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
275,DRR162466,DRX153085,DRS083146,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.,,,,brain sample from 2 mpf zebrafish replicate5,SAMD00152414,,sample name:b02 5|age:2 month|biological replicate:5|tissue:brain,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152414,DRX153085,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,2000Application ReadForward11Application ReadReverse101,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152414,,,,1184455800.0,5922279.0,DRR162466,0:100 1:100,A:357035323;C:233685447;G:235595745;T:356085837;N:2053448,100,100,,,357035323,233685447,235595745,356085837,2053448,DRX153085,DRS083146,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.90819,0.87146,0.20659,0.19751,0.71246,0.72251,0.52523,0.52531,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Brain,Nervous System
276,DRR162465,DRX153084,DRS083145,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.,,,,brain sample from 2 mpf zebrafish replicate4,SAMD00152413,,sample name:b02 4|age:2 month|biological replicate:4|tissue:brain,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152413,DRX153084,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,2000Application ReadForward11Application ReadReverse101,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152413,,,,1389141000.0,6945705.0,DRR162465,0:100 1:100,A:423029010;C:270113394;G:270981952;T:422602360;N:2414284,100,100,,,423029010,270113394,270981952,422602360,2414284,DRX153084,DRS083145,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.90961,0.87739,0.21147,0.20152,0.71492,0.72563,0.53639,0.53779,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Brain,Nervous System
277,DRR162464,DRX153083,DRS083144,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.,,,,brain sample from 2 mpf zebrafish replicate3,SAMD00152412,,sample name:b02 3|age:2 month|biological replicate:3|tissue:brain,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152412,DRX153083,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,2000Application ReadForward11Application ReadReverse101,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152412,,,,2322459000.0,11612295.0,DRR162464,0:100 1:100,A:701085106;C:457451297;G:460424165;T:699185460;N:4312972,100,100,,,701085106,457451297,460424165,699185460,4312972,DRX153083,DRS083144,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.92479,0.89382,0.16108,0.1547,0.73312,0.74121,0.55089,0.55507,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Brain,Nervous System
278,DRR162463,DRX153082,DRS083143,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.,,,,brain sample from 2 mpf zebrafish replicate2,SAMD00152411,,sample name:b02 2|age:2 month|biological replicate:2|tissue:brain,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152411,DRX153082,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,2000Application ReadForward11Application ReadReverse101,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152411,,,,1188406400.0,5942032.0,DRR162463,0:100 1:100,A:354575190;C:238508166;G:239587004;T:353623510;N:2112530,100,100,,,354575190,238508166,239587004,353623510,2112530,DRX153082,DRS083143,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.90922,0.8787,0.20709,0.2009,0.71614,0.7362,0.52768,0.53049,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Brain,Nervous System
279,DRR162462,DRX153081,DRS083142,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.,,,,brain sample from 2 mpf zebrafish replicate1,SAMD00152410,,sample name:b02 1|age:2 month|biological replicate:1|tissue:brain,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152410,DRX153081,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,2000Application ReadForward11Application ReadReverse101,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152410,,,,1033492200.0,5167461.0,DRR162462,0:100 1:100,A:310135217;C:205335529;G:207428012;T:308760225;N:1833217,100,100,,,310135217,205335529,207428012,308760225,1833217,DRX153081,DRS083142,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.9176,0.8829,0.18651,0.17848,0.72099,0.73119,0.54307,0.54697,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Brain,Nervous System
26487,SRR26034371,SRX21751586,SRS18859093,SRP459779,PRJNA1015242,Gene expression data from zebrafish SHH medulloblastoma brains and normal brains.,GSE242897,Transcriptome Analysis,Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals 3 individual tp53 mutant and ptch1 crispant animals and 3 individual tp53 heterozygous and ptch1 crispant animals.,,pubmed:39078737,,19521X6 tp53het tumor,GSM7774462,,source name:brain|tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 heterozygous|geo loc name:missing|collection date:missing,19521X6 tp53het tumor,The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts.,brain,Brains were frozen at 80C in RNA stabilization solution QIAGEN.,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.,tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 heterozygous,GSM7774462,GSM7774462: 19521X6 tp53het tumor; Danio rerio; RNA Seq,GSM7774462 r1,GSM7774462,1,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP459779,,loader:fastq load.py,19521X6_220211_A00421_0418_AHGVTMDSX3_S177_L003_R1_001.fastq.gz 19521X6_220211_A00421_0418_AHGVTMDSX3_S177_L003_R2_001.fastq.gz,fastq fastq,13856710696.0,45883148.0,GSM7774462 r1,0:151 1:151,A:3910050404;C:3019565763;G:3183961340;T:3742992264;N:140925,151,151,,,3910050404,3019565763,3183961340,3742992264,140925,SRX21751586,SRS18859093,SRA1710210,Huntsman Cancer Institute,"Oncological Sciences, University of Utah",2,0.8794,0.87909,0.38495,0.38479,0.69753,0.70005,0.49322,0.49442,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,rrna_depletion,trueseq,bulk,bulk,bulk,,United States,2023-09-11,Juvenile,Juvenile,Brain,Nervous System
26488,SRR26034372,SRX21751585,SRS18859092,SRP459779,PRJNA1015242,Gene expression data from zebrafish SHH medulloblastoma brains and normal brains.,GSE242897,Transcriptome Analysis,Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals 3 individual tp53 mutant and ptch1 crispant animals and 3 individual tp53 heterozygous and ptch1 crispant animals.,,pubmed:39078737,,19521X5 tp53het tumor,GSM7774461,,source name:brain|tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 heterozygous|geo loc name:missing|collection date:missing,19521X5 tp53het tumor,The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts.,brain,Brains were frozen at 80C in RNA stabilization solution QIAGEN.,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.,tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 heterozygous,GSM7774461,GSM7774461: 19521X5 tp53het tumor; Danio rerio; RNA Seq,GSM7774461 r1,GSM7774461,1,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP459779,,loader:fastq load.py,19521X5_220211_A00421_0418_AHGVTMDSX3_S176_L003_R1_001.fastq.gz 19521X5_220211_A00421_0418_AHGVTMDSX3_S176_L003_R2_001.fastq.gz,fastq fastq,18644081740.0,61735370.0,GSM7774461 r1,0:151 1:151,A:5198614433;C:4108657498;G:4307546758;T:5029072002;N:191049,151,151,,,5198614433,4108657498,4307546758,5029072002,191049,SRX21751585,SRS18859092,SRA1710210,Huntsman Cancer Institute,"Oncological Sciences, University of Utah",2,0.88544,0.88842,0.35896,0.35863,0.69193,0.69248,0.49682,0.50274,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,rrna_depletion,trueseq,bulk,bulk,bulk,,United States,2023-09-11,Juvenile,Juvenile,Brain,Nervous System
26489,SRR26034373,SRX21751584,SRS18859091,SRP459779,PRJNA1015242,Gene expression data from zebrafish SHH medulloblastoma brains and normal brains.,GSE242897,Transcriptome Analysis,Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals 3 individual tp53 mutant and ptch1 crispant animals and 3 individual tp53 heterozygous and ptch1 crispant animals.,,pubmed:39078737,,19521X4 tp53het tumor,GSM7774460,,source name:brain|tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 heterozygous|geo loc name:missing|collection date:missing,19521X4 tp53het tumor,The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts.,brain,Brains were frozen at 80C in RNA stabilization solution QIAGEN.,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.,tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 heterozygous,GSM7774460,GSM7774460: 19521X4 tp53het tumor; Danio rerio; RNA Seq,GSM7774460 r1,GSM7774460,1,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP459779,,loader:fastq load.py,19521X4_220211_A00421_0418_AHGVTMDSX3_S175_L003_R1_001.fastq.gz 19521X4_220211_A00421_0418_AHGVTMDSX3_S175_L003_R2_001.fastq.gz,fastq fastq,14417628886.0,47740493.0,GSM7774460 r1,0:151 1:151,A:4016299076;C:3183962020;G:3341158152;T:3876059438;N:150200,151,151,,,4016299076,3183962020,3341158152,3876059438,150200,SRX21751584,SRS18859091,SRA1710210,Huntsman Cancer Institute,"Oncological Sciences, University of Utah",2,0.89118,0.89184,0.33812,0.33641,0.68947,0.68954,0.49867,0.50026,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,rrna_depletion,trueseq,bulk,bulk,bulk,,United States,2023-09-11,Juvenile,Juvenile,Brain,Nervous System
26491,SRR26034375,SRX21751582,SRS18859089,SRP459779,PRJNA1015242,Gene expression data from zebrafish SHH medulloblastoma brains and normal brains.,GSE242897,Transcriptome Analysis,Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals 3 individual tp53 mutant and ptch1 crispant animals and 3 individual tp53 heterozygous and ptch1 crispant animals.,,pubmed:39078737,,19521X2 tp53mut tumor,GSM7774458,,source name:brain|tissue:brain|tumor status:tumor|age:8 wpf|genotype:tp53 mutant|geo loc name:missing|collection date:missing,19521X2 tp53mut tumor,The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts.,brain,Brains were frozen at 80C in RNA stabilization solution QIAGEN.,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.,tissue:brain|tumor status:tumor|age:8 wpf|genotype:tp53 mutant,GSM7774458,GSM7774458: 19521X2 tp53mut tumor; Danio rerio; RNA Seq,GSM7774458 r1,GSM7774458,1,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP459779,,loader:fastq load.py,19521X2_220211_A00421_0418_AHGVTMDSX3_S173_L003_R1_001.fastq.gz 19521X2_220211_A00421_0418_AHGVTMDSX3_S173_L003_R2_001.fastq.gz,fastq fastq,14064076580.0,46569790.0,GSM7774458 r1,0:151 1:151,A:3935649548;C:3089754695;G:3257286821;T:3781242542;N:142974,151,151,,,3935649548,3089754695,3257286821,3781242542,142974,SRX21751582,SRS18859089,SRA1710210,Huntsman Cancer Institute,"Oncological Sciences, University of Utah",2,0.89595,0.89655,0.35454,0.35431,0.68927,0.69077,0.47888,0.47831,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,rrna_depletion,trueseq,bulk,bulk,bulk,,United States,2023-09-11,Juvenile,Juvenile,Brain,Nervous System
26492,SRR26034376,SRX21751581,SRS18859088,SRP459779,PRJNA1015242,Gene expression data from zebrafish SHH medulloblastoma brains and normal brains.,GSE242897,Transcriptome Analysis,Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals 3 individual tp53 mutant and ptch1 crispant animals and 3 individual tp53 heterozygous and ptch1 crispant animals.,,pubmed:39078737,,19521X1 tp53mut tumor,GSM7774457,,source name:brain|tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 mutant|geo loc name:missing|collection date:missing,19521X1 tp53mut tumor,The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts.,brain,Brains were frozen at 80C in RNA stabilization solution QIAGEN.,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.,tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 mutant,GSM7774457,GSM7774457: 19521X1 tp53mut tumor; Danio rerio; RNA Seq,GSM7774457 r1,GSM7774457,1,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP459779,,loader:fastq load.py,19521X1_220211_A00421_0418_AHGVTMDSX3_S172_L003_R1_001.fastq.gz 19521X1_220211_A00421_0418_AHGVTMDSX3_S172_L003_R2_001.fastq.gz,fastq fastq,16911500190.0,55998345.0,GSM7774457 r1,0:151 1:151,A:4750241986;C:3698380612;G:3890633834;T:4572071732;N:172026,151,151,,,4750241986,3698380612,3890633834,4572071732,172026,SRX21751581,SRS18859088,SRA1710210,Huntsman Cancer Institute,"Oncological Sciences, University of Utah",2,0.89695,0.89831,0.3562,0.35542,0.68392,0.68369,0.48172,0.48641,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,rrna_depletion,trueseq,bulk,bulk,bulk,,United States,2023-09-11,Juvenile,Juvenile,Brain,Nervous System
33360,SRR30140788,SRX25609257,SRS22255959,SRP524310,PRJNA1144219,Danio rerio Raw sequence reads,PRJNA1144219,Whole Genome Sequencing,post exposure to bisphenol S for 50 days zebrafish brain tissue was performed by RNA seq,,,,DMSO 1,DMSO 1,,strain:AB|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:50 days|dev stage:DMSO 1|collection date:not collected|geo loc name:China: Qingdao|sex:intersex|tissue:Brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish Danio rerio,S886,S886,normal RNA seq of Danio rerio,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524310,,,DMSO_1_1.fq.gz DMSO_1_2.fq.gz,fastq fastq,6848352600.0,22827842.0,DMSO 1 1.fq.gz,0:150 1:150,A:2042619042;C:1408327078;G:1392721721;T:2004605654;N:79105,150,150,,,2042619042,1408327078,1392721721,2004605654,79105,SRX25609257,SRS22255959,SRA1940694,Ocean University of China|College of Marine Life Sciences,Ocean University of China,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-08-06,Juvenile,Juvenile,Brain,Nervous System
33361,SRR30140789,SRX25609256,SRS22255958,SRP524310,PRJNA1144219,Danio rerio Raw sequence reads,PRJNA1144219,Whole Genome Sequencing,post exposure to bisphenol S for 50 days zebrafish brain tissue was performed by RNA seq,,,,DMSO 2,DMSO 2,,strain:AB|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:50 days|dev stage:DMSO 2|collection date:not collected|geo loc name:China: Qingdao|sex:intersex|tissue:Brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish Danio rerio,S887,S887,normal RNA seq of Danio rerio,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524310,,,DMSO_2_1.fq.gz DMSO_2_2.fq.gz,fastq fastq,6722867400.0,22409558.0,DMSO 2 1.fq.gz,0:150 1:150,A:1987471480;C:1402576521;G:1384470516;T:1948276779;N:72104,150,150,,,1987471480,1402576521,1384470516,1948276779,72104,SRX25609256,SRS22255958,SRA1940694,Ocean University of China|College of Marine Life Sciences,Ocean University of China,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-08-06,Juvenile,Juvenile,Brain,Nervous System
33362,SRR30140790,SRX25609255,SRS22255957,SRP524310,PRJNA1144219,Danio rerio Raw sequence reads,PRJNA1144219,Whole Genome Sequencing,post exposure to bisphenol S for 50 days zebrafish brain tissue was performed by RNA seq,,,,DMSO 3,DMSO 3,,strain:AB|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:50 days|dev stage:DMSO 3|collection date:not collected|geo loc name:China: Qingdao|sex:intersex|tissue:Brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish Danio rerio,S888,S888,normal RNA seq of Danio rerio,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524310,,,DMSO_3_1.fq.gz DMSO_3_2.fq.gz,fastq fastq,6385524600.0,21285082.0,DMSO 3 1.fq.gz,0:150 1:150,A:1858080423;C:1360978750;G:1348505877;T:1817909740;N:49810,150,150,,,1858080423,1360978750,1348505877,1817909740,49810,SRX25609255,SRS22255957,SRA1940694,Ocean University of China|College of Marine Life Sciences,Ocean University of China,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-08-06,Juvenile,Juvenile,Brain,Nervous System
33363,SRR30140791,SRX25609254,SRS22255956,SRP524310,PRJNA1144219,Danio rerio Raw sequence reads,PRJNA1144219,Whole Genome Sequencing,post exposure to bisphenol S for 50 days zebrafish brain tissue was performed by RNA seq,,,,BPS1 1,BPS1 1,,strain:AB|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:50 days|dev stage:BPS1 1|collection date:not collected|geo loc name:China: Qingdao|sex:intersex|tissue:Brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish Danio rerio,S889,S889,normal RNA seq of Danio rerio,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524310,,,BPS1_1_1.fq.gz BPS1_1_2.fq.gz,fastq fastq,6677891400.0,22259638.0,BPS1 1 1.fq.gz,0:150 1:150,A:1942755547;C:1419146767;G:1404962384;T:1910952784;N:73918,150,150,,,1942755547,1419146767,1404962384,1910952784,73918,SRX25609254,SRS22255956,SRA1940694,Ocean University of China|College of Marine Life Sciences,Ocean University of China,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-08-06,Juvenile,Juvenile,Brain,Nervous System
33364,SRR30140792,SRX25609253,SRS22255955,SRP524310,PRJNA1144219,Danio rerio Raw sequence reads,PRJNA1144219,Whole Genome Sequencing,post exposure to bisphenol S for 50 days zebrafish brain tissue was performed by RNA seq,,,,BPS1 2,BPS1 2,,strain:AB|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:50 days|dev stage:BPS1 2|collection date:not collected|geo loc name:China: Qingdao|sex:intersex|tissue:Brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish Danio rerio,S890,S890,normal RNA seq of Danio rerio,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524310,,,BPS1_2_1.fq.gz BPS1_2_2.fq.gz,fastq fastq,6521417700.0,21738059.0,BPS1 2 1.fq.gz,0:150 1:150,A:1909300221;C:1371099464;G:1358671002;T:1882282904;N:64109,150,150,,,1909300221,1371099464,1358671002,1882282904,64109,SRX25609253,SRS22255955,SRA1940694,Ocean University of China|College of Marine Life Sciences,Ocean University of China,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-08-06,Juvenile,Juvenile,Brain,Nervous System
33365,SRR30140793,SRX25609252,SRS22255954,SRP524310,PRJNA1144219,Danio rerio Raw sequence reads,PRJNA1144219,Whole Genome Sequencing,post exposure to bisphenol S for 50 days zebrafish brain tissue was performed by RNA seq,,,,BPS1 3,BPS1 3,,strain:AB|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:50 days|dev stage:BPS1 3|collection date:not collected|geo loc name:China: Qingdao|sex:intersex|tissue:Brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish Danio rerio,S891,S891,normal RNA seq of Danio rerio,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524310,,,BPS1_3_1.fq.gz BPS1_3_2.fq.gz,fastq fastq,6821300100.0,22737667.0,BPS1 3 1.fq.gz,0:150 1:150,A:1996014045;C:1437758871;G:1429644156;T:1957815359;N:67669,150,150,,,1996014045,1437758871,1429644156,1957815359,67669,SRX25609252,SRS22255954,SRA1940694,Ocean University of China|College of Marine Life Sciences,Ocean University of China,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-08-06,Juvenile,Juvenile,Brain,Nervous System
33366,SRR30140794,SRX25609251,SRS22255953,SRP524310,PRJNA1144219,Danio rerio Raw sequence reads,PRJNA1144219,Whole Genome Sequencing,post exposure to bisphenol S for 50 days zebrafish brain tissue was performed by RNA seq,,,,BPS100 1,BPS100 1,,strain:AB|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:50 days|dev stage:BPS100 1|collection date:not collected|geo loc name:China: Qingdao|sex:intersex|tissue:Brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish Danio rerio,S892,S892,normal RNA seq of Danio rerio,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524310,,,BPS100_1_1.fq.gz BPS100_1_2.fq.gz,fastq fastq,6420793800.0,21402646.0,BPS100 1 1.fq.gz,0:150 1:150,A:1856129124;C:1374411655;G:1366071243;T:1824132054;N:49724,150,150,,,1856129124,1374411655,1366071243,1824132054,49724,SRX25609251,SRS22255953,SRA1940694,Ocean University of China|College of Marine Life Sciences,Ocean University of China,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-08-06,Juvenile,Juvenile,Brain,Nervous System
33367,SRR30140795,SRX25609250,SRS22255952,SRP524310,PRJNA1144219,Danio rerio Raw sequence reads,PRJNA1144219,Whole Genome Sequencing,post exposure to bisphenol S for 50 days zebrafish brain tissue was performed by RNA seq,,,,BPS100 2,BPS100 2,,strain:AB|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:50 days|dev stage:BPS100 2|collection date:not collected|geo loc name:China: Qingdao|sex:intersex|tissue:Brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish Danio rerio,S893,S893,normal RNA seq of Danio rerio,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524310,,,BPS100_2_1.fq.gz BPS100_2_2.fq.gz,fastq fastq,6639336600.0,22131122.0,BPS100 2 1.fq.gz,0:150 1:150,A:1901484110;C:1438361866;G:1430361119;T:1869078551;N:50954,150,150,,,1901484110,1438361866,1430361119,1869078551,50954,SRX25609250,SRS22255952,SRA1940694,Ocean University of China|College of Marine Life Sciences,Ocean University of China,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-08-06,Juvenile,Juvenile,Brain,Nervous System
33368,SRR30140796,SRX25609249,SRS22255951,SRP524310,PRJNA1144219,Danio rerio Raw sequence reads,PRJNA1144219,Whole Genome Sequencing,post exposure to bisphenol S for 50 days zebrafish brain tissue was performed by RNA seq,,,,BPS100 3,BPS100 3,,strain:AB|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:50 days|dev stage:BPS100 3|collection date:not collected|geo loc name:China: Qingdao|sex:intersex|tissue:Brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish Danio rerio,S894,S894,normal RNA seq of Danio rerio,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524310,,,BPS100_3_1.fq.gz BPS100_3_2.fq.gz,fastq fastq,6586231800.0,21954106.0,BPS100 3 1.fq.gz,0:150 1:150,A:1875041634;C:1438699475;G:1425868891;T:1846570793;N:51007,150,150,,,1875041634,1438699475,1425868891,1846570793,51007,SRX25609249,SRS22255951,SRA1940694,Ocean University of China|College of Marine Life Sciences,Ocean University of China,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-08-06,Juvenile,Juvenile,Brain,Nervous System
42221,SRR5837492,SRX3013998,SRS2363592,SRP112722,PRJNA385064,Transcriptomic effects of 17 alpha methyltestosterone on zebrafish brain sexual development.,PRJNA385064,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic hormonal and environmental factors can influence sexual development. Androgen treatment triggers phenotypic and behavioural masculinisation in zebrafish. 17 alpha methyltestosterone MT a synthetic androgen is routinely used in aquaculture for production of all male populations. However the molecular mechanisms underlying 17 alpha methyltestosterone induced brain and behavioural masculinisation in fish are poorly understood. In this study we analysed brain transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with brain transcriptomes of untreated female and male zebrafish. These data give insight into the role of androgens in teleost brain sexual differentiation.,,,,,60CFB1,,strain:Tgvas:egfp|age:60 dpf|dev stage:juvenile|sex:female|tissue:brain|genotype:Tgvas:egfp|sample type:whole brain|treatment:untreated|replicate:60 dpf control female brain Replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 60 dpf untreated female brain,60CFB1,60CFB1,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP112722,,,BC1JJDACXX_NZGL00075_60SCFB1_AGTCAA_L005_R1_001.fastq.gz BC1JJDACXX_NZGL00075_60SCFB1_AGTCAA_L005_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60SCFB1_AGTCAA_L003_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCFB1_AGTCAA_L003_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60SCFB1_AGTCAA_L004_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCFB1_AGTCAA_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq,3969892400.0,19849462.0,C1PF2ACXX NZGL00075 60SCFB1 AGTCAA L004 R1 001.fastq.gz,0:100 1:100,A:1094818823;C:893895690;G:881549121;T:1090706413;N:8922353,100,100,,,1094818823,893895690,881549121,1090706413,8922353,SRX3013998,SRS2363592,SRA588281,University of Otago|Anatomy,University of Otago,2,0.94266,0.94424,0.1002,0.10048,0.69487,0.69424,0.50397,0.50085,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2018-07-31,Juvenile,Juvenile,Brain,Nervous System
42222,SRR5837493,SRX3013997,SRS2363591,SRP112722,PRJNA385064,Transcriptomic effects of 17 alpha methyltestosterone on zebrafish brain sexual development.,PRJNA385064,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic hormonal and environmental factors can influence sexual development. Androgen treatment triggers phenotypic and behavioural masculinisation in zebrafish. 17 alpha methyltestosterone MT a synthetic androgen is routinely used in aquaculture for production of all male populations. However the molecular mechanisms underlying 17 alpha methyltestosterone induced brain and behavioural masculinisation in fish are poorly understood. In this study we analysed brain transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with brain transcriptomes of untreated female and male zebrafish. These data give insight into the role of androgens in teleost brain sexual differentiation.,,,,,40CFB3,,strain:Tgvas:egfp|age:40 dpf|dev stage:juvenile|sex:female|tissue:brain|genotype:Tgvas:egfp|sample type:whole brain|treatment:untreated|replicate:40 dpf control female brain Replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 40 dpf untreated female brain,40CFB3,40CFB3,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP112722,,,BC1JJDACXX_NZGL00075_40SCFB3_ACTTGA_L005_R1_001.fastq.gz BC1JJDACXX_NZGL00075_40SCFB3_ACTTGA_L005_R2_001.fastq.gz C1PF2ACXX_NZGL00075_40SCFB3_ACTTGA_L003_R1_001.fastq.gz C1PF2ACXX_NZGL00075_40SCFB3_ACTTGA_L003_R2_001.fastq.gz C1PF2ACXX_NZGL00075_40SCFB3_ACTTGA_L004_R1_001.fastq.gz C1PF2ACXX_NZGL00075_40SCFB3_ACTTGA_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq,4666625600.0,23333128.0,BC1JJDACXX NZGL00075 40SCFB3 ACTTGA L005 R1 001.fastq.gz,0:100 1:100,A:1278337365;C:1058348384;G:1046272422;T:1273517804;N:10149625,100,100,,,1278337365,1058348384,1046272422,1273517804,10149625,SRX3013997,SRS2363591,SRA588281,University of Otago|Anatomy,University of Otago,2,0.93927,0.93973,0.11474,0.11356,0.69296,0.69094,0.49888,0.50165,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2018-07-31,Juvenile,Juvenile,Brain,Nervous System
42223,SRR5837494,SRX3013996,SRS2363593,SRP112722,PRJNA385064,Transcriptomic effects of 17 alpha methyltestosterone on zebrafish brain sexual development.,PRJNA385064,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic hormonal and environmental factors can influence sexual development. Androgen treatment triggers phenotypic and behavioural masculinisation in zebrafish. 17 alpha methyltestosterone MT a synthetic androgen is routinely used in aquaculture for production of all male populations. However the molecular mechanisms underlying 17 alpha methyltestosterone induced brain and behavioural masculinisation in fish are poorly understood. In this study we analysed brain transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with brain transcriptomes of untreated female and male zebrafish. These data give insight into the role of androgens in teleost brain sexual differentiation.,,,,,40CFB2,,strain:Tgvas:egfp|age:40 dpf|dev stage:juvenile|sex:female|tissue:brain|genotype:Tgvas:egfp|sample type:whole brain|treatment:untreated|replicate:40 dpf control female brain Replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 40 dpf untreated female brain,40CFB2,40CFB2,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP112722,,,BC1JJDACXX_NZGL00075_40SCFB2_TTAGGC_L005_R1_001.fastq.gz BC1JJDACXX_NZGL00075_40SCFB2_TTAGGC_L005_R2_001.fastq.gz C1PF2ACXX_NZGL00075_40SCFB2_TTAGGC_L003_R1_001.fastq.gz C1PF2ACXX_NZGL00075_40SCFB2_TTAGGC_L003_R2_001.fastq.gz C1PF2ACXX_NZGL00075_40SCFB2_TTAGGC_L004_R1_001.fastq.gz C1PF2ACXX_NZGL00075_40SCFB2_TTAGGC_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq,4705471600.0,23527358.0,C1PF2ACXX NZGL00075 40SCFB2 TTAGGC L003 R2 001.fastq.gz,0:100 1:100,A:1295830944;C:1061229949;G:1046418784;T:1291698494;N:10293429,100,100,,,1295830944,1061229949,1046418784,1291698494,10293429,SRX3013996,SRS2363593,SRA588281,University of Otago|Anatomy,University of Otago,2,0.94019,0.94149,0.1211,0.12046,0.69296,0.69057,0.49768,0.49689,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2018-07-31,Juvenile,Juvenile,Brain,Nervous System
42224,SRR5837495,SRX3013995,SRS2363590,SRP112722,PRJNA385064,Transcriptomic effects of 17 alpha methyltestosterone on zebrafish brain sexual development.,PRJNA385064,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic hormonal and environmental factors can influence sexual development. Androgen treatment triggers phenotypic and behavioural masculinisation in zebrafish. 17 alpha methyltestosterone MT a synthetic androgen is routinely used in aquaculture for production of all male populations. However the molecular mechanisms underlying 17 alpha methyltestosterone induced brain and behavioural masculinisation in fish are poorly understood. In this study we analysed brain transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with brain transcriptomes of untreated female and male zebrafish. These data give insight into the role of androgens in teleost brain sexual differentiation.,,,,,40CFB1,,strain:Tgvas:egfp|age:40 dpf|dev stage:juvenile|sex:female|tissue:brain|genotype:Tgvas:egfp|sample type:whole brain|treatment:untreated|replicate:40 dpf control female brain Replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 40 dpf untreated female brain,40CFB1,40CFB1,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP112722,,,BC1JJDACXX_NZGL00075_40SCFB1_ATCACG_L005_R1_001.fastq.gz BC1JJDACXX_NZGL00075_40SCFB1_ATCACG_L005_R2_001.fastq.gz C1PF2ACXX_NZGL00075_40SCFB1_ATCACG_L003_R1_001.fastq.gz C1PF2ACXX_NZGL00075_40SCFB1_ATCACG_L003_R2_001.fastq.gz C1PF2ACXX_NZGL00075_40SCFB1_ATCACG_L004_R1_001.fastq.gz C1PF2ACXX_NZGL00075_40SCFB1_ATCACG_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq,3868551800.0,19342759.0,C1PF2ACXX NZGL00075 40SCFB1 ATCACG L004 R1 001.fastq.gz,0:100 1:100,A:1064777174;C:873167844;G:861300163;T:1060844147;N:8462472,100,100,,,1064777174,873167844,861300163,1060844147,8462472,SRX3013995,SRS2363590,SRA588281,University of Otago|Anatomy,University of Otago,2,0.94408,0.9437,0.11215,0.11277,0.69802,0.69921,0.50432,0.50459,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2018-07-31,Juvenile,Juvenile,Brain,Nervous System
42225,SRR5837496,SRX3013994,SRS2363589,SRP112722,PRJNA385064,Transcriptomic effects of 17 alpha methyltestosterone on zebrafish brain sexual development.,PRJNA385064,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic hormonal and environmental factors can influence sexual development. Androgen treatment triggers phenotypic and behavioural masculinisation in zebrafish. 17 alpha methyltestosterone MT a synthetic androgen is routinely used in aquaculture for production of all male populations. However the molecular mechanisms underlying 17 alpha methyltestosterone induced brain and behavioural masculinisation in fish are poorly understood. In this study we analysed brain transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with brain transcriptomes of untreated female and male zebrafish. These data give insight into the role of androgens in teleost brain sexual differentiation.,,,,,40MTB3,,strain:Tgvas:egfp|age:40 dpf|dev stage:juvenile|sex:male|tissue:brain|genotype:Tgvas:egfp|sample type:whole brain|treatment:methyltestoster1 treated|replicate:40 dpf MT treated male brain Replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 40 dpf methyltestoster1 treated male brain,40MTB3,40MTB3,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP112722,,,C1PF2ACXX_NZGL00075_40MTMB3_GGCTAC_L003_R1_001.fastq.gz C1PF2ACXX_NZGL00075_40MTMB3_GGCTAC_L003_R2_001.fastq.gz C1PF2ACXX_NZGL00075_40MTMB3_GGCTAC_L004_R1_001.fastq.gz C1PF2ACXX_NZGL00075_40MTMB3_GGCTAC_L004_R2_001.fastq.gz BC1JJDACXX_NZGL00075_40MTMB3_GGCTAC_L005_R2_001.fastq.gz BC1JJDACXX_NZGL00075_40MTMB3_GGCTAC_L005_R1_001.fastq.gz,fastq fastq fastq fastq fastq fastq,3476188200.0,17380941.0,C1PF2ACXX NZGL00075 40MTMB3 GGCTAC L003 R1 001.fastq.gz,0:100 1:100,A:969766943;C:771530527;G:761101800;T:966163718;N:7625212,100,100,,,969766943,771530527,761101800,966163718,7625212,SRX3013994,SRS2363589,SRA588281,University of Otago|Anatomy,University of Otago,2,0.93915,0.93776,0.13576,0.13477,0.6966,0.69743,0.50796,0.50794,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2018-07-31,Juvenile,Juvenile,Brain,Nervous System
42226,SRR5837497,SRX3013993,SRS2363587,SRP112722,PRJNA385064,Transcriptomic effects of 17 alpha methyltestosterone on zebrafish brain sexual development.,PRJNA385064,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic hormonal and environmental factors can influence sexual development. Androgen treatment triggers phenotypic and behavioural masculinisation in zebrafish. 17 alpha methyltestosterone MT a synthetic androgen is routinely used in aquaculture for production of all male populations. However the molecular mechanisms underlying 17 alpha methyltestosterone induced brain and behavioural masculinisation in fish are poorly understood. In this study we analysed brain transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with brain transcriptomes of untreated female and male zebrafish. These data give insight into the role of androgens in teleost brain sexual differentiation.,,,,,40MTB2,,strain:Tgvas:egfp|age:40 dpf|dev stage:juvenile|sex:male|tissue:brain|genotype:Tgvas:egfp|sample type:whole brain|treatment:methyltestoster1 treated|replicate:40 dpf MT treated male brain Replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 40 dpf methyltestoster1 treated male brain,40MTB2,40MTB2,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP112722,,,BC1JJDACXX_NZGL00075_40MTMB2_TAGCTT_L005_R1_001.fastq.gz BC1JJDACXX_NZGL00075_40MTMB2_TAGCTT_L005_R2_001.fastq.gz C1PF2ACXX_NZGL00075_40MTMB2_TAGCTT_L003_R1_001.fastq.gz C1PF2ACXX_NZGL00075_40MTMB2_TAGCTT_L003_R2_001.fastq.gz C1PF2ACXX_NZGL00075_40MTMB2_TAGCTT_L004_R1_001.fastq.gz C1PF2ACXX_NZGL00075_40MTMB2_TAGCTT_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq,3838481200.0,19192406.0,C1PF2ACXX NZGL00075 40MTMB2 TAGCTT L004 R1 001.fastq.gz,0:100 1:100,A:1076294083;C:847249175;G:833793251;T:1072626237;N:8518454,100,100,,,1076294083,847249175,833793251,1072626237,8518454,SRX3013993,SRS2363587,SRA588281,University of Otago|Anatomy,University of Otago,2,0.93771,0.93855,0.13889,0.1404,0.69408,0.69459,0.51453,0.50946,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2018-07-31,Juvenile,Juvenile,Brain,Nervous System
