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 30572,SRR27848813,SRX23511754,SRS20362222,SRP487850,PRJNA1072679,Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish,GSE254948,Transcriptome Analysis,Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.,,,,Wildtype 7,GSM8061015,,source name:Retina|tissue:Retina|genotype:Wildtype|geo loc name:missing|collection date:missing,Wildtype 7,Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.,Retina,,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,tissue:Retina|genotype:Wildtype,GSM8061015,GSM8061015: Wildtype 7; Danio rerio; RNA Seq,GSM8061015 r1,GSM8061015,1,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487850,,loader:fastq load.py,WT7_1.fq.gz WT7_2.fq.gz,fastq fastq,16387213200.0,54624044.0,GSM8061015 r1,0:150 1:150,A:4787207224;C:3312386758;G:3384738324;T:4902574775;N:306119,150,150,,,4787207224,3312386758,3384738324,4902574775,306119,SRX23511754,SRS20362222,SRA1796957,The Francis Crick Institute,The Francis Crick Institute,2,0.92431,0.91825,0.16903,0.16976,0.74067,0.75189,0.50167,0.50261,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2024-02-02,Undetermined,Embryo,Eye,Sensory System 30573,SRR27848814,SRX23511753,SRS20362221,SRP487850,PRJNA1072679,Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish,GSE254948,Transcriptome Analysis,Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.,,,,Wildtype 6,GSM8061014,,source name:Retina|tissue:Retina|genotype:Wildtype|geo loc name:missing|collection date:missing,Wildtype 6,Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.,Retina,,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,tissue:Retina|genotype:Wildtype,GSM8061014,GSM8061014: Wildtype 6; Danio rerio; RNA Seq,GSM8061014 r1,GSM8061014,1,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487850,,loader:fastq load.py,WT6_1.fq.gz WT6_2.fq.gz,fastq fastq,19114278900.0,63714263.0,GSM8061014 r1,0:150 1:150,A:5885874877;C:3513555230;G:3610119151;T:6104379853;N:349789,150,150,,,5885874877,3513555230,3610119151,6104379853,349789,SRX23511753,SRS20362221,SRA1796957,The Francis Crick Institute,The Francis Crick Institute,2,0.88104,0.87237,0.33066,0.33508,0.7357,0.7499,0.52706,0.51369,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2024-02-02,Undetermined,Embryo,Eye,Sensory System 30574,SRR27848815,SRX23511752,SRS20362220,SRP487850,PRJNA1072679,Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish,GSE254948,Transcriptome Analysis,Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.,,,,Wildtype 5,GSM8061013,,source name:Retina|tissue:Retina|genotype:Wildtype|geo loc name:missing|collection date:missing,Wildtype 5,Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.,Retina,,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,tissue:Retina|genotype:Wildtype,GSM8061013,GSM8061013: Wildtype 5; Danio rerio; RNA Seq,GSM8061013 r1,GSM8061013,1,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487850,,loader:fastq load.py,WT5_2.fq.gz WT5_1.fq.gz,fastq fastq,16120305900.0,53734353.0,GSM8061013 r1,0:150 1:150,A:4774586081;C:3152393582;G:3245217813;T:4947808687;N:299737,150,150,,,4774586081,3152393582,3245217813,4947808687,299737,SRX23511752,SRS20362220,SRA1796957,The Francis Crick Institute,The Francis Crick Institute,2,0.90351,0.89372,0.19598,0.19188,0.74468,0.76037,0.49643,0.5012,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2024-02-02,Undetermined,Embryo,Eye,Sensory System 30575,SRR27848816,SRX23511751,SRS20362219,SRP487850,PRJNA1072679,Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish,GSE254948,Transcriptome Analysis,Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.,,,,Wildtype 4,GSM8061012,,source name:Retina|tissue:Retina|genotype:Wildtype|geo loc name:missing|collection date:missing,Wildtype 4,Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.,Retina,,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,tissue:Retina|genotype:Wildtype,GSM8061012,GSM8061012: Wildtype 4; Danio rerio; RNA Seq,GSM8061012 r1,GSM8061012,1,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487850,,loader:fastq load.py,WT4_1.fq.gz WT4_2.fq.gz,fastq fastq,15545813700.0,51819379.0,GSM8061012 r1,0:150 1:150,A:4735339999;C:2883223993;G:2979819364;T:4947148649;N:281695,150,150,,,4735339999,2883223993,2979819364,4947148649,281695,SRX23511751,SRS20362219,SRA1796957,The Francis Crick Institute,The Francis Crick Institute,2,0.88431,0.87409,0.2472,0.24596,0.74675,0.76534,0.50472,0.51348,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2024-02-02,Undetermined,Embryo,Eye,Sensory System 30576,SRR27848817,SRX23511750,SRS20362218,SRP487850,PRJNA1072679,Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish,GSE254948,Transcriptome Analysis,Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.,,,,Wildtype 3,GSM8061011,,source name:Retina|tissue:Retina|genotype:Wildtype|geo loc name:missing|collection date:missing,Wildtype 3,Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.,Retina,,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,tissue:Retina|genotype:Wildtype,GSM8061011,GSM8061011: Wildtype 3; Danio rerio; RNA Seq,GSM8061011 r1,GSM8061011,1,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487850,,loader:fastq load.py,WT3_1.fq.gz WT3_2.fq.gz,fastq fastq,17883593700.0,59611979.0,GSM8061011 r1,0:150 1:150,A:5305029339;C:3503937995;G:3594774195;T:5479523425;N:328746,150,150,,,5305029339,3503937995,3594774195,5479523425,328746,SRX23511750,SRS20362218,SRA1796957,The Francis Crick Institute,The Francis Crick Institute,2,0.90376,0.89786,0.22127,0.22019,0.72941,0.74257,0.49283,0.4977,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2024-02-02,Undetermined,Embryo,Eye,Sensory System 30577,SRR27848818,SRX23511749,SRS20362217,SRP487850,PRJNA1072679,Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish,GSE254948,Transcriptome Analysis,Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.,,,,Wildtype 2,GSM8061010,,source name:Retina|tissue:Retina|genotype:Wildtype|geo loc name:missing|collection date:missing,Wildtype 2,Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.,Retina,,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,tissue:Retina|genotype:Wildtype,GSM8061010,GSM8061010: Wildtype 2; Danio rerio; RNA Seq,GSM8061010 r1,GSM8061010,1,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487850,,loader:fastq load.py,WT2_1.fq.gz WT2_2.fq.gz,fastq fastq,15921002400.0,53070008.0,GSM8061010 r1,0:150 1:150,A:4801739158;C:2898179014;G:3037454009;T:5183338180;N:292039,150,150,,,4801739158,2898179014,3037454009,5183338180,292039,SRX23511749,SRS20362217,SRA1796957,The Francis Crick Institute,The Francis Crick Institute,2,0.88935,0.87616,0.22376,0.2085,0.75367,0.78123,0.53443,0.51122,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2024-02-02,Undetermined,Embryo,Eye,Sensory System 30578,SRR27848819,SRX23511748,SRS20362216,SRP487850,PRJNA1072679,Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish,GSE254948,Transcriptome Analysis,Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.,,,,Wildtype 1,GSM8061009,,source name:Retina|tissue:Retina|genotype:Wildtype|geo loc name:missing|collection date:missing,Wildtype 1,Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.,Retina,,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,tissue:Retina|genotype:Wildtype,GSM8061009,GSM8061009: Wildtype 1; Danio rerio; RNA Seq,GSM8061009 r1,GSM8061009,1,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487850,,loader:fastq load.py,WT1_1.fq.gz WT1_2.fq.gz,fastq fastq,15664926900.0,52216423.0,GSM8061009 r1,0:150 1:150,A:4654413024;C:3082161368;G:3150203371;T:4777859952;N:289185,150,150,,,4654413024,3082161368,3150203371,4777859952,289185,SRX23511748,SRS20362216,SRA1796957,The Francis Crick Institute,The Francis Crick Institute,2,0.9012,0.89646,0.22096,0.21863,0.73507,0.7475,0.4816,0.4726,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2024-02-02,Undetermined,Embryo,Eye,Sensory System 30579,SRR27848820,SRX23511747,SRS20362215,SRP487850,PRJNA1072679,Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish,GSE254948,Transcriptome Analysis,Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.,,,,Choroideremia 7,GSM8061008,,source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing,Choroideremia 7,Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.,Retina,,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,tissue:Retina|genotype:Choroideremia,GSM8061008,GSM8061008: Choroideremia 7; Danio rerio; RNA Seq,GSM8061008 r1,GSM8061008,1,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487850,,loader:fastq load.py,CHM7_2.fq.gz CHM7_1.fq.gz,fastq fastq,16991281200.0,56637604.0,GSM8061008 r1,0:150 1:150,A:4896856485;C:3497447652;G:3598783228;T:4998138764;N:55071,150,150,,,4896856485,3497447652,3598783228,4998138764,55071,SRX23511747,SRS20362215,SRA1796957,The Francis Crick Institute,The Francis Crick Institute,2,0.926,0.92518,0.16779,0.16551,0.72393,0.73513,0.51723,0.51214,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2024-02-02,Undetermined,Embryo,Eye,Sensory System 30580,SRR27848821,SRX23511746,SRS20362214,SRP487850,PRJNA1072679,Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish,GSE254948,Transcriptome Analysis,Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.,,,,Choroideremia 6,GSM8061007,,source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing,Choroideremia 6,Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.,Retina,,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,tissue:Retina|genotype:Choroideremia,GSM8061007,GSM8061007: Choroideremia 6; Danio rerio; RNA Seq,GSM8061007 r1,GSM8061007,1,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487850,,loader:fastq load.py,CHM6_1.fq.gz CHM6_2.fq.gz,fastq fastq,18881901900.0,62939673.0,GSM8061007 r1,0:150 1:150,A:5796692721;C:3348140904;G:3547934333;T:6189072751;N:61191,150,150,,,5796692721,3348140904,3547934333,6189072751,61191,SRX23511746,SRS20362214,SRA1796957,The Francis Crick Institute,The Francis Crick Institute,2,0.86869,0.86484,0.26053,0.2569,0.75057,0.77705,0.66121,0.65975,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2024-02-02,Undetermined,Embryo,Eye,Sensory System 30581,SRR27848822,SRX23511745,SRS20362213,SRP487850,PRJNA1072679,Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish,GSE254948,Transcriptome Analysis,Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.,,,,Choroideremia 5,GSM8061006,,source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing,Choroideremia 5,Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.,Retina,,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,tissue:Retina|genotype:Choroideremia,GSM8061006,GSM8061006: Choroideremia 5; Danio rerio; RNA Seq,GSM8061006 r1,GSM8061006,1,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487850,,loader:fastq load.py,CHM5_2.fq.gz CHM5_1.fq.gz,fastq fastq,17802156900.0,59340523.0,GSM8061006 r1,0:150 1:150,A:5198674613;C:3599354426;G:3698229931;T:5305840019;N:57911,150,150,,,5198674613,3599354426,3698229931,5305840019,57911,SRX23511745,SRS20362213,SRA1796957,The Francis Crick Institute,The Francis Crick Institute,2,0.9109,0.91251,0.18901,0.18793,0.72354,0.73456,0.51839,0.52348,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2024-02-02,Undetermined,Embryo,Eye,Sensory System 30582,SRR27848823,SRX23511744,SRS20362212,SRP487850,PRJNA1072679,Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish,GSE254948,Transcriptome Analysis,Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.,,,,Choroideremia 4,GSM8061005,,source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing,Choroideremia 4,Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.,Retina,,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,tissue:Retina|genotype:Choroideremia,GSM8061005,GSM8061005: Choroideremia 4; Danio rerio; RNA Seq,GSM8061005 r1,GSM8061005,1,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487850,,loader:fastq load.py,CHM4_2.fq.gz CHM4_1.fq.gz,fastq fastq,15944831400.0,53149438.0,GSM8061005 r1,0:150 1:150,A:4833633886;C:2870981386;G:3055307522;T:5184819306;N:89300,150,150,,,4833633886,2870981386,3055307522,5184819306,89300,SRX23511744,SRS20362212,SRA1796957,The Francis Crick Institute,The Francis Crick Institute,2,0.88929,0.88364,0.25277,0.24996,0.75317,0.77826,0.64914,0.65907,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2024-02-02,Undetermined,Embryo,Eye,Sensory System 30583,SRR27848824,SRX23511743,SRS20362211,SRP487850,PRJNA1072679,Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish,GSE254948,Transcriptome Analysis,Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.,,,,Choroideremia 3,GSM8061004,,source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing,Choroideremia 3,Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.,Retina,,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,tissue:Retina|genotype:Choroideremia,GSM8061004,GSM8061004: Choroideremia 3; Danio rerio; RNA Seq,GSM8061004 r1,GSM8061004,1,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487850,,loader:fastq load.py,CHM3_1.fq.gz CHM3_2.fq.gz,fastq fastq,16028608800.0,53428696.0,GSM8061004 r1,0:150 1:150,A:4842495383;C:2966448486;G:3084331699;T:5135033798;N:299434,150,150,,,4842495383,2966448486,3084331699,5135033798,299434,SRX23511743,SRS20362211,SRA1796957,The Francis Crick Institute,The Francis Crick Institute,2,0.89747,0.88445,0.23706,0.23597,0.72904,0.75187,0.5514,0.45471,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2024-02-02,Undetermined,Embryo,Eye,Sensory System 30584,SRR27848825,SRX23511742,SRS20362210,SRP487850,PRJNA1072679,Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish,GSE254948,Transcriptome Analysis,Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.,,,,Choroideremia 2,GSM8061003,,source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing,Choroideremia 2,Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.,Retina,,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,tissue:Retina|genotype:Choroideremia,GSM8061003,GSM8061003: Choroideremia 2; Danio rerio; RNA Seq,GSM8061003 r1,GSM8061003,1,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487850,,loader:fastq load.py,CHM2_1.fq.gz CHM2_2.fq.gz,fastq fastq,14968884300.0,49896281.0,GSM8061003 r1,0:150 1:150,A:4575866591;C:2606132581;G:2819446784;T:4967389772;N:48572,150,150,,,4575866591,2606132581,2819446784,4967389772,48572,SRX23511742,SRS20362210,SRA1796957,The Francis Crick Institute,The Francis Crick Institute,2,0.88022,0.87326,0.29312,0.29812,0.7335,0.76228,0.5854,0.57614,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2024-02-02,Undetermined,Embryo,Eye,Sensory System 30585,SRR27848826,SRX23511741,SRS20362209,SRP487850,PRJNA1072679,Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish,GSE254948,Transcriptome Analysis,Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.,,,,Choroideremia 1,GSM8061002,,source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing,Choroideremia 1,Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.,Retina,,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,tissue:Retina|genotype:Choroideremia,GSM8061002,GSM8061002: Choroideremia 1; Danio rerio; RNA Seq,GSM8061002 r1,GSM8061002,1,Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN ≥ 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487850,,loader:fastq load.py,CHM1_2.fq.gz CHM1_1.fq.gz,fastq fastq,15862639500.0,52875465.0,GSM8061002 r1,0:150 1:150,A:4812544148;C:2881706406;G:3014671171;T:5153419977;N:297798,150,150,,,4812544148,2881706406,3014671171,5153419977,297798,SRX23511741,SRS20362209,SRA1796957,The Francis Crick Institute,The Francis Crick Institute,2,0.89157,0.87804,0.24616,0.24284,0.73884,0.76232,0.58251,0.58918,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2024-02-02,Undetermined,Embryo,Eye,Sensory System 33304,SRR29927538,SRX25421512,SRS22081668,SRP521592,PRJNA1139127,Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration,PRJNA1139127,Other,Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.,,,,INL 3d rep2,MCWR 2019 000138,,strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin Milwaukee|sex:male|tissue:retina|treatment:INL 3d rep2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 3 day post optic nerve injury inner nuclear layer,INL 3d rep2,INL 3d rep2,SMART Seqv4,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP521592,,,MCWR_2019_000138_S10_L001_R1_001.fastq.gz MCWR_2019_000138_S10_L001_R2_001.fastq.gz MCWR_2019_000138_S10_L002_R1_001.fastq.gz MCWR_2019_000138_S10_L002_R2_001.fastq.gz,fastq fastq fastq fastq,12792286105.0,42489107.0,MCWR 2019 000138 S10 L001 R1 001.fastq.gz,0:150.53 1:150.54,A:3362192057;C:3017281691;G:3072735924;T:3339916027;N:160406,150,150,,,3362192057,3017281691,3072735924,3339916027,160406,SRX25421512,SRS22081668,SRA1930690,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.95023,0.94904,0.10306,0.10406,0.71167,0.71305,0.46929,0.47143,149,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2024-07-23,Adult,Adult,Eye,Sensory System 33305,SRR29927539,SRX25421511,SRS22081667,SRP521592,PRJNA1139127,Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration,PRJNA1139127,Other,Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.,,,,INL 3d rep1,MCWR 2019 000137,,strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin Milwaukee|sex:male|tissue:retina|treatment:INL 3d rep1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 3 day post optic nerve injury inner nuclear layer,INL 3d rep1,INL 3d rep1,SMART Seqv4,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP521592,,,MCWR_2019_000137_S9_L001_R1_001.fastq.gz MCWR_2019_000137_S9_L001_R2_001.fastq.gz MCWR_2019_000137_S9_L002_R1_001.fastq.gz MCWR_2019_000137_S9_L002_R2_001.fastq.gz,fastq fastq fastq fastq,11290383949.0,37500632.0,MCWR 2019 000137 S9 L001 R1 001.fastq.gz,0:150.53 1:150.54,A:2978304239;C:2650227687;G:2709306614;T:2952404306;N:141103,150,150,,,2978304239,2650227687,2709306614,2952404306,141103,SRX25421511,SRS22081667,SRA1930690,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.95037,0.94915,0.09395,0.0939,0.71019,0.71143,0.47425,0.46854,151,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2024-07-23,Adult,Adult,Eye,Sensory System 33306,SRR29927540,SRX25421510,SRS22081666,SRP521592,PRJNA1139127,Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration,PRJNA1139127,Other,Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.,,,,INL Control rep3,MCWR 2019 000136,,strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin Milwaukee|sex:male|tissue:retina|treatment:INL Control rep3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: naive inner nuclear layer,INL Control rep3,INL Control rep3,SMART Seqv4,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP521592,,,MCWR_2019_000136_S8_L001_R1_001.fastq.gz MCWR_2019_000136_S8_L001_R2_001.fastq.gz MCWR_2019_000136_S8_L002_R1_001.fastq.gz MCWR_2019_000136_S8_L002_R2_001.fastq.gz,fastq fastq fastq fastq,10926876847.0,36289612.0,MCWR 2019 000136 S8 L001 R1 001.fastq.gz,0:150.54 1:150.56,A:2876719537;C:2534137531;G:2628404662;T:2887478941;N:136176,150,150,,,2876719537,2534137531,2628404662,2887478941,136176,SRX25421510,SRS22081666,SRA1930690,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.9413,0.94085,0.12465,0.12554,0.71565,0.71536,0.47866,0.47866,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2024-07-23,Adult,Adult,Eye,Sensory System 33307,SRR29927541,SRX25421509,SRS22081665,SRP521592,PRJNA1139127,Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration,PRJNA1139127,Other,Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.,,,,INL Control rep2,MCWR 2019 000135,,strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin Milwaukee|sex:male|tissue:retina|treatment:INL Control rep2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: naive inner nuclear layer,INL Control rep2,INL Control rep2,SMART Seqv4,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP521592,,,MCWR_2019_000135_S7_L001_R1_001.fastq.gz MCWR_2019_000135_S7_L001_R2_001.fastq.gz MCWR_2019_000135_S7_L002_R1_001.fastq.gz MCWR_2019_000135_S7_L002_R2_001.fastq.gz,fastq fastq fastq fastq,11015573968.0,36586451.0,MCWR 2019 000135 S7 L001 R1 001.fastq.gz,0:150.54 1:150.54,A:2922133009;C:2558945272;G:2631247657;T:2903110333;N:137697,150,150,,,2922133009,2558945272,2631247657,2903110333,137697,SRX25421509,SRS22081665,SRA1930690,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.94458,0.94452,0.1088,0.10943,0.71167,0.71161,0.48464,0.48393,149,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2024-07-23,Adult,Adult,Eye,Sensory System 33308,SRR29927542,SRX25421508,SRS22081664,SRP521592,PRJNA1139127,Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration,PRJNA1139127,Other,Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.,,,,INL Control rep1,MCWR 2019 000134,,strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin Milwaukee|sex:male|tissue:retina|treatment:INL Control rep1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: naive inner nuclear layer,INL Control rep1,INL Control rep1,SMART Seqv4,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP521592,,,MCWR_2019_000134_S6_L001_R1_001.fastq.gz MCWR_2019_000134_S6_L001_R2_001.fastq.gz MCWR_2019_000134_S6_L002_R1_001.fastq.gz MCWR_2019_000134_S6_L002_R2_001.fastq.gz,fastq fastq fastq fastq,12065204348.0,40074475.0,MCWR 2019 000134 S6 L001 R1 001.fastq.gz,0:150.53 1:150.54,A:3229181479;C:2787700756;G:2849413410;T:3198752940;N:155763,150,150,,,3229181479,2787700756,2849413410,3198752940,155763,SRX25421508,SRS22081664,SRA1930690,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.94249,0.94233,0.10755,0.10774,0.71427,0.71449,0.48361,0.48286,151,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2024-07-23,Adult,Adult,Eye,Sensory System 33309,SRR29927543,SRX25421507,SRS22081663,SRP521592,PRJNA1139127,Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration,PRJNA1139127,Other,Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.,,,,GCL 3d rep3,MCWR 2019 000133,,strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin Milwaukee|sex:male|tissue:retina|treatment:GCL 3d rep3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 3 day post optic nerve injury ganglion cell layer,GCL 3d rep3,GCL 3d rep3,SMART Seqv4,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP521592,,,MCWR_2019_000133_S5_L001_R1_001.fastq.gz MCWR_2019_000133_S5_L001_R2_001.fastq.gz MCWR_2019_000133_S5_L002_R1_001.fastq.gz MCWR_2019_000133_S5_L002_R2_001.fastq.gz,fastq fastq fastq fastq,11567455830.0,38423805.0,MCWR 2019 000133 S5 L001 R1 001.fastq.gz,0:150.52 1:150.52,A:3334076845;C:2423637444;G:2488288638;T:3321309876;N:143027,150,150,,,3334076845,2423637444,2488288638,3321309876,143027,SRX25421507,SRS22081663,SRA1930690,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.90351,0.90273,0.20071,0.20036,0.7443,0.74588,0.57805,0.58483,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2024-07-23,Adult,Adult,Eye,Sensory System 33310,SRR29927544,SRX25421506,SRS22081662,SRP521592,PRJNA1139127,Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration,PRJNA1139127,Other,Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.,,,,GCL 3d rep2,MCWR 2019 000132,,strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin Milwaukee|sex:male|tissue:retina|treatment:GCL 3d rep2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 3 day post optic nerve injury ganglion cell layer,GCL 3d rep2,GCL 3d rep2,SMART Seqv4,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP521592,,,MCWR_2019_000132_S4_L001_R1_001.fastq.gz MCWR_2019_000132_S4_L001_R2_001.fastq.gz MCWR_2019_000132_S4_L002_R1_001.fastq.gz MCWR_2019_000132_S4_L002_R2_001.fastq.gz,fastq fastq fastq fastq,9928742591.0,32979607.0,MCWR 2019 000132 S4 L001 R1 001.fastq.gz,0:150.53 1:150.53,A:2670122365;C:2289339998;G:2333968379;T:2635186637;N:125212,150,150,,,2670122365,2289339998,2333968379,2635186637,125212,SRX25421506,SRS22081662,SRA1930690,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.94453,0.9429,0.1039,0.10476,0.72032,0.72184,0.51703,0.51652,148,149,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2024-07-23,Adult,Adult,Eye,Sensory System 33313,SRR29927547,SRX25421503,SRS22081659,SRP521592,PRJNA1139127,Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration,PRJNA1139127,Other,Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.,,,,GCL 