rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
34447,SRR31768861,SRX27130600,SRS23587604,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #3,GSM8691385,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 7|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #3,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 7,GSM8691385,GSM8691385: adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #3; Danio rerio; RNA Seq,GSM8691385 r1,GSM8691385,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,7DPI_uninjured_03_S30_R1_001.fastq.gz 7DPI_uninjured_03_S30_R2_001.fastq.gz,fastq fastq,5698047024.0,29362783.0,GSM8691385 r1,0:97.02 1:97.03,A:1667059209;C:1124020328;G:1186053751;T:1719272359;N:1641377,97,97,,,1667059209,1124020328,1186053751,1719272359,1641377,SRX27130600,SRS23587604,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34448,SRR31768862,SRX27130599,SRS23587603,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #2,GSM8691384,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 7|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #2,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 7,GSM8691384,GSM8691384: adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #2; Danio rerio; RNA Seq,GSM8691384 r1,GSM8691384,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,7DPI_uninjured_02_S29_R1_001.fastq.gz 7DPI_uninjured_02_S29_R2_001.fastq.gz,fastq fastq,6167521979.0,31682719.0,GSM8691384 r1,0:97.33 1:97.33,A:1801911913;C:1219391300;G:1283420442;T:1861159517;N:1638807,97,97,,,1801911913,1219391300,1283420442,1861159517,1638807,SRX27130599,SRS23587603,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34449,SRR31768863,SRX27130598,SRS23587602,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #1,GSM8691383,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 7|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #1,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 7,GSM8691383,GSM8691383: adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #1; Danio rerio; RNA Seq,GSM8691383 r1,GSM8691383,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,7DPI_uninjured_01_S28_R1_001.fastq.gz 7DPI_uninjured_01_S28_R2_001.fastq.gz,fastq fastq,6017592709.0,30979971.0,GSM8691383 r1,0:97.12 1:97.12,A:1777015201;C:1171009321;G:1236169034;T:1831770286;N:1628867,97,97,,,1777015201,1171009321,1236169034,1831770286,1628867,SRX27130598,SRS23587602,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34450,SRR31768864,SRX27130597,SRS23587601,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #3,GSM8691382,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #3,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury,GSM8691382,GSM8691382: adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #3; Danio rerio; RNA Seq,GSM8691382 r1,GSM8691382,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,7DPI_injured_03_S27_R1_001.fastq.gz 7DPI_injured_03_S27_R2_001.fastq.gz,fastq fastq,6341961565.0,32524944.0,GSM8691382 r1,0:97.49 1:97.49,A:1851283556;C:1264914896;G:1328636652;T:1895553719;N:1572742,97,97,,,1851283556,1264914896,1328636652,1895553719,1572742,SRX27130597,SRS23587601,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34451,SRR31768865,SRX27130596,SRS23587600,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #2,GSM8691381,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #2,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury,GSM8691381,GSM8691381: adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #2; Danio rerio; RNA Seq,GSM8691381 r1,GSM8691381,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,7DPI_injured_02_S26_R1_001.fastq.gz 7DPI_injured_02_S26_R2_001.fastq.gz,fastq fastq,6235870535.0,31994279.0,GSM8691381 r1,0:97.45 1:97.46,A:1822480684;C:1235794789;G:1300588308;T:1875414630;N:1592124,97,97,,,1822480684,1235794789,1300588308,1875414630,1592124,SRX27130596,SRS23587600,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34452,SRR31768866,SRX27130595,SRS23587599,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #1,GSM8691380,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #1,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury,GSM8691380,GSM8691380: adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #1; Danio rerio; RNA Seq,GSM8691380 r1,GSM8691380,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,7DPI_injured_01_S25_R1_001.fastq.gz 7DPI_injured_01_S25_R2_001.fastq.gz,fastq fastq,6174385200.0,31622915.0,GSM8691380 r1,0:97.62 1:97.63,A:1787576071;C:1247968531;G:1306271111;T:1831148003;N:1421484,97,97,,,1787576071,1247968531,1306271111,1831148003,1421484,SRX27130595,SRS23587599,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34453,SRR31768867,SRX27130594,SRS23587598,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  day 5 uninjured  fish set #3,GSM8691379,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 5|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  day 5 uninjured  fish set #3,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 5,GSM8691379,GSM8691379: adult zebrafish retinal ganglion cells  day 5 uninjured  fish set #3; Danio rerio; RNA Seq,GSM8691379 r1,GSM8691379,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,5DPI_uninjured_03_S24_R1_001.fastq.gz 5DPI_uninjured_03_S24_R2_001.fastq.gz,fastq fastq,6412343629.0,34154945.0,GSM8691379 r1,0:93.86 1:93.88,A:1885512926;C:1263616925;G:1311969388;T:1947630859;N:3613531,93,93,,,1885512926,1263616925,1311969388,1947630859,3613531,SRX27130594,SRS23587598,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34454,SRR31768868,SRX27130593,SRS23587597,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  day 5 uninjured  fish set #2,GSM8691378,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 5|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  day 5 uninjured  fish set #2,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 5,GSM8691378,GSM8691378: adult zebrafish retinal ganglion cells  day 5 uninjured  fish set #2; Danio rerio; RNA Seq,GSM8691378 r1,GSM8691378,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,5DPI_uninjured_02_S23_R1_001.fastq.gz 5DPI_uninjured_02_S23_R2_001.fastq.gz,fastq fastq,6672888700.0,34007957.0,GSM8691378 r1,0:98.11 1:98.11,A:1934192871;C:1346688691;G:1405041934;T:1985769861;N:1195343,98,98,,,1934192871,1346688691,1405041934,1985769861,1195343,SRX27130593,SRS23587597,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34455,SRR31768869,SRX27130592,SRS23587596,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  day 5 uninjured  fish set #1,GSM8691377,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 5|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  day 5 uninjured  fish set #1,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 5,GSM8691377,GSM8691377: adult zebrafish retinal ganglion cells  day 5 uninjured  fish set #1; Danio rerio; RNA Seq,GSM8691377 r1,GSM8691377,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,5DPI_uninjured_01_S22_R1_001.fastq.gz 5DPI_uninjured_01_S22_R2_001.fastq.gz,fastq fastq,6710121204.0,35640240.0,GSM8691377 r1,0:94.13 1:94.14,A:1930817182;C:1378539334;G:1418299809;T:1979047683;N:3417196,94,94,,,1930817182,1378539334,1418299809,1979047683,3417196,SRX27130592,SRS23587596,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34456,SRR31768870,SRX27130591,SRS23587595,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  5 xxx post injury  fish set #3,GSM8691376,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  5 xxx post injury  fish set #3,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury,GSM8691376,GSM8691376: adult zebrafish retinal ganglion cells  5 xxx post injury  fish set #3; Danio rerio; RNA Seq,GSM8691376 r1,GSM8691376,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,5DPI_injured_03_S21_R1_001.fastq.gz 5DPI_injured_03_S21_R2_001.fastq.gz,fastq fastq,5815478166.0,29829330.0,GSM8691376 r1,0:97.47 1:97.49,A:1686233316;C:1173233216;G:1223299576;T:1731320900;N:1391158,97,97,,,1686233316,1173233216,1223299576,1731320900,1391158,SRX27130591,SRS23587595,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34457,SRR31768871,SRX27130590,SRS23587594,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  5 xxx post injury  fish set #2,GSM8691375,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  5 xxx post injury  fish set #2,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury,GSM8691375,GSM8691375: adult zebrafish retinal ganglion cells  5 xxx post injury  fish set #2; Danio rerio; RNA Seq,GSM8691375 r1,GSM8691375,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,5DPI_injured_02_S20_R1_001.fastq.gz 5DPI_injured_02_S20_R2_001.fastq.gz,fastq fastq,6463184463.0,33031735.0,GSM8691375 r1,0:97.83 1:97.84,A:1869116597;C:1303631450;G:1365056296;T:1924007964;N:1372156,97,97,,,1869116597,1303631450,1365056296,1924007964,1372156,SRX27130590,SRS23587594,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34458,SRR31768872,SRX27130589,SRS23587593,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  5 xxx post injury  fish set #1,GSM8691374,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  5 xxx post injury  fish set #1,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury,GSM8691374,GSM8691374: adult zebrafish retinal ganglion cells  5 xxx post injury  fish set #1; Danio rerio; RNA Seq,GSM8691374 r1,GSM8691374,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,5DPI_injured_01_S19_R1_001.fastq.gz 5DPI_injured_01_S19_R2_001.fastq.gz,fastq fastq,5770277062.0,29421167.0,GSM8691374 r1,0:98.06 1:98.07,A:1659818839;C:1176285041;G:1230578027;T:1702467577;N:1127578,98,98,,,1659818839,1176285041,1230578027,1702467577,1127578,SRX27130589,SRS23587593,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34459,SRR31768873,SRX27130588,SRS23587592,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #3,GSM8691373,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 1|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #3,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 1,GSM8691373,GSM8691373: adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #3; Danio rerio; RNA Seq,GSM8691373 r1,GSM8691373,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,1DPI_uninjured_03_S18_R1_001.fastq.gz 1DPI_uninjured_03_S18_R2_001.fastq.gz,fastq fastq,6268800701.0,32414990.0,GSM8691373 r1,0:96.68 1:96.71,A:1808208631;C:1259950394;G:1326103117;T:1872600468;N:1938091,96,96,,,1808208631,1259950394,1326103117,1872600468,1938091,SRX27130588,SRS23587592,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34460,SRR31768874,SRX27130587,SRS23587591,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #2,GSM8691372,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 1|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #2,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 1,GSM8691372,GSM8691372: adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #2; Danio rerio; RNA Seq,GSM8691372 r1,GSM8691372,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,1DPI_uninjured_02_S17_R1_001.fastq.gz 1DPI_uninjured_02_S17_R2_001.fastq.gz,fastq fastq,6475037338.0,33641146.0,GSM8691372 r1,0:96.23 1:96.24,A:1875658518;C:1291113851;G:1361172356;T:1944790051;N:2302562,96,96,,,1875658518,1291113851,1361172356,1944790051,2302562,SRX27130587,SRS23587591,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34461,SRR31768875,SRX27130586,SRS23587590,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #1,GSM8691371,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 1|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #1,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 1,GSM8691371,GSM8691371: adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #1; Danio rerio; RNA Seq,GSM8691371 r1,GSM8691371,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,1DPI_uninjured_01_S16_R1_001.fastq.gz 1DPI_uninjured_01_S16_R2_001.fastq.gz,fastq fastq,6400897196.0,33022714.0,GSM8691371 r1,0:96.92 1:96.91,A:1846404518;C:1284124731;G:1356841105;T:1911572894;N:1953948,96,96,,,1846404518,1284124731,1356841105,1911572894,1953948,SRX27130586,SRS23587590,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34462,SRR31768876,SRX27130585,SRS23587589,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #3,GSM8691370,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #3,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury,GSM8691370,GSM8691370: adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #3; Danio rerio; RNA Seq,GSM8691370 r1,GSM8691370,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,1DPI_injured_03_S15_R1_001.fastq.gz 1DPI_injured_03_S15_R2_001.fastq.gz,fastq fastq,5946459133.0,30587969.0,GSM8691370 r1,0:97.20 1:97.21,A:1716543360;C:1195543685;G:1259830252;T:1772896957;N:1644879,97,97,,,1716543360,1195543685,1259830252,1772896957,1644879,SRX27130585,SRS23587589,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34463,SRR31768877,SRX27130584,SRS23587588,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #2,GSM8691369,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #2,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury,GSM8691369,GSM8691369: adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #2; Danio rerio; RNA Seq,GSM8691369 r1,GSM8691369,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,1DPI_injured_02_S14_R1_001.fastq.gz 1DPI_injured_02_S14_R2_001.fastq.gz,fastq fastq,6366392345.0,32994721.0,GSM8691369 r1,0:96.48 1:96.47,A:1861203729;C:1243094742;G:1336477656;T:1923087937;N:2528281,96,96,,,1861203729,1243094742,1336477656,1923087937,2528281,SRX27130584,SRS23587588,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34464,SRR31768878,SRX27130583,SRS23587587,SRP552464,PRJNA1200121,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA Seq],GSE284728,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Nine bulk RNA seq libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue post optic nerve transection at each of 3 timepoints: 1  5  and 7 xxx post injury dpi  and three from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #1,GSM8691368,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #1,Raw read data were imported to the CLC Genomics Workbench Qiagen Digital Insights licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh. Differential gene expression analysis was performed on Injured versus Uninjured groups  post genes with TPM=0 in one or more replicates were excluded. DEGs from 1  5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5  absolute fold change >1.5  FDR P value <0.05. Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 https://david.ncifcrf.gov and using the KEGG database. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited BulkRNAseq raw counts.tsv file has raw gene counts for each Sample,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury,GSM8691368,GSM8691368: adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #1; Danio rerio; RNA Seq,GSM8691368 r1,GSM8691368,1,1  5 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into SmartSeq HT lysis buffer Takara Bio for mRNA extraction. cDNA sequencing libraries were prepared using a SmartSeq HT kit Takara Bio and Illumina Nextera XT kit Illumina Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP552464,,,1DPI_injured_01_S13_R1_001.fastq.gz 1DPI_injured_01_S13_R2_001.fastq.gz,fastq fastq,6378025205.0,33385333.0,GSM8691368 r1,0:95.51 1:95.53,A:1875735808;C:1227743564;G:1334467564;T:1936726852;N:3351417,95,95,,,1875735808,1227743564,1334467564,1936726852,3351417,SRX27130583,SRS23587587,SRA2037426,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34913,SRR32335084,SRX27670022,SRS24074877,SRP563805,PRJNA1223441,A zebrafish model of crim1 loss of function has small and misshapen lenses with dysregulated clic4 and fgf1b expression ,GSE289562,Transcriptome Analysis,We c ompared gene expression in dissected whole eyes from crim1 /  zebrafish compared to wildtype contros at 72 hpf.  This work will be published as Le et al.  2025: A zebrafish model of crim1 loss of function has small and misshapen lenses with dysregulated clic4 and fgf1b expression. Heterozygous deletions predicting haploinsufficiency for the Cysteine Rich Motor Neuron 1 CRIM1 gene have been identified in two families with macrophthalmia  colobomatous  with microcornea MACOM  an autosomal dominant trait. Crim1 encodes a type I transmembrane protein that is expressed at the cell membrane of lens epithelial and fiber cells at the stage of lens pit formation. Decreased Crim1 expression in the mouse reduced the number of lens epithelial cells and caused defective adhesion between lens epithelial cells and between the epithelial and fiber cells. We present three patients with heterozygous deletions and truncating variants predicted to result in haploinsufficiency for CRIM1 as further evidence for the role of this gene in eye defects  including retinal coloboma  optic pallor  and glaucoma. We used Clustered Regularly Interspaced Short Palindromic Repeats CRISPR/Cas9 to make a stable Danio rerio model of crim1 deficiency  generating zebrafish that were homozygous for a 2 basepair deletion  c.339 340delCT p.Leu112Leufs*3  in crim1. Homozygous  crim1 /  larvae demonstrated smaller eyes and small and misshapen lenses compared to controls  but we did not observe colobomas. Bulk RNA Seq using dissected eyes from crim1 /  larvae and controls at 72 hpf showed significant downregulation of crim1 and chloride intracellular channel 4 clic4 and upregulation of fibroblast growth factor 1b fgf1b and complement component 1  q subcomponent c1q  amongst other dysregulated genes. Our work strengthens the association between haploinsufficiency for CRIM1 and eye defects and characterizes a stable model of crim1 loss of function for future research. Overall design: We c ompared gene expression in dissected whole eyes from crim1 /  zebrafish compared to wildtype contros at 72 hpf. Wildtype and crim1 /  have two replicates.,,pubmed:40114969,,crim1 knockdown whole eyes  72 hpf  sample 3,GSM8794307,,source name:Whole eye|tissue:Whole eye|cell type:All|genotype:crim1 / |geo loc name:missing|collection date:missing,crim1 knockdown whole eyes  72 hpf  sample 3,The quality of raw single end reads of RNA Seq dataset was tested by FastQC http:// www.bioinformatics.babraham.ac.uk/projects/fastqc/ to evaluate the per base sequence quality  quality scores  sequence length distribution and overrepresented adapter/primer sequences.  