42227,SRR5837498,SRX3013992,SRS2363586,SRP112722,PRJNA385064,Transcriptomic effects of 17 alpha methyltestosterone on zebrafish brain sexual development.,PRJNA385064,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic hormonal and environmental factors can influence sexual development. Androgen treatment triggers phenotypic and behavioural masculinisation in zebrafish. 17 alpha methyltestosterone MT a synthetic androgen is routinely used in aquaculture for production of all male populations. However the molecular mechanisms underlying 17 alpha methyltestosterone induced brain and behavioural masculinisation in fish are poorly understood. In this study we analysed brain transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with brain transcriptomes of untreated female and male zebrafish. These data give insight into the role of androgens in teleost brain sexual differentiation.,,,,,40MTB1,,strain:Tgvas:egfp|age:40 dpf|dev stage:juvenile|sex:male|tissue:brain|genotype:Tgvas:egfp|sample type:whole brain|treatment:methyltestoster1 treated|replicate:40 dpf MT treated male brain Replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 40 dpf methyltestoster1 treated male brain,40MTB1,40MTB1,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP112722,,,BC1JJDACXX_NZGL00075_40MTMB1_GATCAG_L005_R1_001.fastq.gz BC1JJDACXX_NZGL00075_40MTMB1_GATCAG_L005_R2_001.fastq.gz C1PF2ACXX_NZGL00075_40MTMB1_GATCAG_L003_R1_001.fastq.gz C1PF2ACXX_NZGL00075_40MTMB1_GATCAG_L003_R2_001.fastq.gz C1PF2ACXX_NZGL00075_40MTMB1_GATCAG_L004_R1_001.fastq.gz C1PF2ACXX_NZGL00075_40MTMB1_GATCAG_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq,3626521400.0,18132607.0,C1PF2ACXX NZGL00075 40MTMB1 GATCAG L004 R2 001.fastq.gz,0:100 1:100,A:1008131839;C:809568850;G:796148693;T:1004689114;N:7982904,100,100,,,1008131839,809568850,796148693,1004689114,7982904,SRX3013992,SRS2363586,SRA588281,University of Otago|Anatomy,University of Otago,2,0.94168,0.94206,0.12488,0.12478,0.69656,0.69514,0.51439,0.51446,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2018-07-31,Juvenile,Juvenile,Brain,Nervous System
42228,SRR5837499,SRX3013991,SRS2363585,SRP112722,PRJNA385064,Transcriptomic effects of 17 alpha methyltestosterone on zebrafish brain sexual development.,PRJNA385064,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic hormonal and environmental factors can influence sexual development. Androgen treatment triggers phenotypic and behavioural masculinisation in zebrafish. 17 alpha methyltestosterone MT a synthetic androgen is routinely used in aquaculture for production of all male populations. However the molecular mechanisms underlying 17 alpha methyltestosterone induced brain and behavioural masculinisation in fish are poorly understood. In this study we analysed brain transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with brain transcriptomes of untreated female and male zebrafish. These data give insight into the role of androgens in teleost brain sexual differentiation.,,,,,40CMB3,,strain:Tgvas:egfp|age:40 dpf|dev stage:juvenile|sex:male|tissue:brain|genotype:Tgvas:egfp|sample type:whole brain|treatment:untreated|replicate:40 dpf control male brain Replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 40 dpf untreated male brain,40CMB3,40CMB3,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP112722,,,BC1JJDACXX_NZGL00075_40SCMB3_GTGAAA_L005_R1_001.fastq.gz BC1JJDACXX_NZGL00075_40SCMB3_GTGAAA_L005_R2_001.fastq.gz C1PF2ACXX_NZGL00075_40SCMB3_GTGAAA_L003_R1_001.fastq.gz C1PF2ACXX_NZGL00075_40SCMB3_GTGAAA_L003_R2_001.fastq.gz C1PF2ACXX_NZGL00075_40SCMB3_GTGAAA_L004_R1_001.fastq.gz C1PF2ACXX_NZGL00075_40SCMB3_GTGAAA_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq,3897797400.0,19488987.0,C1PF2ACXX NZGL00075 40SCMB3 GTGAAA L004 R2 001.fastq.gz,0:100 1:100,A:1053339607;C:898719753;G:886558644;T:1050511593;N:8667803,100,100,,,1053339607,898719753,886558644,1050511593,8667803,SRX3013991,SRS2363585,SRA588281,University of Otago|Anatomy,University of Otago,2,0.94114,0.9399,0.08922,0.0874,0.67466,0.67379,0.48939,0.49225,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2018-07-31,Juvenile,Juvenile,Brain,Nervous System
42229,SRR5837500,SRX3013990,SRS2363584,SRP112722,PRJNA385064,Transcriptomic effects of 17 alpha methyltestosterone on zebrafish brain sexual development.,PRJNA385064,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic hormonal and environmental factors can influence sexual development. Androgen treatment triggers phenotypic and behavioural masculinisation in zebrafish. 17 alpha methyltestosterone MT a synthetic androgen is routinely used in aquaculture for production of all male populations. However the molecular mechanisms underlying 17 alpha methyltestosterone induced brain and behavioural masculinisation in fish are poorly understood. In this study we analysed brain transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with brain transcriptomes of untreated female and male zebrafish. These data give insight into the role of androgens in teleost brain sexual differentiation.,,,,,40CMB2,,strain:Tgvas:egfp|age:40 dpf|dev stage:juvenile|sex:male|tissue:brain|genotype:Tgvas:egfp|sample type:whole brain|treatment:untreated|replicate:40 dpf control male brain Replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 40 dpf untreated male brain,40CMB2,40CMB2,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP112722,,,BC1JJDACXX_NZGL00075_40SCMB2_GTCCGC_L005_R1_001.fastq.gz BC1JJDACXX_NZGL00075_40SCMB2_GTCCGC_L005_R2_001.fastq.gz C1PF2ACXX_NZGL00075_40SCMB2_GTCCGC_L003_R1_001.fastq.gz C1PF2ACXX_NZGL00075_40SCMB2_GTCCGC_L003_R2_001.fastq.gz C1PF2ACXX_NZGL00075_40SCMB2_GTCCGC_L004_R1_001.fastq.gz C1PF2ACXX_NZGL00075_40SCMB2_GTCCGC_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq,4138204400.0,20691022.0,BC1JJDACXX NZGL00075 40SCMB2 GTCCGC L005 R2 001.fastq.gz,0:100 1:100,A:1146985455;C:926307445;G:915147615;T:1140576343;N:9187542,100,100,,,1146985455,926307445,915147615,1140576343,9187542,SRX3013990,SRS2363584,SRA588281,University of Otago|Anatomy,University of Otago,2,0.94656,0.94443,0.10918,0.10786,0.70859,0.70847,0.50618,0.51039,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2018-07-31,Juvenile,Juvenile,Brain,Nervous System
42230,SRR5837501,SRX3013989,SRS2363583,SRP112722,PRJNA385064,Transcriptomic effects of 17 alpha methyltestosterone on zebrafish brain sexual development.,PRJNA385064,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic hormonal and environmental factors can influence sexual development. Androgen treatment triggers phenotypic and behavioural masculinisation in zebrafish. 17 alpha methyltestosterone MT a synthetic androgen is routinely used in aquaculture for production of all male populations. However the molecular mechanisms underlying 17 alpha methyltestosterone induced brain and behavioural masculinisation in fish are poorly understood. In this study we analysed brain transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with brain transcriptomes of untreated female and male zebrafish. These data give insight into the role of androgens in teleost brain sexual differentiation.,,,,,40CMB1,,strain:Tgvas:egfp|age:40 dpf|dev stage:juvenile|sex:male|tissue:brain|genotype:Tgvas:egfp|sample type:whole brain|treatment:untreated|replicate:40 dpf control male brain Replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 40 dpf untreated male brain,40CMB1,40CMB1,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP112722,,,BC1JJDACXX_NZGL00075_40SCMB1_CCGTCC_L005_R1_001.fastq.gz BC1JJDACXX_NZGL00075_40SCMB1_CCGTCC_L005_R2_001.fastq.gz C1PF2ACXX_NZGL00075_40SCMB1_CCGTCC_L003_R1_001.fastq.gz C1PF2ACXX_NZGL00075_40SCMB1_CCGTCC_L003_R2_001.fastq.gz C1PF2ACXX_NZGL00075_40SCMB1_CCGTCC_L004_R1_001.fastq.gz C1PF2ACXX_NZGL00075_40SCMB1_CCGTCC_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq,4102419600.0,20512098.0,C1PF2ACXX NZGL00075 40SCMB1 CCGTCC L003 R2 001.fastq.gz,0:100 1:100,A:1120567185;C:932846455;G:922719371;T:1117046836;N:9239753,100,100,,,1120567185,932846455,922719371,1117046836,9239753,SRX3013989,SRS2363583,SRA588281,University of Otago|Anatomy,University of Otago,2,0.94107,0.94051,0.11806,0.1174,0.69152,0.69213,0.49414,0.4974,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2018-07-31,Juvenile,Juvenile,Brain,Nervous System
42231,SRR5837502,SRX3013988,SRS2363582,SRP112722,PRJNA385064,Transcriptomic effects of 17 alpha methyltestosterone on zebrafish brain sexual development.,PRJNA385064,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic hormonal and environmental factors can influence sexual development. Androgen treatment triggers phenotypic and behavioural masculinisation in zebrafish. 17 alpha methyltestosterone MT a synthetic androgen is routinely used in aquaculture for production of all male populations. However the molecular mechanisms underlying 17 alpha methyltestosterone induced brain and behavioural masculinisation in fish are poorly understood. In this study we analysed brain transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with brain transcriptomes of untreated female and male zebrafish. These data give insight into the role of androgens in teleost brain sexual differentiation.,,,,,60MTB1,,strain:Tgvas:egfp|age:60 dpf|dev stage:juvenile|sex:male|tissue:brain|genotype:Tgvas:egfp|sample type:whole brain|treatment:methyltestoster1 treated|replicate:60 dpf MT treated male brain Replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 60 dpf methyltestoster1 treated male brain,60MTB1,60MTB1,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP112722,,,BC1JJDACXX_NZGL00075_60MTMB1_GCCAAT_L005_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60MTMB1_GCCAAT_L004_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60MTMB1_GCCAAT_L004_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60MTMB1_GCCAAT_L003_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60MTMB1_GCCAAT_L003_R1_001.fastq.gz BC1JJDACXX_NZGL00075_60MTMB1_GCCAAT_L005_R1_001.fastq.gz,fastq fastq fastq fastq fastq fastq,4328218200.0,21641091.0,BC1JJDACXX NZGL00075 60MTMB1 GCCAAT L005 R1 001.fastq.gz,0:100 1:100,A:1195035464;C:972547624;G:959246715;T:1191685906;N:9702491,100,100,,,1195035464,972547624,959246715,1191685906,9702491,SRX3013988,SRS2363582,SRA588281,University of Otago|Anatomy,University of Otago,2,0.93495,0.93683,0.12955,0.12886,0.68566,0.68353,0.50052,0.50293,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2018-07-31,Juvenile,Juvenile,Brain,Nervous System
42232,SRR5837503,SRX3013987,SRS2363581,SRP112722,PRJNA385064,Transcriptomic effects of 17 alpha methyltestosterone on zebrafish brain sexual development.,PRJNA385064,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic hormonal and environmental factors can influence sexual development. Androgen treatment triggers phenotypic and behavioural masculinisation in zebrafish. 17 alpha methyltestosterone MT a synthetic androgen is routinely used in aquaculture for production of all male populations. However the molecular mechanisms underlying 17 alpha methyltestosterone induced brain and behavioural masculinisation in fish are poorly understood. In this study we analysed brain transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with brain transcriptomes of untreated female and male zebrafish. These data give insight into the role of androgens in teleost brain sexual differentiation.,,,,,60CMB3,,strain:Tgvas:egfp|age:60 dpf|dev stage:juvenile|sex:male|tissue:brain|genotype:Tgvas:egfp|sample type:whole brain|treatment:untreated|replicate:60 dpf control male brain Replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 60 dpf untreated male brain,60CMB3,60CMB3,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP112722,,,BC1JJDACXX_NZGL00075_60SCMB3_ACAGTG_L005_R1_001.fastq.gz BC1JJDACXX_NZGL00075_60SCMB3_ACAGTG_L005_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMB3_ACAGTG_L003_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMB3_ACAGTG_L003_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMB3_ACAGTG_L004_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMB3_ACAGTG_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq,4417459400.0,22087297.0,C1PF2ACXX NZGL00075 60SCMB3 ACAGTG L004 R1 001.fastq.gz,0:100 1:100,A:1211897318;C:1001188415;G:986068554;T:1208370764;N:9934349,100,100,,,1211897318,1001188415,986068554,1208370764,9934349,SRX3013987,SRS2363581,SRA588281,University of Otago|Anatomy,University of Otago,2,0.93969,0.94136,0.10711,0.10789,0.69041,0.69134,0.48977,0.48815,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2018-07-31,Juvenile,Juvenile,Brain,Nervous System
42233,SRR5837504,SRX3013986,SRS2363588,SRP112722,PRJNA385064,Transcriptomic effects of 17 alpha methyltestosterone on zebrafish brain sexual development.,PRJNA385064,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic hormonal and environmental factors can influence sexual development. Androgen treatment triggers phenotypic and behavioural masculinisation in zebrafish. 17 alpha methyltestosterone MT a synthetic androgen is routinely used in aquaculture for production of all male populations. However the molecular mechanisms underlying 17 alpha methyltestosterone induced brain and behavioural masculinisation in fish are poorly understood. In this study we analysed brain transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with brain transcriptomes of untreated female and male zebrafish. These data give insight into the role of androgens in teleost brain sexual differentiation.,,,,,60MTB3,,strain:Tgvas:egfp|age:60 dpf|dev stage:juvenile|sex:male|tissue:brain|genotype:Tgvas:egfp|sample type:whole brain|treatment:methyltestoster1 treated|replicate:60 dpf MT treated male brain Replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 60 dpf methyltestoster1 treated male brain,60MTB3,60MTB3,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP112722,,,BC1JJDACXX_NZGL00075_60MTMB3_CTTGTA_L005_R1_001.fastq.gz BC1JJDACXX_NZGL00075_60MTMB3_CTTGTA_L005_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60MTMB3_CTTGTA_L003_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60MTMB3_CTTGTA_L003_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60MTMB3_CTTGTA_L004_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60MTMB3_CTTGTA_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq,4413607000.0,22068035.0,C1PF2ACXX NZGL00075 60MTMB3 CTTGTA L004 R2 001.fastq.gz,0:100 1:100,A:1227802610;C:982523348;G:968660161;T:1224693461;N:9927420,100,100,,,1227802610,982523348,968660161,1224693461,9927420,SRX3013986,SRS2363588,SRA588281,University of Otago|Anatomy,University of Otago,2,0.93584,0.93789,0.13242,0.13255,0.68787,0.68726,0.50157,0.49922,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2018-07-31,Juvenile,Juvenile,Brain,Nervous System
42234,SRR5837505,SRX3013985,SRS2363580,SRP112722,PRJNA385064,Transcriptomic effects of 17 alpha methyltestosterone on zebrafish brain sexual development.,PRJNA385064,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic hormonal and environmental factors can influence sexual development. Androgen treatment triggers phenotypic and behavioural masculinisation in zebrafish. 17 alpha methyltestosterone MT a synthetic androgen is routinely used in aquaculture for production of all male populations. However the molecular mechanisms underlying 17 alpha methyltestosterone induced brain and behavioural masculinisation in fish are poorly understood. In this study we analysed brain transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with brain transcriptomes of untreated female and male zebrafish. These data give insight into the role of androgens in teleost brain sexual differentiation.,,,,,60MTB2,,strain:Tgvas:egfp|age:60 dpf|dev stage:juvenile|sex:male|tissue:brain|genotype:Tgvas:egfp|sample type:whole brain|treatment:methyltestoster1 treated|replicate:60 dpf MT treated male brain brain Replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 60 dpf methyltestoster1 treated male brain,60MTB2,60MTB2,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP112722,,,BC1JJDACXX_NZGL00075_60MTMB2_CAGATC_L005_R1_001.fastq.gz BC1JJDACXX_NZGL00075_60MTMB2_CAGATC_L005_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60MTMB2_CAGATC_L003_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60MTMB2_CAGATC_L003_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60MTMB2_CAGATC_L004_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60MTMB2_CAGATC_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq,3732059600.0,18660298.0,BC1JJDACXX NZGL00075 60MTMB2 CAGATC L005 R1 001.fastq.gz,0:100 1:100,A:1031304662;C:837410272;G:826692599;T:1028351953;N:8300114,100,100,,,1031304662,837410272,826692599,1028351953,8300114,SRX3013985,SRS2363580,SRA588281,University of Otago|Anatomy,University of Otago,2,0.93789,0.93935,0.12645,0.12581,0.68722,0.68562,0.49512,0.49656,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2018-07-31,Juvenile,Juvenile,Brain,Nervous System
42235,SRR5837506,SRX3013984,SRS2363578,SRP112722,PRJNA385064,Transcriptomic effects of 17 alpha methyltestosterone on zebrafish brain sexual development.,PRJNA385064,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic hormonal and environmental factors can influence sexual development. Androgen treatment triggers phenotypic and behavioural masculinisation in zebrafish. 17 alpha methyltestosterone MT a synthetic androgen is routinely used in aquaculture for production of all male populations. However the molecular mechanisms underlying 17 alpha methyltestosterone induced brain and behavioural masculinisation in fish are poorly understood. In this study we analysed brain transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with brain transcriptomes of untreated female and male zebrafish. These data give insight into the role of androgens in teleost brain sexual differentiation.,,,,,60CFB3,,strain:Tgvas:egfp|age:60 dpf|dev stage:juvenile|sex:female|tissue:brain|genotype:Tgvas:egfp|sample type:whole brain|treatment:untreated|replicate:60 dpf control female brain Replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 60 dpf untreated female brain,60CFB3,60CFB3,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP112722,,,BC1JJDACXX_NZGL00075_60SCFB3_ATGTCA_L005_R1_001.fastq.gz BC1JJDACXX_NZGL00075_60SCFB3_ATGTCA_L005_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60SCFB3_ATGTCA_L003_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCFB3_ATGTCA_L003_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60SCFB3_ATGTCA_L004_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCFB3_ATGTCA_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq,3937677400.0,19688387.0,BC1JJDACXX NZGL00075 60SCFB3 ATGTCA L005 R1 001.fastq.gz,0:100 1:100,A:1079137862;C:892796857;G:881342121;T:1075647268;N:8753292,100,100,,,1079137862,892796857,881342121,1075647268,8753292,SRX3013984,SRS2363578,SRA588281,University of Otago|Anatomy,University of Otago,2,0.94036,0.9419,0.10516,0.1048,0.68878,0.68643,0.49926,0.50072,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2018-07-31,Juvenile,Juvenile,Brain,Nervous System
42236,SRR5837507,SRX3013983,SRS2363579,SRP112722,PRJNA385064,Transcriptomic effects of 17 alpha methyltestosterone on zebrafish brain sexual development.,PRJNA385064,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic hormonal and environmental factors can influence sexual development. Androgen treatment triggers phenotypic and behavioural masculinisation in zebrafish. 17 alpha methyltestosterone MT a synthetic androgen is routinely used in aquaculture for production of all male populations. However the molecular mechanisms underlying 17 alpha methyltestosterone induced brain and behavioural masculinisation in fish are poorly understood. In this study we analysed brain transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with brain transcriptomes of untreated female and male zebrafish. These data give insight into the role of androgens in teleost brain sexual differentiation.,,,,,60CFB2,,strain:Tgvas:egfp|age:60 dpf|dev stage:juvenile|sex:female|tissue:brain|genotype:Tgvas:egfp|sample type:whole brain|treatment:untreated|replicate:60 dpf control female brain Replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 60 dpf untreated female brain,60CFB2,60CFB2,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP112722,,,BC1JJDACXX_NZGL00075_60SCFB2_AGTTCC_L005_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCFB2_AGTTCC_L003_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCFB2_AGTTCC_L003_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60SCFB2_AGTTCC_L004_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCFB2_AGTTCC_L004_R2_001.fastq.gz BC1JJDACXX_NZGL00075_60SCFB2_AGTTCC_L005_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq,3985340600.0,19926703.0,C1PF2ACXX NZGL00075 60SCFB2 AGTTCC L003 R1 001.fastq.gz,0:100 1:100,A:1097563742;C:899092355;G:886428117;T:1093249437;N:9006949,100,100,,,1097563742,899092355,886428117,1093249437,9006949,SRX3013983,SRS2363579,SRA588281,University of Otago|Anatomy,University of Otago,2,0.94308,0.94178,0.1009,0.10139,0.69161,0.69232,0.49007,0.49729,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2018-07-31,Juvenile,Juvenile,Brain,Nervous System
42237,SRR5837508,SRX3013982,SRS2363576,SRP112722,PRJNA385064,Transcriptomic effects of 17 alpha methyltestosterone on zebrafish brain sexual development.,PRJNA385064,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic hormonal and environmental factors can influence sexual development. Androgen treatment triggers phenotypic and behavioural masculinisation in zebrafish. 17 alpha methyltestosterone MT a synthetic androgen is routinely used in aquaculture for production of all male populations. However the molecular mechanisms underlying 17 alpha methyltestosterone induced brain and behavioural masculinisation in fish are poorly understood. In this study we analysed brain transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with brain transcriptomes of untreated female and male zebrafish. These data give insight into the role of androgens in teleost brain sexual differentiation.,,,,,60CMB2,,strain:Tgvas:egfp|age:60 dpf|dev stage:juvenile|sex:male|tissue:brain|genotype:Tgvas:egfp|sample type:whole brain|treatment:untreated|replicate:60 dpf control male brain Replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 60 dpf untreated male brain,60CMB2,60CMB2,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP112722,,,BC1JJDACXX_NZGL00075_60SCMB2_TGACCA_L005_R1_001.fastq.gz BC1JJDACXX_NZGL00075_60SCMB2_TGACCA_L005_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMB2_TGACCA_L003_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMB2_TGACCA_L003_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMB2_TGACCA_L004_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMB2_TGACCA_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq,4197412400.0,20987062.0,C1PF2ACXX NZGL00075 60SCMB2 TGACCA L004 R2 001.fastq.gz,0:100 1:100,A:1145515323;C:956583345;G:943561936;T:1142460826;N:9290970,100,100,,,1145515323,956583345,943561936,1142460826,9290970,SRX3013982,SRS2363576,SRA588281,University of Otago|Anatomy,University of Otago,2,0.94131,0.94062,0.10548,0.10508,0.68838,0.68767,0.4885,0.49667,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2018-07-31,Juvenile,Juvenile,Brain,Nervous System
42238,SRR5837509,SRX3013981,SRS2363577,SRP112722,PRJNA385064,Transcriptomic effects of 17 alpha methyltestosterone on zebrafish brain sexual development.,PRJNA385064,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic hormonal and environmental factors can influence sexual development. Androgen treatment triggers phenotypic and behavioural masculinisation in zebrafish. 17 alpha methyltestosterone MT a synthetic androgen is routinely used in aquaculture for production of all male populations. However the molecular mechanisms underlying 17 alpha methyltestosterone induced brain and behavioural masculinisation in fish are poorly understood. In this study we analysed brain transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with brain transcriptomes of untreated female and male zebrafish. These data give insight into the role of androgens in teleost brain sexual differentiation.,,,,,60CMB1,,strain:Tgvas:egfp|age:60 dpf|dev stage:juvenile|sex:male|tissue:brain|genotype:Tgvas:egfp|sample type:whole brain|treatment:untreated|replicate:60 dpf control male brain Replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 60 dpf untreated male brain,60CMB1,60CMB1,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP112722,,,BC1JJDACXX_NZGL00075_60SCMB1_CGATGT_L005_R1_001.fastq.gz BC1JJDACXX_NZGL00075_60SCMB1_CGATGT_L005_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMB1_CGATGT_L003_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMB1_CGATGT_L003_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMB1_CGATGT_L004_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMB1_CGATGT_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq,3656502200.0,18282511.0,C1PF2ACXX NZGL00075 60SCMB1 CGATGT L004 R1 001.fastq.gz,0:100 1:100,A:1006097362;C:825773612;G:813254919;T:1003161970;N:8214337,100,100,,,1006097362,825773612,813254919,1003161970,8214337,SRX3013981,SRS2363577,SRA588281,University of Otago|Anatomy,University of Otago,2,0.9381,0.93994,0.11219,0.113,0.69002,0.69053,0.49163,0.48747,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2018-07-31,Juvenile,Juvenile,Brain,Nervous System
53495,SRR9886611,SRX6639067,SRS5209782,SRP217245,PRJNA558074,Transcriptomic analysis of dj 1 / zebrafish brains compared to wild type siblings,GSE135271,Transcriptome Analysis,RNA Seq comparing transcript expression in the brains of 3 dj 1 / mutant zebrafish and 3 wild type siblings at 16 wpf Overall design: Brain mRNA profiles of 16 wpf wild type and park7dj 1 / zebrafish were generated by deep sequencing in triplicate using Illumina HiSeq 3000,,pubmed:32859696,,GH6,GSM4002525,,source name:Brain|strain:LWT|tissue:Brain|age:12 wpf dj 1 / ,GH6,A quality check was carried out using FastQC to make sure there were enough high quality reads. The adaptor sequences were trimmed with cutadapt 1.16 Salmon 0.10.2 was used for pseudo alignment of reads to the transcriptome. Sleuth 0.30.0 was used to test for differential expression. Genome build: GRCZ11 Supplementary files format and content: tab delimited text file including RPKM values for each transcript hypertext markup language document including read counts per sample,Brain,,Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.,,strain:LWT|tissue:Brain|age:12 wpf dj 1 / ,GSM4002525,GSM4002525: GH6; Danio rerio; RNA Seq,GSM4002525,,1,Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.,GEO Accession:GSM4002525,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP217245,,,GH6_S41_L004_R1_001.fastq-004.gz GH6_S41_L004_R2_001.fastq-009.gz,fastq fastq,16197223984.0,53633192.0,GSM4002525 r1,0:151 1:151,A:4524520245;C:3580881754;G:3728671047;T:4362276906;N:874032,151,151,,,4524520245,3580881754,3728671047,4362276906,874032,SRX6639067,SRS5209782,SRA931013,GEO,"Biology, University of York",2,0.91745,0.9163,0.15171,0.14974,0.69826,0.70161,0.49509,0.48979,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United Kingdom,2019-08-01,Juvenile,Juvenile,Brain,Nervous System
53496,SRR9886610,SRX6639066,SRS5209781,SRP217245,PRJNA558074,Transcriptomic analysis of dj 1 / zebrafish brains compared to wild type siblings,GSE135271,Transcriptome Analysis,RNA Seq comparing transcript expression in the brains of 3 dj 1 / mutant zebrafish and 3 wild type siblings at 16 wpf Overall design: Brain mRNA profiles of 16 wpf wild type and park7dj 1 / zebrafish were generated by deep sequencing in triplicate using Illumina HiSeq 3000,,pubmed:32859696,,GH5,GSM4002524,,source name:Brain|strain:LWT|tissue:Brain|age:12 wpf dj 1 / ,GH5,A quality check was carried out using FastQC to make sure there were enough high quality reads. The adaptor sequences were trimmed with cutadapt 1.16 Salmon 0.10.2 was used for pseudo alignment of reads to the transcriptome. Sleuth 0.30.0 was used to test for differential expression. Genome build: GRCZ11 Supplementary files format and content: tab delimited text file including RPKM values for each transcript hypertext markup language document including read counts per sample,Brain,,Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.,,strain:LWT|tissue:Brain|age:12 wpf dj 1 / ,GSM4002524,GSM4002524: GH5; Danio rerio; RNA Seq,GSM4002524,,1,Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.,GEO Accession:GSM4002524,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP217245,,,GH5_S40_L004_R1_001.fastq-001.gz GH5_S40_L004_R2_001.fastq-003.gz,fastq fastq,14762621304.0,48882852.0,GSM4002524 r1,0:151 1:151,A:4134788753;C:3245817056;G:3388258601;T:3992937107;N:819787,151,151,,,4134788753,3245817056,3388258601,3992937107,819787,SRX6639066,SRS5209781,SRA931013,GEO,"Biology, University of York",2,0.91356,0.91354,0.15637,0.15448,0.69755,0.70177,0.48873,0.49642,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United Kingdom,2019-08-01,Juvenile,Juvenile,Brain,Nervous System
53497,SRR9886609,SRX6639065,SRS5209780,SRP217245,PRJNA558074,Transcriptomic analysis of dj 1 / zebrafish brains compared to wild type siblings,GSE135271,Transcriptome Analysis,RNA Seq comparing transcript expression in the brains of 3 dj 1 / mutant zebrafish and 3 wild type siblings at 16 wpf Overall design: Brain mRNA profiles of 16 wpf wild type and park7dj 1 / zebrafish were generated by deep sequencing in triplicate using Illumina HiSeq 3000,,pubmed:32859696,,GH4,GSM4002523,,source name:Brain|strain:LWT|tissue:Brain|age:12 wpf dj 1 / ,GH4,A quality check was carried out using FastQC to make sure there were enough high quality reads. The adaptor sequences were trimmed with cutadapt 1.16 Salmon 0.10.2 was used for pseudo alignment of reads to the transcriptome. Sleuth 0.30.0 was used to test for differential expression. Genome build: GRCZ11 Supplementary files format and content: tab delimited text file including RPKM values for each transcript hypertext markup language document including read counts per sample,Brain,,Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.,,strain:LWT|tissue:Brain|age:12 wpf dj 1 / ,GSM4002523,GSM4002523: GH4; Danio rerio; RNA Seq,GSM4002523,,1,Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.,GEO Accession:GSM4002523,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP217245,,,GH4_S39_L004_R1_001.fastq-008.gz GH4_S39_L004_R2_001.fastq-011.gz,fastq fastq,17232418376.0,57060988.0,GSM4002523 r1,0:151 1:151,A:4798343141;C:3812370940;G:3947002545;T:4673748329;N:953421,151,151,,,4798343141,3812370940,3947002545,4673748329,953421,SRX6639065,SRS5209780,SRA931013,GEO,"Biology, University of York",2,0.91359,0.91289,0.15791,0.15599,0.70128,0.70585,0.48423,0.48897,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United Kingdom,2019-08-01,Juvenile,Juvenile,Brain,Nervous System
53498,SRR9886608,SRX6639064,SRS5209779,SRP217245,PRJNA558074,Transcriptomic analysis of dj 1 / zebrafish brains compared to wild type siblings,GSE135271,Transcriptome Analysis,RNA Seq comparing transcript expression in the brains of 3 dj 1 / mutant zebrafish and 3 wild type siblings at 16 wpf Overall design: Brain mRNA profiles of 16 wpf wild type and park7dj 1 / zebrafish were generated by deep sequencing in triplicate using Illumina HiSeq 3000,,pubmed:32859696,,GH3,GSM4002522,,source name:Brain|strain:LWT|tissue:Brain|age:12 wpf type,GH3,A quality check was carried out using FastQC to make sure there were enough high quality reads. The adaptor sequences were trimmed with cutadapt 1.16 Salmon 0.10.2 was used for pseudo alignment of reads to the transcriptome. Sleuth 0.30.0 was used to test for differential expression. Genome build: GRCZ11 Supplementary files format and content: tab delimited text file including RPKM values for each transcript hypertext markup language document including read counts per sample,Brain,,Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.,,strain:LWT|tissue:Brain|age:12 wpf type,GSM4002522,GSM4002522: GH3; Danio rerio; RNA Seq,GSM4002522,,1,Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.,GEO Accession:GSM4002522,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP217245,,,GH3_S38_L004_R1_001.fastq-002.gz GH3_S38_L004_R2_001.fastq-005.gz,fastq fastq,15880659430.0,52584965.0,GSM4002522 r1,0:151 1:151,A:4428460730;C:3500855291;G:3647161094;T:4303300463;N:881852,151,151,,,4428460730,3500855291,3647161094,4303300463,881852,SRX6639064,SRS5209779,SRA931013,GEO,"Biology, University of York",2,0.91311,0.91404,0.15734,0.15592,0.69621,0.70092,0.4936,0.48217,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United Kingdom,2019-08-01,Juvenile,Juvenile,Brain,Nervous System