3d rep1,MCWR 2019 000131,,strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin Milwaukee|sex:male|tissue:retina|treatment:GCL 3d rep1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 3 day post optic nerve injury ganglion cell layer,GCL 3d rep1,GCL 3d rep1,SMART Seqv4,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP521592,,,MCWR_2019_000131_S3_L001_R1_001.fastq.gz MCWR_2019_000131_S3_L001_R2_001.fastq.gz MCWR_2019_000131_S3_L002_R1_001.fastq.gz MCWR_2019_000131_S3_L002_R2_001.fastq.gz,fastq fastq fastq fastq,11040747879.0,36674133.0,MCWR 2019 000131 S3 L001 R1 001.fastq.gz,0:150.52 1:150.53,A:3033865749;C:2483236067;G:2540109846;T:2983395404;N:140813,150,150,,,3033865749,2483236067,2540109846,2983395404,140813,SRX25421503,SRS22081659,SRA1930690,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.9328,0.93075,0.12255,0.12345,0.72675,0.72949,0.52776,0.53024,150,149,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2024-07-23,Adult,Adult,Eye,Sensory System 33318,SRR29927552,SRX25421498,SRS22081654,SRP521592,PRJNA1139127,Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration,PRJNA1139127,Other,Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.,,,,ONL 3d rep3,MCWR 2019 000145,,strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin Milwaukee|sex:male|tissue:retina|treatment:ONL 3d rep3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 3 day post optic nerve injury outer nuclear layer,ONL 3d rep3,ONL 3d rep3,SMART Seqv4,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP521592,,,MCWR_2019_000145_S16_L001_R1_001.fastq.gz MCWR_2019_000145_S16_L001_R2_001.fastq.gz MCWR_2019_000145_S16_L002_R1_001.fastq.gz MCWR_2019_000145_S16_L002_R2_001.fastq.gz,fastq fastq fastq fastq,11434401733.0,37973868.0,MCWR 2019 000145 S16 L001 R1 001.fastq.gz,0:150.56 1:150.55,A:2952068036;C:2779158705;G:2786796140;T:2916234156;N:144696,150,150,,,2952068036,2779158705,2786796140,2916234156,144696,SRX25421498,SRS22081654,SRA1930690,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.95416,0.95385,0.07766,0.07806,0.79024,0.78989,0.40138,0.42872,150,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2024-07-23,Adult,Adult,Eye,Sensory System 33319,SRR29927553,SRX25421497,SRS22081653,SRP521592,PRJNA1139127,Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration,PRJNA1139127,Other,Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.,,,,ONL 3d rep2,MCWR 2019 000144,,strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin Milwaukee|sex:male|tissue:retina|treatment:ONL 3d rep2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 3 day post optic nerve injury outer nuclear layer,ONL 3d rep2,ONL 3d rep2,SMART Seqv4,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP521592,,,MCWR_2019_000144_S15_L002_R2_001.fastq.gz MCWR_2019_000144_S15_L002_R1_001.fastq.gz MCWR_2019_000144_S15_L001_R2_001.fastq.gz MCWR_2019_000144_S15_L001_R1_001.fastq.gz,fastq fastq fastq fastq,10784131193.0,35816254.0,MCWR 2019 000144 S15 L001 R1 001.fastq.gz,0:150.55 1:150.55,A:2770521598;C:2622163802;G:2642603869;T:2748709177;N:132747,150,150,,,2770521598,2622163802,2642603869,2748709177,132747,SRX25421497,SRS22081653,SRA1930690,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.95823,0.9574,0.06867,0.06894,0.77055,0.77234,0.43067,0.43052,149,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2024-07-23,Adult,Adult,Eye,Sensory System 33320,SRR29927554,SRX25421496,SRS22081652,SRP521592,PRJNA1139127,Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration,PRJNA1139127,Other,Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.,,,,ONL 3d rep1,MCWR 2019 000143,,strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin Milwaukee|sex:male|tissue:retina|treatment:ONL 3d rep1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 3 day post optic nerve injury outer nuclear layer,ONL 3d rep1,ONL 3d rep1,SMART Seqv4,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP521592,,,MCWR_2019_000143_S14_L001_R1_001.fastq.gz MCWR_2019_000143_S14_L001_R2_001.fastq.gz MCWR_2019_000143_S14_L002_R1_001.fastq.gz MCWR_2019_000143_S14_L002_R2_001.fastq.gz,fastq fastq fastq fastq,10414222985.0,34587231.0,MCWR 2019 000143 S14 L001 R1 001.fastq.gz,0:150.55 1:150.55,A:2640548677;C:2562227240;G:2582839755;T:2628478265;N:129048,150,150,,,2640548677,2562227240,2582839755,2628478265,129048,SRX25421496,SRS22081652,SRA1930690,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.95893,0.95898,0.06693,0.06725,0.78216,0.7833,0.41018,0.40065,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2024-07-23,Adult,Adult,Eye,Sensory System 33321,SRR29927555,SRX25421495,SRS22081651,SRP521592,PRJNA1139127,Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration,PRJNA1139127,Other,Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.,,,,ONL Control rep3,MCWR 2019 000142,,strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin Milwaukee|sex:male|tissue:retina|treatment:ONL Control rep3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: naive outer nuclear layer,ONL Control rep3,ONL Control rep3,SMART Seqv4,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP521592,,,MCWR_2019_000142_S13_L001_R1_001.fastq.gz MCWR_2019_000142_S13_L001_R2_001.fastq.gz MCWR_2019_000142_S13_L002_R1_001.fastq.gz MCWR_2019_000142_S13_L002_R2_001.fastq.gz,fastq fastq fastq fastq,10611460744.0,35241917.0,MCWR 2019 000142 S13 L001 R1 001.fastq.gz,0:150.55 1:150.55,A:2729659216;C:2572974863;G:2597112533;T:2711584081;N:130051,150,150,,,2729659216,2572974863,2597112533,2711584081,130051,SRX25421495,SRS22081651,SRA1930690,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.95524,0.95438,0.08233,0.08236,0.76654,0.76682,0.41657,0.41626,151,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2024-07-23,Adult,Adult,Eye,Sensory System 33322,SRR29927556,SRX25421494,SRS22081650,SRP521592,PRJNA1139127,Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration,PRJNA1139127,Other,Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.,,,,ONL Control rep2,MCWR 2019 000141,,strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin Milwaukee|sex:male|tissue:retina|treatment:ONL Control rep2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: naive outer nuclear layer,ONL Control rep2,ONL Control rep2,SMART Seqv4,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP521592,,,MCWR_2019_000141_S12_L001_R1_001.fastq.gz MCWR_2019_000141_S12_L001_R2_001.fastq.gz MCWR_2019_000141_S12_L002_R1_001.fastq.gz MCWR_2019_000141_S12_L002_R2_001.fastq.gz,fastq fastq fastq fastq,12296763008.0,40838426.0,MCWR 2019 000141 S12 L001 R1 001.fastq.gz,0:150.55 1:150.55,A:3157494503;C:2976873172;G:3025100891;T:3137136259;N:158183,150,150,,,3157494503,2976873172,3025100891,3137136259,158183,SRX25421494,SRS22081650,SRA1930690,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.9531,0.95203,0.08284,0.08254,0.76816,0.76879,0.40735,0.41583,150,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2024-07-23,Adult,Adult,Eye,Sensory System 33323,SRR29927557,SRX25421493,SRS22081649,SRP521592,PRJNA1139127,Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration,PRJNA1139127,Other,Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.,,,,ONL Control rep1,MCWR 2019 000140,,strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin Milwaukee|sex:male|tissue:retina|treatment:ONL Control rep1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: naive outer nuclear layer,ONL Control rep1,ONL Control rep1,SMART Seqv4,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP521592,,,MCWR_2019_000140_S11_L001_R1_001.fastq.gz MCWR_2019_000140_S11_L001_R2_001.fastq.gz MCWR_2019_000140_S11_L002_R1_001.fastq.gz MCWR_2019_000140_S11_L002_R2_001.fastq.gz,fastq fastq fastq fastq,12797441059.0,42498374.0,MCWR 2019 000140 S11 L001 R1 001.fastq.gz,0:150.56 1:150.56,A:3214435348;C:3160301138;G:3218337754;T:3204200743;N:166076,150,150,,,3214435348,3160301138,3218337754,3204200743,166076,SRX25421493,SRS22081649,SRA1930690,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.95836,0.95804,0.0672,0.06787,0.79255,0.7933,0.37626,0.37493,149,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2024-07-23,Adult,Adult,Eye,Sensory System 33324,SRR29927558,SRX25421492,SRS22081648,SRP521592,PRJNA1139127,Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration,PRJNA1139127,Other,Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.,,,,GCL Control rep2,MCWR 2019 000129,,strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin Milwaukee|sex:male|tissue:retina|treatment:GCL Control rep2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: naive ganglion cell layer,GCL Control rep2,GCL Control rep2,SMART Seqv4,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP521592,,,MCWR_2019_000129_S2_L001_R1_001.fastq.gz MCWR_2019_000129_S2_L001_R2_001.fastq.gz MCWR_2019_000129_S2_L002_R1_001.fastq.gz MCWR_2019_000129_S2_L002_R2_001.fastq.gz,fastq fastq fastq fastq,9904585990.0,32898356.0,MCWR 2019 000129 S2 L001 R1 001.fastq.gz,0:150.53 1:150.54,A:2686769990;C:2251531625;G:2320304039;T:2645855407;N:124929,150,150,,,2686769990,2251531625,2320304039,2645855407,124929,SRX25421492,SRS22081648,SRA1930690,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.93013,0.93029,0.10617,0.10657,0.74712,0.74757,0.56746,0.56517,150,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2024-07-23,Adult,Adult,Eye,Sensory System 33325,SRR29927559,SRX25421491,SRS22081647,SRP521592,PRJNA1139127,Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration,PRJNA1139127,Other,Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.,,,,GCL Control rep1,MCWR 2019 000128,,strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin Milwaukee|sex:male|tissue:retina|treatment:GCL Control rep1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: naive ganglion cell layer,GCL Control rep1,GCL Control rep1,SMART Seqv4,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP521592,,,MCWR_2019_000128_S1_L001_R1_001.fastq.gz MCWR_2019_000128_S1_L001_R2_001.fastq.gz MCWR_2019_000128_S1_L002_R1_001.fastq.gz MCWR_2019_000128_S1_L002_R2_001.fastq.gz,fastq fastq fastq fastq,11199698460.0,37200254.0,MCWR 2019 000128 S1 L001 R1 001.fastq.gz,0:150.53 1:150.53,A:3065207886;C:2519670393;G:2596314938;T:3018365726;N:139517,150,150,,,3065207886,2519670393,2596314938,3018365726,139517,SRX25421491,SRS22081647,SRA1930690,"Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy",Medical College of Wisconsin,2,0.93213,0.93206,0.13073,0.13125,0.7305,0.73079,0.5518,0.55133,149,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,United States,2024-07-23,Adult,Adult,Eye,Sensory System 60520,SRR12340458,SRX8840229,SRS7103463,SRP273985,PRJNA649260,THE IMMUNE RESPONSE MODULATES ZEBRAFISH RETINAL PIGMENT EPITHELIUM REGENERATION [RPE],GSE155294,Transcriptome Analysis,Loss of the retinal pigment epithelium RPE due to dysfunction or disease can lead to blindness in humans. Harnessing the intrinsic ability of the RPE to self repair is an attractive therapeutic strategy; however mammalian RPE is limited in its regenerative capacity. Zebrafish possess tremendous intrinsic regenerative potential in ocular tissues including the RPE but little is known about the mechanisms that drive RPE regeneration. Here utilizing zebrafish we identified elements of the immune response as critical mediators of intrinsic RPE regeneration. Macrophages/microglia are responsive to RPE damage and are required for the timely progression of the regenerative response and our data highlight that inflammation post RPE injury is also critical for normal RPE regeneration. These data are the first to identify the molecular and cellular underpinnings of RPE regeneration in any system and hold significant potential for translational approaches aimed towards promoting a pro regenerative environment in mammals. Overall design: RNA seq from FACS purified retinal pigment epithelium RPE post genetic ablation and in unablated controls at 3 timepoints: 2 4 7 xxx post injury dpi. MTZ indicates unablated samples MTZ+ indicates ablated samples.,,pubmed:34006636,,Gross B1 3 1 18 S6 R1 001,GSM4698653,,tissue:retinal pigment epithelium|treatment:MTZ+|time point:7dpi|replicate:3,Gross B1 3 1 18 S6 R1 001,All processing of raw data was performed using the CLC Genomics Workbench v10 Toolbox Reads were trimmed using quality trim limit = 0.05 ambiguous trim = 2 and automatic read through adapter trimming enabled Trim Reads tool v2.1 Reads were mapped to the zebrafish reference genome GRCz10 and TPM expression values were caluclated using the RNA seq Analysis tool v2.16 in CLC Genomics Workbench Genome build: GRCz10 Supplementary files format and content: tab delimited text files containing TPM and total counts for all genes for all samples from each timepoint,retinal pigment epithelium,A subset of larvae 3 replicates from each timepoint were treated with 10mM metronidazole MTZ from 5 6dpf 24 hours to ablate the retinal pigment epithelium,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,Embryos/larvae were treated with 1.5X phenylthiourea PTU in system water from 0.25 5dpf to stop pigmentation. post 5dpf larvae were maintained in system water for the remaining duration of the experiment.,treatment:MTZ+|time point:7dpi|replicate:3,GSM4698653,GSM4698653: Gross B1 3 1 18 S6 R1 001; Danio rerio; RNA Seq,GSM4698653,,1,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,GEO Accession:GSM4698653,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP273985,,,Gross_B1_3_1_18_S6_R1_001.fastq.gz Gross_B1_3_1_18_S6_R2_001.fastq.gz,fastq fastq,8696093700.0,57973958.0,GSM4698653 r1,0:75 1:75,A:2444655785;C:1908991493;G:1829109199;T:2511690358;N:1646865,75,75,,,2444655785,1908991493,1829109199,2511690358,1646865,SRX8840229,SRS7103463,SRA1104764,GEO,"Ophthalmology, University of Pittsburgh School Of Medicine",2,0.88587,0.88723,0.15974,0.15917,0.78248,0.78464,0.59661,0.57767,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2020-07-28,Larval,Larval,Eye,Sensory System 60521,SRR12340457,SRX8840228,SRS7103462,SRP273985,PRJNA649260,THE IMMUNE RESPONSE MODULATES ZEBRAFISH RETINAL PIGMENT EPITHELIUM REGENERATION [RPE],GSE155294,Transcriptome Analysis,Loss of the retinal pigment epithelium RPE due to dysfunction or disease can lead to blindness in humans. Harnessing the intrinsic ability of the RPE to self repair is an attractive therapeutic strategy; however mammalian RPE is limited in its regenerative capacity. Zebrafish possess tremendous intrinsic regenerative potential in ocular tissues including the RPE but little is known about the mechanisms that drive RPE regeneration. Here utilizing zebrafish we identified elements of the immune response as critical mediators of intrinsic RPE regeneration. Macrophages/microglia are responsive to RPE damage and are required for the timely progression of the regenerative response and our data highlight that inflammation post RPE injury is also critical for normal RPE regeneration. These data are the first to identify the molecular and cellular underpinnings of RPE regeneration in any system and hold significant potential for translational approaches aimed towards promoting a pro regenerative environment in mammals. Overall design: RNA seq from FACS purified retinal pigment epithelium RPE post genetic ablation and in unablated controls at 3 timepoints: 2 4 7 xxx post injury dpi. MTZ indicates unablated samples MTZ+ indicates ablated samples.,,pubmed:34006636,,Gross A1 3 1 18 S5 R1 001,GSM4698652,,tissue:retinal pigment epithelium|treatment:MTZ |time point:7dpi|replicate:3,Gross A1 3 1 18 S5 R1 001,All processing of raw data was performed using the CLC Genomics Workbench v10 Toolbox Reads were trimmed using quality trim limit = 0.05 ambiguous trim = 2 and automatic read through adapter trimming enabled Trim Reads tool v2.1 Reads were mapped to the zebrafish reference genome GRCz10 and TPM expression values were caluclated using the RNA seq Analysis tool v2.16 in CLC Genomics Workbench Genome build: GRCz10 Supplementary files format and content: tab delimited text files containing TPM and total counts for all genes for all samples from each timepoint,retinal pigment epithelium,A subset of larvae 3 replicates from each timepoint were treated with 10mM metronidazole MTZ from 5 6dpf 24 hours to ablate the retinal pigment epithelium,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,Embryos/larvae were treated with 1.5X phenylthiourea PTU in system water from 0.25 5dpf to stop pigmentation. post 5dpf larvae were maintained in system water for the remaining duration of the experiment.,treatment:MTZ |time point:7dpi|replicate:3,GSM4698652,GSM4698652: Gross A1 3 1 18 S5 R1 001; Danio rerio; RNA Seq,GSM4698652,,1,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,GEO Accession:GSM4698652,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP273985,,,Gross_A1_3_1_18_S5_R1_001.fastq.gz Gross_A1_3_1_18_S5_R2_001.fastq.gz,fastq fastq,8604655350.0,57364369.0,GSM4698652 r1,0:75 1:75,A:2438039854;C:1874282641;G:1790105674;T:2500628946;N:1598235,75,75,,,2438039854,1874282641,1790105674,2500628946,1598235,SRX8840228,SRS7103462,SRA1104764,GEO,"Ophthalmology, University of Pittsburgh School Of Medicine",2,0.88472,0.88444,0.19788,0.19728,0.79044,0.79403,0.56866,0.56514,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2020-07-28,Larval,Larval,Eye,Sensory System 60522,SRR12340456,SRX8840227,SRS7103461,SRP273985,PRJNA649260,THE IMMUNE RESPONSE MODULATES ZEBRAFISH RETINAL PIGMENT EPITHELIUM REGENERATION [RPE],GSE155294,Transcriptome Analysis,Loss of the retinal pigment epithelium RPE due to dysfunction or disease can lead to blindness in humans. Harnessing the intrinsic ability of the RPE to self repair is an attractive therapeutic strategy; however mammalian RPE is limited in its regenerative capacity. Zebrafish possess tremendous intrinsic regenerative potential in ocular tissues including the RPE but little is known about the mechanisms that drive RPE regeneration. Here utilizing zebrafish we identified elements of the immune response as critical mediators of intrinsic RPE regeneration. Macrophages/microglia are responsive to RPE damage and are required for the timely progression of the regenerative response and our data highlight that inflammation post RPE injury is also critical for normal RPE regeneration. These data are the first to identify the molecular and cellular underpinnings of RPE regeneration in any system and hold significant potential for translational approaches aimed towards promoting a pro regenerative environment in mammals. Overall design: RNA seq from FACS purified retinal pigment epithelium RPE post genetic ablation and in unablated controls at 3 timepoints: 2 4 7 xxx post injury dpi. MTZ indicates unablated samples MTZ+ indicates ablated samples.,,pubmed:34006636,,Gross 4 2 19 18 S8 R1 001,GSM4698651,,tissue:retinal pigment epithelium|treatment:MTZ+|time point:7dpi|replicate:2,Gross 4 2 19 18 S8 R1 001,All processing of raw data was performed using the CLC Genomics Workbench v10 Toolbox Reads were trimmed using quality trim limit = 0.05 ambiguous trim = 2 and automatic read through adapter trimming enabled Trim Reads tool v2.1 Reads were mapped to the zebrafish reference genome GRCz10 and TPM expression values were caluclated using the RNA seq Analysis tool v2.16 in CLC Genomics Workbench Genome build: GRCz10 Supplementary files format and content: tab delimited text files containing TPM and total counts for all genes for all samples from each timepoint,retinal pigment epithelium,A subset of larvae 3 replicates from each timepoint were treated with 10mM metronidazole MTZ from 5 6dpf 24 hours to ablate the retinal pigment epithelium,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,Embryos/larvae were treated with 1.5X phenylthiourea PTU in system water from 0.25 5dpf to stop pigmentation. post 5dpf larvae were maintained in system water for the remaining duration of the experiment.,treatment:MTZ+|time point:7dpi|replicate:2,GSM4698651,GSM4698651: Gross 4 2 19 18 S8 R1 001; Danio rerio; RNA Seq,GSM4698651,,1,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,GEO Accession:GSM4698651,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP273985,,,Gross_4_2_19_18_S8_R1_001.fastq.gz Gross_4_2_19_18_S8_R2_001.fastq.gz,fastq fastq,6302384400.0,42015896.0,GSM4698651 r1,0:75 1:75,A:1786664016;C:1362370577;G:1317481284;T:1834695852;N:1172671,75,75,,,1786664016,1362370577,1317481284,1834695852,1172671,SRX8840227,SRS7103461,SRA1104764,GEO,"Ophthalmology, University of Pittsburgh School Of Medicine",2,0.8904,0.89048,0.15097,0.15117,0.79957,0.8031,0.60565,0.60374,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2020-07-28,Larval,Larval,Eye,Sensory System 60523,SRR12340455,SRX8840226,SRS7103460,SRP273985,PRJNA649260,THE IMMUNE RESPONSE MODULATES ZEBRAFISH RETINAL PIGMENT EPITHELIUM REGENERATION [RPE],GSE155294,Transcriptome Analysis,Loss of the retinal pigment epithelium RPE due to dysfunction or disease can lead to blindness in humans. Harnessing the intrinsic ability of the RPE to self repair is an attractive therapeutic strategy; however mammalian RPE is limited in its regenerative capacity. Zebrafish possess tremendous intrinsic regenerative potential in ocular tissues including the RPE but little is known about the mechanisms that drive RPE regeneration. Here utilizing zebrafish we identified elements of the immune response as critical mediators of intrinsic RPE regeneration. Macrophages/microglia are responsive to RPE damage and are required for the timely progression of the regenerative response and our data highlight that inflammation post RPE injury is also critical for normal RPE regeneration. These data are the first to identify the molecular and cellular underpinnings of RPE regeneration in any system and hold significant potential for translational approaches aimed towards promoting a pro regenerative environment in mammals. Overall design: RNA seq from FACS purified retinal pigment epithelium RPE post genetic ablation and in unablated controls at 3 timepoints: 2 4 7 xxx post injury dpi. MTZ indicates unablated samples MTZ+ indicates ablated samples.,,pubmed:34006636,,Gross 3 2 19 18 S7 R1 001,GSM4698650,,tissue:retinal pigment epithelium|treatment:MTZ |time point:7dpi|replicate:2,Gross 3 2 19 18 S7 R1 001,All processing of raw data was performed using the CLC Genomics Workbench v10 Toolbox Reads were trimmed using quality trim limit = 0.05 ambiguous trim = 2 and automatic read through adapter trimming enabled Trim Reads tool v2.1 Reads were mapped to the zebrafish reference genome GRCz10 and TPM expression values were caluclated using the RNA seq Analysis tool v2.16 in CLC Genomics Workbench Genome build: GRCz10 Supplementary files format and content: tab delimited text files containing TPM and total counts for all genes for all samples from each timepoint,retinal pigment epithelium,A subset of larvae 3 replicates from each timepoint were treated with 10mM metronidazole MTZ from 5 6dpf 24 hours to ablate the retinal pigment epithelium,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,Embryos/larvae were treated with 1.5X phenylthiourea PTU in system water from 0.25 5dpf to stop pigmentation. post 5dpf larvae were maintained in system water for the remaining duration of the experiment.,treatment:MTZ |time point:7dpi|replicate:2,GSM4698650,GSM4698650: Gross 3 2 19 18 S7 R1 001; Danio rerio; RNA Seq,GSM4698650,,1,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,GEO Accession:GSM4698650,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP273985,,,Gross_3_2_19_18_S7_R1_001.fastq.gz Gross_3_2_19_18_S7_R2_001.fastq.gz,fastq fastq,7396105650.0,49307371.0,GSM4698650 r1,0:75 1:75,A:2105808739;C:1588742948;G:1533387574;T:2166793401;N:1372988,75,75,,,2105808739,1588742948,1533387574,2166793401,1372988,SRX8840226,SRS7103460,SRA1104764,GEO,"Ophthalmology, University of Pittsburgh School Of Medicine",2,0.88242,0.88279,0.1914,0.19151,0.79366,0.79717,0.59226,0.60319,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2020-07-28,Larval,Larval,Eye,Sensory System 60524,SRR12340454,SRX8840225,SRS7103459,SRP273985,PRJNA649260,THE