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18 rows where tissue_curation = "Ear" and tissue_curation_coarse = "Sensory System"

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  • Sensory System · 18 ✖

tissue_curation 1

  • Ear · 18 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

devstage_curation_coarse 1

devstage_curation 1

Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
41685 41685 SRR5120134 SRX2435377 SRS1870364 SRP095338 PRJNA358049 Transcriptomic Analysis of Adult Zebrafish Inner Ear Hair Cells GSE92559 Transcriptome Analysis To understand the basic biological property of hair cells HCs from lower vertebrates we examined transcriptomes of adult zebrafish HCs. GFP labeled HCs were isolated from the utricle saccule and lagena the three inner ear sensory epithelia of a pou4f3 promoter driven GAP GFP line of transgenic zebrafish. 2 000 HCs and 2 000 non sensory cells from the inner ear were individually collected by suction pipet technique. RNA sequencing was performed and the resulting sequences were mapped analyzed and compared. Comparisons allow us to identify enriched genes in HCs which may underlie HC specialization. Overall design: Examination of transcriptomes of adult zebrafish inner ear hair cells and surrounding cells individually collected and sorted using pou4f3 promoter driven GFP marking hair cells.   pubmed:29406519   GFP neg surrounding cells 1 Technical 2 GSM2432255   tissue:2 000 Inner ear surrounding cells|cell type:GFP neg cells isolated and pooled from the lagena utricle and saccule|age:11 mpf 13 mpf adult|Sex:female|strain:Tgpou4f3:GAP GFPs273t GFP neg surrounding cells 1 Technical 2 CLC Genomics Workbench software CLC bio Waltham MA USA was used to map the reads to the GRCz10 zebrafish genome and generate gene expression values in the normalized form of reads per kilobase of transcript per million mapped reads RPKM values Genome build: GRCz10 zebrafish genome Supplementary files format and content: Expression data was exported from CLC Genomics Workbench in the form of Microsoft Excel Spreadsheets. 2 000 Inner ear surrounding cells   Qiagen miRNeasy mini plus kit Clontech Smart Seq   cell type:GFP neg cells isolated and pooled from the lagena utricle and saccule|age:11 mpf 13 mpf adult|Sex:female|strain:Tgpou4f3:GAP GFPs273t GSM2432255 GSM2432255: GFP neg surrounding cells 1 Technical 2; Danio rerio; RNA Seq GSM2432255   1 Qiagen miRNeasy mini plus kit Clontech Smart Seq GEO Accession:GSM2432255 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP095338     fish_WT_CGTACTAG-_L002_R1_001.fastq.gz fastq 2079575456.0 20589856.0 GSM2432255 r1 0:101 A:507789042;C:378574589;G:384399617;T:500198055;N:308614153 101       507789042 378574589 384399617 500198055 308614153 SRX2435377 SRS1870364 SRA505331 GEO Department of Biomedical Sciences, Creighton University 1 0.64962   0.22792   0.76148   0.49037   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2016-12-19 Adult Adult Ear Sensory System
41686 41686 SRR5120133 SRX2435376 SRS1870363 SRP095338 PRJNA358049 Transcriptomic Analysis of Adult Zebrafish Inner Ear Hair Cells GSE92559 Transcriptome Analysis To understand the basic biological property of hair cells HCs from lower vertebrates we examined transcriptomes of adult zebrafish HCs. GFP labeled HCs were isolated from the utricle saccule and lagena the three inner ear sensory epithelia of a pou4f3 promoter driven GAP GFP line of transgenic zebrafish. 2 000 HCs and 2 000 non sensory cells from the inner ear were individually collected by suction pipet technique. RNA sequencing was performed and the resulting sequences were mapped analyzed and compared. Comparisons allow us to identify enriched genes in HCs which may underlie HC specialization. Overall design: Examination of transcriptomes of adult zebrafish inner ear hair cells and surrounding cells individually collected and sorted using pou4f3 promoter driven GFP marking hair cells.   pubmed:29406519   GFP neg surrounding cells 1 Technical 1 GSM2432254   tissue:2 000 Inner ear surrounding cells|cell type:GFP neg cells isolated and pooled from the lagena utricle and saccule|age:11 mpf 13 mpf adult|Sex:female|strain:Tgpou4f3:GAP GFPs273t GFP neg surrounding cells 1 Technical 1 CLC Genomics Workbench software CLC bio Waltham MA USA was used to map the reads to the GRCz10 zebrafish genome and generate gene expression values in the normalized form of reads per kilobase of transcript per million mapped reads RPKM values Genome build: GRCz10 zebrafish genome Supplementary files format and content: Expression data was exported from CLC Genomics Workbench in the form of Microsoft Excel Spreadsheets. 2 000 Inner ear surrounding cells   Qiagen miRNeasy mini plus kit Clontech Smart Seq   cell type:GFP neg cells isolated and pooled from the lagena utricle and saccule|age:11 mpf 13 mpf adult|Sex:female|strain:Tgpou4f3:GAP GFPs273t GSM2432254 GSM2432254: GFP neg surrounding cells 1 Technical 1; Danio rerio; RNA Seq GSM2432254   1 Qiagen miRNeasy mini plus kit Clontech Smart Seq GEO Accession:GSM2432254 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP095338     fish_WT_CGTACTAG-_L001_R1_001.fastq.gz fastq 2104552049.0 20837149.0 GSM2432254 r1 0:101 A:514445451;C:383531037;G:389222968;T:506643466;N:310709127 101       514445451 383531037 389222968 506643466 310709127 SRX2435376 SRS1870363 SRA505331 GEO Department of Biomedical Sciences, Creighton University 1 0.6506   0.22936   0.76104   0.48864   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2016-12-19 Adult Adult Ear Sensory System
41687 41687 SRR5120132 SRX2435375 SRS1870362 SRP095338 PRJNA358049 Transcriptomic Analysis of Adult Zebrafish Inner Ear Hair Cells GSE92559 Transcriptome Analysis To understand the basic biological property of hair cells HCs from lower vertebrates we examined transcriptomes of adult zebrafish HCs. GFP labeled HCs were isolated from the utricle saccule and lagena the three inner ear sensory epithelia of a pou4f3 promoter driven GAP GFP line of transgenic zebrafish. 2 000 HCs and 2 000 non sensory cells from the inner ear were individually collected by suction pipet technique. RNA sequencing was performed and the resulting sequences were mapped analyzed and compared. Comparisons allow us to identify enriched genes in HCs which may underlie HC specialization. Overall design: Examination of transcriptomes of adult zebrafish inner ear hair cells and surrounding cells individually collected and sorted using pou4f3 promoter driven GFP marking hair cells.   pubmed:29406519   GFP+ Hair Cells Biological Replicate 2 Technical 2 GSM2432253   tissue:2 000 Inner ear hair cells|cell type:GFP+ Hair Cells isolated and pooled from the lagena utricle and saccule|age:11 mpf 13 mpf adult|Sex:female|strain:Tgpou4f3:GAP GFPs273t GFP+ Hair Cells Biological Replicate 2 Technical 2 CLC Genomics Workbench software CLC bio Waltham MA USA was used to map the reads to the GRCz10 zebrafish genome and generate gene expression values in the normalized form of reads per kilobase of transcript per million mapped reads RPKM values Genome build: GRCz10 zebrafish genome Supplementary files format and content: Expression data was exported from CLC Genomics Workbench in the form of Microsoft Excel Spreadsheets. 2 000 Inner ear hair cells   Qiagen miRNeasy mini plus kit Clontech Smart Seq   cell type:GFP+ Hair Cells isolated and pooled from the lagena utricle and saccule|age:11 mpf 13 mpf adult|Sex:female|strain:Tgpou4f3:GAP GFPs273t GSM2432253 GSM2432253: GFP+ Hair Cells Biological Replicate 2 Technical 2; Danio rerio; RNA Seq GSM2432253   1 Qiagen miRNeasy mini plus kit Clontech Smart Seq GEO Accession:GSM2432253 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP095338     zhc_AGGCAGAA-_L002_R1_001.fastq.gz fastq 6093457260.0 60331260.0 GSM2432253 r1 0:101 A:1471320441;C:1109536878;G:1119505740;T:1436533942;N:956560259 101       1471320441 1109536878 1119505740 1436533942 956560259 SRX2435375 SRS1870362 SRA505331 GEO Department of Biomedical Sciences, Creighton University 1 0.64117   0.14727   0.78145   0.5689   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2016-12-19 Adult Adult Ear Sensory System