post quality control with FastQC  data trimming and clipping was performed using BBDuk and aligned against the zebrafish reference genome GRCz11 using STAR. Alignment results were then assessed to check the quality with Qualimap. RSEM was used to quantify genes. Finally  DESeq2 was used to do the downstream analysis for differentially expressed genes. Statistically significant differentially expressed genes DEGs with log2 fold change greater than ±0.5 with an adjusted p value ≤0.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM ≥1 in all datasets were identified by comparing crim1 /  mutants with control datasets using an in house Python script. Principal component analysis PCA was performed Assembly: GRCz11 Supplementary files format and content: Excel; Statistically significant differentially expressed genes DEGs with log2 fold change greater than ±0.5 with an adjusted p value ≤0.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM ≥1 in all datasets were identified by comparing crim1 /  mutants with control datasets using an in house Python script.,Whole eye,,Whole eyes were dissected fromzebrafish at 72 hpf according to prior methods Krall et al.  2018 We performed ‘bulk’ RNA Seq experiments in dissected eyes from in crossed crim1 /  larvae and controls at 72 hpf according to prior methods Krall et al.  2018. RNA quality and quantity was reviewed with a bioanalyzer 2100 Bioanalyzer  Agilent and libraries were prepared with an Ovation® RNA Seq system V2 kit NuGEN. With this method  total RNA was reverse transcribed to synthesize first strand cDNA using a combination of random hexamers and a poly T chimeric primer Krall et al.  2018. The RNA template was then partially degraded by heating and the second strand cDNA was synthesized using DNA polymerase. The double stranded DNA was then amplified using single primer isothermal amplification SPIA. SPIA is a linear cDNA amplification process in which RNase H degrades RNA in DNA/RNA heteroduplex at the 5′ end of the double  stranded DNA  post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3′ end of the primer by displacement of the existing forward strand Krall et al.  2018. Random hexamers were then used to amplify the second strand cDNA linearly. Finally  libraries from the SPIA amplified cDNA were made using the Ultralow DR library kit NuGEN. The RNA Seq libraries were analyzed for quality and primer dimers by bioanalyzer and quantified by quantitative polymerase chain reaction qPCR prior to sequencing KAPA library quantification kit. High throughput sequencing was done using single end 50 lanes on a HiSeq 4000 instrument Illumina.,,tissue:Whole eye|cell type:All|genotype:crim1 / ,GSM8794307,GSM8794307: crim1 knockdown whole eyes  72 hpf  sample 3; Danio rerio; RNA Seq,GSM8794307 r1,GSM8794307,1,Whole eyes were dissected fromzebrafish at 72 hpf according to prior methods Krall et al.  2018 We performed 'bulk' RNA Seq experiments in dissected eyes from in crossed crim1 /  larvae and controls at 72 hpf according to prior methods Krall et al.  2018. RNA quality and quantity was reviewed with a bioanalyzer 2100 Bioanalyzer  Agilent and libraries were prepared with an Ovation® RNA Seq system V2 kit NuGEN. With this method  total RNA was reverse transcribed to synthesize first strand cDNA using a combination of random hexamers and a poly T chimeric primer Krall et al.  2018. The RNA template was then partially degraded by heating and the second strand cDNA was synthesized using DNA polymerase. The double stranded DNA was then amplified using single primer isothermal amplification SPIA. SPIA is a linear cDNA amplification process in which RNase H degrades RNA in DNA/RNA heteroduplex at the 5′ end of the double  stranded DNA  post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3′ end of the primer by displacement of the existing forward strand Krall et al.  2018. Random hexamers were then used to amplify the second strand cDNA linearly. Finally  libraries from the SPIA amplified cDNA were made using the Ultralow DR library kit NuGEN. The RNA Seq libraries were analyzed for quality and primer dimers by bioanalyzer and quantified by quantitative polymerase chain reaction qPCR prior to sequencing KAPA library quantification kit. High throughput sequencing was done using single end 50 lanes on a HiSeq 4000 instrument Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP563805,,,crim1-dpf-3_S15_L002_R1_001.fastq.gz,fastq,3331893906.0,50483241.0,GSM8794307 r1,0:66,A:873905674;C:752237090;G:742087342;T:963442356;N:221444,66,,,,873905674,752237090,742087342,963442356,221444,SRX27670022,SRS24074877,,,Cincinnati Children's Hospital Medical Center,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,bulk,bulk,,United States,2025-02-13,Larval,Larval,Eye,Sensory System
34914,SRR32335085,SRX27670021,SRS24074876,SRP563805,PRJNA1223441,A zebrafish model of crim1 loss of function has small and misshapen lenses with dysregulated clic4 and fgf1b expression ,GSE289562,Transcriptome Analysis,We c ompared gene expression in dissected whole eyes from crim1 /  zebrafish compared to wildtype contros at 72 hpf.  This work will be published as Le et al.  2025: A zebrafish model of crim1 loss of function has small and misshapen lenses with dysregulated clic4 and fgf1b expression. Heterozygous deletions predicting haploinsufficiency for the Cysteine Rich Motor Neuron 1 CRIM1 gene have been identified in two families with macrophthalmia  colobomatous  with microcornea MACOM  an autosomal dominant trait. Crim1 encodes a type I transmembrane protein that is expressed at the cell membrane of lens epithelial and fiber cells at the stage of lens pit formation. Decreased Crim1 expression in the mouse reduced the number of lens epithelial cells and caused defective adhesion between lens epithelial cells and between the epithelial and fiber cells. We present three patients with heterozygous deletions and truncating variants predicted to result in haploinsufficiency for CRIM1 as further evidence for the role of this gene in eye defects  including retinal coloboma  optic pallor  and glaucoma. We used Clustered Regularly Interspaced Short Palindromic Repeats CRISPR/Cas9 to make a stable Danio rerio model of crim1 deficiency  generating zebrafish that were homozygous for a 2 basepair deletion  c.339 340delCT p.Leu112Leufs*3  in crim1. Homozygous  crim1 /  larvae demonstrated smaller eyes and small and misshapen lenses compared to controls  but we did not observe colobomas. Bulk RNA Seq using dissected eyes from crim1 /  larvae and controls at 72 hpf showed significant downregulation of crim1 and chloride intracellular channel 4 clic4 and upregulation of fibroblast growth factor 1b fgf1b and complement component 1  q subcomponent c1q  amongst other dysregulated genes. Our work strengthens the association between haploinsufficiency for CRIM1 and eye defects and characterizes a stable model of crim1 loss of function for future research. Overall design: We c ompared gene expression in dissected whole eyes from crim1 /  zebrafish compared to wildtype contros at 72 hpf. Wildtype and crim1 /  have two replicates.,,pubmed:40114969,,crim1 knockdown whole eyes  72 hpf  sample 2,GSM8794306,,source name:Whole eye|tissue:Whole eye|cell type:All|genotype:crim1 / |geo loc name:missing|collection date:missing,crim1 knockdown whole eyes  72 hpf  sample 2,The quality of raw single end reads of RNA Seq dataset was tested by FastQC http:// www.bioinformatics.babraham.ac.uk/projects/fastqc/ to evaluate the per base sequence quality  quality scores  sequence length distribution and overrepresented adapter/primer sequences.  post quality control with FastQC  data trimming and clipping was performed using BBDuk and aligned against the zebrafish reference genome GRCz11 using STAR. Alignment results were then assessed to check the quality with Qualimap. RSEM was used to quantify genes. Finally  DESeq2 was used to do the downstream analysis for differentially expressed genes. Statistically significant differentially expressed genes DEGs with log2 fold change greater than ±0.5 with an adjusted p value ≤0.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM ≥1 in all datasets were identified by comparing crim1 /  mutants with control datasets using an in house Python script. Principal component analysis PCA was performed Assembly: GRCz11 Supplementary files format and content: Excel; Statistically significant differentially expressed genes DEGs with log2 fold change greater than ±0.5 with an adjusted p value ≤0.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM ≥1 in all datasets were identified by comparing crim1 /  mutants with control datasets using an in house Python script.,Whole eye,,Whole eyes were dissected fromzebrafish at 72 hpf according to prior methods Krall et al.  2018 We performed ‘bulk’ RNA Seq experiments in dissected eyes from in crossed crim1 /  larvae and controls at 72 hpf according to prior methods Krall et al.  2018. RNA quality and quantity was reviewed with a bioanalyzer 2100 Bioanalyzer  Agilent and libraries were prepared with an Ovation® RNA Seq system V2 kit NuGEN. With this method  total RNA was reverse transcribed to synthesize first strand cDNA using a combination of random hexamers and a poly T chimeric primer Krall et al.  2018. The RNA template was then partially degraded by heating and the second strand cDNA was synthesized using DNA polymerase. The double stranded DNA was then amplified using single primer isothermal amplification SPIA. SPIA is a linear cDNA amplification process in which RNase H degrades RNA in DNA/RNA heteroduplex at the 5′ end of the double  stranded DNA  post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3′ end of the primer by displacement of the existing forward strand Krall et al.  2018. Random hexamers were then used to amplify the second strand cDNA linearly. Finally  libraries from the SPIA amplified cDNA were made using the Ultralow DR library kit NuGEN. The RNA Seq libraries were analyzed for quality and primer dimers by bioanalyzer and quantified by quantitative polymerase chain reaction qPCR prior to sequencing KAPA library quantification kit. High throughput sequencing was done using single end 50 lanes on a HiSeq 4000 instrument Illumina.,,tissue:Whole eye|cell type:All|genotype:crim1 / ,GSM8794306,GSM8794306: crim1 knockdown whole eyes  72 hpf  sample 2; Danio rerio; RNA Seq,GSM8794306 r1,GSM8794306,1,Whole eyes were dissected fromzebrafish at 72 hpf according to prior methods Krall et al.  2018 We performed 'bulk' RNA Seq experiments in dissected eyes from in crossed crim1 /  larvae and controls at 72 hpf according to prior methods Krall et al.  2018. RNA quality and quantity was reviewed with a bioanalyzer 2100 Bioanalyzer  Agilent and libraries were prepared with an Ovation® RNA Seq system V2 kit NuGEN. With this method  total RNA was reverse transcribed to synthesize first strand cDNA using a combination of random hexamers and a poly T chimeric primer Krall et al.  2018. The RNA template was then partially degraded by heating and the second strand cDNA was synthesized using DNA polymerase. The double stranded DNA was then amplified using single primer isothermal amplification SPIA. SPIA is a linear cDNA amplification process in which RNase H degrades RNA in DNA/RNA heteroduplex at the 5′ end of the double  stranded DNA  post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3′ end of the primer by displacement of the existing forward strand Krall et al.  2018. Random hexamers were then used to amplify the second strand cDNA linearly. Finally  libraries from the SPIA amplified cDNA were made using the Ultralow DR library kit NuGEN. The RNA Seq libraries were analyzed for quality and primer dimers by bioanalyzer and quantified by quantitative polymerase chain reaction qPCR prior to sequencing KAPA library quantification kit. High throughput sequencing was done using single end 50 lanes on a HiSeq 4000 instrument Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP563805,,,crim1-dpf-2_S11_L002_R1_001.fastq.gz,fastq,3491059044.0,52894834.0,GSM8794306 r1,0:66,A:907771486;C:794245897;G:783248243;T:1005559302;N:234116,66,,,,907771486,794245897,783248243,1005559302,234116,SRX27670021,SRS24074876,,,Cincinnati Children's Hospital Medical Center,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,bulk,bulk,,United States,2025-02-13,Larval,Larval,Eye,Sensory System
34915,SRR32335086,SRX27670020,SRS24074875,SRP563805,PRJNA1223441,A zebrafish model of crim1 loss of function has small and misshapen lenses with dysregulated clic4 and fgf1b expression ,GSE289562,Transcriptome Analysis,We c ompared gene expression in dissected whole eyes from crim1 /  zebrafish compared to wildtype contros at 72 hpf.  This work will be published as Le et al.  2025: A zebrafish model of crim1 loss of function has small and misshapen lenses with dysregulated clic4 and fgf1b expression. Heterozygous deletions predicting haploinsufficiency for the Cysteine Rich Motor Neuron 1 CRIM1 gene have been identified in two families with macrophthalmia  colobomatous  with microcornea MACOM  an autosomal dominant trait. Crim1 encodes a type I transmembrane protein that is expressed at the cell membrane of lens epithelial and fiber cells at the stage of lens pit formation. Decreased Crim1 expression in the mouse reduced the number of lens epithelial cells and caused defective adhesion between lens epithelial cells and between the epithelial and fiber cells. We present three patients with heterozygous deletions and truncating variants predicted to result in haploinsufficiency for CRIM1 as further evidence for the role of this gene in eye defects  including retinal coloboma  optic pallor  and glaucoma. We used Clustered Regularly Interspaced Short Palindromic Repeats CRISPR/Cas9 to make a stable Danio rerio model of crim1 deficiency  generating zebrafish that were homozygous for a 2 basepair deletion  c.339 340delCT p.Leu112Leufs*3  in crim1. Homozygous  crim1 /  larvae demonstrated smaller eyes and small and misshapen lenses compared to controls  but we did not observe colobomas. Bulk RNA Seq using dissected eyes from crim1 /  larvae and controls at 72 hpf showed significant downregulation of crim1 and chloride intracellular channel 4 clic4 and upregulation of fibroblast growth factor 1b fgf1b and complement component 1  q subcomponent c1q  amongst other dysregulated genes. Our work strengthens the association between haploinsufficiency for CRIM1 and eye defects and characterizes a stable model of crim1 loss of function for future research. Overall design: We c ompared gene expression in dissected whole eyes from crim1 /  zebrafish compared to wildtype contros at 72 hpf. Wildtype and crim1 /  have two replicates.,,pubmed:40114969,,crim1 knockdown whole eyes  72 hpf  sample 1,GSM8794305,,source name:Whole eye|tissue:Whole eye|cell type:All|genotype:crim1 /. |geo loc name:missing|collection date:missing,crim1 knockdown whole eyes  72 hpf  sample 1,The quality of raw single end reads of RNA Seq dataset was tested by FastQC http:// www.bioinformatics.babraham.ac.uk/projects/fastqc/ to evaluate the per base sequence quality  quality scores  sequence length distribution and overrepresented adapter/primer sequences.  post quality control with FastQC  data trimming and clipping was performed using BBDuk and aligned against the zebrafish reference genome GRCz11 using STAR. Alignment results were then assessed to check the quality with Qualimap. RSEM was used to quantify genes. Finally  DESeq2 was used to do the downstream analysis for differentially expressed genes. Statistically significant differentially expressed genes DEGs with log2 fold change greater than ±0.5 with an adjusted p value ≤0.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM ≥1 in all datasets were identified by comparing crim1 /  mutants with control datasets using an in house Python script. Principal component analysis PCA was performed Assembly: GRCz11 Supplementary files format and content: Excel; Statistically significant differentially expressed genes DEGs with log2 fold change greater than ±0.5 with an adjusted p value ≤0.