IMMUNE RESPONSE MODULATES ZEBRAFISH RETINAL PIGMENT EPITHELIUM REGENERATION [RPE],GSE155294,Transcriptome Analysis,Loss of the retinal pigment epithelium RPE due to dysfunction or disease can lead to blindness in humans. Harnessing the intrinsic ability of the RPE to self repair is an attractive therapeutic strategy; however mammalian RPE is limited in its regenerative capacity. Zebrafish possess tremendous intrinsic regenerative potential in ocular tissues including the RPE but little is known about the mechanisms that drive RPE regeneration. Here utilizing zebrafish we identified elements of the immune response as critical mediators of intrinsic RPE regeneration. Macrophages/microglia are responsive to RPE damage and are required for the timely progression of the regenerative response and our data highlight that inflammation post RPE injury is also critical for normal RPE regeneration. These data are the first to identify the molecular and cellular underpinnings of RPE regeneration in any system and hold significant potential for translational approaches aimed towards promoting a pro regenerative environment in mammals. Overall design: RNA seq from FACS purified retinal pigment epithelium RPE post genetic ablation and in unablated controls at 3 timepoints: 2 4 7 xxx post injury dpi. MTZ indicates unablated samples MTZ+ indicates ablated samples.,,pubmed:34006636,,B1 7dpi Mtz positive S4 R1 001,GSM4698649,,tissue:retinal pigment epithelium|treatment:MTZ+|time point:7dpi|replicate:1,B1 7dpi Mtz positive S4 R1 001,All processing of raw data was performed using the CLC Genomics Workbench v10 Toolbox Reads were trimmed using quality trim limit = 0.05 ambiguous trim = 2 and automatic read through adapter trimming enabled Trim Reads tool v2.1 Reads were mapped to the zebrafish reference genome GRCz10 and TPM expression values were caluclated using the RNA seq Analysis tool v2.16 in CLC Genomics Workbench Genome build: GRCz10 Supplementary files format and content: tab delimited text files containing TPM and total counts for all genes for all samples from each timepoint,retinal pigment epithelium,A subset of larvae 3 replicates from each timepoint were treated with 10mM metronidazole MTZ from 5 6dpf 24 hours to ablate the retinal pigment epithelium,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,Embryos/larvae were treated with 1.5X phenylthiourea PTU in system water from 0.25 5dpf to stop pigmentation. post 5dpf larvae were maintained in system water for the remaining duration of the experiment.,treatment:MTZ+|time point:7dpi|replicate:1,GSM4698649,GSM4698649: B1 7dpi Mtz positive S4 R1 001; Danio rerio; RNA Seq,GSM4698649,,1,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,GEO Accession:GSM4698649,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP273985,,,B1_7dpi__Mtz_positive_S4_R1_001.fastq.gz B1_7dpi__Mtz_positive_S4_R2_001.fastq.gz,fastq fastq,9648102450.0,64320683.0,GSM4698649 r1,0:75 1:75,A:2720910424;C:2137814502;G:2043408360;T:2745480288;N:488876,75,75,,,2720910424,2137814502,2043408360,2745480288,488876,SRX8840225,SRS7103459,SRA1104764,GEO,"Ophthalmology, University of Pittsburgh School Of Medicine",2,0.9043,0.90537,0.14589,0.14888,0.77376,0.77885,0.59468,0.59449,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2020-07-28,Larval,Larval,Eye,Sensory System 60525,SRR12340453,SRX8840224,SRS7103458,SRP273985,PRJNA649260,THE IMMUNE RESPONSE MODULATES ZEBRAFISH RETINAL PIGMENT EPITHELIUM REGENERATION [RPE],GSE155294,Transcriptome Analysis,Loss of the retinal pigment epithelium RPE due to dysfunction or disease can lead to blindness in humans. Harnessing the intrinsic ability of the RPE to self repair is an attractive therapeutic strategy; however mammalian RPE is limited in its regenerative capacity. Zebrafish possess tremendous intrinsic regenerative potential in ocular tissues including the RPE but little is known about the mechanisms that drive RPE regeneration. Here utilizing zebrafish we identified elements of the immune response as critical mediators of intrinsic RPE regeneration. Macrophages/microglia are responsive to RPE damage and are required for the timely progression of the regenerative response and our data highlight that inflammation post RPE injury is also critical for normal RPE regeneration. These data are the first to identify the molecular and cellular underpinnings of RPE regeneration in any system and hold significant potential for translational approaches aimed towards promoting a pro regenerative environment in mammals. Overall design: RNA seq from FACS purified retinal pigment epithelium RPE post genetic ablation and in unablated controls at 3 timepoints: 2 4 7 xxx post injury dpi. MTZ indicates unablated samples MTZ+ indicates ablated samples.,,pubmed:34006636,,A1 7dpi Mtz negative S3 R1 001,GSM4698648,,tissue:retinal pigment epithelium|treatment:MTZ |time point:7dpi|replicate:1,A1 7dpi Mtz negative S3 R1 001,All processing of raw data was performed using the CLC Genomics Workbench v10 Toolbox Reads were trimmed using quality trim limit = 0.05 ambiguous trim = 2 and automatic read through adapter trimming enabled Trim Reads tool v2.1 Reads were mapped to the zebrafish reference genome GRCz10 and TPM expression values were caluclated using the RNA seq Analysis tool v2.16 in CLC Genomics Workbench Genome build: GRCz10 Supplementary files format and content: tab delimited text files containing TPM and total counts for all genes for all samples from each timepoint,retinal pigment epithelium,A subset of larvae 3 replicates from each timepoint were treated with 10mM metronidazole MTZ from 5 6dpf 24 hours to ablate the retinal pigment epithelium,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,Embryos/larvae were treated with 1.5X phenylthiourea PTU in system water from 0.25 5dpf to stop pigmentation. post 5dpf larvae were maintained in system water for the remaining duration of the experiment.,treatment:MTZ |time point:7dpi|replicate:1,GSM4698648,GSM4698648: A1 7dpi Mtz negative S3 R1 001; Danio rerio; RNA Seq,GSM4698648,,1,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,GEO Accession:GSM4698648,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP273985,,,A1_7dpi_Mtz_negative_S3_R1_001.fastq.gz A1_7dpi_Mtz_negative_S3_R2_001.fastq.gz,fastq fastq,8796562200.0,58643748.0,GSM4698648 r1,0:75 1:75,A:2514477281;C:1916458284;G:1831625165;T:2533561049;N:440421,75,75,,,2514477281,1916458284,1831625165,2533561049,440421,SRX8840224,SRS7103458,SRA1104764,GEO,"Ophthalmology, University of Pittsburgh School Of Medicine",2,0.8909,0.89141,0.18197,0.18396,0.78301,0.78957,0.53131,0.54216,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2020-07-28,Larval,Larval,Eye,Sensory System 60526,SRR12340470,SRX8840223,SRS7103457,SRP273985,PRJNA649260,THE IMMUNE RESPONSE MODULATES ZEBRAFISH RETINAL PIGMENT EPITHELIUM REGENERATION [RPE],GSE155294,Transcriptome Analysis,Loss of the retinal pigment epithelium RPE due to dysfunction or disease can lead to blindness in humans. Harnessing the intrinsic ability of the RPE to self repair is an attractive therapeutic strategy; however mammalian RPE is limited in its regenerative capacity. Zebrafish possess tremendous intrinsic regenerative potential in ocular tissues including the RPE but little is known about the mechanisms that drive RPE regeneration. Here utilizing zebrafish we identified elements of the immune response as critical mediators of intrinsic RPE regeneration. Macrophages/microglia are responsive to RPE damage and are required for the timely progression of the regenerative response and our data highlight that inflammation post RPE injury is also critical for normal RPE regeneration. These data are the first to identify the molecular and cellular underpinnings of RPE regeneration in any system and hold significant potential for translational approaches aimed towards promoting a pro regenerative environment in mammals. Overall design: RNA seq from FACS purified retinal pigment epithelium RPE post genetic ablation and in unablated controls at 3 timepoints: 2 4 7 xxx post injury dpi. MTZ indicates unablated samples MTZ+ indicates ablated samples.,,pubmed:34006636,,Gross B1 2 26 18 S3 R1 001,GSM4698647,,tissue:retinal pigment epithelium|treatment:MTZ+|time point:4dpi|replicate:3,Gross B1 2 26 18 S3 R1 001,All processing of raw data was performed using the CLC Genomics Workbench v10 Toolbox Reads were trimmed using quality trim limit = 0.05 ambiguous trim = 2 and automatic read through adapter trimming enabled Trim Reads tool v2.1 Reads were mapped to the zebrafish reference genome GRCz10 and TPM expression values were caluclated using the RNA seq Analysis tool v2.16 in CLC Genomics Workbench Genome build: GRCz10 Supplementary files format and content: tab delimited text files containing TPM and total counts for all genes for all samples from each timepoint,retinal pigment epithelium,A subset of larvae 3 replicates from each timepoint were treated with 10mM metronidazole MTZ from 5 6dpf 24 hours to ablate the retinal pigment epithelium,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,Embryos/larvae were treated with 1.5X phenylthiourea PTU in system water from 0.25 5dpf to stop pigmentation. post 5dpf larvae were maintained in system water for the remaining duration of the experiment.,treatment:MTZ+|time point:4dpi|replicate:3,GSM4698647,GSM4698647: Gross B1 2 26 18 S3 R1 001; Danio rerio; RNA Seq,GSM4698647,,1,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,GEO Accession:GSM4698647,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP273985,,,Gross_B1_2_26_18_S3_R1_001.fastq.gz Gross_B1_2_26_18_S3_R2_001.fastq.gz,fastq fastq,10194330000.0,67962200.0,GSM4698647 r1,0:75 1:75,A:2797412483;C:2311301943;G:2234043382;T:2849680027;N:1892165,75,75,,,2797412483,2311301943,2234043382,2849680027,1892165,SRX8840223,SRS7103457,SRA1104764,GEO,"Ophthalmology, University of Pittsburgh School Of Medicine",2,0.91845,0.91935,0.09387,0.09414,0.76644,0.77108,0.54729,0.55175,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2020-07-28,Larval,Larval,Eye,Sensory System 60527,SRR12340469,SRX8840222,SRS7103456,SRP273985,PRJNA649260,THE IMMUNE RESPONSE MODULATES ZEBRAFISH RETINAL PIGMENT EPITHELIUM REGENERATION [RPE],GSE155294,Transcriptome Analysis,Loss of the retinal pigment epithelium RPE due to dysfunction or disease can lead to blindness in humans. Harnessing the intrinsic ability of the RPE to self repair is an attractive therapeutic strategy; however mammalian RPE is limited in its regenerative capacity. Zebrafish possess tremendous intrinsic regenerative potential in ocular tissues including the RPE but little is known about the mechanisms that drive RPE regeneration. Here utilizing zebrafish we identified elements of the immune response as critical mediators of intrinsic RPE regeneration. Macrophages/microglia are responsive to RPE damage and are required for the timely progression of the regenerative response and our data highlight that inflammation post RPE injury is also critical for normal RPE regeneration. These data are the first to identify the molecular and cellular underpinnings of RPE regeneration in any system and hold significant potential for translational approaches aimed towards promoting a pro regenerative environment in mammals. Overall design: RNA seq from FACS purified retinal pigment epithelium RPE post genetic ablation and in unablated controls at 3 timepoints: 2 4 7 xxx post injury dpi. MTZ indicates unablated samples MTZ+ indicates ablated samples.,,pubmed:34006636,,Gross A1 2 26 18 S2 R1 001,GSM4698646,,tissue:retinal pigment epithelium|treatment:MTZ |time point:4dpi|replicate:3,Gross A1 2 26 18 S2 R1 001,All processing of raw data was performed using the CLC Genomics Workbench v10 Toolbox Reads were trimmed using quality trim limit = 0.05 ambiguous trim = 2 and automatic read through adapter trimming enabled Trim Reads tool v2.1 Reads were mapped to the zebrafish reference genome GRCz10 and TPM expression values were caluclated using the RNA seq Analysis tool v2.16 in CLC Genomics Workbench Genome build: GRCz10 Supplementary files format and content: tab delimited text files containing TPM and total counts for all genes for all samples from each timepoint,retinal pigment epithelium,A subset of larvae 3 replicates from each timepoint were treated with 10mM metronidazole MTZ from 5 6dpf 24 hours to ablate the retinal pigment epithelium,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,Embryos/larvae were treated with 1.5X phenylthiourea PTU in system water from 0.25 5dpf to stop pigmentation. post 5dpf larvae were maintained in system water for the remaining duration of the experiment.,treatment:MTZ |time point:4dpi|replicate:3,GSM4698646,GSM4698646: Gross A1 2 26 18 S2 R1 001; Danio rerio; RNA Seq,GSM4698646,,1,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,GEO Accession:GSM4698646,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP273985,,,Gross_A1_2_26_18_S2_R1_001.fastq.gz Gross_A1_2_26_18_S2_R2_001.fastq.gz,fastq fastq,9317069550.0,62113797.0,GSM4698646 r1,0:75 1:75,A:2633250272;C:2031442520;G:1960175177;T:2690457143;N:1744438,75,75,,,2633250272,2031442520,1960175177,2690457143,1744438,SRX8840222,SRS7103456,SRA1104764,GEO,"Ophthalmology, University of Pittsburgh School Of Medicine",2,0.88564,0.88753,0.16256,0.16302,0.78668,0.7894,0.5418,0.53251,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2020-07-28,Larval,Larval,Eye,Sensory System 60528,SRR12340468,SRX8840221,SRS7103455,SRP273985,PRJNA649260,THE IMMUNE RESPONSE MODULATES ZEBRAFISH RETINAL PIGMENT EPITHELIUM REGENERATION [RPE],GSE155294,Transcriptome Analysis,Loss of the retinal pigment epithelium RPE due to dysfunction or disease can lead to blindness in humans. Harnessing the intrinsic ability of the RPE to self repair is an attractive therapeutic strategy; however mammalian RPE is limited in its regenerative capacity. Zebrafish possess tremendous intrinsic regenerative potential in ocular tissues including the RPE but little is known about the mechanisms that drive RPE regeneration. Here utilizing zebrafish we identified elements of the immune response as critical mediators of intrinsic RPE regeneration. Macrophages/microglia are responsive to RPE damage and are required for the timely progression of the regenerative response and our data highlight that inflammation post RPE injury is also critical for normal RPE regeneration. These data are the first to identify the molecular and cellular underpinnings of RPE regeneration in any system and hold significant potential for translational approaches aimed towards promoting a pro regenerative environment in mammals. Overall design: RNA seq from FACS purified retinal pigment epithelium RPE post genetic ablation and in unablated controls at 3 timepoints: 2 4 7 xxx post injury dpi. MTZ indicates unablated samples MTZ+ indicates ablated samples.,,pubmed:34006636,,Gross 2 2 19 18 S9 R1 001,GSM4698645,,tissue:retinal pigment epithelium|treatment:MTZ+|time point:4dpi|replicate:2,Gross 2 2 19 18 S9 R1 001,All processing of raw data was performed using the CLC Genomics Workbench v10 Toolbox Reads were trimmed using quality trim limit = 0.05 ambiguous trim = 2 and automatic read through adapter trimming enabled Trim Reads tool v2.1 Reads were mapped to the zebrafish reference genome GRCz10 and TPM expression values were caluclated using the RNA seq Analysis tool v2.16 in CLC Genomics Workbench Genome build: GRCz10 Supplementary files format and content: tab delimited text files containing TPM and total counts for all genes for all samples from each timepoint,retinal pigment epithelium,A subset of larvae 3 replicates from each timepoint were treated with 10mM metronidazole MTZ from 5 6dpf 24 hours to ablate the retinal pigment epithelium,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,Embryos/larvae were treated with 1.5X phenylthiourea PTU in system water from 0.25 5dpf to stop pigmentation. post 5dpf larvae were maintained in system water for the remaining duration of the experiment.,treatment:MTZ+|time point:4dpi|replicate:2,GSM4698645,GSM4698645: Gross 2 2 19 18 S9 R1 001; Danio rerio; RNA Seq,GSM4698645,,1,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,GEO Accession:GSM4698645,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP273985,,,Gross_2_2_19_18_S9_R1_001.fastq.gz Gross_2_2_19_18_S9_R2_001.fastq.gz,fastq fastq,6943837800.0,46292252.0,GSM4698645 r1,0:75 1:75,A:1886555480;C:1593000206;G:1526721769;T:1937433708;N:126637,75,75,,,1886555480,1593000206,1526721769,1937433708,126637,SRX8840221,SRS7103455,SRA1104764,GEO,"Ophthalmology, University of Pittsburgh School Of Medicine",2,0.91425,0.9151,0.09332,0.09333,0.7651,0.76863,0.55496,0.56315,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2020-07-28,Larval,Larval,Eye,Sensory System 60529,SRR12340467,SRX8840220,SRS7103454,SRP273985,PRJNA649260,THE IMMUNE RESPONSE MODULATES ZEBRAFISH RETINAL PIGMENT EPITHELIUM REGENERATION [RPE],GSE155294,Transcriptome Analysis,Loss of the retinal pigment epithelium RPE due to dysfunction or disease can lead to blindness in humans. Harnessing the intrinsic ability of the RPE to self repair is an attractive therapeutic strategy; however mammalian RPE is limited in its regenerative capacity. Zebrafish possess tremendous intrinsic regenerative potential in ocular tissues including the RPE but little is known about the mechanisms that drive RPE regeneration. Here utilizing zebrafish we identified elements of the immune response as critical mediators of intrinsic RPE regeneration. Macrophages/microglia are responsive to RPE damage and are required for the timely progression of the regenerative response and our data highlight that inflammation post RPE injury is also critical for normal RPE regeneration. These data are the first to identify the molecular and cellular underpinnings of RPE regeneration in any system and hold significant potential for translational approaches aimed towards promoting a pro regenerative environment in mammals. Overall design: RNA seq from FACS purified retinal pigment epithelium RPE post genetic ablation and in unablated controls at 3 timepoints: 2 4 7 xxx post injury dpi. MTZ indicates unablated samples MTZ+ indicates ablated samples.,,pubmed:34006636,,Gross 1 2 19 18 S9 R1 001,GSM4698644,,tissue:retinal pigment epithelium|treatment:MTZ |time point:4dpi|replicate:2,Gross 1 2 19 18 S9 R1 001,All processing of raw data was performed using the CLC Genomics Workbench v10 Toolbox Reads were trimmed using quality trim limit = 0.05 ambiguous trim = 2 and automatic read through adapter trimming enabled Trim Reads tool v2.1 Reads were mapped to the zebrafish reference genome GRCz10 and TPM expression values were caluclated using the RNA seq Analysis tool v2.16 in CLC Genomics Workbench Genome build: GRCz10 Supplementary files format and content: tab delimited text files containing TPM and total counts for all genes for all samples from each timepoint,retinal pigment epithelium,A subset of larvae 3 replicates from each timepoint were treated with 10mM metronidazole MTZ from 5 6dpf 24 hours to ablate the retinal pigment epithelium,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,Embryos/larvae were treated with 1.5X phenylthiourea PTU in system water from 0.25 5dpf to stop pigmentation. post 5dpf larvae were maintained in system water for the remaining duration of the experiment.,treatment:MTZ |time point:4dpi|replicate:2,GSM4698644,GSM4698644: Gross 1 2 19 18 S9 R1 001; Danio rerio; RNA Seq,GSM4698644,,1,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,GEO Accession:GSM4698644,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP273985,,,Gross_1_2_19_18_S9_R1_001.fastq.gz Gross_1_2_19_18_S9_R2_001.fastq.gz,fastq fastq,10078582950.0,67190553.0,GSM4698644 r1,0:75 1:75,A:2785602570;C:2261743354;G:2183115968;T:2846232621;N:1888437,75,75,,,2785602570,2261743354,2183115968,2846232621,1888437,SRX8840220,SRS7103454,SRA1104764,GEO,"Ophthalmology, University of Pittsburgh School Of Medicine",2,0.90636,0.90638,0.13625,0.13748,0.76775,0.77179,0.55101,0.55638,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2020-07-28,Larval,Larval,Eye,Sensory System 60530,SRR12340466,SRX8840219,SRS7103453,SRP273985,PRJNA649260,THE IMMUNE RESPONSE MODULATES ZEBRAFISH RETINAL PIGMENT EPITHELIUM REGENERATION [RPE],GSE155294,Transcriptome Analysis,Loss of the retinal pigment epithelium RPE due to dysfunction or disease can lead to blindness in humans. Harnessing the intrinsic ability of the RPE to self repair is an attractive therapeutic strategy; however mammalian RPE is limited in its regenerative capacity. Zebrafish possess tremendous intrinsic regenerative potential in ocular tissues including the RPE but little is known about the mechanisms that drive RPE regeneration. Here utilizing zebrafish we identified elements of the immune response as critical mediators of intrinsic RPE regeneration. Macrophages/microglia are responsive to RPE damage and are required for the timely progression of the regenerative response and our data highlight that inflammation post RPE injury is also critical for normal RPE regeneration. These data are the first to identify the molecular and cellular underpinnings of RPE regeneration in any system and hold significant potential for translational approaches aimed towards promoting a pro regenerative environment in mammals. Overall design: RNA seq from FACS purified retinal pigment epithelium RPE post genetic ablation and in unablated controls at 3 timepoints: 2 4 7 xxx post injury dpi. MTZ indicates unablated samples MTZ+ indicates ablated samples.,,pubmed:34006636,,4dpi Mtz wellB1 S1 R1 001,GSM4698643,,tissue:retinal pigment epithelium|treatment:MTZ+|time point:4dpi|replicate:1,4dpi Mtz wellB1 S1 R1 001,All processing of raw data was performed using the CLC Genomics Workbench v10 Toolbox Reads were trimmed using quality trim limit = 0.05 ambiguous trim = 2 and automatic read through adapter trimming enabled Trim Reads tool v2.1 Reads were mapped to the zebrafish reference genome GRCz10 and TPM expression values were caluclated using the RNA seq Analysis tool v2.16 in CLC Genomics Workbench Genome build: GRCz10 Supplementary files format and content: tab delimited text files containing TPM and total counts for all genes for all samples from each timepoint,retinal pigment epithelium,A subset of larvae 3 replicates from each timepoint were treated with 10mM metronidazole MTZ from 5 6dpf 24 hours to ablate the retinal pigment epithelium,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,Embryos/larvae were treated with 1.5X phenylthiourea PTU in system water from 0.25 5dpf to stop pigmentation. post 5dpf larvae were maintained in system water for the remaining duration of the experiment.,treatment:MTZ+|time point:4dpi|replicate:1,GSM4698643,GSM4698643: 4dpi Mtz wellB1 S1 R1 001; Danio rerio; RNA Seq,GSM4698643,,1,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,GEO Accession:GSM4698643,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP273985,,,4dpi_Mtz_wellB1_S1_R1_001.fastq.gz 4dpi_Mtz_wellB1_S1_R2_001.fastq.gz,fastq fastq,15174475350.0,101163169.0,GSM4698643 r1,0:75 1:75,A:4489830101;C:3151808637;G:2925260766;T:4606557300;N:1018546,75,75,,,4489830101,3151808637,2925260766,4606557300,1018546,SRX8840219,SRS7103453,SRA1104764,GEO,"Ophthalmology, University of Pittsburgh School Of Medicine",2,0.8966,0.89537,0.20419,0.20662,0.77133,0.77396,0.55333,0.54643,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2020-07-28,Larval,Larval,Eye,Sensory System 60531,SRR12340465,SRX8840218,SRS7103452,SRP273985,PRJNA649260,THE IMMUNE RESPONSE MODULATES ZEBRAFISH RETINAL PIGMENT EPITHELIUM REGENERATION [RPE],GSE155294,Transcriptome Analysis,Loss of the retinal pigment epithelium RPE due to dysfunction or disease can lead to blindness in humans. Harnessing the intrinsic ability of the RPE to self repair is an attractive therapeutic strategy; however mammalian RPE is limited in its regenerative capacity. Zebrafish possess tremendous intrinsic regenerative potential in ocular tissues including the RPE