41688 41688 SRR5120131 SRX2435374 SRS1870361 SRP095338 PRJNA358049 Transcriptomic Analysis of Adult Zebrafish Inner Ear Hair Cells GSE92559 Transcriptome Analysis To understand the basic biological property of hair cells HCs from lower vertebrates we examined transcriptomes of adult zebrafish HCs. GFP labeled HCs were isolated from the utricle saccule and lagena the three inner ear sensory epithelia of a pou4f3 promoter driven GAP GFP line of transgenic zebrafish. 2 000 HCs and 2 000 non sensory cells from the inner ear were individually collected by suction pipet technique. RNA sequencing was performed and the resulting sequences were mapped analyzed and compared. Comparisons allow us to identify enriched genes in HCs which may underlie HC specialization. Overall design: Examination of transcriptomes of adult zebrafish inner ear hair cells and surrounding cells individually collected and sorted using pou4f3 promoter driven GFP marking hair cells.   pubmed:29406519   GFP+ Hair Cells Biological Replicate 2 Technical 1 GSM2432252   tissue:2 000 Inner ear hair cells|cell type:GFP+ Hair Cells isolated and pooled from the lagena utricle and saccule|age:11 mpf 13 mpf adult|Sex:female|strain:Tgpou4f3:GAP GFPs273t GFP+ Hair Cells Biological Replicate 2 Technical 1 CLC Genomics Workbench software CLC bio Waltham MA USA was used to map the reads to the GRCz10 zebrafish genome and generate gene expression values in the normalized form of reads per kilobase of transcript per million mapped reads RPKM values Genome build: GRCz10 zebrafish genome Supplementary files format and content: Expression data was exported from CLC Genomics Workbench in the form of Microsoft Excel Spreadsheets. 2 000 Inner ear hair cells   Qiagen miRNeasy mini plus kit Clontech Smart Seq   cell type:GFP+ Hair Cells isolated and pooled from the lagena utricle and saccule|age:11 mpf 13 mpf adult|Sex:female|strain:Tgpou4f3:GAP GFPs273t GSM2432252 GSM2432252: GFP+ Hair Cells Biological Replicate 2 Technical 1; Danio rerio; RNA Seq GSM2432252   1 Qiagen miRNeasy mini plus kit Clontech Smart Seq GEO Accession:GSM2432252 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP095338     zhc_AGGCAGAA-_L001_R1_001.fastq.gz fastq 6181180911.0 61199811.0 GSM2432252 r1 0:101 A:1493795643;C:1126661332;G:1135879285;T:1459382790;N:965461861 101       1493795643 1126661332 1135879285 1459382790 965461861 SRX2435374 SRS1870361 SRA505331 GEO Department of Biomedical Sciences, Creighton University 1 0.64372   0.14904   0.78301   0.5671   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2016-12-19 Adult Adult Ear Sensory System
41689 41689 SRR5120130 SRX2435373 SRS1870360 SRP095338 PRJNA358049 Transcriptomic Analysis of Adult Zebrafish Inner Ear Hair Cells GSE92559 Transcriptome Analysis To understand the basic biological property of hair cells HCs from lower vertebrates we examined transcriptomes of adult zebrafish HCs. GFP labeled HCs were isolated from the utricle saccule and lagena the three inner ear sensory epithelia of a pou4f3 promoter driven GAP GFP line of transgenic zebrafish. 2 000 HCs and 2 000 non sensory cells from the inner ear were individually collected by suction pipet technique. RNA sequencing was performed and the resulting sequences were mapped analyzed and compared. Comparisons allow us to identify enriched genes in HCs which may underlie HC specialization. Overall design: Examination of transcriptomes of adult zebrafish inner ear hair cells and surrounding cells individually collected and sorted using pou4f3 promoter driven GFP marking hair cells.   pubmed:29406519   GFP+ Hair Cells Biological Replicate 1 Technical 2 GSM2432251   tissue:2 000 Inner ear hair cells|cell type:GFP+ Hair Cells isolated and pooled from the lagena utricle and saccule|age:11 mpf 13 mpf adult|Sex:female|strain:Tgpou4f3:GAP GFPs273t GFP+ Hair Cells Biological Replicate 1 Technical 2 CLC Genomics Workbench software CLC bio Waltham MA USA was used to map the reads to the GRCz10 zebrafish genome and generate gene expression values in the normalized form of reads per kilobase of transcript per million mapped reads RPKM values Genome build: GRCz10 zebrafish genome Supplementary files format and content: Expression data was exported from CLC Genomics Workbench in the form of Microsoft Excel Spreadsheets. 2 000 Inner ear hair cells   Qiagen miRNeasy mini plus kit Clontech Smart Seq   cell type:GFP+ Hair Cells isolated and pooled from the lagena utricle and saccule|age:11 mpf 13 mpf adult|Sex:female|strain:Tgpou4f3:GAP GFPs273t GSM2432251 GSM2432251: GFP+ Hair Cells Biological Replicate 1 Technical 2; Danio rerio; RNA Seq GSM2432251   1 Qiagen miRNeasy mini plus kit Clontech Smart Seq GEO Accession:GSM2432251 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP095338     fish_TAAGGCGA-_L002_R1_001.fastq.gz fastq 1921914355.0 19028855.0 GSM2432251 r1 0:101 A:477226210;C:364711301;G:374540554;T:470661952;N:234774338 101       477226210 364711301 374540554 470661952 234774338 SRX2435373 SRS1870360 SRA505331 GEO Department of Biomedical Sciences, Creighton University 1 0.68061   0.1576   0.7693   0.59569   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2016-12-19 Adult Adult Ear Sensory System
41690 41690 SRR5120129 SRX2435372 SRS1870359 SRP095338 PRJNA358049 Transcriptomic Analysis of Adult Zebrafish Inner Ear Hair Cells GSE92559 Transcriptome Analysis To understand the basic biological property of hair cells HCs from lower vertebrates we examined transcriptomes of adult zebrafish HCs. GFP labeled HCs were isolated from the utricle saccule and lagena the three inner ear sensory epithelia of a pou4f3 promoter driven GAP GFP line of transgenic zebrafish. 2 000 HCs and 2 000 non sensory cells from the inner ear were individually collected by suction pipet technique. RNA sequencing was performed and the resulting sequences were mapped analyzed and compared. Comparisons allow us to identify enriched genes in HCs which may underlie HC specialization. Overall design: Examination of transcriptomes of adult zebrafish inner ear hair cells and surrounding cells individually collected and sorted using pou4f3 promoter driven GFP marking hair cells.   pubmed:29406519   GFP+ Hair Cells Biological Replicate 1 Technical 1 GSM2432250   tissue:2 000 Inner ear hair cells|cell type:GFP+ Hair Cells isolated and pooled from the lagena utricle and saccule|age:11 mpf 13 mpf adult|Sex:female|strain:Tgpou4f3:GAP GFPs273t GFP+ Hair Cells Biological Replicate 1 Technical 1 CLC Genomics Workbench software CLC bio Waltham MA USA was used to map the reads to the GRCz10 zebrafish genome and generate gene expression values in the normalized form of reads per kilobase of transcript per million mapped reads RPKM values Genome build: GRCz10 zebrafish genome Supplementary files format and content: Expression data was exported from CLC Genomics Workbench in the form of Microsoft Excel Spreadsheets. 2 000 Inner ear hair cells   Qiagen miRNeasy mini plus kit Clontech Smart Seq   cell type:GFP+ Hair Cells isolated and pooled from the lagena utricle and saccule|age:11 mpf 13 mpf adult|Sex:female|strain:Tgpou4f3:GAP GFPs273t GSM2432250 GSM2432250: GFP+ Hair Cells Biological Replicate 1 Technical 1; Danio rerio; RNA Seq GSM2432250   1 Qiagen miRNeasy mini plus kit Clontech Smart Seq GEO Accession:GSM2432250 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP095338     fish_TAAGGCGA-_L001_R1_001.fastq.gz fastq 1946906300.0 19276300.0 GSM2432250 r1 0:101 A:483944927;C:369830453;G:379601203;T:477313685;N:236216032 101       483944927 369830453 379601203 477313685 236216032 SRX2435372 SRS1870359 SRA505331 GEO Department of Biomedical Sciences, Creighton University 1 0.68178   0.1597   0.77019   0.59655   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2016-12-19 Adult Adult Ear Sensory System
