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
29092,SRR27010839,SRX22703628,SRS19696103,SRP475450,PRJNA1047749,Differential expression in Muller glia of injured zebrafish in a mycb /  context,GSE249116,Transcriptome Analysis,This experiment studies retinal regeneration using a zebrafish model with a focus on Muller glia reprogramming. Overall design: Three groups: controls Muller glia from uninjured retinas  injured WT Muller glia from injured WT retina at 2 xxx post injury dpi  and injured mycb /  Muller glia from injured mycb /  fish at 2dpi.,parent bioproject:PRJNA1047494,pubmed:38984586,,Muller glia from mycb /  retinas 2 xxx post injury dpi rep2 [7131 ML 8] [7131 ML 8],GSM7926876,,source name:mycb /  Muller glia injured retina|tissue:mycb /  Muller glia injured retina|genotype:mycb / |treatment:injured|geo loc name:missing|collection date:missing,Muller glia from mycb /  retinas 2 xxx post injury dpi rep2 [7131 ML 8] [7131 ML 8],"University of Michigan Bioinformatics Core RNA seq pipeline ""Watermelon"" version 2.4.4 Sequence reads were trimmed for adaptor sequence/low quality sequence using Cutadapt v2.3. FastQC v0.11.8 was used to ensure the quality of data Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a Quantitative count estimates to genes performed with RSEM v1.3.3 Assembly: GRCz11 Supplementary files format and content: RS11 deseq2 raw counts.txt Supplementary files format and content: tab delimited text with include expected counts values for each Sample",mycb /  Muller glia injured retina,Needle poke injury to retina.,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,tissue:mycb /  Muller glia injured retina|genotype:mycb / |treatment:injured,GSM7926876,GSM7926876: Muller glia from mycb /  retinas 2 xxx post injury dpi rep2 [7131 ML 8] [7131 ML 8]; Danio rerio; RNA Seq,GSM7926876 r1,GSM7926876,1,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475450,,loader:fastq load.py,7131-ML-8_GCTGGCCA-GCGTCCGT_S74_R1_001.fastq.gz 7131-ML-8_GCTGGCCA-GCGTCCGT_S74_R2_001.fastq.gz,fastq fastq,27012387282.0,89444991.0,GSM7926876 r1,0:151 1:151,A:7324891140;C:5760958085;G:6796293318;T:7129968103;N:276636,151,151,,,7324891140,5760958085,6796293318,7129968103,276636,SRX22703628,SRS19696103,SRA1761650,University of Michigan,University of Michigan,2,0.88985,0.86096,0.09217,0.08056,0.7473,0.7542,0.59862,0.5926,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2023-12-01,Undetermined,Undetermined,Eye,Sensory System
29093,SRR27010840,SRX22703627,SRS19696102,SRP475450,PRJNA1047749,Differential expression in Muller glia of injured zebrafish in a mycb /  context,GSE249116,Transcriptome Analysis,This experiment studies retinal regeneration using a zebrafish model with a focus on Muller glia reprogramming. Overall design: Three groups: controls Muller glia from uninjured retinas  injured WT Muller glia from injured WT retina at 2 xxx post injury dpi  and injured mycb /  Muller glia from injured mycb /  fish at 2dpi.,parent bioproject:PRJNA1047494,pubmed:38984586,,Muller glia from mycb /  retinas 2 xxx post injury dpi rep1 [7131 ML 7] [7131 ML 7],GSM7926875,,source name:mycb /  Muller glia injured retina|tissue:mycb /  Muller glia injured retina|genotype:mycb / |treatment:injured|geo loc name:missing|collection date:missing,Muller glia from mycb /  retinas 2 xxx post injury dpi rep1 [7131 ML 7] [7131 ML 7],"University of Michigan Bioinformatics Core RNA seq pipeline ""Watermelon"" version 2.4.4 Sequence reads were trimmed for adaptor sequence/low quality sequence using Cutadapt v2.3. FastQC v0.11.8 was used to ensure the quality of data Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a Quantitative count estimates to genes performed with RSEM v1.3.3 Assembly: GRCz11 Supplementary files format and content: RS11 deseq2 raw counts.txt Supplementary files format and content: tab delimited text with include expected counts values for each Sample",mycb /  Muller glia injured retina,Needle poke injury to retina.,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,tissue:mycb /  Muller glia injured retina|genotype:mycb / |treatment:injured,GSM7926875,GSM7926875: Muller glia from mycb /  retinas 2 xxx post injury dpi rep1 [7131 ML 7] [7131 ML 7]; Danio rerio; RNA Seq,GSM7926875 r1,GSM7926875,1,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475450,,loader:fastq load.py,7131-ML-7_TTACGGAC-ATTGGCCA_S73_R1_001.fastq.gz 7131-ML-7_TTACGGAC-ATTGGCCA_S73_R2_001.fastq.gz,fastq fastq,27084816546.0,89684823.0,GSM7926875 r1,0:151 1:151,A:7489987820;C:5729672678;G:6569226079;T:7295655071;N:274898,151,151,,,7489987820,5729672678,6569226079,7295655071,274898,SRX22703627,SRS19696102,SRA1761650,University of Michigan,University of Michigan,2,0.8887,0.84473,0.12952,0.10995,0.73338,0.74211,0.54826,0.56906,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2023-12-01,Undetermined,Undetermined,Eye,Sensory System
29094,SRR27010841,SRX22703626,SRS19696101,SRP475450,PRJNA1047749,Differential expression in Muller glia of injured zebrafish in a mycb /  context,GSE249116,Transcriptome Analysis,This experiment studies retinal regeneration using a zebrafish model with a focus on Muller glia reprogramming. Overall design: Three groups: controls Muller glia from uninjured retinas  injured WT Muller glia from injured WT retina at 2 xxx post injury dpi  and injured mycb /  Muller glia from injured mycb /  fish at 2dpi.,parent bioproject:PRJNA1047494,pubmed:38984586,,Muller glia from WT retinas 2 xxx post injury dpi rep2 [7131 ML 5] [7131 ML 5],GSM7926874,,source name:WT Muller glia injured retina|tissue:WT Muller glia injured retina|genotype:WT|treatment:n1|geo loc name:missing|collection date:missing,Muller glia from WT retinas 2 xxx post injury dpi rep2 [7131 ML 5] [7131 ML 5],"University of Michigan Bioinformatics Core RNA seq pipeline ""Watermelon"" version 2.4.4 Sequence reads were trimmed for adaptor sequence/low quality sequence using Cutadapt v2.3. FastQC v0.11.8 was used to ensure the quality of data Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a Quantitative count estimates to genes performed with RSEM v1.3.3 Assembly: GRCz11 Supplementary files format and content: RS11 deseq2 raw counts.txt Supplementary files format and content: tab delimited text with include expected counts values for each Sample",WT Muller glia injured retina,Needle poke injury to retina.,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,tissue:WT Muller glia injured retina|genotype:WT|treatment:n1,GSM7926874,GSM7926874: Muller glia from WT retinas 2 xxx post injury dpi rep2 [7131 ML 5] [7131 ML 5]; Danio rerio; RNA Seq,GSM7926874 r1,GSM7926874,1,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475450,,loader:fastq load.py,7131-ML-5_CAACCATA-ACCGGTTA_S71_R1_001.fastq.gz 7131-ML-5_CAACCATA-ACCGGTTA_S71_R2_001.fastq.gz,fastq fastq,29094896836.0,96340718.0,GSM7926874 r1,0:151 1:151,A:7739727136;C:6356741244;G:7473778902;T:7524355633;N:293921,151,151,,,7739727136,6356741244,7473778902,7524355633,293921,SRX22703626,SRS19696101,SRA1761650,University of Michigan,University of Michigan,2,0.88966,0.85954,0.08909,0.07794,0.72711,0.73446,0.54596,0.54295,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2023-12-01,Undetermined,Undetermined,Eye,Sensory System
29095,SRR27010842,SRX22703625,SRS19696100,SRP475450,PRJNA1047749,Differential expression in Muller glia of injured zebrafish in a mycb /  context,GSE249116,Transcriptome Analysis,This experiment studies retinal regeneration using a zebrafish model with a focus on Muller glia reprogramming. Overall design: Three groups: controls Muller glia from uninjured retinas  injured WT Muller glia from injured WT retina at 2 xxx post injury dpi  and injured mycb /  Muller glia from injured mycb /  fish at 2dpi.,parent bioproject:PRJNA1047494,pubmed:38984586,,Muller glia from WT retinas 2 xxx post injury dpi rep1 [7131 ML 4] [7131 ML 4],GSM7926873,,source name:WT Muller glia injured retina|tissue:WT Muller glia injured retina|genotype:WT|treatment:n1|geo loc name:missing|collection date:missing,Muller glia from WT retinas 2 xxx post injury dpi rep1 [7131 ML 4] [7131 ML 4],"University of Michigan Bioinformatics Core RNA seq pipeline ""Watermelon"" version 2.4.4 Sequence reads were trimmed for adaptor sequence/low quality sequence using Cutadapt v2.3. FastQC v0.11.8 was used to ensure the quality of data Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a Quantitative count estimates to genes performed with RSEM v1.3.3 Assembly: GRCz11 Supplementary files format and content: RS11 deseq2 raw counts.txt Supplementary files format and content: tab delimited text with include expected counts values for each Sample",WT Muller glia injured retina,Needle poke injury to retina.,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,tissue:WT Muller glia injured retina|genotype:WT|treatment:n1,GSM7926873,GSM7926873: Muller glia from WT retinas 2 xxx post injury dpi rep1 [7131 ML 4] [7131 ML 4]; Danio rerio; RNA Seq,GSM7926873 r1,GSM7926873,1,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475450,,loader:fastq load.py,7131-ML-4_TTAACGGC-CTCCGTCT_S70_R1_001.fastq.gz 7131-ML-4_TTAACGGC-CTCCGTCT_S70_R2_001.fastq.gz,fastq fastq,36567606580.0,121084790.0,GSM7926873 r1,0:151 1:151,A:9477563071;C:8136361552;G:9699876329;T:9253435137;N:370491,151,151,,,9477563071,8136361552,9699876329,9253435137,370491,SRX22703625,SRS19696100,SRA1761650,University of Michigan,University of Michigan,2,0.85059,0.82538,0.08689,0.07693,0.73574,0.74371,0.54735,0.54664,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2023-12-01,Undetermined,Undetermined,Eye,Sensory System
29096,SRR27010843,SRX22703624,SRS19696099,SRP475450,PRJNA1047749,Differential expression in Muller glia of injured zebrafish in a mycb /  context,GSE249116,Transcriptome Analysis,This experiment studies retinal regeneration using a zebrafish model with a focus on Muller glia reprogramming. Overall design: Three groups: controls Muller glia from uninjured retinas  injured WT Muller glia from injured WT retina at 2 xxx post injury dpi  and injured mycb /  Muller glia from injured mycb /  fish at 2dpi.,parent bioproject:PRJNA1047494,pubmed:38984586,,Muller glia from uninjured WT retinas rep2 [7131 ML 2] [7131 ML 2],GSM7926872,,source name:WT Muller retinal glia|tissue:WT Muller retinal glia|genotype:WT|treatment:n1|geo loc name:missing|collection date:missing,Muller glia from uninjured WT retinas rep2 [7131 ML 2] [7131 ML 2],"University of Michigan Bioinformatics Core RNA seq pipeline ""Watermelon"" version 2.4.4 Sequence reads were trimmed for adaptor sequence/low quality sequence using Cutadapt v2.3. FastQC v0.11.8 was used to ensure the quality of data Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a Quantitative count estimates to genes performed with RSEM v1.3.3 Assembly: GRCz11 Supplementary files format and content: RS11 deseq2 raw counts.txt Supplementary files format and content: tab delimited text with include expected counts values for each Sample",WT Muller retinal glia,Needle poke injury to retina.,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,tissue:WT Muller retinal glia|genotype:WT|treatment:n1,GSM7926872,GSM7926872: Muller glia from uninjured WT retinas rep2 [7131 ML 2] [7131 ML 2]; Danio rerio; RNA Seq,GSM7926872 r1,GSM7926872,1,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475450,,loader:fastq load.py,7131-ML-2_ACAGAGAA-GCGGTTAC_S68_R1_001.fastq.gz 7131-ML-2_ACAGAGAA-GCGGTTAC_S68_R2_001.fastq.gz,fastq fastq,31134149118.0,103093209.0,GSM7926872 r1,0:151 1:151,A:8551703439;C:6621403525;G:7636841163;T:8323884132;N:316859,151,151,,,8551703439,6621403525,7636841163,8323884132,316859,SRX22703624,SRS19696099,SRA1761650,University of Michigan,University of Michigan,2,0.89461,0.85335,0.11633,0.10042,0.74302,0.74943,0.5613,0.54558,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2023-12-01,Undetermined,Undetermined,Eye,Sensory System
29097,SRR27010844,SRX22703623,SRS19696098,SRP475450,PRJNA1047749,Differential expression in Muller glia of injured zebrafish in a mycb /  context,GSE249116,Transcriptome Analysis,This experiment studies retinal regeneration using a zebrafish model with a focus on Muller glia reprogramming. Overall design: Three groups: controls Muller glia from uninjured retinas  injured WT Muller glia from injured WT retina at 2 xxx post injury dpi  and injured mycb /  Muller glia from injured mycb /  fish at 2dpi.,parent bioproject:PRJNA1047494,pubmed:38984586,,Muller glia from uninjured WT retinas rep1 [7131 ML 1] [7131 ML 1],GSM7926871,,source name:WT Muller retinal glia|tissue:WT Muller retinal glia|genotype:WT|treatment:n1|geo loc name:missing|collection date:missing,Muller glia from uninjured WT retinas rep1 [7131 ML 1] [7131 ML 1],"University of Michigan Bioinformatics Core RNA seq pipeline ""Watermelon"" version 2.4.4 Sequence reads were trimmed for adaptor sequence/low quality sequence using Cutadapt v2.3. FastQC v0.11.8 was used to ensure the quality of data Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a Quantitative count estimates to genes performed with RSEM v1.3.3 Assembly: GRCz11 Supplementary files format and content: RS11 deseq2 raw counts.txt Supplementary files format and content: tab delimited text with include expected counts values for each Sample",WT Muller retinal glia,Needle poke injury to retina.,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,tissue:WT Muller retinal glia|genotype:WT|treatment:n1,GSM7926871,GSM7926871: Muller glia from uninjured WT retinas rep1 [7131 ML 1] [7131 ML 1]; Danio rerio; RNA Seq,GSM7926871 r1,GSM7926871,1,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475450,,loader:fastq load.py,7131-ML-1_AATGTTGT-TGCTTACA_S67_R1_001.fastq.gz 7131-ML-1_AATGTTGT-TGCTTACA_S67_R2_001.fastq.gz,fastq fastq,30223430972.0,100077586.0,GSM7926871 r1,0:151 1:151,A:8370937172;C:6520369124;G:7146916733;T:8184902603;N:305340,151,151,,,8370937172,6520369124,7146916733,8184902603,305340,SRX22703623,SRS19696098,SRA1761650,University of Michigan,University of Michigan,2,0.91221,0.86081,0.12114,0.10476,0.73164,0.73882,0.54727,0.52951,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2023-12-01,Undetermined,Undetermined,Eye,Sensory System
29098,SRR27010846,SRX22703638,SRS19696113,SRP475451,PRJNA1047750,Differential expression in Muller glia of injured zebrafish in a mych /  context,GSE249115,Transcriptome Analysis,This experiment studies  retinal regeneration using a zebrafish model with a focus on Muller glia reprogramming. Overall design: Three groups: controls Muller glia from uninjured retinas  injured WT Muller glia from injured WT retina at 2 xxx post injury dpi  and injured mych /  Muller glia from injured mych /  fish at 2dpi. Of interest are the WT injury responsive genes  and which injury responsive genes in the WT are differentially expressed in the mych /  fish.,parent bioproject:PRJNA1047494,pubmed:38984586,,Muller glia from mych /  retinas 2 xxx post injury dpi rep3 [5803 ML 10],GSM7926870,,source name:mych /  Muller glia injured retina|tissue:mych /  Muller glia injured retina|genotype:mych / |treatment:injured|geo loc name:missing|collection date:missing,Muller glia from mych /  retinas 2 xxx post injury dpi rep3 [5803 ML 10],"University of Michigan Bioinformatics Core RNA seq pipeline ""Watermelon"" version 2.4.4 Sequence reads were trimmed for adaptor sequence/low quality sequence using Cutadapt v2.3. FastQC v0.11.8 was used to ensure the quality of data Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a Quantitative count estimates to genes performed with RSEM v1.3.3 Assembly: GRCz11 Supplementary files format and content: RS10 deseq2 raw counts.txt Supplementary files format and content: tab delimited text with include expected counts values for each Sample",mych /  Muller glia injured retina,Needle poke injury to retina.,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,tissue:mych /  Muller glia injured retina|genotype:mych / |treatment:injured,GSM7926870,GSM7926870: Muller glia from mych /  retinas 2 xxx post injury dpi rep3 [5803 ML 10]; Danio rerio; RNA Seq,GSM7926870 r1,GSM7926870,1,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475451,,loader:fastq load.py,5803-ML-10_AACAACGG-TTACACCT_S222_R1_001.fastq.gz 5803-ML-10_AACAACGG-TTACACCT_S222_R2_001.fastq.gz,fastq fastq,33066899590.0,109493045.0,GSM7926870 r1,0:151 1:151,A:9045925528;C:7063243555;G:8277253275;T:8680404068;N:73164,151,151,,,9045925528,7063243555,8277253275,8680404068,73164,SRX22703638,SRS19696113,SRA1761648,University of Michigan,University of Michigan,2,0.87174,0.82563,0.12217,0.10466,0.7052,0.71311,0.50335,0.51416,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2023-12-01,Undetermined,Undetermined,Eye,Sensory System
29099,SRR27010847,SRX22703637,SRS19696112,SRP475451,PRJNA1047750,Differential expression in Muller glia of injured zebrafish in a mych /  context,GSE249115,Transcriptome Analysis,This experiment studies  retinal regeneration using a zebrafish model with a focus on Muller glia reprogramming. Overall design: Three groups: controls Muller glia from uninjured retinas  injured WT Muller glia from injured WT retina at 2 xxx post injury dpi  and injured mych /  Muller glia from injured mych /  fish at 2dpi. Of interest are the WT injury responsive genes  and which injury responsive genes in the WT are differentially expressed in the mych /  fish.,parent bioproject:PRJNA1047494,pubmed:38984586,,Muller glia from mych /  retinas 2 xxx post injury dpi rep2 [5803 ML 8],GSM7926869,,source name:mych /  Muller glia injured retina|tissue:mych /  Muller glia injured retina|genotype:mych / |treatment:injured|geo loc name:missing|collection date:missing,Muller glia from mych /  retinas 2 xxx post injury dpi rep2 [5803 ML 8],"University of Michigan Bioinformatics Core RNA seq pipeline ""Watermelon"" version 2.4.4 Sequence reads were trimmed for adaptor sequence/low quality sequence using Cutadapt v2.3. FastQC v0.11.8 was used to ensure the quality of data Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a Quantitative count estimates to genes performed with RSEM v1.3.3 Assembly: GRCz11 Supplementary files format and content: RS10 deseq2 raw counts.txt Supplementary files format and content: tab delimited text with include expected counts values for each Sample",mych /  Muller glia injured retina,Needle poke injury to retina.,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,tissue:mych /  Muller glia injured retina|genotype:mych / |treatment:injured,GSM7926869,GSM7926869: Muller glia from mych /  retinas 2 xxx post injury dpi rep2 [5803 ML 8]; Danio rerio; RNA Seq,GSM7926869 r1,GSM7926869,1,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475451,,loader:fastq load.py,5803-ML-8_CGAGGTGT-CGCCGTTG_S221_R1_001.fastq.gz 5803-ML-8_CGAGGTGT-CGCCGTTG_S221_R2_001.fastq.gz,fastq fastq,45801257486.0,151659793.0,GSM7926869 r1,0:151 1:151,A:12163743496;C:9556065193;G:12415783742;T:11665560316;N:104739,151,151,,,12163743496,9556065193,12415783742,11665560316,104739,SRX22703637,SRS19696112,SRA1761648,University of Michigan,University of Michigan,2,0.82361,0.79223,0.08967,0.0781,0.72614,0.73214,0.51241,0.53445,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2023-12-01,Undetermined,Undetermined,Eye,Sensory System
29100,SRR27010848,SRX22703636,SRS19696111,SRP475451,PRJNA1047750,Differential expression in Muller glia of injured zebrafish in a mych /  context,GSE249115,Transcriptome Analysis,This experiment studies  retinal regeneration using a zebrafish model with a focus on Muller glia reprogramming. Overall design: Three groups: controls Muller glia from uninjured retinas  injured WT Muller glia from injured WT retina at 2 xxx post injury dpi  and injured mych /  Muller glia from injured mych /  fish at 2dpi. Of interest are the WT injury responsive genes  and which injury responsive genes in the WT are differentially expressed in the mych /  fish.,parent bioproject:PRJNA1047494,pubmed:38984586,,Muller glia from mych /  retinas 2 xxx post injury dpi rep1 [5803 ML 7],GSM7926868,,source name:mych /  Muller glia injured retina|tissue:mych /  Muller glia injured retina|genotype:mych / |treatment:injured|geo loc name:missing|collection date:missing,Muller glia from mych /  retinas 2 xxx post injury dpi rep1 [5803 ML 7],"University of Michigan Bioinformatics Core RNA seq pipeline ""Watermelon"" version 2.4.4 Sequence reads were trimmed for adaptor sequence/low quality sequence using Cutadapt v2.3. FastQC v0.11.8 was used to ensure the quality of data Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a Quantitative count estimates to genes performed with RSEM v1.3.3 Assembly: GRCz11 Supplementary files format and content: RS10 deseq2 raw counts.txt Supplementary files format and content: tab delimited text with include expected counts values for each Sample",mych /  Muller glia injured retina,Needle poke injury to retina.,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,tissue:mych /  Muller glia injured retina|genotype:mych / |treatment:injured,GSM7926868,GSM7926868: Muller glia from mych /  retinas 2 xxx post injury dpi rep1 [5803 ML 7]; Danio rerio; RNA Seq,GSM7926868 r1,GSM7926868,1,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475451,,loader:fastq load.py,5803-ML-7_ACCTCCGC-AACCTTCA_S220_R1_001.fastq.gz 5803-ML-7_ACCTCCGC-AACCTTCA_S220_R2_001.fastq.gz,fastq fastq,34323078556.0,113652578.0,GSM7926868 r1,0:151 1:151,A:9212407551;C:7253133739;G:9084057760;T:8773400927;N:78579,151,151,,,9212407551,7253133739,9084057760,8773400927,78579,SRX22703636,SRS19696111,SRA1761648,University of Michigan,University of Michigan,2,0.83258,0.79995,0.10182,0.08869,0.7204,0.72506,0.53438,0.53893,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2023-12-01,Undetermined,Undetermined,Eye,Sensory System
29101,SRR27010849,SRX22703635,SRS19696110,SRP475451,PRJNA1047750,Differential expression in Muller glia of injured zebrafish in a mych /  context,GSE249115,Transcriptome Analysis,This experiment studies  retinal regeneration using a zebrafish model with a focus on Muller glia reprogramming. Overall design: Three groups: controls Muller glia from uninjured retinas  injured WT Muller glia from injured WT retina at 2 xxx post injury dpi  and injured mych /  Muller glia from injured mych /  fish at 2dpi. Of interest are the WT injury responsive genes  and which injury responsive genes in the WT are differentially expressed in the mych /  fish.,parent bioproject:PRJNA1047494,pubmed:38984586,,Muller glia from WT retinas 2 xxx post injury dpi rep3 [5803 ML 6],GSM7926867,,source name:WT Muller glia injured retina|tissue:WT Muller glia injured retina|genotype:WT|treatment:injured|geo loc name:missing|collection date:missing,Muller glia from WT retinas 2 xxx post injury dpi rep3 [5803 ML 6],"University of Michigan Bioinformatics Core RNA seq pipeline ""Watermelon"" version 2.4.4 Sequence reads were trimmed for adaptor sequence/low quality sequence using Cutadapt v2.3. FastQC v0.11.8 was used to ensure the quality of data Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a Quantitative count estimates to genes performed with RSEM v1.3.3 Assembly: GRCz11 Supplementary files format and content: RS10 deseq2 raw counts.txt Supplementary files format and content: tab delimited text with include expected counts values for each Sample",WT Muller glia injured retina,Needle poke injury to retina.,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,tissue:WT Muller glia injured retina|genotype:WT|treatment:injured,GSM7926867,GSM7926867: Muller glia from WT retinas 2 xxx post injury dpi rep3 [5803 ML 6]; Danio rerio; RNA Seq,GSM7926867 r1,GSM7926867,1,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475451,,loader:fastq load.py,5803-ML-6_CTTGAAGG-TAGCGGAG_S219_R1_001.fastq.gz 5803-ML-6_CTTGAAGG-TAGCGGAG_S219_R2_001.fastq.gz,fastq fastq,39633900160.0,131238080.0,GSM7926867 r1,0:151 1:151,A:10574730340;C:8244722619;G:10678580933;T:10135778012;N:88256,151,151,,,10574730340,8244722619,10678580933,10135778012,88256,SRX22703635,SRS19696110,SRA1761648,University of Michigan,University of Michigan,2,0.82908,0.8023,0.08841,0.07628,0.72608,0.73285,0.53006,0.52227,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2023-12-01,Undetermined,Undetermined,Eye,Sensory System
29102,SRR27010850,SRX22703634,SRS19696109,SRP475451,PRJNA1047750,Differential expression in Muller glia of injured zebrafish in a mych /  context,GSE249115,Transcriptome Analysis,This experiment studies  retinal regeneration using a zebrafish model with a focus on Muller glia reprogramming. Overall design: Three groups: controls Muller glia from uninjured retinas  injured WT Muller glia from injured WT retina at 2 xxx post injury dpi  and injured mych /  Muller glia from injured mych /  fish at 2dpi. Of interest are the WT injury responsive genes  and which injury responsive genes in the WT are differentially expressed in the mych /  fish.,parent bioproject:PRJNA1047494,pubmed:38984586,,Muller glia from WT retinas 2 xxx post injury dpi rep2 [5803 ML 5],GSM7926866,,source name:WT Muller glia injured retina|tissue:WT Muller glia injured retina|genotype:WT|treatment:injured|geo loc name:missing|collection date:missing,Muller glia from WT retinas 2 xxx post injury dpi rep2 [5803 ML 5],"University of Michigan Bioinformatics Core RNA seq pipeline ""Watermelon"" version 2.4.4 Sequence reads were trimmed for adaptor sequence/low quality sequence using Cutadapt v2.3. FastQC v0.11.8 was used to ensure the quality of data Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a Quantitative count estimates to genes performed with RSEM v1.3.3 Assembly: GRCz11 Supplementary files format and content: RS10 deseq2 raw counts.txt Supplementary files format and content: tab delimited text with include expected counts values for each Sample",WT Muller glia injured retina,Needle poke injury to retina.,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,tissue:WT Muller glia injured retina|genotype:WT|treatment:injured,GSM7926866,GSM7926866: Muller glia from WT retinas 2 xxx post injury dpi rep2 [5803 ML 5]; Danio rerio; RNA Seq,GSM7926866 r1,GSM7926866,1,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475451,,loader:fastq load.py,5803-ML-5_TCTCGGAG-CCGTGTGT_S218_R1_001.fastq.gz 5803-ML-5_TCTCGGAG-CCGTGTGT_S218_R2_001.fastq.gz,fastq fastq,42813650610.0,141767055.0,GSM7926866 r1,0:151 1:151,A:11307756303;C:9128581274;G:11491585338;T:10885631489;N:96206,151,151,,,11307756303,9128581274,11491585338,10885631489,96206,SRX22703634,SRS19696109,SRA1761648,University of Michigan,University of Michigan,2,0.84717,0.81641,0.07575,0.06577,0.72456,0.72947,0.51796,0.52376,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2023-12-01,Undetermined,Undetermined,Eye,Sensory System
29103,SRR27010851,SRX22703633,SRS19696108,SRP475451,PRJNA1047750,Differential expression in Muller glia of injured zebrafish in a mych /  context,GSE249115,Transcriptome Analysis,This experiment studies  retinal regeneration using a zebrafish model with a focus on Muller glia reprogramming. Overall design: Three groups: controls Muller glia from uninjured retinas  injured WT Muller glia from injured WT retina at 2 xxx post injury dpi  and injured mych /  Muller glia from injured mych /  fish at 2dpi. Of interest are the WT injury responsive genes  and which injury responsive genes in the WT are differentially expressed in the mych /  fish.,parent bioproject:PRJNA1047494,pubmed:38984586,,Muller glia from WT retinas 2 xxx post injury dpi rep1 [5803 ML 4],GSM7926865,,source name:WT Muller glia injured retina|tissue:WT Muller glia injured retina|genotype:WT|treatment:injured|geo loc name:missing|collection date:missing,Muller glia from WT retinas 2 xxx post injury dpi rep1 [5803 ML 4],"University of Michigan Bioinformatics Core RNA seq pipeline ""Watermelon"" version 2.4.4 Sequence reads were trimmed for adaptor sequence/low quality sequence using Cutadapt v2.3. FastQC v0.11.8 was used to ensure the quality of data Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a Quantitative count estimates to genes performed with RSEM v1.3.3 Assembly: GRCz11 Supplementary files format and content: RS10 deseq2 raw counts.txt Supplementary files format and content: tab delimited text with include expected counts values for each Sample",WT Muller glia injured retina,Needle poke injury to retina.,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,tissue:WT Muller glia injured retina|genotype:WT|treatment:injured,GSM7926865,GSM7926865: Muller glia from WT retinas 2 xxx post injury dpi rep1 [5803 ML 4]; Danio rerio; RNA Seq,GSM7926865 r1,GSM7926865,1,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475451,,loader:fastq load.py,5803-ML-4_TTACACAC-AACTCCGA_S217_R1_001.fastq.gz 5803-ML-4_TTACACAC-AACTCCGA_S217_R2_001.fastq.gz,fastq fastq,35641811084.0,118019242.0,GSM7926865 r1,0:151 1:151,A:9509123801;C:7547711759;G:9554254572;T:9030640032;N:80920,151,151,,,9509123801,7547711759,9554254572,9030640032,80920,SRX22703633,SRS19696108,SRA1761648,University of Michigan,University of Michigan,2,0.84325,0.81491,0.09102,0.08021,0.71936,0.72368,0.52206,0.51772,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2023-12-01,Undetermined,Undetermined,Eye,Sensory System