53499,SRR9886607,SRX6639063,SRS5209778,SRP217245,PRJNA558074,Transcriptomic analysis of dj 1 / zebrafish brains compared to wild type siblings,GSE135271,Transcriptome Analysis,RNA Seq comparing transcript expression in the brains of 3 dj 1 / mutant zebrafish and 3 wild type siblings at 16 wpf Overall design: Brain mRNA profiles of 16 wpf wild type and park7dj 1 / zebrafish were generated by deep sequencing in triplicate using Illumina HiSeq 3000,,pubmed:32859696,,GH2,GSM4002521,,source name:Brain|strain:LWT|tissue:Brain|age:12 wpf type,GH2,A quality check was carried out using FastQC to make sure there were enough high quality reads. The adaptor sequences were trimmed with cutadapt 1.16 Salmon 0.10.2 was used for pseudo alignment of reads to the transcriptome. Sleuth 0.30.0 was used to test for differential expression. Genome build: GRCZ11 Supplementary files format and content: tab delimited text file including RPKM values for each transcript hypertext markup language document including read counts per sample,Brain,,Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.,,strain:LWT|tissue:Brain|age:12 wpf type,GSM4002521,GSM4002521: GH2; Danio rerio; RNA Seq,GSM4002521,,1,Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.,GEO Accession:GSM4002521,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP217245,,,GH2_S37_L004_R1_001.fastq-006.gz GH2_S37_L004_R2_001.fastq-012.gz,fastq fastq,17721573816.0,58680708.0,GSM4002521 r1,0:151 1:151,A:4948184152;C:3901958410;G:4066182263;T:4804260891;N:988100,151,151,,,4948184152,3901958410,4066182263,4804260891,988100,SRX6639063,SRS5209778,SRA931013,GEO,"Biology, University of York",2,0.90975,0.90966,0.16242,0.16044,0.69934,0.70339,0.48497,0.49335,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United Kingdom,2019-08-01,Juvenile,Juvenile,Brain,Nervous System
53500,SRR9886606,SRX6639062,SRS5209777,SRP217245,PRJNA558074,Transcriptomic analysis of dj 1 / zebrafish brains compared to wild type siblings,GSE135271,Transcriptome Analysis,RNA Seq comparing transcript expression in the brains of 3 dj 1 / mutant zebrafish and 3 wild type siblings at 16 wpf Overall design: Brain mRNA profiles of 16 wpf wild type and park7dj 1 / zebrafish were generated by deep sequencing in triplicate using Illumina HiSeq 3000,,pubmed:32859696,,GH1,GSM4002520,,source name:Brain|strain:LWT|tissue:Brain|age:12 wpf type,GH1,A quality check was carried out using FastQC to make sure there were enough high quality reads. The adaptor sequences were trimmed with cutadapt 1.16 Salmon 0.10.2 was used for pseudo alignment of reads to the transcriptome. Sleuth 0.30.0 was used to test for differential expression. Genome build: GRCZ11 Supplementary files format and content: tab delimited text file including RPKM values for each transcript hypertext markup language document including read counts per sample,Brain,,Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.,,strain:LWT|tissue:Brain|age:12 wpf type,GSM4002520,GSM4002520: GH1; Danio rerio; RNA Seq,GSM4002520,,1,Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.,GEO Accession:GSM4002520,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP217245,,,GH1_S36_L004_R1_001.fastq-007.gz GH1_S36_L004_R2_001.fastq-010.gz,fastq fastq,16852076254.0,55801577.0,GSM4002520 r1,0:151 1:151,A:4697089825;C:3744087924;G:3878965083;T:4531030410;N:903012,151,151,,,4697089825,3744087924,3878965083,4531030410,903012,SRX6639062,SRS5209777,SRA931013,GEO,"Biology, University of York",2,0.91719,0.91765,0.15136,0.15011,0.69998,0.70455,0.48284,0.48335,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United Kingdom,2019-08-01,Juvenile,Juvenile,Brain,Nervous System
56079,SRR10868206,SRX7538229,SRS5976893,SRP241164,PRJNA600413,Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome,GSE143416,Transcriptome Analysis,Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure – one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio shortfin 'AB' strain of both sexes i.e Male control Female control Male alcohol exposed Female alcohol exposed Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control three replicates of female control two replicates of Male alcohol exposed two replicates of Female alcohol exposed three replicates of Male withdrawal and two replicates of Female withdrawal group. There were 12 samples of liver tissues i.e two replicates for each of the six groups. The sequence reads were quality checked using FastQC mapped to reference genome danRer10 using STAR abundance estimates of transcripts calculated using RSEM and differential expression was performed using EBSeq.,,pubmed:33163595,,WDFB rep2,GSM4259026,,source name:Withdrawal Female Brain 2|strain:short fin 'AB' strain|condition:Withdrawal|Sex:female|tissue:Brain,WDFB rep2,Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR runThreadN 16 runMode alignReads readFilesCommand zcat outSAMstrandField intronMotif outSAMtype BAM SortedByCoordinate quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters rsem calculate expression bam no bam output p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues,Withdrawal Female Brain 2,For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C water salinity of 3 g of sea salt per liter and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations both partners control only male alcohol exposed only female alcohol exposed and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding we kept male and female fish in the same breeding tank a night before the breeding. The next morning breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects.,Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer’s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.,Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty naïve wild type short fin ‘AB’strainD. rerio60 males 60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus each group was composed of 30 fish exclusively either male or female maintained in a 20 L water tank.,strain:short fin 'AB' strain|condition:Withdrawal|Sex:Female|tissue:Brain,GSM4259026,GSM4259026: WDFB rep2; Danio rerio; RNA Seq,GSM4259026,,1,Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.,GEO Accession:GSM4259026,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP241164,,,WDFB2_R1.fastq.gz WDFB2_R2.fastq.gz,fastq fastq,9462270800.0,47311354.0,GSM4259026 r1,0:100 1:100,A:2623324121;C:2128638272;G:2095691781;T:2613931144;N:685482,100,100,,,2623324121,2128638272,2095691781,2613931144,685482,SRX7538229,SRS5976893,SRA1023469,GEO,CSIR Centre for Cellular and Molecular biology,2,0.92749,0.92578,0.12435,0.12374,0.67395,0.67779,0.53341,0.5337,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,India,2020-01-10,Juvenile,Juvenile,Brain,Nervous System
56080,SRR10868205,SRX7538228,SRS5976892,SRP241164,PRJNA600413,Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome,GSE143416,Transcriptome Analysis,Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure – one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio shortfin 'AB' strain of both sexes i.e Male control Female control Male alcohol exposed Female alcohol exposed Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control three replicates of female control two replicates of Male alcohol exposed two replicates of Female alcohol exposed three replicates of Male withdrawal and two replicates of Female withdrawal group. There were 12 samples of liver tissues i.e two replicates for each of the six groups. The sequence reads were quality checked using FastQC mapped to reference genome danRer10 using STAR abundance estimates of transcripts calculated using RSEM and differential expression was performed using EBSeq.,,pubmed:33163595,,WDFB rep1,GSM4259025,,source name:Withdrawal Female Brain 1|strain:short fin 'AB' strain|condition:Withdrawal|Sex:female|tissue:Brain,WDFB rep1,Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR runThreadN 16 runMode alignReads readFilesCommand zcat outSAMstrandField intronMotif outSAMtype BAM SortedByCoordinate quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters rsem calculate expression bam no bam output p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues,Withdrawal Female Brain 1,For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C water salinity of 3 g of sea salt per liter and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations both partners control only male alcohol exposed only female alcohol exposed and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding we kept male and female fish in the same breeding tank a night before the breeding. The next morning breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects.,Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer’s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.,Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty naïve wild type short fin ‘AB’strainD. rerio60 males 60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus each group was composed of 30 fish exclusively either male or female maintained in a 20 L water tank.,strain:short fin 'AB' strain|condition:Withdrawal|Sex:Female|tissue:Brain,GSM4259025,GSM4259025: WDFB rep1; Danio rerio; RNA Seq,GSM4259025,,1,Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.,GEO Accession:GSM4259025,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP241164,,,WDFB1_R1.fastq.gz WDFB1_R2.fastq.gz,fastq fastq,4915307600.0,24576538.0,GSM4259025 r1,0:100 1:100,A:1314857244;C:1204561669;G:1224379519;T:1168856636;N:2652532,100,100,,,1314857244,1204561669,1224379519,1168856636,2652532,SRX7538228,SRS5976892,SRA1023469,GEO,CSIR Centre for Cellular and Molecular biology,2,0.82559,0.82679,0.16477,0.16589,0.75124,0.75345,0.60433,0.60746,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,India,2020-01-10,Juvenile,Juvenile,Brain,Nervous System
56081,SRR10868204,SRX7538227,SRS5976891,SRP241164,PRJNA600413,Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome,GSE143416,Transcriptome Analysis,Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure – one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio shortfin 'AB' strain of both sexes i.e Male control Female control Male alcohol exposed Female alcohol exposed Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control three replicates of female control two replicates of Male alcohol exposed two replicates of Female alcohol exposed three replicates of Male withdrawal and two replicates of Female withdrawal group. There were 12 samples of liver tissues i.e two replicates for each of the six groups. The sequence reads were quality checked using FastQC mapped to reference genome danRer10 using STAR abundance estimates of transcripts calculated using RSEM and differential expression was performed using EBSeq.,,pubmed:33163595,,WDMB rep3,GSM4259024,,source name:Withdrawal Male Brain 3|strain:short fin 'AB' strain|condition:Withdrawal|Sex:male|tissue:Brain,WDMB rep3,Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR runThreadN 16 runMode alignReads readFilesCommand zcat outSAMstrandField intronMotif outSAMtype BAM SortedByCoordinate quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters rsem calculate expression bam no bam output p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues,Withdrawal Male Brain 3,For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C water salinity of 3 g of sea salt per liter and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations both partners control only male alcohol exposed only female alcohol exposed and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding we kept male and female fish in the same breeding tank a night before the breeding. The next morning breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects.,Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer’s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.,Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty naïve wild type short fin ‘AB’strainD. rerio60 males 60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus each group was composed of 30 fish exclusively either male or female maintained in a 20 L water tank.,strain:short fin 'AB' strain|condition:Withdrawal|Sex:Male|tissue:Brain,GSM4259024,GSM4259024: WDMB rep3; Danio rerio; RNA Seq,GSM4259024,,1,Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.,GEO Accession:GSM4259024,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP241164,,,WDMB3_R1.fastq.gz WDMB3_R2.fastq.gz,fastq fastq,6528723800.0,32643619.0,GSM4259024 r1,0:100 1:100,A:1756898202;C:1512672011;G:1529360542;T:1725931518;N:3861527,100,100,,,1756898202,1512672011,1529360542,1725931518,3861527,SRX7538227,SRS5976891,SRA1023469,GEO,CSIR Centre for Cellular and Molecular biology,2,0.94324,0.94244,0.1178,0.1183,0.68394,0.68663,0.51456,0.51726,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,India,2020-01-10,Juvenile,Juvenile,Brain,Nervous System
56082,SRR10868203,SRX7538226,SRS5976890,SRP241164,PRJNA600413,Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome,GSE143416,Transcriptome Analysis,Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure – one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio shortfin 'AB' strain of both sexes i.e Male control Female control Male alcohol exposed Female alcohol exposed Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control three replicates of female control two replicates of Male alcohol exposed two replicates of Female alcohol exposed three replicates of Male withdrawal and two replicates of Female withdrawal group. There were 12 samples of liver tissues i.e two replicates for each of the six groups. The sequence reads were quality checked using FastQC mapped to reference genome danRer10 using STAR abundance estimates of transcripts calculated using RSEM and differential expression was performed using EBSeq.,,pubmed:33163595,,WDMB rep2,GSM4259023,,source name:Withdrawal Male Brain 2|strain:short fin 'AB' strain|condition:Withdrawal|Sex:male|tissue:Brain,WDMB rep2,Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR runThreadN 16 runMode alignReads readFilesCommand zcat outSAMstrandField intronMotif outSAMtype BAM SortedByCoordinate quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters rsem calculate expression bam no bam output p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues,Withdrawal Male Brain 2,For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C water salinity of 3 g of sea salt per liter and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations both partners control only male alcohol exposed only female alcohol exposed and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding we kept male and female fish in the same breeding tank a night before the breeding. The next morning breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects.,Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer’s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.,Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty naïve wild type short fin ‘AB’strainD. rerio60 males 60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus each group was composed of 30 fish exclusively either male or female maintained in a 20 L water tank.,strain:short fin 'AB' strain|condition:Withdrawal|Sex:Male|tissue:Brain,GSM4259023,GSM4259023: WDMB rep2; Danio rerio; RNA Seq,GSM4259023,,1,Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.,GEO Accession:GSM4259023,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP241164,,,WDMB2_R1.fastq.gz WDMB2_R2.fastq.gz,fastq fastq,7911217000.0,39556085.0,GSM4259023 r1,0:100 1:100,A:2166287949;C:1800275915;G:1804637340;T:2135900682;N:4115114,100,100,,,2166287949,1800275915,1804637340,2135900682,4115114,SRX7538226,SRS5976890,SRA1023469,GEO,CSIR Centre for Cellular and Molecular biology,2,0.93471,0.93064,0.12564,0.12609,0.68592,0.6912,0.52362,0.52186,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,India,2020-01-10,Juvenile,Juvenile,Brain,Nervous System
56083,SRR10868202,SRX7538225,SRS5976889,SRP241164,PRJNA600413,Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome,GSE143416,Transcriptome Analysis,Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure – one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio shortfin 'AB' strain of both sexes i.e Male control Female control Male alcohol exposed Female alcohol exposed Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control three replicates of female control two replicates of Male alcohol exposed two replicates of Female alcohol exposed three replicates of Male withdrawal and two replicates of Female withdrawal group. There were 12 samples of liver tissues i.e two replicates for each of the six groups. The sequence reads were quality checked using FastQC mapped to reference genome danRer10 using STAR abundance estimates of transcripts calculated using RSEM and differential expression was performed using EBSeq.,,pubmed:33163595,,WDMB rep1,GSM4259022,,source name:Withdrawal Male Brain 1|strain:short fin 'AB' strain|condition:Withdrawal|Sex:male|tissue:Brain,WDMB rep1,Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR runThreadN 16 runMode alignReads readFilesCommand zcat outSAMstrandField intronMotif outSAMtype BAM SortedByCoordinate quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters rsem calculate expression bam no bam output p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues,Withdrawal Male Brain 1,For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C water salinity of 3 g of sea salt per liter and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations both partners control only male alcohol exposed only female alcohol exposed and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding we kept male and female fish in the same breeding tank a night before the breeding. The next morning breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects.,Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer’s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.,Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty naïve wild type short fin ‘AB’strainD. rerio60 males 60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus each group was composed of 30 fish exclusively either male or female maintained in a 20 L water tank.,strain:short fin 'AB' strain|condition:Withdrawal|Sex:Male|tissue:Brain,GSM4259022,GSM4259022: WDMB rep1; Danio rerio; RNA Seq,GSM4259022,,1,Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.,GEO Accession:GSM4259022,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP241164,,,WDMB1_R1.fastq.gz WDMB1_R2.fastq.gz,fastq fastq,10067526400.0,50337632.0,GSM4259022 r1,0:100 1:100,A:2697183588;C:2346903448;G:2320543779;T:2697791982;N:5103603,100,100,,,2697183588,2346903448,2320543779,2697791982,5103603,SRX7538225,SRS5976889,SRA1023469,GEO,CSIR Centre for Cellular and Molecular biology,2,0.94143,0.94125,0.11819,0.11997,0.68316,0.68667,0.51146,0.51233,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,India,2020-01-10,Juvenile,Juvenile,Brain,Nervous System
56084,SRR10868201,SRX7538224,SRS5976888,SRP241164,PRJNA600413,Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome,GSE143416,Transcriptome Analysis,Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure – one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio shortfin 'AB' strain of both sexes i.e Male control Female control Male alcohol exposed Female alcohol exposed Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control three replicates of female control two replicates of Male alcohol exposed two replicates of Female alcohol exposed three replicates of Male withdrawal and two replicates of Female withdrawal group. There were 12 samples of liver tissues i.e two replicates for each of the six groups. The sequence reads were quality checked using FastQC mapped to reference genome danRer10 using STAR abundance estimates of transcripts calculated using RSEM and differential expression was performed using EBSeq.,,pubmed:33163595,,ALFB rep2,GSM4259021,,source name:Alcohol exposed Female Brain 2|strain:short fin 'AB' strain|condition:Alcohol exposed|Sex:female|tissue:Brain,ALFB rep2,Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR runThreadN 16 runMode alignReads readFilesCommand zcat outSAMstrandField intronMotif outSAMtype BAM SortedByCoordinate quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters rsem calculate expression bam no bam output p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues,Alcohol exposed Female Brain 2,For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C water salinity of 3 g of sea salt per liter and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations both partners control only male alcohol exposed only female alcohol exposed and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding we kept male and female fish in the same breeding tank a night before the breeding. The next morning breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects.,Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer’s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.,Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty naïve wild type short fin ‘AB’strainD. rerio60 males 60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus each group was composed of 30 fish exclusively either male or female maintained in a 20 L water tank.,strain:short fin 'AB' strain|condition:Alcohol exposed|Sex:Female|tissue:Brain,GSM4259021,GSM4259021: ALFB rep2; Danio rerio; RNA Seq,GSM4259021,,1,Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.,GEO Accession:GSM4259021,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP241164,,,ALFB2_R1.fastq.gz ALFB2_R2.fastq.gz,fastq fastq,5723348000.0,28616740.0,GSM4259021 r1,0:100 1:100,A:1619162291;C:1257502494;G:1230192905;T:1616232776;N:257534,100,100,,,1619162291,1257502494,1230192905,1616232776,257534,SRX7538224,SRS5976888,SRA1023469,GEO,CSIR Centre for Cellular and Molecular biology,2,0.88464,0.88121,0.19765,0.19699,0.61306,0.61968,0.4979,0.4979,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,India,2020-01-10,Juvenile,Juvenile,Brain,Nervous System
56085,SRR10868200,SRX7538223,SRS5976887,SRP241164,PRJNA600413,Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome,GSE143416,Transcriptome Analysis,Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure – one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio shortfin 'AB' strain of both sexes i.e Male control Female control Male alcohol exposed Female alcohol exposed Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control three replicates of female control two replicates of Male alcohol exposed two replicates of Female alcohol exposed three replicates of Male withdrawal and two replicates of Female withdrawal group. There were 12 samples of liver tissues i.e two replicates for each of the six groups. The sequence reads were quality checked using FastQC mapped to reference genome danRer10 using STAR abundance estimates of transcripts calculated using RSEM and differential expression was performed using EBSeq.,,pubmed:33163595,,ALFB rep1,GSM4259020,,source name:Alcohol exposed Female Brain 1|strain:short fin 'AB' strain|condition:Alcohol exposed|Sex:female|tissue:Brain,ALFB rep1,Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR runThreadN 16 runMode alignReads readFilesCommand zcat outSAMstrandField intronMotif outSAMtype BAM SortedByCoordinate quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters rsem calculate expression bam no bam output p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues,Alcohol exposed Female Brain 1,For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C water salinity of 3 g of sea salt per liter and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations both partners control only male alcohol exposed only female alcohol exposed and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding we kept male and female fish in the same breeding tank a night before the breeding. The next morning breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects.,Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer’s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.,Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty naïve wild type short fin ‘AB’strainD. rerio60 males 60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus each group was composed of 30 fish exclusively either male or female maintained in a 20 L water tank.,strain:short fin 'AB' strain|condition:Alcohol exposed|Sex:Female|tissue:Brain,GSM4259020,GSM4259020: ALFB rep1; Danio rerio; RNA Seq,GSM4259020,,1,Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.,GEO Accession:GSM4259020,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP241164,,,ALFB1_R2.fastq.gz ALFB1_R1.fastq.gz,fastq fastq,5003967000.0,25019835.0,GSM4259020 r1,0:100 1:100,A:1403773550;C:1111375452;G:1087806444;T:1400663587;N:347967,100,100,,,1403773550,1111375452,1087806444,1400663587,347967,SRX7538223,SRS5976887,SRA1023469,GEO,CSIR Centre for Cellular and Molecular biology,2,0.89689,0.89387,0.18681,0.18574,0.61456,0.62018,0.49315,0.48622,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,India,2020-01-10,Juvenile,Juvenile,Brain,Nervous System
56086,SRR10868199,SRX7538222,SRS5976886,SRP241164,PRJNA600413,Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome,GSE143416,Transcriptome Analysis,Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure – one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio shortfin 'AB' strain of both sexes i.e Male control Female control Male alcohol exposed Female alcohol exposed Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control three replicates of female control two replicates of Male alcohol exposed two replicates of Female alcohol exposed three replicates of Male withdrawal and two replicates of Female withdrawal group. There were 12 samples of liver tissues i.e two replicates for each of the six groups. The sequence reads were quality checked using FastQC mapped to reference genome danRer10 using STAR abundance estimates of transcripts calculated using RSEM and differential expression was performed using EBSeq.,,pubmed:33163595,,ALMB rep2,GSM4259019,,source name:Alcohol exposed Male Brain 2|strain:short fin 'AB' strain|condition:Alcohol exposed|Sex:male|tissue:Brain,ALMB rep2,Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR runThreadN 16 runMode alignReads readFilesCommand zcat outSAMstrandField intronMotif outSAMtype BAM SortedByCoordinate quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters rsem calculate expression bam no bam output p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues,Alcohol exposed Male Brain 2,For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C water salinity of 3 g of sea salt per liter and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations both partners control only male alcohol exposed only female alcohol exposed and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding we kept male and female fish in the same breeding tank a night before the breeding. The next morning breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects.,Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer’s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.,Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty naïve wild type short fin ‘AB’strainD. rerio60 males 60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus each group was composed of 30 fish exclusively either male or female maintained in a 20 L water tank.,strain:short fin 'AB' strain|condition:Alcohol exposed|Sex:Male|tissue:Brain,GSM4259019,GSM4259019: ALMB rep2; Danio rerio; RNA Seq,GSM4259019,,1,Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.,GEO Accession:GSM4259019,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP241164,,,ALMB2_R1.fastq.gz ALMB2_R2.fastq.gz,fastq fastq,5772158400.0,28860792.0,GSM4259019 r1,0:100 1:100,A:1578072067;C:1311721894;G:1290868364;T:1591106232;N:389843,100,100,,,1578072067,1311721894,1290868364,1591106232,389843,SRX7538222,SRS5976886,SRA1023469,GEO,CSIR Centre for Cellular and Molecular biology,2,0.89619,0.89577,0.16969,0.16964,0.62998,0.63126,0.48949,0.49072,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,India,2020-01-10,Juvenile,Juvenile,Brain,Nervous System
56087,SRR10868198,SRX7538221,SRS5976885,SRP241164,PRJNA600413,Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome,GSE143416,Transcriptome Analysis,Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure – one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio shortfin 'AB' strain of both sexes i.e Male control Female control Male alcohol exposed Female alcohol exposed Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control three replicates of female control two replicates of Male alcohol exposed two replicates of Female alcohol exposed three replicates of Male withdrawal and two replicates of Female withdrawal group. There were 12 samples of liver tissues i.e two replicates for each of the six groups. The sequence reads were quality checked using FastQC mapped to reference genome danRer10 using STAR abundance estimates of transcripts calculated using RSEM and differential expression was performed using EBSeq.,,pubmed:33163595,,ALMB rep1,GSM4259018,,source name:Alcohol exposed Male Brain 1|strain:short fin 'AB' strain|condition:Alcohol exposed|Sex:male|tissue:Brain,ALMB rep1,Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR runThreadN 16 runMode alignReads readFilesCommand zcat outSAMstrandField intronMotif outSAMtype BAM SortedByCoordinate quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters rsem calculate expression bam no bam output p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues,Alcohol exposed Male Brain 1,For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C water salinity of 3 g of sea salt per liter and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations both partners control only male alcohol exposed only female alcohol exposed and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding we kept male and female fish in the same breeding tank a night before the breeding. The next morning breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects.,Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer’s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.,Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty naïve wild type short fin ‘AB’strainD. rerio60 males 60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus each group was composed of 30 fish exclusively either male or female maintained in a 20 L water tank.,strain:short fin 'AB' strain|condition:Alcohol exposed|Sex:Male|tissue:Brain,GSM4259018,GSM4259018: ALMB rep1; Danio rerio; RNA Seq,GSM4259018,,1,Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.,GEO Accession:GSM4259018,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP241164,,,ALMB1_R1.fastq.gz ALMB1_R2.fastq.gz,fastq fastq,6680441600.0,33402208.0,GSM4259018 r1,0:100 1:100,A:1866324371;C:1493146465;G:1461482647;T:1858729697;N:758420,100,100,,,1866324371,1493146465,1461482647,1858729697,758420,SRX7538221,SRS5976885,SRA1023469,GEO,CSIR Centre for Cellular and Molecular biology,2,0.88801,0.88327,0.18822,0.1864,0.62134,0.62412,0.50471,0.49503,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,India,2020-01-10,Juvenile,Juvenile,Brain,Nervous System