42948 42948 SRR5853089 SRX3022436 SRS2371721 SRP113243 PRJNA395227 RNA sequencing of Adult Zebrafish Inner Ear Hair Cells GSE101693 Transcriptome Analysis To understand the basic biological properties of inner ear hair cells HCs from non mammalian vertebrates we examined the transcriptome of adult zebrafish auditory and vestibular HCs. GFP labeled HCs were isolated from inner ear sensory epithelia of a pou4f3 promoter driven GAP GFP line of transgenic zebrafish. One thousand HCs and 1 000 non sensory surrounding cells nsSCs were separately collected for each biological replicate using the suction pipette technique. RNA sequencing of three biological replicates for the two cell types was performed. The resulting sequenced reads were mapped. Comparisons between HCs and nsSCs allow identification of enriched genes in HCs which may underlie HC specialization. Our dataset provides an extensive resource for understanding the molecular mechanisms underlying morphology function and pathology of adult zebrafish HCs. It also establishes a framework for future characterization of the genes expressed in HCs and for the study of HC evolution. Overall design: One thousand HCs and 1 000 nsSCs were separately collected for each biological replicate using the suction pipette technique. RNA sequencing of three biological replicates for the two cell types was performed. The resulting sequenced reads were mapped. Comparisons between HCs and nsSCs allow identification of enriched genes in HCs which may underlie HC specialization.   pubmed:29406519   GFP neg Control surrounding cells 3 GSM2712284   tissue:1 000 Inner ear surrounding cells|cell type:GFP neg cells isolated and pooled from the lagena utricle and saccule|passages:11 mpf 13 mpf adult female zebrafish|strain:Tgpou4f3:GAP GFPs273t GFP neg Control surrounding cells 3 CLC Genomics Workbench software CLC bio Waltham MA USA was used to map the reads to the GRCz10 zebrafish genome and generate gene expression values in the normalized form of reads per kilobase of transcript per million mapped reads RPKM values Genome build: GRCz10 zebrafish genome Supplementary files format and content: Excel file of expression data of hair cells and surrounding control cells using RPKM values 1 000 Inner ear surrounding cells   Qiagen miRNeasy mini plus kit Clontech Smart Seq   cell type:GFP neg cells isolated and pooled from the lagena utricle and saccule|passages:11 mpf 13 mpf adult female zebrafish|strain:Tgpou4f3:GAP GFPs273t GSM2712284 GSM2712284: GFP neg Control surrounding cells 3; Danio rerio; RNA Seq GSM2712284   1 Qiagen miRNeasy mini plus kit Clontech Smart Seq GEO Accession:GSM2712284 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP113243     ZFControl3_S3_L001_R1_001.fastq.gz ZFControl3_S3_L001_R2_001.fastq.gz fastq fastq 4109673117.0 45498619.0 GSM2712284 r1 0:90.33 1:0 A:1180209080;C:857937316;G:867108081;T:1202304007;N:2114633 90 0     1180209080 857937316 867108081 1202304007 2114633 SRX3022436 SRS2371721 SRA589592 GEO Department of Biomedical Sciences, Creighton University 1 0.89781   0.12518   0.74966   0.65157   40   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2017-07-20 Adult Adult Ear Sensory System
42949 42949 SRR5853087 SRX3022435 SRS2371720 SRP113243 PRJNA395227 RNA sequencing of Adult Zebrafish Inner Ear Hair Cells GSE101693 Transcriptome Analysis To understand the basic biological properties of inner ear hair cells HCs from non mammalian vertebrates we examined the transcriptome of adult zebrafish auditory and vestibular HCs. GFP labeled HCs were isolated from inner ear sensory epithelia of a pou4f3 promoter driven GAP GFP line of transgenic zebrafish. One thousand HCs and 1 000 non sensory surrounding cells nsSCs were separately collected for each biological replicate using the suction pipette technique. RNA sequencing of three biological replicates for the two cell types was performed. The resulting sequenced reads were mapped. Comparisons between HCs and nsSCs allow identification of enriched genes in HCs which may underlie HC specialization. Our dataset provides an extensive resource for understanding the molecular mechanisms underlying morphology function and pathology of adult zebrafish HCs. It also establishes a framework for future characterization of the genes expressed in HCs and for the study of HC evolution. Overall design: One thousand HCs and 1 000 nsSCs were separately collected for each biological replicate using the suction pipette technique. RNA sequencing of three biological replicates for the two cell types was performed. The resulting sequenced reads were mapped. Comparisons between HCs and nsSCs allow identification of enriched genes in HCs which may underlie HC specialization.   pubmed:29406519   GFP neg Control surrounding cells 2 GSM2712283   tissue:1 000 Inner ear surrounding cells|cell type:GFP neg cells isolated and pooled from the lagena utricle and saccule|passages:11 mpf 13 mpf adult female zebrafish|strain:Tgpou4f3:GAP GFPs273t GFP neg Control surrounding cells 2 CLC Genomics Workbench software CLC bio Waltham MA USA was used to map the reads to the GRCz10 zebrafish genome and generate gene expression values in the normalized form of reads per kilobase of transcript per million mapped reads RPKM values Genome build: GRCz10 zebrafish genome Supplementary files format and content: Excel file of expression data of hair cells and surrounding control cells using RPKM values 1 000 Inner ear surrounding cells   Qiagen miRNeasy mini plus kit Clontech Smart Seq   cell type:GFP neg cells isolated and pooled from the lagena utricle and saccule|passages:11 mpf 13 mpf adult female zebrafish|strain:Tgpou4f3:GAP GFPs273t GSM2712283 GSM2712283: GFP neg Control surrounding cells 2; Danio rerio; RNA Seq GSM2712283   1 Qiagen miRNeasy mini plus kit Clontech Smart Seq GEO Accession:GSM2712283 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP113243     ZFControl2_S2_L001_R1_001.fastq.gz ZFControl2_S2_L001_R2_001.fastq.gz fastq fastq 5277482903.0 59741039.0 GSM2712283 r1 0:88.34 1:0 A:1487835111;C:1133268730;G:1145158631;T:1508220719;N:2999712 88 0     1487835111 1133268730 1145158631 1508220719 2999712 SRX3022435 SRS2371720 SRA589592 GEO Department of Biomedical Sciences, Creighton University 1 0.89608   0.11913   0.74452   0.64488   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2017-07-20 Adult Adult Ear Sensory System
