metadata: run_metadata: 11 rows where experiment.library_layout = "SINGLE", technology = "bulk" and tissue

11 rows where experiment.library_layout = "SINGLE", technology = "bulk" and tissue_curation = "Spinal Cord"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	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.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
62931	62931	SRR13447020	SRX9860256	SRS8040687	SRP301982	PRJNA692493	Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq]	GSE164943	Transcriptome Analysis	mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue.	parent bioproject:PRJNA692492	pubmed:33609461	Z 14 3 wpi sc 2	GSM5023609	source name:21 xxx post injury dpi whole bulk spinal cord\|tissue:bulk spinal cord\|timepoint:21 xxx post injury	Z 14 3 wpi sc 2	Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11	21 xxx post injury dpi whole bulk spinal cord	Adult zebrafish were subjected to complete spinal cord transection or sham injured control.	For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads	tissue:bulk spinal cord\|timepoint:21 xxx post injury	GSM5023609	GSM5023609: Z 14 3 wpi sc 2; Danio rerio; RNA Seq	GSM5023609	1	For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads	GEO Accession:GSM5023609	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP301982	run_2941_s_5_withindex_sequence.txt_GGTTTCG.fq.gz	fastq	1344754850.0	26895097.0	GSM5023609 r1	0:50 1:0	A:368949168;C:303436511;G:303863091;T:368250015;N:256065	50	368949168	303436511	303863091	368250015	256065	SRX9860256	SRS8040687	SRA1184552	GEO	Developmental Biology, Washington University	1	0.90723	0.15091	0.70701	0.50468	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2021-01-15	Adult	Adult	Spinal Cord	Nervous System
62932	62932	SRR13447019	SRX9860255	SRS8040686	SRP301982	PRJNA692493	Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq]	GSE164943	Transcriptome Analysis	mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue.	parent bioproject:PRJNA692492	pubmed:33609461	Z 10 3 wpi sc 1	GSM5023608	source name:21 xxx post injury dpi whole bulk spinal cord\|tissue:bulk spinal cord\|timepoint:21 xxx post injury	Z 10 3 wpi sc 1	Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11	21 xxx post injury dpi whole bulk spinal cord	Adult zebrafish were subjected to complete spinal cord transection or sham injured control.	For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads	tissue:bulk spinal cord\|timepoint:21 xxx post injury	GSM5023608	GSM5023608: Z 10 3 wpi sc 1; Danio rerio; RNA Seq	GSM5023608	1	For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads	GEO Accession:GSM5023608	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP301982	run_2941_s_5_withindex_sequence.txt_GACCGAA.fq.gz	fastq	1479770950.0	29595419.0	GSM5023608 r1	0:50 1:0	A:405566463;C:336370965;G:334352978;T:403198702;N:281842	50	405566463	336370965	334352978	403198702	281842	SRX9860255	SRS8040686	SRA1184552	GEO	Developmental Biology, Washington University	1	0.90956	0.14428	0.70666	0.40811	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2021-01-15	Adult	Adult	Spinal Cord	Nervous System
62933	62933	SRR13447018	SRX9860254	SRS8040685	SRP301982	PRJNA692493	Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq]	GSE164943	Transcriptome Analysis	mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue.	parent bioproject:PRJNA692492	pubmed:33609461	Z 13 10 dpi sc 2	GSM5023607	source name:10 xxx post injury dpi whole bulk spinal cord\|tissue:bulk spinal cord\|timepoint:10 xxx post injury	Z 13 10 dpi sc 2	Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11	10 xxx post injury dpi whole bulk spinal cord	Adult zebrafish were subjected to complete spinal cord transection or sham injured control.	For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads	tissue:bulk spinal cord\|timepoint:10 xxx post injury	GSM5023607	GSM5023607: Z 13 10 dpi sc 2; Danio rerio; RNA Seq	GSM5023607	1	For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads	GEO Accession:GSM5023607	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP301982	run_2941_s_5_withindex_sequence.txt_TTACCGT.fq.gz	fastq	2001230650.0	40024613.0	GSM5023607 r1	0:50 1:0	A:563937717;C:433011935;G:427243197;T:576659283;N:378518	50	563937717	433011935	427243197	576659283	378518	SRX9860254	SRS8040685	SRA1184552	GEO	Developmental Biology, Washington University	1	0.88738	0.25515	0.74576	0.61121	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2021-01-15	Adult	Adult	Spinal Cord	Nervous System