29104,SRR27010852,SRX22703632,SRS19696107,SRP475451,PRJNA1047750,Differential expression in Muller glia of injured zebrafish in a mych /  context,GSE249115,Transcriptome Analysis,This experiment studies  retinal regeneration using a zebrafish model with a focus on Muller glia reprogramming. Overall design: Three groups: controls Muller glia from uninjured retinas  injured WT Muller glia from injured WT retina at 2 xxx post injury dpi  and injured mych /  Muller glia from injured mych /  fish at 2dpi. Of interest are the WT injury responsive genes  and which injury responsive genes in the WT are differentially expressed in the mych /  fish.,parent bioproject:PRJNA1047494,pubmed:38984586,,Muller glia from uninjured WT retinas rep3 [5803 ML 3],GSM7926864,,source name:WT Muller glia uninjured retina|tissue:WT Muller glia uninjured retina|genotype:WT|treatment:n1|geo loc name:missing|collection date:missing,Muller glia from uninjured WT retinas rep3 [5803 ML 3],"University of Michigan Bioinformatics Core RNA seq pipeline ""Watermelon"" version 2.4.4 Sequence reads were trimmed for adaptor sequence/low quality sequence using Cutadapt v2.3. FastQC v0.11.8 was used to ensure the quality of data Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a Quantitative count estimates to genes performed with RSEM v1.3.3 Assembly: GRCz11 Supplementary files format and content: RS10 deseq2 raw counts.txt Supplementary files format and content: tab delimited text with include expected counts values for each Sample",WT Muller glia uninjured retina,Needle poke injury to retina.,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,tissue:WT Muller glia uninjured retina|genotype:WT|treatment:n1,GSM7926864,GSM7926864: Muller glia from uninjured WT retinas rep3 [5803 ML 3]; Danio rerio; RNA Seq,GSM7926864 r1,GSM7926864,1,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475451,,loader:fastq load.py,5803-ML-3_CCTTATGG-GCACGCTT_S216_R2_001.fastq.gz 5803-ML-3_CCTTATGG-GCACGCTT_S216_R1_001.fastq.gz,fastq fastq,44024352302.0,145776001.0,GSM7926864 r1,0:151 1:151,A:12035679681;C:9067037632;G:11325935498;T:11595599635;N:99856,151,151,,,12035679681,9067037632,11325935498,11595599635,99856,SRX22703632,SRS19696107,SRA1761648,University of Michigan,University of Michigan,2,0.83165,0.79093,0.139,0.11939,0.73539,0.74148,0.52839,0.52569,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2023-12-01,Undetermined,Undetermined,Eye,Sensory System
29105,SRR27010853,SRX22703631,SRS19696106,SRP475451,PRJNA1047750,Differential expression in Muller glia of injured zebrafish in a mych /  context,GSE249115,Transcriptome Analysis,This experiment studies  retinal regeneration using a zebrafish model with a focus on Muller glia reprogramming. Overall design: Three groups: controls Muller glia from uninjured retinas  injured WT Muller glia from injured WT retina at 2 xxx post injury dpi  and injured mych /  Muller glia from injured mych /  fish at 2dpi. Of interest are the WT injury responsive genes  and which injury responsive genes in the WT are differentially expressed in the mych /  fish.,parent bioproject:PRJNA1047494,pubmed:38984586,,Muller glia from uninjured WT retinas rep2 [5803 ML 2],GSM7926863,,source name:WT Muller glia uninjured retina|tissue:WT Muller glia uninjured retina|genotype:WT|treatment:n1|geo loc name:missing|collection date:missing,Muller glia from uninjured WT retinas rep2 [5803 ML 2],"University of Michigan Bioinformatics Core RNA seq pipeline ""Watermelon"" version 2.4.4 Sequence reads were trimmed for adaptor sequence/low quality sequence using Cutadapt v2.3. FastQC v0.11.8 was used to ensure the quality of data Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a Quantitative count estimates to genes performed with RSEM v1.3.3 Assembly: GRCz11 Supplementary files format and content: RS10 deseq2 raw counts.txt Supplementary files format and content: tab delimited text with include expected counts values for each Sample",WT Muller glia uninjured retina,Needle poke injury to retina.,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,tissue:WT Muller glia uninjured retina|genotype:WT|treatment:n1,GSM7926863,GSM7926863: Muller glia from uninjured WT retinas rep2 [5803 ML 2]; Danio rerio; RNA Seq,GSM7926863 r1,GSM7926863,1,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475451,,loader:fastq load.py,5803-ML-2_AGGTCTAT-CCGTGAGA_S215_R1_001.fastq.gz 5803-ML-2_AGGTCTAT-CCGTGAGA_S215_R2_001.fastq.gz,fastq fastq,30776465150.0,101908825.0,GSM7926863 r1,0:151 1:151,A:8433807492;C:6356747786;G:7933043571;T:8052796793;N:69508,151,151,,,8433807492,6356747786,7933043571,8052796793,69508,SRX22703631,SRS19696106,SRA1761648,University of Michigan,University of Michigan,2,0.84084,0.79586,0.14119,0.12143,0.74067,0.74718,0.52859,0.5313,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2023-12-01,Undetermined,Undetermined,Eye,Sensory System
29106,SRR27010854,SRX22703630,SRS19696105,SRP475451,PRJNA1047750,Differential expression in Muller glia of injured zebrafish in a mych /  context,GSE249115,Transcriptome Analysis,This experiment studies  retinal regeneration using a zebrafish model with a focus on Muller glia reprogramming. Overall design: Three groups: controls Muller glia from uninjured retinas  injured WT Muller glia from injured WT retina at 2 xxx post injury dpi  and injured mych /  Muller glia from injured mych /  fish at 2dpi. Of interest are the WT injury responsive genes  and which injury responsive genes in the WT are differentially expressed in the mych /  fish.,parent bioproject:PRJNA1047494,pubmed:38984586,,Muller glia from uninjured WT retinas rep1 [5803 ML 1 ],GSM7926862,,source name:WT Muller glia uninjured retina|tissue:WT Muller glia uninjured retina|genotype:WT|treatment:n1|geo loc name:missing|collection date:missing,Muller glia from uninjured WT retinas rep1 [5803 ML 1 ],"University of Michigan Bioinformatics Core RNA seq pipeline ""Watermelon"" version 2.4.4 Sequence reads were trimmed for adaptor sequence/low quality sequence using Cutadapt v2.3. FastQC v0.11.8 was used to ensure the quality of data Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a Quantitative count estimates to genes performed with RSEM v1.3.3 Assembly: GRCz11 Supplementary files format and content: RS10 deseq2 raw counts.txt Supplementary files format and content: tab delimited text with include expected counts values for each Sample",WT Muller glia uninjured retina,Needle poke injury to retina.,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,tissue:WT Muller glia uninjured retina|genotype:WT|treatment:n1,GSM7926862,GSM7926862: Muller glia from uninjured WT retinas rep1 [5803 ML 1 ]; Danio rerio; RNA Seq,GSM7926862 r1,GSM7926862,1,Retinas from gfap:GFP transgenic zebrafish were dissected from fish eyes  tissue was dissociated using Papain Dissociation system Worthington Biochemical and GFP+ Muller glia isolated by FACS. RNA was purified using Directzol RNA microprep kit Zymo Research. Illumina RNA PolyA enrichment library prep kit was used according to manufacturer's directions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP475451,,loader:fastq load.py,5803-ML-1_AAGGACCG-GACACAAG_S214_R1_001.fastq.gz 5803-ML-1_AAGGACCG-GACACAAG_S214_R2_001.fastq.gz,fastq fastq,35814764672.0,118591936.0,GSM7926862 r1,0:151 1:151,A:10118857494;C:7312994344;G:8767136259;T:9615695615;N:80960,151,151,,,10118857494,7312994344,8767136259,9615695615,80960,SRX22703630,SRS19696105,SRA1761648,University of Michigan,University of Michigan,2,0.84915,0.79824,0.17335,0.14475,0.72103,0.73097,0.51291,0.4893,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2023-12-01,Undetermined,Undetermined,Eye,Sensory System
33846,SRR30769771,SRX26172026,SRS22716039,SRP534198,PRJNA1164198,Analysis of The Senescence Secretome During Zebrafish Retina Regeneration,GSE277792,Transcriptome Analysis,Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with Müller glia serving as resident stem cells. Recently  we discovered that this process is aided by a population of damage induced senescent immune cells.  As part of the Senescence Associated Secretory Phenotype SASP  senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However  the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here  we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors post retina injury  including two distinct acute damage regimens  as well as a chronic  genetic model of retina degeneration. We discovered a 31 factor “Regeneration associated Senescence Signature” RASS that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated post damage. Among these  we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration post both acute and chronic retinal damage. Overall design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT 263 senolytic agents. Whole retinas were collected at 3  12  and 20 xxx post injury and samples were collected using Trizol based RNA extraction techniques.,,pubmed:40308558,,NMDA+Senolytic 20dpi Rep 3,GSM8530629,,source name:Retina|tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263|geo loc name:missing|collection date:missing,NMDA+Senolytic 20dpi Rep 3,Adapter sequences and low quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10  a wrapper for CutAdapt v4.8  using the   paired and   illumina parameters. Trimmed reads were quantified using Salmon v1.10.3 in quasi mapping mode with the optional paramaters   validateMappings and   gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome  with the primary assembly from the same release serving as decoys. Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0. Assembly: GRCz11.111 Supplementary files format and content: tab delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi mapping mode,Retina,,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263,GSM8530629,GSM8530629: NMDA+Senolytic 20dpi Rep 3; Danio rerio; RNA Seq,GSM8530629 r1,GSM8530629,1,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP534198,,,11384-GK-0018_S1_L005_R1_001.fastq.gz 11384-GK-0018_S1_L005_R2_001.fastq.gz,fastq fastq,22610089492.0,74867846.0,GSM8530629 r1,0:151 1:151,A:6096322158;C:5038348469;G:5495879212;T:5975532315;N:4007338,151,151,,,6096322158,5038348469,5495879212,5975532315,4007338,SRX26172026,SRS22716039,SRA1977341,"Patton Lab, Biological Sciences, Vanderbilt University","Patton Lab, Biological Sciences, Vanderbilt University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-09-23,Undetermined,Undetermined,Eye,Sensory System
33847,SRR30769772,SRX26172025,SRS22716040,SRP534198,PRJNA1164198,Analysis of The Senescence Secretome During Zebrafish Retina Regeneration,GSE277792,Transcriptome Analysis,Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with Müller glia serving as resident stem cells. Recently  we discovered that this process is aided by a population of damage induced senescent immune cells.  As part of the Senescence Associated Secretory Phenotype SASP  senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However  the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here  we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors post retina injury  including two distinct acute damage regimens  as well as a chronic  genetic model of retina degeneration. We discovered a 31 factor “Regeneration associated Senescence Signature” RASS that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated post damage. Among these  we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration post both acute and chronic retinal damage. Overall design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT 263 senolytic agents. Whole retinas were collected at 3  12  and 20 xxx post injury and samples were collected using Trizol based RNA extraction techniques.,,pubmed:40308558,,NMDA+Senolytic 20dpi Rep 2,GSM8530628,,source name:Retina|tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263|geo loc name:missing|collection date:missing,NMDA+Senolytic 20dpi Rep 2,Adapter sequences and low quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10  a wrapper for CutAdapt v4.8  using the   paired and   illumina parameters. Trimmed reads were quantified using Salmon v1.10.3 in quasi mapping mode with the optional paramaters   validateMappings and   gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome  with the primary assembly from the same release serving as decoys. Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0. Assembly: GRCz11.111 Supplementary files format and content: tab delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi mapping mode,Retina,,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263,GSM8530628,GSM8530628: NMDA+Senolytic 20dpi Rep 2; Danio rerio; RNA Seq,GSM8530628 r1,GSM8530628,1,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP534198,,,11384-GK-0017_S1_L005_R1_001.fastq.gz 11384-GK-0017_S1_L005_R2_001.fastq.gz,fastq fastq,15883255120.0,52593560.0,GSM8530628 r1,0:151 1:151,A:4234691081;C:3596643174;G:3921904429;T:4127066479;N:2949957,151,151,,,4234691081,3596643174,3921904429,4127066479,2949957,SRX26172025,SRS22716040,SRA1977341,"Patton Lab, Biological Sciences, Vanderbilt University","Patton Lab, Biological Sciences, Vanderbilt University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-09-23,Undetermined,Undetermined,Eye,Sensory System
33848,SRR30769773,SRX26172024,SRS22716038,SRP534198,PRJNA1164198,Analysis of The Senescence Secretome During Zebrafish Retina Regeneration,GSE277792,Transcriptome Analysis,Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with Müller glia serving as resident stem cells. Recently  we discovered that this process is aided by a population of damage induced senescent immune cells.  As part of the Senescence Associated Secretory Phenotype SASP  senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However  the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here  we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors post retina injury  including two distinct acute damage regimens  as well as a chronic  genetic model of retina degeneration. We discovered a 31 factor “Regeneration associated Senescence Signature” RASS that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated post damage. Among these  we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration post both acute and chronic retinal damage. Overall design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT 263 senolytic agents. Whole retinas were collected at 3  12  and 20 xxx post injury and samples were collected using Trizol based RNA extraction techniques.,,pubmed:40308558,,NMDA+Senolytic 20dpi Rep 1,GSM8530627,,source name:Retina|tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263|geo loc name:missing|collection date:missing,NMDA+Senolytic 20dpi Rep 1,Adapter sequences and low quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10  a wrapper for CutAdapt v4.8  using the   paired and   illumina parameters. Trimmed reads were quantified using Salmon v1.10.3 in quasi mapping mode with the optional paramaters   validateMappings and   gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome  with the primary assembly from the same release serving as decoys. Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0. Assembly: GRCz11.111 Supplementary files format and content: tab delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi mapping mode,Retina,,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263,GSM8530627,GSM8530627: NMDA+Senolytic 20dpi Rep 1; Danio rerio; RNA Seq,GSM8530627 r1,GSM8530627,1,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP534198,,,11384-GK-0016_S1_L005_R1_001.fastq.gz 11384-GK-0016_S1_L005_R2_001.fastq.gz,fastq fastq,20074224484.0,66470942.0,GSM8530627 r1,0:151 1:151,A:5366083942;C:4521905793;G:4941071454;T:5241584345;N:3578950,151,151,,,5366083942,4521905793,4941071454,5241584345,3578950,SRX26172024,SRS22716038,SRA1977341,"Patton Lab, Biological Sciences, Vanderbilt University","Patton Lab, Biological Sciences, Vanderbilt University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-09-23,Undetermined,Undetermined,Eye,Sensory System
33849,SRR30769774,SRX26172023,SRS22716037,SRP534198,PRJNA1164198,Analysis of The Senescence Secretome During Zebrafish Retina Regeneration,GSE277792,Transcriptome Analysis,Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with Müller glia serving as resident stem cells. Recently  we discovered that this process is aided by a population of damage induced senescent immune cells.  As part of the Senescence Associated Secretory Phenotype SASP  senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However  the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here  we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors post retina injury  including two distinct acute damage regimens  as well as a chronic  genetic model of retina degeneration. We discovered a 31 factor “Regeneration associated Senescence Signature” RASS that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated post damage. Among these  we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration post both acute and chronic retinal damage. Overall design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT 263 senolytic agents. Whole retinas were collected at 3  12  and 20 xxx post injury and samples were collected using Trizol based RNA extraction techniques.,,pubmed:40308558,,NMDA Only 20dpi Rep 3,GSM8530626,,source name:Retina|tissue:Retina|genotype:NMDA Damage|treatment:Control|geo loc name:missing|collection date:missing,NMDA Only 20dpi Rep 3,Adapter sequences and low quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10  a wrapper for CutAdapt v4.8  using the   paired and   illumina parameters. Trimmed reads were quantified using Salmon v1.10.3 in quasi mapping mode with the optional paramaters   validateMappings and   gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome  with the primary assembly from the same release serving as decoys. Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0. Assembly: GRCz11.111 Supplementary files format and content: tab delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi mapping mode,Retina,,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,tissue:Retina|genotype:NMDA Damage|treatment:Control,GSM8530626,GSM8530626: NMDA Only 20dpi Rep 3; Danio rerio; RNA Seq,GSM8530626 r1,GSM8530626,1,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP534198,,,11384-GK-0015_S1_L005_R1_001.fastq.gz 11384-GK-0015_S1_L005_R2_001.fastq.gz,fastq fastq,16764864392.0,55512796.0,GSM8530626 r1,0:151 1:151,A:4465019974;C:3832519977;G:4089874744;T:4374403116;N:3046581,151,151,,,4465019974,3832519977,4089874744,4374403116,3046581,SRX26172023,SRS22716037,SRA1977341,"Patton Lab, Biological Sciences, Vanderbilt University","Patton Lab, Biological Sciences, Vanderbilt University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-09-23,Undetermined,Undetermined,Eye,Sensory System
33850,SRR30769775,SRX26172022,SRS22716036,SRP534198,PRJNA1164198,Analysis of The Senescence Secretome During Zebrafish Retina Regeneration,GSE277792,Transcriptome Analysis,Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with Müller glia serving as resident stem cells. Recently  we discovered that this process is aided by a population of damage induced senescent immune cells.  As part of the Senescence Associated Secretory Phenotype SASP  senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However  the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here  we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors post retina injury  including two distinct acute damage regimens  as well as a chronic  genetic model of retina degeneration. We discovered a 31 factor “Regeneration associated Senescence Signature” RASS that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated post damage. Among these  we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration post both acute and chronic retinal damage. Overall design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT 263 senolytic agents. Whole retinas were collected at 3  12  and 20 xxx post injury and samples were collected using Trizol based RNA extraction techniques.,,pubmed:40308558,,NMDA Only 20dpi Rep 2,GSM8530625,,source name:Retina|tissue:Retina|genotype:NMDA Damage|treatment:Control|geo loc name:missing|collection date:missing,NMDA Only 20dpi Rep 2,Adapter sequences and low quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10  a wrapper for CutAdapt v4.8  using the   paired and   illumina parameters. Trimmed reads were quantified using Salmon v1.10.3 in quasi mapping mode with the optional paramaters   validateMappings and   gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome  with the primary assembly from the same release serving as decoys. Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0. Assembly: GRCz11.111 Supplementary files format and content: tab delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi mapping mode,Retina,,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,tissue:Retina|genotype:NMDA Damage|treatment:Control,GSM8530625,GSM8530625: NMDA Only 20dpi Rep 2; Danio rerio; RNA Seq,GSM8530625 r1,GSM8530625,1,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP534198,,,11384-GK-0014_S1_L005_R1_001.fastq.gz 11384-GK-0014_S1_L005_R2_001.fastq.gz,fastq fastq,17587013488.0,58235144.0,GSM8530625 r1,0:151 1:151,A:4702159471;C:3973231615;G:4291531323;T:4616815802;N:3275277,151,151,,,4702159471,3973231615,4291531323,4616815802,3275277,SRX26172022,SRS22716036,SRA1977341,"Patton Lab, Biological Sciences, Vanderbilt University","Patton Lab, Biological Sciences, Vanderbilt University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-09-23,Undetermined,Undetermined,Eye,Sensory System
33851,SRR30769776,SRX26172021,SRS22716035,SRP534198,PRJNA1164198,Analysis of The Senescence Secretome During Zebrafish Retina Regeneration,GSE277792,Transcriptome Analysis,Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with Müller glia serving as resident stem cells. Recently  we discovered that this process is aided by a population of damage induced senescent immune cells.  As part of the Senescence Associated Secretory Phenotype SASP  senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However  the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here  we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors post retina injury  including two distinct acute damage regimens  as well as a chronic  genetic model of retina degeneration. We discovered a 31 factor “Regeneration associated Senescence Signature” RASS that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated post damage. Among these  we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration post both acute and chronic retinal damage. Overall design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT 263 senolytic agents. Whole retinas were collected at 3  12  and 20 xxx post injury and samples were collected using Trizol based RNA extraction techniques.,,pubmed:40308558,,NMDA Only 20dpi Rep 1,GSM8530624,,source name:Retina|tissue:Retina|genotype:NMDA Damage|treatment:Control|geo loc name:missing|collection date:missing,NMDA Only 20dpi Rep 1,Adapter sequences and low quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10  a wrapper for CutAdapt v4.8  using the   paired and   illumina parameters. Trimmed reads were quantified using Salmon v1.10.3 in quasi mapping mode with the optional paramaters   validateMappings and   gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome  with the primary assembly from the same release serving as decoys. Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0. Assembly: GRCz11.111 Supplementary files format and content: tab delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi mapping mode,Retina,,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,tissue:Retina|genotype:NMDA Damage|treatment:Control,GSM8530624,GSM8530624: NMDA Only 20dpi Rep 1; Danio rerio; RNA Seq,GSM8530624 r1,GSM8530624,1,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP534198,,,11384-GK-0013_S1_L005_R1_001.fastq.gz 11384-GK-0013_S1_L005_R2_001.fastq.gz,fastq fastq,17211645306.0,56992203.0,GSM8530624 r1,0:151 1:151,A:4570848139;C:3941519932;G:4229510898;T:4466558031;N:3208306,151,151,,,4570848139,3941519932,4229510898,4466558031,3208306,SRX26172021,SRS22716035,SRA1977341,"Patton Lab, Biological Sciences, Vanderbilt University","Patton Lab, Biological Sciences, Vanderbilt University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-09-23,Undetermined,Undetermined,Eye,Sensory System
33852,SRR30769777,SRX26172020,SRS22716034,SRP534198,PRJNA1164198,Analysis of The Senescence Secretome During Zebrafish Retina Regeneration,GSE277792,Transcriptome Analysis,Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with Müller glia serving as resident stem cells. Recently  we discovered that this process is aided by a population of damage induced senescent immune cells.  As part of the Senescence Associated Secretory Phenotype SASP  senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However  the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here  we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors post retina injury  including two distinct acute damage regimens  as well as a chronic  genetic model of retina degeneration. We discovered a 31 factor “Regeneration associated Senescence Signature” RASS that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated post damage. Among these  we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration post both acute and chronic retinal damage. Overall design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT 263 senolytic agents. Whole retinas were collected at 3  12  and 20 xxx post injury and samples were collected using Trizol based RNA extraction techniques.,,pubmed:40308558,,NMDA+Senolytic 12dpi Rep 3,GSM8530623,,source name:Retina|tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263|geo loc name:missing|collection date:missing,NMDA+Senolytic 12dpi Rep 3,Adapter sequences and low quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10  a wrapper for CutAdapt v4.8  using the   paired and   illumina parameters. Trimmed reads were quantified using Salmon v1.10.3 in quasi mapping mode with the optional paramaters   validateMappings and   gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome  with the primary assembly from the same release serving as decoys. Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0. Assembly: GRCz11.111 Supplementary files format and content: tab delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi mapping mode,Retina,,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263,GSM8530623,GSM8530623: NMDA+Senolytic 12dpi Rep 3; Danio rerio; RNA Seq,GSM8530623 r1,GSM8530623,1,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP534198,,,11384-GK-0012_S1_L005_R1_001.fastq.gz 11384-GK-0012_S1_L005_R2_001.fastq.gz,fastq fastq,19519830400.0,64635200.0,GSM8530623 r1,0:151 1:151,A:5213575107;C:4426193150;G:4758365858;T:5118199883;N:3496402,151,151,,,5213575107,4426193150,4758365858,5118199883,3496402,SRX26172020,SRS22716034,SRA1977341,"Patton Lab, Biological Sciences, Vanderbilt University","Patton Lab, Biological Sciences, Vanderbilt University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-09-23,Undetermined,Undetermined,Eye,Sensory System
33853,SRR30769778,SRX26172019,SRS22716032,SRP534198,PRJNA1164198,Analysis of The Senescence Secretome During Zebrafish Retina Regeneration,GSE277792,Transcriptome Analysis,Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with Müller glia serving as resident stem cells. Recently  we discovered that this process is aided by a population of damage induced senescent immune cells.  As part of the Senescence Associated Secretory Phenotype SASP  senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However  the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here  we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors post retina injury  including two distinct acute damage regimens  as well as a chronic  genetic model of retina degeneration. We discovered a 31 factor “Regeneration associated Senescence Signature” RASS that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated post damage. Among these  we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration post both acute and chronic retinal damage. Overall design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT 263 senolytic agents. Whole retinas were collected at 3  12  and 20 xxx post injury and samples were collected using Trizol based RNA extraction techniques.,,pubmed:40308558,,NMDA+Senolytic 12dpi Rep 2,GSM8530622,,source name:Retina|tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263|geo loc name:missing|collection date:missing,NMDA+Senolytic 12dpi Rep 2,Adapter sequences and low quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10  a wrapper for CutAdapt v4.8  using the   paired and   illumina parameters. Trimmed reads were quantified using Salmon v1.10.3 in quasi mapping mode with the optional paramaters   validateMappings and   gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome  with the primary assembly from the same release serving as decoys. Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0. Assembly: GRCz11.111 Supplementary files format and content: tab delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi mapping mode,Retina,,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263,GSM8530622,GSM8530622: NMDA+Senolytic 12dpi Rep 2; Danio rerio; RNA Seq,GSM8530622 r1,GSM8530622,1,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP534198,,,11384-GK-0011_S1_L005_R1_001.fastq.gz 11384-GK-0011_S1_L005_R2_001.fastq.gz,fastq fastq,15020818318.0,49737809.0,GSM8530622 r1,0:151 1:151,A:4035098361;C:3327301881;G:3685533773;T:3970171718;N:2712585,151,151,,,4035098361,3327301881,3685533773,3970171718,2712585,SRX26172019,SRS22716032,SRA1977341,"Patton Lab, Biological Sciences, Vanderbilt University","Patton Lab, Biological Sciences, Vanderbilt University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-09-23,Undetermined,Undetermined,Eye,Sensory System
