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
59187,SRR11773518,SRX8326557,SRS6646245,SRP261174,PRJNA631796,Analysis of gene network branching during optic cup morphogenesis in zebrafish RNA Seq,GSE150346,Transcriptome Analysis,We characterize transcriptomic landscape using RNA seq in isolated NR and RPE populations in zebrafish. Overall design: RNA seq profile of sorted zebrafish cell populations of retinal progenitors  NR at 18 hpf  NR at 23 hpf  RPE at 18 hpf and RPE at 23 hpf,,pubmed:34162866,,NR23 3,GSM4547302,,tissue:sorted neural retinal cells|cell type:sorted neural retinal cells|developmental stage:23 hpf|transgenic line:tgvsx2.2:GFP,NR23 3,Each sample was mapped against the index genome built from danRer10 assembly using Tophat v2.1.0 The aligned read BAM files were assembled into transcripts and their abundance was estimated by Cufflinks  v2.2.1 Genome build: danRer10 Supplementary files format and content: txt file including the FPKM values for all genes in each eye domain,sorted neural retinal cells,Zebrafish cells were dissociated and prepared for FACS as described in Manoli and Driever  2012,Total RNA was extracted by TRIzol Invitrogen following manufacturer’s protocol. Possible DNA contamination was eliminated treating the RNA samples with with TURBO DNAse free Ambion. Ribo Zero® rRNA Removal Kit Illumina,Zebrafish embryos were raised in E3 medium at 28 °C,cell type:sorted neural retinal cells|developmental stage:23 hpf|transgenic line:tgvsx2.2:GFP,GSM4547302,GSM4547302: NR23 3; Danio rerio; RNA Seq,GSM4547302,,1,Total RNA was extracted by TRIzol Invitrogen following manufacturer's protocol. Possible DNA contamination was eliminated treating the RNA samples with with TURBO DNAse free Ambion. Ribo Zero® rRNA Removal Kit Illumina,GEO Accession:GSM4547302,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP261174,,,NR23_3_R2.fastq.gz NR23_3_R1.fastq.gz,fastq fastq,11441580000.0,45766320.0,GSM4547302 r1,0:125 1:125,A:3193544242;C:2507284318;G:2578059588;T:3124649357;N:38042495,125,125,,,3193544242,2507284318,2578059588,3124649357,38042495,SRX8326557,SRS6646245,SRA1074492,GEO,CABD,2,0.89036,0.87126,0.2869,0.27767,0.7235,0.73062,0.46892,0.47913,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,Spain,2020-05-11,Segmentation,Embryo,Eye,Sensory System
59188,SRR11773517,SRX8326556,SRS6646244,SRP261174,PRJNA631796,Analysis of gene network branching during optic cup morphogenesis in zebrafish RNA Seq,GSE150346,Transcriptome Analysis,We characterize transcriptomic landscape using RNA seq in isolated NR and RPE populations in zebrafish. Overall design: RNA seq profile of sorted zebrafish cell populations of retinal progenitors  NR at 18 hpf  NR at 23 hpf  RPE at 18 hpf and RPE at 23 hpf,,pubmed:34162866,,NR23 2,GSM4547301,,tissue:sorted neural retinal cells|cell type:sorted neural retinal cells|developmental stage:23 hpf|transgenic line:tgvsx2.2:GFP,NR23 2,Each sample was mapped against the index genome built from danRer10 assembly using Tophat v2.1.0 The aligned read BAM files were assembled into transcripts and their abundance was estimated by Cufflinks  v2.2.1 Genome build: danRer10 Supplementary files format and content: txt file including the FPKM values for all genes in each eye domain,sorted neural retinal cells,Zebrafish cells were dissociated and prepared for FACS as described in Manoli and Driever  2012,Total RNA was extracted by TRIzol Invitrogen following manufacturer’s protocol. Possible DNA contamination was eliminated treating the RNA samples with with TURBO DNAse free Ambion. Ribo Zero® rRNA Removal Kit Illumina,Zebrafish embryos were raised in E3 medium at 28 °C,cell type:sorted neural retinal cells|developmental stage:23 hpf|transgenic line:tgvsx2.2:GFP,GSM4547301,GSM4547301: NR23 2; Danio rerio; RNA Seq,GSM4547301,,1,Total RNA was extracted by TRIzol Invitrogen following manufacturer's protocol. Possible