62934	62934	SRR13447017	SRX9860253	SRS8040684	SRP301982	PRJNA692493	Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq]	GSE164943	Transcriptome Analysis	mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue.	parent bioproject:PRJNA692492	pubmed:33609461	Z 9 10 dpi sc 1	GSM5023606	source name:10 xxx post injury dpi whole bulk spinal cord\|tissue:bulk spinal cord\|timepoint:10 xxx post injury	Z 9 10 dpi sc 1	Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11	10 xxx post injury dpi whole bulk spinal cord	Adult zebrafish were subjected to complete spinal cord transection or sham injured control.	For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads	tissue:bulk spinal cord\|timepoint:10 xxx post injury	GSM5023606	GSM5023606: Z 9 10 dpi sc 1; Danio rerio; RNA Seq	GSM5023606	1	For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads	GEO Accession:GSM5023606	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP301982	run_2941_s_5_withindex_sequence.txt_TAGGATG.fq.gz	fastq	1228530350.0	24570607.0	GSM5023606 r1	0:50 1:0	A:336797190;C:276687423;G:274112310;T:340700127;N:233300	50	336797190	276687423	274112310	340700127	233300	SRX9860253	SRS8040684	SRA1184552	GEO	Developmental Biology, Washington University	1	0.90494	0.17991	0.69789	0.43663	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2021-01-15	Adult	Adult	Spinal Cord	Nervous System
62935	62935	SRR13447016	SRX9860252	SRS8040683	SRP301982	PRJNA692493	Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq]	GSE164943	Transcriptome Analysis	mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue.	parent bioproject:PRJNA692492	pubmed:33609461	Z 12 5 dpi sc 2	GSM5023605	source name:5 xxx post injury dpi whole bulk spinal cord\|tissue:bulk spinal cord\|timepoint:5 xxx post injury	Z 12 5 dpi sc 2	Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11	5 xxx post injury dpi whole bulk spinal cord	Adult zebrafish were subjected to complete spinal cord transection or sham injured control.	For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads	tissue:bulk spinal cord\|timepoint:5 xxx post injury	GSM5023605	GSM5023605: Z 12 5 dpi sc 2; Danio rerio; RNA Seq	GSM5023605	1	For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads	GEO Accession:GSM5023605	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP301982	run_2941_s_5_withindex_sequence.txt_CGCCGTA.fq.gz	fastq	1304617300.0	26092346.0	GSM5023605 r1	0:50 1:0	A:354720856;C:300934683;G:299416035;T:349298501;N:247225	50	354720856	300934683	299416035	349298501	247225	SRX9860252	SRS8040683	SRA1184552	GEO	Developmental Biology, Washington University	1	0.91217	0.12965	0.69609	0.45367	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2021-01-15	Adult	Adult	Spinal Cord	Nervous System
62936	62936	SRR13447015	SRX9860251	SRS8040682	SRP301982	PRJNA692493	Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq]	GSE164943	Transcriptome Analysis	mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue.	parent bioproject:PRJNA692492	pubmed:33609461	Z 8 5 dpi sc 1	GSM5023604	source name:5 xxx post injury dpi whole bulk spinal cord\|tissue:bulk spinal cord\|timepoint:5 xxx post injury	Z 8 5 dpi sc 1	Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11	5 xxx post injury dpi whole bulk spinal cord	Adult zebrafish were subjected to complete spinal cord transection or sham injured control.	For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads	tissue:bulk spinal cord\|timepoint:5 xxx post injury	GSM5023604	GSM5023604: Z 8 5 dpi sc 1; Danio rerio; RNA Seq	GSM5023604	1	For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads	GEO Accession:GSM5023604	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP301982	run_2941_s_5_withindex_sequence.txt_CATACTG.fq.gz	fastq	1396287400.0	27925748.0	GSM5023604 r1	0:50 1:0	A:377321251;C:319668467;G:314347283;T:384684913;N:265486	50	377321251	319668467	314347283	384684913	265486	SRX9860251	SRS8040682	SRA1184552	GEO	Developmental Biology, Washington University	1	0.91125	0.14506	0.69777	0.4557	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2021-01-15	Adult	Adult	Spinal Cord	Nervous System