33854,SRR30769779,SRX26172018,SRS22716033,SRP534198,PRJNA1164198,Analysis of The Senescence Secretome During Zebrafish Retina Regeneration,GSE277792,Transcriptome Analysis,Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with Müller glia serving as resident stem cells. Recently  we discovered that this process is aided by a population of damage induced senescent immune cells.  As part of the Senescence Associated Secretory Phenotype SASP  senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However  the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here  we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors post retina injury  including two distinct acute damage regimens  as well as a chronic  genetic model of retina degeneration. We discovered a 31 factor “Regeneration associated Senescence Signature” RASS that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated post damage. Among these  we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration post both acute and chronic retinal damage. Overall design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT 263 senolytic agents. Whole retinas were collected at 3  12  and 20 xxx post injury and samples were collected using Trizol based RNA extraction techniques.,,pubmed:40308558,,NMDA+Senolytic 12dpi Rep 1,GSM8530621,,source name:Retina|tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263|geo loc name:missing|collection date:missing,NMDA+Senolytic 12dpi Rep 1,Adapter sequences and low quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10  a wrapper for CutAdapt v4.8  using the   paired and   illumina parameters. Trimmed reads were quantified using Salmon v1.10.3 in quasi mapping mode with the optional paramaters   validateMappings and   gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome  with the primary assembly from the same release serving as decoys. Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0. Assembly: GRCz11.111 Supplementary files format and content: tab delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi mapping mode,Retina,,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263,GSM8530621,GSM8530621: NMDA+Senolytic 12dpi Rep 1; Danio rerio; RNA Seq,GSM8530621 r1,GSM8530621,1,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP534198,,,11384-GK-0010_S1_L005_R1_001.fastq.gz 11384-GK-0010_S1_L005_R2_001.fastq.gz,fastq fastq,21313476652.0,70574426.0,GSM8530621 r1,0:151 1:151,A:5681259287;C:4844892428;G:5203514513;T:5579854696;N:3955728,151,151,,,5681259287,4844892428,5203514513,5579854696,3955728,SRX26172018,SRS22716033,SRA1977341,"Patton Lab, Biological Sciences, Vanderbilt University","Patton Lab, Biological Sciences, Vanderbilt University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-09-23,Undetermined,Undetermined,Eye,Sensory System
33855,SRR30769780,SRX26172017,SRS22716030,SRP534198,PRJNA1164198,Analysis of The Senescence Secretome During Zebrafish Retina Regeneration,GSE277792,Transcriptome Analysis,Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with Müller glia serving as resident stem cells. Recently  we discovered that this process is aided by a population of damage induced senescent immune cells.  As part of the Senescence Associated Secretory Phenotype SASP  senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However  the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here  we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors post retina injury  including two distinct acute damage regimens  as well as a chronic  genetic model of retina degeneration. We discovered a 31 factor “Regeneration associated Senescence Signature” RASS that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated post damage. Among these  we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration post both acute and chronic retinal damage. Overall design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT 263 senolytic agents. Whole retinas were collected at 3  12  and 20 xxx post injury and samples were collected using Trizol based RNA extraction techniques.,,pubmed:40308558,,NMDA Only 12dpi Rep 3,GSM8530620,,source name:Retina|tissue:Retina|genotype:NMDA Damage|treatment:Control|geo loc name:missing|collection date:missing,NMDA Only 12dpi Rep 3,Adapter sequences and low quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10  a wrapper for CutAdapt v4.8  using the   paired and   illumina parameters. Trimmed reads were quantified using Salmon v1.10.3 in quasi mapping mode with the optional paramaters   validateMappings and   gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome  with the primary assembly from the same release serving as decoys. Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0. Assembly: GRCz11.111 Supplementary files format and content: tab delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi mapping mode,Retina,,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,tissue:Retina|genotype:NMDA Damage|treatment:Control,GSM8530620,GSM8530620: NMDA Only 12dpi Rep 3; Danio rerio; RNA Seq,GSM8530620 r1,GSM8530620,1,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP534198,,,11384-GK-0009_S1_L005_R1_001.fastq.gz 11384-GK-0009_S1_L005_R2_001.fastq.gz,fastq fastq,15559919726.0,51522913.0,GSM8530620 r1,0:151 1:151,A:4218748488;C:3440121432;G:3770196530;T:4128045704;N:2807572,151,151,,,4218748488,3440121432,3770196530,4128045704,2807572,SRX26172017,SRS22716030,SRA1977341,"Patton Lab, Biological Sciences, Vanderbilt University","Patton Lab, Biological Sciences, Vanderbilt University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-09-23,Undetermined,Undetermined,Eye,Sensory System
33856,SRR30769781,SRX26172016,SRS22716028,SRP534198,PRJNA1164198,Analysis of The Senescence Secretome During Zebrafish Retina Regeneration,GSE277792,Transcriptome Analysis,Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with Müller glia serving as resident stem cells. Recently  we discovered that this process is aided by a population of damage induced senescent immune cells.  As part of the Senescence Associated Secretory Phenotype SASP  senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However  the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here  we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors post retina injury  including two distinct acute damage regimens  as well as a chronic  genetic model of retina degeneration. We discovered a 31 factor “Regeneration associated Senescence Signature” RASS that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated post damage. Among these  we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration post both acute and chronic retinal damage. Overall design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT 263 senolytic agents. Whole retinas were collected at 3  12  and 20 xxx post injury and samples were collected using Trizol based RNA extraction techniques.,,pubmed:40308558,,NMDA Only 12dpi Rep 2,GSM8530619,,source name:Retina|tissue:Retina|genotype:NMDA Damage|treatment:Control|geo loc name:missing|collection date:missing,NMDA Only 12dpi Rep 2,Adapter sequences and low quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10  a wrapper for CutAdapt v4.8  using the   paired and   illumina parameters. Trimmed reads were quantified using Salmon v1.10.3 in quasi mapping mode with the optional paramaters   validateMappings and   gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome  with the primary assembly from the same release serving as decoys. Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0. Assembly: GRCz11.111 Supplementary files format and content: tab delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi mapping mode,Retina,,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,tissue:Retina|genotype:NMDA Damage|treatment:Control,GSM8530619,GSM8530619: NMDA Only 12dpi Rep 2; Danio rerio; RNA Seq,GSM8530619 r1,GSM8530619,1,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP534198,,,11384-GK-0008_S1_L005_R1_001.fastq.gz 11384-GK-0008_S1_L005_R2_001.fastq.gz,fastq fastq,16929495162.0,56057931.0,GSM8530619 r1,0:151 1:151,A:4580671833;C:3751371251;G:4108279016;T:4486053060;N:3120002,151,151,,,4580671833,3751371251,4108279016,4486053060,3120002,SRX26172016,SRS22716028,SRA1977341,"Patton Lab, Biological Sciences, Vanderbilt University","Patton Lab, Biological Sciences, Vanderbilt University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-09-23,Undetermined,Undetermined,Eye,Sensory System
33857,SRR30769782,SRX26172015,SRS22716029,SRP534198,PRJNA1164198,Analysis of The Senescence Secretome During Zebrafish Retina Regeneration,GSE277792,Transcriptome Analysis,Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with Müller glia serving as resident stem cells. Recently  we discovered that this process is aided by a population of damage induced senescent immune cells.  As part of the Senescence Associated Secretory Phenotype SASP  senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However  the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here  we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors post retina injury  including two distinct acute damage regimens  as well as a chronic  genetic model of retina degeneration. We discovered a 31 factor “Regeneration associated Senescence Signature” RASS that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated post damage. Among these  we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration post both acute and chronic retinal damage. Overall design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT 263 senolytic agents. Whole retinas were collected at 3  12  and 20 xxx post injury and samples were collected using Trizol based RNA extraction techniques.,,pubmed:40308558,,NMDA Only 12dpi Rep 1,GSM8530618,,source name:Retina|tissue:Retina|genotype:NMDA Damage|treatment:Control|geo loc name:missing|collection date:missing,NMDA Only 12dpi Rep 1,Adapter sequences and low quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10  a wrapper for CutAdapt v4.8  using the   paired and   illumina parameters. Trimmed reads were quantified using Salmon v1.10.3 in quasi mapping mode with the optional paramaters   validateMappings and   gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome  with the primary assembly from the same release serving as decoys. Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0. Assembly: GRCz11.111 Supplementary files format and content: tab delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi mapping mode,Retina,,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,tissue:Retina|genotype:NMDA Damage|treatment:Control,GSM8530618,GSM8530618: NMDA Only 12dpi Rep 1; Danio rerio; RNA Seq,GSM8530618 r1,GSM8530618,1,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP534198,,,11384-GK-0007_S1_L005_R1_001.fastq.gz 11384-GK-0007_S1_L005_R2_001.fastq.gz,fastq fastq,14797480862.0,48998281.0,GSM8530618 r1,0:151 1:151,A:3900528784;C:3418459440;G:3652120707;T:3823647040;N:2724891,151,151,,,3900528784,3418459440,3652120707,3823647040,2724891,SRX26172015,SRS22716029,SRA1977341,"Patton Lab, Biological Sciences, Vanderbilt University","Patton Lab, Biological Sciences, Vanderbilt University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-09-23,Undetermined,Undetermined,Eye,Sensory System
33858,SRR30769783,SRX26172014,SRS22716031,SRP534198,PRJNA1164198,Analysis of The Senescence Secretome During Zebrafish Retina Regeneration,GSE277792,Transcriptome Analysis,Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with Müller glia serving as resident stem cells. Recently  we discovered that this process is aided by a population of damage induced senescent immune cells.  As part of the Senescence Associated Secretory Phenotype SASP  senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However  the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here  we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors post retina injury  including two distinct acute damage regimens  as well as a chronic  genetic model of retina degeneration. We discovered a 31 factor “Regeneration associated Senescence Signature” RASS that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated post damage. Among these  we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration post both acute and chronic retinal damage. Overall design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT 263 senolytic agents. Whole retinas were collected at 3  12  and 20 xxx post injury and samples were collected using Trizol based RNA extraction techniques.,,pubmed:40308558,,NMDA+Senolytic 3dpi Rep 3,GSM8530617,,source name:Retina|tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263|geo loc name:missing|collection date:missing,NMDA+Senolytic 3dpi Rep 3,Adapter sequences and low quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10  a wrapper for CutAdapt v4.8  using the   paired and   illumina parameters. Trimmed reads were quantified using Salmon v1.10.3 in quasi mapping mode with the optional paramaters   validateMappings and   gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome  with the primary assembly from the same release serving as decoys. Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0. Assembly: GRCz11.111 Supplementary files format and content: tab delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi mapping mode,Retina,,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263,GSM8530617,GSM8530617: NMDA+Senolytic 3dpi Rep 3; Danio rerio; RNA Seq,GSM8530617 r1,GSM8530617,1,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP534198,,,11384-GK-0006_S1_L005_R1_001.fastq.gz 11384-GK-0006_S1_L005_R2_001.fastq.gz,fastq fastq,21007284892.0,69560546.0,GSM8530617 r1,0:151 1:151,A:5599691886;C:4713794227;G:5216907301;T:5473147077;N:3744401,151,151,,,5599691886,4713794227,5216907301,5473147077,3744401,SRX26172014,SRS22716031,SRA1977341,"Patton Lab, Biological Sciences, Vanderbilt University","Patton Lab, Biological Sciences, Vanderbilt University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-09-23,Undetermined,Undetermined,Eye,Sensory System
33859,SRR30769784,SRX26172013,SRS22716027,SRP534198,PRJNA1164198,Analysis of The Senescence Secretome During Zebrafish Retina Regeneration,GSE277792,Transcriptome Analysis,Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with Müller glia serving as resident stem cells. Recently  we discovered that this process is aided by a population of damage induced senescent immune cells.  As part of the Senescence Associated Secretory Phenotype SASP  senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However  the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here  we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors post retina injury  including two distinct acute damage regimens  as well as a chronic  genetic model of retina degeneration. We discovered a 31 factor “Regeneration associated Senescence Signature” RASS that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated post damage. Among these  we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration post both acute and chronic retinal damage. Overall design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT 263 senolytic agents. Whole retinas were collected at 3  12  and 20 xxx post injury and samples were collected using Trizol based RNA extraction techniques.,,pubmed:40308558,,NMDA+Senolytic 3dpi Rep 2,GSM8530616,,source name:Retina|tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263|geo loc name:missing|collection date:missing,NMDA+Senolytic 3dpi Rep 2,Adapter sequences and low quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10  a wrapper for CutAdapt v4.8  using the   paired and   illumina parameters. Trimmed reads were quantified using Salmon v1.10.3 in quasi mapping mode with the optional paramaters   validateMappings and   gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome  with the primary assembly from the same release serving as decoys. Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0. Assembly: GRCz11.111 Supplementary files format and content: tab delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi mapping mode,Retina,,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263,GSM8530616,GSM8530616: NMDA+Senolytic 3dpi Rep 2; Danio rerio; RNA Seq,GSM8530616 r1,GSM8530616,1,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP534198,,,11384-GK-0005_S1_L005_R1_001.fastq.gz 11384-GK-0005_S1_L005_R2_001.fastq.gz,fastq fastq,21284313418.0,70477859.0,GSM8530616 r1,0:151 1:151,A:5662907550;C:4819337573;G:5250600393;T:5547505694;N:3962208,151,151,,,5662907550,4819337573,5250600393,5547505694,3962208,SRX26172013,SRS22716027,SRA1977341,"Patton Lab, Biological Sciences, Vanderbilt University","Patton Lab, Biological Sciences, Vanderbilt University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-09-23,Undetermined,Undetermined,Eye,Sensory System
33860,SRR30769785,SRX26172012,SRS22716026,SRP534198,PRJNA1164198,Analysis of The Senescence Secretome During Zebrafish Retina Regeneration,GSE277792,Transcriptome Analysis,Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with Müller glia serving as resident stem cells. Recently  we discovered that this process is aided by a population of damage induced senescent immune cells.  As part of the Senescence Associated Secretory Phenotype SASP  senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However  the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here  we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors post retina injury  including two distinct acute damage regimens  as well as a chronic  genetic model of retina degeneration. We discovered a 31 factor “Regeneration associated Senescence Signature” RASS that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated post damage. Among these  we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration post both acute and chronic retinal damage. Overall design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT 263 senolytic agents. Whole retinas were collected at 3  12  and 20 xxx post injury and samples were collected using Trizol based RNA extraction techniques.,,pubmed:40308558,,NMDA+Senolytic 3dpi Rep 1,GSM8530615,,source name:Retina|tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263|geo loc name:missing|collection date:missing,NMDA+Senolytic 3dpi Rep 1,Adapter sequences and low quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10  a wrapper for CutAdapt v4.8  using the   paired and   illumina parameters. Trimmed reads were quantified using Salmon v1.10.3 in quasi mapping mode with the optional paramaters   validateMappings and   gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome  with the primary assembly from the same release serving as decoys. Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0. Assembly: GRCz11.111 Supplementary files format and content: tab delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi mapping mode,Retina,,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,tissue:Retina|genotype:NMDA Damage|treatment:Metformin+ABT263,GSM8530615,GSM8530615: NMDA+Senolytic 3dpi Rep 1; Danio rerio; RNA Seq,GSM8530615 r1,GSM8530615,1,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP534198,,,11384-GK-0004_S1_L005_R1_001.fastq.gz 11384-GK-0004_S1_L005_R2_001.fastq.gz,fastq fastq,21278249862.0,70457781.0,GSM8530615 r1,0:151 1:151,A:5702525360;C:4765542588;G:5213022165;T:5593300201;N:3859548,151,151,,,5702525360,4765542588,5213022165,5593300201,3859548,SRX26172012,SRS22716026,SRA1977341,"Patton Lab, Biological Sciences, Vanderbilt University","Patton Lab, Biological Sciences, Vanderbilt University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-09-23,Undetermined,Undetermined,Eye,Sensory System
33861,SRR30769786,SRX26172011,SRS22716024,SRP534198,PRJNA1164198,Analysis of The Senescence Secretome During Zebrafish Retina Regeneration,GSE277792,Transcriptome Analysis,Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with Müller glia serving as resident stem cells. Recently  we discovered that this process is aided by a population of damage induced senescent immune cells.  As part of the Senescence Associated Secretory Phenotype SASP  senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However  the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here  we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors post retina injury  including two distinct acute damage regimens  as well as a chronic  genetic model of retina degeneration. We discovered a 31 factor “Regeneration associated Senescence Signature” RASS that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated post damage. Among these  we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration post both acute and chronic retinal damage. Overall design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT 263 senolytic agents. Whole retinas were collected at 3  12  and 20 xxx post injury and samples were collected using Trizol based RNA extraction techniques.,,pubmed:40308558,,NMDA Only 3dpi Rep 3,GSM8530614,,source name:Retina|tissue:Retina|genotype:NMDA Damage|treatment:Control|geo loc name:missing|collection date:missing,NMDA Only 3dpi Rep 3,Adapter sequences and low quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10  a wrapper for CutAdapt v4.8  using the   paired and   illumina parameters. Trimmed reads were quantified using Salmon v1.10.3 in quasi mapping mode with the optional paramaters   validateMappings and   gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome  with the primary assembly from the same release serving as decoys. Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0. Assembly: GRCz11.111 Supplementary files format and content: tab delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi mapping mode,Retina,,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,tissue:Retina|genotype:NMDA Damage|treatment:Control,GSM8530614,GSM8530614: NMDA Only 3dpi Rep 3; Danio rerio; RNA Seq,GSM8530614 r1,GSM8530614,1,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP534198,,,11384-GK-0003_S1_L005_R1_001.fastq.gz 11384-GK-0003_S1_L005_R2_001.fastq.gz,fastq fastq,15643493696.0,51799648.0,GSM8530614 r1,0:151 1:151,A:4146494742;C:3543481293;G:3863646000;T:4086984951;N:2886710,151,151,,,4146494742,3543481293,3863646000,4086984951,2886710,SRX26172011,SRS22716024,SRA1977341,"Patton Lab, Biological Sciences, Vanderbilt University","Patton Lab, Biological Sciences, Vanderbilt University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-09-23,Undetermined,Undetermined,Eye,Sensory System
33862,SRR30769787,SRX26172010,SRS22716025,SRP534198,PRJNA1164198,Analysis of The Senescence Secretome During Zebrafish Retina Regeneration,GSE277792,Transcriptome Analysis,Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with Müller glia serving as resident stem cells. Recently  we discovered that this process is aided by a population of damage induced senescent immune cells.  As part of the Senescence Associated Secretory Phenotype SASP  senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However  the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here  we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors post retina injury  including two distinct acute damage regimens  as well as a chronic  genetic model of retina degeneration. We discovered a 31 factor “Regeneration associated Senescence Signature” RASS that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated post damage. Among these  we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration post both acute and chronic retinal damage. Overall design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT 263 senolytic agents. Whole retinas were collected at 3  12  and 20 xxx post injury and samples were collected using Trizol based RNA extraction techniques.,,pubmed:40308558,,NMDA Only 3dpi Rep 2,GSM8530613,,source name:Retina|tissue:Retina|genotype:NMDA Damage|treatment:Control|geo loc name:missing|collection date:missing,NMDA Only 3dpi Rep 2,Adapter sequences and low quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10  a wrapper for CutAdapt v4.8  using the   paired and   illumina parameters. Trimmed reads were quantified using Salmon v1.10.3 in quasi mapping mode with the optional paramaters   validateMappings and   gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome  with the primary assembly from the same release serving as decoys. Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0. Assembly: GRCz11.111 Supplementary files format and content: tab delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi mapping mode,Retina,,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,tissue:Retina|genotype:NMDA Damage|treatment:Control,GSM8530613,GSM8530613: NMDA Only 3dpi Rep 2; Danio rerio; RNA Seq,GSM8530613 r1,GSM8530613,1,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP534198,,,11384-GK-0002_S1_L005_R1_001.fastq.gz 11384-GK-0002_S1_L005_R2_001.fastq.gz,fastq fastq,20806359158.0,68895229.0,GSM8530613 r1,0:151 1:151,A:5575454543;C:4587009803;G:5186849961;T:5453371159;N:3673692,151,151,,,5575454543,4587009803,5186849961,5453371159,3673692,SRX26172010,SRS22716025,SRA1977341,"Patton Lab, Biological Sciences, Vanderbilt University","Patton Lab, Biological Sciences, Vanderbilt University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-09-23,Undetermined,Undetermined,Eye,Sensory System
33863,SRR30769788,SRX26172009,SRS22716023,SRP534198,PRJNA1164198,Analysis of The Senescence Secretome During Zebrafish Retina Regeneration,GSE277792,Transcriptome Analysis,Zebrafish possess the innate ability to regenerate any lost or damaged retinal cell type with Müller glia serving as resident stem cells. Recently  we discovered that this process is aided by a population of damage induced senescent immune cells.  As part of the Senescence Associated Secretory Phenotype SASP  senescent cells secrete numerous factors that can play a role in the modulation of inflammation and remodeling of the retinal microenvironment during regeneration. However  the identity of specific SASP factors that drive initiation and progression of retina regeneration remain unclear. Here  we mined the SASP Atlas and RNAseq datasets to identify differentially expressed SASP factors post retina injury  including two distinct acute damage regimens  as well as a chronic  genetic model of retina degeneration. We discovered a 31 factor “Regeneration associated Senescence Signature” RASS that represents SASP factors and senescence markers that are conserved across all data sets and are upregulated post damage. Among these  we show that depletion of npm1a inhibits retina regeneration. Our data support the model that differential expression of SASP factors promotes regeneration post both acute and chronic retinal damage. Overall design: Adult AB zebrafish were injected with either NMDA damaging agent alone or in combination with Metformin and ABT 263 senolytic agents. Whole retinas were collected at 3  12  and 20 xxx post injury and samples were collected using Trizol based RNA extraction techniques.,,pubmed:40308558,,NMDA Only 3dpi Rep 1,GSM8530612,,source name:Retina|tissue:Retina|genotype:NMDA Damage|treatment:Control|geo loc name:missing|collection date:missing,NMDA Only 3dpi Rep 1,Adapter sequences and low quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10  a wrapper for CutAdapt v4.8  using the   paired and   illumina parameters. Trimmed reads were quantified using Salmon v1.10.3 in quasi mapping mode with the optional paramaters   validateMappings and   gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome  with the primary assembly from the same release serving as decoys. Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0. Assembly: GRCz11.111 Supplementary files format and content: tab delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi mapping mode,Retina,,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,tissue:Retina|genotype:NMDA Damage|treatment:Control,GSM8530612,GSM8530612: NMDA Only 3dpi Rep 1; Danio rerio; RNA Seq,GSM8530612 r1,GSM8530612,1,RNA was harvested using Trizol and Phenol chloroform extraction Libraries were prepared utilizing the stranded mRNA polyA selected library preparation kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP534198,,,11384-GK-0001_S1_L005_R1_001.fastq.gz 11384-GK-0001_S1_L005_R2_001.fastq.gz,fastq fastq,23410570088.0,77518444.0,GSM8530612 r1,0:151 1:151,A:6303961643;C:5167049097;G:5768221140;T:6167033748;N:4304460,151,151,,,6303961643,5167049097,5768221140,6167033748,4304460,SRX26172009,SRS22716023,SRA1977341,"Patton Lab, Biological Sciences, Vanderbilt University","Patton Lab, Biological Sciences, Vanderbilt University",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-09-23,Undetermined,Undetermined,Eye,Sensory System