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM ≥1 in all datasets were identified by comparing crim1 /  mutants with control datasets using an in house Python script.,Whole eye,,Whole eyes were dissected fromzebrafish at 72 hpf according to prior methods Krall et al.  2018 We performed ‘bulk’ RNA Seq experiments in dissected eyes from in crossed crim1 /  larvae and controls at 72 hpf according to prior methods Krall et al.  2018. RNA quality and quantity was reviewed with a bioanalyzer 2100 Bioanalyzer  Agilent and libraries were prepared with an Ovation® RNA Seq system V2 kit NuGEN. With this method  total RNA was reverse transcribed to synthesize first strand cDNA using a combination of random hexamers and a poly T chimeric primer Krall et al.  2018. The RNA template was then partially degraded by heating and the second strand cDNA was synthesized using DNA polymerase. The double stranded DNA was then amplified using single primer isothermal amplification SPIA. SPIA is a linear cDNA amplification process in which RNase H degrades RNA in DNA/RNA heteroduplex at the 5′ end of the double  stranded DNA  post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3′ end of the primer by displacement of the existing forward strand Krall et al.  2018. Random hexamers were then used to amplify the second strand cDNA linearly. Finally  libraries from the SPIA amplified cDNA were made using the Ultralow DR library kit NuGEN. The RNA Seq libraries were analyzed for quality and primer dimers by bioanalyzer and quantified by quantitative polymerase chain reaction qPCR prior to sequencing KAPA library quantification kit. High throughput sequencing was done using single end 50 lanes on a HiSeq 4000 instrument Illumina.,,tissue:Whole eye|cell type:All|genotype:crim1 /. ,GSM8794305,GSM8794305: crim1 knockdown whole eyes  72 hpf  sample 1; Danio rerio; RNA Seq,GSM8794305 r1,GSM8794305,1,Whole eyes were dissected fromzebrafish at 72 hpf according to prior methods Krall et al.  2018 We performed 'bulk' RNA Seq experiments in dissected eyes from in crossed crim1 /  larvae and controls at 72 hpf according to prior methods Krall et al.  2018. RNA quality and quantity was reviewed with a bioanalyzer 2100 Bioanalyzer  Agilent and libraries were prepared with an Ovation® RNA Seq system V2 kit NuGEN. With this method  total RNA was reverse transcribed to synthesize first strand cDNA using a combination of random hexamers and a poly T chimeric primer Krall et al.  2018. The RNA template was then partially degraded by heating and the second strand cDNA was synthesized using DNA polymerase. The double stranded DNA was then amplified using single primer isothermal amplification SPIA. SPIA is a linear cDNA amplification process in which RNase H degrades RNA in DNA/RNA heteroduplex at the 5′ end of the double  stranded DNA  post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3′ end of the primer by displacement of the existing forward strand Krall et al.  2018. Random hexamers were then used to amplify the second strand cDNA linearly. Finally  libraries from the SPIA amplified cDNA were made using the Ultralow DR library kit NuGEN. The RNA Seq libraries were analyzed for quality and primer dimers by bioanalyzer and quantified by quantitative polymerase chain reaction qPCR prior to sequencing KAPA library quantification kit. High throughput sequencing was done using single end 50 lanes on a HiSeq 4000 instrument Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP563805,,,crim1-dpf-1_S16_L003_R1_001.fastq.gz,fastq,2751667380.0,41691930.0,GSM8794305 r1,0:66,A:714065903;C:618520760;G:607652792;T:811160146;N:267779,66,,,,714065903,618520760,607652792,811160146,267779,SRX27670020,SRS24074875,,,Cincinnati Children's Hospital Medical Center,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,bulk,bulk,,United States,2025-02-13,Larval,Larval,Eye,Sensory System
34916,SRR32335087,SRX27670019,SRS24074874,SRP563805,PRJNA1223441,A zebrafish model of crim1 loss of function has small and misshapen lenses with dysregulated clic4 and fgf1b expression ,GSE289562,Transcriptome Analysis,We c ompared gene expression in dissected whole eyes from crim1 /  zebrafish compared to wildtype contros at 72 hpf.  This work will be published as Le et al.  2025: A zebrafish model of crim1 loss of function has small and misshapen lenses with dysregulated clic4 and fgf1b expression. Heterozygous deletions predicting haploinsufficiency for the Cysteine Rich Motor Neuron 1 CRIM1 gene have been identified in two families with macrophthalmia  colobomatous  with microcornea MACOM  an autosomal dominant trait. Crim1 encodes a type I transmembrane protein that is expressed at the cell membrane of lens epithelial and fiber cells at the stage of lens pit formation. Decreased Crim1 expression in the mouse reduced the number of lens epithelial cells and caused defective adhesion between lens epithelial cells and between the epithelial and fiber cells. We present three patients with heterozygous deletions and truncating variants predicted to result in haploinsufficiency for CRIM1 as further evidence for the role of this gene in eye defects  including retinal coloboma  optic pallor  and glaucoma. We used Clustered Regularly Interspaced Short Palindromic Repeats CRISPR/Cas9 to make a stable Danio rerio model of crim1 deficiency  generating zebrafish that were homozygous for a 2 basepair deletion  c.339 340delCT p.Leu112Leufs*3  in crim1. Homozygous  crim1 /  larvae demonstrated smaller eyes and small and misshapen lenses compared to controls  but we did not observe colobomas. Bulk RNA Seq using dissected eyes from crim1 /  larvae and controls at 72 hpf showed significant downregulation of crim1 and chloride intracellular channel 4 clic4 and upregulation of fibroblast growth factor 1b fgf1b and complement component 1  q subcomponent c1q  amongst other dysregulated genes. Our work strengthens the association between haploinsufficiency for CRIM1 and eye defects and characterizes a stable model of crim1 loss of function for future research. Overall design: We c ompared gene expression in dissected whole eyes from crim1 /  zebrafish compared to wildtype contros at 72 hpf. Wildtype and crim1 /  have two replicates.,,pubmed:40114969,,wildtype whole eyes  72 hpf  sample 3,GSM8794304,,source name:Whole eye|tissue:Whole eye|cell type:All|genotype:Wildtype|geo loc name:missing|collection date:missing,wildtype whole eyes  72 hpf  sample 3,The quality of raw single end reads of RNA Seq dataset was tested by FastQC http:// www.bioinformatics.babraham.ac.uk/projects/fastqc/ to evaluate the per base sequence quality  quality scores  sequence length distribution and overrepresented adapter/primer sequences.  post quality control with FastQC  data trimming and clipping was performed using BBDuk and aligned against the zebrafish reference genome GRCz11 using STAR. Alignment results were then assessed to check the quality with Qualimap. RSEM was used to quantify genes. Finally  DESeq2 was used to do the downstream analysis for differentially expressed genes. Statistically significant differentially expressed genes DEGs with log2 fold change greater than ±0.5 with an adjusted p value ≤0.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM ≥1 in all datasets were identified by comparing crim1 /  mutants with control datasets using an in house Python script. Principal component analysis PCA was performed Assembly: GRCz11 Supplementary files format and content: Excel; Statistically significant differentially expressed genes DEGs with log2 fold change greater than ±0.5 with an adjusted p value ≤0.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM ≥1 in all datasets were identified by comparing crim1 /  mutants with control datasets using an in house Python script.,Whole eye,,Whole eyes were dissected fromzebrafish at 72 hpf according to prior methods Krall et al.  2018 We performed ‘bulk’ RNA Seq experiments in dissected eyes from in crossed crim1 /  larvae and controls at 72 hpf according to prior methods Krall et al.  2018. RNA quality and quantity was reviewed with a bioanalyzer 2100 Bioanalyzer  Agilent and libraries were prepared with an Ovation® RNA Seq system V2 kit NuGEN. With this method  total RNA was reverse transcribed to synthesize first strand cDNA using a combination of random hexamers and a poly T chimeric primer Krall et al.  2018. The RNA template was then partially degraded by heating and the second strand cDNA was synthesized using DNA polymerase. The double stranded DNA was then amplified using single primer isothermal amplification SPIA. SPIA is a linear cDNA amplification process in which RNase H degrades RNA in DNA/RNA heteroduplex at the 5′ end of the double  stranded DNA  post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3′ end of the primer by displacement of the existing forward strand Krall et al.  2018. Random hexamers were then used to amplify the second strand cDNA linearly. Finally  libraries from the SPIA amplified cDNA were made using the Ultralow DR library kit NuGEN. The RNA Seq libraries were analyzed for quality and primer dimers by bioanalyzer and quantified by quantitative polymerase chain reaction qPCR prior to sequencing KAPA library quantification kit. High throughput sequencing was done using single end 50 lanes on a HiSeq 4000 instrument Illumina.,,tissue:Whole eye|cell type:All|genotype:Wildtype,GSM8794304,GSM8794304: wildtype whole eyes  72 hpf  sample 3; Danio rerio; RNA Seq,GSM8794304 r1,GSM8794304,1,Whole eyes were dissected fromzebrafish at 72 hpf according to prior methods Krall et al.  2018 We performed 'bulk' RNA Seq experiments in dissected eyes from in crossed crim1 /  larvae and controls at 72 hpf according to prior methods Krall et al.  2018. RNA quality and quantity was reviewed with a bioanalyzer 2100 Bioanalyzer  Agilent and libraries were prepared with an Ovation® RNA Seq system V2 kit NuGEN. With this method  total RNA was reverse transcribed to synthesize first strand cDNA using a combination of random hexamers and a poly T chimeric primer Krall et al.  2018. The RNA template was then partially degraded by heating and the second strand cDNA was synthesized using DNA polymerase. The double stranded DNA was then amplified using single primer isothermal amplification SPIA. SPIA is a linear cDNA amplification process in which RNase H degrades RNA in DNA/RNA heteroduplex at the 5′ end of the double  stranded DNA  post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3′ end of the primer by displacement of the existing forward strand Krall et al.  2018. Random hexamers were then used to amplify the second strand cDNA linearly. Finally  libraries from the SPIA amplified cDNA were made using the Ultralow DR library kit NuGEN. The RNA Seq libraries were analyzed for quality and primer dimers by bioanalyzer and quantified by quantitative polymerase chain reaction qPCR prior to sequencing KAPA library quantification kit. High throughput sequencing was done using single end 50 lanes on a HiSeq 4000 instrument Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP563805,,,crim1-ctr-3_S12_L002_R1_001.fastq.gz,fastq,2881865976.0,43664636.0,GSM8794304 r1,0:66,A:759373846;C:644323432;G:637932338;T:840046555;N:189805,66,,,,759373846,644323432,637932338,840046555,189805,SRX27670019,SRS24074874,,,Cincinnati Children's Hospital Medical Center,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,bulk,bulk,,United States,2025-02-13,Larval,Larval,Eye,Sensory System
34917,SRR32335088,SRX27670018,SRS24074873,SRP563805,PRJNA1223441,A zebrafish model of crim1 loss of function has small and misshapen lenses with dysregulated clic4 and fgf1b expression ,GSE289562,Transcriptome Analysis,We c ompared gene expression in dissected whole eyes from crim1 /  zebrafish compared to wildtype contros at 72 hpf.  This work will be published as Le et al.  2025: A zebrafish model of crim1 loss of function has small and misshapen lenses with dysregulated clic4 and fgf1b expression. Heterozygous deletions predicting haploinsufficiency for the Cysteine Rich Motor Neuron 1 CRIM1 gene have been identified in two families with macrophthalmia  colobomatous  with microcornea MACOM  an autosomal dominant trait. Crim1 encodes a type I transmembrane protein that is expressed at the cell membrane of lens epithelial and fiber cells at the stage of lens pit formation. Decreased Crim1 expression in the mouse reduced the number of lens epithelial cells and caused defective adhesion between lens epithelial cells and between the epithelial and fiber cells. We present three patients with heterozygous deletions and truncating variants predicted to result in haploinsufficiency for CRIM1 as further evidence for the role of this gene in eye defects  including retinal coloboma  optic pallor  and glaucoma. We used Clustered Regularly Interspaced Short Palindromic Repeats CRISPR/Cas9 to make a stable Danio rerio model of crim1 deficiency  generating zebrafish that were homozygous for a 2 basepair deletion  c.339 340delCT p.Leu112Leufs*3  in crim1. Homozygous  crim1 /  larvae demonstrated smaller eyes and small and misshapen lenses compared to controls  but we did not observe colobomas. Bulk RNA Seq using dissected eyes from crim1 /  larvae and controls at 72 hpf showed significant downregulation of crim1 and chloride intracellular channel 4 clic4 and upregulation of fibroblast growth factor 1b fgf1b and complement component 1  q subcomponent c1q  amongst other dysregulated genes. Our work strengthens the association between haploinsufficiency for CRIM1 and eye defects and characterizes a stable model of crim1 loss of function for future research. Overall design: We c ompared gene expression in dissected whole eyes from crim1 /  zebrafish compared to wildtype contros at 72 hpf. Wildtype and crim1 /  have two replicates.,,pubmed:40114969,,wildtype whole eyes  72 hpf  sample 2,GSM8794303,,source name:Whole eye|tissue:Whole eye|cell type:All|genotype:Wildtype|geo loc name:missing|collection date:missing,wildtype whole eyes  72 hpf  sample 2,The quality of raw single end reads of RNA Seq dataset was tested by FastQC http:// www.bioinformatics.babraham.ac.uk/projects/fastqc/ to evaluate the per base sequence quality  quality scores  sequence length distribution and overrepresented adapter/primer sequences.  post quality control with FastQC  data trimming and clipping was performed using BBDuk and aligned against the zebrafish reference genome GRCz11 using STAR. Alignment results were then assessed to check the quality with Qualimap. RSEM was used to quantify genes. Finally  DESeq2 was used to do the downstream analysis for differentially expressed genes. Statistically significant differentially expressed genes DEGs with log2 fold change greater than ±0.5 with an adjusted p value ≤0.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM ≥1 in all datasets were identified by comparing crim1 /  mutants with control datasets using an in house Python script. Principal component analysis PCA was performed Assembly: GRCz11 Supplementary files format and content: Excel; Statistically significant differentially expressed genes DEGs with log2 fold change greater than ±0.5 with an adjusted p value ≤0.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM ≥1 in all datasets were identified by comparing crim1 /  mutants with control datasets using an in house Python script.,Whole eye,,Whole eyes were dissected fromzebrafish at 72 hpf according to prior methods Krall et al.  2018 We performed ‘bulk’ RNA Seq experiments in dissected eyes from in crossed crim1 /  larvae and controls at 72 hpf according to prior methods Krall et al.  2018. RNA quality and quantity was reviewed with a bioanalyzer 2100 Bioanalyzer  Agilent and libraries were prepared with an Ovation® RNA Seq system V2 kit NuGEN. With this method  total RNA was reverse transcribed to synthesize first strand cDNA using a combination of random hexamers and a poly T chimeric primer Krall et al.  2018. The RNA template was then partially degraded by heating and the second strand cDNA was synthesized using DNA polymerase. The double stranded DNA was then amplified using single primer isothermal amplification SPIA. SPIA is a linear cDNA amplification process in which RNase H degrades RNA in DNA/RNA heteroduplex at the 5′ end of the double  stranded DNA  post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3′ end of the primer by displacement of the existing forward strand Krall et al.  2018. Random hexamers were then used to amplify the second strand cDNA linearly. Finally  libraries from the SPIA amplified cDNA were made using the Ultralow DR library kit NuGEN. The RNA Seq libraries were analyzed for quality and primer dimers by bioanalyzer and quantified by quantitative polymerase chain reaction qPCR prior to sequencing KAPA library quantification kit. High throughput sequencing was done using single end 50 lanes on a HiSeq 4000 instrument Illumina.,,tissue:Whole eye|cell type:All|genotype:Wildtype,GSM8794303,GSM8794303: wildtype whole eyes  72 hpf  sample 2; Danio rerio; RNA Seq,GSM8794303 r1,GSM8794303,1,Whole eyes were dissected fromzebrafish at 72 hpf according to prior methods Krall et al.  2018 We performed 'bulk' RNA Seq experiments in dissected eyes from in crossed crim1 /  larvae and controls at 72 hpf according to prior methods Krall et al.  2018. RNA quality and quantity was reviewed with a bioanalyzer 2100 Bioanalyzer  Agilent and libraries were prepared with an Ovation® RNA Seq system V2 kit NuGEN. With this method  total RNA was reverse transcribed to synthesize first strand cDNA using a combination of random hexamers and a poly T chimeric primer Krall et al.  2018. The RNA template was then partially degraded by heating and the second strand cDNA was synthesized using DNA polymerase. The double stranded DNA was then amplified using single primer isothermal amplification SPIA. SPIA is a linear cDNA amplification process in which RNase H degrades RNA in DNA/RNA heteroduplex at the 5′ end of the double  stranded DNA  post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3′ end of the primer by displacement of the existing forward strand Krall et al.  2018. Random hexamers were then used to amplify the second strand cDNA linearly. Finally  libraries from the SPIA amplified cDNA were made using the Ultralow DR library kit NuGEN. The RNA Seq libraries were analyzed for quality and primer dimers by bioanalyzer and quantified by quantitative polymerase chain reaction qPCR prior to sequencing KAPA library quantification kit. High throughput sequencing was done using single end 50 lanes on a HiSeq 4000 instrument Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP563805,,,crim1-ctr-2_S20_L003_R1_001.fastq.gz,fastq,2380780182.0,36072427.0,GSM8794303 r1,0:66,A:617266566;C:538355433;G:528639561;T:696293971;N:224651,66,,,,617266566,538355433,528639561,696293971,224651,SRX27670018,SRS24074873,,,Cincinnati Children's Hospital Medical Center,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,bulk,bulk,,United States,2025-02-13,Larval,Larval,Eye,Sensory System
