metadata: run_metadata: 12 rows where technology = "smartseq", tissue_curation = "Ear" and tissue_curation

12 rows where technology = "smartseq", tissue_curation = "Ear" and tissue_curation_coarse = "Sensory System"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	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.study_ref	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.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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	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

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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");;