39680,SRR2039721,SRX1038073,SRS945231,SRP058706,PRJNA284916,Cyp27c1 red shifts the spectral sensitivity of photoreceptors by converting vitamin A1 into A2,GSE69219,Other,The goal of this project was to identify the dehydrogenase enzyme that converts vitamin A1 into A2  resulting in red shifted spectral sensitivity of the visual system.  We conducted next generation sequencing of mRNA derived from the retinal pigment epithelium RPE of two animal models that use vitamin A2 as a chromophore to identify this enzyme. Zebrafish switch from vitamin A1 to A2 when treated with thyroid hormone  so we profiled the RPE from TH  and vehicle treated zebrafish n=3. The adult American bullfrog sequesters vitamin A2 within the dorsal part of the retina  but lacks vitamin A2 in the ventral retina. We therefore also profiled dorsal and ventral American bullfrog RPE n=3. Using this approach  we identified cytochrome p450 family member cyp27c1 as strongly enriched in both datasets  and determined through additional experiments that cyp27c1 is both necessary and sufficient for vitamin A2 production. Overall design: Differential gene expression analysis in TH treated vs. control zebrafish RPE and dorsal vs. ventral bullfrog RPE  conducted in triplicate,,pubmed:26549260,,zebrafish RPE V3,GSM1695527,,source name:retinal pigment epithelium RPE|treatment:Vehicle control|region of rpe:N/A|tissue:retinal pigment epithelium,zebrafish RPE V3,bullfrog de novo transcriptome assembly using Trinity version r2013 11 10 de novo transcritome assembly filtered to include only predicted open frames > 100 aa  trinity TransDecoder plugin bowtie libraries generated for bullfrog de novo transcriptome and previously published zebrafish transcriptome PLoS One  2013. 87: p. e67801 using bowtie build reads aligned to transcriptome using bowtie version 0.12.7 count table constructed from bowtie output file using custom perl script differential gene expression called using edgeR Genome build: bullfrog RPE Trinity.fasta included with this dataset  curated zebrafish transcriptome with cyp27 family transcripts added PLoS One  2013. 87: p. e67801  included with this dataset Supplementary files format and content: excel spreadsheets contain raw counts and RPKM for each transcript  as well as the output from edgeR Supplementary files format and content: fasta files contain the transcriptome assembly used for alignment of bullfrog and zebrafish sequencing data,retinal pigment epithelium RPE,,Zebrafish RPE was isolated by dissection  and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection  and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit  and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.,Zebrafish were treated for three weeks with TH or a vehicle control.,treatment:Vehicle control|region of rpe:N/A|tissue:retinal pigment epithelium,GSM1695527,GSM1695527: zebrafish RPE V3; Danio rerio; RNA Seq,GSM1695527,,1,Zebrafish RPE was isolated by dissection  and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection  and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit  and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.,GEO Accession:GSM1695527,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP058706,,,zebrafish_RPE_V3.fq.gz,fastq,1398879800.0,27977596.0,GSM1695527 r1,0:50,A:372827112;C:318907071;G:322799013;T:383834897;N:511707,50,,,,372827112,318907071,322799013,383834897,511707,SRX1038073,SRS945231,SRA269915,GEO,Washington University School of Medicine,1,0.86882,,0.25203,,0.75572,,0.65651,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2015-05-26,Undetermined,Undetermined,Eye,Sensory System
39681,SRR2039720,SRX1038072,SRS945232,SRP058706,PRJNA284916,Cyp27c1 red shifts the spectral sensitivity of photoreceptors by converting vitamin A1 into A2,GSE69219,Other,The goal of this project was to identify the dehydrogenase enzyme that converts vitamin A1 into A2  resulting in red shifted spectral sensitivity of the visual system.  We conducted next generation sequencing of mRNA derived from the retinal pigment epithelium RPE of two animal models that use vitamin A2 as a chromophore to identify this enzyme. Zebrafish switch from vitamin A1 to A2 when treated with thyroid hormone  so we profiled the RPE from TH  and vehicle treated zebrafish n=3. The adult American bullfrog sequesters vitamin A2 within the dorsal part of the retina  but lacks vitamin A2 in the ventral retina. We therefore also profiled dorsal and ventral American bullfrog RPE n=3. Using this approach  we identified cytochrome p450 family member cyp27c1 as strongly enriched in both datasets  and determined through additional experiments that cyp27c1 is both necessary and sufficient for vitamin A2 production. Overall design: Differential gene expression analysis in TH treated vs. control zebrafish RPE and dorsal vs. ventral bullfrog RPE  conducted in triplicate,,pubmed:26549260,,zebrafish RPE V2,GSM1695526,,source name:retinal pigment epithelium RPE|treatment:Vehicle control|region of rpe:N/A|tissue:retinal pigment epithelium,zebrafish RPE V2,bullfrog de novo transcriptome assembly using Trinity version r2013 11 10 de novo transcritome assembly filtered to include only predicted open frames > 100 aa  trinity TransDecoder plugin bowtie libraries generated for bullfrog de novo transcriptome and previously published zebrafish transcriptome PLoS One  2013. 87: p. e67801 using bowtie build reads aligned to transcriptome using bowtie version 0.12.7 count table constructed from bowtie output file using custom perl script differential gene expression called using edgeR Genome build: bullfrog RPE Trinity.fasta included with this dataset  curated zebrafish transcriptome with cyp27 family transcripts added PLoS One  2013. 87: p. e67801  included with this dataset Supplementary files format and content: excel spreadsheets contain raw counts and RPKM for each transcript  as well as the output from edgeR Supplementary files format and content: fasta files contain the transcriptome assembly used for alignment of bullfrog and zebrafish sequencing data,retinal pigment epithelium RPE,,Zebrafish RPE was isolated by dissection  and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection  and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit  and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.,Zebrafish were treated for three weeks with TH or a vehicle control.,treatment:Vehicle control|region of rpe:N/A|tissue:retinal pigment epithelium,GSM1695526,GSM1695526: zebrafish RPE V2; Danio rerio; RNA Seq,GSM1695526,,1,Zebrafish RPE was isolated by dissection  and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection  and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit  and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.,GEO Accession:GSM1695526,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP058706,,,zebrafish_RPE_V2.fq.gz,fastq,1424267450.0,28485349.0,GSM1695526 r1,0:50,A:384966484;C:318922158;G:323424610;T:396433148;N:521050,50,,,,384966484,318922158,323424610,396433148,521050,SRX1038072,SRS945232,SRA269915,GEO,Washington University School of Medicine,1,0.85592,,0.26231,,0.74614,,0.63068,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2015-05-26,Undetermined,Undetermined,Eye,Sensory System
39682,SRR2039719,SRX1038071,SRS945233,SRP058706,PRJNA284916,Cyp27c1 red shifts the spectral sensitivity of photoreceptors by converting vitamin A1 into A2,GSE69219,Other,The goal of this project was to identify the dehydrogenase enzyme that converts vitamin A1 into A2  resulting in red shifted spectral sensitivity of the visual system.  We conducted next generation sequencing of mRNA derived from the retinal pigment epithelium RPE of two animal models that use vitamin A2 as a chromophore to identify this enzyme. Zebrafish switch from vitamin A1 to A2 when treated with thyroid hormone  so we profiled the RPE from TH  and vehicle treated zebrafish n=3. The adult American bullfrog sequesters vitamin A2 within the dorsal part of the retina  but lacks vitamin A2 in the ventral retina. We therefore also profiled dorsal and ventral American bullfrog RPE n=3. Using this approach  we identified cytochrome p450 family member cyp27c1 as strongly enriched in both datasets  and determined through additional experiments that cyp27c1 is both necessary and sufficient for vitamin A2 production. Overall design: Differential gene expression analysis in TH treated vs. control zebrafish RPE and dorsal vs. ventral bullfrog RPE  conducted in triplicate,,pubmed:26549260,,zebrafish RPE V1,GSM1695525,,source name:retinal pigment epithelium RPE|treatment:Vehicle control|region of rpe:N/A|tissue:retinal pigment epithelium,zebrafish RPE V1,bullfrog de novo transcriptome assembly using Trinity version r2013 11 10 de novo transcritome assembly filtered to include only predicted open frames > 100 aa  trinity TransDecoder plugin bowtie libraries generated for bullfrog de novo transcriptome and previously published zebrafish transcriptome PLoS One  2013. 87: p. e67801 using bowtie build reads aligned to transcriptome using bowtie version 0.12.7 count table constructed from bowtie output file using custom perl script differential gene expression called using edgeR Genome build: bullfrog RPE Trinity.fasta included with this dataset  curated zebrafish transcriptome with cyp27 family transcripts added PLoS One  2013. 87: p. e67801  included with this dataset Supplementary files format and content: excel spreadsheets contain raw counts and RPKM for each transcript  as well as the output from edgeR Supplementary files format and content: fasta files contain the transcriptome assembly used for alignment of bullfrog and zebrafish sequencing data,retinal pigment epithelium RPE,,Zebrafish RPE was isolated by dissection  and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection  and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit  and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.,Zebrafish were treated for three weeks with TH or a vehicle control.,treatment:Vehicle control|region of rpe:N/A|tissue:retinal pigment epithelium,GSM1695525,GSM1695525: zebrafish RPE V1; Danio rerio; RNA Seq,GSM1695525,,1,Zebrafish RPE was isolated by dissection  and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection  and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit  and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.,GEO Accession:GSM1695525,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP058706,,,zebrafish_RPE_V1.fq.gz,fastq,1562666150.0,31253323.0,GSM1695525 r1,0:50,A:425809315;C:346680173;G:352748774;T:436855950;N:571938,50,,,,425809315,346680173,352748774,436855950,571938,SRX1038071,SRS945233,SRA269915,GEO,Washington University School of Medicine,1,0.8622,,0.24448,,0.74659,,0.63481,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2015-05-26,Undetermined,Undetermined,Eye,Sensory System
39683,SRR2039718,SRX1038070,SRS945234,SRP058706,PRJNA284916,Cyp27c1 red shifts the spectral sensitivity of photoreceptors by converting vitamin A1 into A2,GSE69219,Other,The goal of this project was to identify the dehydrogenase enzyme that converts vitamin A1 into A2  resulting in red shifted spectral sensitivity of the visual system.  We conducted next generation sequencing of mRNA derived from the retinal pigment epithelium RPE of two animal models that use vitamin A2 as a chromophore to identify this enzyme. Zebrafish switch from vitamin A1 to A2 when treated with thyroid hormone  so we profiled the RPE from TH  and vehicle treated zebrafish n=3. The adult American bullfrog sequesters vitamin A2 within the dorsal part of the retina  but lacks vitamin A2 in the ventral retina. We therefore also profiled dorsal and ventral American bullfrog RPE n=3. Using this approach  we identified cytochrome p450 family member cyp27c1 as strongly enriched in both datasets  and determined through additional experiments that cyp27c1 is both necessary and sufficient for vitamin A2 production. Overall design: Differential gene expression analysis in TH treated vs. control zebrafish RPE and dorsal vs. ventral bullfrog RPE  conducted in triplicate,,pubmed:26549260,,zebrafish RPE T3,GSM1695524,,source name:retinal pigment epithelium RPE|treatment:Thyroid horm1|region of rpe:N/A|tissue:retinal pigment epithelium,zebrafish RPE T3,bullfrog de novo transcriptome assembly using Trinity version r2013 11 10 de novo transcritome assembly filtered to include only predicted open frames > 100 aa  trinity TransDecoder plugin bowtie libraries generated for bullfrog de novo transcriptome and previously published zebrafish transcriptome PLoS One  2013. 87: p. e67801 using bowtie build reads aligned to transcriptome using bowtie version 0.12.7 count table constructed from bowtie output file using custom perl script differential gene expression called using edgeR Genome build: bullfrog RPE Trinity.fasta included with this dataset  curated zebrafish transcriptome with cyp27 family transcripts added PLoS One  2013. 87: p. e67801  included with this dataset Supplementary files format and content: excel spreadsheets contain raw counts and RPKM for each transcript  as well as the output from edgeR Supplementary files format and content: fasta files contain the transcriptome assembly used for alignment of bullfrog and zebrafish sequencing data,retinal pigment epithelium RPE,,Zebrafish RPE was isolated by dissection  and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection  and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit  and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.,Zebrafish were treated for three weeks with TH or a vehicle control.,treatment:Thyroid horm1|region of rpe:N/A|tissue:retinal pigment epithelium,GSM1695524,GSM1695524: zebrafish RPE T3; Danio rerio; RNA Seq,GSM1695524,,1,Zebrafish RPE was isolated by dissection  and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection  and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit  and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.,GEO Accession:GSM1695524,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP058706,,,zebrafish_RPE_T3.fq.gz,fastq,1384311250.0,27686225.0,GSM1695524 r1,0:50,A:365623713;C:318733172;G:322931194;T:376515371;N:507800,50,,,,365623713,318733172,322931194,376515371,507800,SRX1038070,SRS945234,SRA269915,GEO,Washington University School of Medicine,1,0.86222,,0.24783,,0.76124,,0.64632,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2015-05-26,Undetermined,Undetermined,Eye,Sensory System
39684,SRR2039717,SRX1038069,SRS945235,SRP058706,PRJNA284916,Cyp27c1 red shifts the spectral sensitivity of photoreceptors by converting vitamin A1 into A2,GSE69219,Other,The goal of this project was to identify the dehydrogenase enzyme that converts vitamin A1 into A2  resulting in red shifted spectral sensitivity of the visual system.  We conducted next generation sequencing of mRNA derived from the retinal pigment epithelium RPE of two animal models that use vitamin A2 as a chromophore to identify this enzyme. Zebrafish switch from vitamin A1 to A2 when treated with thyroid hormone  so we profiled the RPE from TH  and vehicle treated zebrafish n=3. The adult American bullfrog sequesters vitamin A2 within the dorsal part of the retina  but lacks vitamin A2 in the ventral retina. We therefore also profiled dorsal and ventral American bullfrog RPE n=3. Using this approach  we identified cytochrome p450 family member cyp27c1 as strongly enriched in both datasets  and determined through additional experiments that cyp27c1 is both necessary and sufficient for vitamin A2 production. Overall design: Differential gene expression analysis in TH treated vs. control zebrafish RPE and dorsal vs. ventral bullfrog RPE  conducted in triplicate,,pubmed:26549260,,zebrafish RPE T2,GSM1695523,,source name:retinal pigment epithelium RPE|treatment:Thyroid horm1|region of rpe:N/A|tissue:retinal pigment epithelium,zebrafish RPE T2,bullfrog de novo transcriptome assembly using Trinity version r2013 11 10 de novo transcritome assembly filtered to include only predicted open frames > 100 aa  trinity TransDecoder plugin bowtie libraries generated for bullfrog de novo transcriptome and previously published zebrafish transcriptome PLoS One  2013. 87: p. e67801 using bowtie build reads aligned to transcriptome using bowtie version 0.12.7 count table constructed from bowtie output file using custom perl script differential gene expression called using edgeR Genome build: bullfrog RPE Trinity.fasta included with this dataset  curated zebrafish transcriptome with cyp27 family transcripts added PLoS One  2013. 87: p. e67801  included with this dataset Supplementary files format and content: excel spreadsheets contain raw counts and RPKM for each transcript  as well as the output from edgeR Supplementary files format and content: fasta files contain the transcriptome assembly used for alignment of bullfrog and zebrafish sequencing data,retinal pigment epithelium RPE,,Zebrafish RPE was isolated by dissection  and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection  and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit  and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.,Zebrafish were treated for three weeks with TH or a vehicle control.,treatment:Thyroid horm1|region of rpe:N/A|tissue:retinal pigment epithelium,GSM1695523,GSM1695523: zebrafish RPE T2; Danio rerio; RNA Seq,GSM1695523,,1,Zebrafish RPE was isolated by dissection  and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection  and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit  and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.,GEO Accession:GSM1695523,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP058706,,,zebrafish_RPE_T2.fq.gz,fastq,1519161100.0,30383222.0,GSM1695523 r1,0:50,A:400594372;C:350805128;G:354718825;T:412492575;N:550200,50,,,,400594372,350805128,354718825,412492575,550200,SRX1038069,SRS945235,SRA269915,GEO,Washington University School of Medicine,1,0.86836,,0.26137,,0.75022,,0.60251,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2015-05-26,Undetermined,Undetermined,Eye,Sensory System
39685,SRR2039716,SRX1038068,SRS945236,SRP058706,PRJNA284916,Cyp27c1 red shifts the spectral sensitivity of photoreceptors by converting vitamin A1 into A2,GSE69219,Other,The goal of this project was to identify the dehydrogenase enzyme that converts vitamin A1 into A2  resulting in red shifted spectral sensitivity of the visual system.  We conducted next generation sequencing of mRNA derived from the retinal pigment epithelium RPE of two animal models that use vitamin A2 as a chromophore to identify this enzyme. Zebrafish switch from vitamin A1 to A2 when treated with thyroid hormone  so we profiled the RPE from TH  and vehicle treated zebrafish n=3. The adult American bullfrog sequesters vitamin A2 within the dorsal part of the retina  but lacks vitamin A2 in the ventral retina. We therefore also profiled dorsal and ventral American bullfrog RPE n=3. Using this approach  we identified cytochrome p450 family member cyp27c1 as strongly enriched in both datasets  and determined through additional experiments that cyp27c1 is both necessary and sufficient for vitamin A2 production. Overall design: Differential gene expression analysis in TH treated vs. control zebrafish RPE and dorsal vs. ventral bullfrog RPE  conducted in triplicate,,pubmed:26549260,,zebrafish RPE T1,GSM1695522,,source name:retinal pigment epithelium RPE|treatment:Thyroid horm1|region of rpe:N/A|tissue:retinal pigment epithelium,zebrafish RPE T1,bullfrog de novo transcriptome assembly using Trinity version r2013 11 10 de novo transcritome assembly filtered to include only predicted open frames > 100 aa  trinity TransDecoder plugin bowtie libraries generated for bullfrog de novo transcriptome and previously published zebrafish transcriptome PLoS One  2013. 87: p. e67801 using bowtie build reads aligned to transcriptome using bowtie version 0.12.7 count table constructed from bowtie output file using custom perl script differential gene expression called using edgeR Genome build: bullfrog RPE Trinity.fasta included with this dataset  curated zebrafish transcriptome with cyp27 family transcripts added PLoS One  2013. 87: p. e67801  included with this dataset Supplementary files format and content: excel spreadsheets contain raw counts and RPKM for each transcript  as well as the output from edgeR Supplementary files format and content: fasta files contain the transcriptome assembly used for alignment of bullfrog and zebrafish sequencing data,retinal pigment epithelium RPE,,Zebrafish RPE was isolated by dissection  and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection  and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit  and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.,Zebrafish were treated for three weeks with TH or a vehicle control.,treatment:Thyroid horm1|region of rpe:N/A|tissue:retinal pigment epithelium,GSM1695522,GSM1695522: zebrafish RPE T1; Danio rerio; RNA Seq,GSM1695522,,1,Zebrafish RPE was isolated by dissection  and RNA was collected using the RNeasy mini kit with DNase treatment step included. Bullfrog RPE was isolated by dissection  and RNA was isolated using phenol/chloroform extraction and treated with DNase. Zebrafish cDNA libraries were constructed using the NuGen Ovation RNA Seq System V2 kit and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq. Bullfrog RNA was depleted of rRNA using a Ribo Zero rRNA Removal Kit  and Illumina adapters were applied to allow for multiplex sequencing. All six samples were run in a single lane on an Illumin HI Seq.,GEO Accession:GSM1695522,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP058706,,,zebrafish_RPE_T1.fq.gz,fastq,805113700.0,16102274.0,GSM1695522 r1,0:50,A:218678280;C:181598232;G:182588099;T:221957441;N:291648,50,,,,218678280,181598232,182588099,221957441,291648,SRX1038068,SRS945236,SRA269915,GEO,Washington University School of Medicine,1,0.86363,,0.25795,,0.7334,,0.5942,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2015-05-26,Undetermined,Undetermined,Eye,Sensory System
61619,SRR12890232,SRX9355403,SRS7578437,SRP288489,PRJNA671696,DAPT dependent regulation of zebrafish Muller glial cell gene expression,GSE160047,Transcriptome Analysis,In this work we identify genes differentially expressed in Muller glia from uninjured retina in zebrafish treated with and without xxx for 1 day. Overall design: Triplicate samples from control DMSO treated and experimental DAPT treated gfap:GFP transgenic zebrafish.,parent bioproject:PRJNA672149,pubmed:34415582,,DAPT 3,GSM4855910,,tissue:Mueller Glia cells|treatment:DAPT,DAPT 3,Alignment with TopHat v2.0.13 and bowtie2 v2.2.1 with   b2 very sensitive htseq count v0.6.1 Genome build: danRer10 Supplementary files format and content: tab delimited text of raw counts,Mueller Glia cells,Fish were immersed in fish water containing DMSO or DAPT,One day post treatment  retinas were isolated  dissociated  and GFP+ Muller glia purified by FACS. RNA was isolated with Trizol. RNA libraries prepared using standard Illumina  protocols,Zebrafish were maintained in aquaria at 28 degrees centrigrade,treatment:DAPT,GSM4855910,GSM4855910: DAPT 3; Danio rerio; RNA Seq,GSM4855910,,1,One day post treatment  retinas were isolated  dissociated  and GFP+ Muller glia purified by FACS. RNA was isolated with Trizol. RNA libraries prepared using standard Illumina  protocols,GEO Accession:GSM4855910,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP288489,,,121570_TTGGACTC-GGAAGCAG_S6_L003_R1_001.fastq.gz,fastq,2901597825.0,56894075.0,GSM4855910 r1,0:51 1:0,A:802507169;C:650000584;G:646034561;T:802559439;N:496072,51,0,,,802507169,650000584,646034561,802559439,496072,SRX9355403,SRS7578437,SRA1147626,GEO,University of Michigan,1,0.89998,,0.17112,,0.73799,,0.45092,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-10-25,Undetermined,Undetermined,Eye,Sensory System
61620,SRR12890231,SRX9355402,SRS7578438,SRP288489,PRJNA671696,DAPT dependent regulation of zebrafish Muller glial cell gene expression,GSE160047,Transcriptome Analysis,In this work we identify genes differentially expressed in Muller glia from uninjured retina in zebrafish treated with and without xxx for 1 day. Overall design: Triplicate samples from control DMSO treated and experimental DAPT treated gfap:GFP transgenic zebrafish.,parent bioproject:PRJNA672149,pubmed:34415582,,DAPT 2,GSM4855909,,tissue:Mueller Glia cells|treatment:DAPT,DAPT 2,Alignment with TopHat v2.0.13 and bowtie2 v2.2.1 with   b2 very sensitive htseq count v0.6.1 Genome build: danRer10 Supplementary files format and content: tab delimited text of raw counts,Mueller Glia cells,Fish were immersed in fish water containing DMSO or DAPT,One day post treatment  retinas were isolated  dissociated  and GFP+ Muller glia purified by FACS. RNA was isolated with Trizol. RNA libraries prepared using standard Illumina  protocols,Zebrafish were maintained in aquaria at 28 degrees centrigrade,treatment:DAPT,GSM4855909,GSM4855909: DAPT 2; Danio rerio; RNA Seq,GSM4855909,,1,One day post treatment  retinas were isolated  dissociated  and GFP+ Muller glia purified by FACS. RNA was isolated with Trizol. RNA libraries prepared using standard Illumina  protocols,GEO Accession:GSM4855909,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP288489,,,121569_CCAAGTCT-AAGGATGA_S5_L003_R1_001.fastq.gz,fastq,3647882406.0,71527106.0,GSM4855909 r1,0:51 1:0,A:1008849046;C:817833961;G:810490148;T:1010074346;N:634905,51,0,,,1008849046,817833961,810490148,1010074346,634905,SRX9355402,SRS7578438,SRA1147626,GEO,University of Michigan,1,0.89982,,0.16575,,0.72951,,0.45464,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-10-25,Undetermined,Undetermined,Eye,Sensory System
61621,SRR12890230,SRX9355401,SRS7578436,SRP288489,PRJNA671696,DAPT dependent regulation of zebrafish Muller glial cell gene expression,GSE160047,Transcriptome Analysis,In this work we identify genes differentially expressed in Muller glia from uninjured retina in zebrafish treated with and without xxx for 1 day. Overall design: Triplicate samples from control DMSO treated and experimental DAPT treated gfap:GFP transgenic zebrafish.,parent bioproject:PRJNA672149,pubmed:34415582,,DAPT 1,GSM4855908,,tissue:Mueller Glia cells|treatment:DAPT,DAPT 1,Alignment with TopHat v2.0.13 and bowtie2 v2.2.1 with   b2 very sensitive htseq count v0.6.1 Genome build: danRer10 Supplementary files format and content: tab delimited text of raw counts,Mueller Glia cells,Fish were immersed in fish water containing DMSO or DAPT,One day post treatment  retinas were isolated  dissociated  and GFP+ Muller glia purified by FACS. RNA was isolated with Trizol. RNA libraries prepared using standard Illumina  protocols,Zebrafish were maintained in aquaria at 28 degrees centrigrade,treatment:DAPT,GSM4855908,GSM4855908: DAPT 1; Danio rerio; RNA Seq,GSM4855908,,1,One day post treatment  retinas were isolated  dissociated  and GFP+ Muller glia purified by FACS. RNA was isolated with Trizol. RNA libraries prepared using standard Illumina  protocols,GEO Accession:GSM4855908,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP288489,,,121568_CTCTCGTC-TATAACCT_S4_L003_R1_001.fastq.gz,fastq,3058754019.0,59975569.0,GSM4855908 r1,0:51 1:0,A:848297031;C:683744926;G:678559921;T:847620525;N:531616,51,0,,,848297031,683744926,678559921,847620525,531616,SRX9355401,SRS7578436,SRA1147626,GEO,University of Michigan,1,0.89817,,0.17371,,0.72665,,0.4669,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-10-25,Undetermined,Undetermined,Eye,Sensory System