34918,SRR32335089,SRX27670017,SRS24074872,SRP563805,PRJNA1223441,A zebrafish model of crim1 loss of function has small and misshapen lenses with dysregulated clic4 and fgf1b expression ,GSE289562,Transcriptome Analysis,We c ompared gene expression in dissected whole eyes from crim1 /  zebrafish compared to wildtype contros at 72 hpf.  This work will be published as Le et al.  2025: A zebrafish model of crim1 loss of function has small and misshapen lenses with dysregulated clic4 and fgf1b expression. Heterozygous deletions predicting haploinsufficiency for the Cysteine Rich Motor Neuron 1 CRIM1 gene have been identified in two families with macrophthalmia  colobomatous  with microcornea MACOM  an autosomal dominant trait. Crim1 encodes a type I transmembrane protein that is expressed at the cell membrane of lens epithelial and fiber cells at the stage of lens pit formation. Decreased Crim1 expression in the mouse reduced the number of lens epithelial cells and caused defective adhesion between lens epithelial cells and between the epithelial and fiber cells. We present three patients with heterozygous deletions and truncating variants predicted to result in haploinsufficiency for CRIM1 as further evidence for the role of this gene in eye defects  including retinal coloboma  optic pallor  and glaucoma. We used Clustered Regularly Interspaced Short Palindromic Repeats CRISPR/Cas9 to make a stable Danio rerio model of crim1 deficiency  generating zebrafish that were homozygous for a 2 basepair deletion  c.339 340delCT p.Leu112Leufs*3  in crim1. Homozygous  crim1 /  larvae demonstrated smaller eyes and small and misshapen lenses compared to controls  but we did not observe colobomas. Bulk RNA Seq using dissected eyes from crim1 /  larvae and controls at 72 hpf showed significant downregulation of crim1 and chloride intracellular channel 4 clic4 and upregulation of fibroblast growth factor 1b fgf1b and complement component 1  q subcomponent c1q  amongst other dysregulated genes. Our work strengthens the association between haploinsufficiency for CRIM1 and eye defects and characterizes a stable model of crim1 loss of function for future research. Overall design: We c ompared gene expression in dissected whole eyes from crim1 /  zebrafish compared to wildtype contros at 72 hpf. Wildtype and crim1 /  have two replicates.,,pubmed:40114969,,wildtype whole eyes  72 hpf  sample 1,GSM8794302,,source name:Whole eye|tissue:Whole eye|cell type:All|genotype:Wildtype|geo loc name:missing|collection date:missing,wildtype whole eyes  72 hpf  sample 1,The quality of raw single end reads of RNA Seq dataset was tested by FastQC http:// www.bioinformatics.babraham.ac.uk/projects/fastqc/ to evaluate the per base sequence quality  quality scores  sequence length distribution and overrepresented adapter/primer sequences.  post quality control with FastQC  data trimming and clipping was performed using BBDuk and aligned against the zebrafish reference genome GRCz11 using STAR. Alignment results were then assessed to check the quality with Qualimap. RSEM was used to quantify genes. Finally  DESeq2 was used to do the downstream analysis for differentially expressed genes. Statistically significant differentially expressed genes DEGs with log2 fold change greater than ±0.5 with an adjusted p value ≤0.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM ≥1 in all datasets were identified by comparing crim1 /  mutants with control datasets using an in house Python script. Principal component analysis PCA was performed Assembly: GRCz11 Supplementary files format and content: Excel; Statistically significant differentially expressed genes DEGs with log2 fold change greater than ±0.5 with an adjusted p value ≤0.05 and the mean Fragments Per Kilobase of Exon Per Million Fragments Mapped FPKM ≥1 in all datasets were identified by comparing crim1 /  mutants with control datasets using an in house Python script.,Whole eye,,Whole eyes were dissected fromzebrafish at 72 hpf according to prior methods Krall et al.  2018 We performed ‘bulk’ RNA Seq experiments in dissected eyes from in crossed crim1 /  larvae and controls at 72 hpf according to prior methods Krall et al.  2018. RNA quality and quantity was reviewed with a bioanalyzer 2100 Bioanalyzer  Agilent and libraries were prepared with an Ovation® RNA Seq system V2 kit NuGEN. With this method  total RNA was reverse transcribed to synthesize first strand cDNA using a combination of random hexamers and a poly T chimeric primer Krall et al.  2018. The RNA template was then partially degraded by heating and the second strand cDNA was synthesized using DNA polymerase. The double stranded DNA was then amplified using single primer isothermal amplification SPIA. SPIA is a linear cDNA amplification process in which RNase H degrades RNA in DNA/RNA heteroduplex at the 5′ end of the double  stranded DNA  post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3′ end of the primer by displacement of the existing forward strand Krall et al.  2018. Random hexamers were then used to amplify the second strand cDNA linearly. Finally  libraries from the SPIA amplified cDNA were made using the Ultralow DR library kit NuGEN. The RNA Seq libraries were analyzed for quality and primer dimers by bioanalyzer and quantified by quantitative polymerase chain reaction qPCR prior to sequencing KAPA library quantification kit. High throughput sequencing was done using single end 50 lanes on a HiSeq 4000 instrument Illumina.,,tissue:Whole eye|cell type:All|genotype:Wildtype,GSM8794302,GSM8794302: wildtype whole eyes  72 hpf  sample 1; Danio rerio; RNA Seq,GSM8794302 r1,GSM8794302,1,Whole eyes were dissected fromzebrafish at 72 hpf according to prior methods Krall et al.  2018 We performed 'bulk' RNA Seq experiments in dissected eyes from in crossed crim1 /  larvae and controls at 72 hpf according to prior methods Krall et al.  2018. RNA quality and quantity was reviewed with a bioanalyzer 2100 Bioanalyzer  Agilent and libraries were prepared with an Ovation® RNA Seq system V2 kit NuGEN. With this method  total RNA was reverse transcribed to synthesize first strand cDNA using a combination of random hexamers and a poly T chimeric primer Krall et al.  2018. The RNA template was then partially degraded by heating and the second strand cDNA was synthesized using DNA polymerase. The double stranded DNA was then amplified using single primer isothermal amplification SPIA. SPIA is a linear cDNA amplification process in which RNase H degrades RNA in DNA/RNA heteroduplex at the 5′ end of the double  stranded DNA  post which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3′ end of the primer by displacement of the existing forward strand Krall et al.  2018. Random hexamers were then used to amplify the second strand cDNA linearly. Finally  libraries from the SPIA amplified cDNA were made using the Ultralow DR library kit NuGEN. The RNA Seq libraries were analyzed for quality and primer dimers by bioanalyzer and quantified by quantitative polymerase chain reaction qPCR prior to sequencing KAPA library quantification kit. High throughput sequencing was done using single end 50 lanes on a HiSeq 4000 instrument Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP563805,,,crim1-ctr-1_S17_L003_R1_001.fastq.gz,fastq,3007758600.0,45572100.0,GSM8794302 r1,0:66,A:783035033;C:680405728;G:668894784;T:875142229;N:280826,66,,,,783035033,680405728,668894784,875142229,280826,SRX27670017,SRS24074872,,,Cincinnati Children's Hospital Medical Center,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,bulk,bulk,,United States,2025-02-13,Larval,Larval,Eye,Sensory System
53513,SRR9906847,SRX6657804,SRS5218265,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAnmdahN36R2,GSM4007833,,source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 2,zfRNAnmdahN36R2,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 2,GSM4007833,GSM4007833: zfRNAnmdahN36R2; Danio rerio; RNA Seq,GSM4007833,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-TF4N_S8_R1_001.fastq.gz THoa-TF4N_S8_R2_001.fastq.gz,fastq fastq,7928700600.0,52858004.0,GSM4007833 r1,0:75 1:75,A:2214653986;C:1699850211;G:1809132429;T:2204054149;N:1009825,75,75,,,2214653986,1699850211,1809132429,2204054149,1009825,SRX6657804,SRS5218265,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.88014,0.90383,0.394,0.41783,0.76607,0.77043,0.5474,0.55256,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53514,SRR9906846,SRX6657803,SRS5218264,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAnmdahN36R1,GSM4007832,,source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 1,zfRNAnmdahN36R1,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 1,GSM4007832,GSM4007832: zfRNAnmdahN36R1; Danio rerio; RNA Seq,GSM4007832,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-TF3N_S7_R1_001.fastq.gz THoa-TF3N_S7_R2_001.fastq.gz,fastq fastq,7863596250.0,52423975.0,GSM4007832 r1,0:75 1:75,A:2245214380;C:1641445245;G:1740385747;T:2235554179;N:996699,75,75,,,2245214380,1641445245,1740385747,2235554179,996699,SRX6657803,SRS5218264,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.86899,0.89643,0.43639,0.46473,0.76631,0.77086,0.53259,0.53462,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53515,SRR9906845,SRX6657802,SRS5218263,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAnmdahN20R2,GSM4007831,,source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:20hr|replicate:Replicate 2,zfRNAnmdahN20R2,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:20hr|replicate:Replicate 2,GSM4007831,GSM4007831: zfRNAnmdahN20R2; Danio rerio; RNA Seq,GSM4007831,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-TF2N_S6_R1_001.fastq.gz THoa-TF2N_S6_R2_001.fastq.gz,fastq fastq,11221029450.0,74806863.0,GSM4007831 r1,0:75 1:75,A:3206652122;C:2349148827;G:2475237997;T:3188565893;N:1424611,75,75,,,3206652122,2349148827,2475237997,3188565893,1424611,SRX6657802,SRS5218263,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.86571,0.89458,0.44089,0.4703,0.77163,0.77573,0.54887,0.54576,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53516,SRR9906844,SRX6657801,SRS5218262,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAnmdahN20R1,GSM4007830,,source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:20hr|replicate:Replicate 1,zfRNAnmdahN20R1,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:20hr|replicate:Replicate 1,GSM4007830,GSM4007830: zfRNAnmdahN20R1; Danio rerio; RNA Seq,GSM4007830,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-TF1N_S5_R1_001.fastq.gz THoa-TF1N_S5_R2_001.fastq.gz,fastq fastq,11263633950.0,75090893.0,GSM4007830 r1,0:75 1:75,A:3198241763;C:2374935676;G:2514695492;T:3174314457;N:1446562,75,75,,,3198241763,2374935676,2514695492,3174314457,1446562,SRX6657801,SRS5218262,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.87624,0.90304,0.39909,0.42417,0.76984,0.77376,0.53406,0.53718,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53517,SRR9906843,SRX6657800,SRS5218261,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAnmdahP36R2,GSM4007829,,source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:36hr|replicate:Replicate 2,zfRNAnmdahP36R2,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:36hr|replicate:Replicate 2,GSM4007829,GSM4007829: zfRNAnmdahP36R2; Danio rerio; RNA Seq,GSM4007829,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-TF4P_S4_R1_001.fastq.gz THoa-TF4P_S4_R2_001.fastq.gz,fastq fastq,10599378900.0,70662526.0,GSM4007829 r1,0:75 1:75,A:2917939167;C:2338922409;G:2472546084;T:2868616483;N:1354757,75,75,,,2917939167,2338922409,2472546084,2868616483,1354757,SRX6657800,SRS5218261,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.89693,0.9159,0.31259,0.33022,0.7371,0.74182,0.56412,0.56559,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53518,SRR9906842,SRX6657799,SRS5218260,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAnmdahP36R1,GSM4007828,,source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:36hr|replicate:Replicate 1,zfRNAnmdahP36R1,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:36hr|replicate:Replicate 1,GSM4007828,GSM4007828: zfRNAnmdahP36R1; Danio rerio; RNA Seq,GSM4007828,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-TF3P_S3_R1_001.fastq.gz THoa-TF3P_S3_R2_001.fastq.gz,fastq fastq,11034687150.0,73564581.0,GSM4007828 r1,0:75 1:75,A:2954740084;C:2509220120;G:2662792371;T:2906521814;N:1412761,75,75,,,2954740084,2509220120,2662792371,2906521814,1412761,SRX6657799,SRS5218260,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.90866,0.9253,0.29649,0.3138,0.7419,0.74793,0.57845,0.59013,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53519,SRR9906841,SRX6657798,SRS5218259,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAnmdahP20R2,GSM4007827,,source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:20hr|replicate:Replicate 2,zfRNAnmdahP20R2,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:20hr|replicate:Replicate 2,GSM4007827,GSM4007827: zfRNAnmdahP20R2; Danio rerio; RNA Seq,GSM4007827,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-TF2P_S2_R1_001.fastq.gz THoa-TF2P_S2_R2_001.fastq.gz,fastq fastq,10416796950.0,69445313.0,GSM4007827 r1,0:75 1:75,A:2846027907;C:2324721617;G:2438862539;T:2805866203;N:1318684,75,75,,,2846027907,2324721617,2438862539,2805866203,1318684,SRX6657798,SRS5218259,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.89999,0.92352,0.30772,0.32822,0.74823,0.75089,0.5489,0.55828,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53520,SRR9906840,SRX6657797,SRS5218258,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAnmdahP20R1,GSM4007826,,source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:20hr|replicate:Replicate 1,zfRNAnmdahP20R1,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:20hr|replicate:Replicate 1,GSM4007826,GSM4007826: zfRNAnmdahP20R1; Danio rerio; RNA Seq,GSM4007826,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-TF1P_S1_R1_001.fastq.gz THoa-TF1P_S1_R2_001.fastq.gz,fastq fastq,11087990850.0,73919939.0,GSM4007826 r1,0:75 1:75,A:3086331907;C:2414289581;G:2547013161;T:3038947630;N:1408571,75,75,,,3086331907,2414289581,2547013161,3038947630,1408571,SRX6657797,SRS5218258,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.89541,0.9175,0.30129,0.32289,0.7417,0.74714,0.55292,0.55122,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53521,SRR9906839,SRX6657796,SRS5218257,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAnmdaN36R2,GSM4007825,,source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 2,zfRNAnmdaN36R2,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 2,GSM4007825,GSM4007825: zfRNAnmdaN36R2; Danio rerio; RNA Seq,GSM4007825,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-DF16N_S7_R1_001.fastq.gz THoa-DF16N_S7_R2_001.fastq.gz,fastq fastq,7593295650.0,50621971.0,GSM4007825 r1,0:75 1:75,A:1842742463;C:1931868500;G:2009769570;T:1805690959;N:3224158,75,75,,,1842742463,1931868500,2009769570,1805690959,3224158,SRX6657796,SRS5218257,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.93981,0.95204,0.24731,0.26265,0.81412,0.81811,0.67154,0.67196,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53522,SRR9906838,SRX6657795,SRS5218256,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAnmdaN36R1,GSM4007824,,source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 1,zfRNAnmdaN36R1,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 1,GSM4007824,GSM4007824: zfRNAnmdaN36R1; Danio rerio; RNA Seq,GSM4007824,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-DF15N_S6_R1_001.fastq.gz THoa-DF15N_S6_R2_001.fastq.gz,fastq fastq,7927875450.0,52852503.0,GSM4007824 r1,0:75 1:75,A:1938512738;C:1988054202;G:2080463145;T:1917497438;N:3347927,75,75,,,1938512738,1988054202,2080463145,1917497438,3347927,SRX6657795,SRS5218256,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.93468,0.94808,0.25462,0.27334,0.81262,0.81548,0.6351,0.66108,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53523,SRR9906837,SRX6657794,SRS5218255,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAnmdaN20R2,GSM4007823,,source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:20hr|replicate:Replicate 2,zfRNAnmdaN20R2,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:20hr|replicate:Replicate 2,GSM4007823,GSM4007823: zfRNAnmdaN20R2; Danio rerio; RNA Seq,GSM4007823,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,DF29N_S7_R1_001.fastq.gz DF29N_S7_R2_001.fastq.gz,fastq fastq,7876840694.0,52829905.0,GSM4007823 r1,0:74.55 1:74.55,A:2010274884;C:1895760244;G:1963812981;T:2004863879;N:2128706,74,74,,,2010274884,1895760244,1963812981,2004863879,2128706,SRX6657794,SRS5218255,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.90858,0.91979,0.28522,0.29978,0.81742,0.82104,0.6582,0.65941,74,75,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53524,SRR9906836,SRX6657793,SRS5218254,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAnmdaN20R1,GSM4007822,,source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:20hr|replicate:Replicate 