56088,SRR10868197,SRX7538220,SRS5976884,SRP241164,PRJNA600413,Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome,GSE143416,Transcriptome Analysis,Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure – one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio shortfin 'AB' strain of both sexes i.e Male control Female control Male alcohol exposed Female alcohol exposed Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control three replicates of female control two replicates of Male alcohol exposed two replicates of Female alcohol exposed three replicates of Male withdrawal and two replicates of Female withdrawal group. There were 12 samples of liver tissues i.e two replicates for each of the six groups. The sequence reads were quality checked using FastQC mapped to reference genome danRer10 using STAR abundance estimates of transcripts calculated using RSEM and differential expression was performed using EBSeq.,,pubmed:33163595,,CTFB rep3,GSM4259017,,source name:Control Female Brain 3|strain:short fin 'AB' strain|condition:Control|Sex:female|tissue:Brain,CTFB rep3,Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR runThreadN 16 runMode alignReads readFilesCommand zcat outSAMstrandField intronMotif outSAMtype BAM SortedByCoordinate quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters rsem calculate expression bam no bam output p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues,Control Female Brain 3,For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C water salinity of 3 g of sea salt per liter and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations both partners control only male alcohol exposed only female alcohol exposed and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding we kept male and female fish in the same breeding tank a night before the breeding. The next morning breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects.,Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer’s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.,Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty naïve wild type short fin ‘AB’strainD. rerio60 males 60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus each group was composed of 30 fish exclusively either male or female maintained in a 20 L water tank.,strain:short fin 'AB' strain|condition:Control|Sex:Female|tissue:Brain,GSM4259017,GSM4259017: CTFB rep3; Danio rerio; RNA Seq,GSM4259017,,1,Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.,GEO Accession:GSM4259017,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP241164,,,CTFB3_R1.fastq.gz CTFB3_R2.fastq.gz,fastq fastq,7118478200.0,35592391.0,GSM4259017 r1,0:100 1:100,A:1971457015;C:1597253419;G:1582003387;T:1963888656;N:3875723,100,100,,,1971457015,1597253419,1582003387,1963888656,3875723,SRX7538220,SRS5976884,SRA1023469,GEO,CSIR Centre for Cellular and Molecular biology,2,0.91947,0.91902,0.13574,0.13767,0.68481,0.68954,0.51218,0.50542,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,India,2020-01-10,Juvenile,Juvenile,Brain,Nervous System
56089,SRR10868196,SRX7538219,SRS5976883,SRP241164,PRJNA600413,Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome,GSE143416,Transcriptome Analysis,Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure – one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio shortfin 'AB' strain of both sexes i.e Male control Female control Male alcohol exposed Female alcohol exposed Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control three replicates of female control two replicates of Male alcohol exposed two replicates of Female alcohol exposed three replicates of Male withdrawal and two replicates of Female withdrawal group. There were 12 samples of liver tissues i.e two replicates for each of the six groups. The sequence reads were quality checked using FastQC mapped to reference genome danRer10 using STAR abundance estimates of transcripts calculated using RSEM and differential expression was performed using EBSeq.,,pubmed:33163595,,CTFB rep2,GSM4259016,,source name:Control Female Brain 2|strain:short fin 'AB' strain|condition:Control|Sex:female|tissue:Brain,CTFB rep2,Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR runThreadN 16 runMode alignReads readFilesCommand zcat outSAMstrandField intronMotif outSAMtype BAM SortedByCoordinate quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters rsem calculate expression bam no bam output p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues,Control Female Brain 2,For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C water salinity of 3 g of sea salt per liter and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations both partners control only male alcohol exposed only female alcohol exposed and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding we kept male and female fish in the same breeding tank a night before the breeding. The next morning breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects.,Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer’s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.,Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty naïve wild type short fin ‘AB’strainD. rerio60 males 60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus each group was composed of 30 fish exclusively either male or female maintained in a 20 L water tank.,strain:short fin 'AB' strain|condition:Control|Sex:Female|tissue:Brain,GSM4259016,GSM4259016: CTFB rep2; Danio rerio; RNA Seq,GSM4259016,,1,Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.,GEO Accession:GSM4259016,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP241164,,,CTFB2_R2.fastq.gz CTFB2_R1.fastq.gz,fastq fastq,8466120400.0,42330602.0,GSM4259016 r1,0:100 1:100,A:2325166132;C:1918127777;G:1912942105;T:2305391168;N:4493218,100,100,,,2325166132,1918127777,1912942105,2305391168,4493218,SRX7538219,SRS5976883,SRA1023469,GEO,CSIR Centre for Cellular and Molecular biology,2,0.93939,0.93646,0.13166,0.13198,0.68424,0.69018,0.53035,0.52204,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,India,2020-01-10,Juvenile,Juvenile,Brain,Nervous System
56090,SRR10868195,SRX7538218,SRS5976882,SRP241164,PRJNA600413,Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome,GSE143416,Transcriptome Analysis,Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure – one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio shortfin 'AB' strain of both sexes i.e Male control Female control Male alcohol exposed Female alcohol exposed Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control three replicates of female control two replicates of Male alcohol exposed two replicates of Female alcohol exposed three replicates of Male withdrawal and two replicates of Female withdrawal group. There were 12 samples of liver tissues i.e two replicates for each of the six groups. The sequence reads were quality checked using FastQC mapped to reference genome danRer10 using STAR abundance estimates of transcripts calculated using RSEM and differential expression was performed using EBSeq.,,pubmed:33163595,,CTFB rep1,GSM4259015,,source name:Control Female Brain 1|strain:short fin 'AB' strain|condition:Control|Sex:female|tissue:Brain,CTFB rep1,Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR runThreadN 16 runMode alignReads readFilesCommand zcat outSAMstrandField intronMotif outSAMtype BAM SortedByCoordinate quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters rsem calculate expression bam no bam output p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues,Control Female Brain 1,For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C water salinity of 3 g of sea salt per liter and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations both partners control only male alcohol exposed only female alcohol exposed and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding we kept male and female fish in the same breeding tank a night before the breeding. The next morning breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects.,Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer’s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.,Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty naïve wild type short fin ‘AB’strainD. rerio60 males 60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus each group was composed of 30 fish exclusively either male or female maintained in a 20 L water tank.,strain:short fin 'AB' strain|condition:Control|Sex:Female|tissue:Brain,GSM4259015,GSM4259015: CTFB rep1; Danio rerio; RNA Seq,GSM4259015,,1,Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.,GEO Accession:GSM4259015,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP241164,,,CTFB1_R1.fastq.gz CTFB1_R2.fastq.gz,fastq fastq,7268191400.0,36340957.0,GSM4259015 r1,0:100 1:100,A:2025221999;C:1631297953;G:1641821598;T:1966011517;N:3838333,100,100,,,2025221999,1631297953,1641821598,1966011517,3838333,SRX7538218,SRS5976882,SRA1023469,GEO,CSIR Centre for Cellular and Molecular biology,2,0.93943,0.93735,0.12747,0.12896,0.68925,0.69475,0.51438,0.50946,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,India,2020-01-10,Juvenile,Juvenile,Brain,Nervous System
56091,SRR10868194,SRX7538217,SRS5976881,SRP241164,PRJNA600413,Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome,GSE143416,Transcriptome Analysis,Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure – one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio shortfin 'AB' strain of both sexes i.e Male control Female control Male alcohol exposed Female alcohol exposed Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control three replicates of female control two replicates of Male alcohol exposed two replicates of Female alcohol exposed three replicates of Male withdrawal and two replicates of Female withdrawal group. There were 12 samples of liver tissues i.e two replicates for each of the six groups. The sequence reads were quality checked using FastQC mapped to reference genome danRer10 using STAR abundance estimates of transcripts calculated using RSEM and differential expression was performed using EBSeq.,,pubmed:33163595,,CTMB rep2,GSM4259014,,source name:Control Male Brain 2|strain:short fin 'AB' strain|condition:Control|Sex:male|tissue:Brain,CTMB rep2,Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR runThreadN 16 runMode alignReads readFilesCommand zcat outSAMstrandField intronMotif outSAMtype BAM SortedByCoordinate quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters rsem calculate expression bam no bam output p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues,Control Male Brain 2,For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C water salinity of 3 g of sea salt per liter and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations both partners control only male alcohol exposed only female alcohol exposed and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding we kept male and female fish in the same breeding tank a night before the breeding. The next morning breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects.,Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer’s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.,Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty naïve wild type short fin ‘AB’strainD. rerio60 males 60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus each group was composed of 30 fish exclusively either male or female maintained in a 20 L water tank.,strain:short fin 'AB' strain|condition:Control|Sex:Male|tissue:Brain,GSM4259014,GSM4259014: CTMB rep2; Danio rerio; RNA Seq,GSM4259014,,1,Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.,GEO Accession:GSM4259014,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP241164,,,CTMB2_R2.fastq.gz CTMB2_R1.fastq.gz,fastq fastq,11274416800.0,56372084.0,GSM4259014 r1,0:100 1:100,A:3218094652;C:2460765567;G:2418902264;T:3176107395;N:546922,100,100,,,3218094652,2460765567,2418902264,3176107395,546922,SRX7538217,SRS5976881,SRA1023469,GEO,CSIR Centre for Cellular and Molecular biology,2,0.92636,0.92291,0.1565,0.15531,0.69757,0.70086,0.53239,0.53374,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,India,2020-01-10,Juvenile,Juvenile,Brain,Nervous System
56092,SRR10868193,SRX7538216,SRS5976880,SRP241164,PRJNA600413,Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome,GSE143416,Transcriptome Analysis,Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure – one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio shortfin 'AB' strain of both sexes i.e Male control Female control Male alcohol exposed Female alcohol exposed Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control three replicates of female control two replicates of Male alcohol exposed two replicates of Female alcohol exposed three replicates of Male withdrawal and two replicates of Female withdrawal group. There were 12 samples of liver tissues i.e two replicates for each of the six groups. The sequence reads were quality checked using FastQC mapped to reference genome danRer10 using STAR abundance estimates of transcripts calculated using RSEM and differential expression was performed using EBSeq.,,pubmed:33163595,,CTMB rep1,GSM4259013,,source name:Control Male Brain 1|strain:short fin 'AB' strain|condition:Control|Sex:male|tissue:Brain,CTMB rep1,Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR runThreadN 16 runMode alignReads readFilesCommand zcat outSAMstrandField intronMotif outSAMtype BAM SortedByCoordinate quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters rsem calculate expression bam no bam output p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues,Control Male Brain 1,For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C water salinity of 3 g of sea salt per liter and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations both partners control only male alcohol exposed only female alcohol exposed and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding we kept male and female fish in the same breeding tank a night before the breeding. The next morning breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects.,Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer’s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.,Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty naïve wild type short fin ‘AB’strainD. rerio60 males 60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus each group was composed of 30 fish exclusively either male or female maintained in a 20 L water tank.,strain:short fin 'AB' strain|condition:Control|Sex:Male|tissue:Brain,GSM4259013,GSM4259013: CTMB rep1; Danio rerio; RNA Seq,GSM4259013,,1,Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.,GEO Accession:GSM4259013,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP241164,,,CTMB1_R2.fastq.gz CTMB1_R1.fastq.gz,fastq fastq,15053412200.0,75267061.0,GSM4259013 r1,0:100 1:100,A:4263297589;C:3314448659;G:3262961765;T:4211848536;N:855651,100,100,,,4263297589,3314448659,3262961765,4211848536,855651,SRX7538216,SRS5976880,SRA1023469,GEO,CSIR Centre for Cellular and Molecular biology,2,0.92714,0.92479,0.14993,0.14892,0.69692,0.69873,0.5153,0.51983,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,India,2020-01-10,Juvenile,Juvenile,Brain,Nervous System
65060,SRR14923998,SRX11237268,SRS9283142,SRP325759,PRJNA741770,Single cell profiling of cranial neural crest diversification across a vertebrate lifetime,GSE178969,Other,The cranial neural crest CNC is a vertebrate specific population that generates a huge diversity of derivatives including the bulk of the connective and skeletal tissues of the head. How neural crest cells generate the appropriate cell types for distinct head regions over time remains unresolved. Here we profile RNA expression scRNAseq and chromatin accessibility snATACseq of the zebrafish cranial neural crest lineage at single cell resolution from embryos to adults. Overall design: To recover the cell heterogeneity and lineage information in the span of a life time of a fish we collected the converted cells from embryonic stages 1.5 2 dpf larval stage 3 5 and 14 dpf juvenile stage 60 dpf to adult stage 150 or 210 dpf. We used a cranial neural crest converted zebrafish line 28.5Sox10:Cre;bactin:BFP to DsRed to permanantly convert and label the CNCC derived cells. The converted cells were collected and subjected to single cell sequencing for both their transcriptome and open chromatin region using Chromium platform of 10X Genomic. For biological and technical control we include replicates for both scRNAseq and snATACseq at various stages. We include an additional line fli1a:eGFP/sox10:dsRed for a biological and positive control of CNCC of 1.5 dpf sample.,,pubmed:35013168,,scRNAseq Sox10 Cre bact BtR 60dpf rep 2,GSM5402440,,tissue:Cranial neural crest derived cells|cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:60 dpf|facs markers:Zombie / dsRed+,scRNAseq Sox10 Cre bact BtR 60dpf rep 2,For scRNAseq libraries Cellranger v3.0.0 10X Genomics was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against zebrafish genome index built with GRCz11.fa and GRCz11.98.gtf. For snATACseq libraries Cellranger ATAC v1.2.0 10X Genomics was used for alignment against zebrafish genome index built with GRCz11.fa JASPAR2020 and GRCz11.98.gtf peak calling and peak by cell count matrix generation with default parameters. QC step for the library was performed along with the Cellranger or Cellranger ATAC alignment process. We performed a second round of peak calling for our snATACseq data using package Snaptools and SnapATAC. We first removed cell debris low quality cells and cell duplicates by setting cutoffs based on percentage of reads in peaks > 30 for 60 dpf > 45 for 210 dpf and > 50 for the rest and fragment number within peaks 5 000 – 30 000 for 5 dpf 1 000 – 11 000 for 14 dpf and 1 000 – 20 000 for the rest. To recover every aligned fragment we binned the genome into 5 kb sections and constructed the bin by cell matrices bmats for each library by Snaptools from the positional sorted bam files generated by cellranger atac. The cells were filtered dimensionally reduced by diffusion map and clustered with inputs of the first 34 dimensions followed the SnapATAC vignette. The specific peaks were called for each cluster by the wrapped MACS2 function in SnapATAC with parameter gsize = 1.5e9 shift = 100 ext = 200 and qval = 5e 2. The finalized and refined peak profile was derived by collapsing and merging all 175 individual peak files to about 450K peaks. The count matrices of both scRNAseq and snATACseq data were analyzed by R package Seurat and Signac. The count matrices of each sample were aggregated if there is any replicate. For scRNAseq data the matrices are normalized NormalizeData and scaled for the top 2 000 variable genes FindVariableFeatures and ScaleData. The scaled matrices were dimensional reduced to 50 principal components 60 components for 150 dpf which then subjected to neighbor finding FindNeighbors k = 20 and clustering FindClusters resolution = 0.8. The data were visualized through UMAP with 50 principal components as input. For snATACseq data the matrices are dimensionally reduced 30 latent semantic indices LSIs through RunTFIDF and RunSVD functions. The neighbor finding clustering and visualization are performed with the second to the thirtieth LSIs as input algoritm = 3 for FindClusters. Genome build: GRCz11 Supplementary files format and content: Each sample comes with four processed data files: a tab delimited cell barcode file tsv a tab delimited feature file with genes for scRNAseq or peaks for snATACseq tsv a sparse matrix of count table mtx and a cluster table tsv. The previous three files are suffice for creating a single cell count matrix. The cluster table can be further added to recreat the corresponding cluster information as published.,Cranial neural crest derived cells,,Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer’s solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5°C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 °C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz’s L15 medium Life Technologies twice. Final volumes of 500 µl resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer’s instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chromatins of the isolated nuclei were targeted and tagged by transposase barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.,The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults in the institute vivarium according to Protocol 20771.,cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:60 dpf|facs markers:Zombie / dsRed+,GSM5402440,GSM5402440: scRNAseq Sox10 Cre bact BtR 60dpf rep 2; Danio rerio; RNA Seq,GSM5402440,,1,Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer's solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5°C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 °C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies twice. Final volumes of 500 µl resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer's instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chromatins of the isolated nuclei were targeted and tagged by transposase barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.,GEO Accession:GSM5402440,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP325759,,,scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_2_S17_L001_R1_001.fastq.gz scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_2_S17_L001_R2_001.fastq.gz,fastq fastq,7297507744.0,49499870.0,GSM5402440 r1,0:27 1:120.42,A:2154834707;C:1571012695;G:1612449699;T:1955051784;N:4158859,27,120,,,2154834707,1571012695,1612449699,1955051784,4158859,SRX11237268,SRS9283142,SRA1250944,GEO,"Crump Lab, Stem Cell, USC",2,0.00118,0.86503,0.00059,0.14289,0.99793,0.85385,0.46902,0.50643,27,119,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-06-27,Juvenile,Juvenile,Brain,Nervous System
65061,SRR14923999,SRX11237268,SRS9283142,SRP325759,PRJNA741770,Single cell profiling of cranial neural crest diversification across a vertebrate lifetime,GSE178969,Other,The cranial neural crest CNC is a vertebrate specific population that generates a huge diversity of derivatives including the bulk of the connective and skeletal tissues of the head. How neural crest cells generate the appropriate cell types for distinct head regions over time remains unresolved. Here we profile RNA expression scRNAseq and chromatin accessibility snATACseq of the zebrafish cranial neural crest lineage at single cell resolution from embryos to adults. Overall design: To recover the cell heterogeneity and lineage information in the span of a life time of a fish we collected the converted cells from embryonic stages 1.5 2 dpf larval stage 3 5 and 14 dpf juvenile stage 60 dpf to adult stage 150 or 210 dpf. We used a cranial neural crest converted zebrafish line 28.5Sox10:Cre;bactin:BFP to DsRed to permanantly convert and label the CNCC derived cells. The converted cells were collected and subjected to single cell sequencing for both their transcriptome and open chromatin region using Chromium platform of 10X Genomic. For biological and technical control we include replicates for both scRNAseq and snATACseq at various stages. We include an additional line fli1a:eGFP/sox10:dsRed for a biological and positive control of CNCC of 1.5 dpf sample.,,pubmed:35013168,,scRNAseq Sox10 Cre bact BtR 60dpf rep 2,GSM5402440,,tissue:Cranial neural crest derived cells|cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:60 dpf|facs markers:Zombie / dsRed+,scRNAseq Sox10 Cre bact BtR 60dpf rep 2,For scRNAseq libraries Cellranger v3.0.0 10X Genomics was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against zebrafish genome index built with GRCz11.fa and GRCz11.98.gtf. For snATACseq libraries Cellranger ATAC v1.2.0 10X Genomics was used for alignment against zebrafish genome index built with GRCz11.fa JASPAR2020 and GRCz11.98.gtf peak calling and peak by cell count matrix generation with default parameters. QC step for the library was performed along with the Cellranger or Cellranger ATAC alignment process. We performed a second round of peak calling for our snATACseq data using package Snaptools and SnapATAC. We first removed cell debris low quality cells and cell duplicates by setting cutoffs based on percentage of reads in peaks > 30 for 60 dpf > 45 for 210 dpf and > 50 for the rest and fragment number within peaks 5 000 – 30 000 for 5 dpf 1 000 – 11 000 for 14 dpf and 1 000 – 20 000 for the rest. To recover every aligned fragment we binned the genome into 5 kb sections and constructed the bin by cell matrices bmats for each library by Snaptools from the positional sorted bam files generated by cellranger atac. The cells were filtered dimensionally reduced by diffusion map and clustered with inputs of the first 34 dimensions followed the SnapATAC vignette. The specific peaks were called for each cluster by the wrapped MACS2 function in SnapATAC with parameter gsize = 1.5e9 shift = 100 ext = 200 and qval = 5e 2. The finalized and refined peak profile was derived by collapsing and merging all 175 individual peak files to about 450K peaks. The count matrices of both scRNAseq and snATACseq data were analyzed by R package Seurat and Signac. The count matrices of each sample were aggregated if there is any replicate. For scRNAseq data the matrices are normalized NormalizeData and scaled for the top 2 000 variable genes FindVariableFeatures and ScaleData. The scaled matrices were dimensional reduced to 50 principal components 60 components for 150 dpf which then subjected to neighbor finding FindNeighbors k = 20 and clustering FindClusters resolution = 0.8. The data were visualized through UMAP with 50 principal components as input. For snATACseq data the matrices are dimensionally reduced 30 latent semantic indices LSIs through RunTFIDF and RunSVD functions. The neighbor finding clustering and visualization are performed with the second to the thirtieth LSIs as input algoritm = 3 for FindClusters. Genome build: GRCz11 Supplementary files format and content: Each sample comes with four processed data files: a tab delimited cell barcode file tsv a tab delimited feature file with genes for scRNAseq or peaks for snATACseq tsv a sparse matrix of count table mtx and a cluster table tsv. The previous three files are suffice for creating a single cell count matrix. The cluster table can be further added to recreat the corresponding cluster information as published.,Cranial neural crest derived cells,,Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer’s solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5°C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 °C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz’s L15 medium Life Technologies twice. Final volumes of 500 µl resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer’s instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chromatins of the isolated nuclei were targeted and tagged by transposase barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.,The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults in the institute vivarium according to Protocol 20771.,cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:60 dpf|facs markers:Zombie / dsRed+,GSM5402440,GSM5402440: scRNAseq Sox10 Cre bact BtR 60dpf rep 2; Danio rerio; RNA Seq,GSM5402440,,1,Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer's solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5°C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 °C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies twice. Final volumes of 500 µl resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer's instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chromatins of the isolated nuclei were targeted and tagged by transposase barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.,GEO Accession:GSM5402440,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP325759,,,scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_2_S18_L001_R1_001.fastq.gz scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_2_S18_L001_R2_001.fastq.gz,fastq fastq,4258953868.0,28889131.0,GSM5402440 r2,0:27 1:120.42,A:1263874552;C:912254586;G:936347287;T:1144040879;N:2436564,27,120,,,1263874552,912254586,936347287,1144040879,2436564,SRX11237268,SRS9283142,SRA1250944,GEO,"Crump Lab, Stem Cell, USC",2,0.00124,0.86353,0.00061,0.14235,0.99782,0.85251,0.45967,0.51575,27,120,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-06-27,Juvenile,Juvenile,Brain,Nervous System
65062,SRR14924000,SRX11237268,SRS9283142,SRP325759,PRJNA741770,Single cell profiling of cranial neural crest diversification across a vertebrate lifetime,GSE178969,Other,The cranial neural crest CNC is a vertebrate specific population that generates a huge diversity of derivatives including the bulk of the connective and skeletal tissues of the head. How neural crest cells generate the appropriate cell types for distinct head regions over time remains unresolved. Here we profile RNA expression scRNAseq and chromatin accessibility snATACseq of the zebrafish cranial neural crest lineage at single cell resolution from embryos to adults. Overall design: To recover the cell heterogeneity and lineage information in the span of a life time of a fish we collected the converted cells from embryonic stages 1.5 2 dpf larval stage 3 5 and 14 dpf juvenile stage 60 dpf to adult stage 150 or 210 dpf. We used a cranial neural crest converted zebrafish line 28.5Sox10:Cre;bactin:BFP to DsRed to permanantly convert and label the CNCC derived cells. The converted cells were collected and subjected to single cell sequencing for both their transcriptome and open chromatin region using Chromium platform of 10X Genomic. For biological and technical control we include replicates for both scRNAseq and snATACseq at various stages. We include an additional line fli1a:eGFP/sox10:dsRed for a biological and positive control of CNCC of 1.5 dpf sample.,,pubmed:35013168,,scRNAseq Sox10 Cre bact BtR 60dpf rep 2,GSM5402440,,tissue:Cranial neural crest derived cells|cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:60 dpf|facs markers:Zombie / dsRed+,scRNAseq Sox10 Cre bact BtR 60dpf rep 2,For scRNAseq libraries Cellranger v3.0.0 10X Genomics was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against zebrafish genome index built with GRCz11.fa and GRCz11.98.gtf. For snATACseq libraries Cellranger ATAC v1.2.0 10X Genomics was used for alignment against zebrafish genome index built with GRCz11.fa JASPAR2020 and GRCz11.98.gtf peak calling and peak by cell count matrix generation with default parameters. QC step for the library was performed along with the Cellranger or Cellranger ATAC alignment process. We performed a second round of peak calling for our snATACseq data using package Snaptools and SnapATAC. We first removed cell debris low quality cells and cell duplicates by setting cutoffs based on percentage of reads in peaks > 30 for 60 dpf > 45 for 210 dpf and > 50 for the rest and fragment number within peaks 5 000 – 30 000 for 5 dpf 1 000 – 11 000 for 14 dpf and 1 000 – 20 000 for the rest. To recover every aligned fragment we binned the genome into 5 kb sections and constructed the bin by cell matrices bmats for each library by Snaptools from the positional sorted bam files generated by cellranger atac. The cells were filtered dimensionally reduced by diffusion map and clustered with inputs of the first 34 dimensions followed the SnapATAC vignette. The specific peaks were called for each cluster by the wrapped MACS2 function in SnapATAC with parameter gsize = 1.5e9 shift = 100 ext = 200 and qval = 5e 2. The finalized and refined peak profile was derived by collapsing and merging all 175 individual peak files to about 450K peaks. The count matrices of both scRNAseq and snATACseq data were analyzed by R package Seurat and Signac. The count matrices of each sample were aggregated if there is any replicate. For scRNAseq data the matrices are normalized NormalizeData and scaled for the top 2 000 variable genes FindVariableFeatures and ScaleData. The scaled matrices were dimensional reduced to 50 principal components 60 components for 150 dpf which then subjected to neighbor finding FindNeighbors k = 20 and clustering FindClusters resolution = 0.8. The data were visualized through UMAP with 50 principal components as input. For snATACseq data the matrices are dimensionally reduced 30 latent semantic indices LSIs through RunTFIDF and RunSVD functions. The neighbor finding clustering and visualization are performed with the second to the thirtieth LSIs as input algoritm = 3 for FindClusters. Genome build: GRCz11 Supplementary files format and content: Each sample comes with four processed data files: a tab delimited cell barcode file tsv a tab delimited feature file with genes for scRNAseq or peaks for snATACseq tsv a sparse matrix of count table mtx and a cluster table tsv. The previous three files are suffice for creating a single cell count matrix. The cluster table can be further added to recreat the corresponding cluster information as published.,Cranial neural crest derived cells,,Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer’s solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5°C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 °C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz’s L15 medium Life Technologies twice. Final volumes of 500 µl resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer’s instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chromatins of the isolated nuclei were targeted and tagged by transposase barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.,The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults in the institute vivarium according to Protocol 20771.,cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:60 dpf|facs markers:Zombie / dsRed+,GSM5402440,GSM5402440: scRNAseq Sox10 Cre bact BtR 60dpf rep 2; Danio rerio; RNA Seq,GSM5402440,,1,Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer's solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5°C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 °C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies twice. Final volumes of 500 µl resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer's instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chromatins of the isolated nuclei were targeted and tagged by transposase barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.,GEO Accession:GSM5402440,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP325759,,,scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_2_S19_L001_R1_001.fastq.gz scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_2_S19_L001_R2_001.fastq.gz,fastq fastq,4050808878.0,27477008.0,GSM5402440 r3,0:27 1:120.43,A:1201699026;C:868704481;G:891671655;T:1086426372;N:2307344,27,120,,,1201699026,868704481,891671655,1086426372,2307344,SRX11237268,SRS9283142,SRA1250944,GEO,"Crump Lab, Stem Cell, USC",2,0.00124,0.86647,0.0006,0.14333,0.99778,0.85407,0.4065,0.52778,27,120,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-06-27,Juvenile,Juvenile,Brain,Nervous System