DNA contamination was eliminated treating the RNA samples with with TURBO DNAse free Ambion. Ribo Zero® rRNA Removal Kit Illumina,GEO Accession:GSM4547301,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP261174,,,NR23_2_R2.fastq.gz NR23_2_R1.fastq.gz,fastq fastq,12118709750.0,48474839.0,GSM4547301 r1,0:125 1:125,A:3357426665;C:2683042785;G:2780933570;T:3256906658;N:40400072,125,125,,,3357426665,2683042785,2780933570,3256906658,40400072,SRX8326556,SRS6646244,SRA1074492,GEO,CABD,2,0.89955,0.882,0.24791,0.24102,0.73456,0.74123,0.49599,0.50353,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,Spain,2020-05-11,Segmentation,Embryo,Eye,Sensory System
59189,SRR11773516,SRX8326555,SRS6646243,SRP261174,PRJNA631796,Analysis of gene network branching during optic cup morphogenesis in zebrafish RNA Seq,GSE150346,Transcriptome Analysis,We characterize transcriptomic landscape using RNA seq in isolated NR and RPE populations in zebrafish. Overall design: RNA seq profile of sorted zebrafish cell populations of retinal progenitors  NR at 18 hpf  NR at 23 hpf  RPE at 18 hpf and RPE at 23 hpf,,pubmed:34162866,,NR23 1,GSM4547300,,tissue:sorted neural retinal cells|cell type:sorted neural retinal cells|developmental stage:23 hpf|transgenic line:tgvsx2.2:GFP,NR23 1,Each sample was mapped against the index genome built from danRer10 assembly using Tophat v2.1.0 The aligned read BAM files were assembled into transcripts and their abundance was estimated by Cufflinks  v2.2.1 Genome build: danRer10 Supplementary files format and content: txt file including the FPKM values for all genes in each eye domain,sorted neural retinal cells,Zebrafish cells were dissociated and prepared for FACS as described in Manoli and Driever  2012,Total RNA was extracted by TRIzol Invitrogen following manufacturer’s protocol. Possible DNA contamination was eliminated treating the RNA samples with with TURBO DNAse free Ambion. Ribo Zero® rRNA Removal Kit Illumina,Zebrafish embryos were raised in E3 medium at 28 °C,cell type:sorted neural retinal cells|developmental stage:23 hpf|transgenic line:tgvsx2.2:GFP,GSM4547300,GSM4547300: NR23 1; Danio rerio; RNA Seq,GSM4547300,,1,Total RNA was extracted by TRIzol Invitrogen following manufacturer's protocol. Possible DNA contamination was eliminated treating the RNA samples with with TURBO DNAse free Ambion. Ribo Zero® rRNA Removal Kit Illumina,GEO Accession:GSM4547300,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP261174,,,NR23_1_R2.fastq.gz NR23_1_R1.fastq.gz,fastq fastq,11283384750.0,45133539.0,GSM4547300 r1,0:125 1:125,A:3166451884;C:2455917792;G:2536626330;T:3086588302;N:37800442,125,125,,,3166451884,2455917792,2536626330,3086588302,37800442,SRX8326555,SRS6646243,SRA1074492,GEO,CABD,2,0.88471,0.86597,0.30542,0.29503,0.74085,0.74692,0.49997,0.49285,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,Spain,2020-05-11,Segmentation,Embryo,Eye,Sensory System
59190,SRR11773515,SRX8326554,SRS6646242,SRP261174,PRJNA631796,Analysis of gene network branching during optic cup morphogenesis in zebrafish RNA Seq,GSE150346,Transcriptome Analysis,We characterize transcriptomic landscape using RNA seq in isolated NR and RPE populations in zebrafish. Overall design: RNA seq profile of sorted zebrafish cell populations of retinal progenitors  NR at 18 hpf  NR at 23 hpf  RPE at 18 hpf and RPE at 23 hpf,,pubmed:34162866,,NR18 3,GSM4547299,,tissue:sorted neural retinal cells|cell type:sorted neural retinal cells|developmental stage:18 hpf|transgenic line:tgvsx2.2:GFP,NR18 3,Each sample was mapped against the index genome built from danRer10 assembly using Tophat v2.1.0 The aligned read BAM files were assembled into transcripts and their abundance was estimated by Cufflinks  v2.2.1 Genome build: danRer10 Supplementary files format and content: txt file including the FPKM values for all genes in each eye domain,sorted neural retinal