1,zfRNAnmdaN20R1,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:20hr|replicate:Replicate 1,GSM4007822,GSM4007822: zfRNAnmdaN20R1; Danio rerio; RNA Seq,GSM4007822,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-DF13N_S5_R1_001.fastq.gz THoa-DF13N_S5_R2_001.fastq.gz,fastq fastq,8003905950.0,53359373.0,GSM4007822 r1,0:75 1:75,A:1925414212;C:2030985118;G:2137411382;T:1906727349;N:3367889,75,75,,,1925414212,2030985118,2137411382,1906727349,3367889,SRX6657793,SRS5218254,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.94476,0.95272,0.22584,0.24304,0.81404,0.8186,0.68349,0.6811,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53525,SRR9906835,SRX6657792,SRS5218253,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAnmdaN10R2,GSM4007821,,source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:10hr|replicate:Replicate 2,zfRNAnmdaN10R2,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:10hr|replicate:Replicate 2,GSM4007821,GSM4007821: zfRNAnmdaN10R2; Danio rerio; RNA Seq,GSM4007821,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-DF12N_S4_R1_001.fastq.gz THoa-DF12N_S4_R2_001.fastq.gz,fastq fastq,7571445300.0,50476302.0,GSM4007821 r1,0:75 1:75,A:1961355978;C:1793618129;G:1874282399;T:1938980874;N:3207920,75,75,,,1961355978,1793618129,1874282399,1938980874,3207920,SRX6657792,SRS5218253,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.91789,0.93655,0.28528,0.30489,0.7989,0.80079,0.6136,0.62523,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53526,SRR9906834,SRX6657791,SRS5218252,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAnmdaN10R1,GSM4007820,,source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:10hr|replicate:Replicate 1,zfRNAnmdaN10R1,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:10hr|replicate:Replicate 1,GSM4007820,GSM4007820: zfRNAnmdaN10R1; Danio rerio; RNA Seq,GSM4007820,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-DF11N_S3_R1_001.fastq.gz THoa-DF11N_S3_R2_001.fastq.gz,fastq fastq,6515556150.0,43437041.0,GSM4007820 r1,0:75 1:75,A:1542198255;C:1688374350;G:1771407578;T:1510810367;N:2765600,75,75,,,1542198255,1688374350,1771407578,1510810367,2765600,SRX6657791,SRS5218252,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.94732,0.95644,0.21363,0.23778,0.82698,0.83019,0.69676,0.69466,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53527,SRR9906833,SRX6657790,SRS5218251,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAnmdaN04R2,GSM4007819,,source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:4hr|replicate:Replicate 2,zfRNAnmdaN04R2,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:4hr|replicate:Replicate 2,GSM4007819,GSM4007819: zfRNAnmdaN04R2; Danio rerio; RNA Seq,GSM4007819,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-DF10N_S2_R1_001.fastq.gz THoa-DF10N_S2_R2_001.fastq.gz,fastq fastq,7522510200.0,50150068.0,GSM4007819 r1,0:75 1:75,A:1828130590;C:1927363004;G:1976726604;T:1787097599;N:3192403,75,75,,,1828130590,1927363004,1976726604,1787097599,3192403,SRX6657790,SRS5218251,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.94502,0.9468,0.20905,0.22188,0.8436,0.8454,0.72316,0.72635,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53528,SRR9906832,SRX6657789,SRS5218250,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAnmdaN04R1,GSM4007818,,source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:4hr|replicate:Replicate 1,zfRNAnmdaN04R1,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP |time:4hr|replicate:Replicate 1,GSM4007818,GSM4007818: zfRNAnmdaN04R1; Danio rerio; RNA Seq,GSM4007818,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-DF9N_S1_R1_001.fastq.gz THoa-DF9N_S1_R2_001.fastq.gz,fastq fastq,7392867750.0,49285785.0,GSM4007818 r1,0:75 1:75,A:1807364965;C:1871069705;G:1942445368;T:1768857698;N:3130014,75,75,,,1807364965,1871069705,1942445368,1768857698,3130014,SRX6657789,SRS5218250,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.93966,0.94358,0.23683,0.25285,0.81785,0.82012,0.67242,0.69507,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53529,SRR9906831,SRX6657788,SRS5218249,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAnmdaP36R2,GSM4007817,,source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:36hr|replicate:Replicate 2,zfRNAnmdaP36R2,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:36hr|replicate:Replicate 2,GSM4007817,GSM4007817: zfRNAnmdaP36R2; Danio rerio; RNA Seq,GSM4007817,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-DF16P_S7_R1_001.fastq.gz THoa-DF16P_S7_R2_001.fastq.gz,fastq fastq,6373735248.0,42722100.0,GSM4007817 r1,0:74.59 1:74.60,A:1515782870;C:1648277663;G:1705206622;T:1501843556;N:2624537,74,74,,,1515782870,1648277663,1705206622,1501843556,2624537,SRX6657788,SRS5218249,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.94124,0.94458,0.14833,0.15451,0.82012,0.8239,0.6622,0.67093,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53530,SRR9906830,SRX6657787,SRS5218248,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAnmdaP36R1,GSM4007816,,source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:36hr|replicate:Replicate 1,zfRNAnmdaP36R1,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:36hr|replicate:Replicate 1,GSM4007816,GSM4007816: zfRNAnmdaP36R1; Danio rerio; RNA Seq,GSM4007816,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-DF15P_S6_R1_001.fastq.gz THoa-DF15P_S6_R2_001.fastq.gz,fastq fastq,6569582369.0,44039507.0,GSM4007816 r1,0:74.58 1:74.59,A:1581167169;C:1668076484;G:1734283999;T:1583362809;N:2691908,74,74,,,1581167169,1668076484,1734283999,1583362809,2691908,SRX6657787,SRS5218248,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.92986,0.93029,0.15525,0.16583,0.80825,0.81172,0.65632,0.67275,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53531,SRR9906829,SRX6657786,SRS5218247,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAnmdaP20R2R2,GSM4007815,,source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:20hr|replicate:Replicate 2,zfRNAnmdaP20R2R2,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:20hr|replicate:Replicate 2,GSM4007815,GSM4007815: zfRNAnmdaP20R2R2; Danio rerio; RNA Seq,GSM4007815,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-DF29P-run2_S7_R1_001.fastq.gz THoa-DF29P-run2_S7_R2_001.fastq.gz,fastq fastq,4138950900.0,27593006.0,GSM4007815 r1,0:75 1:75,A:1036118589;C:1022903513;G:1048995320;T:1027851668;N:3081810,75,75,,,1036118589,1022903513,1048995320,1027851668,3081810,SRX6657786,SRS5218247,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.94004,0.94676,0.14485,0.14607,0.80986,0.8102,0.6594,0.60583,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53532,SRR9906828,SRX6657785,SRS5218246,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAnmdaP20R2R1,GSM4007814,,source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:20hr|replicate:Replicate 2,zfRNAnmdaP20R2R1,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:20hr|replicate:Replicate 2,GSM4007814,GSM4007814: zfRNAnmdaP20R2R1; Danio rerio; RNA Seq,GSM4007814,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-DF29P-run1_S7_R1_001.fastq.gz THoa-DF29P-run1_S7_R2_001.fastq.gz,fastq fastq,2345611650.0,15637411.0,GSM4007814 r1,0:75 1:75,A:586100477;C:579733712;G:596500443;T:582730098;N:546920,75,75,,,586100477,579733712,596500443,582730098,546920,SRX6657785,SRS5218246,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.93951,0.94484,0.14437,0.14581,0.80738,0.80724,0.66526,0.58765,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53533,SRR9906827,SRX6657784,SRS5218245,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAnmdaP20R1,GSM4007813,,source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:20hr|replicate:Replicate 1,zfRNAnmdaP20R1,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:20hr|replicate:Replicate 1,GSM4007813,GSM4007813: zfRNAnmdaP20R1; Danio rerio; RNA Seq,GSM4007813,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-DF13P_S5_R1_001.fastq.gz THoa-DF13P_S5_R2_001.fastq.gz,fastq fastq,7039003072.0,47187560.0,GSM4007813 r1,0:74.58 1:74.59,A:1712945752;C:1757482359;G:1842953199;T:1722863594;N:2758168,74,74,,,1712945752,1757482359,1842953199,1722863594,2758168,SRX6657784,SRS5218245,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.94233,0.94816,0.14168,0.15153,0.79977,0.80549,0.62578,0.64305,72,75,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53534,SRR9906826,SRX6657783,SRS5218244,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAnmdaP10R2,GSM4007812,,source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:10hr|replicate:Replicate 2,zfRNAnmdaP10R2,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:10hr|replicate:Replicate 2,GSM4007812,GSM4007812: zfRNAnmdaP10R2; Danio rerio; RNA Seq,GSM4007812,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-DF12P_S4_R1_001.fastq.gz THoa-DF12P_S4_R2_001.fastq.gz,fastq fastq,5745697684.0,38525032.0,GSM4007812 r1,0:74.57 1:74.57,A:1416523959;C:1432155681;G:1476691642;T:1417880795;N:2445607,74,74,,,1416523959,1432155681,1476691642,1417880795,2445607,SRX6657783,SRS5218244,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.93423,0.94349,0.1837,0.191,0.81146,0.81446,0.64969,0.65118,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53535,SRR9906825,SRX6657782,SRS5218243,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAnmdaP10R1,GSM4007811,,source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:10hr|replicate:Replicate 1,zfRNAnmdaP10R1,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:10hr|replicate:Replicate 1,GSM4007811,GSM4007811: zfRNAnmdaP10R1; Danio rerio; RNA Seq,GSM4007811,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-DF11P_S3_R1_001.fastq.gz THoa-DF11P_S3_R2_001.fastq.gz,fastq fastq,4687597951.0,31430998.0,GSM4007811 r1,0:74.56 1:74.58,A:1186920007;C:1133558971;G:1178442772;T:1186839573;N:1836628,74,74,,,1186920007,1133558971,1178442772,1186839573,1836628,SRX6657782,SRS5218243,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.93636,0.94612,0.16988,0.17882,0.80014,0.80424,0.63955,0.63931,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53536,SRR9906824,SRX6657781,SRS5218242,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAnmdaP04R2,GSM4007810,,source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:4hr|replicate:Replicate 2,zfRNAnmdaP04R2,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:4hr|replicate:Replicate 2,GSM4007810,GSM4007810: zfRNAnmdaP04R2; Danio rerio; RNA Seq,GSM4007810,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-DF10P_S2_R1_001.fastq.gz THoa-DF10P_S2_R2_001.fastq.gz,fastq fastq,5482033611.0,36761528.0,GSM4007810 r1,0:74.56 1:74.57,A:1399163955;C:1327953597;G:1360796447;T:1391846223;N:2273389,74,74,,,1399163955,1327953597,1360796447,1391846223,2273389,SRX6657781,SRS5218242,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.86015,0.87027,0.18565,0.19683,0.83349,0.83666,0.62827,0.63846,72,75,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53537,SRR9906823,SRX6657780,SRS5218241,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAnmdaP04R1,GSM4007809,,source name:Retina|tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:4hr|replicate:Replicate 1,zfRNAnmdaP04R1,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:GFP]mi2001  AB|condition:NMDA treatment|cell population of facs sorting:GFP+|time:4hr|replicate:Replicate 1,GSM4007809,GSM4007809: zfRNAnmdaP04R1; Danio rerio; RNA Seq,GSM4007809,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-DF9P_S1_R1_001.fastq.gz THoa-DF9P_S1_R2_001.fastq.gz,fastq fastq,21735411065.0,145822702.0,GSM4007809 r1,0:74.54 1:74.51,A:5770843248;C:4924186554;G:5223386393;T:5808415210;N:8579660,74,74,,,5770843248,4924186554,5223386393,5808415210,8579660,SRX6657780,SRS5218241,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.32804,0.332,0.08428,0.08869,0.87584,0.87969,0.63905,0.65793,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53538,SRR9906822,SRX6657779,SRS5218240,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAldtN36R2,GSM4007808,,source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 2,zfRNAldtN36R2,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 2,GSM4007808,GSM4007808: zfRNAldtN36R2; Danio rerio; RNA Seq,GSM4007808,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-DF8N_S9_R1_001.fastq.gz THoa-DF8N_S9_R2_001.fastq.gz,fastq fastq,7461557400.0,49743716.0,GSM4007808 r1,0:75 1:75,A:1829397197;C:1872660811;G:1943038567;T:1813306644;N:3154181,75,75,,,1829397197,1872660811,1943038567,1813306644,3154181,SRX6657779,SRS5218240,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.9181,0.93155,0.26114,0.27679,0.80152,0.8045,0.67335,0.67474,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53539,SRR9906821,SRX6657778,SRS5218239,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAldtN36R1,GSM4007807,,source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 1,zfRNAldtN36R1,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 1,GSM4007807,GSM4007807: zfRNAldtN36R1; Danio rerio; RNA Seq,GSM4007807,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-DF7N_S8_R1_001.fastq.gz THoa-DF7N_S8_R2_001.fastq.gz,fastq fastq,7310480700.0,48736538.0,GSM4007807 r1,0:75 1:75,A:1851060267;C:1761439990;G:1858394380;T:1836486630;N:3099433,75,75,,,1851060267,1761439990,1858394380,1836486630,3099433,SRX6657778,SRS5218239,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.92044,0.93499,0.28396,0.29825,0.77948,0.7825,0.62758,0.63403,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53540,SRR9906820,SRX6657777,SRS5218238,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAldtN20R2,GSM4007806,,source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP |time:20hr|replicate:Replicate 2,zfRNAldtN20R2,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP |time:20hr|replicate:Replicate 2,GSM4007806,GSM4007806: zfRNAldtN20R2; Danio rerio; RNA Seq,GSM4007806,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-DF6N_S9_R1_001.fastq.gz THoa-DF6N_S9_R2_001.fastq.gz,fastq fastq,7098730131.0,47579801.0,GSM4007806 r1,0:74.60 1:74.59,A:1717050162;C:1797575844;G:1860363186;T:1720884708;N:2856231,74,74,,,1717050162,1797575844,1860363186,1720884708,2856231,SRX6657777,SRS5218238,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.93627,0.93912,0.23916,0.25175,0.80945,0.81418,0.67342,0.68259,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53541,SRR9906819,SRX6657776,SRS5218237,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAldtN20R1,GSM4007805,,source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP |time:20hr|replicate:Replicate 1,zfRNAldtN20R1,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP |time:20hr|replicate:Replicate 1,GSM4007805,GSM4007805: zfRNAldtN20R1; Danio rerio; RNA Seq,GSM4007805,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-DF5N_S8_R1_001.fastq.gz THoa-DF5N_S8_R2_001.fastq.gz,fastq fastq,7507942092.0,50334342.0,GSM4007805 r1,0:74.59 1:74.57,A:1866081920;C:1827112880;G:1922774342;T:1888960357;N:3012593,74,74,,,1866081920,1827112880,1922774342,1888960357,3012593,SRX6657776,SRS5218237,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.92572,0.93469,0.27326,0.28815,0.79084,0.79707,0.61558,0.63121,75,74,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53542,SRR9906818,SRX6657775,SRS5218236,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAldtN10R2,GSM4007804,,source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP |time:10hr|replicate:Replicate 2,zfRNAldtN10R2,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP |time:10hr|replicate:Replicate 2,GSM4007804,GSM4007804: zfRNAldtN10R2; Danio rerio; RNA Seq,GSM4007804,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-DF4N_S4_R1_001.fastq.gz THoa-DF4N_S4_R2_001.fastq.gz,fastq fastq,9118674847.0,60348350.0,GSM4007804 r1,0:75.55 1:75.55,A:2354247285;C:2165731401;G:2244032848;T:2353621167;N:1042146,75,75,,,2354247285,2165731401,2244032848,2353621167,1042146,SRX6657775,SRS5218236,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.90175,0.91595,0.25813,0.27158,0.79125,0.7931,0.62118,0.61894,76,75,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53543,SRR9906817,SRX6657774,SRS5218235,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAldtN10R1R2,GSM4007803,,source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP |time:10hr|replicate:Replicate 1,zfRNAldtN10R1R2,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP |time:10hr|replicate:Replicate 1,GSM4007803,GSM4007803: zfRNAldtN10R1R2; Danio rerio; RNA Seq,GSM4007803,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-DF2N_S4_R1_001.fastq.gz THoa-DF2N_S4_R2_001.fastq.gz,fastq fastq,6920389304.0,45528877.0,GSM4007803 r1,0:76 1:76,A:1832467265;C:1590107325;G:1661000950;T:1836680423;N:133341,76,76,,,1832467265,1590107325,1661000950,1836680423,133341,SRX6657774,SRS5218235,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.89667,0.91615,0.32531,0.34748,0.78407,0.78628,0.61109,0.59996,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53544,SRR9906816,SRX6657773,SRS5218234,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAldtN10R1R1,GSM4007802,,source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP |time:10hr|replicate:Replicate 1,zfRNAldtN10R1R1,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP |time:10hr|replicate:Replicate 1,GSM4007802,GSM4007802: zfRNAldtN10R1R1; Danio rerio; RNA Seq,GSM4007802,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,DF2N_S4_R1_001.fastq.gz DF2N_S4_R2_001.fastq.gz,fastq fastq,6701567912.0,44400966.0,GSM4007802 r1,0:75.49 