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6 rows where experiment.library_layout = "SINGLE", experiment.platform = "ILLUMINA" and tissue_curation = "Ear"

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tissue_curation_coarse 1

tissue_curation 1

technology 1

experiment.platform 1

  • ILLUMINA · 6 ✖

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

experiment.library_layout 1

  • SINGLE · 6 ✖

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

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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");;