42950 42950 SRR5853085 SRX3022434 SRS2371718 SRP113243 PRJNA395227 RNA sequencing of Adult Zebrafish Inner Ear Hair Cells GSE101693 Transcriptome Analysis To understand the basic biological properties of inner ear hair cells HCs from non mammalian vertebrates we examined the transcriptome of adult zebrafish auditory and vestibular HCs. GFP labeled HCs were isolated from inner ear sensory epithelia of a pou4f3 promoter driven GAP GFP line of transgenic zebrafish. One thousand HCs and 1 000 non sensory surrounding cells nsSCs were separately collected for each biological replicate using the suction pipette technique. RNA sequencing of three biological replicates for the two cell types was performed. The resulting sequenced reads were mapped. Comparisons between HCs and nsSCs allow identification of enriched genes in HCs which may underlie HC specialization. Our dataset provides an extensive resource for understanding the molecular mechanisms underlying morphology function and pathology of adult zebrafish HCs. It also establishes a framework for future characterization of the genes expressed in HCs and for the study of HC evolution. Overall design: One thousand HCs and 1 000 nsSCs were separately collected for each biological replicate using the suction pipette technique. RNA sequencing of three biological replicates for the two cell types was performed. The resulting sequenced reads were mapped. Comparisons between HCs and nsSCs allow identification of enriched genes in HCs which may underlie HC specialization.   pubmed:29406519   GFP neg Control surrounding cells 1 GSM2712282   tissue:1 000 Inner ear surrounding cells|cell type:GFP neg cells isolated and pooled from the lagena utricle and saccule|passages:11 mpf 13 mpf adult female zebrafish|strain:Tgpou4f3:GAP GFPs273t GFP neg Control surrounding cells 1 CLC Genomics Workbench software CLC bio Waltham MA USA was used to map the reads to the GRCz10 zebrafish genome and generate gene expression values in the normalized form of reads per kilobase of transcript per million mapped reads RPKM values Genome build: GRCz10 zebrafish genome Supplementary files format and content: Excel file of expression data of hair cells and surrounding control cells using RPKM values 1 000 Inner ear surrounding cells   Qiagen miRNeasy mini plus kit Clontech Smart Seq   cell type:GFP neg cells isolated and pooled from the lagena utricle and saccule|passages:11 mpf 13 mpf adult female zebrafish|strain:Tgpou4f3:GAP GFPs273t GSM2712282 GSM2712282: GFP neg Control surrounding cells 1; Danio rerio; RNA Seq GSM2712282   1 Qiagen miRNeasy mini plus kit Clontech Smart Seq GEO Accession:GSM2712282 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP113243     ZFControl1_S1_L001_R1_001.fastq.gz ZFControl1_S1_L001_R2_001.fastq.gz fastq fastq 4884084264.0 54844980.0 GSM2712282 r1 0:89.05 1:0 A:1416754694;C:1002154600;G:1012874728;T:1449240729;N:3059513 89 0     1416754694 1002154600 1012874728 1449240729 3059513 SRX3022434 SRS2371718 SRA589592 GEO Department of Biomedical Sciences, Creighton University 1 0.89495   0.12873   0.74961   0.65345   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2017-07-20 Adult Adult Ear Sensory System
42951 42951 SRR5853084 SRX3022433 SRS2371719 SRP113243 PRJNA395227 RNA sequencing of Adult Zebrafish Inner Ear Hair Cells GSE101693 Transcriptome Analysis To understand the basic biological properties of inner ear hair cells HCs from non mammalian vertebrates we examined the transcriptome of adult zebrafish auditory and vestibular HCs. GFP labeled HCs were isolated from inner ear sensory epithelia of a pou4f3 promoter driven GAP GFP line of transgenic zebrafish. One thousand HCs and 1 000 non sensory surrounding cells nsSCs were separately collected for each biological replicate using the suction pipette technique. RNA sequencing of three biological replicates for the two cell types was performed. The resulting sequenced reads were mapped. Comparisons between HCs and nsSCs allow identification of enriched genes in HCs which may underlie HC specialization. Our dataset provides an extensive resource for understanding the molecular mechanisms underlying morphology function and pathology of adult zebrafish HCs. It also establishes a framework for future characterization of the genes expressed in HCs and for the study of HC evolution. Overall design: One thousand HCs and 1 000 nsSCs were separately collected for each biological replicate using the suction pipette technique. RNA sequencing of three biological replicates for the two cell types was performed. The resulting sequenced reads were mapped. Comparisons between HCs and nsSCs allow identification of enriched genes in HCs which may underlie HC specialization.   pubmed:29406519   GFP+ Zebrafish Hair Cells Biological Replicate 3 GSM2712281   tissue:1 000 Inner ear hair cells|cell type:GFP+ Hair Cells isolated and pooled from the lagena utricle and saccule|passages:11 mpf 13 mpf adult female zebrafish|strain:Tgpou4f3:GAP GFPs273t GFP+ Zebrafish Hair Cells Biological Replicate 3 CLC Genomics Workbench software CLC bio Waltham MA USA was used to map the reads to the GRCz10 zebrafish genome and generate gene expression values in the normalized form of reads per kilobase of transcript per million mapped reads RPKM values Genome build: GRCz10 zebrafish genome Supplementary files format and content: Excel file of expression data of hair cells and surrounding control cells using RPKM values 1 000 Inner ear hair cells   Qiagen miRNeasy mini plus kit Clontech Smart Seq   cell type:GFP+ Hair Cells isolated and pooled from the lagena utricle and saccule|passages:11 mpf 13 mpf adult female zebrafish|strain:Tgpou4f3:GAP GFPs273t GSM2712281 GSM2712281: GFP+ Zebrafish Hair Cells Biological Replicate 3; Danio rerio; RNA Seq GSM2712281   1 Qiagen miRNeasy mini plus kit Clontech Smart Seq GEO Accession:GSM2712281 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP113243     ZFgfp+3_S6_L001_R2_001.fastq.gz ZFgfp+3_S6_L001_R1_001.fastq.gz fastq fastq 4519238829.0 50912071.0 GSM2712281 r1 0:88.77 1:0 A:1293161930;C:955006076;G:967428880;T:1300944329;N:2697614 88 0     1293161930 955006076 967428880 1300944329 2697614 SRX3022433 SRS2371719 SRA589592 GEO Department of Biomedical Sciences, Creighton University 1 0.92939   0.14631   0.75485   0.53515   98   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2017-07-20 Adult Adult Ear Sensory System