but little is known about the mechanisms that drive RPE regeneration. Here utilizing zebrafish we identified elements of the immune response as critical mediators of intrinsic RPE regeneration. Macrophages/microglia are responsive to RPE damage and are required for the timely progression of the regenerative response and our data highlight that inflammation post RPE injury is also critical for normal RPE regeneration. These data are the first to identify the molecular and cellular underpinnings of RPE regeneration in any system and hold significant potential for translational approaches aimed towards promoting a pro regenerative environment in mammals. Overall design: RNA seq from FACS purified retinal pigment epithelium RPE post genetic ablation and in unablated controls at 3 timepoints: 2 4 7 xxx post injury dpi. MTZ indicates unablated samples MTZ+ indicates ablated samples.,,pubmed:34006636,,4dpi Mtz positive S2 R1 001,GSM4698642,,tissue:retinal pigment epithelium|treatment:MTZ |time point:4dpi|replicate:1,4dpi Mtz positive S2 R1 001,All processing of raw data was performed using the CLC Genomics Workbench v10 Toolbox Reads were trimmed using quality trim limit = 0.05 ambiguous trim = 2 and automatic read through adapter trimming enabled Trim Reads tool v2.1 Reads were mapped to the zebrafish reference genome GRCz10 and TPM expression values were caluclated using the RNA seq Analysis tool v2.16 in CLC Genomics Workbench Genome build: GRCz10 Supplementary files format and content: tab delimited text files containing TPM and total counts for all genes for all samples from each timepoint,retinal pigment epithelium,A subset of larvae 3 replicates from each timepoint were treated with 10mM metronidazole MTZ from 5 6dpf 24 hours to ablate the retinal pigment epithelium,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,Embryos/larvae were treated with 1.5X phenylthiourea PTU in system water from 0.25 5dpf to stop pigmentation. post 5dpf larvae were maintained in system water for the remaining duration of the experiment.,treatment:MTZ |time point:4dpi|replicate:1,GSM4698642,GSM4698642: 4dpi Mtz positive S2 R1 001; Danio rerio; RNA Seq,GSM4698642,,1,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,GEO Accession:GSM4698642,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP273985,,,4dpi_Mtz_positive_S2_R1_001.fastq.gz 4dpi_Mtz_positive_S2_R2_001.fastq.gz,fastq fastq,14465275500.0,96435170.0,GSM4698642 r1,0:75 1:75,A:4305203858;C:2972696214;G:2770662543;T:4415737295;N:975590,75,75,,,4305203858,2972696214,2770662543,4415737295,975590,SRX8840218,SRS7103452,SRA1104764,GEO,"Ophthalmology, University of Pittsburgh School Of Medicine",2,0.88931,0.8886,0.21414,0.21629,0.79186,0.79364,0.52573,0.53764,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2020-07-28,Larval,Larval,Eye,Sensory System 60532,SRR12340464,SRX8840217,SRS7103451,SRP273985,PRJNA649260,THE IMMUNE RESPONSE MODULATES ZEBRAFISH RETINAL PIGMENT EPITHELIUM REGENERATION [RPE],GSE155294,Transcriptome Analysis,Loss of the retinal pigment epithelium RPE due to dysfunction or disease can lead to blindness in humans. Harnessing the intrinsic ability of the RPE to self repair is an attractive therapeutic strategy; however mammalian RPE is limited in its regenerative capacity. Zebrafish possess tremendous intrinsic regenerative potential in ocular tissues including the RPE but little is known about the mechanisms that drive RPE regeneration. Here utilizing zebrafish we identified elements of the immune response as critical mediators of intrinsic RPE regeneration. Macrophages/microglia are responsive to RPE damage and are required for the timely progression of the regenerative response and our data highlight that inflammation post RPE injury is also critical for normal RPE regeneration. These data are the first to identify the molecular and cellular underpinnings of RPE regeneration in any system and hold significant potential for translational approaches aimed towards promoting a pro regenerative environment in mammals. Overall design: RNA seq from FACS purified retinal pigment epithelium RPE post genetic ablation and in unablated controls at 3 timepoints: 2 4 7 xxx post injury dpi. MTZ indicates unablated samples MTZ+ indicates ablated samples.,,pubmed:34006636,,Gross 4 2 14 18 S3 R1 001,GSM4698641,,tissue:retinal pigment epithelium|treatment:MTZ+|time point:2dpi|replicate:3,Gross 4 2 14 18 S3 R1 001,All processing of raw data was performed using the CLC Genomics Workbench v10 Toolbox Reads were trimmed using quality trim limit = 0.05 ambiguous trim = 2 and automatic read through adapter trimming enabled Trim Reads tool v2.1 Reads were mapped to the zebrafish reference genome GRCz10 and TPM expression values were caluclated using the RNA seq Analysis tool v2.16 in CLC Genomics Workbench Genome build: GRCz10 Supplementary files format and content: tab delimited text files containing TPM and total counts for all genes for all samples from each timepoint,retinal pigment epithelium,A subset of larvae 3 replicates from each timepoint were treated with 10mM metronidazole MTZ from 5 6dpf 24 hours to ablate the retinal pigment epithelium,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,Embryos/larvae were treated with 1.5X phenylthiourea PTU in system water from 0.25 5dpf to stop pigmentation. post 5dpf larvae were maintained in system water for the remaining duration of the experiment.,treatment:MTZ+|time point:2dpi|replicate:3,GSM4698641,GSM4698641: Gross 4 2 14 18 S3 R1 001; Danio rerio; RNA Seq,GSM4698641,,1,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,GEO Accession:GSM4698641,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP273985,,,Gross_4_2_14_18_S3_R1_001.fastq.gz Gross_4_2_14_18_S3_R2_001.fastq.gz,fastq fastq,7323035250.0,48820235.0,GSM4698641 r1,0:75 1:75,A:2037050672;C:1630520360;G:1553208990;T:2102111453;N:143775,75,75,,,2037050672,1630520360,1553208990,2102111453,143775,SRX8840217,SRS7103451,SRA1104764,GEO,"Ophthalmology, University of Pittsburgh School Of Medicine",2,0.89319,0.89329,0.08809,0.08734,0.80994,0.81213,0.48819,0.48268,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2020-07-28,Larval,Larval,Eye,Sensory System 60533,SRR12340463,SRX8840216,SRS7103450,SRP273985,PRJNA649260,THE IMMUNE RESPONSE MODULATES ZEBRAFISH RETINAL PIGMENT EPITHELIUM REGENERATION [RPE],GSE155294,Transcriptome Analysis,Loss of the retinal pigment epithelium RPE due to dysfunction or disease can lead to blindness in humans. Harnessing the intrinsic ability of the RPE to self repair is an attractive therapeutic strategy; however mammalian RPE is limited in its regenerative capacity. Zebrafish possess tremendous intrinsic regenerative potential in ocular tissues including the RPE but little is known about the mechanisms that drive RPE regeneration. Here utilizing zebrafish we identified elements of the immune response as critical mediators of intrinsic RPE regeneration. Macrophages/microglia are responsive to RPE damage and are required for the timely progression of the regenerative response and our data highlight that inflammation post RPE injury is also critical for normal RPE regeneration. These data are the first to identify the molecular and cellular underpinnings of RPE regeneration in any system and hold significant potential for translational approaches aimed towards promoting a pro regenerative environment in mammals. Overall design: RNA seq from FACS purified retinal pigment epithelium RPE post genetic ablation and in unablated controls at 3 timepoints: 2 4 7 xxx post injury dpi. MTZ indicates unablated samples MTZ+ indicates ablated samples.,,pubmed:34006636,,Gross 3 2 14 18 S1 R1 001,GSM4698640,,tissue:retinal pigment epithelium|treatment:MTZ |time point:2dpi|replicate:3,Gross 3 2 14 18 S1 R1 001,All processing of raw data was performed using the CLC Genomics Workbench v10 Toolbox Reads were trimmed using quality trim limit = 0.05 ambiguous trim = 2 and automatic read through adapter trimming enabled Trim Reads tool v2.1 Reads were mapped to the zebrafish reference genome GRCz10 and TPM expression values were caluclated using the RNA seq Analysis tool v2.16 in CLC Genomics Workbench Genome build: GRCz10 Supplementary files format and content: tab delimited text files containing TPM and total counts for all genes for all samples from each timepoint,retinal pigment epithelium,A subset of larvae 3 replicates from each timepoint were treated with 10mM metronidazole MTZ from 5 6dpf 24 hours to ablate the retinal pigment epithelium,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,Embryos/larvae were treated with 1.5X phenylthiourea PTU in system water from 0.25 5dpf to stop pigmentation. post 5dpf larvae were maintained in system water for the remaining duration of the experiment.,treatment:MTZ |time point:2dpi|replicate:3,GSM4698640,GSM4698640: Gross 3 2 14 18 S1 R1 001; Danio rerio; RNA Seq,GSM4698640,,1,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,GEO Accession:GSM4698640,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP273985,,,Gross_3_2_14_18_S1_R1_001.fastq.gz Gross_3_2_14_18_S1_R2_001.fastq.gz,fastq fastq,10449829350.0,69665529.0,GSM4698640 r1,0:75 1:75,A:2934953274;C:2299836580;G:2220469343;T:2992611133;N:1959020,75,75,,,2934953274,2299836580,2220469343,2992611133,1959020,SRX8840216,SRS7103450,SRA1104764,GEO,"Ophthalmology, University of Pittsburgh School Of Medicine",2,0.90164,0.9031,0.09259,0.09215,0.81893,0.82205,0.55977,0.55441,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2020-07-28,Larval,Larval,Eye,Sensory System 60534,SRR12340462,SRX8840215,SRS7103449,SRP273985,PRJNA649260,THE IMMUNE RESPONSE MODULATES ZEBRAFISH RETINAL PIGMENT EPITHELIUM REGENERATION [RPE],GSE155294,Transcriptome Analysis,Loss of the retinal pigment epithelium RPE due to dysfunction or disease can lead to blindness in humans. Harnessing the intrinsic ability of the RPE to self repair is an attractive therapeutic strategy; however mammalian RPE is limited in its regenerative capacity. Zebrafish possess tremendous intrinsic regenerative potential in ocular tissues including the RPE but little is known about the mechanisms that drive RPE regeneration. Here utilizing zebrafish we identified elements of the immune response as critical mediators of intrinsic RPE regeneration. Macrophages/microglia are responsive to RPE damage and are required for the timely progression of the regenerative response and our data highlight that inflammation post RPE injury is also critical for normal RPE regeneration. These data are the first to identify the molecular and cellular underpinnings of RPE regeneration in any system and hold significant potential for translational approaches aimed towards promoting a pro regenerative environment in mammals. Overall design: RNA seq from FACS purified retinal pigment epithelium RPE post genetic ablation and in unablated controls at 3 timepoints: 2 4 7 xxx post injury dpi. MTZ indicates unablated samples MTZ+ indicates ablated samples.,,pubmed:34006636,,Gross 2 2 14 18 S2 R1 001,GSM4698639,,tissue:retinal pigment epithelium|treatment:MTZ+|time point:2dpi|replicate:2,Gross 2 2 14 18 S2 R1 001,All processing of raw data was performed using the CLC Genomics Workbench v10 Toolbox Reads were trimmed using quality trim limit = 0.05 ambiguous trim = 2 and automatic read through adapter trimming enabled Trim Reads tool v2.1 Reads were mapped to the zebrafish reference genome GRCz10 and TPM expression values were caluclated using the RNA seq Analysis tool v2.16 in CLC Genomics Workbench Genome build: GRCz10 Supplementary files format and content: tab delimited text files containing TPM and total counts for all genes for all samples from each timepoint,retinal pigment epithelium,A subset of larvae 3 replicates from each timepoint were treated with 10mM metronidazole MTZ from 5 6dpf 24 hours to ablate the retinal pigment epithelium,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,Embryos/larvae were treated with 1.5X phenylthiourea PTU in system water from 0.25 5dpf to stop pigmentation. post 5dpf larvae were maintained in system water for the remaining duration of the experiment.,treatment:MTZ+|time point:2dpi|replicate:2,GSM4698639,GSM4698639: Gross 2 2 14 18 S2 R1 001; Danio rerio; RNA Seq,GSM4698639,,1,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,GEO Accession:GSM4698639,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP273985,,,Gross_2_2_14_18_S2_R1_001.fastq.gz Gross_2_2_14_18_S2_R2_001.fastq.gz,fastq fastq,7118058000.0,47453720.0,GSM4698639 r1,0:75 1:75,A:1970099255;C:1599508735;G:1534887607;T:2013422747;N:139656,75,75,,,1970099255,1599508735,1534887607,2013422747,139656,SRX8840215,SRS7103449,SRA1104764,GEO,"Ophthalmology, University of Pittsburgh School Of Medicine",2,0.91287,0.91242,0.09748,0.09714,0.80497,0.80779,0.57396,0.58098,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2020-07-28,Larval,Larval,Eye,Sensory System 60535,SRR12340461,SRX8840214,SRS7103448,SRP273985,PRJNA649260,THE IMMUNE RESPONSE MODULATES ZEBRAFISH RETINAL PIGMENT EPITHELIUM REGENERATION [RPE],GSE155294,Transcriptome Analysis,Loss of the retinal pigment epithelium RPE due to dysfunction or disease can lead to blindness in humans. Harnessing the intrinsic ability of the RPE to self repair is an attractive therapeutic strategy; however mammalian RPE is limited in its regenerative capacity. Zebrafish possess tremendous intrinsic regenerative potential in ocular tissues including the RPE but little is known about the mechanisms that drive RPE regeneration. Here utilizing zebrafish we identified elements of the immune response as critical mediators of intrinsic RPE regeneration. Macrophages/microglia are responsive to RPE damage and are required for the timely progression of the regenerative response and our data highlight that inflammation post RPE injury is also critical for normal RPE regeneration. These data are the first to identify the molecular and cellular underpinnings of RPE regeneration in any system and hold significant potential for translational approaches aimed towards promoting a pro regenerative environment in mammals. Overall design: RNA seq from FACS purified retinal pigment epithelium RPE post genetic ablation and in unablated controls at 3 timepoints: 2 4 7 xxx post injury dpi. MTZ indicates unablated samples MTZ+ indicates ablated samples.,,pubmed:34006636,,Gross 1 2 14 18 S1 R1 001,GSM4698638,,tissue:retinal pigment epithelium|treatment:MTZ |time point:2dpi|replicate:2,Gross 1 2 14 18 S1 R1 001,All processing of raw data was performed using the CLC Genomics Workbench v10 Toolbox Reads were trimmed using quality trim limit = 0.05 ambiguous trim = 2 and automatic read through adapter trimming enabled Trim Reads tool v2.1 Reads were mapped to the zebrafish reference genome GRCz10 and TPM expression values were caluclated using the RNA seq Analysis tool v2.16 in CLC Genomics Workbench Genome build: GRCz10 Supplementary files format and content: tab delimited text files containing TPM and total counts for all genes for all samples from each timepoint,retinal pigment epithelium,A subset of larvae 3 replicates from each timepoint were treated with 10mM metronidazole MTZ from 5 6dpf 24 hours to ablate the retinal pigment epithelium,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,Embryos/larvae were treated with 1.5X phenylthiourea PTU in system water from 0.25 5dpf to stop pigmentation. post 5dpf larvae were maintained in system water for the remaining duration of the experiment.,treatment:MTZ |time point:2dpi|replicate:2,GSM4698638,GSM4698638: Gross 1 2 14 18 S1 R1 001; Danio rerio; RNA Seq,GSM4698638,,1,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,GEO Accession:GSM4698638,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP273985,,,Gross_1_2_14_18_S1_R1_001.fastq.gz Gross_1_2_14_18_S1_R2_001.fastq.gz,fastq fastq,7440843750.0,49605625.0,GSM4698638 r1,0:75 1:75,A:2059279583;C:1673204623;G:1607893745;T:2100319660;N:146139,75,75,,,2059279583,1673204623,1607893745,2100319660,146139,SRX8840214,SRS7103448,SRA1104764,GEO,"Ophthalmology, University of Pittsburgh School Of Medicine",2,0.9049,0.90435,0.09492,0.09533,0.80645,0.8102,0.5878,0.58909,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2020-07-28,Larval,Larval,Eye,Sensory System 60536,SRR12340460,SRX8840213,SRS7103447,SRP273985,PRJNA649260,THE IMMUNE RESPONSE MODULATES ZEBRAFISH RETINAL PIGMENT EPITHELIUM REGENERATION [RPE],GSE155294,Transcriptome Analysis,Loss of the retinal pigment epithelium RPE due to dysfunction or disease can lead to blindness in humans. Harnessing the intrinsic ability of the RPE to self repair is an attractive therapeutic strategy; however mammalian RPE is limited in its regenerative capacity. Zebrafish possess tremendous intrinsic regenerative potential in ocular tissues including the RPE but little is known about the mechanisms that drive RPE regeneration. Here utilizing zebrafish we identified elements of the immune response as critical mediators of intrinsic RPE regeneration. Macrophages/microglia are responsive to RPE damage and are required for the timely progression of the regenerative response and our data highlight that inflammation post RPE injury is also critical for normal RPE regeneration. These data are the first to identify the molecular and cellular underpinnings of RPE regeneration in any system and hold significant potential for translational approaches aimed towards promoting a pro regenerative environment in mammals. Overall design: RNA seq from FACS purified retinal pigment epithelium RPE post genetic ablation and in unablated controls at 3 timepoints: 2 4 7 xxx post injury dpi. MTZ indicates unablated samples MTZ+ indicates ablated samples.,,pubmed:34006636,,C1 2dpi Mtz positive S2 R1 001,GSM4698637,,tissue:retinal pigment epithelium|treatment:MTZ+|time point:2dpi|replicate:1,C1 2dpi Mtz positive S2 R1 001,All processing of raw data was performed using the CLC Genomics Workbench v10 Toolbox Reads were trimmed using quality trim limit = 0.05 ambiguous trim = 2 and automatic read through adapter trimming enabled Trim Reads tool v2.1 Reads were mapped to the zebrafish reference genome GRCz10 and TPM expression values were caluclated using the RNA seq Analysis tool v2.16 in CLC Genomics Workbench Genome build: GRCz10 Supplementary files format and content: tab delimited text files containing TPM and total counts for all genes for all samples from each timepoint,retinal pigment epithelium,A subset of larvae 3 replicates from each timepoint were treated with 10mM metronidazole MTZ from 5 6dpf 24 hours to ablate the retinal pigment epithelium,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,Embryos/larvae were treated with 1.5X phenylthiourea PTU in system water from 0.25 5dpf to stop pigmentation. post 5dpf larvae were maintained in system water for the remaining duration of the experiment.,treatment:MTZ+|time point:2dpi|replicate:1,GSM4698637,GSM4698637: C1 2dpi Mtz positive S2 R1 001; Danio rerio; RNA Seq,GSM4698637,,1,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,GEO Accession:GSM4698637,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP273985,,,C1_2dpi_Mtz_positive_S2_R1_001.fastq.gz C1_2dpi_Mtz_positive_S2_R2_001.fastq.gz,fastq fastq,7579414950.0,50529433.0,GSM4698637 r1,0:75 1:75,A:2182688073;C:1636273330;G:1575885137;T:2184180583;N:387827,75,75,,,2182688073,1636273330,1575885137,2184180583,387827,SRX8840213,SRS7103447,SRA1104764,GEO,"Ophthalmology, University of Pittsburgh School Of Medicine",2,0.92297,0.92402,0.10638,0.10797,0.77924,0.78429,0.53277,0.54049,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2020-07-28,Larval,Larval,Eye,Sensory System 60537,SRR12340459,SRX8840212,SRS7103446,SRP273985,PRJNA649260,THE IMMUNE RESPONSE MODULATES ZEBRAFISH RETINAL PIGMENT EPITHELIUM REGENERATION [RPE],GSE155294,Transcriptome Analysis,Loss of the retinal pigment epithelium RPE due to dysfunction or disease can lead to blindness in humans. Harnessing the intrinsic ability of the RPE to self repair is an attractive therapeutic strategy; however mammalian RPE is limited in its regenerative capacity. Zebrafish possess tremendous intrinsic regenerative potential in ocular tissues including the RPE but little is known about the mechanisms that drive RPE regeneration. Here utilizing zebrafish we identified elements of the immune response as critical mediators of intrinsic RPE regeneration. Macrophages/microglia are responsive to RPE damage and are required for the timely progression of the regenerative response and our data highlight that inflammation post RPE injury is also critical for normal RPE regeneration. These data are the first to identify the molecular and cellular underpinnings of RPE regeneration in any system and hold significant potential for translational approaches aimed towards promoting a pro regenerative environment in mammals. Overall design: RNA seq from FACS purified retinal pigment epithelium RPE post genetic ablation and in unablated controls at 3 timepoints: 2 4 7 xxx post injury dpi. MTZ indicates unablated samples MTZ+ indicates ablated samples.,,pubmed:34006636,,B1 2dpi Mtz negative S1 R1 001,GSM4698636,,tissue:retinal pigment epithelium|treatment:MTZ |time point:2dpi|replicate:1,B1 2dpi Mtz negative S1 R1 001,All processing of raw data was performed using the CLC Genomics Workbench v10 Toolbox Reads were trimmed using quality trim limit = 0.05 ambiguous trim = 2 and automatic read through adapter trimming enabled Trim Reads tool v2.1 Reads were mapped to the zebrafish reference genome GRCz10 and TPM expression values were caluclated using the RNA seq Analysis tool v2.16 in CLC Genomics Workbench Genome build: GRCz10 Supplementary files format and content: tab delimited text files containing TPM and total counts for all genes for all samples from each timepoint,retinal pigment epithelium,A subset of larvae 3 replicates from each timepoint were treated with 10mM metronidazole MTZ from 5 6dpf 24 hours to ablate the retinal pigment epithelium,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,Embryos/larvae were treated with 1.5X phenylthiourea PTU in system water from 0.25 5dpf to stop pigmentation. post 5dpf larvae were maintained in system water for the remaining duration of the experiment.,treatment:MTZ |time point:2dpi|replicate:1,GSM4698636,GSM4698636: B1 2dpi Mtz negative S1 R1 001; Danio rerio; RNA Seq,GSM4698636,,1,≤1000 eGFP positive cells from dissociated enuculeated larval eyes were FACS sorted directly into buffer from the SMART Seq v4 Ultra Low Input RNA Kit from Takara Bio Inc. cDNA synthesis amplification and purification was performed using the SMART Seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina following manufacterer's instructions,GEO Accession:GSM4698636,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP273985,,,B1_2dpi_Mtz_negative_S1_R1_001.fastq.gz B1_2dpi_Mtz_negative_S1_R2_001.fastq.gz,fastq fastq,8671548300.0,57810322.0,GSM4698636 r1,0:75 1:75,A:2503462417;C:1865690082;G:1792760262;T:2509196085;N:439454,75,75,,,2503462417,1865690082,1792760262,2509196085,439454,SRX8840212,SRS7103446,SRA1104764,GEO,"Ophthalmology, University of Pittsburgh School Of Medicine",2,0.91854,0.91883,0.11281,0.11376,0.78064,0.78563,0.56466,0.5741,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2020-07-28,Larval,Larval,Eye,Sensory System 66932,SRR16905258,SRX13097745,SRS11034058,SRP345451,PRJNA779419,Transcriptomic profiling of adult zebrafish photoreceptors,GSE188560,Transcriptome Analysis,Identifying the transcription factors required to specify photoreceptor subtypes is critical to understand the normal development of the retina and to inform cell replacement therapies to restore vision. RNA seq is a powerful way to identify novel genes expressed in particular cell subtypes. Although RNA seq approaches have been used to identify genes differentially expressed between photoreceptor subtypes in many species the limited transcriptome depth derived from single cell techniques constitutes a barrier in the reliable detection of transcription factors. To obtain a deep high quality RNA seq dataset