65063,SRR14924001,SRX11237268,SRS9283142,SRP325759,PRJNA741770,Single cell profiling of cranial neural crest diversification across a vertebrate lifetime,GSE178969,Other,The cranial neural crest CNC is a vertebrate specific population that generates a huge diversity of derivatives including the bulk of the connective and skeletal tissues of the head. How neural crest cells generate the appropriate cell types for distinct head regions over time remains unresolved. Here we profile RNA expression scRNAseq and chromatin accessibility snATACseq of the zebrafish cranial neural crest lineage at single cell resolution from embryos to adults. Overall design: To recover the cell heterogeneity and lineage information in the span of a life time of a fish we collected the converted cells from embryonic stages 1.5 2 dpf larval stage 3 5 and 14 dpf juvenile stage 60 dpf to adult stage 150 or 210 dpf. We used a cranial neural crest converted zebrafish line 28.5Sox10:Cre;bactin:BFP to DsRed to permanantly convert and label the CNCC derived cells. The converted cells were collected and subjected to single cell sequencing for both their transcriptome and open chromatin region using Chromium platform of 10X Genomic. For biological and technical control we include replicates for both scRNAseq and snATACseq at various stages. We include an additional line fli1a:eGFP/sox10:dsRed for a biological and positive control of CNCC of 1.5 dpf sample.,,pubmed:35013168,,scRNAseq Sox10 Cre bact BtR 60dpf rep 2,GSM5402440,,tissue:Cranial neural crest derived cells|cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:60 dpf|facs markers:Zombie / dsRed+,scRNAseq Sox10 Cre bact BtR 60dpf rep 2,For scRNAseq libraries Cellranger v3.0.0 10X Genomics was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against zebrafish genome index built with GRCz11.fa and GRCz11.98.gtf. For snATACseq libraries Cellranger ATAC v1.2.0 10X Genomics was used for alignment against zebrafish genome index built with GRCz11.fa JASPAR2020 and GRCz11.98.gtf peak calling and peak by cell count matrix generation with default parameters. QC step for the library was performed along with the Cellranger or Cellranger ATAC alignment process. We performed a second round of peak calling for our snATACseq data using package Snaptools and SnapATAC. We first removed cell debris low quality cells and cell duplicates by setting cutoffs based on percentage of reads in peaks > 30 for 60 dpf > 45 for 210 dpf and > 50 for the rest and fragment number within peaks 5 000 – 30 000 for 5 dpf 1 000 – 11 000 for 14 dpf and 1 000 – 20 000 for the rest. To recover every aligned fragment we binned the genome into 5 kb sections and constructed the bin by cell matrices bmats for each library by Snaptools from the positional sorted bam files generated by cellranger atac. The cells were filtered dimensionally reduced by diffusion map and clustered with inputs of the first 34 dimensions followed the SnapATAC vignette. The specific peaks were called for each cluster by the wrapped MACS2 function in SnapATAC with parameter gsize = 1.5e9 shift = 100 ext = 200 and qval = 5e 2. The finalized and refined peak profile was derived by collapsing and merging all 175 individual peak files to about 450K peaks. The count matrices of both scRNAseq and snATACseq data were analyzed by R package Seurat and Signac. The count matrices of each sample were aggregated if there is any replicate. For scRNAseq data the matrices are normalized NormalizeData and scaled for the top 2 000 variable genes FindVariableFeatures and ScaleData. The scaled matrices were dimensional reduced to 50 principal components 60 components for 150 dpf which then subjected to neighbor finding FindNeighbors k = 20 and clustering FindClusters resolution = 0.8. The data were visualized through UMAP with 50 principal components as input. For snATACseq data the matrices are dimensionally reduced 30 latent semantic indices LSIs through RunTFIDF and RunSVD functions. The neighbor finding clustering and visualization are performed with the second to the thirtieth LSIs as input algoritm = 3 for FindClusters. Genome build: GRCz11 Supplementary files format and content: Each sample comes with four processed data files: a tab delimited cell barcode file tsv a tab delimited feature file with genes for scRNAseq or peaks for snATACseq tsv a sparse matrix of count table mtx and a cluster table tsv. The previous three files are suffice for creating a single cell count matrix. The cluster table can be further added to recreat the corresponding cluster information as published.,Cranial neural crest derived cells,,Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer’s solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5°C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 °C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz’s L15 medium Life Technologies twice. Final volumes of 500 µl resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer’s instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chromatins of the isolated nuclei were targeted and tagged by transposase barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.,The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults in the institute vivarium according to Protocol 20771.,cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:60 dpf|facs markers:Zombie / dsRed+,GSM5402440,GSM5402440: scRNAseq Sox10 Cre bact BtR 60dpf rep 2; Danio rerio; RNA Seq,GSM5402440,,1,Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer's solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5°C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 °C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies twice. Final volumes of 500 µl resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer's instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chromatins of the isolated nuclei were targeted and tagged by transposase barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.,GEO Accession:GSM5402440,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP325759,,,scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_2_S20_L001_R1_001.fastq.gz scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_2_S20_L001_R2_001.fastq.gz,fastq fastq,5532406222.0,37527113.0,GSM5402440 r4,0:27 1:120.42,A:1639053013;C:1186314122;G:1218280877;T:1485607687;N:3150523,27,120,,,1639053013,1186314122,1218280877,1485607687,3150523,SRX11237268,SRS9283142,SRA1250944,GEO,"Crump Lab, Stem Cell, USC",2,0.00122,0.86507,0.00058,0.14242,0.99772,0.85385,0.4,0.51687,27,120,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-06-27,Juvenile,Juvenile,Brain,Nervous System
65064,SRR14923994,SRX11237267,SRS9283141,SRP325759,PRJNA741770,Single cell profiling of cranial neural crest diversification across a vertebrate lifetime,GSE178969,Other,The cranial neural crest CNC is a vertebrate specific population that generates a huge diversity of derivatives including the bulk of the connective and skeletal tissues of the head. How neural crest cells generate the appropriate cell types for distinct head regions over time remains unresolved. Here we profile RNA expression scRNAseq and chromatin accessibility snATACseq of the zebrafish cranial neural crest lineage at single cell resolution from embryos to adults. Overall design: To recover the cell heterogeneity and lineage information in the span of a life time of a fish we collected the converted cells from embryonic stages 1.5 2 dpf larval stage 3 5 and 14 dpf juvenile stage 60 dpf to adult stage 150 or 210 dpf. We used a cranial neural crest converted zebrafish line 28.5Sox10:Cre;bactin:BFP to DsRed to permanantly convert and label the CNCC derived cells. The converted cells were collected and subjected to single cell sequencing for both their transcriptome and open chromatin region using Chromium platform of 10X Genomic. For biological and technical control we include replicates for both scRNAseq and snATACseq at various stages. We include an additional line fli1a:eGFP/sox10:dsRed for a biological and positive control of CNCC of 1.5 dpf sample.,,pubmed:35013168,,scRNAseq Sox10 Cre bact BtR 60dpf rep 1,GSM5402439,,tissue:Cranial neural crest derived cells|cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:60 dpf|facs markers:Zombie / dsRed+,scRNAseq Sox10 Cre bact BtR 60dpf rep 1,For scRNAseq libraries Cellranger v3.0.0 10X Genomics was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against zebrafish genome index built with GRCz11.fa and GRCz11.98.gtf. For snATACseq libraries Cellranger ATAC v1.2.0 10X Genomics was used for alignment against zebrafish genome index built with GRCz11.fa JASPAR2020 and GRCz11.98.gtf peak calling and peak by cell count matrix generation with default parameters. QC step for the library was performed along with the Cellranger or Cellranger ATAC alignment process. We performed a second round of peak calling for our snATACseq data using package Snaptools and SnapATAC. We first removed cell debris low quality cells and cell duplicates by setting cutoffs based on percentage of reads in peaks > 30 for 60 dpf > 45 for 210 dpf and > 50 for the rest and fragment number within peaks 5 000 – 30 000 for 5 dpf 1 000 – 11 000 for 14 dpf and 1 000 – 20 000 for the rest. To recover every aligned fragment we binned the genome into 5 kb sections and constructed the bin by cell matrices bmats for each library by Snaptools from the positional sorted bam files generated by cellranger atac. The cells were filtered dimensionally reduced by diffusion map and clustered with inputs of the first 34 dimensions followed the SnapATAC vignette. The specific peaks were called for each cluster by the wrapped MACS2 function in SnapATAC with parameter gsize = 1.5e9 shift = 100 ext = 200 and qval = 5e 2. The finalized and refined peak profile was derived by collapsing and merging all 175 individual peak files to about 450K peaks. The count matrices of both scRNAseq and snATACseq data were analyzed by R package Seurat and Signac. The count matrices of each sample were aggregated if there is any replicate. For scRNAseq data the matrices are normalized NormalizeData and scaled for the top 2 000 variable genes FindVariableFeatures and ScaleData. The scaled matrices were dimensional reduced to 50 principal components 60 components for 150 dpf which then subjected to neighbor finding FindNeighbors k = 20 and clustering FindClusters resolution = 0.8. The data were visualized through UMAP with 50 principal components as input. For snATACseq data the matrices are dimensionally reduced 30 latent semantic indices LSIs through RunTFIDF and RunSVD functions. The neighbor finding clustering and visualization are performed with the second to the thirtieth LSIs as input algoritm = 3 for FindClusters. Genome build: GRCz11 Supplementary files format and content: Each sample comes with four processed data files: a tab delimited cell barcode file tsv a tab delimited feature file with genes for scRNAseq or peaks for snATACseq tsv a sparse matrix of count table mtx and a cluster table tsv. The previous three files are suffice for creating a single cell count matrix. The cluster table can be further added to recreat the corresponding cluster information as published.,Cranial neural crest derived cells,,Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer’s solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5°C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 °C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz’s L15 medium Life Technologies twice. Final volumes of 500 µl resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer’s instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chromatins of the isolated nuclei were targeted and tagged by transposase barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.,The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults in the institute vivarium according to Protocol 20771.,cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:60 dpf|facs markers:Zombie / dsRed+,GSM5402439,GSM5402439: scRNAseq Sox10 Cre bact BtR 60dpf rep 1; Danio rerio; RNA Seq,GSM5402439,,1,Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer's solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5°C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 °C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies twice. Final volumes of 500 µl resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer's instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chromatins of the isolated nuclei were targeted and tagged by transposase barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.,GEO Accession:GSM5402439,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP325759,,,scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_1_S13_L001_R1_001.fastq.gz scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_1_S13_L001_R2_001.fastq.gz,fastq fastq,9936865506.0,67405339.0,GSM5402439 r1,0:27 1:120.42,A:2906745689;C:2166283632;G:2206772222;T:2651323922;N:5740041,27,120,,,2906745689,2166283632,2206772222,2651323922,5740041,SRX11237267,SRS9283141,SRA1250944,GEO,"Crump Lab, Stem Cell, USC",2,0.00134,0.84917,0.0006,0.12877,0.99746,0.84944,0.36363,0.52247,27,119,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-06-27,Juvenile,Juvenile,Brain,Nervous System
65065,SRR14923995,SRX11237267,SRS9283141,SRP325759,PRJNA741770,Single cell profiling of cranial neural crest diversification across a vertebrate lifetime,GSE178969,Other,The cranial neural crest CNC is a vertebrate specific population that generates a huge diversity of derivatives including the bulk of the connective and skeletal tissues of the head. How neural crest cells generate the appropriate cell types for distinct head regions over time remains unresolved. Here we profile RNA expression scRNAseq and chromatin accessibility snATACseq of the zebrafish cranial neural crest lineage at single cell resolution from embryos to adults. Overall design: To recover the cell heterogeneity and lineage information in the span of a life time of a fish we collected the converted cells from embryonic stages 1.5 2 dpf larval stage 3 5 and 14 dpf juvenile stage 60 dpf to adult stage 150 or 210 dpf. We used a cranial neural crest converted zebrafish line 28.5Sox10:Cre;bactin:BFP to DsRed to permanantly convert and label the CNCC derived cells. The converted cells were collected and subjected to single cell sequencing for both their transcriptome and open chromatin region using Chromium platform of 10X Genomic. For biological and technical control we include replicates for both scRNAseq and snATACseq at various stages. We include an additional line fli1a:eGFP/sox10:dsRed for a biological and positive control of CNCC of 1.5 dpf sample.,,pubmed:35013168,,scRNAseq Sox10 Cre bact BtR 60dpf rep 1,GSM5402439,,tissue:Cranial neural crest derived cells|cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:60 dpf|facs markers:Zombie / dsRed+,scRNAseq Sox10 Cre bact BtR 60dpf rep 1,For scRNAseq libraries Cellranger v3.0.0 10X Genomics was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against zebrafish genome index built with GRCz11.fa and GRCz11.98.gtf. For snATACseq libraries Cellranger ATAC v1.2.0 10X Genomics was used for alignment against zebrafish genome index built with GRCz11.fa JASPAR2020 and GRCz11.98.gtf peak calling and peak by cell count matrix generation with default parameters. QC step for the library was performed along with the Cellranger or Cellranger ATAC alignment process. We performed a second round of peak calling for our snATACseq data using package Snaptools and SnapATAC. We first removed cell debris low quality cells and cell duplicates by setting cutoffs based on percentage of reads in peaks > 30 for 60 dpf > 45 for 210 dpf and > 50 for the rest and fragment number within peaks 5 000 – 30 000 for 5 dpf 1 000 – 11 000 for 14 dpf and 1 000 – 20 000 for the rest. To recover every aligned fragment we binned the genome into 5 kb sections and constructed the bin by cell matrices bmats for each library by Snaptools from the positional sorted bam files generated by cellranger atac. The cells were filtered dimensionally reduced by diffusion map and clustered with inputs of the first 34 dimensions followed the SnapATAC vignette. The specific peaks were called for each cluster by the wrapped MACS2 function in SnapATAC with parameter gsize = 1.5e9 shift = 100 ext = 200 and qval = 5e 2. The finalized and refined peak profile was derived by collapsing and merging all 175 individual peak files to about 450K peaks. The count matrices of both scRNAseq and snATACseq data were analyzed by R package Seurat and Signac. The count matrices of each sample were aggregated if there is any replicate. For scRNAseq data the matrices are normalized NormalizeData and scaled for the top 2 000 variable genes FindVariableFeatures and ScaleData. The scaled matrices were dimensional reduced to 50 principal components 60 components for 150 dpf which then subjected to neighbor finding FindNeighbors k = 20 and clustering FindClusters resolution = 0.8. The data were visualized through UMAP with 50 principal components as input. For snATACseq data the matrices are dimensionally reduced 30 latent semantic indices LSIs through RunTFIDF and RunSVD functions. The neighbor finding clustering and visualization are performed with the second to the thirtieth LSIs as input algoritm = 3 for FindClusters. Genome build: GRCz11 Supplementary files format and content: Each sample comes with four processed data files: a tab delimited cell barcode file tsv a tab delimited feature file with genes for scRNAseq or peaks for snATACseq tsv a sparse matrix of count table mtx and a cluster table tsv. The previous three files are suffice for creating a single cell count matrix. The cluster table can be further added to recreat the corresponding cluster information as published.,Cranial neural crest derived cells,,Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer’s solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5°C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 °C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz’s L15 medium Life Technologies twice. Final volumes of 500 µl resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer’s instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chromatins of the isolated nuclei were targeted and tagged by transposase barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.,The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults in the institute vivarium according to Protocol 20771.,cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:60 dpf|facs markers:Zombie / dsRed+,GSM5402439,GSM5402439: scRNAseq Sox10 Cre bact BtR 60dpf rep 1; Danio rerio; RNA Seq,GSM5402439,,1,Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer's solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5°C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 °C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies twice. Final volumes of 500 µl resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer's instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chromatins of the isolated nuclei were targeted and tagged by transposase barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.,GEO Accession:GSM5402439,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP325759,,,scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_1_S14_L001_R1_001.fastq.gz scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_1_S14_L001_R2_001.fastq.gz,fastq fastq,7897275260.0,53567183.0,GSM5402439 r2,0:27 1:120.43,A:2323096260;C:1712849172;G:1740350109;T:2116414828;N:4564891,27,120,,,2323096260,1712849172,1740350109,2116414828,4564891,SRX11237267,SRS9283141,SRA1250944,GEO,"Crump Lab, Stem Cell, USC",2,0.00136,0.85419,0.00056,0.13524,0.99709,0.85989,0.38853,0.51984,27,120,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-06-27,Juvenile,Juvenile,Brain,Nervous System
65066,SRR14923996,SRX11237267,SRS9283141,SRP325759,PRJNA741770,Single cell profiling of cranial neural crest diversification across a vertebrate lifetime,GSE178969,Other,The cranial neural crest CNC is a vertebrate specific population that generates a huge diversity of derivatives including the bulk of the connective and skeletal tissues of the head. How neural crest cells generate the appropriate cell types for distinct head regions over time remains unresolved. Here we profile RNA expression scRNAseq and chromatin accessibility snATACseq of the zebrafish cranial neural crest lineage at single cell resolution from embryos to adults. Overall design: To recover the cell heterogeneity and lineage information in the span of a life time of a fish we collected the converted cells from embryonic stages 1.5 2 dpf larval stage 3 5 and 14 dpf juvenile stage 60 dpf to adult stage 150 or 210 dpf. We used a cranial neural crest converted zebrafish line 28.5Sox10:Cre;bactin:BFP to DsRed to permanantly convert and label the CNCC derived cells. The converted cells were collected and subjected to single cell sequencing for both their transcriptome and open chromatin region using Chromium platform of 10X Genomic. For biological and technical control we include replicates for both scRNAseq and snATACseq at various stages. We include an additional line fli1a:eGFP/sox10:dsRed for a biological and positive control of CNCC of 1.5 dpf sample.,,pubmed:35013168,,scRNAseq Sox10 Cre bact BtR 60dpf rep 1,GSM5402439,,tissue:Cranial neural crest derived cells|cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:60 dpf|facs markers:Zombie / dsRed+,scRNAseq Sox10 Cre bact BtR 60dpf rep 1,For scRNAseq libraries Cellranger v3.0.0 10X Genomics was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against zebrafish genome index built with GRCz11.fa and GRCz11.98.gtf. For snATACseq libraries Cellranger ATAC v1.2.0 10X Genomics was used for alignment against zebrafish genome index built with GRCz11.fa JASPAR2020 and GRCz11.98.gtf peak calling and peak by cell count matrix generation with default parameters. QC step for the library was performed along with the Cellranger or Cellranger ATAC alignment process. We performed a second round of peak calling for our snATACseq data using package Snaptools and SnapATAC. We first removed cell debris low quality cells and cell duplicates by setting cutoffs based on percentage of reads in peaks > 30 for 60 dpf > 45 for 210 dpf and > 50 for the rest and fragment number within peaks 5 000 – 30 000 for 5 dpf 1 000 – 11 000 for 14 dpf and 1 000 – 20 000 for the rest. To recover every aligned fragment we binned the genome into 5 kb sections and constructed the bin by cell matrices bmats for each library by Snaptools from the positional sorted bam files generated by cellranger atac. The cells were filtered dimensionally reduced by diffusion map and clustered with inputs of the first 34 dimensions followed the SnapATAC vignette. The specific peaks were called for each cluster by the wrapped MACS2 function in SnapATAC with parameter gsize = 1.5e9 shift = 100 ext = 200 and qval = 5e 2. The finalized and refined peak profile was derived by collapsing and merging all 175 individual peak files to about 450K peaks. The count matrices of both scRNAseq and snATACseq data were analyzed by R package Seurat and Signac. The count matrices of each sample were aggregated if there is any replicate. For scRNAseq data the matrices are normalized NormalizeData and scaled for the top 2 000 variable genes FindVariableFeatures and ScaleData. The scaled matrices were dimensional reduced to 50 principal components 60 components for 150 dpf which then subjected to neighbor finding FindNeighbors k = 20 and clustering FindClusters resolution = 0.8. The data were visualized through UMAP with 50 principal components as input. For snATACseq data the matrices are dimensionally reduced 30 latent semantic indices LSIs through RunTFIDF and RunSVD functions. The neighbor finding clustering and visualization are performed with the second to the thirtieth LSIs as input algoritm = 3 for FindClusters. Genome build: GRCz11 Supplementary files format and content: Each sample comes with four processed data files: a tab delimited cell barcode file tsv a tab delimited feature file with genes for scRNAseq or peaks for snATACseq tsv a sparse matrix of count table mtx and a cluster table tsv. The previous three files are suffice for creating a single cell count matrix. The cluster table can be further added to recreat the corresponding cluster information as published.,Cranial neural crest derived cells,,Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer’s solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5°C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 °C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz’s L15 medium Life Technologies twice. Final volumes of 500 µl resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer’s instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chromatins of the isolated nuclei were targeted and tagged by transposase barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.,The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults in the institute vivarium according to Protocol 20771.,cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:60 dpf|facs markers:Zombie / dsRed+,GSM5402439,GSM5402439: scRNAseq Sox10 Cre bact BtR 60dpf rep 1; Danio rerio; RNA Seq,GSM5402439,,1,Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer's solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5°C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 °C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies twice. Final volumes of 500 µl resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer's instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chromatins of the isolated nuclei were targeted and tagged by transposase barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.,GEO Accession:GSM5402439,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP325759,,,scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_1_S15_L001_R1_001.fastq.gz scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_1_S15_L001_R2_001.fastq.gz,fastq fastq,7765136197.0,52676458.0,GSM5402439 r3,0:27 1:120.41,A:2285912113;C:1683626385;G:1719251520;T:2071793622;N:4552557,27,120,,,2285912113,1683626385,1719251520,2071793622,4552557,SRX11237267,SRS9283141,SRA1250944,GEO,"Crump Lab, Stem Cell, USC",2,0.00115,0.85166,0.00046,0.13288,0.99766,0.85163,0.35877,0.5154,27,121,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-06-27,Juvenile,Juvenile,Brain,Nervous System
65067,SRR14923997,SRX11237267,SRS9283141,SRP325759,PRJNA741770,Single cell profiling of cranial neural crest diversification across a vertebrate lifetime,GSE178969,Other,The cranial neural crest CNC is a vertebrate specific population that generates a huge diversity of derivatives including the bulk of the connective and skeletal tissues of the head. How neural crest cells generate the appropriate cell types for distinct head regions over time remains unresolved. Here we profile RNA expression scRNAseq and chromatin accessibility snATACseq of the zebrafish cranial neural crest lineage at single cell resolution from embryos to adults. Overall design: To recover the cell heterogeneity and lineage information in the span of a life time of a fish we collected the converted cells from embryonic stages 1.5 2 dpf larval stage 3 5 and 14 dpf juvenile stage 60 dpf to adult stage 150 or 210 dpf. We used a cranial neural crest converted zebrafish line 28.5Sox10:Cre;bactin:BFP to DsRed to permanantly convert and label the CNCC derived cells. The converted cells were collected and subjected to single cell sequencing for both their transcriptome and open chromatin region using Chromium platform of 10X Genomic. For biological and technical control we include replicates for both scRNAseq and snATACseq at various stages. We include an additional line fli1a:eGFP/sox10:dsRed for a biological and positive control of CNCC of 1.5 dpf sample.,,pubmed:35013168,,scRNAseq Sox10 Cre bact BtR 60dpf rep 1,GSM5402439,,tissue:Cranial neural crest derived cells|cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:60 dpf|facs markers:Zombie / dsRed+,scRNAseq Sox10 Cre bact BtR 60dpf rep 1,For scRNAseq libraries Cellranger v3.0.0 10X Genomics was used for demultiplexing alignment and raw count matrix generation. The alignment was performed against zebrafish genome index built with GRCz11.fa and GRCz11.98.gtf. For snATACseq libraries Cellranger ATAC v1.2.0 10X Genomics was used for alignment against zebrafish genome index built with GRCz11.fa JASPAR2020 and GRCz11.98.gtf peak calling and peak by cell count matrix generation with default parameters. QC step for the library was performed along with the Cellranger or Cellranger ATAC alignment process. We performed a second round of peak calling for our snATACseq data using package Snaptools and SnapATAC. We first removed cell debris low quality cells and cell duplicates by setting cutoffs based on percentage of reads in peaks > 30 for 60 dpf > 45 for 210 dpf and > 50 for the rest and fragment number within peaks 5 000 – 30 000 for 5 dpf 1 000 – 11 000 for 14 dpf and 1 000 – 20 000 for the rest. To recover every aligned fragment we binned the genome into 5 kb sections and constructed the bin by cell matrices bmats for each library by Snaptools from the positional sorted bam files generated by cellranger atac. The cells were filtered dimensionally reduced by diffusion map and clustered with inputs of the first 34 dimensions followed the SnapATAC vignette. The specific peaks were called for each cluster by the wrapped MACS2 function in SnapATAC with parameter gsize = 1.5e9 shift = 100 ext = 200 and qval = 5e 2. The finalized and refined peak profile was derived by collapsing and merging all 175 individual peak files to about 450K peaks. The count matrices of both scRNAseq and snATACseq data were analyzed by R package Seurat and Signac. The count matrices of each sample were aggregated if there is any replicate. For scRNAseq data the matrices are normalized NormalizeData and scaled for the top 2 000 variable genes FindVariableFeatures and ScaleData. The scaled matrices were dimensional reduced to 50 principal components 60 components for 150 dpf which then subjected to neighbor finding FindNeighbors k = 20 and clustering FindClusters resolution = 0.8. The data were visualized through UMAP with 50 principal components as input. For snATACseq data the matrices are dimensionally reduced 30 latent semantic indices LSIs through RunTFIDF and RunSVD functions. The neighbor finding clustering and visualization are performed with the second to the thirtieth LSIs as input algoritm = 3 for FindClusters. Genome build: GRCz11 Supplementary files format and content: Each sample comes with four processed data files: a tab delimited cell barcode file tsv a tab delimited feature file with genes for scRNAseq or peaks for snATACseq tsv a sparse matrix of count table mtx and a cluster table tsv. The previous three files are suffice for creating a single cell count matrix. The cluster table can be further added to recreat the corresponding cluster information as published.,Cranial neural crest derived cells,,Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer’s solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5°C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 °C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz’s L15 medium Life Technologies twice. Final volumes of 500 µl resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer’s instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chromatins of the isolated nuclei were targeted and tagged by transposase barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.,The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults in the institute vivarium according to Protocol 20771.,cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:60 dpf|facs markers:Zombie / dsRed+,GSM5402439,GSM5402439: scRNAseq Sox10 Cre bact BtR 60dpf rep 1; Danio rerio; RNA Seq,GSM5402439,,1,Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer's solution 5 10 min followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution 0.25% trypsin Life Technologies 15090 046 1 mM EDTA and 400 mg/ml Collagenase D Sigma 11088882001 in PBS and incubated at 28.5°C for 20 30 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm 5 minute 4 °C and resuspended in suspension media 1% FBS 0.8 mM CaCl2 50 U/ml penicillin and 0.05 mg/ml streptomycin Sigma Aldrich St. Louis MO in phenol red free Leibovitz's L15 medium Life Technologies twice. Final volumes of 500 µl resuspended cells were placed on ice and sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend 423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction we used the same cell dissociation and sorting protocol as for scRNAseq with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer's instructions 10X Genomic protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq the cell lysis polyA pull down tagging with cell barcode and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq the open chromatins of the isolated nuclei were targeted and tagged by transposase barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.,GEO Accession:GSM5402439,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP325759,,,scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_1_S16_L001_R1_001.fastq.gz scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_1_S16_L001_R2_001.fastq.gz,fastq fastq,10430563739.0,70754033.0,GSM5402439 r4,0:27 1:120.42,A:3057357215;C:2269896192;G:2312685494;T:2784595449;N:6029389,27,120,,,3057357215,2269896192,2312685494,2784595449,6029389,SRX11237267,SRS9283141,SRA1250944,GEO,"Crump Lab, Stem Cell, USC",2,0.00148,0.85451,0.00069,0.13182,0.99715,0.85397,0.41721,0.50684,27,121,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-06-27,Juvenile,Juvenile,Brain,Nervous System