cells,Zebrafish cells were dissociated and prepared for FACS as described in Manoli and Driever  2012,Total RNA was extracted by TRIzol Invitrogen following manufacturer’s protocol. Possible DNA contamination was eliminated treating the RNA samples with with TURBO DNAse free Ambion. Ribo Zero® rRNA Removal Kit Illumina,Zebrafish embryos were raised in E3 medium at 28 °C,cell type:sorted neural retinal cells|developmental stage:18 hpf|transgenic line:tgvsx2.2:GFP,GSM4547299,GSM4547299: NR18 3; Danio rerio; RNA Seq,GSM4547299,,1,Total RNA was extracted by TRIzol Invitrogen following manufacturer's protocol. Possible DNA contamination was eliminated treating the RNA samples with with TURBO DNAse free Ambion. Ribo Zero® rRNA Removal Kit Illumina,GEO Accession:GSM4547299,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP261174,,,NR18_3_R1.fastq.gz NR18_3_R2.fastq.gz,fastq fastq,20765853000.0,83063412.0,GSM4547299 r1,0:125 1:125,A:5453638173;C:4893182050;G:5092402153;T:5318552251;N:8078373,125,125,,,5453638173,4893182050,5092402153,5318552251,8078373,SRX8326554,SRS6646242,SRA1074492,GEO,CABD,2,0.9495,0.94981,0.19027,0.18835,0.72147,0.72429,0.48833,0.48746,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,Spain,2020-05-11,Segmentation,Embryo,Eye,Sensory System
59191,SRR11773514,SRX8326553,SRS6646241,SRP261174,PRJNA631796,Analysis of gene network branching during optic cup morphogenesis in zebrafish RNA Seq,GSE150346,Transcriptome Analysis,We characterize transcriptomic landscape using RNA seq in isolated NR and RPE populations in zebrafish. Overall design: RNA seq profile of sorted zebrafish cell populations of retinal progenitors  NR at 18 hpf  NR at 23 hpf  RPE at 18 hpf and RPE at 23 hpf,,pubmed:34162866,,NR18 2,GSM4547298,,tissue:sorted neural retinal cells|cell type:sorted neural retinal cells|developmental stage:18 hpf|transgenic line:tgvsx2.2:GFP,NR18 2,Each sample was mapped against the index genome built from danRer10 assembly using Tophat v2.1.0 The aligned read BAM files were assembled into transcripts and their abundance was estimated by Cufflinks  v2.2.1 Genome build: danRer10 Supplementary files format and content: txt file including the FPKM values for all genes in each eye domain,sorted neural retinal cells,Zebrafish cells were dissociated and prepared for FACS as described in Manoli and Driever  2012,Total RNA was extracted by TRIzol Invitrogen following manufacturer’s protocol. Possible DNA contamination was eliminated treating the RNA samples with with TURBO DNAse free Ambion. Ribo Zero® rRNA Removal Kit Illumina,Zebrafish embryos were raised in E3 medium at 28 °C,cell type:sorted neural retinal cells|developmental stage:18 hpf|transgenic line:tgvsx2.2:GFP,GSM4547298,GSM4547298: NR18 2; Danio rerio; RNA Seq,GSM4547298,,1,Total RNA was extracted by TRIzol Invitrogen following manufacturer's protocol. Possible DNA contamination was eliminated treating the RNA samples with with TURBO DNAse free Ambion. Ribo Zero® rRNA Removal Kit Illumina,GEO Accession:GSM4547298,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP261174,,,NR18_2_R2.fastq.gz NR18_2_R1.fastq.gz,fastq fastq,16104497500.0,64417990.0,GSM4547298 r1,0:125 1:125,A:4426657875;C:3597354985;G:3719329924;T:4355202597;N:5952119,125,125,,,4426657875,3597354985,3719329924,4355202597,5952119,SRX8326553,SRS6646241,SRA1074492,GEO,CABD,2,0.92888,0.92961,0.2646,0.26484,0.71869,0.72046,0.47089,0.46472,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,Spain,2020-05-11,Segmentation,Embryo,Eye,Sensory System