42952 42952 SRR5853083 SRX3022432 SRS2371717 SRP113243 PRJNA395227 RNA sequencing of Adult Zebrafish Inner Ear Hair Cells GSE101693 Transcriptome Analysis To understand the basic biological properties of inner ear hair cells HCs from non mammalian vertebrates we examined the transcriptome of adult zebrafish auditory and vestibular HCs. GFP labeled HCs were isolated from inner ear sensory epithelia of a pou4f3 promoter driven GAP GFP line of transgenic zebrafish. One thousand HCs and 1 000 non sensory surrounding cells nsSCs were separately collected for each biological replicate using the suction pipette technique. RNA sequencing of three biological replicates for the two cell types was performed. The resulting sequenced reads were mapped. Comparisons between HCs and nsSCs allow identification of enriched genes in HCs which may underlie HC specialization. Our dataset provides an extensive resource for understanding the molecular mechanisms underlying morphology function and pathology of adult zebrafish HCs. It also establishes a framework for future characterization of the genes expressed in HCs and for the study of HC evolution. Overall design: One thousand HCs and 1 000 nsSCs were separately collected for each biological replicate using the suction pipette technique. RNA sequencing of three biological replicates for the two cell types was performed. The resulting sequenced reads were mapped. Comparisons between HCs and nsSCs allow identification of enriched genes in HCs which may underlie HC specialization.   pubmed:29406519   GFP+ Zebrafish Hair Cells Biological Replicate 2 GSM2712280   tissue:1 000 Inner ear hair cells|cell type:GFP+ Hair Cells isolated and pooled from the lagena utricle and saccule|passages:11 mpf 13 mpf adult female zebrafish|strain:Tgpou4f3:GAP GFPs273t GFP+ Zebrafish Hair Cells Biological Replicate 2 CLC Genomics Workbench software CLC bio Waltham MA USA was used to map the reads to the GRCz10 zebrafish genome and generate gene expression values in the normalized form of reads per kilobase of transcript per million mapped reads RPKM values Genome build: GRCz10 zebrafish genome Supplementary files format and content: Excel file of expression data of hair cells and surrounding control cells using RPKM values 1 000 Inner ear hair cells   Qiagen miRNeasy mini plus kit Clontech Smart Seq   cell type:GFP+ Hair Cells isolated and pooled from the lagena utricle and saccule|passages:11 mpf 13 mpf adult female zebrafish|strain:Tgpou4f3:GAP GFPs273t GSM2712280 GSM2712280: GFP+ Zebrafish Hair Cells Biological Replicate 2; Danio rerio; RNA Seq GSM2712280   1 Qiagen miRNeasy mini plus kit Clontech Smart Seq GEO Accession:GSM2712280 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP113243     ZFgfp+2_S5_L001_R1_001.fastq.gz ZFgfp+2_S5_L001_R2_001.fastq.gz fastq fastq 9048065761.0 100567605.0 GSM2712280 r1 0:89.97 1:0 A:2534571144;C:1972906517;G:2001215942;T:2534611481;N:4760677 89 0     2534571144 1972906517 2001215942 2534611481 4760677 SRX3022432 SRS2371717 SRA589592 GEO Department of Biomedical Sciences, Creighton University 1 0.93842   0.12913   0.75402   0.53067   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2017-07-20 Adult Adult Ear Sensory System
42953 42953 SRR5853082 SRX3022431 SRS2371716 SRP113243 PRJNA395227 RNA sequencing of Adult Zebrafish Inner Ear Hair Cells GSE101693 Transcriptome Analysis To understand the basic biological properties of inner ear hair cells HCs from non mammalian vertebrates we examined the transcriptome of adult zebrafish auditory and vestibular HCs. GFP labeled HCs were isolated from inner ear sensory epithelia of a pou4f3 promoter driven GAP GFP line of transgenic zebrafish. One thousand HCs and 1 000 non sensory surrounding cells nsSCs were separately collected for each biological replicate using the suction pipette technique. RNA sequencing of three biological replicates for the two cell types was performed. The resulting sequenced reads were mapped. Comparisons between HCs and nsSCs allow identification of enriched genes in HCs which may underlie HC specialization. Our dataset provides an extensive resource for understanding the molecular mechanisms underlying morphology function and pathology of adult zebrafish HCs. It also establishes a framework for future characterization of the genes expressed in HCs and for the study of HC evolution. Overall design: One thousand HCs and 1 000 nsSCs were separately collected for each biological replicate using the suction pipette technique. RNA sequencing of three biological replicates for the two cell types was performed. The resulting sequenced reads were mapped. Comparisons between HCs and nsSCs allow identification of enriched genes in HCs which may underlie HC specialization.   pubmed:29406519   GFP+ Zebrafish Hair Cells Biological Replicate 1 GSM2712279   tissue:1 000 Inner ear hair cells|cell type:GFP+ Hair Cells isolated and pooled from the lagena utricle and saccule|passages:11 mpf 13 mpf adult female zebrafish|strain:Tgpou4f3:GAP GFPs273t GFP+ Zebrafish Hair Cells Biological Replicate 1 CLC Genomics Workbench software CLC bio Waltham MA USA was used to map the reads to the GRCz10 zebrafish genome and generate gene expression values in the normalized form of reads per kilobase of transcript per million mapped reads RPKM values Genome build: GRCz10 zebrafish genome Supplementary files format and content: Excel file of expression data of hair cells and surrounding control cells using RPKM values 1 000 Inner ear hair cells   Qiagen miRNeasy mini plus kit Clontech Smart Seq   cell type:GFP+ Hair Cells isolated and pooled from the lagena utricle and saccule|passages:11 mpf 13 mpf adult female zebrafish|strain:Tgpou4f3:GAP GFPs273t GSM2712279 GSM2712279: GFP+ Zebrafish Hair Cells Biological Replicate 1; Danio rerio; RNA Seq GSM2712279   1 Qiagen miRNeasy mini plus kit Clontech Smart Seq GEO Accession:GSM2712279 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP113243     ZFgfp+1_S4_L001_R1_001.fastq.gz ZFgfp+1_S4_L001_R2_001.fastq.gz fastq fastq 1315401262.0 14413064.0 GSM2712279 r1 0:91.26 1:0 A:370914131;C:284206703;G:289196987;T:370556334;N:527107 91 0     370914131 284206703 289196987 370556334 527107 SRX3022431 SRS2371716 SRA589592 GEO Department of Biomedical Sciences, Creighton University 1 0.93705   0.13551   0.75471   0.53888   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2017-07-20 Adult Adult Ear Sensory System
67897 67897 SRR17413278 SRX13584925 SRS11474973 SRP353328 PRJNA793867 A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish GSE192947 Other Using adult zebrafish inner ears as a model for sensorineural regeneration we performed a targeted ablation of the mechanosensory receptors in the saccule and utricle and characterized the single cell epigenome and transcriptome at consecutive time points following hair cell death. Overall design: To elucidate the transcriptional regulatory network that controls tissue regeneration we characterized the gene expression profiles scRNA seq and the map of accessible regions scATAC seq associated with the response to hair cell ablation in adult zebrafish sensory epithelia. We dissected out saccules and utricles at three time points: Days 4 5 and 7 post DT and each were processed separately in both scRNA seq and scATAC seq experiments. Untreated Tgmyo6b:DTR transgenic zebrafish and wild type DT injected and untreated zebrafish lacking the Tgmyo6b:DTR transgene were used as non regenerating controls. Cell suspensions of isolated sensory epithelia were subjected to single cell sequencing for both their transcriptome and open chromatin regions using 10X Genomics Chromium Single Cell Gene Expression and Single Cell ATAC Sequencing. We also include biological triplicates of untreated wild type saccules and utricles for bulk ATAC seq.   pubmed:36212030   Day7 DTR Saccule scRNAseq GSM5769451   tissue:Regenerating adult zebrafish saccule|strain:myo6b:hDTR|embryo age:6 mpf 10 mpf adult zebrafish|treatment:0.05 ng/ul Diphtheria Toxin Day7 DTR Saccule scRNAseq Binary Base Call BCL files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics. Cell Ranger Version 3.0.2 10x Genomics was used to demultiplex for barcode processing for single cell gene counts for single cell accessibility counts and aggregating files. For bulk ATAC seq libraries were sequenced on an Illumina HiSeq 2500 platform and run as indexed 