66831,SRR16674680,SRX12875367,SRS10818487,SRP343978,PRJNA776712,RNA seq analysis of nde1 mutant zebrafish,PRJNA776712,Other,We perform RNA sequencing to detect defferential expressed genes of nde1 deficiency mutant zebrafish brains compared to wild type.,,,,,brain nde1KO,,strain:nde1KO|dev stage:2mpf|sex:male|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of nde1 ko Danio rerio brain,B8,B8,RNA seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina San Diego CA using 5g of total RNA. Shortly messenger RNA was isolated according to polyA selection method by oligodT beads and then fragmented by fragmentation buffer firstly. Secondly double stranded cDNA was synthesized using a SuperScript double stranded cDNA synthesis kit Invitrogen CA with random hexamer primers Illumina. Then the synthesized cDNA was subjected to end repair phosphorylation and A base addition according to Illuminas library construction protocol. Libraries were size selected for cDNA target fragments of 200300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. post quantified by TBS380 paired end RNA seq sequencing library was sequenced with the Illumina HiSeq 4000 2 150bp read length.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP343978,,,B8.R1.fastq.gz B8.R2.fastq.gz,fastq fastq,6730442668.0,22286234.0,B8.R1.fastq.gz,0:151 1:151,A:1861252434;C:1503025278;G:1520846977;T:1845259260;N:58719,151,151,,,1861252434,1503025278,1520846977,1845259260,58719,SRX12875367,SRS10818487,,,Children's Hospital of Fudan University,2,0.94017,0.93241,0.13042,0.12914,0.68958,0.69132,0.48508,0.48284,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,China,2021-11-01,Juvenile,Juvenile,Brain,Nervous System
66832,SRR16674681,SRX12875366,SRS10818487,SRP343978,PRJNA776712,RNA seq analysis of nde1 mutant zebrafish,PRJNA776712,Other,We perform RNA sequencing to detect defferential expressed genes of nde1 deficiency mutant zebrafish brains compared to wild type.,,,,,brain nde1KO,,strain:nde1KO|dev stage:2mpf|sex:male|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of nde1 ko Danio rerio brain,B5,B5,RNA seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina San Diego CA using 5g of total RNA. Shortly messenger RNA was isolated according to polyA selection method by oligodT beads and then fragmented by fragmentation buffer firstly. Secondly double stranded cDNA was synthesized using a SuperScript double stranded cDNA synthesis kit Invitrogen CA with random hexamer primers Illumina. Then the synthesized cDNA was subjected to end repair phosphorylation and A base addition according to Illuminas library construction protocol. Libraries were size selected for cDNA target fragments of 200300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. post quantified by TBS380 paired end RNA seq sequencing library was sequenced with the Illumina HiSeq 4000 2 150bp read length.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP343978,,,B5.R1.fastq.gz B5.R2.fastq.gz,fastq fastq,7110747040.0,23545520.0,B5.R1.fastq.gz,0:151 1:151,A:1977355863;C:1580608625;G:1601936422;T:1950785340;N:60790,151,151,,,1977355863,1580608625,1601936422,1950785340,60790,SRX12875366,SRS10818487,,,Children's Hospital of Fudan University,2,0.93839,0.92891,0.1351,0.13386,0.69175,0.69424,0.49143,0.49249,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,China,2021-11-01,Juvenile,Juvenile,Brain,Nervous System
66833,SRR16674682,SRX12875365,SRS10818487,SRP343978,PRJNA776712,RNA seq analysis of nde1 mutant zebrafish,PRJNA776712,Other,We perform RNA sequencing to detect defferential expressed genes of nde1 deficiency mutant zebrafish brains compared to wild type.,,,,,brain nde1KO,,strain:nde1KO|dev stage:2mpf|sex:male|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of nde1 ko Danio rerio brain,B2,B2,RNA seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina San Diego CA using 5g of total RNA. Shortly messenger RNA was isolated according to polyA selection method by oligodT beads and then fragmented by fragmentation buffer firstly. Secondly double stranded cDNA was synthesized using a SuperScript double stranded cDNA synthesis kit Invitrogen CA with random hexamer primers Illumina. Then the synthesized cDNA was subjected to end repair phosphorylation and A base addition according to Illuminas library construction protocol. Libraries were size selected for cDNA target fragments of 200300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. post quantified by TBS380 paired end RNA seq sequencing library was sequenced with the Illumina HiSeq 4000 2 150bp read length.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP343978,,,B2.R1.fastq.gz B2.R2.fastq.gz,fastq fastq,8547028538.0,28301419.0,B2.R1.fastq.gz,0:151 1:151,A:2378598350;C:1891330158;G:1921569124;T:2355455648;N:75258,151,151,,,2378598350,1891330158,1921569124,2355455648,75258,SRX12875365,SRS10818487,,,Children's Hospital of Fudan University,2,0.94029,0.92534,0.13616,0.13373,0.68949,0.69219,0.47948,0.48398,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,China,2021-11-01,Juvenile,Juvenile,Brain,Nervous System
66834,SRR16674683,SRX12875364,SRS10818488,SRP343978,PRJNA776712,RNA seq analysis of nde1 mutant zebrafish,PRJNA776712,Other,We perform RNA sequencing to detect defferential expressed genes of nde1 deficiency mutant zebrafish brains compared to wild type.,,,,,brain WT,,strain:TU|dev stage:2mpf|sex:male|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio brain,B7,B7,RNA seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina San Diego CA using 5g of total RNA. Shortly messenger RNA was isolated according to polyA selection method by oligodT beads and then fragmented by fragmentation buffer firstly. Secondly double stranded cDNA was synthesized using a SuperScript double stranded cDNA synthesis kit Invitrogen CA with random hexamer primers Illumina. Then the synthesized cDNA was subjected to end repair phosphorylation and A base addition according to Illuminas library construction protocol. Libraries were size selected for cDNA target fragments of 200300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. post quantified by TBS380 paired end RNA seq sequencing library was sequenced with the Illumina HiSeq 4000 2 150bp read length.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP343978,,,B7.R1.fastq.gz B7.R2.fastq.gz,fastq fastq,6685388496.0,22137048.0,B7.R1.fastq.gz,0:151 1:151,A:1860264075;C:1483831512;G:1503216220;T:1838014556;N:62133,151,151,,,1860264075,1483831512,1503216220,1838014556,62133,SRX12875364,SRS10818488,,,Children's Hospital of Fudan University,2,0.94254,0.93341,0.13834,0.13689,0.69355,0.69755,0.49201,0.49217,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,China,2021-11-01,Juvenile,Juvenile,Brain,Nervous System
66835,SRR16674684,SRX12875363,SRS10818488,SRP343978,PRJNA776712,RNA seq analysis of nde1 mutant zebrafish,PRJNA776712,Other,We perform RNA sequencing to detect defferential expressed genes of nde1 deficiency mutant zebrafish brains compared to wild type.,,,,,brain WT,,strain:TU|dev stage:2mpf|sex:male|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio brain,B4,B4,RNA seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina San Diego CA using 5g of total RNA. Shortly messenger RNA was isolated according to polyA selection method by oligodT beads and then fragmented by fragmentation buffer firstly. Secondly double stranded cDNA was synthesized using a SuperScript double stranded cDNA synthesis kit Invitrogen CA with random hexamer primers Illumina. Then the synthesized cDNA was subjected to end repair phosphorylation and A base addition according to Illuminas library construction protocol. Libraries were size selected for cDNA target fragments of 200300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. post quantified by TBS380 paired end RNA seq sequencing library was sequenced with the Illumina HiSeq 4000 2 150bp read length.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP343978,,,B4.R1.fastq.gz B4.R2.fastq.gz,fastq fastq,7546711220.0,24989110.0,B4.R1.fastq.gz,0:151 1:151,A:2099092660;C:1670910951;G:1699960602;T:2076680479;N:66528,151,151,,,2099092660,1670910951,1699960602,2076680479,66528,SRX12875363,SRS10818488,,,Children's Hospital of Fudan University,2,0.94254,0.92745,0.13347,0.13114,0.69225,0.69424,0.48413,0.49124,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,China,2021-11-01,Juvenile,Juvenile,Brain,Nervous System
66836,SRR16674685,SRX12875362,SRS10818488,SRP343978,PRJNA776712,RNA seq analysis of nde1 mutant zebrafish,PRJNA776712,Other,We perform RNA sequencing to detect defferential expressed genes of nde1 deficiency mutant zebrafish brains compared to wild type.,,,,,brain WT,,strain:TU|dev stage:2mpf|sex:male|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio brain,B1,B1,RNA seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina San Diego CA using 5g of total RNA. Shortly messenger RNA was isolated according to polyA selection method by oligodT beads and then fragmented by fragmentation buffer firstly. Secondly double stranded cDNA was synthesized using a SuperScript double stranded cDNA synthesis kit Invitrogen CA with random hexamer primers Illumina. Then the synthesized cDNA was subjected to end repair phosphorylation and A base addition according to Illuminas library construction protocol. Libraries were size selected for cDNA target fragments of 200300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. post quantified by TBS380 paired end RNA seq sequencing library was sequenced with the Illumina HiSeq 4000 2 150bp read length.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP343978,,,B1.R1.fastq.gz B1.R2.fastq.gz,fastq fastq,6758464342.0,22379021.0,B1.R1.fastq.gz,0:151 1:151,A:1881676275;C:1495234309;G:1519420774;T:1862074223;N:58761,151,151,,,1881676275,1495234309,1519420774,1862074223,58761,SRX12875362,SRS10818488,,,Children's Hospital of Fudan University,2,0.94263,0.92421,0.13676,0.13324,0.69505,0.697,0.48389,0.48239,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,China,2021-11-02,Juvenile,Juvenile,Brain,Nervous System
68554,SRR18010263,SRX14164590,SRS11988750,SRP359660,PRJNA806676,Transcriptome analysis of nomo1 homologous deficiency zebrafish,PRJNA806676,Other,This analysis revealed transcriptome level changes of brain of nomo1 homologous deficiency zebrafish.,,,,,nomo1,,strain:nomo / |dev stage:2mpf|sex:male|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rario: nomo1,nomo,nomo,RNA seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina San Diego CA using 5g of total RNA. Shortly messenger RNA was isolated according to polyA selection method by oligodT beads and then fragmented by fragmentation buffer firstly. Secondly double stranded cDNA was synthesized using a SuperScript double stranded cDNA synthesis kit Invitrogen CA with random hexamer primers Illumina. Then the synthesized cDNA was subjected to end repair phosphorylation and A base addition according to Illuminas library construction protocol. Libraries were size selected for cDNA target fragments of 200300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. post quantified by TBS380 paired end RNA seq sequencing library was sequenced with the Illumina HiSeq 4000 2 150bp read length.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP359660,,,NOMO_1.fq.gz NOMO_2.fq.gz,fastq fastq,7423945800.0,24746486.0,NOMO 1.fq.gz,0:150 1:150,A:2079187833;C:1643658691;G:1652867282;T:2048199003;N:32991,150,150,,,2079187833,1643658691,1652867282,2048199003,32991,SRX14164590,SRS11988750,,,Children's Hospital of Fudan University,2,0.93796,0.93625,0.16379,0.1632,0.69643,0.69842,0.48865,0.48976,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,China,2022-02-13,Juvenile,Juvenile,Brain,Nervous System
68555,SRR18010264,SRX14164589,SRS11988749,SRP359660,PRJNA806676,Transcriptome analysis of nomo1 homologous deficiency zebrafish,PRJNA806676,Other,This analysis revealed transcriptome level changes of brain of nomo1 homologous deficiency zebrafish.,,,,,WT,,strain:tu|dev stage:2mpf|sex:male|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rario: TU,TU,TU,RNA seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina San Diego CA using 5g of total RNA. Shortly messenger RNA was isolated according to polyA selection method by oligodT beads and then fragmented by fragmentation buffer firstly. Secondly double stranded cDNA was synthesized using a SuperScript double stranded cDNA synthesis kit Invitrogen CA with random hexamer primers Illumina. Then the synthesized cDNA was subjected to end repair phosphorylation and A base addition according to Illuminas library construction protocol. Libraries were size selected for cDNA target fragments of 200300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. post quantified by TBS380 paired end RNA seq sequencing library was sequenced with the Illumina HiSeq 4000 2 150bp read length.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP359660,,,TU_1.fq.gz TU_2.fq.gz,fastq fastq,7981027200.0,26603424.0,TU 1.fq.gz,0:150 1:150,A:2246332345;C:1756444706;G:1767372264;T:2210842856;N:35029,150,150,,,2246332345,1756444706,1767372264,2210842856,35029,SRX14164589,SRS11988749,,,Children's Hospital of Fudan University,2,0.93375,0.93291,0.17081,0.17028,0.69755,0.69875,0.48942,0.49405,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,China,2022-02-13,Juvenile,Juvenile,Brain,Nervous System
70192,SRR19571672,SRX15623697,SRS13323926,SRP378890,PRJNA846700,Telomerase Dependent Ageing In The Zebrafish Brain,GSE205601,Transcriptome Analysis,Decreased telomerase expression telomere shortening senescence associated markers and inflammation have all been independently observed in the ageing brain and associated with disease. However causality between limited telomerase expression and brain senescence and neuro inflammation in the natural ageing setting is yet to be established. Here we address these questions using the zebrafish as an ageing model which akin to humans displays premature ageing and death in the absence of telomerase and where telomere shortening is a driver of cellular senescence. Our work shows for the first time that telomerase deficiency tert / accelerates key hallmarks of ageing identified in the Wild Type WT zebrafish brain at transcriptional cellular tissue and functional levels. We show that Tert dependent transcriptomic changes associated with dysregulation of gene expression stress response and dysregulation of immune genes are accompanied by accelerated accumulation of senescence associated markers and inflammation in the aged brain. Importantly In vivo these changes correlate with increased blood brain barrier permeability and altered cognitive behaviour. Of note telomerase dependent accumulation of senescence associated markers in the brain occurs not only in the expected proliferative areas but also in non proliferative ones where it is unlikely due to telomere dependent replicative exhaustion suggesting that non canonical roles of telomerase may be involved. Together our work suggests that telomerase has a protective role in the zebrafish brain against the accumulation of senescence and neuro inflammation and is required for blood brain barrier integrity. Overall design: RNA Sequencing of whole brain tissues throughout the lifespan of WT and telomerase deficient tert / fish. The data 4 age groups of WT 2 9 22 and >30 month corresponding to young adult median lifespan and old; and 3 age groups of telomerase deficient fish 2 9 and 22 month which correspond to young medium lifespan and old. Each group has a sample size of 3 animals. To identify signatures of ageing WT brain samples were subjected separately to DESEq2 analysis comparing the time points 9 22 and >30 month with the time point of 2 month. Then tert / samples at 2 9 month and 22 month were compared with WT at 2 month to identify telomerase dependent ageing processes.,,,,Brain tert 2months rep3,GSM6215412,,source name:brain|tissue:brain|strain:AB background|genotype:tert |age:2 month,Brain tert 2months rep3,Quality control was performed using MultiQC version 1.9. Cutadapt version 3.0 was used for trimming the first 13 bases from the reads to remove poor quality base pairs in the reads. Read alignment: Single end reads were aligned against the reference genome Danio rerio.GRCz11.dna. primary assembly.fa using STAR. A bespoke alignment index was built using annotation file Danio rerio.GRCz11.103.gtf and an expected read length of 88 bp. Ht seq count was run in non stranded mode to obtain per gene read counts. Assembly: Danio rerio.GRCz11.dna. Supplementary files format and content: tab delimited text files include RPKM values for each Sample,brain,,Whole tissues were dissected in cold PBS Sigma Aldrich transferred to a microcentrifuge tube containing 100 μl of Trizol Thermo Fisher Scientific snap frozen in dry ice and stored at 80°. To isolate the RNA extra 50 μl of Trizol was added to each sample and the tissue was homogenized with a mechanical homogenizer VWR International and a 1.5 pestle Kimble Chase Vineland NJ USA. post 5 min incubation at room temperature RT 30 μl of chloroform 1:5 VWR International was added and the samples were incubated for further 3 min at RT before centrifuged at 13 000g for 30 min at 4°C. Isopropanol Thermo Fisher Scientific was then added to the aqueous phase of the solution and the resultant mix was incubated for 10 min at RT before centrifuged 13 000g for 15 min at 4°C. Finally the pellet was twice washed in 250 μl of ice cold 75% ethanol and left to air dry before resuspended in 14 μl of nuclease free water. RNA integrity was assessed with the bioanalyzer Agilent 2100 Bioanalyzer Agilent Santa Clara CA USA. All the samples had a RNA integrity number RIN ≥9. Library preparation was performed following the Illumina methodology. mRNA was extracted from 500 ng of RNA with oligo dT beads capturing polyA tails using the NEBNext PolyA mRNA Magnetic Isolation Module New England Biolabs Inc. cDNA libraries were made with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina following the manufacturer’s instructions New England Biolabs Inc.,Zebrafish were maintained at the standard conditions of 27 28ºC in a 14:10 hour light dark cycle and fed twice a day with Artemia live rotifers and Sparus dry food.,tissue:brain|strain:AB background|genotype:tert |age:2 month,GSM6215412,GSM6215412: Brain tert 2months rep3; Danio rerio; RNA Seq,GSM6215412 r1,GSM6215412,1,Whole tissues were dissected in cold PBS Sigma Aldrich transferred to a microcentrifuge tube containing 100 μl of Trizol Thermo Fisher Scientific snap frozen in dry ice and stored at 80°. To isolate the RNA extra 50 μl of Trizol was added to each sample and the tissue was homogenized with a mechanical homogenizer VWR International and a 1.5 pestle Kimble Chase Vineland NJ USA. post 5 min incubation at room temperature RT 30 μl of chloroform 1:5 VWR International was added and the samples were incubated for further 3 min at RT before centrifuged at 13 000g for 30 min at 4°C. Isopropanol Thermo Fisher Scientific was then added to the aqueous phase of the solution and the resultant mix was incubated for 10 min at RT before centrifuged 13 000g for 15 min at 4°C. Finally the pellet was twice washed in 250 μl of ice cold 75% ethanol and left to air dry before resuspended in 14 μl of nuclease free water. RNA integrity was assessed with the bioanalyzer Agilent 2100 Bioanalyzer Agilent Santa Clara CA USA. All the samples had a RNA integrity number RIN ≥9. Library preparation was performed following the Illumina methodology. mRNA was extracted from 500 ng of RNA with oligo dT beads capturing polyA tails using the NEBNext PolyA mRNA Magnetic Isolation Module New England Biolabs Inc. cDNA libraries were made with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina following the manufacturer's instructions New England Biolabs Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiScanSQ,,SRP378890,,,B23.fastq.gz,fastq,1518961321.0,15039221.0,GSM6215412 r1,0:101 1:0,A:409595352;C:338757295;G:334460970;T:428742126;N:7405578,101,0,,,409595352,338757295,334460970,428742126,7405578,SRX15623697,SRS13323926,SRA1433223,"Tissue Repair & Immunity in ageing, Oncology & Metabolism, The University of Sheffield","Tissue Repair & Immunity in ageing, Oncology & Metabolism, The University of Sheffield",1,0.93103,,0.15922,,0.68856,,0.49773,,101,,B,,usable mapping rate,illumina,early_illumina,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2022-06-07,Juvenile,Juvenile,Brain,Nervous System
70193,SRR19571673,SRX15623696,SRS13323925,SRP378890,PRJNA846700,Telomerase Dependent Ageing In The Zebrafish Brain,GSE205601,Transcriptome Analysis,Decreased telomerase expression telomere shortening senescence associated markers and inflammation have all been independently observed in the ageing brain and associated with disease. However causality between limited telomerase expression and brain senescence and neuro inflammation in the natural ageing setting is yet to be established. Here we address these questions using the zebrafish as an ageing model which akin to humans displays premature ageing and death in the absence of telomerase and where telomere shortening is a driver of cellular senescence. Our work shows for the first time that telomerase deficiency tert / accelerates key hallmarks of ageing identified in the Wild Type WT zebrafish brain at transcriptional cellular tissue and functional levels. We show that Tert dependent transcriptomic changes associated with dysregulation of gene expression stress response and dysregulation of immune genes are accompanied by accelerated accumulation of senescence associated markers and inflammation in the aged brain. Importantly In vivo these changes correlate with increased blood brain barrier permeability and altered cognitive behaviour. Of note telomerase dependent accumulation of senescence associated markers in the brain occurs not only in the expected proliferative areas but also in non proliferative ones where it is unlikely due to telomere dependent replicative exhaustion suggesting that non canonical roles of telomerase may be involved. Together our work suggests that telomerase has a protective role in the zebrafish brain against the accumulation of senescence and neuro inflammation and is required for blood brain barrier integrity. Overall design: RNA Sequencing of whole brain tissues throughout the lifespan of WT and telomerase deficient tert / fish. The data 4 age groups of WT 2 9 22 and >30 month corresponding to young adult median lifespan and old; and 3 age groups of telomerase deficient fish 2 9 and 22 month which correspond to young medium lifespan and old. Each group has a sample size of 3 animals. To identify signatures of ageing WT brain samples were subjected separately to DESEq2 analysis comparing the time points 9 22 and >30 month with the time point of 2 month. Then tert / samples at 2 9 month and 22 month were compared with WT at 2 month to identify telomerase dependent ageing processes.,,,,Brain tert 2months rep2,GSM6215411,,source name:brain|tissue:brain|strain:AB background|genotype:tert |age:2 month,Brain tert 2months rep2,Quality control was performed using MultiQC version 1.9. Cutadapt version 3.0 was used for trimming the first 13 bases from the reads to remove poor quality base pairs in the reads. Read alignment: Single end reads were aligned against the reference genome Danio rerio.GRCz11.dna. primary assembly.fa using STAR. A bespoke alignment index was built using annotation file Danio rerio.GRCz11.103.gtf and an expected read length of 88 bp. Ht seq count was run in non stranded mode to obtain per gene read counts. Assembly: Danio rerio.GRCz11.dna. Supplementary files format and content: tab delimited text files include RPKM values for each Sample,brain,,Whole tissues were dissected in cold PBS Sigma Aldrich transferred to a microcentrifuge tube containing 100 μl of Trizol Thermo Fisher Scientific snap frozen in dry ice and stored at 80°. To isolate the RNA extra 50 μl of Trizol was added to each sample and the tissue was homogenized with a mechanical homogenizer VWR International and a 1.5 pestle Kimble Chase Vineland NJ USA. post 5 min incubation at room temperature RT 30 μl of chloroform 1:5 VWR International was added and the samples were incubated for further 3 min at RT before centrifuged at 13 000g for 30 min at 4°C. Isopropanol Thermo Fisher Scientific was then added to the aqueous phase of the solution and the resultant mix was incubated for 10 min at RT before centrifuged 13 000g for 15 min at 4°C. Finally the pellet was twice washed in 250 μl of ice cold 75% ethanol and left to air dry before resuspended in 14 μl of nuclease free water. RNA integrity was assessed with the bioanalyzer Agilent 2100 Bioanalyzer Agilent Santa Clara CA USA. All the samples had a RNA integrity number RIN ≥9. Library preparation was performed following the Illumina methodology. mRNA was extracted from 500 ng of RNA with oligo dT beads capturing polyA tails using the NEBNext PolyA mRNA Magnetic Isolation Module New England Biolabs Inc. cDNA libraries were made with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina following the manufacturer’s instructions New England Biolabs Inc.,Zebrafish were maintained at the standard conditions of 27 28ºC in a 14:10 hour light dark cycle and fed twice a day with Artemia live rotifers and Sparus dry food.,tissue:brain|strain:AB background|genotype:tert |age:2 month,GSM6215411,GSM6215411: Brain tert 2months rep2; Danio rerio; RNA Seq,GSM6215411 r1,GSM6215411,1,Whole tissues were dissected in cold PBS Sigma Aldrich transferred to a microcentrifuge tube containing 100 μl of Trizol Thermo Fisher Scientific snap frozen in dry ice and stored at 80°. To isolate the RNA extra 50 μl of Trizol was added to each sample and the tissue was homogenized with a mechanical homogenizer VWR International and a 1.5 pestle Kimble Chase Vineland NJ USA. post 5 min incubation at room temperature RT 30 μl of chloroform 1:5 VWR International was added and the samples were incubated for further 3 min at RT before centrifuged at 13 000g for 30 min at 4°C. Isopropanol Thermo Fisher Scientific was then added to the aqueous phase of the solution and the resultant mix was incubated for 10 min at RT before centrifuged 13 000g for 15 min at 4°C. Finally the pellet was twice washed in 250 μl of ice cold 75% ethanol and left to air dry before resuspended in 14 μl of nuclease free water. RNA integrity was assessed with the bioanalyzer Agilent 2100 Bioanalyzer Agilent Santa Clara CA USA. All the samples had a RNA integrity number RIN ≥9. Library preparation was performed following the Illumina methodology. mRNA was extracted from 500 ng of RNA with oligo dT beads capturing polyA tails using the NEBNext PolyA mRNA Magnetic Isolation Module New England Biolabs Inc. cDNA libraries were made with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina following the manufacturer's instructions New England Biolabs Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiScanSQ,,SRP378890,,,B20.fastq.gz,fastq,1589807064.0,15740664.0,GSM6215411 r1,0:101 1:0,A:425523566;C:356671503;G:351309194;T:448559151;N:7743650,101,0,,,425523566,356671503,351309194,448559151,7743650,SRX15623696,SRS13323925,SRA1433223,"Tissue Repair & Immunity in ageing, Oncology & Metabolism, The University of Sheffield","Tissue Repair & Immunity in ageing, Oncology & Metabolism, The University of Sheffield",1,0.93342,,0.15617,,0.68801,,0.49533,,101,,B,,usable mapping rate,illumina,early_illumina,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2022-06-07,Juvenile,Juvenile,Brain,Nervous System