59192,SRR11773513,SRX8326552,SRS6646240,SRP261174,PRJNA631796,Analysis of gene network branching during optic cup morphogenesis in zebrafish RNA Seq,GSE150346,Transcriptome Analysis,We characterize transcriptomic landscape using RNA seq in isolated NR and RPE populations in zebrafish. Overall design: RNA seq profile of sorted zebrafish cell populations of retinal progenitors  NR at 18 hpf  NR at 23 hpf  RPE at 18 hpf and RPE at 23 hpf,,pubmed:34162866,,NR18 1,GSM4547297,,tissue:sorted neural retinal cells|cell type:sorted neural retinal cells|developmental stage:18 hpf|transgenic line:tgvsx2.2:GFP,NR18 1,Each sample was mapped against the index genome built from danRer10 assembly using Tophat v2.1.0 The aligned read BAM files were assembled into transcripts and their abundance was estimated by Cufflinks  v2.2.1 Genome build: danRer10 Supplementary files format and content: txt file including the FPKM values for all genes in each eye domain,sorted neural retinal cells,Zebrafish cells were dissociated and prepared for FACS as described in Manoli and Driever  2012,Total RNA was extracted by TRIzol Invitrogen following manufacturer’s protocol. Possible DNA contamination was eliminated treating the RNA samples with with TURBO DNAse free Ambion. Ribo Zero® rRNA Removal Kit Illumina,Zebrafish embryos were raised in E3 medium at 28 °C,cell type:sorted neural retinal cells|developmental stage:18 hpf|transgenic line:tgvsx2.2:GFP,GSM4547297,GSM4547297: NR18 1; Danio rerio; RNA Seq,GSM4547297,,1,Total RNA was extracted by TRIzol Invitrogen following manufacturer's protocol. Possible DNA contamination was eliminated treating the RNA samples with with TURBO DNAse free Ambion. Ribo Zero® rRNA Removal Kit Illumina,GEO Accession:GSM4547297,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP261174,,,NR18_1_R2.fastq.gz NR18_1_R1.fastq.gz,fastq fastq,15427246750.0,61708987.0,GSM4547297 r1,0:125 1:125,A:4141782324;C:3545523818;G:3664555510;T:4069654010;N:5731088,125,125,,,4141782324,3545523818,3664555510,4069654010,5731088,SRX8326552,SRS6646240,SRA1074492,GEO,CABD,2,0.93716,0.93931,0.25986,0.25981,0.70701,0.70954,0.46766,0.47027,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,Spain,2020-05-11,Segmentation,Embryo,Eye,Sensory System
59193,SRR11773512,SRX8326551,SRS6646239,SRP261174,PRJNA631796,Analysis of gene network branching during optic cup morphogenesis in zebrafish RNA Seq,GSE150346,Transcriptome Analysis,We characterize transcriptomic landscape using RNA seq in isolated NR and RPE populations in zebrafish. Overall design: RNA seq profile of sorted zebrafish cell populations of retinal progenitors  NR at 18 hpf  NR at 23 hpf  RPE at 18 hpf and RPE at 23 hpf,,pubmed:34162866,,PG 3,GSM4547296,,tissue:sorted retinal progenitor cells|cell type:sorted retinal progenitor cells|developmental stage:16 hpf|transgenic line:tgvsx2.2:GFP,PG 3,Each sample was mapped against the index genome built from danRer10 assembly using Tophat v2.1.0 The aligned read BAM files were assembled into transcripts and their abundance was estimated by Cufflinks  v2.2.1 Genome build: danRer10 Supplementary files format and content: txt file including the FPKM values for all genes in each eye domain,sorted retinal progenitor cells,Zebrafish cells were dissociated and prepared for FACS as described in Manoli and Driever  2012,Total RNA was extracted by TRIzol Invitrogen following manufacturer’s protocol. Possible DNA contamination was eliminated treating the RNA samples with with TURBO DNAse free Ambion. Ribo Zero® rRNA Removal Kit Illumina,Zebrafish embryos were raised in E3 medium at 28 °C,cell type:sorted retinal progenitor cells|developmental stage:16 hpf|transgenic line:tgvsx2.2:GFP,GSM4547296,GSM4547296: PG 3; Danio rerio; RNA Seq,GSM4547296,,1,Total RNA was extracted by TRIzol Invitrogen following manufacturer's protocol. Possible DNA contamination was eliminated treating the RNA samples with with TURBO DNAse free Ambion. Ribo Zero® rRNA Removal Kit Illumina,GEO Accession:GSM4547296,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP261174,,,PG16_3_R1.fastq.gz,fastq,8842268375.0,70738147.0,GSM4547296 r1,0:125 1:0,A:2352817479;C:1996147557;G:1967653614;T:2525589488;N:60237,125,0,,,2352817479,1996147557,1967653614,2525589488,60237,SRX8326551,SRS6646239,SRA1074492,GEO,CABD,1,0.90222,,0.34198,,0.70853,,0.48133,,125,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,Spain,2020-05-11,Segmentation,Embryo,Eye,Sensory System