61622,SRR12890229,SRX9355400,SRS7578434,SRP288489,PRJNA671696,DAPT dependent regulation of zebrafish Muller glial cell gene expression,GSE160047,Transcriptome Analysis,In this work we identify genes differentially expressed in Muller glia from uninjured retina in zebrafish treated with and without xxx for 1 day. Overall design: Triplicate samples from control DMSO treated and experimental DAPT treated gfap:GFP transgenic zebrafish.,parent bioproject:PRJNA672149,pubmed:34415582,,DMSO 3,GSM4855907,,tissue:Mueller Glia cells|treatment:DMSO,DMSO 3,Alignment with TopHat v2.0.13 and bowtie2 v2.2.1 with   b2 very sensitive htseq count v0.6.1 Genome build: danRer10 Supplementary files format and content: tab delimited text of raw counts,Mueller Glia cells,Fish were immersed in fish water containing DMSO or DAPT,One day post treatment  retinas were isolated  dissociated  and GFP+ Muller glia purified by FACS. RNA was isolated with Trizol. RNA libraries prepared using standard Illumina  protocols,Zebrafish were maintained in aquaria at 28 degrees centrigrade,treatment:DMSO,GSM4855907,GSM4855907: DMSO 3; Danio rerio; RNA Seq,GSM4855907,,1,One day post treatment  retinas were isolated  dissociated  and GFP+ Muller glia purified by FACS. RNA was isolated with Trizol. RNA libraries prepared using standard Illumina  protocols,GEO Accession:GSM4855907,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP288489,,,121567_TCTCTACT-CGCGGTTC_S3_L003_R1_001.fastq.gz,fastq,3443292132.0,67515532.0,GSM4855907 r1,0:51 1:0,A:957058450;C:767123229;G:759473336;T:959030874;N:606243,51,0,,,957058450,767123229,759473336,959030874,606243,SRX9355400,SRS7578434,SRA1147626,GEO,University of Michigan,1,0.89998,,0.18055,,0.72048,,0.47997,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-10-25,Undetermined,Undetermined,Eye,Sensory System
61623,SRR12890228,SRX9355399,SRS7578435,SRP288489,PRJNA671696,DAPT dependent regulation of zebrafish Muller glial cell gene expression,GSE160047,Transcriptome Analysis,In this work we identify genes differentially expressed in Muller glia from uninjured retina in zebrafish treated with and without xxx for 1 day. Overall design: Triplicate samples from control DMSO treated and experimental DAPT treated gfap:GFP transgenic zebrafish.,parent bioproject:PRJNA672149,pubmed:34415582,,DMSO 2,GSM4855906,,tissue:Mueller Glia cells|treatment:DMSO,DMSO 2,Alignment with TopHat v2.0.13 and bowtie2 v2.2.1 with   b2 very sensitive htseq count v0.6.1 Genome build: danRer10 Supplementary files format and content: tab delimited text of raw counts,Mueller Glia cells,Fish were immersed in fish water containing DMSO or DAPT,One day post treatment  retinas were isolated  dissociated  and GFP+ Muller glia purified by FACS. RNA was isolated with Trizol. RNA libraries prepared using standard Illumina  protocols,Zebrafish were maintained in aquaria at 28 degrees centrigrade,treatment:DMSO,GSM4855906,GSM4855906: DMSO 2; Danio rerio; RNA Seq,GSM4855906,,1,One day post treatment  retinas were isolated  dissociated  and GFP+ Muller glia purified by FACS. RNA was isolated with Trizol. RNA libraries prepared using standard Illumina  protocols,GEO Accession:GSM4855906,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP288489,,,121566_GACCTGAA-TTGGTGAG_S2_L003_R1_001.fastq.gz,fastq,3264529941.0,64010391.0,GSM4855906 r1,0:51 1:0,A:923700093;C:710395473;G:705063079;T:924792878;N:578418,51,0,,,923700093,710395473,705063079,924792878,578418,SRX9355399,SRS7578435,SRA1147626,GEO,University of Michigan,1,0.88907,,0.23013,,0.72123,,0.48896,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-10-25,Undetermined,Undetermined,Eye,Sensory System
61624,SRR12890227,SRX9355398,SRS7578433,SRP288489,PRJNA671696,DAPT dependent regulation of zebrafish Muller glial cell gene expression,GSE160047,Transcriptome Analysis,In this work we identify genes differentially expressed in Muller glia from uninjured retina in zebrafish treated with and without xxx for 1 day. Overall design: Triplicate samples from control DMSO treated and experimental DAPT treated gfap:GFP transgenic zebrafish.,parent bioproject:PRJNA672149,pubmed:34415582,,DMSO 1,GSM4855905,,tissue:Mueller Glia cells|treatment:DMSO,DMSO 1,Alignment with TopHat v2.0.13 and bowtie2 v2.2.1 with   b2 very sensitive htseq count v0.6.1 Genome build: danRer10 Supplementary files format and content: tab delimited text of raw counts,Mueller Glia cells,Fish were immersed in fish water containing DMSO or DAPT,One day post treatment  retinas were isolated  dissociated  and GFP+ Muller glia purified by FACS. RNA was isolated with Trizol. RNA libraries prepared using standard Illumina  protocols,Zebrafish were maintained in aquaria at 28 degrees centrigrade,treatment:DMSO,GSM4855905,GSM4855905: DMSO 1; Danio rerio; RNA Seq,GSM4855905,,1,One day post treatment  retinas were isolated  dissociated  and GFP+ Muller glia purified by FACS. RNA was isolated with Trizol. RNA libraries prepared using standard Illumina  protocols,GEO Accession:GSM4855905,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP288489,,,121565_AGTTCAGG-CCAACAGA_S1_L003_R1_001.fastq.gz,fastq,3286081521.0,64432971.0,GSM4855905 r1,0:51 1:0,A:929491040;C:715061853;G:711802428;T:929156880;N:569320,51,0,,,929491040,715061853,711802428,929156880,569320,SRX9355398,SRS7578433,SRA1147626,GEO,University of Michigan,1,0.88921,,0.21621,,0.72583,,0.47557,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-10-25,Undetermined,Undetermined,Eye,Sensory System
61625,SRR12892309,SRX9357451,SRS7580778,SRP288490,PRJNA671699,DN MAML dependent regulation of zebrafish Muller glial cell gene expression,GSE160051,Transcriptome Analysis,In this work we identify genes differentially expressed in Muller glia from uninjured retina in zebrafish treated with and without xxx MAML for 1 day. Overall design: Triplicate samples from control heat shock treated gfap:GFP transgenic zebrafish and heat shock treated gfap:GFP;hsp70:DN MAML transgenic zebrafish.,parent bioproject:PRJNA672149,pubmed:34415582,,uninj MAML HS MG3,GSM4859290,,tissue:Mueller glia cells|genotype/variation:gfap:GFP;hsp70:DN MAML,uninj MAML HS MG3,Alignment with STAR v2.6.1b Count estimates with RSEM v1.3.1 Genome build: danRer11 Supplementary files format and content: tab delimited text of raw counts,Mueller glia cells,Fish received a 1 hour heat shock at 37 degrees centrigrade  every 6 hours for a 24 hour period.,One day post treatment  retinas were isolated  dissociated  and GFP+ Muller glia purified by FACS. RNA was isolated with Trizol. RNA libraries prepared using standard Illumina  protocols,Zebrafish were maintained in aquaria at 28 degrees centrigrade,genotype/variation:gfap:GFP;hsp70:DN MAML,GSM4859290,GSM4859290: uninj MAML HS MG3; Danio rerio; RNA Seq,GSM4859290,,1,One day post treatment  retinas were isolated  dissociated  and GFP+ Muller glia purified by FACS. RNA was isolated with Trizol. RNA libraries prepared using standard Illumina  protocols,GEO Accession:GSM4859290,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP288490,,,128298_ACCTTGGC-GGCCTCAT_S95_R1_001.fastq.gz 128298_ACCTTGGC-GGCCTCAT_S95_R2_001.fastq.gz,fastq fastq,11304585438.0,110829269.0,GSM4859290 r1,0:51 1:51,A:3120893883;C:2553158451;G:2535848779;T:3094615308;N:69017,51,51,,,3120893883,2553158451,2535848779,3094615308,69017,SRX9357451,SRS7580778,SRA1147632,GEO,University of Michigan,2,0.90996,0.90778,0.16923,0.16894,0.71496,0.71565,0.47014,0.46624,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-10-25,Undetermined,Undetermined,Eye,Sensory System
61626,SRR12892308,SRX9357450,SRS7580777,SRP288490,PRJNA671699,DN MAML dependent regulation of zebrafish Muller glial cell gene expression,GSE160051,Transcriptome Analysis,In this work we identify genes differentially expressed in Muller glia from uninjured retina in zebrafish treated with and without xxx MAML for 1 day. Overall design: Triplicate samples from control heat shock treated gfap:GFP transgenic zebrafish and heat shock treated gfap:GFP;hsp70:DN MAML transgenic zebrafish.,parent bioproject:PRJNA672149,pubmed:34415582,,uninj MAML HS MG2,GSM4859289,,tissue:Mueller glia cells|genotype/variation:gfap:GFP;hsp70:DN MAML,uninj MAML HS MG2,Alignment with STAR v2.6.1b Count estimates with RSEM v1.3.1 Genome build: danRer11 Supplementary files format and content: tab delimited text of raw counts,Mueller glia cells,Fish received a 1 hour heat shock at 37 degrees centrigrade  every 6 hours for a 24 hour period.,One day post treatment  retinas were isolated  dissociated  and GFP+ Muller glia purified by FACS. RNA was isolated with Trizol. RNA libraries prepared using standard Illumina  protocols,Zebrafish were maintained in aquaria at 28 degrees centrigrade,genotype/variation:gfap:GFP;hsp70:DN MAML,GSM4859289,GSM4859289: uninj MAML HS MG2; Danio rerio; RNA Seq,GSM4859289,,1,One day post treatment  retinas were isolated  dissociated  and GFP+ Muller glia purified by FACS. RNA was isolated with Trizol. RNA libraries prepared using standard Illumina  protocols,GEO Accession:GSM4859289,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP288490,,,128297_GTTCCAAT-AATTCTGC_S94_R1_001.fastq.gz 128297_GTTCCAAT-AATTCTGC_S94_R2_001.fastq.gz,fastq fastq,16253506098.0,159348099.0,GSM4859289 r1,0:51 1:51,A:4552341347;C:3604463399;G:3574350555;T:4522248115;N:102682,51,51,,,4552341347,3604463399,3574350555,4522248115,102682,SRX9357450,SRS7580777,SRA1147632,GEO,University of Michigan,2,0.92937,0.92879,0.21013,0.21006,0.7024,0.70343,0.46032,0.46249,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-10-25,Undetermined,Undetermined,Eye,Sensory System
61627,SRR12892307,SRX9357449,SRS7580774,SRP288490,PRJNA671699,DN MAML dependent regulation of zebrafish Muller glial cell gene expression,GSE160051,Transcriptome Analysis,In this work we identify genes differentially expressed in Muller glia from uninjured retina in zebrafish treated with and without xxx MAML for 1 day. Overall design: Triplicate samples from control heat shock treated gfap:GFP transgenic zebrafish and heat shock treated gfap:GFP;hsp70:DN MAML transgenic zebrafish.,parent bioproject:PRJNA672149,pubmed:34415582,,uninj MAML HS MG1,GSM4859288,,tissue:Mueller glia cells|genotype/variation:gfap:GFP;hsp70:DN MAML,uninj MAML HS MG1,Alignment with STAR v2.6.1b Count estimates with RSEM v1.3.1 Genome build: danRer11 Supplementary files format and content: tab delimited text of raw counts,Mueller glia cells,Fish received a 1 hour heat shock at 37 degrees centrigrade  every 6 hours for a 24 hour period.,One day post treatment  retinas were isolated  dissociated  and GFP+ Muller glia purified by FACS. RNA was isolated with Trizol. RNA libraries prepared using standard Illumina  protocols,Zebrafish were maintained in aquaria at 28 degrees centrigrade,genotype/variation:gfap:GFP;hsp70:DN MAML,GSM4859288,GSM4859288: uninj MAML HS MG1; Danio rerio; RNA Seq,GSM4859288,,1,One day post treatment  retinas were isolated  dissociated  and GFP+ Muller glia purified by FACS. RNA was isolated with Trizol. RNA libraries prepared using standard Illumina  protocols,GEO Accession:GSM4859288,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP288490,,,128296_GCAATGCA-GGAACGTT_S93_R1_001.fastq.gz 128296_GCAATGCA-GGAACGTT_S93_R2_001.fastq.gz,fastq fastq,11640710220.0,114124610.0,GSM4859288 r1,0:51 1:51,A:3231432736;C:2614327875;G:2598832880;T:3196044849;N:71880,51,51,,,3231432736,2614327875,2598832880,3196044849,71880,SRX9357449,SRS7580774,SRA1147632,GEO,University of Michigan,2,0.93459,0.9331,0.16634,0.16587,0.70467,0.70364,0.4641,0.47067,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-10-25,Undetermined,Undetermined,Eye,Sensory System
61628,SRR12892306,SRX9357448,SRS7580776,SRP288490,PRJNA671699,DN MAML dependent regulation of zebrafish Muller glial cell gene expression,GSE160051,Transcriptome Analysis,In this work we identify genes differentially expressed in Muller glia from uninjured retina in zebrafish treated with and without xxx MAML for 1 day. Overall design: Triplicate samples from control heat shock treated gfap:GFP transgenic zebrafish and heat shock treated gfap:GFP;hsp70:DN MAML transgenic zebrafish.,parent bioproject:PRJNA672149,pubmed:34415582,,uninj HS MG3,GSM4859287,,tissue:Mueller glia cells|genotype/variation:gfap:GFP transgenic,uninj HS MG3,Alignment with STAR v2.6.1b Count estimates with RSEM v1.3.1 Genome build: danRer11 Supplementary files format and content: tab delimited text of raw counts,Mueller glia cells,Fish received a 1 hour heat shock at 37 degrees centrigrade  every 6 hours for a 24 hour period.,One day post treatment  retinas were isolated  dissociated  and GFP+ Muller glia purified by FACS. RNA was isolated with Trizol. RNA libraries prepared using standard Illumina  protocols,Zebrafish were maintained in aquaria at 28 degrees centrigrade,genotype/variation:gfap:GFP transgenic,GSM4859287,GSM4859287: uninj HS MG3; Danio rerio; RNA Seq,GSM4859287,,1,One day post treatment  retinas were isolated  dissociated  and GFP+ Muller glia purified by FACS. RNA was isolated with Trizol. RNA libraries prepared using standard Illumina  protocols,GEO Accession:GSM4859287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP288490,,,128295_ATGGCATG-AAGGTACC_S92_R1_001.fastq.gz 128295_ATGGCATG-AAGGTACC_S92_R2_001.fastq.gz,fastq fastq,15027240780.0,147325890.0,GSM4859287 r1,0:51 1:51,A:4223415769;C:3311166178;G:3302916926;T:4189645819;N:96088,51,51,,,4223415769,3311166178,3302916926,4189645819,96088,SRX9357448,SRS7580776,SRA1147632,GEO,University of Michigan,2,0.93194,0.92948,0.21634,0.21516,0.71303,0.71607,0.46322,0.46154,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-10-25,Undetermined,Undetermined,Eye,Sensory System
61629,SRR12892305,SRX9357447,SRS7580775,SRP288490,PRJNA671699,DN MAML dependent regulation of zebrafish Muller glial cell gene expression,GSE160051,Transcriptome Analysis,In this work we identify genes differentially expressed in Muller glia from uninjured retina in zebrafish treated with and without xxx MAML for 1 day. Overall design: Triplicate samples from control heat shock treated gfap:GFP transgenic zebrafish and heat shock treated gfap:GFP;hsp70:DN MAML transgenic zebrafish.,parent bioproject:PRJNA672149,pubmed:34415582,,uninj HS MG2,GSM4859286,,tissue:Mueller glia cells|genotype/variation:gfap:GFP transgenic,uninj HS MG2,Alignment with STAR v2.6.1b Count estimates with RSEM v1.3.1 Genome build: danRer11 Supplementary files format and content: tab delimited text of raw counts,Mueller glia cells,Fish received a 1 hour heat shock at 37 degrees centrigrade  every 6 hours for a 24 hour period.,One day post treatment  retinas were isolated  dissociated  and GFP+ Muller glia purified by FACS. RNA was isolated with Trizol. RNA libraries prepared using standard Illumina  protocols,Zebrafish were maintained in aquaria at 28 degrees centrigrade,genotype/variation:gfap:GFP transgenic,GSM4859286,GSM4859286: uninj HS MG2; Danio rerio; RNA Seq,GSM4859286,,1,One day post treatment  retinas were isolated  dissociated  and GFP+ Muller glia purified by FACS. RNA was isolated with Trizol. RNA libraries prepared using standard Illumina  protocols,GEO Accession:GSM4859286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP288490,,,128294_GGAGCGTC-GTCCGTGC_S91_R1_001.fastq.gz 128294_GGAGCGTC-GTCCGTGC_S91_R2_001.fastq.gz,fastq fastq,13937272860.0,136639930.0,GSM4859286 r1,0:51 1:51,A:3870514089;C:3125765850;G:3103028736;T:3837876483;N:87702,51,51,,,3870514089,3125765850,3103028736,3837876483,87702,SRX9357447,SRS7580775,SRA1147632,GEO,University of Michigan,2,0.93217,0.93085,0.18039,0.18003,0.71612,0.7177,0.45988,0.45871,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-10-25,Undetermined,Undetermined,Eye,Sensory System
61630,SRR12892304,SRX9357446,SRS7580773,SRP288490,PRJNA671699,DN MAML dependent regulation of zebrafish Muller glial cell gene expression,GSE160051,Transcriptome Analysis,In this work we identify genes differentially expressed in Muller glia from uninjured retina in zebrafish treated with and without xxx MAML for 1 day. Overall design: Triplicate samples from control heat shock treated gfap:GFP transgenic zebrafish and heat shock treated gfap:GFP;hsp70:DN MAML transgenic zebrafish.,parent bioproject:PRJNA672149,pubmed:34415582,,uninj HS MG1,GSM4859285,,tissue:Mueller glia cells|genotype/variation:gfap:GFP transgenic,uninj HS MG1,Alignment with STAR v2.6.1b Count estimates with RSEM v1.3.1 Genome build: danRer11 Supplementary files format and content: tab delimited text of raw counts,Mueller glia cells,Fish received a 1 hour heat shock at 37 degrees centrigrade  every 6 hours for a 24 hour period.,One day post treatment  retinas were isolated  dissociated  and GFP+ Muller glia purified by FACS. RNA was isolated with Trizol. RNA libraries prepared using standard Illumina  protocols,Zebrafish were maintained in aquaria at 28 degrees centrigrade,genotype/variation:gfap:GFP transgenic,GSM4859285,GSM4859285: uninj HS MG1; Danio rerio; RNA Seq,GSM4859285,,1,One day post treatment  retinas were isolated  dissociated  and GFP+ Muller glia purified by FACS. RNA was isolated with Trizol. RNA libraries prepared using standard Illumina  protocols,GEO Accession:GSM4859285,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP288490,,,128293_AAGATACT-ACTTACAT_S90_R1_001.fastq.gz 128293_AAGATACT-ACTTACAT_S90_R2_001.fastq.gz,fastq fastq,15386698674.0,150849987.0,GSM4859285 r1,0:51 1:51,A:4316453490;C:3400011671;G:3382273332;T:4287862448;N:97733,51,51,,,4316453490,3400011671,3382273332,4287862448,97733,SRX9357446,SRS7580773,SRA1147632,GEO,University of Michigan,2,0.92975,0.92816,0.2114,0.21184,0.719,0.71973,0.46141,0.46428,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-10-25,Undetermined,Undetermined,Eye,Sensory System
64991,SRR14883467,SRX11200547,SRS9255526,SRP325167,PRJNA740056,Transcriptome RNA seq analysis of the retina of crumbs 2a crb2a m289/m289 zebrafish model of Leber congenital amaurosis and retinitis pigmentosa.,GSE178709,Transcriptome Analysis,The crumbs cell polarity complex plays a crucial role in apical basal epithelial polarity. When human CRB1 is mutated  it results in autosomal recessive Leber congenital amaurosis and retinitis pigmentosa  with no established genotype phenotype correlation. Using the oko meduzym289/m289 crb2a /  zebrafish model  we performed integrative transcriptomic and methylomic analysis to identify dysregulated genes and pathways. We reveal delayed retinal cell type specification confirmed in patient derived retinal organoids  with disruption to cell cycle modulation and epigenetic transcriptional control. Hence  using reduced representation bisulphite sequencing RRBS we explored differential DNA methylation  identifying hypermethylated pathways involving biological adhesion  Hippo and transforming growth factor beta TGFbeta signalling. Functional epigenetic modules FEM were highlighted through the integration of RNA seq and RRBS  confirming cell cycle involvement and disturbance of TGFbeta  BMP  Hippo and SMAD protein signal transduction. Taken together our work provides insights for epigenetic regulation in early retinal development and considerations for future therapeutic development. Overall design: We used RNA seq to identify differentially expressed genes between the zebrafish model of CRB  crb2a m289. Samples were isolated retinal regions of the dorsal retina at 56 hpf; crb2a /  and control wildtype. Biological replicates were taken.,,pubmed:36656098,,wildtype retina rep 5 [R56 WT05],GSM5396388,,source name:wildtype retina|genotype:wildtype A/B|hpf:56|tissue:dorsal retina,wildtype retina rep 5 [R56 WT05],Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using trimgalore Reads were aligned to the genome and transcriptome using HISAT2 v2.2.1 using using standard paired end based parameters. Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates Count files were created using featurecounts v2 and modelled using DESeq2 v1.30.1 Genome build: GRCz11 Supplementary files format and content: tab delimited text files include raw count values for each sample,wildtype retina,,RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols,zebrafish were harvested at appropriate time points hpf  retinal regions dissected,genotype:wildtype A/B|hpf:56|tissue:dorsal retina,GSM5396388,GSM5396388: wildtype retina rep 5 [R56 WT05]; Danio rerio; RNA Seq,GSM5396388,,1,RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols,GEO Accession:GSM5396388,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP325167,,,R56-WT05_R1.fastq.gz R56-WT05_R2.fastq.gz,fastq fastq,3021678200.0,15108391.0,GSM5396388 r1,0:100 1:100,A:842653749;C:670303060;G:690387728;T:815456479;N:2877184,100,100,,,842653749,670303060,690387728,815456479,2877184,SRX11200547,SRS9255526,SRA1249569,GEO,"Institute of Ophthalmology, UCL",2,0.94619,0.94625,0.15092,0.15062,0.74647,0.74836,0.48911,0.4957,100,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2021-06-22,Undetermined,Undetermined,Eye,Sensory System
64992,SRR14883466,SRX11200546,SRS9255524,SRP325167,PRJNA740056,Transcriptome RNA seq analysis of the retina of crumbs 2a crb2a m289/m289 zebrafish model of Leber congenital amaurosis and retinitis pigmentosa.,GSE178709,Transcriptome Analysis,The crumbs cell polarity complex plays a crucial role in apical basal epithelial polarity. When human CRB1 is mutated  it results in autosomal recessive Leber congenital amaurosis and retinitis pigmentosa  with no established genotype phenotype correlation. Using the oko meduzym289/m289 crb2a /  zebrafish model  we performed integrative transcriptomic and methylomic analysis to identify dysregulated genes and pathways. We reveal delayed retinal cell type specification confirmed in patient derived retinal organoids  with disruption to cell cycle modulation and epigenetic transcriptional control. Hence  using reduced representation bisulphite sequencing RRBS we explored differential DNA methylation  identifying hypermethylated pathways involving biological adhesion  Hippo and transforming growth factor beta TGFbeta signalling. Functional epigenetic modules FEM were highlighted through the integration of RNA seq and RRBS  confirming cell cycle involvement and disturbance of TGFbeta  BMP  Hippo and SMAD protein signal transduction. Taken together our work provides insights for epigenetic regulation in early retinal development and considerations for future therapeutic development. Overall design: We used RNA seq to identify differentially expressed genes between the zebrafish model of CRB  crb2a m289. Samples were isolated retinal regions of the dorsal retina at 56 hpf; crb2a /  and control wildtype. Biological replicates were taken.,,pubmed:36656098,,wildtype retina rep 4 [R56 WT04],GSM5396387,,source name:wildtype retina|genotype:wildtype A/B|hpf:56|tissue:dorsal retina,wildtype retina rep 4 [R56 WT04],Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using trimgalore Reads were aligned to the genome and transcriptome using HISAT2 v2.2.1 using using standard paired end based parameters. Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates Count files were created using featurecounts v2 and modelled using DESeq2 v1.30.1 Genome build: GRCz11 Supplementary files format and content: tab delimited text files include raw count values for each sample,wildtype retina,,RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols,zebrafish were harvested at appropriate time points hpf  retinal regions dissected,genotype:wildtype A/B|hpf:56|tissue:dorsal retina,GSM5396387,GSM5396387: wildtype retina rep 4 [R56 WT04]; Danio rerio; RNA Seq,GSM5396387,,1,RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols,GEO Accession:GSM5396387,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP325167,,,R56-WT04_R1.fastq.gz R56-WT04_R2.fastq.gz,fastq fastq,2575355000.0,12876775.0,GSM5396387 r1,0:100 1:100,A:719372734;C:569208001;G:591353722;T:692825451;N:2595092,100,100,,,719372734,569208001,591353722,692825451,2595092,SRX11200546,SRS9255524,SRA1249569,GEO,"Institute of Ophthalmology, UCL",2,0.94198,0.94214,0.14241,0.14231,0.74462,0.74572,0.48739,0.4875,100,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2021-06-22,Undetermined,Undetermined,Eye,Sensory System
64993,SRR14883465,SRX11200545,SRS9255525,SRP325167,PRJNA740056,Transcriptome RNA seq analysis of the retina of crumbs 2a crb2a m289/m289 zebrafish model of Leber congenital amaurosis and retinitis pigmentosa.,GSE178709,Transcriptome Analysis,The crumbs cell polarity complex plays a crucial role in apical basal epithelial polarity. When human CRB1 is mutated  it results in autosomal recessive Leber congenital amaurosis and retinitis pigmentosa  with no established genotype phenotype correlation. Using the oko meduzym289/m289 crb2a /  zebrafish model  we performed integrative transcriptomic and methylomic analysis to identify dysregulated genes and pathways. We reveal delayed retinal cell type specification confirmed in patient derived retinal organoids  with disruption to cell cycle modulation and epigenetic transcriptional control. Hence  using reduced representation bisulphite sequencing RRBS we explored differential DNA methylation  identifying hypermethylated pathways involving biological adhesion  Hippo and transforming growth factor beta TGFbeta signalling. Functional epigenetic modules FEM were highlighted through the integration of RNA seq and RRBS  confirming cell cycle involvement and disturbance of TGFbeta  BMP  Hippo and SMAD protein signal transduction. Taken together our work provides insights for epigenetic regulation in early retinal development and considerations for future therapeutic development. Overall design: We used RNA seq to identify differentially expressed genes between the zebrafish model of CRB  crb2a m289. Samples were isolated retinal regions of the dorsal retina at 56 hpf; crb2a /  and control wildtype. Biological replicates were taken.,,pubmed:36656098,,wildtype retina rep 3 [R56 WT03],GSM5396386,,source name:wildtype retina|genotype:wildtype A/B|hpf:56|tissue:dorsal retina,wildtype retina rep 3 [R56 WT03],Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using trimgalore Reads were aligned to the genome and transcriptome using HISAT2 v2.2.1 using using standard paired end based parameters. Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates Count files were created using featurecounts v2 and modelled using DESeq2 v1.30.1 Genome build: GRCz11 Supplementary files format and content: tab delimited text files include raw count values for each sample,wildtype retina,,RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols,zebrafish were harvested at appropriate time points hpf  retinal regions dissected,genotype:wildtype A/B|hpf:56|tissue:dorsal retina,GSM5396386,GSM5396386: wildtype retina rep 3 [R56 WT03]; Danio rerio; RNA Seq,GSM5396386,,1,RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols,GEO Accession:GSM5396386,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP325167,,,R56-WT03_R1.fastq.gz R56-WT03_R2.fastq.gz,fastq fastq,2836655800.0,14183279.0,GSM5396386 r1,0:100 1:100,A:796999987;C:622654837;G:648405815;T:765641148;N:2954013,100,100,,,796999987,622654837,648405815,765641148,2954013,SRX11200545,SRS9255525,SRA1249569,GEO,"Institute of Ophthalmology, UCL",2,0.94063,0.94078,0.15658,0.15536,0.74406,0.74523,0.49509,0.49589,100,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2021-06-22,Undetermined,Undetermined,Eye,Sensory System
64994,SRR14883464,SRX11200544,SRS9255523,SRP325167,PRJNA740056,Transcriptome RNA seq analysis of the retina of crumbs 2a crb2a m289/m289 zebrafish model of Leber congenital amaurosis and retinitis pigmentosa.,GSE178709,Transcriptome Analysis,The crumbs cell polarity complex plays a crucial role in apical basal epithelial polarity. When human CRB1 is mutated  it results in autosomal recessive Leber congenital amaurosis and retinitis pigmentosa  with no established genotype phenotype correlation. Using the oko meduzym289/m289 crb2a /  zebrafish model  we performed integrative transcriptomic and methylomic analysis to identify dysregulated genes and pathways. We reveal delayed retinal cell type specification confirmed in patient derived retinal organoids  with disruption to cell cycle modulation and epigenetic transcriptional control. Hence  using reduced representation bisulphite sequencing RRBS we explored differential DNA methylation  identifying hypermethylated pathways involving biological adhesion  Hippo and transforming growth factor beta TGFbeta signalling. Functional epigenetic modules FEM were highlighted through the integration of RNA seq and RRBS  confirming cell cycle involvement and disturbance of TGFbeta  BMP  Hippo and SMAD protein signal transduction. Taken together our work provides insights for epigenetic regulation in early retinal development and considerations for future therapeutic development. Overall design: We used RNA seq to identify differentially expressed genes between the zebrafish model of CRB  crb2a m289. Samples were isolated retinal regions of the dorsal retina at 56 hpf; crb2a /  and control wildtype. Biological replicates were taken.,,pubmed:36656098,,wildtype retina rep 2 [R56 WT02],GSM5396385,,source name:wildtype retina|genotype:wildtype A/B|hpf:56|tissue:dorsal retina,wildtype retina rep 2 [R56 WT02],Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using trimgalore Reads were aligned to the genome and transcriptome using HISAT2 v2.2.1 using using standard paired end based parameters. Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates Count files were created using featurecounts v2 and modelled using DESeq2 v1.30.1 Genome build: GRCz11 Supplementary files format and content: tab delimited text files include raw count values for each sample,wildtype retina,,RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols,zebrafish were harvested at appropriate time points hpf  retinal regions dissected,genotype:wildtype A/B|hpf:56|tissue:dorsal retina,GSM5396385,GSM5396385: wildtype retina rep 2 [R56 WT02]; Danio rerio; RNA Seq,GSM5396385,,1,RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols,GEO Accession:GSM5396385,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP325167,,,R56-WT02_R1.fastq.gz R56-WT02_R2.fastq.gz,fastq fastq,2736567000.0,13682835.0,GSM5396385 r1,0:100 1:100,A:774624618;C:594658601;G:615415962;T:749131027;N:2736792,100,100,,,774624618,594658601,615415962,749131027,2736792,SRX11200544,SRS9255523,SRA1249569,GEO,"Institute of Ophthalmology, UCL",2,0.93365,0.93451,0.17399,0.17557,0.74237,0.74483,0.51877,0.50425,100,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2021-06-22,Undetermined,Undetermined,Eye,Sensory System