from zebrafish photoreceptors we manually collected pools of photoreceptors of a single subtype. Overall design: We identified photoreceptors using well characterized transgenic lines that express fluorescent proteins in each subtype with high specificity including rods—TgxOPS:GFP UV cones—Tgopn1sw1:GFP S cones—Tgopn1sw2:GFP M cones—Tgopn1mw2:GFP and L cones—Tgthrb:tdTomato. We manually collected pools of 20 dissociated but healthy photoreceptors of a single subtype for each of our samples while actively avoiding cellular debris and other contaminants.,,pubmed:36745553,,Lc1s06,GSM5685606,,tissue:Dissociated adult photoreceptors|transgenic line:Tgthrb:tdTomato|cell type:L c1s|age:Adult,Lc1s06,Illumina software used for base calling and demultiplexing Sequences for primers and adapters removed using Trimmomatic Trimmomatic 0.36 phred33 /adapters/TruSeq2 PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:70 Reads aligned to zebrafish genome Danio rerio.GRCz11 using HiSat2 hisat2 p 8 rna strandness FR Transcript assembly and counts derived using StringTie Differential gene expression analysis using DESeq2 Genome build: Danio rerio.GRCz11 Supplementary files format and content: Comma separated values files include FPKM values for each Sample Comma separated values files include DESeq2 analysis results comparing Rods vs. Cones GTF files post trimming alignment to genome and transcript assembly RDS Seurat v03 file including count data for all samples,Dissociated adult photoreceptors,post euthanasia retinas from adult zebrafish were collected. Dissociated photoreceptors were obtained post enzymatic treatment with papain gentle mechanic trituration and filtering.,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,transgenic line:Tgthrb:tdTomato|cell type:L c1s|age:Adult,GSM5685606,GSM5685606: Lc1s06; Danio rerio; RNA Seq,GSM5685606 r1,GSM5685606,1,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP345451,,,M7_R1.fastq.gz M7_R2.fastq.gz,fastq fastq,4479967296.0,17777648.0,GSM5685606 r1,0:126 1:126,A:1237334310;C:1008032807;G:1039640738;T:1193669258;N:1290183,126,126,,,1237334310,1008032807,1039640738,1193669258,1290183,SRX13097745,SRS11034058,SRA1538252,"Wei Li, Unit of Retinal Neurophysiology, National Eye Institute","Wei Li, Unit of Retinal Neurophysiology, National Eye Institute",2,0.92181,0.92355,0.08891,0.09213,0.88008,0.87965,0.61525,0.61487,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-11-10,Adult,Adult,Eye,Sensory System 66933,SRR16905259,SRX13097744,SRS11034056,SRP345451,PRJNA779419,Transcriptomic profiling of adult zebrafish photoreceptors,GSE188560,Transcriptome Analysis,Identifying the transcription factors required to specify photoreceptor subtypes is critical to understand the normal development of the retina and to inform cell replacement therapies to restore vision. RNA seq is a powerful way to identify novel genes expressed in particular cell subtypes. Although RNA seq approaches have been used to identify genes differentially expressed between photoreceptor subtypes in many species the limited transcriptome depth derived from single cell techniques constitutes a barrier in the reliable detection of transcription factors. To obtain a deep high quality RNA seq dataset from zebrafish photoreceptors we manually collected pools of photoreceptors of a single subtype. Overall design: We identified photoreceptors using well characterized transgenic lines that express fluorescent proteins in each subtype with high specificity including rods—TgxOPS:GFP UV cones—Tgopn1sw1:GFP S cones—Tgopn1sw2:GFP M cones—Tgopn1mw2:GFP and L cones—Tgthrb:tdTomato. We manually collected pools of 20 dissociated but healthy photoreceptors of a single subtype for each of our samples while actively avoiding cellular debris and other contaminants.,,pubmed:36745553,,Lc1s05,GSM5685605,,tissue:Dissociated adult photoreceptors|transgenic line:Tgthrb:tdTomato|cell type:L c1s|age:Adult,Lc1s05,Illumina software used for base calling and demultiplexing Sequences for primers and adapters removed using Trimmomatic Trimmomatic 0.36 phred33 /adapters/TruSeq2 PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:70 Reads aligned to zebrafish genome Danio rerio.GRCz11 using HiSat2 hisat2 p 8 rna strandness FR Transcript assembly and counts derived using StringTie Differential gene expression analysis using DESeq2 Genome build: Danio rerio.GRCz11 Supplementary files format and content: Comma separated values files include FPKM values for each Sample Comma separated values files include DESeq2 analysis results comparing Rods vs. Cones GTF files post trimming alignment to genome and transcript assembly RDS Seurat v03 file including count data for all samples,Dissociated adult photoreceptors,post euthanasia retinas from adult zebrafish were collected. Dissociated photoreceptors were obtained post enzymatic treatment with papain gentle mechanic trituration and filtering.,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,transgenic line:Tgthrb:tdTomato|cell type:L c1s|age:Adult,GSM5685605,GSM5685605: Lc1s05; Danio rerio; RNA Seq,GSM5685605 r1,GSM5685605,1,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP345451,,,M6_R1.fastq.gz M6_R2.fastq.gz,fastq fastq,4677938748.0,18563249.0,GSM5685605 r1,0:126 1:126,A:1300596747;C:1041273522;G:1072983193;T:1261726964;N:1358322,126,126,,,1300596747,1041273522,1072983193,1261726964,1358322,SRX13097744,SRS11034056,SRA1538252,"Wei Li, Unit of Retinal Neurophysiology, National Eye Institute","Wei Li, Unit of Retinal Neurophysiology, National Eye Institute",2,0.89583,0.89778,0.1022,0.1062,0.86586,0.86671,0.61763,0.61712,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-11-10,Adult,Adult,Eye,Sensory System 66934,SRR16905260,SRX13097743,SRS11034055,SRP345451,PRJNA779419,Transcriptomic profiling of adult zebrafish photoreceptors,GSE188560,Transcriptome Analysis,Identifying the transcription factors required to specify photoreceptor subtypes is critical to understand the normal development of the retina and to inform cell replacement therapies to restore vision. RNA seq is a powerful way to identify novel genes expressed in particular cell subtypes. Although RNA seq approaches have been used to identify genes differentially expressed between photoreceptor subtypes in many species the limited transcriptome depth derived from single cell techniques constitutes a barrier in the reliable detection of transcription factors. To obtain a deep high quality RNA seq dataset from zebrafish photoreceptors we manually collected pools of photoreceptors of a single subtype. Overall design: We identified photoreceptors using well characterized transgenic lines that express fluorescent proteins in each subtype with high specificity including rods—TgxOPS:GFP UV cones—Tgopn1sw1:GFP S cones—Tgopn1sw2:GFP M cones—Tgopn1mw2:GFP and L cones—Tgthrb:tdTomato. We manually collected pools of 20 dissociated but healthy photoreceptors of a single subtype for each of our samples while actively avoiding cellular debris and other contaminants.,,pubmed:36745553,,Lc1s04,GSM5685604,,tissue:Dissociated adult photoreceptors|transgenic line:Tgthrb:tdTomato|cell type:L c1s|age:Adult,Lc1s04,Illumina software used for base calling and demultiplexing Sequences for primers and adapters removed using Trimmomatic Trimmomatic 0.36 phred33 /adapters/TruSeq2 PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:70 Reads aligned to zebrafish genome Danio rerio.GRCz11 using HiSat2 hisat2 p 8 rna strandness FR Transcript assembly and counts derived using StringTie Differential gene expression analysis using DESeq2 Genome build: Danio rerio.GRCz11 Supplementary files format and content: Comma separated values files include FPKM values for each Sample Comma separated values files include DESeq2 analysis results comparing Rods vs. Cones GTF files post trimming alignment to genome and transcript assembly RDS Seurat v03 file including count data for all samples,Dissociated adult photoreceptors,post euthanasia retinas from adult zebrafish were collected. Dissociated photoreceptors were obtained post enzymatic treatment with papain gentle mechanic trituration and filtering.,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,transgenic line:Tgthrb:tdTomato|cell type:L c1s|age:Adult,GSM5685604,GSM5685604: Lc1s04; Danio rerio; RNA Seq,GSM5685604 r1,GSM5685604,1,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP345451,,,M5_R1.fastq.gz M5_R2.fastq.gz,fastq fastq,4268566260.0,16938755.0,GSM5685604 r1,0:126 1:126,A:1202633828;C:936978100;G:961878404;T:1165842444;N:1233484,126,126,,,1202633828,936978100,961878404,1165842444,1233484,SRX13097743,SRS11034055,SRA1538252,"Wei Li, Unit of Retinal Neurophysiology, National Eye Institute","Wei Li, Unit of Retinal Neurophysiology, National Eye Institute",2,0.9028,0.90383,0.13013,0.1345,0.86162,0.86247,0.61071,0.61449,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-11-10,Adult,Adult,Eye,Sensory System 66935,SRR16905261,SRX13097742,SRS11034057,SRP345451,PRJNA779419,Transcriptomic profiling of adult zebrafish photoreceptors,GSE188560,Transcriptome Analysis,Identifying the transcription factors required to specify photoreceptor subtypes is critical to understand the normal development of the retina and to inform cell replacement therapies to restore vision. RNA seq is a powerful way to identify novel genes expressed in particular cell subtypes. Although RNA seq approaches have been used to identify genes differentially expressed between photoreceptor subtypes in many species the limited transcriptome depth derived from single cell techniques constitutes a barrier in the reliable detection of transcription factors. To obtain a deep high quality RNA seq dataset from zebrafish photoreceptors we manually collected pools of photoreceptors of a single subtype. Overall design: We identified photoreceptors using well characterized transgenic lines that express fluorescent proteins in each subtype with high specificity including rods—TgxOPS:GFP UV cones—Tgopn1sw1:GFP S cones—Tgopn1sw2:GFP M cones—Tgopn1mw2:GFP and L cones—Tgthrb:tdTomato. We manually collected pools of 20 dissociated but healthy photoreceptors of a single subtype for each of our samples while actively avoiding cellular debris and other contaminants.,,pubmed:36745553,,Lc1s03,GSM5685603,,tissue:Dissociated adult photoreceptors|transgenic line:Tgthrb:tdTomato|cell type:L c1s|age:Adult,Lc1s03,Illumina software used for base calling and demultiplexing Sequences for primers and adapters removed using Trimmomatic Trimmomatic 0.36 phred33 /adapters/TruSeq2 PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:70 Reads aligned to zebrafish genome Danio rerio.GRCz11 using HiSat2 hisat2 p 8 rna strandness FR Transcript assembly and counts derived using StringTie Differential gene expression analysis using DESeq2 Genome build: Danio rerio.GRCz11 Supplementary files format and content: Comma separated values files include FPKM values for each Sample Comma separated values files include DESeq2 analysis results comparing Rods vs. Cones GTF files post trimming alignment to genome and transcript assembly RDS Seurat v03 file including count data for all samples,Dissociated adult photoreceptors,post euthanasia retinas from adult zebrafish were collected. Dissociated photoreceptors were obtained post enzymatic treatment with papain gentle mechanic trituration and filtering.,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,transgenic line:Tgthrb:tdTomato|cell type:L c1s|age:Adult,GSM5685603,GSM5685603: Lc1s03; Danio rerio; RNA Seq,GSM5685603 r1,GSM5685603,1,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP345451,,,M4_R1.fastq.gz M4_R2.fastq.gz,fastq fastq,4922830836.0,19535043.0,GSM5685603 r1,0:126 1:126,A:1393659289;C:1073965742;G:1104426892;T:1349360389;N:1418524,126,126,,,1393659289,1073965742,1104426892,1349360389,1418524,SRX13097742,SRS11034057,SRA1538252,"Wei Li, Unit of Retinal Neurophysiology, National Eye Institute","Wei Li, Unit of Retinal Neurophysiology, National Eye Institute",2,0.92949,0.93013,0.1152,0.11877,0.8743,0.87411,0.5533,0.55908,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-11-10,Adult,Adult,Eye,Sensory System 66936,SRR16905262,SRX13097741,SRS11034054,SRP345451,PRJNA779419,Transcriptomic profiling of adult zebrafish photoreceptors,GSE188560,Transcriptome Analysis,Identifying the transcription factors required to specify photoreceptor subtypes is critical to understand the normal development of the retina and to inform cell replacement therapies to restore vision. RNA seq is a powerful way to identify novel genes expressed in particular cell subtypes. Although RNA seq approaches have been used to identify genes differentially expressed between photoreceptor subtypes in many species the limited transcriptome depth derived from single cell techniques constitutes a barrier in the reliable detection of transcription factors. To obtain a deep high quality RNA seq dataset from zebrafish photoreceptors we manually collected pools of photoreceptors of a single subtype. Overall design: We identified photoreceptors using well characterized transgenic lines that express fluorescent proteins in each subtype with high specificity including rods—TgxOPS:GFP UV cones—Tgopn1sw1:GFP S cones—Tgopn1sw2:GFP M cones—Tgopn1mw2:GFP and L cones—Tgthrb:tdTomato. We manually collected pools of 20 dissociated but healthy photoreceptors of a single subtype for each of our samples while actively avoiding cellular debris and other contaminants.,,pubmed:36745553,,Lc1s02,GSM5685602,,tissue:Dissociated adult photoreceptors|transgenic line:Tgthrb:tdTomato|cell type:L c1s|age:Adult,Lc1s02,Illumina software used for base calling and demultiplexing Sequences for primers and adapters removed using Trimmomatic Trimmomatic 0.36 phred33 /adapters/TruSeq2 PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:70 Reads aligned to zebrafish genome Danio rerio.GRCz11 using HiSat2 hisat2 p 8 rna strandness FR Transcript assembly and counts derived using StringTie Differential gene expression analysis using DESeq2 Genome build: Danio rerio.GRCz11 Supplementary files format and content: Comma separated values files include FPKM values for each Sample Comma separated values files include DESeq2 analysis results comparing Rods vs. Cones GTF files post trimming alignment to genome and transcript assembly RDS Seurat v03 file including count data for all samples,Dissociated adult photoreceptors,post euthanasia retinas from adult zebrafish were collected. Dissociated photoreceptors were obtained post enzymatic treatment with papain gentle mechanic trituration and filtering.,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,transgenic line:Tgthrb:tdTomato|cell type:L c1s|age:Adult,GSM5685602,GSM5685602: Lc1s02; Danio rerio; RNA Seq,GSM5685602 r1,GSM5685602,1,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP345451,,,M3_R1.fastq.gz M3_R2.fastq.gz,fastq fastq,3385949616.0,13436308.0,GSM5685602 r1,0:126 1:126,A:945460566;C:750140157;G:771123146;T:918091053;N:1134694,126,126,,,945460566,750140157,771123146,918091053,1134694,SRX13097741,SRS11034054,SRA1538252,"Wei Li, Unit of Retinal Neurophysiology, National Eye Institute","Wei Li, Unit of Retinal Neurophysiology, National Eye Institute",2,0.92512,0.92562,0.08564,0.08823,0.87134,0.87237,0.57466,0.5101,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-11-10,Adult,Adult,Eye,Sensory System 66937,SRR16905263,SRX13097740,SRS11034053,SRP345451,PRJNA779419,Transcriptomic profiling of adult zebrafish photoreceptors,GSE188560,Transcriptome Analysis,Identifying the transcription factors required to specify photoreceptor subtypes is critical to understand the normal development of the retina and to inform cell replacement therapies to restore vision. RNA seq is a powerful way to identify novel genes expressed in particular cell subtypes. Although RNA seq approaches have been used to identify genes differentially expressed between photoreceptor subtypes in many species the limited transcriptome depth derived from single cell techniques constitutes a barrier in the reliable detection of transcription factors. To obtain a deep high quality RNA seq dataset from zebrafish photoreceptors we manually collected pools of photoreceptors of a single subtype. Overall design: We identified photoreceptors using well characterized transgenic lines that express fluorescent proteins in each subtype with high specificity including rods—TgxOPS:GFP UV cones—Tgopn1sw1:GFP S cones—Tgopn1sw2:GFP M cones—Tgopn1mw2:GFP and L cones—Tgthrb:tdTomato. We manually collected pools of 20 dissociated but healthy photoreceptors of a single subtype for each of our samples while actively avoiding cellular debris and other contaminants.,,pubmed:36745553,,Lc1s01,GSM5685601,,tissue:Dissociated adult photoreceptors|transgenic line:Tgthrb:tdTomato|cell type:L c1s|age:Adult,Lc1s01,Illumina software used for base calling and demultiplexing Sequences for primers and adapters removed using Trimmomatic Trimmomatic 0.36 phred33 /adapters/TruSeq2 PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:70 Reads aligned to zebrafish genome Danio rerio.GRCz11 using HiSat2 hisat2 p 8 rna strandness FR Transcript assembly and counts derived using StringTie Differential gene expression analysis using DESeq2 Genome build: Danio rerio.GRCz11 Supplementary files format and content: Comma separated values files include FPKM values for each Sample Comma separated values files include DESeq2 analysis results comparing Rods vs. Cones GTF files post trimming alignment to genome and transcript assembly RDS Seurat v03 file including count data for all samples,Dissociated adult photoreceptors,post euthanasia retinas from adult zebrafish were collected. Dissociated photoreceptors were obtained post enzymatic treatment with papain gentle mechanic trituration and filtering.,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,transgenic line:Tgthrb:tdTomato|cell type:L c1s|age:Adult,GSM5685601,GSM5685601: Lc1s01; Danio rerio; RNA Seq,GSM5685601 r1,GSM5685601,1,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP345451,,,M2_R1.fastq.gz M2_R2.fastq.gz,fastq fastq,4022125380.0,15960815.0,GSM5685601 r1,0:126 1:126,A:1122601768;C:890958269;G:918552055;T:1088667547;N:1345741,126,126,,,1122601768,890958269,918552055,1088667547,1345741,SRX13097740,SRS11034053,SRA1538252,"Wei Li, Unit of Retinal Neurophysiology, National Eye Institute","Wei Li, Unit of Retinal Neurophysiology, National Eye Institute",2,0.92058,0.92281,0.10158,0.10522,0.87937,0.88024,0.61938,0.62455,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-11-10,Adult,Adult,Eye,Sensory System 66938,SRR16905264,SRX13097739,SRS11034052,SRP345451,PRJNA779419,Transcriptomic profiling of adult zebrafish photoreceptors,GSE188560,Transcriptome Analysis,Identifying the transcription factors required to specify photoreceptor subtypes is critical to understand the normal development of the retina and to inform cell replacement therapies to restore vision. RNA seq is a powerful way to identify novel genes expressed in particular cell subtypes. Although RNA seq approaches have been used to identify genes differentially expressed between photoreceptor subtypes in many species the limited transcriptome depth derived from single cell techniques constitutes a barrier in the reliable detection of transcription factors. To obtain a deep high quality RNA seq dataset from zebrafish photoreceptors we manually collected pools of photoreceptors of a single subtype. Overall design: We identified photoreceptors using well characterized transgenic lines that express fluorescent proteins in each subtype with high specificity including rods—TgxOPS:GFP UV cones—Tgopn1sw1:GFP S cones—Tgopn1sw2:GFP M cones—Tgopn1mw2:GFP and L cones—Tgthrb:tdTomato. We manually collected pools of 20 dissociated but healthy photoreceptors of a single subtype for each of our samples while actively avoiding cellular debris and other contaminants.,,pubmed:36745553,,Mc1s07,GSM5685600,,tissue:Dissociated adult photoreceptors|transgenic line:Tgopn1mw1:GFP|cell type:M c1s|age:Adult,Mc1s07,Illumina software used for base calling and demultiplexing Sequences for primers and adapters removed using Trimmomatic Trimmomatic 0.36 phred33 /adapters/TruSeq2 PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:70 Reads aligned to zebrafish genome Danio rerio.GRCz11 using HiSat2 hisat2 p 8 rna strandness FR Transcript assembly and counts derived using StringTie Differential gene expression analysis using DESeq2 Genome build: Danio rerio.GRCz11 Supplementary files format and content: Comma separated values files include FPKM values for each Sample Comma separated values files include DESeq2 analysis results comparing Rods vs. Cones GTF files post trimming alignment to genome and transcript assembly RDS Seurat v03 file including count data for all samples,Dissociated adult photoreceptors,post euthanasia retinas from adult zebrafish were collected. Dissociated photoreceptors were obtained post enzymatic treatment with papain gentle mechanic trituration and filtering.,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,transgenic line:Tgopn1mw1:GFP|cell type:M c1s|age:Adult,GSM5685600,GSM5685600: Mc1s07; Danio rerio; RNA Seq,GSM5685600 r1,GSM5685600,1,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP345451,,,M1_R1.fastq.gz M1_R2.fastq.gz,fastq fastq,4912178796.0,19492773.0,GSM5685600 r1,0:126 1:126,A:1364040683;C:1099242822;G:1130576895;T:1316656088;N:1662308,126,126,,,1364040683,1099242822,1130576895,1316656088,1662308,SRX13097739,SRS11034052,SRA1538252,"Wei Li, Unit of Retinal Neurophysiology, National Eye Institute","Wei Li, Unit of Retinal Neurophysiology, National Eye Institute",2,0.92326,0.92568,0.09705,0.09985,0.87113,0.87186,0.61512,0.61584,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-11-10,Adult,Adult,Eye,Sensory System 66939,SRR16905265,SRX13097738,SRS11034051,SRP345451,PRJNA779419,Transcriptomic profiling of adult zebrafish photoreceptors,GSE188560,Transcriptome Analysis,Identifying the transcription factors required to specify photoreceptor subtypes is critical to understand the normal development of the retina and to inform cell replacement therapies to restore vision. RNA seq is a powerful way to identify novel genes expressed in particular cell subtypes. Although RNA seq approaches have been used to identify genes differentially expressed between photoreceptor subtypes in many species the limited transcriptome depth derived from single cell techniques constitutes a barrier in the reliable detection of transcription factors. To obtain a deep high quality RNA seq dataset from zebrafish photoreceptors we manually collected pools of photoreceptors of a single subtype. Overall design: We identified photoreceptors using well characterized transgenic lines that express fluorescent proteins in each subtype with high specificity including rods—TgxOPS:GFP UV cones—Tgopn1sw1:GFP S cones—Tgopn1sw2:GFP M cones—Tgopn1mw2:GFP and L cones—Tgthrb:tdTomato. We manually collected pools of 20 dissociated but healthy photoreceptors of a single subtype for each of our samples while actively avoiding cellular debris and other contaminants.,,pubmed:36745553,,Mc1s06,GSM5685599,,tissue:Dissociated adult photoreceptors|transgenic line:Tgopn1mw1:GFP|cell type:M c1s|age:Adult,Mc1s06,Illumina software used for base calling and demultiplexing Sequences for primers and adapters removed using Trimmomatic Trimmomatic 0.36 phred33 /adapters/TruSeq2 PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:70 Reads aligned to zebrafish genome Danio rerio.GRCz11 using HiSat2 hisat2 p 8 rna strandness FR Transcript assembly and counts derived using StringTie Differential gene expression analysis using DESeq2 Genome build: Danio rerio.GRCz11 Supplementary files format and content: Comma separated values files include FPKM values for each Sample Comma separated values files include DESeq2 analysis results comparing Rods vs. Cones GTF files post trimming alignment to genome and transcript assembly RDS Seurat v03 file including count data for all samples,Dissociated adult