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78 rows where experiment.library_layout = "PAIRED", technology = "smartseq" and tissue_curation = "Eye"

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devstage_curation_coarse 3

devstage_curation 3

experiment.library_selection 2

tissue_curation_coarse 1

tissue_curation 1

  • Eye · 78 ✖

technology 1

  • smartseq · 78 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_layout 1

  • PAIRED · 78 ✖
Link 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;