64995,SRR14883463,SRX11200543,SRS9255522,SRP325167,PRJNA740056,Transcriptome RNA seq analysis of the retina of crumbs 2a crb2a m289/m289 zebrafish model of Leber congenital amaurosis and retinitis pigmentosa.,GSE178709,Transcriptome Analysis,The crumbs cell polarity complex plays a crucial role in apical basal epithelial polarity. When human CRB1 is mutated  it results in autosomal recessive Leber congenital amaurosis and retinitis pigmentosa  with no established genotype phenotype correlation. Using the oko meduzym289/m289 crb2a /  zebrafish model  we performed integrative transcriptomic and methylomic analysis to identify dysregulated genes and pathways. We reveal delayed retinal cell type specification confirmed in patient derived retinal organoids  with disruption to cell cycle modulation and epigenetic transcriptional control. Hence  using reduced representation bisulphite sequencing RRBS we explored differential DNA methylation  identifying hypermethylated pathways involving biological adhesion  Hippo and transforming growth factor beta TGFbeta signalling. Functional epigenetic modules FEM were highlighted through the integration of RNA seq and RRBS  confirming cell cycle involvement and disturbance of TGFbeta  BMP  Hippo and SMAD protein signal transduction. Taken together our work provides insights for epigenetic regulation in early retinal development and considerations for future therapeutic development. Overall design: We used RNA seq to identify differentially expressed genes between the zebrafish model of CRB  crb2a m289. Samples were isolated retinal regions of the dorsal retina at 56 hpf; crb2a /  and control wildtype. Biological replicates were taken.,,pubmed:36656098,,wildtype retina rep 1 [R56 WT01],GSM5396384,,source name:wildtype retina|genotype:wildtype A/B|hpf:56|tissue:dorsal retina,wildtype retina rep 1 [R56 WT01],Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using trimgalore Reads were aligned to the genome and transcriptome using HISAT2 v2.2.1 using using standard paired end based parameters. Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates Count files were created using featurecounts v2 and modelled using DESeq2 v1.30.1 Genome build: GRCz11 Supplementary files format and content: tab delimited text files include raw count values for each sample,wildtype retina,,RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols,zebrafish were harvested at appropriate time points hpf  retinal regions dissected,genotype:wildtype A/B|hpf:56|tissue:dorsal retina,GSM5396384,GSM5396384: wildtype retina rep 1 [R56 WT01]; Danio rerio; RNA Seq,GSM5396384,,1,RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols,GEO Accession:GSM5396384,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP325167,,,R56-WT01_R1.fastq.gz R56-WT01_R2.fastq.gz,fastq fastq,2657160200.0,13285801.0,GSM5396384 r1,0:100 1:100,A:783255245;C:545277836;G:561089398;T:764970589;N:2567132,100,100,,,783255245,545277836,561089398,764970589,2567132,SRX11200543,SRS9255522,SRA1249569,GEO,"Institute of Ophthalmology, UCL",2,0.89394,0.89321,0.38801,0.38892,0.70467,0.70538,0.5052,0.49386,100,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2021-06-22,Undetermined,Undetermined,Eye,Sensory System
64996,SRR14883462,SRX11200542,SRS9255521,SRP325167,PRJNA740056,Transcriptome RNA seq analysis of the retina of crumbs 2a crb2a m289/m289 zebrafish model of Leber congenital amaurosis and retinitis pigmentosa.,GSE178709,Transcriptome Analysis,The crumbs cell polarity complex plays a crucial role in apical basal epithelial polarity. When human CRB1 is mutated  it results in autosomal recessive Leber congenital amaurosis and retinitis pigmentosa  with no established genotype phenotype correlation. Using the oko meduzym289/m289 crb2a /  zebrafish model  we performed integrative transcriptomic and methylomic analysis to identify dysregulated genes and pathways. We reveal delayed retinal cell type specification confirmed in patient derived retinal organoids  with disruption to cell cycle modulation and epigenetic transcriptional control. Hence  using reduced representation bisulphite sequencing RRBS we explored differential DNA methylation  identifying hypermethylated pathways involving biological adhesion  Hippo and transforming growth factor beta TGFbeta signalling. Functional epigenetic modules FEM were highlighted through the integration of RNA seq and RRBS  confirming cell cycle involvement and disturbance of TGFbeta  BMP  Hippo and SMAD protein signal transduction. Taken together our work provides insights for epigenetic regulation in early retinal development and considerations for future therapeutic development. Overall design: We used RNA seq to identify differentially expressed genes between the zebrafish model of CRB  crb2a m289. Samples were isolated retinal regions of the dorsal retina at 56 hpf; crb2a /  and control wildtype. Biological replicates were taken.,,pubmed:36656098,,crb2a m289/m289 retina rep 6 [R56 crb06],GSM5396383,,source name:crb2a m289/m289 retina|genotype:crb2a m289/m289|hpf:56|tissue:dorsal retina,crb2a m289/m289 retina rep 6 [R56 crb06],Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using trimgalore Reads were aligned to the genome and transcriptome using HISAT2 v2.2.1 using using standard paired end based parameters. Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates Count files were created using featurecounts v2 and modelled using DESeq2 v1.30.1 Genome build: GRCz11 Supplementary files format and content: tab delimited text files include raw count values for each sample,crb2a m289/m289 retina,,RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols,zebrafish were harvested at appropriate time points hpf  retinal regions dissected,genotype:crb2a m289/m289|hpf:56|tissue:dorsal retina,GSM5396383,GSM5396383: crb2a m289/m289 retina rep 6 [R56 crb06]; Danio rerio; RNA Seq,GSM5396383,,1,RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols,GEO Accession:GSM5396383,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP325167,,,R56-crb06_R1.fastq.gz R56-crb06_R2.fastq.gz,fastq fastq,2366800400.0,11834002.0,GSM5396383 r1,0:100 1:100,A:674390311;C:510745542;G:533969042;T:645375479;N:2320026,100,100,,,674390311,510745542,533969042,645375479,2320026,SRX11200542,SRS9255521,SRA1249569,GEO,"Institute of Ophthalmology, UCL",2,0.93643,0.93726,0.1222,0.12345,0.7823,0.78397,0.52987,0.51915,100,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2021-06-22,Undetermined,Undetermined,Eye,Sensory System
64997,SRR14883461,SRX11200541,SRS9255520,SRP325167,PRJNA740056,Transcriptome RNA seq analysis of the retina of crumbs 2a crb2a m289/m289 zebrafish model of Leber congenital amaurosis and retinitis pigmentosa.,GSE178709,Transcriptome Analysis,The crumbs cell polarity complex plays a crucial role in apical basal epithelial polarity. When human CRB1 is mutated  it results in autosomal recessive Leber congenital amaurosis and retinitis pigmentosa  with no established genotype phenotype correlation. Using the oko meduzym289/m289 crb2a /  zebrafish model  we performed integrative transcriptomic and methylomic analysis to identify dysregulated genes and pathways. We reveal delayed retinal cell type specification confirmed in patient derived retinal organoids  with disruption to cell cycle modulation and epigenetic transcriptional control. Hence  using reduced representation bisulphite sequencing RRBS we explored differential DNA methylation  identifying hypermethylated pathways involving biological adhesion  Hippo and transforming growth factor beta TGFbeta signalling. Functional epigenetic modules FEM were highlighted through the integration of RNA seq and RRBS  confirming cell cycle involvement and disturbance of TGFbeta  BMP  Hippo and SMAD protein signal transduction. Taken together our work provides insights for epigenetic regulation in early retinal development and considerations for future therapeutic development. Overall design: We used RNA seq to identify differentially expressed genes between the zebrafish model of CRB  crb2a m289. Samples were isolated retinal regions of the dorsal retina at 56 hpf; crb2a /  and control wildtype. Biological replicates were taken.,,pubmed:36656098,,crb2a m289/m289 retina rep 5 [R56 crb05],GSM5396382,,source name:crb2a m289/m289 retina|genotype:crb2a m289/m289|hpf:56|tissue:dorsal retina,crb2a m289/m289 retina rep 5 [R56 crb05],Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using trimgalore Reads were aligned to the genome and transcriptome using HISAT2 v2.2.1 using using standard paired end based parameters. Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates Count files were created using featurecounts v2 and modelled using DESeq2 v1.30.1 Genome build: GRCz11 Supplementary files format and content: tab delimited text files include raw count values for each sample,crb2a m289/m289 retina,,RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols,zebrafish were harvested at appropriate time points hpf  retinal regions dissected,genotype:crb2a m289/m289|hpf:56|tissue:dorsal retina,GSM5396382,GSM5396382: crb2a m289/m289 retina rep 5 [R56 crb05]; Danio rerio; RNA Seq,GSM5396382,,1,RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols,GEO Accession:GSM5396382,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP325167,,,R56-crb05_R1.fastq.gz R56-crb05_R2.fastq.gz,fastq fastq,2182015000.0,10910075.0,GSM5396382 r1,0:100 1:100,A:613679978;C:478180059;G:499240631;T:588697097;N:2217235,100,100,,,613679978,478180059,499240631,588697097,2217235,SRX11200541,SRS9255520,SRA1249569,GEO,"Institute of Ophthalmology, UCL",2,0.84093,0.8406,0.12771,0.12778,0.75799,0.75921,0.51192,0.51305,100,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2021-06-22,Undetermined,Undetermined,Eye,Sensory System
64998,SRR14883460,SRX11200540,SRS9255519,SRP325167,PRJNA740056,Transcriptome RNA seq analysis of the retina of crumbs 2a crb2a m289/m289 zebrafish model of Leber congenital amaurosis and retinitis pigmentosa.,GSE178709,Transcriptome Analysis,The crumbs cell polarity complex plays a crucial role in apical basal epithelial polarity. When human CRB1 is mutated  it results in autosomal recessive Leber congenital amaurosis and retinitis pigmentosa  with no established genotype phenotype correlation. Using the oko meduzym289/m289 crb2a /  zebrafish model  we performed integrative transcriptomic and methylomic analysis to identify dysregulated genes and pathways. We reveal delayed retinal cell type specification confirmed in patient derived retinal organoids  with disruption to cell cycle modulation and epigenetic transcriptional control. Hence  using reduced representation bisulphite sequencing RRBS we explored differential DNA methylation  identifying hypermethylated pathways involving biological adhesion  Hippo and transforming growth factor beta TGFbeta signalling. Functional epigenetic modules FEM were highlighted through the integration of RNA seq and RRBS  confirming cell cycle involvement and disturbance of TGFbeta  BMP  Hippo and SMAD protein signal transduction. Taken together our work provides insights for epigenetic regulation in early retinal development and considerations for future therapeutic development. Overall design: We used RNA seq to identify differentially expressed genes between the zebrafish model of CRB  crb2a m289. Samples were isolated retinal regions of the dorsal retina at 56 hpf; crb2a /  and control wildtype. Biological replicates were taken.,,pubmed:36656098,,crb2a m289/m289 retina rep 4 [R56 crb04],GSM5396381,,source name:crb2a m289/m289 retina|genotype:crb2a m289/m289|hpf:56|tissue:dorsal retina,crb2a m289/m289 retina rep 4 [R56 crb04],Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using trimgalore Reads were aligned to the genome and transcriptome using HISAT2 v2.2.1 using using standard paired end based parameters. Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates Count files were created using featurecounts v2 and modelled using DESeq2 v1.30.1 Genome build: GRCz11 Supplementary files format and content: tab delimited text files include raw count values for each sample,crb2a m289/m289 retina,,RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols,zebrafish were harvested at appropriate time points hpf  retinal regions dissected,genotype:crb2a m289/m289|hpf:56|tissue:dorsal retina,GSM5396381,GSM5396381: crb2a m289/m289 retina rep 4 [R56 crb04]; Danio rerio; RNA Seq,GSM5396381,,1,RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols,GEO Accession:GSM5396381,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP325167,,,R56-crb04_R1.fastq.gz R56-crb04_R2.fastq.gz,fastq fastq,3034970000.0,15174850.0,GSM5396381 r1,0:100 1:100,A:852152156;C:668039682;G:691856017;T:819874164;N:3047981,100,100,,,852152156,668039682,691856017,819874164,3047981,SRX11200540,SRS9255519,SRA1249569,GEO,"Institute of Ophthalmology, UCL",2,0.94841,0.9474,0.12465,0.12425,0.76568,0.76668,0.49983,0.50174,100,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2021-06-22,Undetermined,Undetermined,Eye,Sensory System
64999,SRR14883459,SRX11200539,SRS9255518,SRP325167,PRJNA740056,Transcriptome RNA seq analysis of the retina of crumbs 2a crb2a m289/m289 zebrafish model of Leber congenital amaurosis and retinitis pigmentosa.,GSE178709,Transcriptome Analysis,The crumbs cell polarity complex plays a crucial role in apical basal epithelial polarity. When human CRB1 is mutated  it results in autosomal recessive Leber congenital amaurosis and retinitis pigmentosa  with no established genotype phenotype correlation. Using the oko meduzym289/m289 crb2a /  zebrafish model  we performed integrative transcriptomic and methylomic analysis to identify dysregulated genes and pathways. We reveal delayed retinal cell type specification confirmed in patient derived retinal organoids  with disruption to cell cycle modulation and epigenetic transcriptional control. Hence  using reduced representation bisulphite sequencing RRBS we explored differential DNA methylation  identifying hypermethylated pathways involving biological adhesion  Hippo and transforming growth factor beta TGFbeta signalling. Functional epigenetic modules FEM were highlighted through the integration of RNA seq and RRBS  confirming cell cycle involvement and disturbance of TGFbeta  BMP  Hippo and SMAD protein signal transduction. Taken together our work provides insights for epigenetic regulation in early retinal development and considerations for future therapeutic development. Overall design: We used RNA seq to identify differentially expressed genes between the zebrafish model of CRB  crb2a m289. Samples were isolated retinal regions of the dorsal retina at 56 hpf; crb2a /  and control wildtype. Biological replicates were taken.,,pubmed:36656098,,crb2a m289/m289 retina rep 3 [R56 crb03],GSM5396380,,source name:crb2a m289/m289 retina|genotype:crb2a m289/m289|hpf:56|tissue:dorsal retina,crb2a m289/m289 retina rep 3 [R56 crb03],Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using trimgalore Reads were aligned to the genome and transcriptome using HISAT2 v2.2.1 using using standard paired end based parameters. Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates Count files were created using featurecounts v2 and modelled using DESeq2 v1.30.1 Genome build: GRCz11 Supplementary files format and content: tab delimited text files include raw count values for each sample,crb2a m289/m289 retina,,RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols,zebrafish were harvested at appropriate time points hpf  retinal regions dissected,genotype:crb2a m289/m289|hpf:56|tissue:dorsal retina,GSM5396380,GSM5396380: crb2a m289/m289 retina rep 3 [R56 crb03]; Danio rerio; RNA Seq,GSM5396380,,1,RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols,GEO Accession:GSM5396380,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP325167,,,R56-crb03_R1.fastq.gz R56-crb03_R2.fastq.gz,fastq fastq,3029887200.0,15149436.0,GSM5396380 r1,0:100 1:100,A:843898686;C:678623407;G:719760887;T:784452063;N:3152157,100,100,,,843898686,678623407,719760887,784452063,3152157,SRX11200539,SRS9255518,SRA1249569,GEO,"Institute of Ophthalmology, UCL",2,0.93788,0.93797,0.12236,0.12249,0.78021,0.78019,0.52408,0.5209,100,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2021-06-22,Undetermined,Undetermined,Eye,Sensory System
65000,SRR14883458,SRX11200538,SRS9255517,SRP325167,PRJNA740056,Transcriptome RNA seq analysis of the retina of crumbs 2a crb2a m289/m289 zebrafish model of Leber congenital amaurosis and retinitis pigmentosa.,GSE178709,Transcriptome Analysis,The crumbs cell polarity complex plays a crucial role in apical basal epithelial polarity. When human CRB1 is mutated  it results in autosomal recessive Leber congenital amaurosis and retinitis pigmentosa  with no established genotype phenotype correlation. Using the oko meduzym289/m289 crb2a /  zebrafish model  we performed integrative transcriptomic and methylomic analysis to identify dysregulated genes and pathways. We reveal delayed retinal cell type specification confirmed in patient derived retinal organoids  with disruption to cell cycle modulation and epigenetic transcriptional control. Hence  using reduced representation bisulphite sequencing RRBS we explored differential DNA methylation  identifying hypermethylated pathways involving biological adhesion  Hippo and transforming growth factor beta TGFbeta signalling. Functional epigenetic modules FEM were highlighted through the integration of RNA seq and RRBS  confirming cell cycle involvement and disturbance of TGFbeta  BMP  Hippo and SMAD protein signal transduction. Taken together our work provides insights for epigenetic regulation in early retinal development and considerations for future therapeutic development. Overall design: We used RNA seq to identify differentially expressed genes between the zebrafish model of CRB  crb2a m289. Samples were isolated retinal regions of the dorsal retina at 56 hpf; crb2a /  and control wildtype. Biological replicates were taken.,,pubmed:36656098,,crb2a m289/m289 retina rep 2 [R56 crb02],GSM5396379,,source name:crb2a m289/m289 retina|genotype:crb2a m289/m289|hpf:56|tissue:dorsal retina,crb2a m289/m289 retina rep 2 [R56 crb02],Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using trimgalore Reads were aligned to the genome and transcriptome using HISAT2 v2.2.1 using using standard paired end based parameters. Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates Count files were created using featurecounts v2 and modelled using DESeq2 v1.30.1 Genome build: GRCz11 Supplementary files format and content: tab delimited text files include raw count values for each sample,crb2a m289/m289 retina,,RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols,zebrafish were harvested at appropriate time points hpf  retinal regions dissected,genotype:crb2a m289/m289|hpf:56|tissue:dorsal retina,GSM5396379,GSM5396379: crb2a m289/m289 retina rep 2 [R56 crb02]; Danio rerio; RNA Seq,GSM5396379,,1,RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols,GEO Accession:GSM5396379,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP325167,,,R56-crb02_R1.fastq.gz R56-crb02_R2.fastq.gz,fastq fastq,3961420600.0,19807103.0,GSM5396379 r1,0:100 1:100,A:1167948902;C:867511818;G:934751657;T:987108651;N:4099572,100,100,,,1167948902,867511818,934751657,987108651,4099572,SRX11200538,SRS9255517,SRA1249569,GEO,"Institute of Ophthalmology, UCL",2,0.93631,0.93656,0.1413,0.14192,0.79444,0.79425,0.53478,0.52917,100,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2021-06-22,Undetermined,Undetermined,Eye,Sensory System
65001,SRR14883457,SRX11200537,SRS9255516,SRP325167,PRJNA740056,Transcriptome RNA seq analysis of the retina of crumbs 2a crb2a m289/m289 zebrafish model of Leber congenital amaurosis and retinitis pigmentosa.,GSE178709,Transcriptome Analysis,The crumbs cell polarity complex plays a crucial role in apical basal epithelial polarity. When human CRB1 is mutated  it results in autosomal recessive Leber congenital amaurosis and retinitis pigmentosa  with no established genotype phenotype correlation. Using the oko meduzym289/m289 crb2a /  zebrafish model  we performed integrative transcriptomic and methylomic analysis to identify dysregulated genes and pathways. We reveal delayed retinal cell type specification confirmed in patient derived retinal organoids  with disruption to cell cycle modulation and epigenetic transcriptional control. Hence  using reduced representation bisulphite sequencing RRBS we explored differential DNA methylation  identifying hypermethylated pathways involving biological adhesion  Hippo and transforming growth factor beta TGFbeta signalling. Functional epigenetic modules FEM were highlighted through the integration of RNA seq and RRBS  confirming cell cycle involvement and disturbance of TGFbeta  BMP  Hippo and SMAD protein signal transduction. Taken together our work provides insights for epigenetic regulation in early retinal development and considerations for future therapeutic development. Overall design: We used RNA seq to identify differentially expressed genes between the zebrafish model of CRB  crb2a m289. Samples were isolated retinal regions of the dorsal retina at 56 hpf; crb2a /  and control wildtype. Biological replicates were taken.,,pubmed:36656098,,crb2a m289/m289 retina rep 1 [R56 crb01],GSM5396378,,source name:crb2a m289/m289 retina|genotype:crb2a m289/m289|hpf:56|tissue:dorsal retina,crb2a m289/m289 retina rep 1 [R56 crb01],Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using trimgalore Reads were aligned to the genome and transcriptome using HISAT2 v2.2.1 using using standard paired end based parameters. Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates Count files were created using featurecounts v2 and modelled using DESeq2 v1.30.1 Genome build: GRCz11 Supplementary files format and content: tab delimited text files include raw count values for each sample,crb2a m289/m289 retina,,RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols,zebrafish were harvested at appropriate time points hpf  retinal regions dissected,genotype:crb2a m289/m289|hpf:56|tissue:dorsal retina,GSM5396378,GSM5396378: crb2a m289/m289 retina rep 1 [R56 crb01]; Danio rerio; RNA Seq,GSM5396378,,1,RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols,GEO Accession:GSM5396378,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP325167,,,R56-crb01_R1.fastq.gz R56-crb01_R2.fastq.gz,fastq fastq,2947225600.0,14736128.0,GSM5396378 r1,0:100 1:100,A:906619457;C:624314744;G:678281106;T:735161202;N:2849091,100,100,,,906619457,624314744,678281106,735161202,2849091,SRX11200537,SRS9255516,SRA1249569,GEO,"Institute of Ophthalmology, UCL",2,0.90444,0.90345,0.15985,0.15916,0.81049,0.81067,0.51786,0.52746,100,100,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2021-06-22,Undetermined,Undetermined,Eye,Sensory System
70464,SRR19897787,SRX15940767,SRS13627793,SRP384180,PRJNA854078,The eyes of Danio rerio RNA seq data from white light group  blue light group  white light + cold group and blue light +  cold group,PRJNA854078,Other,zebrafish were placed in a white light emitting diode and a blue light emitting diode and 26 degrees centigrade water body. post pretreatment for two weeks  fish were then transferred to white light and 11degrees centigrade water  respectively.,,,,,CW1,,strain:missing|age:missing|sex:missing|tissue:eye|repulicate:cold + white light repulicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio,CW1,CW1,cold + white light,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP384180,,,CW1_1.fq.gz CW1_2.fq.gz,fastq fastq,6739882500.0,22466275.0,CW1 1.fq.gz,0:150 1:150,A:1848237756;C:1519101210;G:1513969331;T:1858563022;N:11181,150,150,,,1848237756,1519101210,1513969331,1858563022,11181,SRX15940767,SRS13627793,SRA1445974,Zhejiang Ocean University|National Engineering Research Center of Marine Fac,Zhejiang Ocean University,2,0.9202,0.92005,0.10845,0.10844,0.68603,0.68696,0.52694,0.5273,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2022-06-29,Undetermined,Undetermined,Eye,Sensory System
70465,SRR19897788,SRX15940766,SRS13627792,SRP384180,PRJNA854078,The eyes of Danio rerio RNA seq data from white light group  blue light group  white light + cold group and blue light +  cold group,PRJNA854078,Other,zebrafish were placed in a white light emitting diode and a blue light emitting diode and 26 degrees centigrade water body. post pretreatment for two weeks  fish were then transferred to white light and 11degrees centigrade water  respectively.,,,,,CB3,,strain:missing|age:missing|sex:missing|tissue:eye|repulicate:cold + blue light repulicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio,CB3,CB3,cold + blue light,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP384180,,,CB3_1.fq.gz CB3_2.fq.gz,fastq fastq,6616936500.0,22056455.0,CB3 1.fq.gz,0:150 1:150,A:1808345659;C:1499214022;G:1492074811;T:1817144348;N:157660,150,150,,,1808345659,1499214022,1492074811,1817144348,157660,SRX15940766,SRS13627792,SRA1445974,Zhejiang Ocean University|National Engineering Research Center of Marine Fac,Zhejiang Ocean University,2,0.92167,0.92063,0.10246,0.10193,0.6883,0.68832,0.51958,0.52373,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2022-06-29,Undetermined,Undetermined,Eye,Sensory System
70466,SRR19897789,SRX15940765,SRS13627791,SRP384180,PRJNA854078,The eyes of Danio rerio RNA seq data from white light group  blue light group  white light + cold group and blue light +  cold group,PRJNA854078,Other,zebrafish were placed in a white light emitting diode and a blue light emitting diode and 26 degrees centigrade water body. post pretreatment for two weeks  fish were then transferred to white light and 11degrees centigrade water  respectively.,,,,,CB2,,strain:missing|age:missing|sex:missing|tissue:eye|repulicate:cold + blue light repulicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio,CB2,CB2,cold + blue light,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP384180,,,CB2_1.fq.gz CB2_2.fq.gz,fastq fastq,6643125000.0,22143750.0,CB2 1.fq.gz,0:150 1:150,A:1834995141;C:1484447017;G:1478473640;T:1845045394;N:163808,150,150,,,1834995141,1484447017,1478473640,1845045394,163808,SRX15940765,SRS13627791,SRA1445974,Zhejiang Ocean University|National Engineering Research Center of Marine Fac,Zhejiang Ocean University,2,0.91587,0.91485,0.10928,0.10908,0.67271,0.67284,0.53214,0.51839,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2022-06-29,Undetermined,Undetermined,Eye,Sensory System
70467,SRR19897790,SRX15940764,SRS13627790,SRP384180,PRJNA854078,The eyes of Danio rerio RNA seq data from white light group  blue light group  white light + cold group and blue light +  cold group,PRJNA854078,Other,zebrafish were placed in a white light emitting diode and a blue light emitting diode and 26 degrees centigrade water body. post pretreatment for two weeks  fish were then transferred to white light and 11degrees centigrade water  respectively.,,,,,CB1,,strain:missing|age:missing|sex:missing|tissue:eye|repulicate:cold + blue light repulicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio,CB1,CB1,cold + blue light,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP384180,,,CB1_1.fq.gz CB1_2.fq.gz,fastq fastq,6726735900.0,22422453.0,CB1 1.fq.gz,0:150 1:150,A:1854984195;C:1506200798;G:1500739385;T:1864656690;N:154832,150,150,,,1854984195,1506200798,1500739385,1864656690,154832,SRX15940764,SRS13627790,SRA1445974,Zhejiang Ocean University|National Engineering Research Center of Marine Fac,Zhejiang Ocean University,2,0.92107,0.92013,0.11091,0.11046,0.68416,0.68369,0.52205,0.51943,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2022-06-29,Undetermined,Undetermined,Eye,Sensory System