59194,SRR11773511,SRX8326550,SRS6646238,SRP261174,PRJNA631796,Analysis of gene network branching during optic cup morphogenesis in zebrafish RNA Seq,GSE150346,Transcriptome Analysis,We characterize transcriptomic landscape using RNA seq in isolated NR and RPE populations in zebrafish. Overall design: RNA seq profile of sorted zebrafish cell populations of retinal progenitors  NR at 18 hpf  NR at 23 hpf  RPE at 18 hpf and RPE at 23 hpf,,pubmed:34162866,,PG 2,GSM4547295,,tissue:sorted retinal progenitor cells|cell type:sorted retinal progenitor cells|developmental stage:16 hpf|transgenic line:tgvsx2.2:GFP,PG 2,Each sample was mapped against the index genome built from danRer10 assembly using Tophat v2.1.0 The aligned read BAM files were assembled into transcripts and their abundance was estimated by Cufflinks  v2.2.1 Genome build: danRer10 Supplementary files format and content: txt file including the FPKM values for all genes in each eye domain,sorted retinal progenitor cells,Zebrafish cells were dissociated and prepared for FACS as described in Manoli and Driever  2012,Total RNA was extracted by TRIzol Invitrogen following manufacturer’s protocol. Possible DNA contamination was eliminated treating the RNA samples with with TURBO DNAse free Ambion. Ribo Zero® rRNA Removal Kit Illumina,Zebrafish embryos were raised in E3 medium at 28 °C,cell type:sorted retinal progenitor cells|developmental stage:16 hpf|transgenic line:tgvsx2.2:GFP,GSM4547295,GSM4547295: PG 2; Danio rerio; RNA Seq,GSM4547295,,1,Total RNA was extracted by TRIzol Invitrogen following manufacturer's protocol. Possible DNA contamination was eliminated treating the RNA samples with with TURBO DNAse free Ambion. Ribo Zero® rRNA Removal Kit Illumina,GEO Accession:GSM4547295,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP261174,,,PG16_2_R1.fastq.gz,fastq,9860997500.0,78887980.0,GSM4547295 r1,0:125 1:0,A:2453379488;C:2434250915;G:2295560807;T:2677739557;N:66733,125,0,,,2453379488,2434250915,2295560807,2677739557,66733,SRX8326550,SRS6646238,SRA1074492,GEO,CABD,1,0.88896,,0.198,,0.71356,,0.48154,,125,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,Spain,2020-05-11,Segmentation,Embryo,Eye,Sensory System
59195,SRR11773510,SRX8326549,SRS6646237,SRP261174,PRJNA631796,Analysis of gene network branching during optic cup morphogenesis in zebrafish RNA Seq,GSE150346,Transcriptome Analysis,We characterize transcriptomic landscape using RNA seq in isolated NR and RPE populations in zebrafish. Overall design: RNA seq profile of sorted zebrafish cell populations of retinal progenitors  NR at 18 hpf  NR at 23 hpf  RPE at 18 hpf and RPE at 23 hpf,,pubmed:34162866,,PG 1,GSM4547294,,tissue:sorted retinal progenitor cells|cell type:sorted retinal progenitor cells|developmental stage:16 hpf|transgenic line:tgvsx2.2:GFP,PG 1,Each sample was mapped against the index genome built from danRer10 assembly using Tophat v2.1.0 The aligned read BAM files were assembled into transcripts and their abundance was estimated by Cufflinks  v2.2.1 Genome build: danRer10 Supplementary files format and content: txt file including the FPKM values for all genes in each eye domain,sorted retinal progenitor cells,Zebrafish cells were dissociated and prepared for FACS as described in Manoli and Driever  2012,Total RNA was extracted by TRIzol Invitrogen following manufacturer’s protocol. Possible DNA contamination was eliminated treating the RNA samples with with TURBO DNAse free Ambion. Ribo Zero® rRNA Removal Kit Illumina,Zebrafish embryos were raised in E3 medium at 28 °C,cell type:sorted retinal progenitor cells|developmental stage:16 hpf|transgenic line:tgvsx2.2:GFP,GSM4547294,GSM4547294: PG 1; Danio rerio; RNA