photoreceptors,post euthanasia retinas from adult zebrafish were collected. Dissociated photoreceptors were obtained post enzymatic treatment with papain gentle mechanic trituration and filtering.,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,transgenic line:Tgopn1mw1:GFP|cell type:M c1s|age:Adult,GSM5685599,GSM5685599: Mc1s06; Danio rerio; RNA Seq,GSM5685599 r1,GSM5685599,1,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP345451,,,L6_R1.fastq.gz L6_R2.fastq.gz,fastq fastq,5360885208.0,21273354.0,GSM5685599 r1,0:126 1:126,A:1505629300;C:1182511679;G:1221625903;T:1449566489;N:1551837,126,126,,,1505629300,1182511679,1221625903,1449566489,1551837,SRX13097738,SRS11034051,SRA1538252,"Wei Li, Unit of Retinal Neurophysiology, National Eye Institute","Wei Li, Unit of Retinal Neurophysiology, National Eye Institute",2,0.94449,0.94528,0.10857,0.11154,0.86379,0.86452,0.59645,0.59568,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-11-10,Adult,Adult,Eye,Sensory System 66940,SRR16905266,SRX13097737,SRS11034050,SRP345451,PRJNA779419,Transcriptomic profiling of adult zebrafish photoreceptors,GSE188560,Transcriptome Analysis,Identifying the transcription factors required to specify photoreceptor subtypes is critical to understand the normal development of the retina and to inform cell replacement therapies to restore vision. RNA seq is a powerful way to identify novel genes expressed in particular cell subtypes. Although RNA seq approaches have been used to identify genes differentially expressed between photoreceptor subtypes in many species the limited transcriptome depth derived from single cell techniques constitutes a barrier in the reliable detection of transcription factors. To obtain a deep high quality RNA seq dataset from zebrafish photoreceptors we manually collected pools of photoreceptors of a single subtype. Overall design: We identified photoreceptors using well characterized transgenic lines that express fluorescent proteins in each subtype with high specificity including rods—TgxOPS:GFP UV cones—Tgopn1sw1:GFP S cones—Tgopn1sw2:GFP M cones—Tgopn1mw2:GFP and L cones—Tgthrb:tdTomato. We manually collected pools of 20 dissociated but healthy photoreceptors of a single subtype for each of our samples while actively avoiding cellular debris and other contaminants.,,pubmed:36745553,,Mc1s05,GSM5685598,,tissue:Dissociated adult photoreceptors|transgenic line:Tgopn1mw1:GFP|cell type:M c1s|age:Adult,Mc1s05,Illumina software used for base calling and demultiplexing Sequences for primers and adapters removed using Trimmomatic Trimmomatic 0.36 phred33 /adapters/TruSeq2 PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:70 Reads aligned to zebrafish genome Danio rerio.GRCz11 using HiSat2 hisat2 p 8 rna strandness FR Transcript assembly and counts derived using StringTie Differential gene expression analysis using DESeq2 Genome build: Danio rerio.GRCz11 Supplementary files format and content: Comma separated values files include FPKM values for each Sample Comma separated values files include DESeq2 analysis results comparing Rods vs. Cones GTF files post trimming alignment to genome and transcript assembly RDS Seurat v03 file including count data for all samples,Dissociated adult photoreceptors,post euthanasia retinas from adult zebrafish were collected. Dissociated photoreceptors were obtained post enzymatic treatment with papain gentle mechanic trituration and filtering.,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,transgenic line:Tgopn1mw1:GFP|cell type:M c1s|age:Adult,GSM5685598,GSM5685598: Mc1s05; Danio rerio; RNA Seq,GSM5685598 r1,GSM5685598,1,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP345451,,,L5_R1.fastq.gz L5_R2.fastq.gz,fastq fastq,5341124628.0,21194939.0,GSM5685598 r1,0:126 1:126,A:1501482271;C:1174289982;G:1205658468;T:1458129831;N:1564076,126,126,,,1501482271,1174289982,1205658468,1458129831,1564076,SRX13097737,SRS11034050,SRA1538252,"Wei Li, Unit of Retinal Neurophysiology, National Eye Institute","Wei Li, Unit of Retinal Neurophysiology, National Eye Institute",2,0.94708,0.94832,0.1139,0.11733,0.85975,0.86113,0.58445,0.59167,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-11-10,Adult,Adult,Eye,Sensory System 66941,SRR16905267,SRX13097736,SRS11034049,SRP345451,PRJNA779419,Transcriptomic profiling of adult zebrafish photoreceptors,GSE188560,Transcriptome Analysis,Identifying the transcription factors required to specify photoreceptor subtypes is critical to understand the normal development of the retina and to inform cell replacement therapies to restore vision. RNA seq is a powerful way to identify novel genes expressed in particular cell subtypes. Although RNA seq approaches have been used to identify genes differentially expressed between photoreceptor subtypes in many species the limited transcriptome depth derived from single cell techniques constitutes a barrier in the reliable detection of transcription factors. To obtain a deep high quality RNA seq dataset from zebrafish photoreceptors we manually collected pools of photoreceptors of a single subtype. Overall design: We identified photoreceptors using well characterized transgenic lines that express fluorescent proteins in each subtype with high specificity including rods—TgxOPS:GFP UV cones—Tgopn1sw1:GFP S cones—Tgopn1sw2:GFP M cones—Tgopn1mw2:GFP and L cones—Tgthrb:tdTomato. We manually collected pools of 20 dissociated but healthy photoreceptors of a single subtype for each of our samples while actively avoiding cellular debris and other contaminants.,,pubmed:36745553,,Mc1s04,GSM5685597,,tissue:Dissociated adult photoreceptors|transgenic line:Tgopn1mw1:GFP|cell type:M c1s|age:Adult,Mc1s04,Illumina software used for base calling and demultiplexing Sequences for primers and adapters removed using Trimmomatic Trimmomatic 0.36 phred33 /adapters/TruSeq2 PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:70 Reads aligned to zebrafish genome Danio rerio.GRCz11 using HiSat2 hisat2 p 8 rna strandness FR Transcript assembly and counts derived using StringTie Differential gene expression analysis using DESeq2 Genome build: Danio rerio.GRCz11 Supplementary files format and content: Comma separated values files include FPKM values for each Sample Comma separated values files include DESeq2 analysis results comparing Rods vs. Cones GTF files post trimming alignment to genome and transcript assembly RDS Seurat v03 file including count data for all samples,Dissociated adult photoreceptors,post euthanasia retinas from adult zebrafish were collected. Dissociated photoreceptors were obtained post enzymatic treatment with papain gentle mechanic trituration and filtering.,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,transgenic line:Tgopn1mw1:GFP|cell type:M c1s|age:Adult,GSM5685597,GSM5685597: Mc1s04; Danio rerio; RNA Seq,GSM5685597 r1,GSM5685597,1,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP345451,,,L4_R1.fastq.gz L4_R2.fastq.gz,fastq fastq,5578168932.0,22135591.0,GSM5685597 r1,0:126 1:126,A:1578660956;C:1223768295;G:1252061634;T:1522058460;N:1619587,126,126,,,1578660956,1223768295,1252061634,1522058460,1619587,SRX13097736,SRS11034049,SRA1538252,"Wei Li, Unit of Retinal Neurophysiology, National Eye Institute","Wei Li, Unit of Retinal Neurophysiology, National Eye Institute",2,0.94516,0.94489,0.12036,0.12402,0.84137,0.84254,0.57288,0.54404,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-11-10,Adult,Adult,Eye,Sensory System 66942,SRR16905268,SRX13097735,SRS11034048,SRP345451,PRJNA779419,Transcriptomic profiling of adult zebrafish photoreceptors,GSE188560,Transcriptome Analysis,Identifying the transcription factors required to specify photoreceptor subtypes is critical to understand the normal development of the retina and to inform cell replacement therapies to restore vision. RNA seq is a powerful way to identify novel genes expressed in particular cell subtypes. Although RNA seq approaches have been used to identify genes differentially expressed between photoreceptor subtypes in many species the limited transcriptome depth derived from single cell techniques constitutes a barrier in the reliable detection of transcription factors. To obtain a deep high quality RNA seq dataset from zebrafish photoreceptors we manually collected pools of photoreceptors of a single subtype. Overall design: We identified photoreceptors using well characterized transgenic lines that express fluorescent proteins in each subtype with high specificity including rods—TgxOPS:GFP UV cones—Tgopn1sw1:GFP S cones—Tgopn1sw2:GFP M cones—Tgopn1mw2:GFP and L cones—Tgthrb:tdTomato. We manually collected pools of 20 dissociated but healthy photoreceptors of a single subtype for each of our samples while actively avoiding cellular debris and other contaminants.,,pubmed:36745553,,Mc1s03,GSM5685596,,tissue:Dissociated adult photoreceptors|transgenic line:Tgopn1mw1:GFP|cell type:M c1s|age:Adult,Mc1s03,Illumina software used for base calling and demultiplexing Sequences for primers and adapters removed using Trimmomatic Trimmomatic 0.36 phred33 /adapters/TruSeq2 PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:70 Reads aligned to zebrafish genome Danio rerio.GRCz11 using HiSat2 hisat2 p 8 rna strandness FR Transcript assembly and counts derived using StringTie Differential gene expression analysis using DESeq2 Genome build: Danio rerio.GRCz11 Supplementary files format and content: Comma separated values files include FPKM values for each Sample Comma separated values files include DESeq2 analysis results comparing Rods vs. Cones GTF files post trimming alignment to genome and transcript assembly RDS Seurat v03 file including count data for all samples,Dissociated adult photoreceptors,post euthanasia retinas from adult zebrafish were collected. Dissociated photoreceptors were obtained post enzymatic treatment with papain gentle mechanic trituration and filtering.,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,transgenic line:Tgopn1mw1:GFP|cell type:M c1s|age:Adult,GSM5685596,GSM5685596: Mc1s03; Danio rerio; RNA Seq,GSM5685596 r1,GSM5685596,1,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP345451,,,L3_R1.fastq.gz L3_R2.fastq.gz,fastq fastq,5271009660.0,20916705.0,GSM5685596 r1,0:126 1:126,A:1485442147;C:1154338217;G:1186231551;T:1443223057;N:1774688,126,126,,,1485442147,1154338217,1186231551,1443223057,1774688,SRX13097735,SRS11034048,SRA1538252,"Wei Li, Unit of Retinal Neurophysiology, National Eye Institute","Wei Li, Unit of Retinal Neurophysiology, National Eye Institute",2,0.94468,0.94523,0.13201,0.13554,0.84329,0.84492,0.57095,0.54365,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-11-10,Adult,Adult,Eye,Sensory System 66943,SRR16905269,SRX13097734,SRS11034047,SRP345451,PRJNA779419,Transcriptomic profiling of adult zebrafish photoreceptors,GSE188560,Transcriptome Analysis,Identifying the transcription factors required to specify photoreceptor subtypes is critical to understand the normal development of the retina and to inform cell replacement therapies to restore vision. RNA seq is a powerful way to identify novel genes expressed in particular cell subtypes. Although RNA seq approaches have been used to identify genes differentially expressed between photoreceptor subtypes in many species the limited transcriptome depth derived from single cell techniques constitutes a barrier in the reliable detection of transcription factors. To obtain a deep high quality RNA seq dataset from zebrafish photoreceptors we manually collected pools of photoreceptors of a single subtype. Overall design: We identified photoreceptors using well characterized transgenic lines that express fluorescent proteins in each subtype with high specificity including rods—TgxOPS:GFP UV cones—Tgopn1sw1:GFP S cones—Tgopn1sw2:GFP M cones—Tgopn1mw2:GFP and L cones—Tgthrb:tdTomato. We manually collected pools of 20 dissociated but healthy photoreceptors of a single subtype for each of our samples while actively avoiding cellular debris and other contaminants.,,pubmed:36745553,,Mc1s02,GSM5685595,,tissue:Dissociated adult photoreceptors|transgenic line:Tgopn1mw1:GFP|cell type:M c1s|age:Adult,Mc1s02,Illumina software used for base calling and demultiplexing Sequences for primers and adapters removed using Trimmomatic Trimmomatic 0.36 phred33 /adapters/TruSeq2 PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:70 Reads aligned to zebrafish genome Danio rerio.GRCz11 using HiSat2 hisat2 p 8 rna strandness FR Transcript assembly and counts derived using StringTie Differential gene expression analysis using DESeq2 Genome build: Danio rerio.GRCz11 Supplementary files format and content: Comma separated values files include FPKM values for each Sample Comma separated values files include DESeq2 analysis results comparing Rods vs. Cones GTF files post trimming alignment to genome and transcript assembly RDS Seurat v03 file including count data for all samples,Dissociated adult photoreceptors,post euthanasia retinas from adult zebrafish were collected. Dissociated photoreceptors were obtained post enzymatic treatment with papain gentle mechanic trituration and filtering.,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,transgenic line:Tgopn1mw1:GFP|cell type:M c1s|age:Adult,GSM5685595,GSM5685595: Mc1s02; Danio rerio; RNA Seq,GSM5685595 r1,GSM5685595,1,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP345451,,,L2_R1.fastq.gz L2_R2.fastq.gz,fastq fastq,5138924868.0,20392559.0,GSM5685595 r1,0:126 1:126,A:1430260105;C:1141131866;G:1170941238;T:1394865738;N:1725921,126,126,,,1430260105,1141131866,1170941238,1394865738,1725921,SRX13097734,SRS11034047,SRA1538252,"Wei Li, Unit of Retinal Neurophysiology, National Eye Institute","Wei Li, Unit of Retinal Neurophysiology, National Eye Institute",2,0.94907,0.94979,0.09443,0.09721,0.86342,0.86431,0.57214,0.57443,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-11-10,Adult,Adult,Eye,Sensory System 66944,SRR16905270,SRX13097733,SRS11034046,SRP345451,PRJNA779419,Transcriptomic profiling of adult zebrafish photoreceptors,GSE188560,Transcriptome Analysis,Identifying the transcription factors required to specify photoreceptor subtypes is critical to understand the normal development of the retina and to inform cell replacement therapies to restore vision. RNA seq is a powerful way to identify novel genes expressed in particular cell subtypes. Although RNA seq approaches have been used to identify genes differentially expressed between photoreceptor subtypes in many species the limited transcriptome depth derived from single cell techniques constitutes a barrier in the reliable detection of transcription factors. To obtain a deep high quality RNA seq dataset from zebrafish photoreceptors we manually collected pools of photoreceptors of a single subtype. Overall design: We identified photoreceptors using well characterized transgenic lines that express fluorescent proteins in each subtype with high specificity including rods—TgxOPS:GFP UV cones—Tgopn1sw1:GFP S cones—Tgopn1sw2:GFP M cones—Tgopn1mw2:GFP and L cones—Tgthrb:tdTomato. We manually collected pools of 20 dissociated but healthy photoreceptors of a single subtype for each of our samples while actively avoiding cellular debris and other contaminants.,,pubmed:36745553,,Mc1s01,GSM5685594,,tissue:Dissociated adult photoreceptors|transgenic line:Tgopn1mw1:GFP|cell type:M c1s|age:Adult,Mc1s01,Illumina software used for base calling and demultiplexing Sequences for primers and adapters removed using Trimmomatic Trimmomatic 0.36 phred33 /adapters/TruSeq2 PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:70 Reads aligned to zebrafish genome Danio rerio.GRCz11 using HiSat2 hisat2 p 8 rna strandness FR Transcript assembly and counts derived using StringTie Differential gene expression analysis using DESeq2 Genome build: Danio rerio.GRCz11 Supplementary files format and content: Comma separated values files include FPKM values for each Sample Comma separated values files include DESeq2 analysis results comparing Rods vs. Cones GTF files post trimming alignment to genome and transcript assembly RDS Seurat v03 file including count data for all samples,Dissociated adult photoreceptors,post euthanasia retinas from adult zebrafish were collected. Dissociated photoreceptors were obtained post enzymatic treatment with papain gentle mechanic trituration and filtering.,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,transgenic line:Tgopn1mw1:GFP|cell type:M c1s|age:Adult,GSM5685594,GSM5685594: Mc1s01; Danio rerio; RNA Seq,GSM5685594 r1,GSM5685594,1,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP345451,,,L1_R1.fastq.gz L1_R2.fastq.gz,fastq fastq,4850595540.0,19248395.0,GSM5685594 r1,0:126 1:126,A:1357107734;C:1073830302;G:1101729243;T:1316296351;N:1631910,126,126,,,1357107734,1073830302,1101729243,1316296351,1631910,SRX13097733,SRS11034046,SRA1538252,"Wei Li, Unit of Retinal Neurophysiology, National Eye Institute","Wei Li, Unit of Retinal Neurophysiology, National Eye Institute",2,0.94799,0.94746,0.11829,0.12268,0.86066,0.86117,0.58516,0.58453,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-11-10,Adult,Adult,Eye,Sensory System 66945,SRR16905271,SRX13097732,SRS11034045,SRP345451,PRJNA779419,Transcriptomic profiling of adult zebrafish photoreceptors,GSE188560,Transcriptome Analysis,Identifying the transcription factors required to specify photoreceptor subtypes is critical to understand the normal development of the retina and to inform cell replacement therapies to restore vision. RNA seq is a powerful way to identify novel genes expressed in particular cell subtypes. Although RNA seq approaches have been used to identify genes differentially expressed between photoreceptor subtypes in many species the limited transcriptome depth derived from single cell techniques constitutes a barrier in the reliable detection of transcription factors. To obtain a deep high quality RNA seq dataset from zebrafish photoreceptors we manually collected pools of photoreceptors of a single subtype. Overall design: We identified photoreceptors using well characterized transgenic lines that express fluorescent proteins in each subtype with high specificity including rods—TgxOPS:GFP UV cones—Tgopn1sw1:GFP S cones—Tgopn1sw2:GFP M cones—Tgopn1mw2:GFP and L cones—Tgthrb:tdTomato. We manually collected pools of 20 dissociated but healthy photoreceptors of a single subtype for each of our samples while actively avoiding cellular debris and other contaminants.,,pubmed:36745553,,Sc1s06,GSM5685593,,tissue:Dissociated adult photoreceptors|transgenic line:Tgopn1sw2:GFP|cell type:S c1s|age:Adult,Sc1s06,Illumina software used for base calling and demultiplexing Sequences for primers and adapters removed using Trimmomatic Trimmomatic 0.36 phred33 /adapters/TruSeq2 PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:70 Reads aligned to zebrafish genome Danio rerio.GRCz11 using HiSat2 hisat2 p 8 rna strandness FR Transcript assembly and counts derived using StringTie Differential gene expression analysis using DESeq2 Genome build: Danio rerio.GRCz11 Supplementary files format and content: Comma separated values files include FPKM values for each Sample Comma separated values files include DESeq2 analysis results comparing Rods vs. Cones GTF files post trimming alignment to genome and transcript assembly RDS Seurat v03 file including count data for all samples,Dissociated adult photoreceptors,post euthanasia retinas from adult zebrafish were collected. Dissociated photoreceptors were obtained post enzymatic treatment with papain gentle mechanic trituration and filtering.,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,transgenic line:Tgopn1sw2:GFP|cell type:S c1s|age:Adult,GSM5685593,GSM5685593: Sc1s06; Danio rerio; RNA Seq,GSM5685593 r1,GSM5685593,1,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP345451,,,S6_R1.fastq.gz S6_R2.fastq.gz,fastq fastq,5358169152.0,21262576.0,GSM5685593 r1,0:126 1:126,A:1509635456;C:1173625207;G:1208688053;T:1464661887;N:1558549,126,126,,,1509635456,1173625207,1208688053,1464661887,1558549,SRX13097732,SRS11034045,SRA1538252,"Wei Li, Unit of Retinal Neurophysiology, National Eye Institute","Wei Li, Unit of Retinal Neurophysiology, National Eye Institute",2,0.91206,0.91488,0.10909,0.11229,0.88134,0.88114,0.65434,0.64924,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-11-10,Adult,Adult,Eye,Sensory System 66946,SRR16905272,SRX13097731,SRS11034044,SRP345451,PRJNA779419,Transcriptomic profiling of adult zebrafish photoreceptors,GSE188560,Transcriptome Analysis,Identifying the transcription factors required to specify photoreceptor subtypes is critical to understand the normal development of the retina and to inform cell replacement therapies to restore vision. RNA seq is a powerful way to identify novel genes expressed in particular cell subtypes. Although RNA seq approaches have been used to identify genes differentially expressed between photoreceptor subtypes in many species the limited transcriptome depth derived from single cell techniques constitutes a barrier in the reliable detection of transcription factors. To obtain a deep high quality RNA seq dataset from zebrafish photoreceptors we manually collected pools of photoreceptors of a single subtype. Overall design: We identified photoreceptors using well characterized transgenic lines that express fluorescent proteins in each subtype with high specificity including rods—TgxOPS:GFP UV cones—Tgopn1sw1:GFP S cones—Tgopn1sw2:GFP M cones—Tgopn1mw2:GFP and L cones—Tgthrb:tdTomato. We manually collected pools of 20 dissociated but healthy photoreceptors of a single subtype for each of our samples while actively avoiding cellular debris and other contaminants.,,pubmed:36745553,,Sc1s05,GSM5685592,,tissue:Dissociated adult photoreceptors|transgenic line:Tgopn1sw2:GFP|cell type:S c1s|age:Adult,Sc1s05,Illumina software used for base calling and demultiplexing Sequences for primers and adapters removed using Trimmomatic Trimmomatic 0.36 phred33 /adapters/TruSeq2 PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:70 Reads aligned to zebrafish genome Danio rerio.GRCz11 using HiSat2 hisat2 p 8 rna strandness FR Transcript assembly and counts derived using StringTie Differential gene expression analysis using DESeq2 Genome build: Danio rerio.GRCz11 Supplementary files format and content: Comma separated values files include FPKM values for each Sample Comma separated values files include DESeq2 analysis results comparing Rods vs. Cones GTF files post trimming alignment to genome and transcript assembly RDS Seurat v03 file including count data for all samples,Dissociated adult photoreceptors,post euthanasia retinas from adult zebrafish were collected. Dissociated photoreceptors were obtained post enzymatic treatment with papain gentle mechanic trituration and filtering.,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,transgenic line:Tgopn1sw2:GFP|cell type:S c1s|age:Adult,GSM5685592,GSM5685592: Sc1s05; Danio rerio; RNA Seq,GSM5685592 r1,GSM5685592,1,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP345451,,,S5_R1.fastq.gz S5_R2.fastq.gz,fastq fastq,6509121444.0,25829847.0,GSM5685592 r1,0:126 1:126,A:1836417327;C:1425249461;G:1465375194;T:1780196185;N:1883277,126,126,,,1836417327,1425249461,1465375194,1780196185,1883277,SRX13097731,SRS11034044,SRA1538252,"Wei Li, Unit of Retinal Neurophysiology, National Eye Institute","Wei Li, Unit of Retinal Neurophysiology, National Eye Institute",2,0.91956,0.9207,0.12443,0.12844,0.86711,0.86817,0.64231,0.53996,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-11-10,Adult,Adult,Eye,Sensory System 66947,SRR16905273,SRX13097730,SRS11034043,SRP345451,PRJNA779419,Transcriptomic profiling of adult zebrafish photoreceptors,GSE188560,Transcriptome Analysis,Identifying the transcription factors required to specify photoreceptor subtypes is critical to understand the normal development of the retina and to inform cell replacement therapies to restore vision. RNA seq is a powerful way to identify novel genes expressed in particular cell subtypes. Although RNA seq approaches have been used to identify genes