1:75.44,A:1688384411;C:1625844846;G:1698926520;T:1686384951;N:2027184,75,75,,,1688384411,1625844846,1698926520,1686384951,2027184,SRX6657773,SRS5218234,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.91379,0.93036,0.29573,0.31837,0.80034,0.8017,0.638,0.65469,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53545,SRR9906815,SRX6657772,SRS5218233,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAldtN04R2,GSM4007801,,source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP |time:4hr|replicate:Replicate 2,zfRNAldtN04R2,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP |time:4hr|replicate:Replicate 2,GSM4007801,GSM4007801: zfRNAldtN04R2; Danio rerio; RNA Seq,GSM4007801,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-DF3N_S3_R1_001.fastq.gz THoa-DF3N_S3_R2_001.fastq.gz,fastq fastq,9452762624.0,62556061.0,GSM4007801 r1,0:75.55 1:75.56,A:2418410246;C:2278741513;G:2354276985;T:2400236180;N:1097700,75,75,,,2418410246,2278741513,2354276985,2400236180,1097700,SRX6657772,SRS5218233,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.90533,0.91159,0.20572,0.21726,0.81349,0.81436,0.6425,0.64845,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53546,SRR9906814,SRX6657771,SRS5218232,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAldtN04R1R2,GSM4007800,,source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP |time:4hr|replicate:Replicate 1,zfRNAldtN04R1R2,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP |time:4hr|replicate:Replicate 1,GSM4007800,GSM4007800: zfRNAldtN04R1R2; Danio rerio; RNA Seq,GSM4007800,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-DF1N_S3_R1_001.fastq.gz THoa-DF1N_S3_R2_001.fastq.gz,fastq fastq,6443366488.0,42390569.0,GSM4007800 r1,0:76 1:76,A:1668027282;C:1512803937;G:1592154543;T:1670256264;N:124462,76,76,,,1668027282,1512803937,1592154543,1670256264,124462,SRX6657771,SRS5218232,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.90685,0.92348,0.30206,0.32259,0.80016,0.80156,0.63847,0.61929,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53547,SRR9906813,SRX6657770,SRS5218231,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAldtP36R2R2,GSM4007799,,source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP+|time:36hr|replicate:Replicate 2,zfRNAldtP36R2R2,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP+|time:36hr|replicate:Replicate 2,GSM4007799,GSM4007799: zfRNAldtP36R2R2; Danio rerio; RNA Seq,GSM4007799,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-DF8P_S9_R1_001.fastq.gz THoa-DF8P_S9_R2_001.fastq.gz,fastq fastq,6236494032.0,41029566.0,GSM4007799 r1,0:76 1:76,A:1465414386;C:1634912062;G:1681819477;T:1454230315;N:117792,76,76,,,1465414386,1634912062,1681819477,1454230315,117792,SRX6657770,SRS5218231,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.94408,0.94952,0.15494,0.16176,0.82404,0.82544,0.67236,0.65741,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53548,SRR9906812,SRX6657769,SRS5218230,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAldtP36R1R2,GSM4007798,,source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP+|time:36hr|replicate:Replicate 1,zfRNAldtP36R1R2,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP+|time:36hr|replicate:Replicate 1,GSM4007798,GSM4007798: zfRNAldtP36R1R2; Danio rerio; RNA Seq,GSM4007798,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-DF7P_S10_R1_001.fastq.gz THoa-DF7P_S10_R2_001.fastq.gz,fastq fastq,7484077973.0,50162298.0,GSM4007798 r1,0:74.59 1:74.61,A:1782486863;C:1922264544;G:1989068688;T:1787280217;N:2977661,74,74,,,1782486863,1922264544,1989068688,1787280217,2977661,SRX6657769,SRS5218230,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.95471,0.95346,0.15186,0.1567,0.80332,0.80736,0.64996,0.66954,74,74,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53549,SRR9906811,SRX6657768,SRS5218229,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAldtP20R3,GSM4007797,,source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP+|time:20hr|replicate:Replicate 2,zfRNAldtP20R3,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP+|time:20hr|replicate:Replicate 2,GSM4007797,GSM4007797: zfRNAldtP20R3; Danio rerio; RNA Seq,GSM4007797,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,DF31P_S8_R1_001.fastq.gz DF31P_S8_R2_001.fastq.gz,fastq fastq,8153845075.0,54684638.0,GSM4007797 r1,0:74.54 1:74.57,A:2035354223;C:2023329236;G:2076788826;T:2016246616;N:2126174,74,74,,,2035354223,2023329236,2076788826,2016246616,2126174,SRX6657768,SRS5218229,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.93265,0.94088,0.15684,0.16053,0.80846,0.81044,0.67966,0.68311,75,72,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53550,SRR9906810,SRX6657767,SRS5218228,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAldtP20R1R2,GSM4007796,,source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP+|time:20hr|replicate:Replicate 1,zfRNAldtP20R1R2,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP+|time:20hr|replicate:Replicate 1,GSM4007796,GSM4007796: zfRNAldtP20R1R2; Danio rerio; RNA Seq,GSM4007796,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-DF5P_S7_R1_001.fastq.gz THoa-DF5P_S7_R2_001.fastq.gz,fastq fastq,7112121496.0,46790273.0,GSM4007796 r1,0:76 1:76,A:1739973400;C:1792717453;G:1855648989;T:1723646755;N:134899,76,76,,,1739973400,1792717453,1855648989,1723646755,134899,SRX6657767,SRS5218228,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.879,0.88409,0.13484,0.14289,0.83542,0.83646,0.67507,0.70811,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53551,SRR9906809,SRX6657766,SRS5218227,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAldtP10R3R2,GSM4007795,,source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP+|time:10hr|replicate:Replicate 2,zfRNAldtP10R3R2,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP+|time:10hr|replicate:Replicate 2,GSM4007795,GSM4007795: zfRNAldtP10R3R2; Danio rerio; RNA Seq,GSM4007795,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,Thoa-DF30P-run2_S8_R1_001.fastq.gz Thoa-DF30P-run2_S8_R2_001.fastq.gz,fastq fastq,12756789300.0,85045262.0,GSM4007795 r1,0:75 1:75,A:3411640312;C:2880127219;G:3046896925;T:3408585301;N:9539543,75,75,,,3411640312,2880127219,3046896925,3408585301,9539543,SRX6657766,SRS5218227,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.33812,0.34433,0.0768,0.0802,0.86082,0.86058,0.65811,0.65755,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53552,SRR9906808,SRX6657765,SRS5218226,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAldtP10R3R1,GSM4007794,,source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP+|time:10hr|replicate:Replicate 2,zfRNAldtP10R3R1,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP+|time:10hr|replicate:Replicate 2,GSM4007794,GSM4007794: zfRNAldtP10R3R1; Danio rerio; RNA Seq,GSM4007794,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-DF30P-run1_S8_R1_001.fastq.gz THoa-DF30P-run1_S8_R2_001.fastq.gz,fastq fastq,7263559800.0,48423732.0,GSM4007794 r1,0:75 1:75,A:1936778022;C:1641879024;G:1743981633;T:1939224391;N:1696730,75,75,,,1936778022,1641879024,1743981633,1939224391,1696730,SRX6657765,SRS5218226,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.33555,0.34158,0.07618,0.07959,0.85847,0.8594,0.66386,0.65576,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53553,SRR9906807,SRX6657764,SRS5218225,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAldtP10R1R2,GSM4007793,,source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP+|time:10hr|replicate:Replicate 1,zfRNAldtP10R1R2,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP+|time:10hr|replicate:Replicate 1,GSM4007793,GSM4007793: zfRNAldtP10R1R2; Danio rerio; RNA Seq,GSM4007793,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-DF2P_S2_R1_001.fastq.gz THoa-DF2P_S2_R2_001.fastq.gz,fastq fastq,6707936472.0,44131161.0,GSM4007793 r1,0:76 1:76,A:1740799990;C:1575292568;G:1651597418;T:1740118005;N:128491,76,76,,,1740799990,1575292568,1651597418,1740118005,128491,SRX6657764,SRS5218225,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.8382,0.85278,0.22937,0.24498,0.79046,0.79228,0.65323,0.64817,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53554,SRR9906806,SRX6657763,SRS5218224,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAldtP04R2R2,GSM4007792,,source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP+|time:4hr|replicate:Replicate 2,zfRNAldtP04R2R2,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP+|time:4hr|replicate:Replicate 2,GSM4007792,GSM4007792: zfRNAldtP04R2R2; Danio rerio; RNA Seq,GSM4007792,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-DF3P_S5_R1_001.fastq.gz THoa-DF3P_S5_R2_001.fastq.gz,fastq fastq,6486340688.0,42673294.0,GSM4007792 r1,0:76 1:76,A:1620859265;C:1595766403;G:1651838644;T:1617753810;N:122566,76,76,,,1620859265,1595766403,1651838644,1617753810,122566,SRX6657763,SRS5218224,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.9266,0.93745,0.22272,0.23594,0.80693,0.80886,0.66624,0.66443,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53555,SRR9906805,SRX6657762,SRS5218223,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAldtP04R2R1,GSM4007791,,source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP+|time:4hr|replicate:Replicate 2,zfRNAldtP04R2R1,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP+|time:4hr|replicate:Replicate 2,GSM4007791,GSM4007791: zfRNAldtP04R2R1; Danio rerio; RNA Seq,GSM4007791,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,DF3P_S5_R1_001.fastq.gz DF3P_S5_R2_001.fastq.gz,fastq fastq,6232060716.0,41263515.0,GSM4007791 r1,0:75.53 1:75.50,A:1454262167;C:1640522906;G:1684030380;T:1451528226;N:1717037,75,75,,,1454262167,1640522906,1684030380,1451528226,1717037,SRX6657762,SRS5218223,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.94564,0.95222,0.21542,0.23023,0.8339,0.83707,0.69637,0.6205,76,75,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53556,SRR9906804,SRX6657761,SRS5218222,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAldtP04R1R2,GSM4007790,,source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP+|time:4hr|replicate:Replicate 1,zfRNAldtP04R1R2,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP+|time:4hr|replicate:Replicate 1,GSM4007790,GSM4007790: zfRNAldtP04R1R2; Danio rerio; RNA Seq,GSM4007790,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-DF1P_S1_R1_001.fastq.gz THoa-DF1P_S1_R2_001.fastq.gz,fastq fastq,7005274768.0,46087334.0,GSM4007790 r1,0:76 1:76,A:1776496242;C:1692239427;G:1767588879;T:1768815957;N:134263,76,76,,,1776496242,1692239427,1767588879,1768815957,134263,SRX6657761,SRS5218222,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.90794,0.9194,0.26514,0.28336,0.81077,0.81124,0.63299,0.65518,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53557,SRR9906803,SRX6657760,SRS5218221,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAldtP04R1R1,GSM4007789,,source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP+|time:4hr|replicate:Replicate 1,zfRNAldtP04R1R1,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP+|time:4hr|replicate:Replicate 1,GSM4007789,GSM4007789: zfRNAldtP04R1R1; Danio rerio; RNA Seq,GSM4007789,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,DF1P_S1_R1_001.fastq.gz DF1P_S1_R2_001.fastq.gz,fastq fastq,6061320621.0,40165032.0,GSM4007789 r1,0:75.46 1:75.45,A:1512598083;C:1489834050;G:1544112556;T:1512543832;N:2232100,75,75,,,1512598083,1489834050,1544112556,1512543832,2232100,SRX6657760,SRS5218221,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.88455,0.89692,0.25418,0.26915,0.82625,0.82769,0.65697,0.64732,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53558,SRR9906802,SRX6657759,SRS5218220,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAadtN00R2,GSM4007788,,source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Control|cell population of facs sorting:GFP |time:Adult|replicate:Replicate 2,zfRNAadtN00R2,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Control|cell population of facs sorting:GFP |time:Adult|replicate:Replicate 2,GSM4007788,GSM4007788: zfRNAadtN00R2; Danio rerio; RNA Seq,GSM4007788,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-N2_S2_R1_001.fastq.gz THoa-N2_S2_R2_001.fastq.gz,fastq fastq,8845507010.0,58568328.0,GSM4007788 r1,0:75.51 1:75.51,A:2454613681;C:1922905558;G:2022484926;T:2444448951;N:1053894,75,75,,,2454613681,1922905558,2022484926,2444448951,1053894,SRX6657759,SRS5218220,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.89621,0.91455,0.27054,0.28804,0.79703,0.79906,0.59135,0.58068,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53559,SRR9906801,SRX6657758,SRS5218219,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAadtN00R1,GSM4007787,,source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Control|cell population of facs sorting:GFP |time:Adult|replicate:Replicate 1,zfRNAadtN00R1,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Control|cell population of facs sorting:GFP |time:Adult|replicate:Replicate 1,GSM4007787,GSM4007787: zfRNAadtN00R1; Danio rerio; RNA Seq,GSM4007787,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,THoa-N1_S1_R1_001.fastq.gz THoa-N1_S1_R2_001.fastq.gz,fastq fastq,8187702247.0,54214303.0,GSM4007787 r1,0:75.52 1:75.51,A:2264577330;C:1793888388;G:1895064861;T:2233150910;N:1020758,75,75,,,2264577330,1793888388,1895064861,2233150910,1020758,SRX6657758,SRS5218219,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.88635,0.90124,0.22483,0.23897,0.81237,0.81568,0.55133,0.54969,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53560,SRR9906800,SRX6657757,SRS5218218,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAadtP00R2,GSM4007786,,source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Control|cell population of facs sorting:GFP+|time:Adult|replicate:Replicate 2,zfRNAadtP00R2,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Control|cell population of facs sorting:GFP+|time:Adult|replicate:Replicate 2,GSM4007786,GSM4007786: zfRNAadtP00R2; Danio rerio; RNA Seq,GSM4007786,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,Lds0P2_S4_R1_001.fastq.gz Lds0P2_S4_R2_001.fastq.gz,fastq fastq,8063674328.0,53050489.0,GSM4007786 r1,0:76 1:76,A:2142932036;C:1892279645;G:1965160014;T:2062649309;N:653324,76,76,,,2142932036,1892279645,1965160014,2062649309,653324,SRX6657757,SRS5218218,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.93858,0.94315,0.16694,0.16908,0.83782,0.84161,0.69345,0.73603,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53561,SRR9906799,SRX6657756,SRS5218217,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAadtP00R1,GSM4007785,,source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Control|cell population of facs sorting:GFP+|time:Adult|replicate:Replicate 1,zfRNAadtP00R1,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Control|cell population of facs sorting:GFP+|time:Adult|replicate:Replicate 1,GSM4007785,GSM4007785: zfRNAadtP00R1; Danio rerio; RNA Seq,GSM4007785,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,Lds0P1_S3_R1_001.fastq.gz Lds0P1_S3_R2_001.fastq.gz,fastq fastq,8088589256.0,53214403.0,GSM4007785 r1,0:76 1:76,A:2075935926;C:1970959110;G:2022264326;T:2018771586;N:658308,76,76,,,2075935926,1970959110,2022264326,2018771586,658308,SRX6657756,SRS5218217,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.92645,0.93309,0.17732,0.18266,0.84743,0.85121,0.72406,0.73766,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53562,SRR9906798,SRX6657755,SRS5218216,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAldN36R2,GSM4007784,,source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 2,zfRNAldN36R2,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 2,GSM4007784,GSM4007784: zfRNAldN36R2; Danio rerio; RNA Seq,GSM4007784,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,TD36_2Neg_S8_R1_001.fastq.gz TD36_2Neg_S8_R2_001.fastq.gz,fastq fastq,5585507129.0,36977321.0,GSM4007784 r1,0:75.53 1:75.52,A:1441608710;C:1299899157;G:1382489435;T:1460670876;N:838951,75,75,,,1441608710,1299899157,1382489435,1460670876,838951,SRX6657755,SRS5218216,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.90161,0.90954,0.34163,0.36762,0.77208,0.77475,0.62098,0.62291,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53563,SRR9906797,SRX6657754,SRS5218215,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAldN36R1,GSM4007783,,source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 1,zfRNAldN36R1,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP |time:36hr|replicate:Replicate 1,GSM4007783,GSM4007783: zfRNAldN36R1; Danio rerio; RNA Seq,GSM4007783,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,TD36_1Neg_S7_R1_001.fastq.gz TD36_1Neg_S7_R2_001.fastq.gz,fastq fastq,5251880856.0,34783967.0,GSM4007783 r1,0:75.50 1:75.48,A:1444102469;C:1132662042;G:1193758518;T:1480759618;N:598209,75,75,,,1444102469,1132662042,1193758518,1480759618,598209,SRX6657754,SRS5218215,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.8912,0.90553,0.35443,0.38081,0.76712,0.77212,0.53833,0.52968,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53564,SRR9906796,SRX6657753,SRS5218214,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAldN00R2,GSM4007782,,source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Control|cell population of facs sorting:GFP |time:Adult|replicate:Replicate 2,zfRNAldN00R2,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Control|cell population of facs sorting:GFP |time:Adult|replicate:Replicate 2,GSM4007782,GSM4007782: zfRNAldN00R2; Danio rerio; RNA Seq,GSM4007782,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,TC2Neg_S12_R1_001.fastq.gz TC2Neg_S12_R2_001.fastq.gz,fastq fastq,5514036114.0,36521658.0,GSM4007782 r1,0:75.50 