Seq,GSM4547294,,1,Total RNA was extracted by TRIzol Invitrogen following manufacturer's protocol. Possible DNA contamination was eliminated treating the RNA samples with with TURBO DNAse free Ambion. Ribo Zero® rRNA Removal Kit Illumina,GEO Accession:GSM4547294,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP261174,,,PG16_1_R1.fastq.gz,fastq,8274354750.0,66194838.0,GSM4547294 r1,0:125 1:0,A:2111248116;C:2064819412;G:1927992450;T:2170238125;N:56647,125,0,,,2111248116,2064819412,1927992450,2170238125,56647,SRX8326549,SRS6646237,SRA1074492,GEO,CABD,1,0.62887,,0.14778,,0.75521,,0.5602,,125,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,Spain,2020-05-11,Segmentation,Embryo,Eye,Sensory System
67814,SRR17313507,SRX13490114,SRS11385977,SRP352175,PRJNA791684,Translational profiling of zebrafish retina cells using translating ribosome affinity purification methods,GSE192511,Other,Translating ribosome affinity purification TRAP methods allow cell specific recovery of polyribosome associated RNAs by genetic tagging of ribosomes in selected cell populations. In this study  we purified and analysed the polyribosome associated RNA fraction of zebrafish embryo´s retinas at 22 hpf To this aim  we generated a transgenic strain in which the tagged ribosomes expression is restricted to the retina cells due to the activity of a specific promoter. Overall design: Analysis of ribosome associated mRNAs in zebrafish retina cells,,pubmed:35174174,,Vsx2:TRAP 22hpf 3,GSM5750326,,tissue:Vsx2:TRAP|strain:Vsx2:TRAP|developmental stage:22 hpf embryos only retina cells tagged,Vsx2:TRAP 22hpf 3,Base calling performed using HiSeq Control Software 2.2.58 Quality of reads was checked using FastQC v.0.72 Reads were aligned to Danio rerio GRCz11 genome assembly using Hisat2 with default parameters v. 2.2.1 Raw counts of reads were obtained through the featureCounts software using the zebrafish genome GRCz11 annotation from Ensembl Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample,Vsx2:TRAP,,Tagged ribosomes with mRNA attached to them were purified through inmunoprecipitation. postwards  the RNA was isolated. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:Vsx2:TRAP|developmental stage:22 hpf embryos only retina cells tagged,GSM5750326,GSM5750326: Vsx2:TRAP 22hpf 3; Danio rerio; RNA Seq,GSM5750326 r1,GSM5750326,1,Tagged ribosomes with mRNA attached to them were purified through inmunoprecipitation. postwards  the RNA was isolated. RNA libraries were prepared for sequencing using standard Illumina protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP352175,,,TRAP3_00523AAA_GTGGCC_read1.fastq.gz TRAP3_00523AAA_GTGGCC_read2.fastq.gz,fastq fastq,8792826250.0,35171305.0,GSM5750326 r1,0:125 1:125,A:1760289035;C:2642082686;G:2620444494;T:1768120361;N:1889674,125,125,,,1760289035,2642082686,2620444494,1768120361,1889674,SRX13490114,SRS11385977,SRA1347903,CABD,CABD,2,0.9712,0.97179,0.28473,0.27911,0.96327,0.96341,0.84082,0.81514,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Spain,2021-12-22,Segmentation,Embryo,Eye,Sensory System
67815,SRR17313508,SRX13490113,SRS11385975,SRP352175,PRJNA791684,Translational profiling of zebrafish retina cells using translating ribosome affinity purification methods,GSE192511,Other,Translating ribosome affinity purification TRAP methods allow cell specific recovery of polyribosome associated RNAs by genetic tagging of ribosomes in selected cell populations. In this study  we purified and analysed the polyribosome associated RNA fraction of zebrafish embryo´s retinas at 22 hpf To this aim  we generated a transgenic strain in which the tagged ribosomes expression is restricted to the retina cells due to the activity of a specific promoter. Overall design: Analysis of ribosome associated mRNAs in zebrafish retina cells,,pubmed:35174174,,Vsx2:TRAP 22hpf 2,GSM5750325,,tissue:Vsx2:TRAP|strain:Vsx2:TRAP|developmental