70194,SRR19571674,SRX15623695,SRS13323924,SRP378890,PRJNA846700,Telomerase Dependent Ageing In The Zebrafish Brain,GSE205601,Transcriptome Analysis,Decreased telomerase expression telomere shortening senescence associated markers and inflammation have all been independently observed in the ageing brain and associated with disease. However causality between limited telomerase expression and brain senescence and neuro inflammation in the natural ageing setting is yet to be established. Here we address these questions using the zebrafish as an ageing model which akin to humans displays premature ageing and death in the absence of telomerase and where telomere shortening is a driver of cellular senescence. Our work shows for the first time that telomerase deficiency tert / accelerates key hallmarks of ageing identified in the Wild Type WT zebrafish brain at transcriptional cellular tissue and functional levels. We show that Tert dependent transcriptomic changes associated with dysregulation of gene expression stress response and dysregulation of immune genes are accompanied by accelerated accumulation of senescence associated markers and inflammation in the aged brain. Importantly In vivo these changes correlate with increased blood brain barrier permeability and altered cognitive behaviour. Of note telomerase dependent accumulation of senescence associated markers in the brain occurs not only in the expected proliferative areas but also in non proliferative ones where it is unlikely due to telomere dependent replicative exhaustion suggesting that non canonical roles of telomerase may be involved. Together our work suggests that telomerase has a protective role in the zebrafish brain against the accumulation of senescence and neuro inflammation and is required for blood brain barrier integrity. Overall design: RNA Sequencing of whole brain tissues throughout the lifespan of WT and telomerase deficient tert / fish. The data 4 age groups of WT 2 9 22 and >30 month corresponding to young adult median lifespan and old; and 3 age groups of telomerase deficient fish 2 9 and 22 month which correspond to young medium lifespan and old. Each group has a sample size of 3 animals. To identify signatures of ageing WT brain samples were subjected separately to DESEq2 analysis comparing the time points 9 22 and >30 month with the time point of 2 month. Then tert / samples at 2 9 month and 22 month were compared with WT at 2 month to identify telomerase dependent ageing processes.,,,,Brain tert 2months rep1,GSM6215410,,source name:brain|tissue:brain|strain:AB background|genotype:tert |age:2 month,Brain tert 2months rep1,Quality control was performed using MultiQC version 1.9. Cutadapt version 3.0 was used for trimming the first 13 bases from the reads to remove poor quality base pairs in the reads. Read alignment: Single end reads were aligned against the reference genome Danio rerio.GRCz11.dna. primary assembly.fa using STAR. A bespoke alignment index was built using annotation file Danio rerio.GRCz11.103.gtf and an expected read length of 88 bp. Ht seq count was run in non stranded mode to obtain per gene read counts. Assembly: Danio rerio.GRCz11.dna. Supplementary files format and content: tab delimited text files include RPKM values for each Sample,brain,,Whole tissues were dissected in cold PBS Sigma Aldrich transferred to a microcentrifuge tube containing 100 μl of Trizol Thermo Fisher Scientific snap frozen in dry ice and stored at 80°. To isolate the RNA extra 50 μl of Trizol was added to each sample and the tissue was homogenized with a mechanical homogenizer VWR International and a 1.5 pestle Kimble Chase Vineland NJ USA. post 5 min incubation at room temperature RT 30 μl of chloroform 1:5 VWR International was added and the samples were incubated for further 3 min at RT before centrifuged at 13 000g for 30 min at 4°C. Isopropanol Thermo Fisher Scientific was then added to the aqueous phase of the solution and the resultant mix was incubated for 10 min at RT before centrifuged 13 000g for 15 min at 4°C. Finally the pellet was twice washed in 250 μl of ice cold 75% ethanol and left to air dry before resuspended in 14 μl of nuclease free water. RNA integrity was assessed with the bioanalyzer Agilent 2100 Bioanalyzer Agilent Santa Clara CA USA. All the samples had a RNA integrity number RIN ≥9. Library preparation was performed following the Illumina methodology. mRNA was extracted from 500 ng of RNA with oligo dT beads capturing polyA tails using the NEBNext PolyA mRNA Magnetic Isolation Module New England Biolabs Inc. cDNA libraries were made with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina following the manufacturer’s instructions New England Biolabs Inc.,Zebrafish were maintained at the standard conditions of 27 28ºC in a 14:10 hour light dark cycle and fed twice a day with Artemia live rotifers and Sparus dry food.,tissue:brain|strain:AB background|genotype:tert |age:2 month,GSM6215410,GSM6215410: Brain tert 2months rep1; Danio rerio; RNA Seq,GSM6215410 r1,GSM6215410,1,Whole tissues were dissected in cold PBS Sigma Aldrich transferred to a microcentrifuge tube containing 100 μl of Trizol Thermo Fisher Scientific snap frozen in dry ice and stored at 80°. To isolate the RNA extra 50 μl of Trizol was added to each sample and the tissue was homogenized with a mechanical homogenizer VWR International and a 1.5 pestle Kimble Chase Vineland NJ USA. post 5 min incubation at room temperature RT 30 μl of chloroform 1:5 VWR International was added and the samples were incubated for further 3 min at RT before centrifuged at 13 000g for 30 min at 4°C. Isopropanol Thermo Fisher Scientific was then added to the aqueous phase of the solution and the resultant mix was incubated for 10 min at RT before centrifuged 13 000g for 15 min at 4°C. Finally the pellet was twice washed in 250 μl of ice cold 75% ethanol and left to air dry before resuspended in 14 μl of nuclease free water. RNA integrity was assessed with the bioanalyzer Agilent 2100 Bioanalyzer Agilent Santa Clara CA USA. All the samples had a RNA integrity number RIN ≥9. Library preparation was performed following the Illumina methodology. mRNA was extracted from 500 ng of RNA with oligo dT beads capturing polyA tails using the NEBNext PolyA mRNA Magnetic Isolation Module New England Biolabs Inc. cDNA libraries were made with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina following the manufacturer's instructions New England Biolabs Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiScanSQ,,SRP378890,,,B19.fastq.gz,fastq,1565394758.0,15498958.0,GSM6215410 r1,0:101 1:0,A:419284430;C:351126516;G:346272198;T:441081355;N:7630259,101,0,,,419284430,351126516,346272198,441081355,7630259,SRX15623695,SRS13323924,SRA1433223,"Tissue Repair & Immunity in ageing, Oncology & Metabolism, The University of Sheffield","Tissue Repair & Immunity in ageing, Oncology & Metabolism, The University of Sheffield",1,0.9329,,0.14098,,0.69796,,0.49654,,101,,B,,usable mapping rate,illumina,early_illumina,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2022-06-07,Juvenile,Juvenile,Brain,Nervous System
70204,SRR19571684,SRX15623685,SRS13323914,SRP378890,PRJNA846700,Telomerase Dependent Ageing In The Zebrafish Brain,GSE205601,Transcriptome Analysis,Decreased telomerase expression telomere shortening senescence associated markers and inflammation have all been independently observed in the ageing brain and associated with disease. However causality between limited telomerase expression and brain senescence and neuro inflammation in the natural ageing setting is yet to be established. Here we address these questions using the zebrafish as an ageing model which akin to humans displays premature ageing and death in the absence of telomerase and where telomere shortening is a driver of cellular senescence. Our work shows for the first time that telomerase deficiency tert / accelerates key hallmarks of ageing identified in the Wild Type WT zebrafish brain at transcriptional cellular tissue and functional levels. We show that Tert dependent transcriptomic changes associated with dysregulation of gene expression stress response and dysregulation of immune genes are accompanied by accelerated accumulation of senescence associated markers and inflammation in the aged brain. Importantly In vivo these changes correlate with increased blood brain barrier permeability and altered cognitive behaviour. Of note telomerase dependent accumulation of senescence associated markers in the brain occurs not only in the expected proliferative areas but also in non proliferative ones where it is unlikely due to telomere dependent replicative exhaustion suggesting that non canonical roles of telomerase may be involved. Together our work suggests that telomerase has a protective role in the zebrafish brain against the accumulation of senescence and neuro inflammation and is required for blood brain barrier integrity. Overall design: RNA Sequencing of whole brain tissues throughout the lifespan of WT and telomerase deficient tert / fish. The data 4 age groups of WT 2 9 22 and >30 month corresponding to young adult median lifespan and old; and 3 age groups of telomerase deficient fish 2 9 and 22 month which correspond to young medium lifespan and old. Each group has a sample size of 3 animals. To identify signatures of ageing WT brain samples were subjected separately to DESEq2 analysis comparing the time points 9 22 and >30 month with the time point of 2 month. Then tert / samples at 2 9 month and 22 month were compared with WT at 2 month to identify telomerase dependent ageing processes.,,,,Brain WT 2months rep3,GSM6215400,,source name:brain|tissue:brain|strain:AB background|genotype:WT|age:2 month,Brain WT 2months rep3,Quality control was performed using MultiQC version 1.9. Cutadapt version 3.0 was used for trimming the first 13 bases from the reads to remove poor quality base pairs in the reads. Read alignment: Single end reads were aligned against the reference genome Danio rerio.GRCz11.dna. primary assembly.fa using STAR. A bespoke alignment index was built using annotation file Danio rerio.GRCz11.103.gtf and an expected read length of 88 bp. Ht seq count was run in non stranded mode to obtain per gene read counts. Assembly: Danio rerio.GRCz11.dna. Supplementary files format and content: tab delimited text files include RPKM values for each Sample,brain,,Whole tissues were dissected in cold PBS Sigma Aldrich transferred to a microcentrifuge tube containing 100 μl of Trizol Thermo Fisher Scientific snap frozen in dry ice and stored at 80°. To isolate the RNA extra 50 μl of Trizol was added to each sample and the tissue was homogenized with a mechanical homogenizer VWR International and a 1.5 pestle Kimble Chase Vineland NJ USA. post 5 min incubation at room temperature RT 30 μl of chloroform 1:5 VWR International was added and the samples were incubated for further 3 min at RT before centrifuged at 13 000g for 30 min at 4°C. Isopropanol Thermo Fisher Scientific was then added to the aqueous phase of the solution and the resultant mix was incubated for 10 min at RT before centrifuged 13 000g for 15 min at 4°C. Finally the pellet was twice washed in 250 μl of ice cold 75% ethanol and left to air dry before resuspended in 14 μl of nuclease free water. RNA integrity was assessed with the bioanalyzer Agilent 2100 Bioanalyzer Agilent Santa Clara CA USA. All the samples had a RNA integrity number RIN ≥9. Library preparation was performed following the Illumina methodology. mRNA was extracted from 500 ng of RNA with oligo dT beads capturing polyA tails using the NEBNext PolyA mRNA Magnetic Isolation Module New England Biolabs Inc. cDNA libraries were made with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina following the manufacturer’s instructions New England Biolabs Inc.,Zebrafish were maintained at the standard conditions of 27 28ºC in a 14:10 hour light dark cycle and fed twice a day with Artemia live rotifers and Sparus dry food.,tissue:brain|strain:AB background|genotype:WT|age:2 month,GSM6215400,GSM6215400: Brain WT 2months rep3; Danio rerio; RNA Seq,GSM6215400 r1,GSM6215400,1,Whole tissues were dissected in cold PBS Sigma Aldrich transferred to a microcentrifuge tube containing 100 μl of Trizol Thermo Fisher Scientific snap frozen in dry ice and stored at 80°. To isolate the RNA extra 50 μl of Trizol was added to each sample and the tissue was homogenized with a mechanical homogenizer VWR International and a 1.5 pestle Kimble Chase Vineland NJ USA. post 5 min incubation at room temperature RT 30 μl of chloroform 1:5 VWR International was added and the samples were incubated for further 3 min at RT before centrifuged at 13 000g for 30 min at 4°C. Isopropanol Thermo Fisher Scientific was then added to the aqueous phase of the solution and the resultant mix was incubated for 10 min at RT before centrifuged 13 000g for 15 min at 4°C. Finally the pellet was twice washed in 250 μl of ice cold 75% ethanol and left to air dry before resuspended in 14 μl of nuclease free water. RNA integrity was assessed with the bioanalyzer Agilent 2100 Bioanalyzer Agilent Santa Clara CA USA. All the samples had a RNA integrity number RIN ≥9. Library preparation was performed following the Illumina methodology. mRNA was extracted from 500 ng of RNA with oligo dT beads capturing polyA tails using the NEBNext PolyA mRNA Magnetic Isolation Module New England Biolabs Inc. cDNA libraries were made with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina following the manufacturer's instructions New England Biolabs Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiScanSQ,,SRP378890,,,B4.fastq.gz,fastq,1685443863.0,16687563.0,GSM6215400 r1,0:101 1:0,A:450415537;C:379565206;G:372769588;T:474474996;N:8218536,101,0,,,450415537,379565206,372769588,474474996,8218536,SRX15623685,SRS13323914,SRA1433223,"Tissue Repair & Immunity in ageing, Oncology & Metabolism, The University of Sheffield","Tissue Repair & Immunity in ageing, Oncology & Metabolism, The University of Sheffield",1,0.93133,,0.15452,,0.69363,,0.49019,,101,,B,,usable mapping rate,illumina,early_illumina,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2022-06-07,Juvenile,Juvenile,Brain,Nervous System
70205,SRR19571685,SRX15623684,SRS13323913,SRP378890,PRJNA846700,Telomerase Dependent Ageing In The Zebrafish Brain,GSE205601,Transcriptome Analysis,Decreased telomerase expression telomere shortening senescence associated markers and inflammation have all been independently observed in the ageing brain and associated with disease. However causality between limited telomerase expression and brain senescence and neuro inflammation in the natural ageing setting is yet to be established. Here we address these questions using the zebrafish as an ageing model which akin to humans displays premature ageing and death in the absence of telomerase and where telomere shortening is a driver of cellular senescence. Our work shows for the first time that telomerase deficiency tert / accelerates key hallmarks of ageing identified in the Wild Type WT zebrafish brain at transcriptional cellular tissue and functional levels. We show that Tert dependent transcriptomic changes associated with dysregulation of gene expression stress response and dysregulation of immune genes are accompanied by accelerated accumulation of senescence associated markers and inflammation in the aged brain. Importantly In vivo these changes correlate with increased blood brain barrier permeability and altered cognitive behaviour. Of note telomerase dependent accumulation of senescence associated markers in the brain occurs not only in the expected proliferative areas but also in non proliferative ones where it is unlikely due to telomere dependent replicative exhaustion suggesting that non canonical roles of telomerase may be involved. Together our work suggests that telomerase has a protective role in the zebrafish brain against the accumulation of senescence and neuro inflammation and is required for blood brain barrier integrity. Overall design: RNA Sequencing of whole brain tissues throughout the lifespan of WT and telomerase deficient tert / fish. The data 4 age groups of WT 2 9 22 and >30 month corresponding to young adult median lifespan and old; and 3 age groups of telomerase deficient fish 2 9 and 22 month which correspond to young medium lifespan and old. Each group has a sample size of 3 animals. To identify signatures of ageing WT brain samples were subjected separately to DESEq2 analysis comparing the time points 9 22 and >30 month with the time point of 2 month. Then tert / samples at 2 9 month and 22 month were compared with WT at 2 month to identify telomerase dependent ageing processes.,,,,Brain WT 2months rep1,GSM6215399,,source name:brain|tissue:brain|strain:AB background|genotype:WT|age:2 month,Brain WT 2months rep1,Quality control was performed using MultiQC version 1.9. Cutadapt version 3.0 was used for trimming the first 13 bases from the reads to remove poor quality base pairs in the reads. Read alignment: Single end reads were aligned against the reference genome Danio rerio.GRCz11.dna. primary assembly.fa using STAR. A bespoke alignment index was built using annotation file Danio rerio.GRCz11.103.gtf and an expected read length of 88 bp. Ht seq count was run in non stranded mode to obtain per gene read counts. Assembly: Danio rerio.GRCz11.dna. Supplementary files format and content: tab delimited text files include RPKM values for each Sample,brain,,Whole tissues were dissected in cold PBS Sigma Aldrich transferred to a microcentrifuge tube containing 100 μl of Trizol Thermo Fisher Scientific snap frozen in dry ice and stored at 80°. To isolate the RNA extra 50 μl of Trizol was added to each sample and the tissue was homogenized with a mechanical homogenizer VWR International and a 1.5 pestle Kimble Chase Vineland NJ USA. post 5 min incubation at room temperature RT 30 μl of chloroform 1:5 VWR International was added and the samples were incubated for further 3 min at RT before centrifuged at 13 000g for 30 min at 4°C. Isopropanol Thermo Fisher Scientific was then added to the aqueous phase of the solution and the resultant mix was incubated for 10 min at RT before centrifuged 13 000g for 15 min at 4°C. Finally the pellet was twice washed in 250 μl of ice cold 75% ethanol and left to air dry before resuspended in 14 μl of nuclease free water. RNA integrity was assessed with the bioanalyzer Agilent 2100 Bioanalyzer Agilent Santa Clara CA USA. All the samples had a RNA integrity number RIN ≥9. Library preparation was performed following the Illumina methodology. mRNA was extracted from 500 ng of RNA with oligo dT beads capturing polyA tails using the NEBNext PolyA mRNA Magnetic Isolation Module New England Biolabs Inc. cDNA libraries were made with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina following the manufacturer’s instructions New England Biolabs Inc.,Zebrafish were maintained at the standard conditions of 27 28ºC in a 14:10 hour light dark cycle and fed twice a day with Artemia live rotifers and Sparus dry food.,tissue:brain|strain:AB background|genotype:WT|age:2 month,GSM6215399,GSM6215399: Brain WT 2months rep1; Danio rerio; RNA Seq,GSM6215399 r1,GSM6215399,1,Whole tissues were dissected in cold PBS Sigma Aldrich transferred to a microcentrifuge tube containing 100 μl of Trizol Thermo Fisher Scientific snap frozen in dry ice and stored at 80°. To isolate the RNA extra 50 μl of Trizol was added to each sample and the tissue was homogenized with a mechanical homogenizer VWR International and a 1.5 pestle Kimble Chase Vineland NJ USA. post 5 min incubation at room temperature RT 30 μl of chloroform 1:5 VWR International was added and the samples were incubated for further 3 min at RT before centrifuged at 13 000g for 30 min at 4°C. Isopropanol Thermo Fisher Scientific was then added to the aqueous phase of the solution and the resultant mix was incubated for 10 min at RT before centrifuged 13 000g for 15 min at 4°C. Finally the pellet was twice washed in 250 μl of ice cold 75% ethanol and left to air dry before resuspended in 14 μl of nuclease free water. RNA integrity was assessed with the bioanalyzer Agilent 2100 Bioanalyzer Agilent Santa Clara CA USA. All the samples had a RNA integrity number RIN ≥9. Library preparation was performed following the Illumina methodology. mRNA was extracted from 500 ng of RNA with oligo dT beads capturing polyA tails using the NEBNext PolyA mRNA Magnetic Isolation Module New England Biolabs Inc. cDNA libraries were made with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina following the manufacturer's instructions New England Biolabs Inc.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiScanSQ,,SRP378890,,,B2.fastq.gz,fastq,1656790668.0,16403868.0,GSM6215399 r1,0:101 1:0,A:449703718;C:368586926;G:363343184;T:467072556;N:8084284,101,0,,,449703718,368586926,363343184,467072556,8084284,SRX15623684,SRS13323913,SRA1433223,"Tissue Repair & Immunity in ageing, Oncology & Metabolism, The University of Sheffield","Tissue Repair & Immunity in ageing, Oncology & Metabolism, The University of Sheffield",1,0.92658,,0.16686,,0.69731,,0.49794,,101,,B,,usable mapping rate,illumina,early_illumina,unknown,poly_a,nebnext,bulk,unknown,unknown,,United Kingdom,2022-06-07,Juvenile,Juvenile,Brain,Nervous System
71012,SRR21091434,SRX17106010,SRS14681480,SRP392532,PRJNA870087,RNA sequencing katnb1 / 30dpf brains from fish with scoliosis,PRJNA870087,Other,RNA sequencing examining the expression in katnb1 / 30dpf brains from fish with scoliosis vs. wildtype 30dpf brains,,,,katnb1+/ with straight spine,control,,strain:not applicable|age:30 dof|sex:not applicable|tissue:Brain|genotype:katnb1 mh102+/ |phenotype:Straight spine|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of scoliotic zebrafish brains: 30dpf control straight spine brains,katnStrC5,katnStrC5,3 brains were pooled from 30 dpf scoliotic fish and RNA extracted with an RNA extraction kit. RNA sample quality was assessed using an Agilent Bioanalyzer. Library prep and subsequent sequencing was performed by The Centre for Applied Genomics at The Hospital for Sick Children SickKids using the NEBNext stranded RNA.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP392532,,,KatnStrC5.bam,bam,18788598694.0,63985901.0,KatnStrC5.bam,0:146.10 1:147.53,A:5114182464;C:4272224571;G:4325361406;T:5076743348;N:86905,146,147,,,5114182464,4272224571,4325361406,5076743348,86905,SRX17106010,SRS14681480,SRA1477007,The Hospital for Sick Children|Developmental and Stem Cell Biology,The Hospital for Sick Children,2,0.96542,0.93972,0.09288,0.08734,0.68964,0.69351,0.51701,0.50667,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,Canada,2022-08-16,Juvenile,Juvenile,Brain,Nervous System
71013,SRR21091435,SRX17106009,SRS14681480,SRP392532,PRJNA870087,RNA sequencing katnb1 / 30dpf brains from fish with scoliosis,PRJNA870087,Other,RNA sequencing examining the expression in katnb1 / 30dpf brains from fish with scoliosis vs. wildtype 30dpf brains,,,,katnb1+/ with straight spine,control,,strain:not applicable|age:30 dof|sex:not applicable|tissue:Brain|genotype:katnb1 mh102+/ |phenotype:Straight spine|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of scoliotic zebrafish brains: 30dpf control straight spine brains,katnStrB2,katnStrB2,3 brains were pooled from 30 dpf scoliotic fish and RNA extracted with an RNA extraction kit. RNA sample quality was assessed using an Agilent Bioanalyzer. Library prep and subsequent sequencing was performed by The Centre for Applied Genomics at The Hospital for Sick Children SickKids using the NEBNext stranded RNA.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP392532,,,KatnStrB2.bam,bam,20078804506.0,68106137.0,KatnStrB2.bam,0:146.89 1:147.92,A:5421281907;C:4618285403;G:4664274499;T:5374870022;N:92675,146,147,,,5421281907,4618285403,4664274499,5374870022,92675,SRX17106009,SRS14681480,SRA1477007,The Hospital for Sick Children|Developmental and Stem Cell Biology,The Hospital for Sick Children,2,0.96744,0.94847,0.08978,0.08524,0.68247,0.6856,0.50498,0.5051,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,Canada,2022-08-16,Juvenile,Juvenile,Brain,Nervous System
71014,SRR21091436,SRX17106008,SRS14681480,SRP392532,PRJNA870087,RNA sequencing katnb1 / 30dpf brains from fish with scoliosis,PRJNA870087,Other,RNA sequencing examining the expression in katnb1 / 30dpf brains from fish with scoliosis vs. wildtype 30dpf brains,,,,katnb1+/ with straight spine,control,,strain:not applicable|age:30 dof|sex:not applicable|tissue:Brain|genotype:katnb1 mh102+/ |phenotype:Straight spine|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of scoliotic zebrafish brains: 30dpf control straight spine brains,katnStrA2,katnStrA2,3 brains were pooled from 30 dpf scoliotic fish and RNA extracted with an RNA extraction kit. RNA sample quality was assessed using an Agilent Bioanalyzer. Library prep and subsequent sequencing was performed by The Centre for Applied Genomics at The Hospital for Sick Children SickKids using the NEBNext stranded RNA.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP392532,,assembly:GCA 000002035.4,KatnStrA2.sorted.bam,bam,14745184752.0,49982168.0,KatnStrA2.bam,0:146.99 1:148.02,A:4006566088;C:3365043851;G:3398771138;T:3974735621;N:68054,146,148,,,4006566088,3365043851,3398771138,3974735621,68054,SRX17106008,SRS14681480,SRA1477007,The Hospital for Sick Children|Developmental and Stem Cell Biology,The Hospital for Sick Children,2,0.96701,0.94847,0.09023,0.0851,0.69355,0.69595,0.51631,0.51894,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,Canada,2022-08-23,Juvenile,Juvenile,Brain,Nervous System
71015,SRR21091437,SRX17106007,SRS14681479,SRP392532,PRJNA870087,RNA sequencing katnb1 / 30dpf brains from fish with scoliosis,PRJNA870087,Other,RNA sequencing examining the expression in katnb1 / 30dpf brains from fish with scoliosis vs. wildtype 30dpf brains,,,,katnb1 / with scoliosis,katnb1,,strain:not applicable|age:30 dpf|sex:not applicable|tissue:Brain|genotype:katnb1 mh102 / |phenotype:Scoliosis|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of scoliotic zebrafish brains: 30dpf katnb1 / scoliotic brains,katnCurveC5,katnCurveC5,3 brains were pooled from 30 dpf scoliotic fish and RNA extracted with an RNA extraction kit. RNA sample quality was assessed using an Agilent Bioanalyzer. Library prep and subsequent sequencing was performed by The Centre for Applied Genomics at The Hospital for Sick Children SickKids using the NEBNext stranded RNA.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP392532,,,KatnCurveC5.bam,bam,17238328774.0,58363500.0,KatnCurveC5.bam,0:147.19 1:148.17,A:4653368298;C:3966638334;G:4006013577;T:4612229382;N:79183,147,148,,,4653368298,3966638334,4006013577,4612229382,79183,SRX17106007,SRS14681479,SRA1477007,The Hospital for Sick Children|Developmental and Stem Cell Biology,The Hospital for Sick Children,2,0.96717,0.94875,0.08768,0.08345,0.69599,0.69907,0.50576,0.51639,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,Canada,2022-08-16,Juvenile,Juvenile,Brain,Nervous System
71016,SRR21091438,SRX17106006,SRS14681479,SRP392532,PRJNA870087,RNA sequencing katnb1 / 30dpf brains from fish with scoliosis,PRJNA870087,Other,RNA sequencing examining the expression in katnb1 / 30dpf brains from fish with scoliosis vs. wildtype 30dpf brains,,,,katnb1 / with scoliosis,katnb1,,strain:not applicable|age:30 dpf|sex:not applicable|tissue:Brain|genotype:katnb1 mh102 / |phenotype:Scoliosis|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of scoliotic zebrafish brains: 30dpf katnb1 / scoliotic brains,katnCurveC3,katnCurveC3,3 brains were pooled from 30 dpf scoliotic fish and RNA extracted with an RNA extraction kit. RNA sample quality was assessed using an Agilent Bioanalyzer. Library prep and subsequent sequencing was performed by The Centre for Applied Genomics at The Hospital for Sick Children SickKids using the NEBNext stranded RNA.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP392532,,,KatnCurveC3.bam,bam,22702292739.0,76912847.0,KatnCurveC3.bam,0:147.07 1:148.10,A:6175143542;C:5174336497;G:5230446382;T:6122261437;N:104881,147,148,,,6175143542,5174336497,5230446382,6122261437,104881,SRX17106006,SRS14681479,SRA1477007,The Hospital for Sick Children|Developmental and Stem Cell Biology,The Hospital for Sick Children,2,0.96417,0.94507,0.0955,0.08929,0.69367,0.6981,0.50366,0.51208,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,Canada,2022-08-16,Juvenile,Juvenile,Brain,Nervous System
71017,SRR21091439,SRX17106005,SRS14681479,SRP392532,PRJNA870087,RNA sequencing katnb1 / 30dpf brains from fish with scoliosis,PRJNA870087,Other,RNA sequencing examining the expression in katnb1 / 30dpf brains from fish with scoliosis vs. wildtype 30dpf brains,,,,katnb1 / with scoliosis,katnb1,,strain:not applicable|age:30 dpf|sex:not applicable|tissue:Brain|genotype:katnb1 mh102 / |phenotype:Scoliosis|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of scoliotic zebrafish brains: 30dpf katnb1 / scoliotic brains,katnCurveA2,katnCurveA2,3 brains were pooled from 30 dpf scoliotic fish and RNA extracted with an RNA extraction kit. RNA sample quality was assessed using an Agilent Bioanalyzer. Library prep and subsequent sequencing was performed by The Centre for Applied Genomics at The Hospital for Sick Children SickKids using the NEBNext stranded RNA.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP392532,,,KatnCurveA2.bam,bam,17338927218.0,58528866.0,KatnCurveA2.bam,0:147.72 1:148.53,A:4739833700;C:3943593929;G:3973633658;T:4681786227;N:79704,147,148,,,4739833700,3943593929,3973633658,4681786227,79704,SRX17106005,SRS14681479,SRA1477007,The Hospital for Sick Children|Developmental and Stem Cell Biology,The Hospital for Sick Children,2,0.9623,0.94913,0.10094,0.09521,0.69414,0.69649,0.50529,0.51246,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,Canada,2022-08-18,Juvenile,Juvenile,Brain,Nervous System
74187,SRR23592269,SRX19477372,SRS16868715,SRP424004,PRJNA937732,Integrative single cell transcriptomics clarifies adult neurogenesis and macroglia evolution,GSE225863,Transcriptome Analysis,The evolution of nervous systems hinges on cell type diversification and specialization. Neural glia also called macroglia make up a large percentage of the total cell numbers in the brain of several species including humans and perform critical functions related to producing maintaining and assiting neurons. Despite their importance glial cells have been much less studied than neurons. Here in order to investigate the heterogeneity of adult radial glial cells in zebrafish and to study the evolution of macroglia and the adult neurogenesis process they support we generated a single cell RNAseq dataset of the adult zebrafish telencephalon enriched for radial glial cells using a sox2:gfp transgenic line. Overall design: Cells from the telencephalon of 12wpf Tgsox2:gfp/+ fish were isolated by Fluorescence Activated Cell Sorting FACS. GFP positive cells were enriched to increase the relative proportion of radial glial cells and the resulting samples were processed for scRNA seq.,,pubmed:38518783,,Replicate3,GSM7058866,,source name:Telencephalon|tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks,Replicate3,The demultiplexing barcoded processing and gene countings were made using the Cell Ranger software. We did not use the implemented aggregation method and the data provided here corresponds to individual replicates. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,Telencephalon,,Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks,GSM7058866,GSM7058866: Replicate3; Danio rerio; RNA Seq,GSM7058866 r1,GSM7058866,1,Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP424004,,loader:fastq load.py,Replicate3_S6_L002_I1_001.fastq.gz Replicate3_S6_L002_R1_001.fastq.gz Replicate3_S6_L002_R2_001.fastq.gz,fastq fastq fastq,10975505112.0,83147766.0,GSM7058866 r1,0:8 1:26 2:98,A:2426282254;C:1547059106;G:1673155133;T:2499529455;N:2455120,8,26,98,,2426282254,1547059106,1673155133,2499529455,2455120,SRX19477372,SRS16868715,SRA1594515,"Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur","Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur",1,0.88458,,0.25806,,0.75777,,0.51359,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,France,2023-02-22,Juvenile,Juvenile,Brain,Nervous System
74188,SRR23592270,SRX19477372,SRS16868715,SRP424004,PRJNA937732,Integrative single cell transcriptomics clarifies adult neurogenesis and macroglia evolution,GSE225863,Transcriptome Analysis,The evolution of nervous systems hinges on cell type diversification and specialization. Neural glia also called macroglia make up a large percentage of the total cell numbers in the brain of several species including humans and perform critical functions related to producing maintaining and assiting neurons. Despite their importance glial cells have been much less studied than neurons. Here in order to investigate the heterogeneity of adult radial glial cells in zebrafish and to study the evolution of macroglia and the adult neurogenesis process they support we generated a single cell RNAseq dataset of the adult zebrafish telencephalon enriched for radial glial cells using a sox2:gfp transgenic line. Overall design: Cells from the telencephalon of 12wpf Tgsox2:gfp/+ fish were isolated by Fluorescence Activated Cell Sorting FACS. GFP positive cells were enriched to increase the relative proportion of radial glial cells and the resulting samples were processed for scRNA seq.,,pubmed:38518783,,Replicate3,GSM7058866,,source name:Telencephalon|tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks,Replicate3,The demultiplexing barcoded processing and gene countings were made using the Cell Ranger software. We did not use the implemented aggregation method and the data provided here corresponds to individual replicates. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,Telencephalon,,Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks,GSM7058866,GSM7058866: Replicate3; Danio rerio; RNA Seq,GSM7058866 r1,GSM7058866,1,Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP424004,,loader:fastq load.py,Replicate3_S6_L003_I1_001.fastq.gz Replicate3_S6_L003_R1_001.fastq.gz Replicate3_S6_L003_R2_001.fastq.gz,fastq fastq fastq,10997748828.0,83316279.0,GSM7058866 r2,0:8 1:26 2:98,A:2431471247;C:1548269509;G:1677317277;T:2505450138;N:2487171,8,26,98,,2431471247,1548269509,1677317277,2505450138,2487171,SRX19477372,SRS16868715,SRA1594515,"Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur","Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur",1,0.87918,,0.25527,,0.76077,,0.5112,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,France,2023-02-22,Juvenile,Juvenile,Brain,Nervous System