50 base single end reads. Bulk ATAC seq reads were aligned to reference zebrafish genome danRer11 using bowtie2. Peaks were called by MACS2 from individual replicate. Genome build: danRer11 Supplementary files format and content: scRNA seq and scATAC seq outputs were generated using the 10x Cell Ranger pipeline. scRNA seq H5 filtered feature bc matrix files contain the UMI counts for each cell. scATAC seq processed data files include three file formats per sample: CSV TBI and H5. CSV singlecell.csv files contain per barcode QC information associated with the fragments per barcode ATAC signal per barcode and cell calling information. TBI Fragments.tsv.gz.tbi files are tabix index of the fragment intervals. H5 filtered peak bc matrix.h5 files contain only detected cellular barcodes. For bulk ATAC seq narrowPeak files contain MACS2 called peaks in BED format. Regenerating adult zebrafish saccule   For single cell experiments non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics. For scATAC seq libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111 10X Genomics. For bulk ATAC seq libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.   strain:myo6b:hDTR|embryo age:6 mpf 10 mpf adult zebrafish|treatment:0.05 ng/ul Diphtheria Toxin GSM5769451 GSM5769451: Day7 DTR Saccule scRNAseq; Danio rerio; RNA Seq GSM5769451 r1 GSM5769451 1 For single cell experiments non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics. For scATAC seq libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111 10X Genomics. For bulk ATAC seq libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP353328   assembly:danRer11|intentional duplicate Day7_DTR_S.bam 10X Genomics bam file 2977382681.0 32718491.0 GSM5769451 r1 0:91 A:897353356;C:606781567;G:635522033;T:834175973;N:3549752 91       897353356 606781567 635522033 834175973 3549752 SRX13584925 SRS11474973 SRA1351664 Shawn Burgess, NHGRI, NIH Shawn Burgess, NHGRI, NIH 1 0.90368   0.24681   0.80545   0.63964   91   B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_droplet 10x   United States 2022-01-03 Adult Adult Ear Sensory System
67899 67899 SRR17413280 SRX13584923 SRS11474971 SRP353328 PRJNA793867 A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish GSE192947 Other Using adult zebrafish inner ears as a model for sensorineural regeneration we performed a targeted ablation of the mechanosensory receptors in the saccule and utricle and characterized the single cell epigenome and transcriptome at consecutive time points following hair cell death. Overall design: To elucidate the transcriptional regulatory network that controls tissue regeneration we characterized the gene expression profiles scRNA seq and the map of accessible regions scATAC seq associated with the response to hair cell ablation in adult zebrafish sensory epithelia. We dissected out saccules and utricles at three time points: Days 4 5 and 7 post DT and each were processed separately in both scRNA seq and scATAC seq experiments. Untreated Tgmyo6b:DTR transgenic zebrafish and wild type DT injected and untreated zebrafish lacking the Tgmyo6b:DTR transgene were used as non regenerating controls. Cell suspensions of isolated sensory epithelia were subjected to single cell sequencing for both their transcriptome and open chromatin regions using 10X Genomics Chromium Single Cell Gene Expression and Single Cell ATAC Sequencing. We also include biological triplicates of untreated wild type saccules and utricles for bulk ATAC seq.   pubmed:36212030   Day5 DTR Saccule scRNAseq GSM5769449   tissue:Regenerating adult zebrafish saccule|strain:myo6b:hDTR|embryo age:6 mpf 10 mpf adult zebrafish|treatment:0.05 ng/ul Diphtheria Toxin Day5 DTR Saccule scRNAseq Binary Base Call BCL files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics. Cell Ranger Version 3.0.2 10x Genomics was used to demultiplex for barcode processing for single cell gene counts for single cell accessibility counts and aggregating files. For bulk ATAC seq libraries were sequenced on an Illumina HiSeq 2500 platform and run as indexed 50 base single end reads. Bulk ATAC seq reads were aligned to reference zebrafish genome danRer11 using bowtie2. Peaks were called by MACS2 from individual replicate. Genome build: danRer11 Supplementary files format and content: scRNA seq and scATAC seq outputs were generated using the 10x Cell Ranger pipeline. scRNA seq H5 filtered feature bc matrix files contain the UMI counts for each cell. scATAC seq processed data files include three file formats per sample: CSV TBI and H5. CSV singlecell.csv files contain per barcode QC information associated with the fragments per barcode ATAC signal per barcode and cell calling information. TBI Fragments.tsv.gz.tbi files are tabix index of the fragment intervals. H5 filtered peak bc matrix.h5 files contain only detected cellular barcodes. For bulk ATAC seq narrowPeak files contain MACS2 called peaks in BED format. Regenerating adult zebrafish saccule   For single cell experiments non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics. For scATAC seq libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111 10X Genomics. For bulk ATAC seq libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.   strain:myo6b:hDTR|embryo age:6 mpf 10 mpf adult zebrafish|treatment:0.05 ng/ul Diphtheria Toxin GSM5769449 GSM5769449: Day5 DTR Saccule scRNAseq; Danio rerio; RNA Seq GSM5769449 r1 GSM5769449 1 For single cell experiments non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics. For scATAC seq libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111 10X Genomics. For bulk ATAC seq libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP353328   assembly:danRer11|intentional duplicate Day5_DTR_S.bam 10X Genomics bam file 2743635167.0 30149837.0 GSM5769449 r1 0:91 A:824173714;C:546471747;G:619313829;T:750434697;N:3241180 91       824173714 546471747 619313829 750434697 3241180 SRX13584923 SRS11474971 SRA1351664 Shawn Burgess, NHGRI, NIH Shawn Burgess, NHGRI, NIH 1 0.89351   0.24046   0.79547   0.55401   91   B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_droplet 10x   United States 2022-01-03 Adult Adult Ear Sensory System
67901 67901 SRR17413282 SRX13584921 SRS11474969 SRP353328 PRJNA793867 A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish GSE192947 Other Using adult zebrafish inner ears as a model for sensorineural regeneration we performed a targeted ablation of the mechanosensory receptors in the saccule and utricle and characterized the single cell epigenome and transcriptome at consecutive time points following hair cell death. Overall design: To elucidate the transcriptional regulatory network that controls tissue regeneration we characterized the gene expression profiles scRNA seq and the map of accessible regions scATAC seq associated with the response to hair cell ablation in adult zebrafish sensory epithelia. We dissected out saccules and utricles at three time points: Days 4 5 and 7 post DT and each were processed separately in both scRNA seq and scATAC seq experiments. Untreated Tgmyo6b:DTR transgenic zebrafish and wild type DT injected and untreated zebrafish lacking the Tgmyo6b:DTR transgene were used as non regenerating controls. Cell suspensions of isolated sensory epithelia were subjected to single cell sequencing for both their transcriptome and open chromatin regions using 10X Genomics Chromium Single Cell Gene Expression and Single Cell ATAC