stage:22 hpf embryos only retina cells tagged,Vsx2:TRAP 22hpf 2,Base calling performed using HiSeq Control Software 2.2.58 Quality of reads was checked using FastQC v.0.72 Reads were aligned to Danio rerio GRCz11 genome assembly using Hisat2 with default parameters v. 2.2.1 Raw counts of reads were obtained through the featureCounts software using the zebrafish genome GRCz11 annotation from Ensembl Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample,Vsx2:TRAP,,Tagged ribosomes with mRNA attached to them were purified through inmunoprecipitation. postwards  the RNA was isolated. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:Vsx2:TRAP|developmental stage:22 hpf embryos only retina cells tagged,GSM5750325,GSM5750325: Vsx2:TRAP 22hpf 2; Danio rerio; RNA Seq,GSM5750325 r1,GSM5750325,1,Tagged ribosomes with mRNA attached to them were purified through inmunoprecipitation. postwards  the RNA was isolated. RNA libraries were prepared for sequencing using standard Illumina protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP352175,,,TRAP2_00522AAA_TAGCTT_read1.fastq.gz TRAP2_00522AAA_TAGCTT_read2.fastq.gz,fastq fastq,12349898250.0,49399593.0,GSM5750325 r1,0:125 1:125,A:2491151924;C:3690583678;G:3664104797;T:2501408401;N:2649450,125,125,,,2491151924,3690583678,3664104797,2501408401,2649450,SRX13490113,SRS11385975,SRA1347903,CABD,CABD,2,0.97277,0.97397,0.27672,0.27092,0.95578,0.95556,0.84157,0.84013,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Spain,2021-12-22,Segmentation,Embryo,Eye,Sensory System
67816,SRR17313509,SRX13490112,SRS11385976,SRP352175,PRJNA791684,Translational profiling of zebrafish retina cells using translating ribosome affinity purification methods,GSE192511,Other,Translating ribosome affinity purification TRAP methods allow cell specific recovery of polyribosome associated RNAs by genetic tagging of ribosomes in selected cell populations. In this study  we purified and analysed the polyribosome associated RNA fraction of zebrafish embryo´s retinas at 22 hpf To this aim  we generated a transgenic strain in which the tagged ribosomes expression is restricted to the retina cells due to the activity of a specific promoter. Overall design: Analysis of ribosome associated mRNAs in zebrafish retina cells,,pubmed:35174174,,Vsx2:TRAP 22hpf 1,GSM5750324,,tissue:Vsx2:TRAP|strain:Vsx2:TRAP|developmental stage:22 hpf embryos only retina cells tagged,Vsx2:TRAP 22hpf 1,Base calling performed using HiSeq Control Software 2.2.58 Quality of reads was checked using FastQC v.0.72 Reads were aligned to Danio rerio GRCz11 genome assembly using Hisat2 with default parameters v. 2.2.1 Raw counts of reads were obtained through the featureCounts software using the zebrafish genome GRCz11 annotation from Ensembl Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample,Vsx2:TRAP,,Tagged ribosomes with mRNA attached to them were purified through inmunoprecipitation. postwards  the RNA was isolated. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:Vsx2:TRAP|developmental stage:22 hpf embryos only retina cells tagged,GSM5750324,GSM5750324: Vsx2:TRAP 22hpf 1; Danio rerio; RNA Seq,GSM5750324 r1,GSM5750324,1,Tagged ribosomes with mRNA attached to them were purified through inmunoprecipitation. postwards  the RNA was isolated. RNA libraries were prepared for sequencing using standard Illumina protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP352175,,,TRAP1_00521AAA_ATCACG_read1.fastq.gz TRAP1_00521AAA_ATCACG_read2.fastq.gz,fastq fastq,11455245000.0,45820980.0,GSM5750324 r1,0:125 1:125,A:2301920784;C:3440804776;G:3403731502;T:2306319875;N:2468063,125,125,,,2301920784,3440804776,3403731502,2306319875,2468063,SRX13490112,SRS11385976,SRA1347903,CABD,CABD,2,0.99269,0.99316,0.29021,0.28458,0.96311,0.96331,0.80398,0.80477,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Spain,2021-12-22,Segmentation,Embryo,Eye,Sensory System