70468,SRR19897791,SRX15940763,SRS13627789,SRP384180,PRJNA854078,The eyes of Danio rerio RNA seq data from white light group  blue light group  white light + cold group and blue light +  cold group,PRJNA854078,Other,zebrafish were placed in a white light emitting diode and a blue light emitting diode and 26 degrees centigrade water body. post pretreatment for two weeks  fish were then transferred to white light and 11degrees centigrade water  respectively.,,,,,W3,,strain:missing|age:missing|sex:missing|tissue:eye|repulicate:white repulicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio,W3,W3,white light,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP384180,,,W3_1.fq.gz W3_2.fq.gz,fastq fastq,6768510900.0,22561703.0,W3 1.fq.gz,0:150 1:150,A:1854668626;C:1528356228;G:1523098237;T:1862376595;N:11214,150,150,,,1854668626,1528356228,1523098237,1862376595,11214,SRX15940763,SRS13627789,SRA1445974,Zhejiang Ocean University|National Engineering Research Center of Marine Fac,Zhejiang Ocean University,2,0.92284,0.92018,0.10477,0.10423,0.68032,0.68105,0.52004,0.52091,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2022-06-29,Undetermined,Undetermined,Eye,Sensory System
70469,SRR19897792,SRX15940762,SRS13627788,SRP384180,PRJNA854078,The eyes of Danio rerio RNA seq data from white light group  blue light group  white light + cold group and blue light +  cold group,PRJNA854078,Other,zebrafish were placed in a white light emitting diode and a blue light emitting diode and 26 degrees centigrade water body. post pretreatment for two weeks  fish were then transferred to white light and 11degrees centigrade water  respectively.,,,,,W2,,strain:missing|age:missing|sex:missing|tissue:eye|repulicate:white repulicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio,W2,W2,white light,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP384180,,,W2_1.fq.gz W2_2.fq.gz,fastq fastq,6680260200.0,22267534.0,W2 1.fq.gz,0:150 1:150,A:1823317259;C:1515290462;G:1509530485;T:1832110882;N:11112,150,150,,,1823317259,1515290462,1509530485,1832110882,11112,SRX15940762,SRS13627788,SRA1445974,Zhejiang Ocean University|National Engineering Research Center of Marine Fac,Zhejiang Ocean University,2,0.92292,0.92065,0.09554,0.09545,0.67551,0.6757,0.50849,0.51222,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2022-06-29,Undetermined,Undetermined,Eye,Sensory System
70470,SRR19897793,SRX15940761,SRS13627787,SRP384180,PRJNA854078,The eyes of Danio rerio RNA seq data from white light group  blue light group  white light + cold group and blue light +  cold group,PRJNA854078,Other,zebrafish were placed in a white light emitting diode and a blue light emitting diode and 26 degrees centigrade water body. post pretreatment for two weeks  fish were then transferred to white light and 11degrees centigrade water  respectively.,,,,,W1,,strain:missing|age:missing|sex:missing|tissue:eye|repulicate:white repulicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio,W1,W1,white light,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP384180,,,W1_1.fq.gz W1_2.fq.gz,fastq fastq,6781992000.0,22606640.0,W1 1.fq.gz,0:150 1:150,A:1844053579;C:1544613499;G:1543816397;T:1849496814;N:11711,150,150,,,1844053579,1544613499,1543816397,1849496814,11711,SRX15940761,SRS13627787,SRA1445974,Zhejiang Ocean University|National Engineering Research Center of Marine Fac,Zhejiang Ocean University,2,0.92064,0.91964,0.09713,0.09743,0.67667,0.67746,0.5212,0.50218,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2022-06-29,Undetermined,Undetermined,Eye,Sensory System
70471,SRR19897794,SRX15940760,SRS13627786,SRP384180,PRJNA854078,The eyes of Danio rerio RNA seq data from white light group  blue light group  white light + cold group and blue light +  cold group,PRJNA854078,Other,zebrafish were placed in a white light emitting diode and a blue light emitting diode and 26 degrees centigrade water body. post pretreatment for two weeks  fish were then transferred to white light and 11degrees centigrade water  respectively.,,,,,B3,,strain:missing|age:missing|sex:missing|tissue:eye|repulicate:blue repulicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio,B3,B3,blue light,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP384180,,,B3_1.fq.gz B3_2.fq.gz,fastq fastq,6656595900.0,22188653.0,B3 1.fq.gz,0:150 1:150,A:1805784355;C:1520422218;G:1518168444;T:1812078392;N:142491,150,150,,,1805784355,1520422218,1518168444,1812078392,142491,SRX15940760,SRS13627786,SRA1445974,Zhejiang Ocean University|National Engineering Research Center of Marine Fac,Zhejiang Ocean University,2,0.92236,0.91914,0.09522,0.09395,0.67661,0.67722,0.518,0.51697,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2022-06-29,Undetermined,Undetermined,Eye,Sensory System
70472,SRR19897795,SRX15940759,SRS13627785,SRP384180,PRJNA854078,The eyes of Danio rerio RNA seq data from white light group  blue light group  white light + cold group and blue light +  cold group,PRJNA854078,Other,zebrafish were placed in a white light emitting diode and a blue light emitting diode and 26 degrees centigrade water body. post pretreatment for two weeks  fish were then transferred to white light and 11degrees centigrade water  respectively.,,,,,CW3,,strain:missing|age:missing|sex:missing|tissue:eye|repulicate:cold + white light repulicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio,CW3,CW3,cold + white light,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP384180,,,CW3_1.fq.gz CW3_2.fq.gz,fastq fastq,6747757500.0,22492525.0,CW3 1.fq.gz,0:150 1:150,A:1879771229;C:1493093261;G:1485694977;T:1889044111;N:153922,150,150,,,1879771229,1493093261,1485694977,1889044111,153922,SRX15940759,SRS13627785,SRA1445974,Zhejiang Ocean University|National Engineering Research Center of Marine Fac,Zhejiang Ocean University,2,0.91511,0.9134,0.11866,0.11919,0.67667,0.67744,0.53077,0.53216,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2022-06-29,Undetermined,Undetermined,Eye,Sensory System
70473,SRR19897796,SRX15940758,SRS13627784,SRP384180,PRJNA854078,The eyes of Danio rerio RNA seq data from white light group  blue light group  white light + cold group and blue light +  cold group,PRJNA854078,Other,zebrafish were placed in a white light emitting diode and a blue light emitting diode and 26 degrees centigrade water body. post pretreatment for two weeks  fish were then transferred to white light and 11degrees centigrade water  respectively.,,,,,CW2,,strain:missing|age:missing|sex:missing|tissue:eye|repulicate:cold + white light repulicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio,CW2,CW2,cold + white light,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP384180,,,CW2_1.fq.gz CW2_2.fq.gz,fastq fastq,6683398200.0,22277994.0,CW2 1.fq.gz,0:150 1:150,A:1843667678;C:1495135303;G:1486210450;T:1858373680;N:11089,150,150,,,1843667678,1495135303,1486210450,1858373680,11089,SRX15940758,SRS13627784,SRA1445974,Zhejiang Ocean University|National Engineering Research Center of Marine Fac,Zhejiang Ocean University,2,0.91857,0.91787,0.11123,0.11217,0.68753,0.68858,0.5306,0.49945,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2022-06-29,Undetermined,Undetermined,Eye,Sensory System
70474,SRR19897797,SRX15940757,SRS13627783,SRP384180,PRJNA854078,The eyes of Danio rerio RNA seq data from white light group  blue light group  white light + cold group and blue light +  cold group,PRJNA854078,Other,zebrafish were placed in a white light emitting diode and a blue light emitting diode and 26 degrees centigrade water body. post pretreatment for two weeks  fish were then transferred to white light and 11degrees centigrade water  respectively.,,,,,B2,,strain:missing|age:missing|sex:missing|tissue:eye|repulicate:blue repulicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio,B2,B2,blue light,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP384180,,,B2_1.fq.gz B2_2.fq.gz,fastq fastq,6727692000.0,22425640.0,B2 1.fq.gz,0:150 1:150,A:1850003227;C:1513202517;G:1506953883;T:1857378373;N:154000,150,150,,,1850003227,1513202517,1506953883,1857378373,154000,SRX15940757,SRS13627783,SRA1445974,Zhejiang Ocean University|National Engineering Research Center of Marine Fac,Zhejiang Ocean University,2,0.91912,0.91906,0.1068,0.10681,0.6733,0.67247,0.52417,0.51448,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2022-06-29,Undetermined,Undetermined,Eye,Sensory System
70475,SRR19897798,SRX15940756,SRS13627782,SRP384180,PRJNA854078,The eyes of Danio rerio RNA seq data from white light group  blue light group  white light + cold group and blue light +  cold group,PRJNA854078,Other,zebrafish were placed in a white light emitting diode and a blue light emitting diode and 26 degrees centigrade water body. post pretreatment for two weeks  fish were then transferred to white light and 11degrees centigrade water  respectively.,,,,,B1,,strain:missing|age:missing|sex:missing|tissue:eye|repulicate:blue repulicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio,B1,B1,blue light,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP384180,,,B1_1.fq.gz B1_2.fq.gz,fastq fastq,6763694400.0,22545648.0,B1 1.fq.gz,0:150 1:150,A:1864141494;C:1516607505;G:1508752023;T:1874030068;N:163310,150,150,,,1864141494,1516607505,1508752023,1874030068,163310,SRX15940756,SRS13627782,SRA1445974,Zhejiang Ocean University|National Engineering Research Center of Marine Fac,Zhejiang Ocean University,2,0.91777,0.91753,0.11235,0.11188,0.68065,0.68069,0.51959,0.52086,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2022-06-29,Undetermined,Undetermined,Eye,Sensory System
76691,SRR25253548,SRX20999601,SRS18272874,SRP449239,PRJNA994180,Evolution of neuronal cell classes and types in the vertebrate retina [Zebrafish],GSE237214,Transcriptome Analysis,The basic plan of the retina is conserved across vertebrates  yet species differ profoundly in their visual needs Baden et al.  2020. One might expect that retinal cell types evolved to accommodate these varied needs  but this has not been systematically studied. Here  we generated and integrated single cell transcriptomic atlases of the retina from 17 species: humans  two non human primates  four rodents  three ungulates  opossum  ferret  tree shrew  a teleost fish  a bird  a reptile and a lamprey. Molecular conservation of the six retinal cell classes photoreceptors  horizontal cells  bipolar cells  amacrine cells  retinal ganglion cells [RGCs] and Müller glia is striking  with transcriptomic differences across species correlated with evolutionary distance. Major subclasses are also conserved  whereas variation among types within classes or subclasses is more pronounced. However  an integrative analysis revealed that numerous types are shared across species based on conserved gene expression programs that likely trace back to the common ancestor of jawed vertebrates. The degree of variation among types increases from the outer retina photoreceptors to the inner retina RGCs  suggesting that evolution acts preferentially to shape the retinal output. Finally  we identified mammalian orthologs of midget RGCs  which comprise >80% of RGCs in the human retina  subserve high acuity vision  and were believed to be primate specific Berson  2008; in contrast  the mouse orthologs comprise <2% of mouse RGCs. Projections both primate and mouse orthologous types are overrepresented in the thalamus  which supplies the primary visual cortex. We suggest that midget RGCs are not primate innovations  but descendants of evolutionarily ancient types that decreased in size and increased in number as primates evolved  thereby facilitating high visual acuity and increased cortical processing of visual information. Overall design: Single cell RNA seq was performed on cells isolated from fresh retina. Fluorescence activated cell sorting was used to collect Calcein blueCB positive live cells. For some collections  CB+ cells were further seprated using CD90/THY1 and/or CD73 expression as an strategy to enrich for RGCs and/or to deplete phototreceptors  respectively Please note that he enrichment strategy was not effective for some species/samples. Approximately 8000 cells were recovered from each sample  and each cell was sequenced to a depth of 40000 reads.,parent bioproject:PRJNA994164,pubmed:38092908,,Zebrafish BC8,GSM7596942,,source name:Retina|tissue:Retina|cell type:Retinal neurons|geo loc name:missing|collection date:missing,Zebrafish BC8,We used cellranger v7.0  10X Genomics to align the sc  and snRNA seq datasets  following manufacturer’s instructions. For each species  sequencing reads were demultiplexed into distinct samples and the .fastq.gz files corresponding to each sample were aligned to reference transcriptomes to obtain binary alignment map .bam files. Assembly: Zv82 Supplementary files format and content: To include both exonic and intronic reads in the quantification of gene expression for each sample  regardless of cellular or nuclear origin  we applied velocyto to the corresponding .bam files. This generated two separate gene expression matrices GEMs; genes x cells for each sample  corresponding to “spliced” and “unspliced” reads. The two GEMs were summed element by element to obtain “total” GEM for each sample. Supplementary files format and content: GEMs from different sample runs were combined column wise concatenated to yield a full species’ GEM.,Retina,None,Retinas were dissected in Ames solution Sigma Aldrich; equilibrated with 95% O2/5% CO2 for all use immediately following enucleation. They were dissociated in papain  followed by FACS sorting. Cells were stained for either THY1/CD90 to enrich for RGCs or for CD73 to deplete photoreceptors. Single cell libraries were generated using the Chromium 3’ V3 platform 10X Genomics  Pleasanton  CA according to the manufacturer’s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs where nuclear lysis and barcoded reverse transcription of RNA would take place to yield full length cDNA; this was followed by amplification  enzymatic fragmentation  and 5’ adaptor and sample index attachment to yield the final libraries. Single cell RNA sequecning 10X Genomics,,tissue:Retina|cell type:Retinal neurons,GSM7596942,GSM7596942: Zebrafish BC8; Danio rerio; RNA Seq,GSM7596942 r1,GSM7596942,1,Retinas were dissected in Ames solution Sigma Aldrich; equilibrated with 95% O2/5% CO2 for all use immediately following enucleation. They were dissociated in papain  followed by FACS sorting. Cells were stained for either THY1/CD90 to enrich for RGCs or for CD73 to deplete photoreceptors. Single cell libraries were generated using the Chromium three prime V3 platform 10X Genomics  Pleasanton  CA according to the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs where nuclear lysis and barcoded reverse transcription of RNA would take place to yield full length cDNA; this was followed by amplification  enzymatic fragmentation  and five prime adaptor and sample index attachment to yield the final libraries. Single cell RNA sequecning 10X Genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP449239,,intentional duplicate,ZfishBC8.bam,10X Genomics bam file,8580337178.0,87554461.0,GSM7596942 r1,0:98,A:2489735011;C:1687426244;G:1785339875;T:2616019593;N:1816455,98,,,,2489735011,1687426244,1785339875,2616019593,1816455,SRX20999601,SRS18272874,SRA1672086,"Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley","Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley",1,0.87916,,0.24205,,0.81217,,0.50856,,98,,B,,usable mapping rate,illumina,novaseq_era,full_length,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-07-12,Undetermined,Undetermined,Eye,Sensory System
76692,SRR25253549,SRX20999600,SRS18272873,SRP449239,PRJNA994180,Evolution of neuronal cell classes and types in the vertebrate retina [Zebrafish],GSE237214,Transcriptome Analysis,The basic plan of the retina is conserved across vertebrates  yet species differ profoundly in their visual needs Baden et al.  2020. One might expect that retinal cell types evolved to accommodate these varied needs  but this has not been systematically studied. Here  we generated and integrated single cell transcriptomic atlases of the retina from 17 species: humans  two non human primates  four rodents  three ungulates  opossum  ferret  tree shrew  a teleost fish  a bird  a reptile and a lamprey. Molecular conservation of the six retinal cell classes photoreceptors  horizontal cells  bipolar cells  amacrine cells  retinal ganglion cells [RGCs] and Müller glia is striking  with transcriptomic differences across species correlated with evolutionary distance. Major subclasses are also conserved  whereas variation among types within classes or subclasses is more pronounced. However  an integrative analysis revealed that numerous types are shared across species based on conserved gene expression programs that likely trace back to the common ancestor of jawed vertebrates. The degree of variation among types increases from the outer retina photoreceptors to the inner retina RGCs  suggesting that evolution acts preferentially to shape the retinal output. Finally  we identified mammalian orthologs of midget RGCs  which comprise >80% of RGCs in the human retina  subserve high acuity vision  and were believed to be primate specific Berson  2008; in contrast  the mouse orthologs comprise <2% of mouse RGCs. Projections both primate and mouse orthologous types are overrepresented in the thalamus  which supplies the primary visual cortex. We suggest that midget RGCs are not primate innovations  but descendants of evolutionarily ancient types that decreased in size and increased in number as primates evolved  thereby facilitating high visual acuity and increased cortical processing of visual information. Overall design: Single cell RNA seq was performed on cells isolated from fresh retina. Fluorescence activated cell sorting was used to collect Calcein blueCB positive live cells. For some collections  CB+ cells were further seprated using CD90/THY1 and/or CD73 expression as an strategy to enrich for RGCs and/or to deplete phototreceptors  respectively Please note that he enrichment strategy was not effective for some species/samples. Approximately 8000 cells were recovered from each sample  and each cell was sequenced to a depth of 40000 reads.,parent bioproject:PRJNA994164,pubmed:38092908,,Zebrafish BC7,GSM7596941,,source name:Retina|tissue:Retina|cell type:Retinal neurons|geo loc name:missing|collection date:missing,Zebrafish BC7,We used cellranger v7.0  10X Genomics to align the sc  and snRNA seq datasets  following manufacturer’s instructions. For each species  sequencing reads were demultiplexed into distinct samples and the .fastq.gz files corresponding to each sample were aligned to reference transcriptomes to obtain binary alignment map .bam files. Assembly: Zv82 Supplementary files format and content: To include both exonic and intronic reads in the quantification of gene expression for each sample  regardless of cellular or nuclear origin  we applied velocyto to the corresponding .bam files. This generated two separate gene expression matrices GEMs; genes x cells for each sample  corresponding to “spliced” and “unspliced” reads. The two GEMs were summed element by element to obtain “total” GEM for each sample. Supplementary files format and content: GEMs from different sample runs were combined column wise concatenated to yield a full species’ GEM.,Retina,None,Retinas were dissected in Ames solution Sigma Aldrich; equilibrated with 95% O2/5% CO2 for all use immediately following enucleation. They were dissociated in papain  followed by FACS sorting. Cells were stained for either THY1/CD90 to enrich for RGCs or for CD73 to deplete photoreceptors. Single cell libraries were generated using the Chromium 3’ V3 platform 10X Genomics  Pleasanton  CA according to the manufacturer’s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs where nuclear lysis and barcoded reverse transcription of RNA would take place to yield full length cDNA; this was followed by amplification  enzymatic fragmentation  and 5’ adaptor and sample index attachment to yield the final libraries. Single cell RNA sequecning 10X Genomics,,tissue:Retina|cell type:Retinal neurons,GSM7596941,GSM7596941: Zebrafish BC7; Danio rerio; RNA Seq,GSM7596941 r1,GSM7596941,1,Retinas were dissected in Ames solution Sigma Aldrich; equilibrated with 95% O2/5% CO2 for all use immediately following enucleation. They were dissociated in papain  followed by FACS sorting. Cells were stained for either THY1/CD90 to enrich for RGCs or for CD73 to deplete photoreceptors. Single cell libraries were generated using the Chromium three prime V3 platform 10X Genomics  Pleasanton  CA according to the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs where nuclear lysis and barcoded reverse transcription of RNA would take place to yield full length cDNA; this was followed by amplification  enzymatic fragmentation  and five prime adaptor and sample index attachment to yield the final libraries. Single cell RNA sequecning 10X Genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP449239,,intentional duplicate,ZfishBC7.bam,10X Genomics bam file,5495018662.0,56071619.0,GSM7596941 r1,0:98,A:1599986794;C:1077631009;G:1137108891;T:1679156666;N:1135302,98,,,,1599986794,1077631009,1137108891,1679156666,1135302,SRX20999600,SRS18272873,SRA1672086,"Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley","Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley",1,0.87849,,0.24695,,0.81201,,0.50341,,98,,B,,usable mapping rate,illumina,novaseq_era,full_length,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-07-12,Undetermined,Undetermined,Eye,Sensory System
76693,SRR25253550,SRX20999599,SRS18272872,SRP449239,PRJNA994180,Evolution of neuronal cell classes and types in the vertebrate retina [Zebrafish],GSE237214,Transcriptome Analysis,The basic plan of the retina is conserved across vertebrates  yet species differ profoundly in their visual needs Baden et al.  2020. One might expect that retinal cell types evolved to accommodate these varied needs  but this has not been systematically studied. Here  we generated and integrated single cell transcriptomic atlases of the retina from 17 species: humans  two non human primates  four rodents  three ungulates  opossum  ferret  tree shrew  a teleost fish  a bird  a reptile and a lamprey. Molecular conservation of the six retinal cell classes photoreceptors  horizontal cells  bipolar cells  amacrine cells  retinal ganglion cells [RGCs] and Müller glia is striking  with transcriptomic differences across species correlated with evolutionary distance. Major subclasses are also conserved  whereas variation among types within classes or subclasses is more pronounced. However  an integrative analysis revealed that numerous types are shared across species based on conserved gene expression programs that likely trace back to the common ancestor of jawed vertebrates. The degree of variation among types increases from the outer retina photoreceptors to the inner retina RGCs  suggesting that evolution acts preferentially to shape the retinal output. Finally  we identified mammalian orthologs of midget RGCs  which comprise >80% of RGCs in the human retina  subserve high acuity vision  and were believed to be primate specific Berson  2008; in contrast  the mouse orthologs comprise <2% of mouse RGCs. Projections both primate and mouse orthologous types are overrepresented in the thalamus  which supplies the primary visual cortex. We suggest that midget RGCs are not primate innovations  but descendants of evolutionarily ancient types that decreased in size and increased in number as primates evolved  thereby facilitating high visual acuity and increased cortical processing of visual information. Overall design: Single cell RNA seq was performed on cells isolated from fresh retina. Fluorescence activated cell sorting was used to collect Calcein blueCB positive live cells. For some collections  CB+ cells were further seprated using CD90/THY1 and/or CD73 expression as an strategy to enrich for RGCs and/or to deplete phototreceptors  respectively Please note that he enrichment strategy was not effective for some species/samples. Approximately 8000 cells were recovered from each sample  and each cell was sequenced to a depth of 40000 reads.,parent bioproject:PRJNA994164,pubmed:38092908,,Zebrafish BC6,GSM7596940,,source name:Retina|tissue:Retina|cell type:Retinal neurons|geo loc name:missing|collection date:missing,Zebrafish BC6,We used cellranger v7.0  10X Genomics to align the sc  and snRNA seq datasets  following manufacturer’s instructions. For each species  sequencing reads were demultiplexed into distinct samples and the .fastq.gz files corresponding to each sample were aligned to reference transcriptomes to obtain binary alignment map .bam files. Assembly: Zv82 Supplementary files format and content: To include both exonic and intronic reads in the quantification of gene expression for each sample  regardless of cellular or nuclear origin  we applied velocyto to the corresponding .bam files. This generated two separate gene expression matrices GEMs; genes x cells for each sample  corresponding to “spliced” and “unspliced” reads. The two GEMs were summed element by element to obtain “total” GEM for each sample. Supplementary files format and content: GEMs from different sample runs were combined column wise concatenated to yield a full species’ GEM.,Retina,None,Retinas were dissected in Ames solution Sigma Aldrich; equilibrated with 95% O2/5% CO2 for all use immediately following enucleation. They were dissociated in papain  followed by FACS sorting. Cells were stained for either THY1/CD90 to enrich for RGCs or for CD73 to deplete photoreceptors. Single cell libraries were generated using the Chromium 3’ V3 platform 10X Genomics  Pleasanton  CA according to the manufacturer’s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs where nuclear lysis and barcoded reverse transcription of RNA would take place to yield full length cDNA; this was followed by amplification  enzymatic fragmentation  and 5’ adaptor and sample index attachment to yield the final libraries. Single cell RNA sequecning 10X Genomics,,tissue:Retina|cell type:Retinal neurons,GSM7596940,GSM7596940: Zebrafish BC6; Danio rerio; RNA Seq,GSM7596940 r1,GSM7596940,1,Retinas were dissected in Ames solution Sigma Aldrich; equilibrated with 95% O2/5% CO2 for all use immediately following enucleation. They were dissociated in papain  followed by FACS sorting. Cells were stained for either THY1/CD90 to enrich for RGCs or for CD73 to deplete photoreceptors. Single cell libraries were generated using the Chromium three prime V3 platform 10X Genomics  Pleasanton  CA according to the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs where nuclear lysis and barcoded reverse transcription of RNA would take place to yield full length cDNA; this was followed by amplification  enzymatic fragmentation  and five prime adaptor and sample index attachment to yield the final libraries. Single cell RNA sequecning 10X Genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP449239,,intentional duplicate,ZfishBC6.bam,10X Genomics bam file,5448150848.0,55593376.0,GSM7596940 r1,0:98,A:1618648587;C:1039410282;G:1103144747;T:1685792809;N:1154423,98,,,,1618648587,1039410282,1103144747,1685792809,1154423,SRX20999599,SRS18272872,SRA1672086,"Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley","Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley",1,0.8629,,0.27443,,0.80641,,0.50269,,98,,B,,usable mapping rate,illumina,novaseq_era,full_length,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-07-12,Undetermined,Undetermined,Eye,Sensory System