Sequencing. We also include biological triplicates of untreated wild type saccules and utricles for bulk ATAC seq.   pubmed:36212030   Day4 DTR Saccule scRNAseq GSM5769447   tissue:Regenerating adult zebrafish saccule|strain:myo6b:hDTR|embryo age:6 mpf 10 mpf adult zebrafish|treatment:0.05 ng/ul Diphtheria Toxin Day4 DTR Saccule scRNAseq Binary Base Call BCL files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics. Cell Ranger Version 3.0.2 10x Genomics was used to demultiplex for barcode processing for single cell gene counts for single cell accessibility counts and aggregating files. For bulk ATAC seq libraries were sequenced on an Illumina HiSeq 2500 platform and run as indexed 50 base single end reads. Bulk ATAC seq reads were aligned to reference zebrafish genome danRer11 using bowtie2. Peaks were called by MACS2 from individual replicate. Genome build: danRer11 Supplementary files format and content: scRNA seq and scATAC seq outputs were generated using the 10x Cell Ranger pipeline. scRNA seq H5 filtered feature bc matrix files contain the UMI counts for each cell. scATAC seq processed data files include three file formats per sample: CSV TBI and H5. CSV singlecell.csv files contain per barcode QC information associated with the fragments per barcode ATAC signal per barcode and cell calling information. TBI Fragments.tsv.gz.tbi files are tabix index of the fragment intervals. H5 filtered peak bc matrix.h5 files contain only detected cellular barcodes. For bulk ATAC seq narrowPeak files contain MACS2 called peaks in BED format. Regenerating adult zebrafish saccule   For single cell experiments non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics. For scATAC seq libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111 10X Genomics. For bulk ATAC seq libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.   strain:myo6b:hDTR|embryo age:6 mpf 10 mpf adult zebrafish|treatment:0.05 ng/ul Diphtheria Toxin GSM5769447 GSM5769447: Day4 DTR Saccule scRNAseq; Danio rerio; RNA Seq GSM5769447 r1 GSM5769447 1 For single cell experiments non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics. For scATAC seq libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111 10X Genomics. For bulk ATAC seq libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP353328   assembly:danRer11|intentional duplicate Day4_DTR_S.bam 10X Genomics bam file 2212530229.0 24313519.0 GSM5769447 r1 0:91 A:662453123;C:446920712;G:485929921;T:614604891;N:2621582 91       662453123 446920712 485929921 614604891 2621582 SRX13584921 SRS11474969 SRA1351664 Shawn Burgess, NHGRI, NIH Shawn Burgess, NHGRI, NIH 1 0.90066   0.25447   0.80255   0.6844   91   B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_droplet 10x   United States 2022-01-03 Adult Adult Ear Sensory System
67903 67903 SRR17413284 SRX13584919 SRS11474967 SRP353328 PRJNA793867 A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish GSE192947 Other Using adult zebrafish inner ears as a model for sensorineural regeneration we performed a targeted ablation of the mechanosensory receptors in the saccule and utricle and characterized the single cell epigenome and transcriptome at consecutive time points following hair cell death. Overall design: To elucidate the transcriptional regulatory network that controls tissue regeneration we characterized the gene expression profiles scRNA seq and the map of accessible regions scATAC seq associated with the response to hair cell ablation in adult zebrafish sensory epithelia. We dissected out saccules and utricles at three time points: Days 4 5 and 7 post DT and each were processed separately in both scRNA seq and scATAC seq experiments. Untreated Tgmyo6b:DTR transgenic zebrafish and wild type DT injected and untreated zebrafish lacking the Tgmyo6b:DTR transgene were used as non regenerating controls. Cell suspensions of isolated sensory epithelia were subjected to single cell sequencing for both their transcriptome and open chromatin regions using 10X Genomics Chromium Single Cell Gene Expression and Single Cell ATAC Sequencing. We also include biological triplicates of untreated wild type saccules and utricles for bulk ATAC seq.   pubmed:36212030   Untreated DTR Saccule scRNAseq GSM5769445   tissue:Untreated DTR saccule|strain:myo6b:hDTR|embryo age:6 mpf 10 mpf adult zebrafish|treatment:N1 Untreated DTR Saccule scRNAseq Binary Base Call BCL files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics. Cell Ranger Version 3.0.2 10x Genomics was used to demultiplex for barcode processing for single cell gene counts for single cell accessibility counts and aggregating files. For bulk ATAC seq libraries were sequenced on an Illumina HiSeq 2500 platform and run as indexed 50 base single end reads. Bulk ATAC seq reads were aligned to reference zebrafish genome danRer11 using bowtie2. Peaks were called by MACS2 from individual replicate. Genome build: danRer11 Supplementary files format and content: scRNA seq and scATAC seq outputs were generated using the 10x Cell Ranger pipeline. scRNA seq H5 filtered feature bc matrix files contain the UMI counts for each cell. scATAC seq processed data files include three file formats per sample: CSV TBI and H5. CSV singlecell.csv files contain per barcode QC information associated with the fragments per barcode ATAC signal per barcode and cell calling information. TBI Fragments.tsv.gz.tbi files are tabix index of the fragment intervals. H5 filtered peak bc matrix.h5 files contain only detected cellular barcodes. For bulk ATAC seq narrowPeak files contain MACS2 called peaks in BED format. Untreated DTR saccule   For single cell experiments non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics. For scATAC seq libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111 10X Genomics. For bulk ATAC seq libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.   strain:myo6b:hDTR|embryo age:6 mpf 10 mpf adult zebrafish|treatment:N1 GSM5769445 GSM5769445: Untreated DTR Saccule scRNAseq; Danio rerio; RNA Seq GSM5769445 r1 GSM5769445 1 For single cell experiments non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics. For scATAC seq libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111 10X Genomics. For bulk ATAC seq libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP353328   assembly:danRer11|intentional duplicate DTR_S.bam 10X Genomics bam file 2688090860.0 29539460.0 GSM5769445 r1 0:91 A:809804738;C:543094593;G:588432755;T:743564790;N:3193984 91       809804738 543094593 588432755 743564790 3193984 SRX13584919 SRS11474967 SRA1351664 Shawn Burgess, NHGRI, NIH Shawn Burgess, NHGRI, NIH 1 0.91096   0.22811   0.82672   0.70832   91   B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_droplet 10x   United States 2022-01-03 Adult Adult Ear Sensory System