differentially expressed between photoreceptor subtypes in many species the limited transcriptome depth derived from single cell techniques constitutes a barrier in the reliable detection of transcription factors. To obtain a deep high quality RNA seq dataset from zebrafish photoreceptors we manually collected pools of photoreceptors of a single subtype. Overall design: We identified photoreceptors using well characterized transgenic lines that express fluorescent proteins in each subtype with high specificity including rods—TgxOPS:GFP UV cones—Tgopn1sw1:GFP S cones—Tgopn1sw2:GFP M cones—Tgopn1mw2:GFP and L cones—Tgthrb:tdTomato. We manually collected pools of 20 dissociated but healthy photoreceptors of a single subtype for each of our samples while actively avoiding cellular debris and other contaminants.,,pubmed:36745553,,Sc1s04,GSM5685591,,tissue:Dissociated adult photoreceptors|transgenic line:Tgopn1sw2:GFP|cell type:S c1s|age:Adult,Sc1s04,Illumina software used for base calling and demultiplexing Sequences for primers and adapters removed using Trimmomatic Trimmomatic 0.36 phred33 /adapters/TruSeq2 PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:70 Reads aligned to zebrafish genome Danio rerio.GRCz11 using HiSat2 hisat2 p 8 rna strandness FR Transcript assembly and counts derived using StringTie Differential gene expression analysis using DESeq2 Genome build: Danio rerio.GRCz11 Supplementary files format and content: Comma separated values files include FPKM values for each Sample Comma separated values files include DESeq2 analysis results comparing Rods vs. Cones GTF files post trimming alignment to genome and transcript assembly RDS Seurat v03 file including count data for all samples,Dissociated adult photoreceptors,post euthanasia retinas from adult zebrafish were collected. Dissociated photoreceptors were obtained post enzymatic treatment with papain gentle mechanic trituration and filtering.,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,transgenic line:Tgopn1sw2:GFP|cell type:S c1s|age:Adult,GSM5685591,GSM5685591: Sc1s04; Danio rerio; RNA Seq,GSM5685591 r1,GSM5685591,1,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP345451,,,S4_R1.fastq.gz S4_R2.fastq.gz,fastq fastq,7552946520.0,29972010.0,GSM5685591 r1,0:126 1:126,A:2119122249;C:1660029834;G:1723217776;T:2048829099;N:1747562,126,126,,,2119122249,1660029834,1723217776,2048829099,1747562,SRX13097730,SRS11034043,SRA1538252,"Wei Li, Unit of Retinal Neurophysiology, National Eye Institute","Wei Li, Unit of Retinal Neurophysiology, National Eye Institute",2,0.9112,0.91617,0.10328,0.10662,0.86849,0.86902,0.57363,0.58769,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-11-10,Adult,Adult,Eye,Sensory System 66948,SRR16905274,SRX13097729,SRS11034042,SRP345451,PRJNA779419,Transcriptomic profiling of adult zebrafish photoreceptors,GSE188560,Transcriptome Analysis,Identifying the transcription factors required to specify photoreceptor subtypes is critical to understand the normal development of the retina and to inform cell replacement therapies to restore vision. RNA seq is a powerful way to identify novel genes expressed in particular cell subtypes. Although RNA seq approaches have been used to identify genes differentially expressed between photoreceptor subtypes in many species the limited transcriptome depth derived from single cell techniques constitutes a barrier in the reliable detection of transcription factors. To obtain a deep high quality RNA seq dataset from zebrafish photoreceptors we manually collected pools of photoreceptors of a single subtype. Overall design: We identified photoreceptors using well characterized transgenic lines that express fluorescent proteins in each subtype with high specificity including rods—TgxOPS:GFP UV cones—Tgopn1sw1:GFP S cones—Tgopn1sw2:GFP M cones—Tgopn1mw2:GFP and L cones—Tgthrb:tdTomato. We manually collected pools of 20 dissociated but healthy photoreceptors of a single subtype for each of our samples while actively avoiding cellular debris and other contaminants.,,pubmed:36745553,,Sc1s03,GSM5685590,,tissue:Dissociated adult photoreceptors|transgenic line:Tgopn1sw2:GFP|cell type:S c1s|age:Adult,Sc1s03,Illumina software used for base calling and demultiplexing Sequences for primers and adapters removed using Trimmomatic Trimmomatic 0.36 phred33 /adapters/TruSeq2 PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:70 Reads aligned to zebrafish genome Danio rerio.GRCz11 using HiSat2 hisat2 p 8 rna strandness FR Transcript assembly and counts derived using StringTie Differential gene expression analysis using DESeq2 Genome build: Danio rerio.GRCz11 Supplementary files format and content: Comma separated values files include FPKM values for each Sample Comma separated values files include DESeq2 analysis results comparing Rods vs. Cones GTF files post trimming alignment to genome and transcript assembly RDS Seurat v03 file including count data for all samples,Dissociated adult photoreceptors,post euthanasia retinas from adult zebrafish were collected. Dissociated photoreceptors were obtained post enzymatic treatment with papain gentle mechanic trituration and filtering.,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,transgenic line:Tgopn1sw2:GFP|cell type:S c1s|age:Adult,GSM5685590,GSM5685590: Sc1s03; Danio rerio; RNA Seq,GSM5685590 r1,GSM5685590,1,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP345451,,,S3_R1.fastq.gz S3_R2.fastq.gz,fastq fastq,4714229016.0,18707258.0,GSM5685590 r1,0:126 1:126,A:1297789070;C:1055844065;G:1094044166;T:1265457138;N:1094577,126,126,,,1297789070,1055844065,1094044166,1265457138,1094577,SRX13097729,SRS11034042,SRA1538252,"Wei Li, Unit of Retinal Neurophysiology, National Eye Institute","Wei Li, Unit of Retinal Neurophysiology, National Eye Institute",2,0.90603,0.90991,0.10831,0.11103,0.88079,0.88156,0.56446,0.56732,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-11-10,Adult,Adult,Eye,Sensory System 66949,SRR16905275,SRX13097728,SRS11034041,SRP345451,PRJNA779419,Transcriptomic profiling of adult zebrafish photoreceptors,GSE188560,Transcriptome Analysis,Identifying the transcription factors required to specify photoreceptor subtypes is critical to understand the normal development of the retina and to inform cell replacement therapies to restore vision. RNA seq is a powerful way to identify novel genes expressed in particular cell subtypes. Although RNA seq approaches have been used to identify genes differentially expressed between photoreceptor subtypes in many species the limited transcriptome depth derived from single cell techniques constitutes a barrier in the reliable detection of transcription factors. To obtain a deep high quality RNA seq dataset from zebrafish photoreceptors we manually collected pools of photoreceptors of a single subtype. Overall design: We identified photoreceptors using well characterized transgenic lines that express fluorescent proteins in each subtype with high specificity including rods—TgxOPS:GFP UV cones—Tgopn1sw1:GFP S cones—Tgopn1sw2:GFP M cones—Tgopn1mw2:GFP and L cones—Tgthrb:tdTomato. We manually collected pools of 20 dissociated but healthy photoreceptors of a single subtype for each of our samples while actively avoiding cellular debris and other contaminants.,,pubmed:36745553,,Sc1s02,GSM5685589,,tissue:Dissociated adult photoreceptors|transgenic line:Tgopn1sw2:GFP|cell type:S c1s|age:Adult,Sc1s02,Illumina software used for base calling and demultiplexing Sequences for primers and adapters removed using Trimmomatic Trimmomatic 0.36 phred33 /adapters/TruSeq2 PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:70 Reads aligned to zebrafish genome Danio rerio.GRCz11 using HiSat2 hisat2 p 8 rna strandness FR Transcript assembly and counts derived using StringTie Differential gene expression analysis using DESeq2 Genome build: Danio rerio.GRCz11 Supplementary files format and content: Comma separated values files include FPKM values for each Sample Comma separated values files include DESeq2 analysis results comparing Rods vs. Cones GTF files post trimming alignment to genome and transcript assembly RDS Seurat v03 file including count data for all samples,Dissociated adult photoreceptors,post euthanasia retinas from adult zebrafish were collected. Dissociated photoreceptors were obtained post enzymatic treatment with papain gentle mechanic trituration and filtering.,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,transgenic line:Tgopn1sw2:GFP|cell type:S c1s|age:Adult,GSM5685589,GSM5685589: Sc1s02; Danio rerio; RNA Seq,GSM5685589 r1,GSM5685589,1,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP345451,,,S2_R1.fastq.gz S2_R2.fastq.gz,fastq fastq,4715583264.0,18712632.0,GSM5685589 r1,0:126 1:126,A:1326599158;C:1033755270;G:1074748315;T:1279389764;N:1090757,126,126,,,1326599158,1033755270,1074748315,1279389764,1090757,SRX13097728,SRS11034041,SRA1538252,"Wei Li, Unit of Retinal Neurophysiology, National Eye Institute","Wei Li, Unit of Retinal Neurophysiology, National Eye Institute",2,0.91422,0.91687,0.12099,0.12449,0.88556,0.88566,0.53084,0.52789,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-11-10,Adult,Adult,Eye,Sensory System 66950,SRR16905276,SRX13097727,SRS11034040,SRP345451,PRJNA779419,Transcriptomic profiling of adult zebrafish photoreceptors,GSE188560,Transcriptome Analysis,Identifying the transcription factors required to specify photoreceptor subtypes is critical to understand the normal development of the retina and to inform cell replacement therapies to restore vision. RNA seq is a powerful way to identify novel genes expressed in particular cell subtypes. Although RNA seq approaches have been used to identify genes differentially expressed between photoreceptor subtypes in many species the limited transcriptome depth derived from single cell techniques constitutes a barrier in the reliable detection of transcription factors. To obtain a deep high quality RNA seq dataset from zebrafish photoreceptors we manually collected pools of photoreceptors of a single subtype. Overall design: We identified photoreceptors using well characterized transgenic lines that express fluorescent proteins in each subtype with high specificity including rods—TgxOPS:GFP UV cones—Tgopn1sw1:GFP S cones—Tgopn1sw2:GFP M cones—Tgopn1mw2:GFP and L cones—Tgthrb:tdTomato. We manually collected pools of 20 dissociated but healthy photoreceptors of a single subtype for each of our samples while actively avoiding cellular debris and other contaminants.,,pubmed:36745553,,Sc1s01,GSM5685588,,tissue:Dissociated adult photoreceptors|transgenic line:Tgopn1sw2:GFP|cell type:S c1s|age:Adult,Sc1s01,Illumina software used for base calling and demultiplexing Sequences for primers and adapters removed using Trimmomatic Trimmomatic 0.36 phred33 /adapters/TruSeq2 PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:70 Reads aligned to zebrafish genome Danio rerio.GRCz11 using HiSat2 hisat2 p 8 rna strandness FR Transcript assembly and counts derived using StringTie Differential gene expression analysis using DESeq2 Genome build: Danio rerio.GRCz11 Supplementary files format and content: Comma separated values files include FPKM values for each Sample Comma separated values files include DESeq2 analysis results comparing Rods vs. Cones GTF files post trimming alignment to genome and transcript assembly RDS Seurat v03 file including count data for all samples,Dissociated adult photoreceptors,post euthanasia retinas from adult zebrafish were collected. Dissociated photoreceptors were obtained post enzymatic treatment with papain gentle mechanic trituration and filtering.,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,transgenic line:Tgopn1sw2:GFP|cell type:S c1s|age:Adult,GSM5685588,GSM5685588: Sc1s01; Danio rerio; RNA Seq,GSM5685588 r1,GSM5685588,1,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP345451,,,S1_R1.fastq.gz S1_R2.fastq.gz,fastq fastq,4491370044.0,17822897.0,GSM5685588 r1,0:126 1:126,A:1250356330;C:994050165;G:1029964584;T:1215960945;N:1038020,126,126,,,1250356330,994050165,1029964584,1215960945,1038020,SRX13097727,SRS11034040,SRA1538252,"Wei Li, Unit of Retinal Neurophysiology, National Eye Institute","Wei Li, Unit of Retinal Neurophysiology, National Eye Institute",2,0.92746,0.93073,0.10175,0.1045,0.88868,0.88927,0.56703,0.56725,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-11-10,Adult,Adult,Eye,Sensory System 66951,SRR16905277,SRX13097726,SRS11034039,SRP345451,PRJNA779419,Transcriptomic profiling of adult zebrafish photoreceptors,GSE188560,Transcriptome Analysis,Identifying the transcription factors required to specify photoreceptor subtypes is critical to understand the normal development of the retina and to inform cell replacement therapies to restore vision. RNA seq is a powerful way to identify novel genes expressed in particular cell subtypes. Although RNA seq approaches have been used to identify genes differentially expressed between photoreceptor subtypes in many species the limited transcriptome depth derived from single cell techniques constitutes a barrier in the reliable detection of transcription factors. To obtain a deep high quality RNA seq dataset from zebrafish photoreceptors we manually collected pools of photoreceptors of a single subtype. Overall design: We identified photoreceptors using well characterized transgenic lines that express fluorescent proteins in each subtype with high specificity including rods—TgxOPS:GFP UV cones—Tgopn1sw1:GFP S cones—Tgopn1sw2:GFP M cones—Tgopn1mw2:GFP and L cones—Tgthrb:tdTomato. We manually collected pools of 20 dissociated but healthy photoreceptors of a single subtype for each of our samples while actively avoiding cellular debris and other contaminants.,,pubmed:36745553,,UVc1s05,GSM5685587,,tissue:Dissociated adult photoreceptors|transgenic line:Tgopn1sw1:GFP|cell type:UV c1s|age:Adult,UVc1s05,Illumina software used for base calling and demultiplexing Sequences for primers and adapters removed using Trimmomatic Trimmomatic 0.36 phred33 /adapters/TruSeq2 PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:70 Reads aligned to zebrafish genome Danio rerio.GRCz11 using HiSat2 hisat2 p 8 rna strandness FR Transcript assembly and counts derived using StringTie Differential gene expression analysis using DESeq2 Genome build: Danio rerio.GRCz11 Supplementary files format and content: Comma separated values files include FPKM values for each Sample Comma separated values files include DESeq2 analysis results comparing Rods vs. Cones GTF files post trimming alignment to genome and transcript assembly RDS Seurat v03 file including count data for all samples,Dissociated adult photoreceptors,post euthanasia retinas from adult zebrafish were collected. Dissociated photoreceptors were obtained post enzymatic treatment with papain gentle mechanic trituration and filtering.,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,transgenic line:Tgopn1sw1:GFP|cell type:UV c1s|age:Adult,GSM5685587,GSM5685587: UVc1s05; Danio rerio; RNA Seq,GSM5685587 r1,GSM5685587,1,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP345451,,,U5_R1.fastq.gz U5_R2.fastq.gz,fastq fastq,5676629868.0,22526309.0,GSM5685587 r1,0:126 1:126,A:1545654536;C:1295170307;G:1330357853;T:1503534377;N:1912795,126,126,,,1545654536,1295170307,1330357853,1503534377,1912795,SRX13097726,SRS11034039,SRA1538252,"Wei Li, Unit of Retinal Neurophysiology, National Eye Institute","Wei Li, Unit of Retinal Neurophysiology, National Eye Institute",2,0.82624,0.82848,0.11559,0.12029,0.87503,0.8757,0.37839,0.37885,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-11-10,Adult,Adult,Eye,Sensory System 66952,SRR16905278,SRX13097725,SRS11034038,SRP345451,PRJNA779419,Transcriptomic profiling of adult zebrafish photoreceptors,GSE188560,Transcriptome Analysis,Identifying the transcription factors required to specify photoreceptor subtypes is critical to understand the normal development of the retina and to inform cell replacement therapies to restore vision. RNA seq is a powerful way to identify novel genes expressed in particular cell subtypes. Although RNA seq approaches have been used to identify genes differentially expressed between photoreceptor subtypes in many species the limited transcriptome depth derived from single cell techniques constitutes a barrier in the reliable detection of transcription factors. To obtain a deep high quality RNA seq dataset from zebrafish photoreceptors we manually collected pools of photoreceptors of a single subtype. Overall design: We identified photoreceptors using well characterized transgenic lines that express fluorescent proteins in each subtype with high specificity including rods—TgxOPS:GFP UV cones—Tgopn1sw1:GFP S cones—Tgopn1sw2:GFP M cones—Tgopn1mw2:GFP and L cones—Tgthrb:tdTomato. We manually collected pools of 20 dissociated but healthy photoreceptors of a single subtype for each of our samples while actively avoiding cellular debris and other contaminants.,,pubmed:36745553,,UVc1s04,GSM5685586,,tissue:Dissociated adult photoreceptors|transgenic line:Tgopn1sw1:GFP|cell type:UV c1s|age:Adult,UVc1s04,Illumina software used for base calling and demultiplexing Sequences for primers and adapters removed using Trimmomatic Trimmomatic 0.36 phred33 /adapters/TruSeq2 PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:70 Reads aligned to zebrafish genome Danio rerio.GRCz11 using HiSat2 hisat2 p 8 rna strandness FR Transcript assembly and counts derived using StringTie Differential gene expression analysis using DESeq2 Genome build: Danio rerio.GRCz11 Supplementary files format and content: Comma separated values files include FPKM values for each Sample Comma separated values files include DESeq2 analysis results comparing Rods vs. Cones GTF files post trimming alignment to genome and transcript assembly RDS Seurat v03 file including count data for all samples,Dissociated adult photoreceptors,post euthanasia retinas from adult zebrafish were collected. Dissociated photoreceptors were obtained post enzymatic treatment with papain gentle mechanic trituration and filtering.,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,transgenic line:Tgopn1sw1:GFP|cell type:UV c1s|age:Adult,GSM5685586,GSM5685586: UVc1s04; Danio rerio; RNA Seq,GSM5685586 r1,GSM5685586,1,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP345451,,,U4_R1.fastq.gz U4_R2.fastq.gz,fastq fastq,4442855760.0,17630380.0,GSM5685586 r1,0:126 1:126,A:1228795139;C:992181736;G:1025373281;T:1195476912;N:1028692,126,126,,,1228795139,992181736,1025373281,1195476912,1028692,SRX13097725,SRS11034038,SRA1538252,"Wei Li, Unit of Retinal Neurophysiology, National Eye Institute","Wei Li, Unit of Retinal Neurophysiology, National Eye Institute",2,0.89666,0.90048,0.10818,0.1113,0.86565,0.86576,0.45376,0.45358,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-11-10,Adult,Adult,Eye,Sensory System 66953,SRR16905279,SRX13097724,SRS11034037,SRP345451,PRJNA779419,Transcriptomic profiling of adult zebrafish photoreceptors,GSE188560,Transcriptome Analysis,Identifying the transcription factors required to specify photoreceptor subtypes is critical to understand the normal development of the retina and to inform cell replacement therapies to restore vision. RNA seq is a powerful way to identify novel genes expressed in particular cell subtypes. Although RNA seq approaches have been used to identify genes differentially expressed between photoreceptor subtypes in many species the limited transcriptome depth derived from single cell techniques constitutes a barrier in the reliable detection of transcription factors. To obtain a deep high quality RNA seq dataset from zebrafish photoreceptors we manually collected pools of photoreceptors of a single subtype. Overall design: We identified photoreceptors using well characterized transgenic lines that express fluorescent proteins in each subtype with high specificity including rods—TgxOPS:GFP UV cones—Tgopn1sw1:GFP S cones—Tgopn1sw2:GFP M cones—Tgopn1mw2:GFP and L cones—Tgthrb:tdTomato. We manually collected pools of 20 dissociated but healthy photoreceptors of a single subtype for each of our samples while actively avoiding cellular debris and other contaminants.,,pubmed:36745553,,UVc1s03,GSM5685585,,tissue:Dissociated adult photoreceptors|transgenic line:Tgopn1sw1:GFP|cell type:UV c1s|age:Adult,UVc1s03,Illumina software used for base calling and demultiplexing Sequences for primers and adapters removed using Trimmomatic Trimmomatic 0.36 phred33 /adapters/TruSeq2 PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:70 Reads aligned to zebrafish genome Danio rerio.GRCz11 using HiSat2 hisat2 p 8 rna strandness FR Transcript assembly and counts derived using StringTie Differential gene expression analysis using DESeq2 Genome build: Danio rerio.GRCz11 Supplementary files format and content: Comma separated values files include FPKM values for each Sample Comma separated values files include DESeq2 analysis results comparing Rods vs. Cones GTF files post trimming alignment to genome and transcript assembly RDS Seurat v03 file including count data for all samples,Dissociated adult photoreceptors,post euthanasia retinas from adult zebrafish were collected. Dissociated photoreceptors were obtained post enzymatic treatment with papain gentle mechanic trituration and filtering.,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,transgenic line:Tgopn1sw1:GFP|cell type:UV c1s|age:Adult,GSM5685585,GSM5685585: UVc1s03; Danio rerio; RNA Seq,GSM5685585 r1,GSM5685585,1,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP345451,,,U3_R1.fastq.gz U3_R2.fastq.gz,fastq fastq,5071833900.0,20126325.0,GSM5685585 r1,0:126 1:126,A:1420392734;C:1115192663;G:1152057964;T:1383013429;N:1177110,126,126,,,1420392734,1115192663,1152057964,1383013429,1177110,SRX13097724,SRS11034037,SRA1538252,"Wei Li, Unit of Retinal Neurophysiology, National Eye Institute","Wei Li, Unit of Retinal Neurophysiology, National Eye Institute",2,0.8932,0.89753,0.12444,0.12759,0.87612,0.87677,0.47554,0.48693,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-11-10,Adult,Adult,Eye,Sensory System 66954,SRR16905280,SRX13097723,SRS11034036,SRP345451,PRJNA779419,Transcriptomic profiling of adult zebrafish photoreceptors,GSE188560,Transcriptome Analysis,Identifying the transcription factors required to specify photoreceptor subtypes is critical to understand the normal development of the retina and to inform cell replacement therapies to restore vision. RNA seq is a powerful way to identify novel genes expressed in particular cell subtypes. Although RNA seq approaches have been used to identify genes differentially expressed between photoreceptor subtypes in many species the limited transcriptome depth derived from single cell techniques constitutes a barrier in the reliable detection of transcription factors. To obtain a deep high quality RNA seq dataset from zebrafish photoreceptors we manually collected pools of photoreceptors of a single subtype. Overall design: We identified photoreceptors using well characterized transgenic lines that express fluorescent proteins in each subtype with high specificity including rods—TgxOPS:GFP UV cones—Tgopn1sw1:GFP S cones—Tgopn1sw2:GFP M cones—Tgopn1mw2:GFP and L cones—Tgthrb:tdTomato. We manually collected pools of 20 dissociated but healthy photoreceptors of a single subtype for each of our samples while actively avoiding cellular debris and other contaminants.,,pubmed:36745553,,UVc1s02,GSM5685584,,tissue:Dissociated adult photoreceptors|transgenic line:Tgopn1sw1:GFP|cell type:UV c1s|age:Adult,UVc1s02,Illumina software used for base calling and demultiplexing Sequences for primers and adapters removed using Trimmomatic Trimmomatic 0.36 phred33 /adapters/TruSeq2 PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:70 Reads aligned to zebrafish genome Danio rerio.GRCz11 using HiSat2 hisat2 p 8 rna strandness FR Transcript assembly and counts derived using StringTie Differential gene expression analysis using DESeq2 Genome build: Danio rerio.GRCz11 Supplementary files format and content: Comma separated values files include