76694,SRR25253551,SRX20999598,SRS18272871,SRP449239,PRJNA994180,Evolution of neuronal cell classes and types in the vertebrate retina [Zebrafish],GSE237214,Transcriptome Analysis,The basic plan of the retina is conserved across vertebrates  yet species differ profoundly in their visual needs Baden et al.  2020. One might expect that retinal cell types evolved to accommodate these varied needs  but this has not been systematically studied. Here  we generated and integrated single cell transcriptomic atlases of the retina from 17 species: humans  two non human primates  four rodents  three ungulates  opossum  ferret  tree shrew  a teleost fish  a bird  a reptile and a lamprey. Molecular conservation of the six retinal cell classes photoreceptors  horizontal cells  bipolar cells  amacrine cells  retinal ganglion cells [RGCs] and Müller glia is striking  with transcriptomic differences across species correlated with evolutionary distance. Major subclasses are also conserved  whereas variation among types within classes or subclasses is more pronounced. However  an integrative analysis revealed that numerous types are shared across species based on conserved gene expression programs that likely trace back to the common ancestor of jawed vertebrates. The degree of variation among types increases from the outer retina photoreceptors to the inner retina RGCs  suggesting that evolution acts preferentially to shape the retinal output. Finally  we identified mammalian orthologs of midget RGCs  which comprise >80% of RGCs in the human retina  subserve high acuity vision  and were believed to be primate specific Berson  2008; in contrast  the mouse orthologs comprise <2% of mouse RGCs. Projections both primate and mouse orthologous types are overrepresented in the thalamus  which supplies the primary visual cortex. We suggest that midget RGCs are not primate innovations  but descendants of evolutionarily ancient types that decreased in size and increased in number as primates evolved  thereby facilitating high visual acuity and increased cortical processing of visual information. Overall design: Single cell RNA seq was performed on cells isolated from fresh retina. Fluorescence activated cell sorting was used to collect Calcein blueCB positive live cells. For some collections  CB+ cells were further seprated using CD90/THY1 and/or CD73 expression as an strategy to enrich for RGCs and/or to deplete phototreceptors  respectively Please note that he enrichment strategy was not effective for some species/samples. Approximately 8000 cells were recovered from each sample  and each cell was sequenced to a depth of 40000 reads.,parent bioproject:PRJNA994164,pubmed:38092908,,Zebrafish BC5,GSM7596939,,source name:Retina|tissue:Retina|cell type:Retinal neurons|geo loc name:missing|collection date:missing,Zebrafish BC5,We used cellranger v7.0  10X Genomics to align the sc  and snRNA seq datasets  following manufacturer’s instructions. For each species  sequencing reads were demultiplexed into distinct samples and the .fastq.gz files corresponding to each sample were aligned to reference transcriptomes to obtain binary alignment map .bam files. Assembly: Zv82 Supplementary files format and content: To include both exonic and intronic reads in the quantification of gene expression for each sample  regardless of cellular or nuclear origin  we applied velocyto to the corresponding .bam files. This generated two separate gene expression matrices GEMs; genes x cells for each sample  corresponding to “spliced” and “unspliced” reads. The two GEMs were summed element by element to obtain “total” GEM for each sample. Supplementary files format and content: GEMs from different sample runs were combined column wise concatenated to yield a full species’ GEM.,Retina,None,Retinas were dissected in Ames solution Sigma Aldrich; equilibrated with 95% O2/5% CO2 for all use immediately following enucleation. They were dissociated in papain  followed by FACS sorting. Cells were stained for either THY1/CD90 to enrich for RGCs or for CD73 to deplete photoreceptors. Single cell libraries were generated using the Chromium 3’ V3 platform 10X Genomics  Pleasanton  CA according to the manufacturer’s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs where nuclear lysis and barcoded reverse transcription of RNA would take place to yield full length cDNA; this was followed by amplification  enzymatic fragmentation  and 5’ adaptor and sample index attachment to yield the final libraries. Single cell RNA sequecning 10X Genomics,,tissue:Retina|cell type:Retinal neurons,GSM7596939,GSM7596939: Zebrafish BC5; Danio rerio; RNA Seq,GSM7596939 r1,GSM7596939,1,Retinas were dissected in Ames solution Sigma Aldrich; equilibrated with 95% O2/5% CO2 for all use immediately following enucleation. They were dissociated in papain  followed by FACS sorting. Cells were stained for either THY1/CD90 to enrich for RGCs or for CD73 to deplete photoreceptors. Single cell libraries were generated using the Chromium three prime V3 platform 10X Genomics  Pleasanton  CA according to the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs where nuclear lysis and barcoded reverse transcription of RNA would take place to yield full length cDNA; this was followed by amplification  enzymatic fragmentation  and five prime adaptor and sample index attachment to yield the final libraries. Single cell RNA sequecning 10X Genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP449239,,intentional duplicate,ZfishBC5.bam,10X Genomics bam file,5999974344.0,61224228.0,GSM7596939 r1,0:98,A:1800524734;C:1128470469;G:1198385405;T:1871305613;N:1288123,98,,,,1800524734,1128470469,1198385405,1871305613,1288123,SRX20999598,SRS18272871,SRA1672086,"Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley","Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley",1,0.85583,,0.2784,,0.80549,,0.50577,,98,,B,,usable mapping rate,illumina,novaseq_era,full_length,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-07-12,Undetermined,Undetermined,Eye,Sensory System
76695,SRR25253552,SRX20999597,SRS18272870,SRP449239,PRJNA994180,Evolution of neuronal cell classes and types in the vertebrate retina [Zebrafish],GSE237214,Transcriptome Analysis,The basic plan of the retina is conserved across vertebrates  yet species differ profoundly in their visual needs Baden et al.  2020. One might expect that retinal cell types evolved to accommodate these varied needs  but this has not been systematically studied. Here  we generated and integrated single cell transcriptomic atlases of the retina from 17 species: humans  two non human primates  four rodents  three ungulates  opossum  ferret  tree shrew  a teleost fish  a bird  a reptile and a lamprey. Molecular conservation of the six retinal cell classes photoreceptors  horizontal cells  bipolar cells  amacrine cells  retinal ganglion cells [RGCs] and Müller glia is striking  with transcriptomic differences across species correlated with evolutionary distance. Major subclasses are also conserved  whereas variation among types within classes or subclasses is more pronounced. However  an integrative analysis revealed that numerous types are shared across species based on conserved gene expression programs that likely trace back to the common ancestor of jawed vertebrates. The degree of variation among types increases from the outer retina photoreceptors to the inner retina RGCs  suggesting that evolution acts preferentially to shape the retinal output. Finally  we identified mammalian orthologs of midget RGCs  which comprise >80% of RGCs in the human retina  subserve high acuity vision  and were believed to be primate specific Berson  2008; in contrast  the mouse orthologs comprise <2% of mouse RGCs. Projections both primate and mouse orthologous types are overrepresented in the thalamus  which supplies the primary visual cortex. We suggest that midget RGCs are not primate innovations  but descendants of evolutionarily ancient types that decreased in size and increased in number as primates evolved  thereby facilitating high visual acuity and increased cortical processing of visual information. Overall design: Single cell RNA seq was performed on cells isolated from fresh retina. Fluorescence activated cell sorting was used to collect Calcein blueCB positive live cells. For some collections  CB+ cells were further seprated using CD90/THY1 and/or CD73 expression as an strategy to enrich for RGCs and/or to deplete phototreceptors  respectively Please note that he enrichment strategy was not effective for some species/samples. Approximately 8000 cells were recovered from each sample  and each cell was sequenced to a depth of 40000 reads.,parent bioproject:PRJNA994164,pubmed:38092908,,Zebrafish BC4,GSM7596938,,source name:Retina|tissue:Retina|cell type:Retinal neurons|geo loc name:missing|collection date:missing,Zebrafish BC4,We used cellranger v7.0  10X Genomics to align the sc  and snRNA seq datasets  following manufacturer’s instructions. For each species  sequencing reads were demultiplexed into distinct samples and the .fastq.gz files corresponding to each sample were aligned to reference transcriptomes to obtain binary alignment map .bam files. Assembly: Zv82 Supplementary files format and content: To include both exonic and intronic reads in the quantification of gene expression for each sample  regardless of cellular or nuclear origin  we applied velocyto to the corresponding .bam files. This generated two separate gene expression matrices GEMs; genes x cells for each sample  corresponding to “spliced” and “unspliced” reads. The two GEMs were summed element by element to obtain “total” GEM for each sample. Supplementary files format and content: GEMs from different sample runs were combined column wise concatenated to yield a full species’ GEM.,Retina,None,Retinas were dissected in Ames solution Sigma Aldrich; equilibrated with 95% O2/5% CO2 for all use immediately following enucleation. They were dissociated in papain  followed by FACS sorting. Cells were stained for either THY1/CD90 to enrich for RGCs or for CD73 to deplete photoreceptors. Single cell libraries were generated using the Chromium 3’ V3 platform 10X Genomics  Pleasanton  CA according to the manufacturer’s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs where nuclear lysis and barcoded reverse transcription of RNA would take place to yield full length cDNA; this was followed by amplification  enzymatic fragmentation  and 5’ adaptor and sample index attachment to yield the final libraries. Single cell RNA sequecning 10X Genomics,,tissue:Retina|cell type:Retinal neurons,GSM7596938,GSM7596938: Zebrafish BC4; Danio rerio; RNA Seq,GSM7596938 r1,GSM7596938,1,Retinas were dissected in Ames solution Sigma Aldrich; equilibrated with 95% O2/5% CO2 for all use immediately following enucleation. They were dissociated in papain  followed by FACS sorting. Cells were stained for either THY1/CD90 to enrich for RGCs or for CD73 to deplete photoreceptors. Single cell libraries were generated using the Chromium three prime V3 platform 10X Genomics  Pleasanton  CA according to the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs where nuclear lysis and barcoded reverse transcription of RNA would take place to yield full length cDNA; this was followed by amplification  enzymatic fragmentation  and five prime adaptor and sample index attachment to yield the final libraries. Single cell RNA sequecning 10X Genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP449239,,intentional duplicate,ZfishBC4.bam,10X Genomics bam file,3888885196.0,39682502.0,GSM7596938 r1,0:98,A:1137239303;C:751206133;G:783572508;T:1216050370;N:816882,98,,,,1137239303,751206133,783572508,1216050370,816882,SRX20999597,SRS18272870,SRA1672086,"Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley","Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley",1,0.86728,,0.21876,,0.81578,,0.49956,,98,,B,,usable mapping rate,illumina,novaseq_era,full_length,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-07-12,Undetermined,Undetermined,Eye,Sensory System
76696,SRR25253553,SRX20999596,SRS18272869,SRP449239,PRJNA994180,Evolution of neuronal cell classes and types in the vertebrate retina [Zebrafish],GSE237214,Transcriptome Analysis,The basic plan of the retina is conserved across vertebrates  yet species differ profoundly in their visual needs Baden et al.  2020. One might expect that retinal cell types evolved to accommodate these varied needs  but this has not been systematically studied. Here  we generated and integrated single cell transcriptomic atlases of the retina from 17 species: humans  two non human primates  four rodents  three ungulates  opossum  ferret  tree shrew  a teleost fish  a bird  a reptile and a lamprey. Molecular conservation of the six retinal cell classes photoreceptors  horizontal cells  bipolar cells  amacrine cells  retinal ganglion cells [RGCs] and Müller glia is striking  with transcriptomic differences across species correlated with evolutionary distance. Major subclasses are also conserved  whereas variation among types within classes or subclasses is more pronounced. However  an integrative analysis revealed that numerous types are shared across species based on conserved gene expression programs that likely trace back to the common ancestor of jawed vertebrates. The degree of variation among types increases from the outer retina photoreceptors to the inner retina RGCs  suggesting that evolution acts preferentially to shape the retinal output. Finally  we identified mammalian orthologs of midget RGCs  which comprise >80% of RGCs in the human retina  subserve high acuity vision  and were believed to be primate specific Berson  2008; in contrast  the mouse orthologs comprise <2% of mouse RGCs. Projections both primate and mouse orthologous types are overrepresented in the thalamus  which supplies the primary visual cortex. We suggest that midget RGCs are not primate innovations  but descendants of evolutionarily ancient types that decreased in size and increased in number as primates evolved  thereby facilitating high visual acuity and increased cortical processing of visual information. Overall design: Single cell RNA seq was performed on cells isolated from fresh retina. Fluorescence activated cell sorting was used to collect Calcein blueCB positive live cells. For some collections  CB+ cells were further seprated using CD90/THY1 and/or CD73 expression as an strategy to enrich for RGCs and/or to deplete phototreceptors  respectively Please note that he enrichment strategy was not effective for some species/samples. Approximately 8000 cells were recovered from each sample  and each cell was sequenced to a depth of 40000 reads.,parent bioproject:PRJNA994164,pubmed:38092908,,Zebrafish BC3,GSM7596937,,source name:Retina|tissue:Retina|cell type:Retinal neurons|geo loc name:missing|collection date:missing,Zebrafish BC3,We used cellranger v7.0  10X Genomics to align the sc  and snRNA seq datasets  following manufacturer’s instructions. For each species  sequencing reads were demultiplexed into distinct samples and the .fastq.gz files corresponding to each sample were aligned to reference transcriptomes to obtain binary alignment map .bam files. Assembly: Zv82 Supplementary files format and content: To include both exonic and intronic reads in the quantification of gene expression for each sample  regardless of cellular or nuclear origin  we applied velocyto to the corresponding .bam files. This generated two separate gene expression matrices GEMs; genes x cells for each sample  corresponding to “spliced” and “unspliced” reads. The two GEMs were summed element by element to obtain “total” GEM for each sample. Supplementary files format and content: GEMs from different sample runs were combined column wise concatenated to yield a full species’ GEM.,Retina,None,Retinas were dissected in Ames solution Sigma Aldrich; equilibrated with 95% O2/5% CO2 for all use immediately following enucleation. They were dissociated in papain  followed by FACS sorting. Cells were stained for either THY1/CD90 to enrich for RGCs or for CD73 to deplete photoreceptors. Single cell libraries were generated using the Chromium 3’ V3 platform 10X Genomics  Pleasanton  CA according to the manufacturer’s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs where nuclear lysis and barcoded reverse transcription of RNA would take place to yield full length cDNA; this was followed by amplification  enzymatic fragmentation  and 5’ adaptor and sample index attachment to yield the final libraries. Single cell RNA sequecning 10X Genomics,,tissue:Retina|cell type:Retinal neurons,GSM7596937,GSM7596937: Zebrafish BC3; Danio rerio; RNA Seq,GSM7596937 r1,GSM7596937,1,Retinas were dissected in Ames solution Sigma Aldrich; equilibrated with 95% O2/5% CO2 for all use immediately following enucleation. They were dissociated in papain  followed by FACS sorting. Cells were stained for either THY1/CD90 to enrich for RGCs or for CD73 to deplete photoreceptors. Single cell libraries were generated using the Chromium three prime V3 platform 10X Genomics  Pleasanton  CA according to the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs where nuclear lysis and barcoded reverse transcription of RNA would take place to yield full length cDNA; this was followed by amplification  enzymatic fragmentation  and five prime adaptor and sample index attachment to yield the final libraries. Single cell RNA sequecning 10X Genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP449239,,intentional duplicate,ZfishBC3.bam,10X Genomics bam file,4133686256.0,42180472.0,GSM7596937 r1,0:98,A:1223733383;C:788484354;G:823319620;T:1297264565;N:884334,98,,,,1223733383,788484354,823319620,1297264565,884334,SRX20999596,SRS18272869,SRA1672086,"Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley","Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley",1,0.85846,,0.22015,,0.81716,,0.48798,,98,,B,,usable mapping rate,illumina,novaseq_era,full_length,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-07-12,Undetermined,Undetermined,Eye,Sensory System
76697,SRR25253554,SRX20999595,SRS18272868,SRP449239,PRJNA994180,Evolution of neuronal cell classes and types in the vertebrate retina [Zebrafish],GSE237214,Transcriptome Analysis,The basic plan of the retina is conserved across vertebrates  yet species differ profoundly in their visual needs Baden et al.  2020. One might expect that retinal cell types evolved to accommodate these varied needs  but this has not been systematically studied. Here  we generated and integrated single cell transcriptomic atlases of the retina from 17 species: humans  two non human primates  four rodents  three ungulates  opossum  ferret  tree shrew  a teleost fish  a bird  a reptile and a lamprey. Molecular conservation of the six retinal cell classes photoreceptors  horizontal cells  bipolar cells  amacrine cells  retinal ganglion cells [RGCs] and Müller glia is striking  with transcriptomic differences across species correlated with evolutionary distance. Major subclasses are also conserved  whereas variation among types within classes or subclasses is more pronounced. However  an integrative analysis revealed that numerous types are shared across species based on conserved gene expression programs that likely trace back to the common ancestor of jawed vertebrates. The degree of variation among types increases from the outer retina photoreceptors to the inner retina RGCs  suggesting that evolution acts preferentially to shape the retinal output. Finally  we identified mammalian orthologs of midget RGCs  which comprise >80% of RGCs in the human retina  subserve high acuity vision  and were believed to be primate specific Berson  2008; in contrast  the mouse orthologs comprise <2% of mouse RGCs. Projections both primate and mouse orthologous types are overrepresented in the thalamus  which supplies the primary visual cortex. We suggest that midget RGCs are not primate innovations  but descendants of evolutionarily ancient types that decreased in size and increased in number as primates evolved  thereby facilitating high visual acuity and increased cortical processing of visual information. Overall design: Single cell RNA seq was performed on cells isolated from fresh retina. Fluorescence activated cell sorting was used to collect Calcein blueCB positive live cells. For some collections  CB+ cells were further seprated using CD90/THY1 and/or CD73 expression as an strategy to enrich for RGCs and/or to deplete phototreceptors  respectively Please note that he enrichment strategy was not effective for some species/samples. Approximately 8000 cells were recovered from each sample  and each cell was sequenced to a depth of 40000 reads.,parent bioproject:PRJNA994164,pubmed:38092908,,Zebrafish BC2,GSM7596936,,source name:Retina|tissue:Retina|cell type:Retinal neurons|geo loc name:missing|collection date:missing,Zebrafish BC2,We used cellranger v7.0  10X Genomics to align the sc  and snRNA seq datasets  following manufacturer’s instructions. For each species  sequencing reads were demultiplexed into distinct samples and the .fastq.gz files corresponding to each sample were aligned to reference transcriptomes to obtain binary alignment map .bam files. Assembly: Zv82 Supplementary files format and content: To include both exonic and intronic reads in the quantification of gene expression for each sample  regardless of cellular or nuclear origin  we applied velocyto to the corresponding .bam files. This generated two separate gene expression matrices GEMs; genes x cells for each sample  corresponding to “spliced” and “unspliced” reads. The two GEMs were summed element by element to obtain “total” GEM for each sample. Supplementary files format and content: GEMs from different sample runs were combined column wise concatenated to yield a full species’ GEM.,Retina,None,Retinas were dissected in Ames solution Sigma Aldrich; equilibrated with 95% O2/5% CO2 for all use immediately following enucleation. They were dissociated in papain  followed by FACS sorting. Cells were stained for either THY1/CD90 to enrich for RGCs or for CD73 to deplete photoreceptors. Single cell libraries were generated using the Chromium 3’ V3 platform 10X Genomics  Pleasanton  CA according to the manufacturer’s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs where nuclear lysis and barcoded reverse transcription of RNA would take place to yield full length cDNA; this was followed by amplification  enzymatic fragmentation  and 5’ adaptor and sample index attachment to yield the final libraries. Single cell RNA sequecning 10X Genomics,,tissue:Retina|cell type:Retinal neurons,GSM7596936,GSM7596936: Zebrafish BC2; Danio rerio; RNA Seq,GSM7596936 r1,GSM7596936,1,Retinas were dissected in Ames solution Sigma Aldrich; equilibrated with 95% O2/5% CO2 for all use immediately following enucleation. They were dissociated in papain  followed by FACS sorting. Cells were stained for either THY1/CD90 to enrich for RGCs or for CD73 to deplete photoreceptors. Single cell libraries were generated using the Chromium three prime V3 platform 10X Genomics  Pleasanton  CA according to the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs where nuclear lysis and barcoded reverse transcription of RNA would take place to yield full length cDNA; this was followed by amplification  enzymatic fragmentation  and five prime adaptor and sample index attachment to yield the final libraries. Single cell RNA sequecning 10X Genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP449239,,intentional duplicate,ZfishBC2.bam,10X Genomics bam file,6321874454.0,64508923.0,GSM7596936 r1,0:98,A:1876697721;C:1233227329;G:1289921693;T:1921011454;N:1016257,98,,,,1876697721,1233227329,1289921693,1921011454,1016257,SRX20999595,SRS18272868,SRA1672086,"Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley","Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley",1,0.85024,,0.27225,,0.81314,,0.48938,,98,,B,,usable mapping rate,illumina,novaseq_era,full_length,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-07-12,Undetermined,Undetermined,Eye,Sensory System
76698,SRR25253555,SRX20999594,SRS18272867,SRP449239,PRJNA994180,Evolution of neuronal cell classes and types in the vertebrate retina [Zebrafish],GSE237214,Transcriptome Analysis,The basic plan of the retina is conserved across vertebrates  yet species differ profoundly in their visual needs Baden et al.  2020. One might expect that retinal cell types evolved to accommodate these varied needs  but this has not been systematically studied. Here  we generated and integrated single cell transcriptomic atlases of the retina from 17 species: humans  two non human primates  four rodents  three ungulates  opossum  ferret  tree shrew  a teleost fish  a bird  a reptile and a lamprey. Molecular conservation of the six retinal cell classes photoreceptors  horizontal cells  bipolar cells  amacrine cells  retinal ganglion cells [RGCs] and Müller glia is striking  with transcriptomic differences across species correlated with evolutionary distance. Major subclasses are also conserved  whereas variation among types within classes or subclasses is more pronounced. However  an integrative analysis revealed that numerous types are shared across species based on conserved gene expression programs that likely trace back to the common ancestor of jawed vertebrates. The degree of variation among types increases from the outer retina photoreceptors to the inner retina RGCs  suggesting that evolution acts preferentially to shape the retinal output. Finally  we identified mammalian orthologs of midget RGCs  which comprise >80% of RGCs in the human retina  subserve high acuity vision  and were believed to be primate specific Berson  2008; in contrast  the mouse orthologs comprise <2% of mouse RGCs. Projections both primate and mouse orthologous types are overrepresented in the thalamus  which supplies the primary visual cortex. We suggest that midget RGCs are not primate innovations  but descendants of evolutionarily ancient types that decreased in size and increased in number as primates evolved  thereby facilitating high visual acuity and increased cortical processing of visual information. Overall design: Single cell RNA seq was performed on cells isolated from fresh retina. Fluorescence activated cell sorting was used to collect Calcein blueCB positive live cells. For some collections  CB+ cells were further seprated using CD90/THY1 and/or CD73 expression as an strategy to enrich for RGCs and/or to deplete phototreceptors  respectively Please note that he enrichment strategy was not effective for some species/samples. Approximately 8000 cells were recovered from each sample  and each cell was sequenced to a depth of 40000 reads.,parent bioproject:PRJNA994164,pubmed:38092908,,Zebrafish BC1,GSM7596935,,source name:Retina|tissue:Retina|cell type:Retinal neurons|geo loc name:missing|collection date:missing,Zebrafish BC1,We used cellranger v7.0  10X Genomics to align the sc  and snRNA seq datasets  following manufacturer’s instructions. For each species  sequencing reads were demultiplexed into distinct samples and the .fastq.gz files corresponding to each sample were aligned to reference transcriptomes to obtain binary alignment map .bam files. Assembly: Zv82 Supplementary files format and content: To include both exonic and intronic reads in the quantification of gene expression for each sample  regardless of cellular or nuclear origin  we applied velocyto to the corresponding .bam files. This generated two separate gene expression matrices GEMs; genes x cells for each sample  corresponding to “spliced” and “unspliced” reads. The two GEMs were summed element by element to obtain “total” GEM for each sample. Supplementary files format and content: GEMs from different sample runs were combined column wise concatenated to yield a full species’ GEM.,Retina,None,Retinas were dissected in Ames solution Sigma Aldrich; equilibrated with 95% O2/5% CO2 for all use immediately following enucleation. They were dissociated in papain  followed by FACS sorting. Cells were stained for either THY1/CD90 to enrich for RGCs or for CD73 to deplete photoreceptors. Single cell libraries were generated using the Chromium 3’ V3 platform 10X Genomics  Pleasanton  CA according to the manufacturer’s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs where nuclear lysis and barcoded reverse transcription of RNA would take place to yield full length cDNA; this was followed by amplification  enzymatic fragmentation  and 5’ adaptor and sample index attachment to yield the final libraries. Single cell RNA sequecning 10X Genomics,,tissue:Retina|cell type:Retinal neurons,GSM7596935,GSM7596935: Zebrafish BC1; Danio rerio; RNA Seq,GSM7596935 r1,GSM7596935,1,Retinas were dissected in Ames solution Sigma Aldrich; equilibrated with 95% O2/5% CO2 for all use immediately following enucleation. They were dissociated in papain  followed by FACS sorting. Cells were stained for either THY1/CD90 to enrich for RGCs or for CD73 to deplete photoreceptors. Single cell libraries were generated using the Chromium three prime V3 platform 10X Genomics  Pleasanton  CA according to the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs where nuclear lysis and barcoded reverse transcription of RNA would take place to yield full length cDNA; this was followed by amplification  enzymatic fragmentation  and five prime adaptor and sample index attachment to yield the final libraries. Single cell RNA sequecning 10X Genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP449239,,intentional duplicate,ZfishBC1.bam,10X Genomics bam file,6529192180.0,66624410.0,GSM7596935 r1,0:98,A:1937703976;C:1274004687;G:1327972080;T:1988461414;N:1050023,98,,,,1937703976,1274004687,1327972080,1988461414,1050023,SRX20999594,SRS18272867,SRA1672086,"Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley","Karthik Shekhar, Chemical and Biomolecular Engineering, UC Berkeley",1,0.84848,,0.27131,,0.81233,,0.48186,,98,,B,,usable mapping rate,illumina,novaseq_era,full_length,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-07-12,Undetermined,Undetermined,Eye,Sensory System