67905 67905 SRR17413286 SRX13584917 SRS11474965 SRP353328 PRJNA793867 A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish GSE192947 Other Using adult zebrafish inner ears as a model for sensorineural regeneration we performed a targeted ablation of the mechanosensory receptors in the saccule and utricle and characterized the single cell epigenome and transcriptome at consecutive time points following hair cell death. Overall design: To elucidate the transcriptional regulatory network that controls tissue regeneration we characterized the gene expression profiles scRNA seq and the map of accessible regions scATAC seq associated with the response to hair cell ablation in adult zebrafish sensory epithelia. We dissected out saccules and utricles at three time points: Days 4 5 and 7 post DT and each were processed separately in both scRNA seq and scATAC seq experiments. Untreated Tgmyo6b:DTR transgenic zebrafish and wild type DT injected and untreated zebrafish lacking the Tgmyo6b:DTR transgene were used as non regenerating controls. Cell suspensions of isolated sensory epithelia were subjected to single cell sequencing for both their transcriptome and open chromatin regions using 10X Genomics Chromium Single Cell Gene Expression and Single Cell ATAC Sequencing. We also include biological triplicates of untreated wild type saccules and utricles for bulk ATAC seq.   pubmed:36212030   Day4 WT Saccule scRNAseq GSM5769443   tissue:Day 4 post DT wild type saccule|strain:TAB 5|embryo age:6 mpf 10 mpf adult zebrafish|treatment:0.05 ng/ul Diphtheria Toxin Day4 WT Saccule scRNAseq Binary Base Call BCL files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics. Cell Ranger Version 3.0.2 10x Genomics was used to demultiplex for barcode processing for single cell gene counts for single cell accessibility counts and aggregating files. For bulk ATAC seq libraries were sequenced on an Illumina HiSeq 2500 platform and run as indexed 50 base single end reads. Bulk ATAC seq reads were aligned to reference zebrafish genome danRer11 using bowtie2. Peaks were called by MACS2 from individual replicate. Genome build: danRer11 Supplementary files format and content: scRNA seq and scATAC seq outputs were generated using the 10x Cell Ranger pipeline. scRNA seq H5 filtered feature bc matrix files contain the UMI counts for each cell. scATAC seq processed data files include three file formats per sample: CSV TBI and H5. CSV singlecell.csv files contain per barcode QC information associated with the fragments per barcode ATAC signal per barcode and cell calling information. TBI Fragments.tsv.gz.tbi files are tabix index of the fragment intervals. H5 filtered peak bc matrix.h5 files contain only detected cellular barcodes. For bulk ATAC seq narrowPeak files contain MACS2 called peaks in BED format. Day 4 post DT wild type saccule   For single cell experiments non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics. For scATAC seq libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111 10X Genomics. For bulk ATAC seq libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.   strain:TAB 5|embryo age:6 mpf 10 mpf adult zebrafish|treatment:0.05 ng/ul Diphtheria Toxin GSM5769443 GSM5769443: Day4 WT Saccule scRNAseq; Danio rerio; RNA Seq GSM5769443 r1 GSM5769443 1 For single cell experiments non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics. For scATAC seq libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111 10X Genomics. For bulk ATAC seq libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP353328   assembly:danRer11|intentional duplicate Day4_WT_S.bam 10X Genomics bam file 2443716548.0 26854028.0 GSM5769443 r1 0:91 A:723842022;C:489011349;G:542403323;T:685572222;N:2887632 91       723842022 489011349 542403323 685572222 2887632 SRX13584917 SRS11474965 SRA1351664 Shawn Burgess, NHGRI, NIH Shawn Burgess, NHGRI, NIH 1 0.90861   0.21636   0.82193   0.70068   91   B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_droplet 10x   United States 2022-01-03 Adult Adult Ear Sensory System
67907 67907 SRR17413288 SRX13584915 SRS11474963 SRP353328 PRJNA793867 A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish GSE192947 Other Using adult zebrafish inner ears as a model for sensorineural regeneration we performed a targeted ablation of the mechanosensory receptors in the saccule and utricle and characterized the single cell epigenome and transcriptome at consecutive time points following hair cell death. Overall design: To elucidate the transcriptional regulatory network that controls tissue regeneration we characterized the gene expression profiles scRNA seq and the map of accessible regions scATAC seq associated with the response to hair cell ablation in adult zebrafish sensory epithelia. We dissected out saccules and utricles at three time points: Days 4 5 and 7 post DT and each were processed separately in both scRNA seq and scATAC seq experiments. Untreated Tgmyo6b:DTR transgenic zebrafish and wild type DT injected and untreated zebrafish lacking the Tgmyo6b:DTR transgene were used as non regenerating controls. Cell suspensions of isolated sensory epithelia were subjected to single cell sequencing for both their transcriptome and open chromatin regions using 10X Genomics Chromium Single Cell Gene Expression and Single Cell ATAC Sequencing. We also include biological triplicates of untreated wild type saccules and utricles for bulk ATAC seq.   pubmed:36212030   Untreated WT Saccule scRNAseq GSM5769441   tissue:Untreated wild type saccule|strain:TAB 5|embryo age:6 mpf 10 mpf adult zebrafish|treatment:N1 Untreated WT Saccule scRNAseq Binary Base Call BCL files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics. Cell Ranger Version 3.0.2 10x Genomics was used to demultiplex for barcode processing for single cell gene counts for single cell accessibility counts and aggregating files. For bulk ATAC seq libraries were sequenced on an Illumina HiSeq 2500 platform and run as indexed 50 base single end reads. Bulk ATAC seq reads were aligned to reference zebrafish genome danRer11 using bowtie2. Peaks were called by MACS2 from individual replicate. Genome build: danRer11 Supplementary files format and content: scRNA seq and scATAC seq outputs were generated using the 10x Cell Ranger pipeline. scRNA seq H5 filtered feature bc matrix files contain the UMI counts for each cell. scATAC seq processed data files include three file formats per sample: CSV TBI and H5. CSV singlecell.csv files contain per barcode QC information associated with the fragments per barcode ATAC signal per barcode and cell calling information. TBI Fragments.tsv.gz.tbi files are tabix index of the fragment intervals. H5 filtered peak bc matrix.h5 files contain only detected cellular barcodes. For bulk ATAC seq narrowPeak files contain MACS2 called peaks in BED format. Untreated wild type saccule   For single cell experiments non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics. For scATAC seq libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111 10X Genomics. For bulk ATAC seq libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.   strain:TAB 5|embryo age:6 mpf 10 mpf adult zebrafish|treatment:N1 GSM5769441 GSM5769441: Untreated WT Saccule scRNAseq; Danio rerio; RNA Seq GSM5769441 r1 GSM5769441 1 For single cell experiments non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics. For scATAC seq libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111 10X Genomics. For bulk ATAC seq libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP353328   assembly:danRer11|intentional duplicate WT_S.bam 10X Genomics bam file 2371392114.0 26059254.0 GSM5769441 r1 0:91 A:717065741;C:489303110;G:485561048;T:676653943;N:2808272 91       717065741 489303110 485561048 676653943 2808272 SRX13584915 SRS11474963 SRA1351664 Shawn Burgess, NHGRI, NIH Shawn Burgess, NHGRI, NIH 1 0.92038   0.23016   0.82771   0.61794   91   B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_droplet 10x   United States 2022-01-03 Adult Adult Ear Sensory System

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