1:75.48,A:1534160858;C:1171528199;G:1254297458;T:1553209609;N:839990,75,75,,,1534160858,1171528199,1254297458,1553209609,839990,SRX6657753,SRS5218214,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.87319,0.89652,0.42952,0.45836,0.76822,0.7725,0.55467,0.54896,74,76,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53565,SRR9906795,SRX6657752,SRS5218213,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAldN00R1,GSM4007781,,source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Control|cell population of facs sorting:GFP |time:Adult|replicate:Replicate 1,zfRNAldN00R1,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Control|cell population of facs sorting:GFP |time:Adult|replicate:Replicate 1,GSM4007781,GSM4007781: zfRNAldN00R1; Danio rerio; RNA Seq,GSM4007781,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,TC1Neg_S11_R1_001.fastq.gz TC1Neg_S11_R2_001.fastq.gz,fastq fastq,6356582607.0,42101680.0,GSM4007781 r1,0:75.50 1:75.49,A:1786373439;C:1330051743;G:1429422994;T:1809862022;N:872409,75,75,,,1786373439,1330051743,1429422994,1809862022,872409,SRX6657752,SRS5218213,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.86968,0.89454,0.42965,0.45666,0.76684,0.76954,0.53875,0.5273,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53566,SRR9906794,SRX6657751,SRS5218212,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAldP36R2,GSM4007780,,source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP+|time:36hr|replicate:Replicate 2,zfRNAldP36R2,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP+|time:36hr|replicate:Replicate 2,GSM4007780,GSM4007780: zfRNAldP36R2; Danio rerio; RNA Seq,GSM4007780,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,TD36_2Pos_S6_R1_001.fastq.gz TD36_2Pos_S6_R2_001.fastq.gz,fastq fastq,4538979938.0,30037021.0,GSM4007780 r1,0:75.56 1:75.56,A:1121835185;C:1107349762;G:1178657723;T:1130551790;N:585478,75,75,,,1121835185,1107349762,1178657723,1130551790,585478,SRX6657751,SRS5218212,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.92939,0.93856,0.26301,0.28237,0.78127,0.78484,0.63081,0.64308,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53567,SRR9906793,SRX6657750,SRS5218211,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAldP36R1,GSM4007779,,source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP+|time:36hr|replicate:Replicate 1,zfRNAldP36R1,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Light damage|cell population of facs sorting:GFP+|time:36hr|replicate:Replicate 1,GSM4007779,GSM4007779: zfRNAldP36R1; Danio rerio; RNA Seq,GSM4007779,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,TD36_1Pos_S5_R1_001.fastq.gz TD36_1Pos_S5_R2_001.fastq.gz,fastq fastq,4731594110.0,31316303.0,GSM4007779 r1,0:75.55 1:75.54,A:1185964667;C:1138861246;G:1209345019;T:1196771621;N:651557,75,75,,,1185964667,1138861246,1209345019,1196771621,651557,SRX6657750,SRS5218211,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.9246,0.93426,0.26174,0.28336,0.77479,0.77784,0.60646,0.60843,74,76,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53568,SRR9906792,SRX6657749,SRS5218210,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAldP00R2,GSM4007778,,source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Control|cell population of facs sorting:GFP+|time:Adult|replicate:Replicate 2,zfRNAldP00R2,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Control|cell population of facs sorting:GFP+|time:Adult|replicate:Replicate 2,GSM4007778,GSM4007778: zfRNAldP00R2; Danio rerio; RNA Seq,GSM4007778,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,TC2Pos_S10_R1_001.fastq.gz TC2Pos_S10_R2_001.fastq.gz,fastq fastq,5591137280.0,37029316.0,GSM4007778 r1,0:75.50 1:75.49,A:1526678021;C:1222716619;G:1298242890;T:1542649889;N:849861,75,75,,,1526678021,1222716619,1298242890,1542649889,849861,SRX6657749,SRS5218210,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.88181,0.90227,0.37932,0.4036,0.79768,0.79989,0.56364,0.5577,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
53569,SRR9906791,SRX6657748,SRS5218209,SRP217505,PRJNA558770,Comparative transcriptomic and epigenomic analysis identifies key regulators of injury response and neurogenic competence in retinal glia,GSE135406,Other,Injury induces retinal Muller glia of non mammalian  but not mammalian  vertebrates to generate neurons.  To identify gene regulatory networks that control neurogenic competence in retinal glia  we used bulk and single cell RNA seq and ATAC seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish  chick and mice.  This was conducted during glial development  following inner and outer retinal injury  as well as following treatment with extrinsic factors that induce glial reprogramming.   Integration of these data  together with functional analysis of candidate genes  identified evolutionarily conserved and species specific gene regulatory networks controlling glial quiescence  gliosis  and neurogenic competence.  In zebrafish and chick  transition from quiescence to gliosis is a necessary stage in acquisition of neurogenic competence  while in mice a dedicated network suppresses this transition and rapidly restores quiescence.  These findings may help guide the design of cell based therapies aimed at restoring retinal neurons lost to disease. Overall design: In this study  to comprehensively identify transcriptional and epigenetic regulators of neurogenic competence in MG  we profiled mRNA levels using bulk RNA seq and chromatin accessibility using ATAC Assay for Transposase Accessible Chromatin sequencing technology in zebrafish and mouse in response to multiple neuronal injury models  as well as growth factor treatment. In total  we generated 105 bulk RNA Seq libraries including 5 technical replicates and 40 bulk ATAC Seq libraries.,,pubmed:33004674;pubmed:35259089;pubmed:38123561,,zfRNAldP00R1,GSM4007777,,source name:Retina|tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Control|cell population of facs sorting:GFP+|time:Adult|replicate:Replicate 1,zfRNAldP00R1,Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR Raw counts of genes were further used to calculate FPKM Fragments Per Kilobase Of Exon Per Million and identify differentially expressed genes through EdgeR post removing adaptors using cutadapt 58  50bp paired end ATAC Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters We filtered reads from chromosome M and Y  and included high mapping quality reads MAPQ score > 10 through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program. ATAC Seq peak regions were called using MACS2 with parameters   nomodel   shift  100   extsize 200. The blacklisted regions in mouse were excluded from peak regions https://www.encodeproject.org/annotations/ENCSR636HFF/. We counted the raw fragments for each peak region using HTSeq. Genome build: GRCm38/mm10 and GRCz10/danRer10 Supplementary files format and content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome  start  stop  name  length of peak region  strand  integer score for display  fold change   log10pvalue   log10qvalue  relative summit position to peak start.,Retina,For NMDA damage  adult mice  either CD1 or GLASTCreERT2; Sun1 sGFP mice at 2 month of age  were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt ended needle. Mice were sacrificed  and retinas were collected at indicated timepoints. For light damage  the mice were reared in cyclic 12 hour low light/12 hour dark conditions at the University of Florida animal housing facility. Prior to light damage  mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter Thermo Fisher Scientific Inc.  Waltham  MA and set to 2000 lux. To induce death of rods and cones  adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days  then transferred to clear polycarbonate tanks placed between four fluorescent bulbs 20 000 lux and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water. To induce amacrine and ganglion cell death  we injected N methyl D aspartic acid NMDA Sigma Aldrich; St. Louis  MO intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2 phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2 phenoxyethanol in system water.,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,To induce Cre recombination  GLASTCreERT2; Sun1 sGFP mice at 2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for xxx consecutive days at xxxmg/dose. Nfialox/lox; Nfiblox/lox  and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1 sGFP mice. To generate MG specific loss of function mutants of NFIa/b/x genes  3 wpf GLASTCreERT2; NFIa/bxlox/lox;Sun1 sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate controlled pathogen free facility on a 14 h 10 h light/dark cycle 07:00 lights on – 19:00 lights off. The adult zebrafish used in these studies were 6 mpf to 12 mpf 3 5cm in length. Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.,tissue:Retina|genotype:Tg[gfap:EGFP]nt11  albino|condition:Control|cell population of facs sorting:GFP+|time:Adult|replicate:Replicate 1,GSM4007777,GSM4007777: zfRNAldP00R1; Danio rerio; RNA Seq,GSM4007777,,1,RNA was extracted from both GFP positive and GFP negative cell fractions using miRNAeasy Mini Kit #217004  Qiagen. Ribosomal RNA was depleted  and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo ZeroTM Gold # 15032619  Illumina. For tagmentation  cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler Illumnia Nextera DNA library prep kit  #FC1211030. DNA was cleaned up using MinElute PCR purification kit #28006  Qiagen and eluted in 10UL of EB buffer. Flow sorted RNA samples were sent to the Deep Sequencing and Microarray Core Johns Hopkins University for library preparation and sequencing. Around 8 10 libraries were pooled and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run  resulting in 45 55 million reads per library. Sorted cells 50k 75k from GFP positive samples were used for ATAC library preparation. Completed ATAC Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired end 75 cycles using the NextSeq 500 system with 400 500 million reads per run.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP217505,,,TC1Pos_S4_R1_001.fastq.gz TC1Pos_S4_R2_001.fastq.gz,fastq fastq,5517591671.0,36535124.0,GSM4007777 r1,0:75.52 1:75.50,A:1482487831;C:1223340071;G:1303339516;T:1507615853;N:808400,75,75,,,1482487831,1223340071,1303339516,1507615853,808400,SRX6657748,SRS5218209,SRA934563,GEO,"Ophthalmology, Johns Hopkins University",2,0.88954,0.90541,0.36969,0.39394,0.79261,0.79299,0.56093,0.576,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,trueseq,sc_generic,bulk,bulk,,United States,2019-08-05,Multi-stage,Multi-stage,Eye,Sensory System
60457,SRR12287401,SRX8790734,SRS7059126,SRP273065,PRJNA647840,Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish,GSE154895,Transcriptome Analysis,We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.,,pubmed:33634099,,36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 3,GSM4681961,,source name:36hpf zebrafish eyes|treatment:Torrin|age:36hpf|tissue:eyes,36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 3,Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681,36hpf zebrafish eyes,,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,,treatment:Torrin|age:36hpf|tissue:eyes,GSM4681961,GSM4681961: 36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 3; Danio rerio; RNA Seq,GSM4681961,,1,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,GEO Accession:GSM4681961,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP273065,,,Tor_3.fq,fastq,611438450.0,12228769.0,GSM4681961 r1,0:50,A:155737074;C:142979561;G:143702101;T:169019714;N:0,50,,,,155737074,142979561,143702101,169019714,0,SRX8790734,SRS7059126,SRA1102335,GEO,"Clark, Ophthalmology and Visual Sciences, Washington University",1,0.96219,,0.1228,,0.73219,,0.50697,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2020-07-22,Pharyngula,Embryo,Eye,Sensory System
60458,SRR12287400,SRX8790733,SRS7059125,SRP273065,PRJNA647840,Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish,GSE154895,Transcriptome Analysis,We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.,,pubmed:33634099,,36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 2,GSM4681960,,source name:36hpf zebrafish eyes|treatment:Torrin|age:36hpf|tissue:eyes,36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 2,Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681,36hpf zebrafish eyes,,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,,treatment:Torrin|age:36hpf|tissue:eyes,GSM4681960,GSM4681960: 36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 2; Danio rerio; RNA Seq,GSM4681960,,1,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,GEO Accession:GSM4681960,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP273065,,,Tor_2.fq,fastq,610161700.0,12203234.0,GSM4681960 r1,0:50,A:153768852;C:143410611;G:145248964;T:167733273;N:0,50,,,,153768852,143410611,145248964,167733273,0,SRX8790733,SRS7059125,SRA1102335,GEO,"Clark, Ophthalmology and Visual Sciences, Washington University",1,0.96418,,0.12127,,0.73521,,0.50591,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2020-07-22,Pharyngula,Embryo,Eye,Sensory System
60459,SRR12287399,SRX8790732,SRS7059124,SRP273065,PRJNA647840,Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish,GSE154895,Transcriptome Analysis,We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.,,pubmed:33634099,,36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 1,GSM4681959,,source name:36hpf zebrafish eyes|treatment:Torrin|age:36hpf|tissue:eyes,36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 1,Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681,36hpf zebrafish eyes,,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,,treatment:Torrin|age:36hpf|tissue:eyes,GSM4681959,GSM4681959: 36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 1; Danio rerio; RNA Seq,GSM4681959,,1,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,GEO Accession:GSM4681959,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP273065,,,Tor_1.fq,fastq,568616650.0,11372333.0,GSM4681959 r1,0:50,A:143342391;C:133596830;G:136056983;T:155620446;N:0,50,,,,143342391,133596830,136056983,155620446,0,SRX8790732,SRS7059124,SRA1102335,GEO,"Clark, Ophthalmology and Visual Sciences, Washington University",1,0.96423,,0.1166,,0.73811,,0.50869,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2020-07-22,Pharyngula,Embryo,Eye,Sensory System
60460,SRR12287398,SRX8790731,SRS7059123,SRP273065,PRJNA647840,Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish,GSE154895,Transcriptome Analysis,We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.,,pubmed:33634099,,36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 3,GSM4681958,,source name:36hpf zebrafish eyes|treatment:DMSO control|age:36hpf|tissue:eyes,36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 3,Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681,36hpf zebrafish eyes,,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,,treatment:DMSO control|age:36hpf|tissue:eyes,GSM4681958,GSM4681958: 36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 3; Danio rerio; RNA Seq,GSM4681958,,1,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,GEO Accession:GSM4681958,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP273065,,,DMSO_3.fq,fastq,710747750.0,14214955.0,GSM4681958 r1,0:50,A:184360596;C:160789051;G:160903077;T:204668511;N:26515,50,,,,184360596,160789051,160903077,204668511,26515,SRX8790731,SRS7059123,SRA1102335,GEO,"Clark, Ophthalmology and Visual Sciences, Washington University",1,0.92693,,0.14102,,0.74233,,0.52477,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2020-07-22,Pharyngula,Embryo,Eye,Sensory System
60461,SRR12287397,SRX8790730,SRS7059122,SRP273065,PRJNA647840,Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish,GSE154895,Transcriptome Analysis,We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.,,pubmed:33634099,,36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 2,GSM4681957,,source name:36hpf zebrafish eyes|treatment:DMSO control|age:36hpf|tissue:eyes,36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 2,Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681,36hpf zebrafish eyes,,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,,treatment:DMSO control|age:36hpf|tissue:eyes,GSM4681957,GSM4681957: 36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 2; Danio rerio; RNA Seq,GSM4681957,,1,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,GEO Accession:GSM4681957,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP273065,,,DMSO_2.fq,fastq,710470350.0,14209407.0,GSM4681957 r1,0:50,A:180578463;C:165554366;G:164357951;T:199952943;N:26627,50,,,,180578463,165554366,164357951,199952943,26627,SRX8790730,SRS7059122,SRA1102335,GEO,"Clark, Ophthalmology and Visual Sciences, Washington University",1,0.92993,,0.12326,,0.73316,,0.50795,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2020-07-22,Pharyngula,Embryo,Eye,Sensory System
60462,SRR12287396,SRX8790729,SRS7059121,SRP273065,PRJNA647840,Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish,GSE154895,Transcriptome Analysis,We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.,,pubmed:33634099,,36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 1,GSM4681956,,source name:36hpf zebrafish eyes|treatment:DMSO control|age:36hpf|tissue:eyes,36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 1,Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681,36hpf zebrafish eyes,,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,,treatment:DMSO control|age:36hpf|tissue:eyes,GSM4681956,GSM4681956: 36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 1; Danio rerio; RNA Seq,GSM4681956,,1,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,GEO Accession:GSM4681956,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP273065,,,DMSO_1.fq,fastq,684145550.0,13682911.0,GSM4681956 r1,0:50,A:176031808;C:157711101;G:157012646;T:193364628;N:25367,50,,,,176031808,157711101,157012646,193364628,25367,SRX8790729,SRS7059121,SRA1102335,GEO,"Clark, Ophthalmology and Visual Sciences, Washington University",1,0.93134,,0.11826,,0.73742,,0.51639,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2020-07-22,Pharyngula,Embryo,Eye,Sensory System