FPKM values for each Sample Comma separated values files include DESeq2 analysis results comparing Rods vs. Cones GTF files post trimming alignment to genome and transcript assembly RDS Seurat v03 file including count data for all samples,Dissociated adult photoreceptors,post euthanasia retinas from adult zebrafish were collected. Dissociated photoreceptors were obtained post enzymatic treatment with papain gentle mechanic trituration and filtering.,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,transgenic line:Tgopn1sw1:GFP|cell type:UV c1s|age:Adult,GSM5685584,GSM5685584: UVc1s02; Danio rerio; RNA Seq,GSM5685584 r1,GSM5685584,1,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP345451,,,U2_R1.fastq.gz U2_R2.fastq.gz,fastq fastq,3575236392.0,14187446.0,GSM5685584 r1,0:126 1:126,A:975203222;C:812648233;G:846540921;T:940013729;N:830287,126,126,,,975203222,812648233,846540921,940013729,830287,SRX13097723,SRS11034036,SRA1538252,"Wei Li, Unit of Retinal Neurophysiology, National Eye Institute","Wei Li, Unit of Retinal Neurophysiology, National Eye Institute",2,0.79703,0.80022,0.11068,0.1139,0.88101,0.88162,0.43397,0.42506,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-11-10,Adult,Adult,Eye,Sensory System 66955,SRR16905281,SRX13097722,SRS11034035,SRP345451,PRJNA779419,Transcriptomic profiling of adult zebrafish photoreceptors,GSE188560,Transcriptome Analysis,Identifying the transcription factors required to specify photoreceptor subtypes is critical to understand the normal development of the retina and to inform cell replacement therapies to restore vision. RNA seq is a powerful way to identify novel genes expressed in particular cell subtypes. Although RNA seq approaches have been used to identify genes differentially expressed between photoreceptor subtypes in many species the limited transcriptome depth derived from single cell techniques constitutes a barrier in the reliable detection of transcription factors. To obtain a deep high quality RNA seq dataset from zebrafish photoreceptors we manually collected pools of photoreceptors of a single subtype. Overall design: We identified photoreceptors using well characterized transgenic lines that express fluorescent proteins in each subtype with high specificity including rods—TgxOPS:GFP UV cones—Tgopn1sw1:GFP S cones—Tgopn1sw2:GFP M cones—Tgopn1mw2:GFP and L cones—Tgthrb:tdTomato. We manually collected pools of 20 dissociated but healthy photoreceptors of a single subtype for each of our samples while actively avoiding cellular debris and other contaminants.,,pubmed:36745553,,UVc1s01,GSM5685583,,tissue:Dissociated adult photoreceptors|transgenic line:Tgopn1sw1:GFP|cell type:UV c1s|age:Adult,UVc1s01,Illumina software used for base calling and demultiplexing Sequences for primers and adapters removed using Trimmomatic Trimmomatic 0.36 phred33 /adapters/TruSeq2 PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:70 Reads aligned to zebrafish genome Danio rerio.GRCz11 using HiSat2 hisat2 p 8 rna strandness FR Transcript assembly and counts derived using StringTie Differential gene expression analysis using DESeq2 Genome build: Danio rerio.GRCz11 Supplementary files format and content: Comma separated values files include FPKM values for each Sample Comma separated values files include DESeq2 analysis results comparing Rods vs. Cones GTF files post trimming alignment to genome and transcript assembly RDS Seurat v03 file including count data for all samples,Dissociated adult photoreceptors,post euthanasia retinas from adult zebrafish were collected. Dissociated photoreceptors were obtained post enzymatic treatment with papain gentle mechanic trituration and filtering.,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,transgenic line:Tgopn1sw1:GFP|cell type:UV c1s|age:Adult,GSM5685583,GSM5685583: UVc1s01; Danio rerio; RNA Seq,GSM5685583 r1,GSM5685583,1,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP345451,,,U1_R1.fastq.gz U1_R2.fastq.gz,fastq fastq,4602778740.0,18264995.0,GSM5685583 r1,0:126 1:126,A:1263708784;C:1041694278;G:1072559354;T:1223758656;N:1057668,126,126,,,1263708784,1041694278,1072559354,1223758656,1057668,SRX13097722,SRS11034035,SRA1538252,"Wei Li, Unit of Retinal Neurophysiology, National Eye Institute","Wei Li, Unit of Retinal Neurophysiology, National Eye Institute",2,0.88814,0.89266,0.11898,0.12278,0.87722,0.87718,0.42734,0.42869,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-11-10,Adult,Adult,Eye,Sensory System 66956,SRR16905282,SRX13097721,SRS11034034,SRP345451,PRJNA779419,Transcriptomic profiling of adult zebrafish photoreceptors,GSE188560,Transcriptome Analysis,Identifying the transcription factors required to specify photoreceptor subtypes is critical to understand the normal development of the retina and to inform cell replacement therapies to restore vision. RNA seq is a powerful way to identify novel genes expressed in particular cell subtypes. Although RNA seq approaches have been used to identify genes differentially expressed between photoreceptor subtypes in many species the limited transcriptome depth derived from single cell techniques constitutes a barrier in the reliable detection of transcription factors. To obtain a deep high quality RNA seq dataset from zebrafish photoreceptors we manually collected pools of photoreceptors of a single subtype. Overall design: We identified photoreceptors using well characterized transgenic lines that express fluorescent proteins in each subtype with high specificity including rods—TgxOPS:GFP UV cones—Tgopn1sw1:GFP S cones—Tgopn1sw2:GFP M cones—Tgopn1mw2:GFP and L cones—Tgthrb:tdTomato. We manually collected pools of 20 dissociated but healthy photoreceptors of a single subtype for each of our samples while actively avoiding cellular debris and other contaminants.,,pubmed:36745553,,Rods06,GSM5685582,,tissue:Dissociated adult photoreceptors|transgenic line:TgxOPS:GFP|cell type:Rods|age:Adult,Rods06,Illumina software used for base calling and demultiplexing Sequences for primers and adapters removed using Trimmomatic Trimmomatic 0.36 phred33 /adapters/TruSeq2 PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:70 Reads aligned to zebrafish genome Danio rerio.GRCz11 using HiSat2 hisat2 p 8 rna strandness FR Transcript assembly and counts derived using StringTie Differential gene expression analysis using DESeq2 Genome build: Danio rerio.GRCz11 Supplementary files format and content: Comma separated values files include FPKM values for each Sample Comma separated values files include DESeq2 analysis results comparing Rods vs. Cones GTF files post trimming alignment to genome and transcript assembly RDS Seurat v03 file including count data for all samples,Dissociated adult photoreceptors,post euthanasia retinas from adult zebrafish were collected. Dissociated photoreceptors were obtained post enzymatic treatment with papain gentle mechanic trituration and filtering.,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,transgenic line:TgxOPS:GFP|cell type:Rods|age:Adult,GSM5685582,GSM5685582: Rods06; Danio rerio; RNA Seq,GSM5685582 r1,GSM5685582,1,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP345451,,,R6_R1.fastq.gz R6_R2.fastq.gz,fastq fastq,4952423700.0,19652475.0,GSM5685582 r1,0:126 1:126,A:1367216877;C:1105189757;G:1137542772;T:1341035495;N:1438799,126,126,,,1367216877,1105189757,1137542772,1341035495,1438799,SRX13097721,SRS11034034,SRA1538252,"Wei Li, Unit of Retinal Neurophysiology, National Eye Institute","Wei Li, Unit of Retinal Neurophysiology, National Eye Institute",2,0.86297,0.86369,0.166,0.17213,0.88355,0.88452,0.47083,0.47346,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-11-10,Adult,Adult,Eye,Sensory System 66957,SRR16905283,SRX13097720,SRS11034033,SRP345451,PRJNA779419,Transcriptomic profiling of adult zebrafish photoreceptors,GSE188560,Transcriptome Analysis,Identifying the transcription factors required to specify photoreceptor subtypes is critical to understand the normal development of the retina and to inform cell replacement therapies to restore vision. RNA seq is a powerful way to identify novel genes expressed in particular cell subtypes. Although RNA seq approaches have been used to identify genes differentially expressed between photoreceptor subtypes in many species the limited transcriptome depth derived from single cell techniques constitutes a barrier in the reliable detection of transcription factors. To obtain a deep high quality RNA seq dataset from zebrafish photoreceptors we manually collected pools of photoreceptors of a single subtype. Overall design: We identified photoreceptors using well characterized transgenic lines that express fluorescent proteins in each subtype with high specificity including rods—TgxOPS:GFP UV cones—Tgopn1sw1:GFP S cones—Tgopn1sw2:GFP M cones—Tgopn1mw2:GFP and L cones—Tgthrb:tdTomato. We manually collected pools of 20 dissociated but healthy photoreceptors of a single subtype for each of our samples while actively avoiding cellular debris and other contaminants.,,pubmed:36745553,,Rods05,GSM5685581,,tissue:Dissociated adult photoreceptors|transgenic line:TgxOPS:GFP|cell type:Rods|age:Adult,Rods05,Illumina software used for base calling and demultiplexing Sequences for primers and adapters removed using Trimmomatic Trimmomatic 0.36 phred33 /adapters/TruSeq2 PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:70 Reads aligned to zebrafish genome Danio rerio.GRCz11 using HiSat2 hisat2 p 8 rna strandness FR Transcript assembly and counts derived using StringTie Differential gene expression analysis using DESeq2 Genome build: Danio rerio.GRCz11 Supplementary files format and content: Comma separated values files include FPKM values for each Sample Comma separated values files include DESeq2 analysis results comparing Rods vs. Cones GTF files post trimming alignment to genome and transcript assembly RDS Seurat v03 file including count data for all samples,Dissociated adult photoreceptors,post euthanasia retinas from adult zebrafish were collected. Dissociated photoreceptors were obtained post enzymatic treatment with papain gentle mechanic trituration and filtering.,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,transgenic line:TgxOPS:GFP|cell type:Rods|age:Adult,GSM5685581,GSM5685581: Rods05; Danio rerio; RNA Seq,GSM5685581 r1,GSM5685581,1,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP345451,,,R5_R1.fastq.gz R5_R2.fastq.gz,fastq fastq,4741972704.0,18817352.0,GSM5685581 r1,0:126 1:126,A:1256424621;C:1113208486;G:1145540246;T:1225431677;N:1367674,126,126,,,1256424621,1113208486,1145540246,1225431677,1367674,SRX13097720,SRS11034033,SRA1538252,"Wei Li, Unit of Retinal Neurophysiology, National Eye Institute","Wei Li, Unit of Retinal Neurophysiology, National Eye Institute",2,0.86034,0.86196,0.10578,0.11012,0.85541,0.85703,0.39962,0.4043,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-11-10,Adult,Adult,Eye,Sensory System 66958,SRR16905284,SRX13097719,SRS11034032,SRP345451,PRJNA779419,Transcriptomic profiling of adult zebrafish photoreceptors,GSE188560,Transcriptome Analysis,Identifying the transcription factors required to specify photoreceptor subtypes is critical to understand the normal development of the retina and to inform cell replacement therapies to restore vision. RNA seq is a powerful way to identify novel genes expressed in particular cell subtypes. Although RNA seq approaches have been used to identify genes differentially expressed between photoreceptor subtypes in many species the limited transcriptome depth derived from single cell techniques constitutes a barrier in the reliable detection of transcription factors. To obtain a deep high quality RNA seq dataset from zebrafish photoreceptors we manually collected pools of photoreceptors of a single subtype. Overall design: We identified photoreceptors using well characterized transgenic lines that express fluorescent proteins in each subtype with high specificity including rods—TgxOPS:GFP UV cones—Tgopn1sw1:GFP S cones—Tgopn1sw2:GFP M cones—Tgopn1mw2:GFP and L cones—Tgthrb:tdTomato. We manually collected pools of 20 dissociated but healthy photoreceptors of a single subtype for each of our samples while actively avoiding cellular debris and other contaminants.,,pubmed:36745553,,Rods04,GSM5685580,,tissue:Dissociated adult photoreceptors|transgenic line:TgxOPS:GFP|cell type:Rods|age:Adult,Rods04,Illumina software used for base calling and demultiplexing Sequences for primers and adapters removed using Trimmomatic Trimmomatic 0.36 phred33 /adapters/TruSeq2 PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:70 Reads aligned to zebrafish genome Danio rerio.GRCz11 using HiSat2 hisat2 p 8 rna strandness FR Transcript assembly and counts derived using StringTie Differential gene expression analysis using DESeq2 Genome build: Danio rerio.GRCz11 Supplementary files format and content: Comma separated values files include FPKM values for each Sample Comma separated values files include DESeq2 analysis results comparing Rods vs. Cones GTF files post trimming alignment to genome and transcript assembly RDS Seurat v03 file including count data for all samples,Dissociated adult photoreceptors,post euthanasia retinas from adult zebrafish were collected. Dissociated photoreceptors were obtained post enzymatic treatment with papain gentle mechanic trituration and filtering.,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,transgenic line:TgxOPS:GFP|cell type:Rods|age:Adult,GSM5685580,GSM5685580: Rods04; Danio rerio; RNA Seq,GSM5685580 r1,GSM5685580,1,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP345451,,,R4_R1.fastq.gz R4_R2.fastq.gz,fastq fastq,6862092552.0,27230526.0,GSM5685580 r1,0:126 1:126,A:1790009645;C:1631339486;G:1675728141;T:1762714572;N:2300708,126,126,,,1790009645,1631339486,1675728141,1762714572,2300708,SRX13097719,SRS11034032,SRA1538252,"Wei Li, Unit of Retinal Neurophysiology, National Eye Institute","Wei Li, Unit of Retinal Neurophysiology, National Eye Institute",2,0.87564,0.8754,0.08143,0.08433,0.87081,0.87213,0.3944,0.31675,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-11-10,Adult,Adult,Eye,Sensory System 66959,SRR16905285,SRX13097718,SRS11034031,SRP345451,PRJNA779419,Transcriptomic profiling of adult zebrafish photoreceptors,GSE188560,Transcriptome Analysis,Identifying the transcription factors required to specify photoreceptor subtypes is critical to understand the normal development of the retina and to inform cell replacement therapies to restore vision. RNA seq is a powerful way to identify novel genes expressed in particular cell subtypes. Although RNA seq approaches have been used to identify genes differentially expressed between photoreceptor subtypes in many species the limited transcriptome depth derived from single cell techniques constitutes a barrier in the reliable detection of transcription factors. To obtain a deep high quality RNA seq dataset from zebrafish photoreceptors we manually collected pools of photoreceptors of a single subtype. Overall design: We identified photoreceptors using well characterized transgenic lines that express fluorescent proteins in each subtype with high specificity including rods—TgxOPS:GFP UV cones—Tgopn1sw1:GFP S cones—Tgopn1sw2:GFP M cones—Tgopn1mw2:GFP and L cones—Tgthrb:tdTomato. We manually collected pools of 20 dissociated but healthy photoreceptors of a single subtype for each of our samples while actively avoiding cellular debris and other contaminants.,,pubmed:36745553,,Rods03,GSM5685579,,tissue:Dissociated adult photoreceptors|transgenic line:TgxOPS:GFP|cell type:Rods|age:Adult,Rods03,Illumina software used for base calling and demultiplexing Sequences for primers and adapters removed using Trimmomatic Trimmomatic 0.36 phred33 /adapters/TruSeq2 PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:70 Reads aligned to zebrafish genome Danio rerio.GRCz11 using HiSat2 hisat2 p 8 rna strandness FR Transcript assembly and counts derived using StringTie Differential gene expression analysis using DESeq2 Genome build: Danio rerio.GRCz11 Supplementary files format and content: Comma separated values files include FPKM values for each Sample Comma separated values files include DESeq2 analysis results comparing Rods vs. Cones GTF files post trimming alignment to genome and transcript assembly RDS Seurat v03 file including count data for all samples,Dissociated adult photoreceptors,post euthanasia retinas from adult zebrafish were collected. Dissociated photoreceptors were obtained post enzymatic treatment with papain gentle mechanic trituration and filtering.,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,transgenic line:TgxOPS:GFP|cell type:Rods|age:Adult,GSM5685579,GSM5685579: Rods03; Danio rerio; RNA Seq,GSM5685579 r1,GSM5685579,1,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP345451,,,R3_R1.fastq.gz R3_R2.fastq.gz,fastq fastq,4355968428.0,17285589.0,GSM5685579 r1,0:126 1:126,A:1140212606;C:1037131472;G:1064701662;T:1112480451;N:1442237,126,126,,,1140212606,1037131472,1064701662,1112480451,1442237,SRX13097718,SRS11034031,SRA1538252,"Wei Li, Unit of Retinal Neurophysiology, National Eye Institute","Wei Li, Unit of Retinal Neurophysiology, National Eye Institute",2,0.87155,0.87283,0.08339,0.0868,0.86121,0.86145,0.38915,0.39476,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-11-10,Adult,Adult,Eye,Sensory System 66960,SRR16905286,SRX13097717,SRS11034030,SRP345451,PRJNA779419,Transcriptomic profiling of adult zebrafish photoreceptors,GSE188560,Transcriptome Analysis,Identifying the transcription factors required to specify photoreceptor subtypes is critical to understand the normal development of the retina and to inform cell replacement therapies to restore vision. RNA seq is a powerful way to identify novel genes expressed in particular cell subtypes. Although RNA seq approaches have been used to identify genes differentially expressed between photoreceptor subtypes in many species the limited transcriptome depth derived from single cell techniques constitutes a barrier in the reliable detection of transcription factors. To obtain a deep high quality RNA seq dataset from zebrafish photoreceptors we manually collected pools of photoreceptors of a single subtype. Overall design: We identified photoreceptors using well characterized transgenic lines that express fluorescent proteins in each subtype with high specificity including rods—TgxOPS:GFP UV cones—Tgopn1sw1:GFP S cones—Tgopn1sw2:GFP M cones—Tgopn1mw2:GFP and L cones—Tgthrb:tdTomato. We manually collected pools of 20 dissociated but healthy photoreceptors of a single subtype for each of our samples while actively avoiding cellular debris and other contaminants.,,pubmed:36745553,,Rods02,GSM5685578,,tissue:Dissociated adult photoreceptors|transgenic line:TgxOPS:GFP|cell type:Rods|age:Adult,Rods02,Illumina software used for base calling and demultiplexing Sequences for primers and adapters removed using Trimmomatic Trimmomatic 0.36 phred33 /adapters/TruSeq2 PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:70 Reads aligned to zebrafish genome Danio rerio.GRCz11 using HiSat2 hisat2 p 8 rna strandness FR Transcript assembly and counts derived using StringTie Differential gene expression analysis using DESeq2 Genome build: Danio rerio.GRCz11 Supplementary files format and content: Comma separated values files include FPKM values for each Sample Comma separated values files include DESeq2 analysis results comparing Rods vs. Cones GTF files post trimming alignment to genome and transcript assembly RDS Seurat v03 file including count data for all samples,Dissociated adult photoreceptors,post euthanasia retinas from adult zebrafish were collected. Dissociated photoreceptors were obtained post enzymatic treatment with papain gentle mechanic trituration and filtering.,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,transgenic line:TgxOPS:GFP|cell type:Rods|age:Adult,GSM5685578,GSM5685578: Rods02; Danio rerio; RNA Seq,GSM5685578 r1,GSM5685578,1,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP345451,,,R2_R1.fastq.gz R2_R2.fastq.gz,fastq fastq,5525706312.0,21927406.0,GSM5685578 r1,0:126 1:126,A:1458005049;C:1298362153;G:1338053805;T:1429420463;N:1864842,126,126,,,1458005049,1298362153,1338053805,1429420463,1864842,SRX13097717,SRS11034030,SRA1538252,"Wei Li, Unit of Retinal Neurophysiology, National Eye Institute","Wei Li, Unit of Retinal Neurophysiology, National Eye Institute",2,0.87831,0.8777,0.09481,0.09849,0.90684,0.9067,0.33599,0.33777,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-11-10,Adult,Adult,Eye,Sensory System 66961,SRR16905287,SRX13097716,SRS11034029,SRP345451,PRJNA779419,Transcriptomic profiling of adult zebrafish photoreceptors,GSE188560,Transcriptome Analysis,Identifying the transcription factors required to specify photoreceptor subtypes is critical to understand the normal development of the retina and to inform cell replacement therapies to restore vision. RNA seq is a powerful way to identify novel genes expressed in particular cell subtypes. Although RNA seq approaches have been used to identify genes differentially expressed between photoreceptor subtypes in many species the limited transcriptome depth derived from single cell techniques constitutes a barrier in the reliable detection of transcription factors. To obtain a deep high quality RNA seq dataset from zebrafish photoreceptors we manually collected pools of photoreceptors of a single subtype. Overall design: We identified photoreceptors using well characterized transgenic lines that express fluorescent proteins in each subtype with high specificity including rods—TgxOPS:GFP UV cones—Tgopn1sw1:GFP S cones—Tgopn1sw2:GFP M cones—Tgopn1mw2:GFP and L cones—Tgthrb:tdTomato. We manually collected pools of 20 dissociated but healthy photoreceptors of a single subtype for each of our samples while actively avoiding cellular debris and other contaminants.,,pubmed:36745553,,Rods01,GSM5685577,,tissue:Dissociated adult photoreceptors|transgenic line:TgxOPS:GFP|cell type:Rods|age:Adult,Rods01,Illumina software used for base calling and demultiplexing Sequences for primers and adapters removed using Trimmomatic Trimmomatic 0.36 phred33 /adapters/TruSeq2 PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:70 Reads aligned to zebrafish genome Danio rerio.GRCz11 using HiSat2 hisat2 p 8 rna strandness FR Transcript assembly and counts derived using StringTie Differential gene expression analysis using DESeq2 Genome build: Danio rerio.GRCz11 Supplementary files format and content: Comma separated values files include FPKM values for each Sample Comma separated values files include DESeq2 analysis results comparing Rods vs. Cones GTF files post trimming alignment to genome and transcript assembly RDS Seurat v03 file including count data for all samples,Dissociated adult photoreceptors,post euthanasia retinas from adult zebrafish were collected. Dissociated photoreceptors were obtained post enzymatic treatment with papain gentle mechanic trituration and filtering.,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,transgenic line:TgxOPS:GFP|cell type:Rods|age:Adult,GSM5685577,GSM5685577: Rods01; Danio rerio; RNA Seq,GSM5685577 r1,GSM5685577,1,Pools of 20 photoreceptors of a single subtype identified by their fluorescence were manually collected and total RNA was obtained and amplified using the SMART seq v4 ultra low input RNA kit for sequencing Takara #634897. cDNA libraries were constructed using the Low Input Library Prep Kit v2 Takara #634899.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP345451,,,R1_R1.fastq.gz R1_R2.fastq.gz,fastq fastq,5291640144.0,20998572.0,GSM5685577 r1,0:126 1:126,A:1420732184;C:1220751611;G:1260778610;T:1387606540;N:1771199,126,126,,,1420732184,1220751611,1260778610,1387606540,1771199,SRX13097716,SRS11034029,SRA1538252,"Wei Li, Unit of Retinal Neurophysiology, National Eye Institute","Wei Li, Unit of Retinal Neurophysiology, National Eye Institute",2,0.89912,0.89977,0.1084,0.11205,0.90098,0.9008,0.43843,0.43583,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-11-10,Adult,Adult,Eye,Sensory System