74189,SRR23592271,SRX19477372,SRS16868715,SRP424004,PRJNA937732,Integrative single cell transcriptomics clarifies adult neurogenesis and macroglia evolution,GSE225863,Transcriptome Analysis,The evolution of nervous systems hinges on cell type diversification and specialization. Neural glia also called macroglia make up a large percentage of the total cell numbers in the brain of several species including humans and perform critical functions related to producing maintaining and assiting neurons. Despite their importance glial cells have been much less studied than neurons. Here in order to investigate the heterogeneity of adult radial glial cells in zebrafish and to study the evolution of macroglia and the adult neurogenesis process they support we generated a single cell RNAseq dataset of the adult zebrafish telencephalon enriched for radial glial cells using a sox2:gfp transgenic line. Overall design: Cells from the telencephalon of 12wpf Tgsox2:gfp/+ fish were isolated by Fluorescence Activated Cell Sorting FACS. GFP positive cells were enriched to increase the relative proportion of radial glial cells and the resulting samples were processed for scRNA seq.,,pubmed:38518783,,Replicate3,GSM7058866,,source name:Telencephalon|tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks,Replicate3,The demultiplexing barcoded processing and gene countings were made using the Cell Ranger software. We did not use the implemented aggregation method and the data provided here corresponds to individual replicates. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,Telencephalon,,Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks,GSM7058866,GSM7058866: Replicate3; Danio rerio; RNA Seq,GSM7058866 r1,GSM7058866,1,Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP424004,,loader:fastq load.py,Replicate3_S6_L004_I1_001.fastq.gz Replicate3_S6_L004_R1_001.fastq.gz Replicate3_S6_L004_R2_001.fastq.gz,fastq fastq fastq,10983946644.0,83211717.0,GSM7058866 r3,0:8 1:26 2:98,A:2429637202;C:1546068983;G:1673189416;T:2503083588;N:2769077,8,26,98,,2429637202,1546068983,1673189416,2503083588,2769077,SRX19477372,SRS16868715,SRA1594515,"Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur","Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur",1,0.88521,,0.2551,,0.76256,,0.50337,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,France,2023-02-22,Juvenile,Juvenile,Brain,Nervous System
74190,SRR23592272,SRX19477372,SRS16868715,SRP424004,PRJNA937732,Integrative single cell transcriptomics clarifies adult neurogenesis and macroglia evolution,GSE225863,Transcriptome Analysis,The evolution of nervous systems hinges on cell type diversification and specialization. Neural glia also called macroglia make up a large percentage of the total cell numbers in the brain of several species including humans and perform critical functions related to producing maintaining and assiting neurons. Despite their importance glial cells have been much less studied than neurons. Here in order to investigate the heterogeneity of adult radial glial cells in zebrafish and to study the evolution of macroglia and the adult neurogenesis process they support we generated a single cell RNAseq dataset of the adult zebrafish telencephalon enriched for radial glial cells using a sox2:gfp transgenic line. Overall design: Cells from the telencephalon of 12wpf Tgsox2:gfp/+ fish were isolated by Fluorescence Activated Cell Sorting FACS. GFP positive cells were enriched to increase the relative proportion of radial glial cells and the resulting samples were processed for scRNA seq.,,pubmed:38518783,,Replicate3,GSM7058866,,source name:Telencephalon|tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks,Replicate3,The demultiplexing barcoded processing and gene countings were made using the Cell Ranger software. We did not use the implemented aggregation method and the data provided here corresponds to individual replicates. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,Telencephalon,,Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks,GSM7058866,GSM7058866: Replicate3; Danio rerio; RNA Seq,GSM7058866 r1,GSM7058866,1,Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP424004,,loader:fastq load.py,Replicate3_S6_L005_I1_001.fastq.gz Replicate3_S6_L005_R1_001.fastq.gz Replicate3_S6_L005_R2_001.fastq.gz,fastq fastq fastq,10968968604.0,83098247.0,GSM7058866 r4,0:8 1:26 2:98,A:2426652777;C:1543610186;G:1671298649;T:2499458002;N:2608592,8,26,98,,2426652777,1543610186,1671298649,2499458002,2608592,SRX19477372,SRS16868715,SRA1594515,"Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur","Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur",1,0.88307,,0.25596,,0.7626,,0.5081,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,France,2023-02-22,Juvenile,Juvenile,Brain,Nervous System
74191,SRR23592273,SRX19477372,SRS16868715,SRP424004,PRJNA937732,Integrative single cell transcriptomics clarifies adult neurogenesis and macroglia evolution,GSE225863,Transcriptome Analysis,The evolution of nervous systems hinges on cell type diversification and specialization. Neural glia also called macroglia make up a large percentage of the total cell numbers in the brain of several species including humans and perform critical functions related to producing maintaining and assiting neurons. Despite their importance glial cells have been much less studied than neurons. Here in order to investigate the heterogeneity of adult radial glial cells in zebrafish and to study the evolution of macroglia and the adult neurogenesis process they support we generated a single cell RNAseq dataset of the adult zebrafish telencephalon enriched for radial glial cells using a sox2:gfp transgenic line. Overall design: Cells from the telencephalon of 12wpf Tgsox2:gfp/+ fish were isolated by Fluorescence Activated Cell Sorting FACS. GFP positive cells were enriched to increase the relative proportion of radial glial cells and the resulting samples were processed for scRNA seq.,,pubmed:38518783,,Replicate3,GSM7058866,,source name:Telencephalon|tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks,Replicate3,The demultiplexing barcoded processing and gene countings were made using the Cell Ranger software. We did not use the implemented aggregation method and the data provided here corresponds to individual replicates. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,Telencephalon,,Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks,GSM7058866,GSM7058866: Replicate3; Danio rerio; RNA Seq,GSM7058866 r1,GSM7058866,1,Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP424004,,loader:fastq load.py,Replicate3_S6_L006_I1_001.fastq.gz Replicate3_S6_L006_R1_001.fastq.gz Replicate3_S6_L006_R2_001.fastq.gz,fastq fastq fastq,11010714792.0,83414506.0,GSM7058866 r5,0:8 1:26 2:98,A:2435577632;C:1549348379;G:1677580141;T:2508999458;N:3115978,8,26,98,,2435577632,1549348379,1677580141,2508999458,3115978,SRX19477372,SRS16868715,SRA1594515,"Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur","Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur",1,0.88298,,0.25581,,0.75996,,0.51556,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,France,2023-02-22,Juvenile,Juvenile,Brain,Nervous System
74192,SRR23592274,SRX19477372,SRS16868715,SRP424004,PRJNA937732,Integrative single cell transcriptomics clarifies adult neurogenesis and macroglia evolution,GSE225863,Transcriptome Analysis,The evolution of nervous systems hinges on cell type diversification and specialization. Neural glia also called macroglia make up a large percentage of the total cell numbers in the brain of several species including humans and perform critical functions related to producing maintaining and assiting neurons. Despite their importance glial cells have been much less studied than neurons. Here in order to investigate the heterogeneity of adult radial glial cells in zebrafish and to study the evolution of macroglia and the adult neurogenesis process they support we generated a single cell RNAseq dataset of the adult zebrafish telencephalon enriched for radial glial cells using a sox2:gfp transgenic line. Overall design: Cells from the telencephalon of 12wpf Tgsox2:gfp/+ fish were isolated by Fluorescence Activated Cell Sorting FACS. GFP positive cells were enriched to increase the relative proportion of radial glial cells and the resulting samples were processed for scRNA seq.,,pubmed:38518783,,Replicate3,GSM7058866,,source name:Telencephalon|tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks,Replicate3,The demultiplexing barcoded processing and gene countings were made using the Cell Ranger software. We did not use the implemented aggregation method and the data provided here corresponds to individual replicates. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,Telencephalon,,Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks,GSM7058866,GSM7058866: Replicate3; Danio rerio; RNA Seq,GSM7058866 r1,GSM7058866,1,Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP424004,,loader:fastq load.py,Replicate3_S6_L007_I1_001.fastq.gz Replicate3_S6_L007_R1_001.fastq.gz Replicate3_S6_L007_R2_001.fastq.gz,fastq fastq fastq,10691125368.0,80993374.0,GSM7058866 r6,0:8 1:26 2:98,A:2364908014;C:1503792848;G:1627924254;T:2438606668;N:2118868,8,26,98,,2364908014,1503792848,1627924254,2438606668,2118868,SRX19477372,SRS16868715,SRA1594515,"Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur","Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur",1,0.88503,,0.2597,,0.76088,,0.49989,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,France,2023-02-22,Juvenile,Juvenile,Brain,Nervous System
74193,SRR23592275,SRX19477372,SRS16868715,SRP424004,PRJNA937732,Integrative single cell transcriptomics clarifies adult neurogenesis and macroglia evolution,GSE225863,Transcriptome Analysis,The evolution of nervous systems hinges on cell type diversification and specialization. Neural glia also called macroglia make up a large percentage of the total cell numbers in the brain of several species including humans and perform critical functions related to producing maintaining and assiting neurons. Despite their importance glial cells have been much less studied than neurons. Here in order to investigate the heterogeneity of adult radial glial cells in zebrafish and to study the evolution of macroglia and the adult neurogenesis process they support we generated a single cell RNAseq dataset of the adult zebrafish telencephalon enriched for radial glial cells using a sox2:gfp transgenic line. Overall design: Cells from the telencephalon of 12wpf Tgsox2:gfp/+ fish were isolated by Fluorescence Activated Cell Sorting FACS. GFP positive cells were enriched to increase the relative proportion of radial glial cells and the resulting samples were processed for scRNA seq.,,pubmed:38518783,,Replicate3,GSM7058866,,source name:Telencephalon|tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks,Replicate3,The demultiplexing barcoded processing and gene countings were made using the Cell Ranger software. We did not use the implemented aggregation method and the data provided here corresponds to individual replicates. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,Telencephalon,,Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks,GSM7058866,GSM7058866: Replicate3; Danio rerio; RNA Seq,GSM7058866 r1,GSM7058866,1,Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP424004,,loader:fastq load.py,Replicate3_S6_L008_I1_001.fastq.gz Replicate3_S6_L008_R1_001.fastq.gz Replicate3_S6_L008_R2_001.fastq.gz,fastq fastq fastq,10670015664.0,80833452.0,GSM7058866 r7,0:8 1:26 2:98,A:2360988524;C:1500040180;G:1624712352;T:2433842237;N:2095003,8,26,98,,2360988524,1500040180,1624712352,2433842237,2095003,SRX19477372,SRS16868715,SRA1594515,"Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur","Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur",1,0.8827,,0.25599,,0.76404,,0.51295,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,France,2023-02-22,Juvenile,Juvenile,Brain,Nervous System
74194,SRR23592276,SRX19477371,SRS16868714,SRP424004,PRJNA937732,Integrative single cell transcriptomics clarifies adult neurogenesis and macroglia evolution,GSE225863,Transcriptome Analysis,The evolution of nervous systems hinges on cell type diversification and specialization. Neural glia also called macroglia make up a large percentage of the total cell numbers in the brain of several species including humans and perform critical functions related to producing maintaining and assiting neurons. Despite their importance glial cells have been much less studied than neurons. Here in order to investigate the heterogeneity of adult radial glial cells in zebrafish and to study the evolution of macroglia and the adult neurogenesis process they support we generated a single cell RNAseq dataset of the adult zebrafish telencephalon enriched for radial glial cells using a sox2:gfp transgenic line. Overall design: Cells from the telencephalon of 12wpf Tgsox2:gfp/+ fish were isolated by Fluorescence Activated Cell Sorting FACS. GFP positive cells were enriched to increase the relative proportion of radial glial cells and the resulting samples were processed for scRNA seq.,,pubmed:38518783,,Replicate2,GSM7058865,,source name:Telencephalon|tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks,Replicate2,The demultiplexing barcoded processing and gene countings were made using the Cell Ranger software. We did not use the implemented aggregation method and the data provided here corresponds to individual replicates. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,Telencephalon,,Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks,GSM7058865,GSM7058865: Replicate2; Danio rerio; RNA Seq,GSM7058865 r1,GSM7058865,1,Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP424004,,loader:fastq load.py,Replicate2_S4_L002_I1_001.fastq.gz Replicate2_S4_L002_R1_001.fastq.gz Replicate2_S4_L002_R2_001.fastq.gz,fastq fastq fastq,9701122992.0,73493356.0,GSM7058865 r1,0:8 1:26 2:98,A:2156760689;C:1368071124;G:1455967716;T:2219399616;N:2149743,8,26,98,,2156760689,1368071124,1455967716,2219399616,2149743,SRX19477371,SRS16868714,SRA1594515,"Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur","Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur",1,0.88255,,0.29986,,0.76455,,0.51063,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,France,2023-02-22,Juvenile,Juvenile,Brain,Nervous System
74195,SRR23592277,SRX19477371,SRS16868714,SRP424004,PRJNA937732,Integrative single cell transcriptomics clarifies adult neurogenesis and macroglia evolution,GSE225863,Transcriptome Analysis,The evolution of nervous systems hinges on cell type diversification and specialization. Neural glia also called macroglia make up a large percentage of the total cell numbers in the brain of several species including humans and perform critical functions related to producing maintaining and assiting neurons. Despite their importance glial cells have been much less studied than neurons. Here in order to investigate the heterogeneity of adult radial glial cells in zebrafish and to study the evolution of macroglia and the adult neurogenesis process they support we generated a single cell RNAseq dataset of the adult zebrafish telencephalon enriched for radial glial cells using a sox2:gfp transgenic line. Overall design: Cells from the telencephalon of 12wpf Tgsox2:gfp/+ fish were isolated by Fluorescence Activated Cell Sorting FACS. GFP positive cells were enriched to increase the relative proportion of radial glial cells and the resulting samples were processed for scRNA seq.,,pubmed:38518783,,Replicate2,GSM7058865,,source name:Telencephalon|tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks,Replicate2,The demultiplexing barcoded processing and gene countings were made using the Cell Ranger software. We did not use the implemented aggregation method and the data provided here corresponds to individual replicates. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,Telencephalon,,Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks,GSM7058865,GSM7058865: Replicate2; Danio rerio; RNA Seq,GSM7058865 r1,GSM7058865,1,Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP424004,,loader:fastq load.py,Replicate2_S4_L003_I1_001.fastq.gz Replicate2_S4_L003_R1_001.fastq.gz Replicate2_S4_L003_R2_001.fastq.gz,fastq fastq fastq,9709605840.0,73557620.0,GSM7058865 r2,0:8 1:26 2:98,A:2158945438;C:1367438603;G:1458088740;T:2222002830;N:2171149,8,26,98,,2158945438,1367438603,1458088740,2222002830,2171149,SRX19477371,SRS16868714,SRA1594515,"Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur","Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur",1,0.87759,,0.2985,,0.76684,,0.5129,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,France,2023-02-22,Juvenile,Juvenile,Brain,Nervous System
74196,SRR23592278,SRX19477371,SRS16868714,SRP424004,PRJNA937732,Integrative single cell transcriptomics clarifies adult neurogenesis and macroglia evolution,GSE225863,Transcriptome Analysis,The evolution of nervous systems hinges on cell type diversification and specialization. Neural glia also called macroglia make up a large percentage of the total cell numbers in the brain of several species including humans and perform critical functions related to producing maintaining and assiting neurons. Despite their importance glial cells have been much less studied than neurons. Here in order to investigate the heterogeneity of adult radial glial cells in zebrafish and to study the evolution of macroglia and the adult neurogenesis process they support we generated a single cell RNAseq dataset of the adult zebrafish telencephalon enriched for radial glial cells using a sox2:gfp transgenic line. Overall design: Cells from the telencephalon of 12wpf Tgsox2:gfp/+ fish were isolated by Fluorescence Activated Cell Sorting FACS. GFP positive cells were enriched to increase the relative proportion of radial glial cells and the resulting samples were processed for scRNA seq.,,pubmed:38518783,,Replicate2,GSM7058865,,source name:Telencephalon|tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks,Replicate2,The demultiplexing barcoded processing and gene countings were made using the Cell Ranger software. We did not use the implemented aggregation method and the data provided here corresponds to individual replicates. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,Telencephalon,,Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks,GSM7058865,GSM7058865: Replicate2; Danio rerio; RNA Seq,GSM7058865 r1,GSM7058865,1,Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP424004,,loader:fastq load.py,Replicate2_S4_L004_I1_001.fastq.gz Replicate2_S4_L004_R1_001.fastq.gz Replicate2_S4_L004_R2_001.fastq.gz,fastq fastq fastq,9708008508.0,73545519.0,GSM7058865 r3,0:8 1:26 2:98,A:2159475104;C:1367156483;G:1455925675;T:2222489574;N:2414026,8,26,98,,2159475104,1367156483,1455925675,2222489574,2414026,SRX19477371,SRS16868714,SRA1594515,"Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur","Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur",1,0.88227,,0.30004,,0.76564,,0.50693,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,France,2023-02-22,Juvenile,Juvenile,Brain,Nervous System
74197,SRR23592279,SRX19477371,SRS16868714,SRP424004,PRJNA937732,Integrative single cell transcriptomics clarifies adult neurogenesis and macroglia evolution,GSE225863,Transcriptome Analysis,The evolution of nervous systems hinges on cell type diversification and specialization. Neural glia also called macroglia make up a large percentage of the total cell numbers in the brain of several species including humans and perform critical functions related to producing maintaining and assiting neurons. Despite their importance glial cells have been much less studied than neurons. Here in order to investigate the heterogeneity of adult radial glial cells in zebrafish and to study the evolution of macroglia and the adult neurogenesis process they support we generated a single cell RNAseq dataset of the adult zebrafish telencephalon enriched for radial glial cells using a sox2:gfp transgenic line. Overall design: Cells from the telencephalon of 12wpf Tgsox2:gfp/+ fish were isolated by Fluorescence Activated Cell Sorting FACS. GFP positive cells were enriched to increase the relative proportion of radial glial cells and the resulting samples were processed for scRNA seq.,,pubmed:38518783,,Replicate2,GSM7058865,,source name:Telencephalon|tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks,Replicate2,The demultiplexing barcoded processing and gene countings were made using the Cell Ranger software. We did not use the implemented aggregation method and the data provided here corresponds to individual replicates. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,Telencephalon,,Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks,GSM7058865,GSM7058865: Replicate2; Danio rerio; RNA Seq,GSM7058865 r1,GSM7058865,1,Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP424004,,loader:fastq load.py,Replicate2_S4_L005_I1_001.fastq.gz Replicate2_S4_L005_R1_001.fastq.gz Replicate2_S4_L005_R2_001.fastq.gz,fastq fastq fastq,9684262896.0,73365628.0,GSM7058865 r4,0:8 1:26 2:98,A:2154636627;C:1363360464;G:1452664065;T:2216892930;N:2277458,8,26,98,,2154636627,1363360464,1452664065,2216892930,2277458,SRX19477371,SRS16868714,SRA1594515,"Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur","Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur",1,0.8814,,0.29837,,0.76601,,0.50864,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,France,2023-02-22,Juvenile,Juvenile,Brain,Nervous System
74198,SRR23592280,SRX19477371,SRS16868714,SRP424004,PRJNA937732,Integrative single cell transcriptomics clarifies adult neurogenesis and macroglia evolution,GSE225863,Transcriptome Analysis,The evolution of nervous systems hinges on cell type diversification and specialization. Neural glia also called macroglia make up a large percentage of the total cell numbers in the brain of several species including humans and perform critical functions related to producing maintaining and assiting neurons. Despite their importance glial cells have been much less studied than neurons. Here in order to investigate the heterogeneity of adult radial glial cells in zebrafish and to study the evolution of macroglia and the adult neurogenesis process they support we generated a single cell RNAseq dataset of the adult zebrafish telencephalon enriched for radial glial cells using a sox2:gfp transgenic line. Overall design: Cells from the telencephalon of 12wpf Tgsox2:gfp/+ fish were isolated by Fluorescence Activated Cell Sorting FACS. GFP positive cells were enriched to increase the relative proportion of radial glial cells and the resulting samples were processed for scRNA seq.,,pubmed:38518783,,Replicate2,GSM7058865,,source name:Telencephalon|tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks,Replicate2,The demultiplexing barcoded processing and gene countings were made using the Cell Ranger software. We did not use the implemented aggregation method and the data provided here corresponds to individual replicates. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,Telencephalon,,Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks,GSM7058865,GSM7058865: Replicate2; Danio rerio; RNA Seq,GSM7058865 r1,GSM7058865,1,Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP424004,,loader:fastq load.py,Replicate2_S4_L006_I1_001.fastq.gz Replicate2_S4_L006_R1_001.fastq.gz Replicate2_S4_L006_R2_001.fastq.gz,fastq fastq fastq,9722510556.0,73655383.0,GSM7058865 r5,0:8 1:26 2:98,A:2163119425;C:1368456380;G:1458295022;T:2225618098;N:2738609,8,26,98,,2163119425,1368456380,1458295022,2225618098,2738609,SRX19477371,SRS16868714,SRA1594515,"Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur","Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur",1,0.88208,,0.29963,,0.76386,,0.50539,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,France,2023-02-22,Juvenile,Juvenile,Brain,Nervous System
74199,SRR23592281,SRX19477371,SRS16868714,SRP424004,PRJNA937732,Integrative single cell transcriptomics clarifies adult neurogenesis and macroglia evolution,GSE225863,Transcriptome Analysis,The evolution of nervous systems hinges on cell type diversification and specialization. Neural glia also called macroglia make up a large percentage of the total cell numbers in the brain of several species including humans and perform critical functions related to producing maintaining and assiting neurons. Despite their importance glial cells have been much less studied than neurons. Here in order to investigate the heterogeneity of adult radial glial cells in zebrafish and to study the evolution of macroglia and the adult neurogenesis process they support we generated a single cell RNAseq dataset of the adult zebrafish telencephalon enriched for radial glial cells using a sox2:gfp transgenic line. Overall design: Cells from the telencephalon of 12wpf Tgsox2:gfp/+ fish were isolated by Fluorescence Activated Cell Sorting FACS. GFP positive cells were enriched to increase the relative proportion of radial glial cells and the resulting samples were processed for scRNA seq.,,pubmed:38518783,,Replicate2,GSM7058865,,source name:Telencephalon|tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks,Replicate2,The demultiplexing barcoded processing and gene countings were made using the Cell Ranger software. We did not use the implemented aggregation method and the data provided here corresponds to individual replicates. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,Telencephalon,,Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks,GSM7058865,GSM7058865: Replicate2; Danio rerio; RNA Seq,GSM7058865 r1,GSM7058865,1,Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP424004,,loader:fastq load.py,Replicate2_S4_L007_I1_001.fastq.gz Replicate2_S4_L007_R1_001.fastq.gz Replicate2_S4_L007_R2_001.fastq.gz,fastq fastq fastq,9472130052.0,71758561.0,GSM7058865 r6,0:8 1:26 2:98,A:2107399564;C:1332856905;G:1419736878;T:2170483176;N:1862455,8,26,98,,2107399564,1332856905,1419736878,2170483176,1862455,SRX19477371,SRS16868714,SRA1594515,"Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur","Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur",1,0.88396,,0.29995,,0.7666,,0.50872,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,France,2023-02-22,Juvenile,Juvenile,Brain,Nervous System
74200,SRR23592282,SRX19477371,SRS16868714,SRP424004,PRJNA937732,Integrative single cell transcriptomics clarifies adult neurogenesis and macroglia evolution,GSE225863,Transcriptome Analysis,The evolution of nervous systems hinges on cell type diversification and specialization. Neural glia also called macroglia make up a large percentage of the total cell numbers in the brain of several species including humans and perform critical functions related to producing maintaining and assiting neurons. Despite their importance glial cells have been much less studied than neurons. Here in order to investigate the heterogeneity of adult radial glial cells in zebrafish and to study the evolution of macroglia and the adult neurogenesis process they support we generated a single cell RNAseq dataset of the adult zebrafish telencephalon enriched for radial glial cells using a sox2:gfp transgenic line. Overall design: Cells from the telencephalon of 12wpf Tgsox2:gfp/+ fish were isolated by Fluorescence Activated Cell Sorting FACS. GFP positive cells were enriched to increase the relative proportion of radial glial cells and the resulting samples were processed for scRNA seq.,,pubmed:38518783,,Replicate2,GSM7058865,,source name:Telencephalon|tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks,Replicate2,The demultiplexing barcoded processing and gene countings were made using the Cell Ranger software. We did not use the implemented aggregation method and the data provided here corresponds to individual replicates. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,Telencephalon,,Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks,GSM7058865,GSM7058865: Replicate2; Danio rerio; RNA Seq,GSM7058865 r1,GSM7058865,1,Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP424004,,loader:fastq load.py,Replicate2_S4_L008_I1_001.fastq.gz Replicate2_S4_L008_R1_001.fastq.gz Replicate2_S4_L008_R2_001.fastq.gz,fastq fastq fastq,9442724016.0,71535788.0,GSM7058865 r7,0:8 1:26 2:98,A:2101696435;C:1327881205;G:1415404738;T:2163690490;N:1834356,8,26,98,,2101696435,1327881205,1415404738,2163690490,1834356,SRX19477371,SRS16868714,SRA1594515,"Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur","Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur",1,0.87989,,0.29895,,0.7668,,0.50886,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,France,2023-02-22,Juvenile,Juvenile,Brain,Nervous System
74201,SRR23592283,SRX19477370,SRS16868713,SRP424004,PRJNA937732,Integrative single cell transcriptomics clarifies adult neurogenesis and macroglia evolution,GSE225863,Transcriptome Analysis,The evolution of nervous systems hinges on cell type diversification and specialization. Neural glia also called macroglia make up a large percentage of the total cell numbers in the brain of several species including humans and perform critical functions related to producing maintaining and assiting neurons. Despite their importance glial cells have been much less studied than neurons. Here in order to investigate the heterogeneity of adult radial glial cells in zebrafish and to study the evolution of macroglia and the adult neurogenesis process they support we generated a single cell RNAseq dataset of the adult zebrafish telencephalon enriched for radial glial cells using a sox2:gfp transgenic line. Overall design: Cells from the telencephalon of 12wpf Tgsox2:gfp/+ fish were isolated by Fluorescence Activated Cell Sorting FACS. GFP positive cells were enriched to increase the relative proportion of radial glial cells and the resulting samples were processed for scRNA seq.,,pubmed:38518783,,Replicate1,GSM7058864,,source name:Telencephalon|tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks,Replicate1,The demultiplexing barcoded processing and gene countings were made using the Cell Ranger software. We did not use the implemented aggregation method and the data provided here corresponds to individual replicates. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,Telencephalon,,Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks,GSM7058864,GSM7058864: Replicate1; Danio rerio; RNA Seq,GSM7058864 r1,GSM7058864,1,Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP424004,,loader:fastq load.py,Replicate1_S2_L002_I1_001.fastq.gz Replicate1_S2_L002_R1_001.fastq.gz Replicate1_S2_L002_R2_001.fastq.gz,fastq fastq fastq,11111432772.0,84177521.0,GSM7058864 r1,0:8 1:26 2:98,A:2488056016;C:1560451855;G:1702518729;T:2495889662;N:2480796,8,26,98,,2488056016,1560451855,1702518729,2495889662,2480796,SRX19477370,SRS16868713,SRA1594515,"Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur","Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur",1,0.86994,,0.32454,,0.75479,,0.50147,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,France,2023-02-22,Juvenile,Juvenile,Brain,Nervous System
74202,SRR23592284,SRX19477370,SRS16868713,SRP424004,PRJNA937732,Integrative single cell transcriptomics clarifies adult neurogenesis and macroglia evolution,GSE225863,Transcriptome Analysis,The evolution of nervous systems hinges on cell type diversification and specialization. Neural glia also called macroglia make up a large percentage of the total cell numbers in the brain of several species including humans and perform critical functions related to producing maintaining and assiting neurons. Despite their importance glial cells have been much less studied than neurons. Here in order to investigate the heterogeneity of adult radial glial cells in zebrafish and to study the evolution of macroglia and the adult neurogenesis process they support we generated a single cell RNAseq dataset of the adult zebrafish telencephalon enriched for radial glial cells using a sox2:gfp transgenic line. Overall design: Cells from the telencephalon of 12wpf Tgsox2:gfp/+ fish were isolated by Fluorescence Activated Cell Sorting FACS. GFP positive cells were enriched to increase the relative proportion of radial glial cells and the resulting samples were processed for scRNA seq.,,pubmed:38518783,,Replicate1,GSM7058864,,source name:Telencephalon|tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks,Replicate1,The demultiplexing barcoded processing and gene countings were made using the Cell Ranger software. We did not use the implemented aggregation method and the data provided here corresponds to individual replicates. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,Telencephalon,,Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,tissue:Telencephalon|genotype:TgSox2:gfp|age:12 weeks,GSM7058864,GSM7058864: Replicate1; Danio rerio; RNA Seq,GSM7058864 r1,GSM7058864,1,Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly telencephalic cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP424004,,loader:fastq load.py,Replicate1_S2_L003_I1_001.fastq.gz Replicate1_S2_L003_R1_001.fastq.gz Replicate1_S2_L003_R2_001.fastq.gz,fastq fastq fastq,11117387952.0,84222636.0,GSM7058864 r2,0:8 1:26 2:98,A:2489475115;C:1559434598;G:1704288588;T:2498112561;N:2507466,8,26,98,,2489475115,1559434598,1704288588,2498112561,2507466,SRX19477370,SRS16868713,SRA1594515,"Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur","Zebrafish Neurogenetics, Developmental and stem cell biology department, Institut Pasteur",1,0.86463,,0.32227,,0.75627,,0.50661,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,France,2023-02-22,Juvenile,Juvenile,Brain,Nervous System