60463,SRR12287395,SRX8790728,SRS7059120,SRP273065,PRJNA647840,Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish,GSE154895,Transcriptome Analysis,We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.,,pubmed:33634099,,36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 3,GSM4681955,,source name:36hpf zebrafish eyes|genotype:Wnt2ba overexpression|age:36hpf|tissue:eyes,36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 3,Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681,36hpf zebrafish eyes,,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,,genotype:Wnt2ba overexpression|age:36hpf|tissue:eyes,GSM4681955,GSM4681955: 36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 3; Danio rerio; RNA Seq,GSM4681955,,1,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,GEO Accession:GSM4681955,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP273065,,,Wnt2b_3.fq,fastq,1683174573.0,33003423.0,GSM4681955 r1,0:51,A:425533518;C:379417030;G:382377050;T:466758495;N:29088480,51,,,,425533518,379417030,382377050,466758495,29088480,SRX8790728,SRS7059120,SRA1102335,GEO,"Clark, Ophthalmology and Visual Sciences, Washington University",1,0.92087,,0.07926,,0.72699,,0.50196,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2020-07-22,Pharyngula,Embryo,Eye,Sensory System
60464,SRR12287394,SRX8790727,SRS7059119,SRP273065,PRJNA647840,Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish,GSE154895,Transcriptome Analysis,We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.,,pubmed:33634099,,36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 2,GSM4681954,,source name:36hpf zebrafish eyes|genotype:Wnt2ba overexpression|age:36hpf|tissue:eyes,36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 2,Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681,36hpf zebrafish eyes,,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,,genotype:Wnt2ba overexpression|age:36hpf|tissue:eyes,GSM4681954,GSM4681954: 36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 2; Danio rerio; RNA Seq,GSM4681954,,1,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,GEO Accession:GSM4681954,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP273065,,,Wnt2b_2.fq,fastq,1491166815.0,29238565.0,GSM4681954 r1,0:51,A:378958250;C:335771876;G:337239729;T:413432220;N:25764740,51,,,,378958250,335771876,337239729,413432220,25764740,SRX8790727,SRS7059119,SRA1102335,GEO,"Clark, Ophthalmology and Visual Sciences, Washington University",1,0.92209,,0.08083,,0.733,,0.51077,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2020-07-22,Pharyngula,Embryo,Eye,Sensory System
60465,SRR12287393,SRX8790726,SRS7059118,SRP273065,PRJNA647840,Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish,GSE154895,Transcriptome Analysis,We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.,,pubmed:33634099,,36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 1,GSM4681953,,source name:36hpf zebrafish eyes|genotype:Wnt2ba overexpression|age:36hpf|tissue:eyes,36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 1,Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681,36hpf zebrafish eyes,,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,,genotype:Wnt2ba overexpression|age:36hpf|tissue:eyes,GSM4681953,GSM4681953: 36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 1; Danio rerio; RNA Seq,GSM4681953,,1,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,GEO Accession:GSM4681953,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP273065,,,Wnt2b_1.fq,fastq,1919112507.0,37629657.0,GSM4681953 r1,0:51,A:477418936;C:433410513;G:453965639;T:530637937;N:23679482,51,,,,477418936,433410513,453965639,530637937,23679482,SRX8790726,SRS7059118,SRA1102335,GEO,"Clark, Ophthalmology and Visual Sciences, Washington University",1,0.78015,,0.06857,,0.73608,,0.49023,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2020-07-22,Pharyngula,Embryo,Eye,Sensory System
60466,SRR12287392,SRX8790725,SRS7059117,SRP273065,PRJNA647840,Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish,GSE154895,Transcriptome Analysis,We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.,,pubmed:33634099,,YapS87A  replicate3,GSM4681952,,source name:36hpf zebrafish eyes|genotype:YapS87A overexpression|age:36hpf|tissue:eyes,YapS87A  replicate3,Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681,36hpf zebrafish eyes,,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,,genotype:YapS87A overexpression|age:36hpf|tissue:eyes,GSM4681952,GSM4681952: YapS87A  replicate3; Danio rerio; RNA Seq,GSM4681952,,1,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,GEO Accession:GSM4681952,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP273065,,,YapS87A_3_sequence.txt,fastq,1680502581.0,32951031.0,GSM4681952 r1,0:51,A:431882743;C:376993099;G:378520286;T:464147117;N:28959336,51,,,,431882743,376993099,378520286,464147117,28959336,SRX8790725,SRS7059117,SRA1102335,GEO,"Clark, Ophthalmology and Visual Sciences, Washington University",1,0.9063,,0.08494,,0.73308,,0.45344,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2020-07-22,Pharyngula,Embryo,Eye,Sensory System
60467,SRR12287391,SRX8790724,SRS7059116,SRP273065,PRJNA647840,Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish,GSE154895,Transcriptome Analysis,We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.,,pubmed:33634099,,YapS87A  replicate2,GSM4681951,,source name:36hpf zebrafish eyes|genotype:YapS87A overexpression|age:36hpf|tissue:eyes,YapS87A  replicate2,Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681,36hpf zebrafish eyes,,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,,genotype:YapS87A overexpression|age:36hpf|tissue:eyes,GSM4681951,GSM4681951: YapS87A  replicate2; Danio rerio; RNA Seq,GSM4681951,,1,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,GEO Accession:GSM4681951,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP273065,,,YapS87A_2_sequence.txt,fastq,1742004705.0,34156955.0,GSM4681951 r1,0:51,A:447373634;C:393295480;G:396777263;T:483090843;N:21467485,51,,,,447373634,393295480,396777263,483090843,21467485,SRX8790724,SRS7059116,SRA1102335,GEO,"Clark, Ophthalmology and Visual Sciences, Washington University",1,0.90564,,0.08572,,0.72721,,0.46483,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2020-07-22,Pharyngula,Embryo,Eye,Sensory System
60468,SRR12287390,SRX8790723,SRS7059115,SRP273065,PRJNA647840,Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish,GSE154895,Transcriptome Analysis,We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.,,pubmed:33634099,,YapS87A  replicate1,GSM4681950,,source name:36hpf zebrafish eyes|genotype:YapS87A overexpression|age:36hpf|tissue:eyes,YapS87A  replicate1,Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681,36hpf zebrafish eyes,,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,,genotype:YapS87A overexpression|age:36hpf|tissue:eyes,GSM4681950,GSM4681950: YapS87A  replicate1; Danio rerio; RNA Seq,GSM4681950,,1,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,GEO Accession:GSM4681950,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP273065,,,YapS87A_1_sequence.txt,fastq,1605602451.0,31482401.0,GSM4681950 r1,0:51,A:416296166;C:357147049;G:359581538;T:444847570;N:27730128,51,,,,416296166,357147049,359581538,444847570,27730128,SRX8790723,SRS7059115,SRA1102335,GEO,"Clark, Ophthalmology and Visual Sciences, Washington University",1,0.90205,,0.08929,,0.72949,,0.47221,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2020-07-22,Pharyngula,Embryo,Eye,Sensory System
60469,SRR12287389,SRX8790722,SRS7059114,SRP273065,PRJNA647840,Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish,GSE154895,Transcriptome Analysis,We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.,,pubmed:33634099,,36hpf zebrafish eyes; WT control for Wnt2b experiments; replicate3,GSM4681949,,source name:36hpf zebrafish eyes|genotype:Gal4 Control for Wnt2b and YapS87A|age:36hpf|tissue:eyes,36hpf zebrafish eyes; WT control for Wnt2b experiments; replicate3,Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681,36hpf zebrafish eyes,,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,,genotype:Gal4 Control for Wnt2b and YapS87A|age:36hpf|tissue:eyes,GSM4681949,GSM4681949: 36hpf zebrafish eyes; WT control for Wnt2b experiments; replicate3; Danio rerio; RNA Seq,GSM4681949,,1,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,GEO Accession:GSM4681949,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP273065,,,WT_3_sequence.txt,fastq,1609588305.0,31560555.0,GSM4681949 r1,0:51,A:412663150;C:358619332;G:364439350;T:446055681;N:27810792,51,,,,412663150,358619332,364439350,446055681,27810792,SRX8790722,SRS7059114,SRA1102335,GEO,"Clark, Ophthalmology and Visual Sciences, Washington University",1,0.92187,,0.07809,,0.73517,,0.46998,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2020-07-22,Pharyngula,Embryo,Eye,Sensory System
60470,SRR12287388,SRX8790721,SRS7059113,SRP273065,PRJNA647840,Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish,GSE154895,Transcriptome Analysis,We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.,,pubmed:33634099,,36hpf zebrafish eyes; WT control for Wnt2b experiments; replicate2,GSM4681948,,source name:36hpf zebrafish eyes|genotype:Gal4 Control for Wnt2b and YapS87A|age:36hpf|tissue:eyes,36hpf zebrafish eyes; WT control for Wnt2b experiments; replicate2,Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681,36hpf zebrafish eyes,,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,,genotype:Gal4 Control for Wnt2b and YapS87A|age:36hpf|tissue:eyes,GSM4681948,GSM4681948: 36hpf zebrafish eyes; WT control for Wnt2b experiments; replicate2; Danio rerio; RNA Seq,GSM4681948,,1,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,GEO Accession:GSM4681948,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP273065,,,WT_2_sequence.txt,fastq,1637145594.0,32100894.0,GSM4681948 r1,0:51,A:414176151;C:369403072;G:372539483;T:452762354;N:28264534,51,,,,414176151,369403072,372539483,452762354,28264534,SRX8790721,SRS7059113,SRA1102335,GEO,"Clark, Ophthalmology and Visual Sciences, Washington University",1,0.92354,,0.08166,,0.73174,,0.47515,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2020-07-22,Pharyngula,Embryo,Eye,Sensory System
60471,SRR12287387,SRX8790720,SRS7059112,SRP273065,PRJNA647840,Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish,GSE154895,Transcriptome Analysis,We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.,,pubmed:33634099,,36hpf zebrafish eyes; WT control for Wnt2b experiments; replicate1,GSM4681947,,source name:36hpf zebrafish eyes|genotype:Gal4 Control for Wnt2b and YapS87A|age:36hpf|tissue:eyes,36hpf zebrafish eyes; WT control for Wnt2b experiments; replicate1,Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681,36hpf zebrafish eyes,,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,,genotype:Gal4 Control for Wnt2b and YapS87A|age:36hpf|tissue:eyes,GSM4681947,GSM4681947: 36hpf zebrafish eyes; WT control for Wnt2b experiments; replicate1; Danio rerio; RNA Seq,GSM4681947,,1,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,GEO Accession:GSM4681947,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP273065,,,WT_1_sequence.txt,fastq,1666445961.0,32675411.0,GSM4681947 r1,0:51,A:421437796;C:380026405;G:379400332;T:465027467;N:20553961,51,,,,421437796,380026405,379400332,465027467,20553961,SRX8790720,SRS7059112,SRA1102335,GEO,"Clark, Ophthalmology and Visual Sciences, Washington University",1,0.91939,,0.07636,,0.73052,,0.4731,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2020-07-22,Pharyngula,Embryo,Eye,Sensory System
60472,SRR12287386,SRX8790719,SRS7059111,SRP273065,PRJNA647840,Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish,GSE154895,Transcriptome Analysis,We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.,,pubmed:33634099,,36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 3,GSM4681946,,source name:36hpf zebrafish eyes|genotype:NICD overexpression|age:36hpf|tissue:eyes,36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 3,Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681,36hpf zebrafish eyes,,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,,genotype:NICD overexpression|age:36hpf|tissue:eyes,GSM4681946,GSM4681946: 36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 3; Danio rerio; RNA Seq,GSM4681946,,1,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,GEO Accession:GSM4681946,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP273065,,,NICD_3.fq,fastq,1687493202.0,33088102.0,GSM4681946 r1,0:51,A:466000780;C:363861781;G:362676818;T:465728464;N:29225359,51,,,,466000780,363861781,362676818,465728464,29225359,SRX8790719,SRS7059111,SRA1102335,GEO,"Clark, Ophthalmology and Visual Sciences, Washington University",1,0.90234,,0.10242,,0.71488,,0.47661,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2020-07-22,Pharyngula,Embryo,Eye,Sensory System
60473,SRR12287385,SRX8790718,SRS7059110,SRP273065,PRJNA647840,Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish,GSE154895,Transcriptome Analysis,We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.,,pubmed:33634099,,36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 2,GSM4681945,,source name:36hpf zebrafish eyes|genotype:NICD overexpression|age:36hpf|tissue:eyes,36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 2,Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681,36hpf zebrafish eyes,,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,,genotype:NICD overexpression|age:36hpf|tissue:eyes,GSM4681945,GSM4681945: 36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 2; Danio rerio; RNA Seq,GSM4681945,,1,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,GEO Accession:GSM4681945,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP273065,,,NICD_2.fq,fastq,1724098248.0,33805848.0,GSM4681945 r1,0:51,A:479329096;C:373215849;G:370751023;T:475738259;N:25064021,51,,,,479329096,373215849,370751023,475738259,25064021,SRX8790718,SRS7059110,SRA1102335,GEO,"Clark, Ophthalmology and Visual Sciences, Washington University",1,0.90041,,0.1068,,0.71571,,0.48007,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2020-07-22,Pharyngula,Embryo,Eye,Sensory System
60474,SRR12287384,SRX8790717,SRS7059109,SRP273065,PRJNA647840,Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish,GSE154895,Transcriptome Analysis,We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.,,pubmed:33634099,,36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 1,GSM4681944,,source name:36hpf zebrafish eyes|genotype:NICD overexpression|age:36hpf|tissue:eyes,36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 1,Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681,36hpf zebrafish eyes,,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,,genotype:NICD overexpression|age:36hpf|tissue:eyes,GSM4681944,GSM4681944: 36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 1; Danio rerio; RNA Seq,GSM4681944,,1,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,GEO Accession:GSM4681944,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP273065,,,NICD_1.fq,fastq,1929410682.0,37831582.0,GSM4681944 r1,0:51,A:531140272;C:421394845;G:418288095;T:530541126;N:28046344,51,,,,531140272,421394845,418288095,530541126,28046344,SRX8790717,SRS7059109,SRA1102335,GEO,"Clark, Ophthalmology and Visual Sciences, Washington University",1,0.90898,,0.10574,,0.71898,,0.47601,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2020-07-22,Pharyngula,Embryo,Eye,Sensory System
60475,SRR12287383,SRX8790716,SRS7059108,SRP273065,PRJNA647840,Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish,GSE154895,Transcriptome Analysis,We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression  compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated  including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4  activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4  activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4  and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.,,pubmed:33634099,,36hpf zebrafish eyes; Gal4 control for NICD experiments; replicate 6,GSM4681943,,source name:36hpf zebrafish eyes|genotype:NICD Control|age:36hpf|tissue:eyes,36hpf zebrafish eyes; Gal4 control for NICD experiments; replicate 6,Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt  and include YapS87A and WT samples from GSE71681,36hpf zebrafish eyes,,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,,genotype:NICD Control|age:36hpf|tissue:eyes,GSM4681943,GSM4681943: 36hpf zebrafish eyes; Gal4 control for NICD experiments; replicate 6; Danio rerio; RNA Seq,GSM4681943,,1,Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads,GEO Accession:GSM4681943,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP273065,,,NICD_Control_6.fq,fastq,2023785927.0,39682077.0,GSM4681943 r1,0:51,A:561742336;C:444105929;G:439290439;T:558958186;N:19689037,51,,,,561742336,444105929,439290439,558958186,19689037,SRX8790716,SRS7059108,SRA1102335,GEO,"Clark, Ophthalmology and Visual Sciences, Washington University",1,0.91779,,0.10376,,0.72468,,0.46199,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2020-07-22,Pharyngula,Embryo,Eye,Sensory System