62937	62937	SRR13447014	SRX9860250	SRS8040681	SRP301982	PRJNA692493	Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq]	GSE164943	Transcriptome Analysis	mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue.	parent bioproject:PRJNA692492	pubmed:33609461	Z 11 uninjured sc 2	GSM5023603	source name:Bulk uninjured spinal cord\|tissue:bulk spinal cord\|timepoint:Uninjured	Z 11 uninjured sc 2	Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11	Bulk uninjured spinal cord	Adult zebrafish were subjected to complete spinal cord transection or sham injured control.	For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads	tissue:bulk spinal cord\|timepoint:Uninjured	GSM5023603	GSM5023603: Z 11 uninjured sc 2; Danio rerio; RNA Seq	GSM5023603	1	For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads	GEO Accession:GSM5023603	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP301982	run_2941_s_5_withindex_sequence.txt_CGTGATA.fq.gz	fastq	1422401500.0	28448030.0	GSM5023603 r1	0:50 1:0	A:383424800;C:325837613;G:322858241;T:390009650;N:271196	50	383424800	325837613	322858241	390009650	271196	SRX9860250	SRS8040681	SRA1184552	GEO	Developmental Biology, Washington University	1	0.918	0.1183	0.7163	0.50669	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2021-01-15	Adult	Adult	Spinal Cord	Nervous System
62938	62938	SRR13447013	SRX9860249	SRS8040680	SRP301982	PRJNA692493	Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq]	GSE164943	Transcriptome Analysis	mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue.	parent bioproject:PRJNA692492	pubmed:33609461	Z 7 uninjured sc 1	GSM5023602	source name:Bulk uninjured spinal cord\|tissue:bulk spinal cord\|timepoint:Uninjured	Z 7 uninjured sc 1	Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11	Bulk uninjured spinal cord	Adult zebrafish were subjected to complete spinal cord transection or sham injured control.	For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads	tissue:bulk spinal cord\|timepoint:Uninjured	GSM5023602	GSM5023602: Z 7 uninjured sc 1; Danio rerio; RNA Seq	GSM5023602	1	For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads	GEO Accession:GSM5023602	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP301982	run_2941_s_5_withindex_sequence.txt_CCCGCTA.fq.gz	fastq	1274023900.0	25480478.0	GSM5023602 r1	0:50 1:0	A:330443270;C:305732881;G:301431401;T:336172878;N:243470	50	330443270	305732881	301431401	336172878	243470	SRX9860249	SRS8040680	SRA1184552	GEO	Developmental Biology, Washington University	1	0.92713	0.09501	0.71776	0.49328	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2021-01-15	Adult	Adult	Spinal Cord	Nervous System
62939	62939	SRR13447012	SRX9860248	SRS8040679	SRP301982	PRJNA692493	Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq]	GSE164943	Transcriptome Analysis	mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue.	parent bioproject:PRJNA692492	pubmed:33609461	Z 3 gp rp rna 1	GSM5023601	source name:FACS sorted ctgfa:mCherry;gfap:EGFP cells\|tissue:ctgfa:mCherry;gfap:EGFP cells\|timepoint:5 xxx post injury	Z 3 gp rp rna 1	Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11	FACS sorted ctgfa:mCherry;gfap:EGFP cells	Adult zebrafish were subjected to complete spinal cord transection or sham injured control.	For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads	tissue:ctgfa:mCherry;gfap:EGFP cells\|timepoint:5 xxx post injury	GSM5023601	GSM5023601: Z 3 gp rp rna 1; Danio rerio; RNA Seq	GSM5023601	1	For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads	GEO Accession:GSM5023601	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP301982	run_2941_s_5_withindex_sequence.txt_ATAGGCT.fq.gz	fastq	1480993150.0	29619863.0	GSM5023601 r1	0:50 1:0	A:407241408;C:335585510;G:332782981;T:405104683;N:278568	50	407241408	335585510	332782981	405104683	278568	SRX9860248	SRS8040679	SRA1184552	GEO	Developmental Biology, Washington University	1	0.90012	0.13909	0.75684	0.59867	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2021-01-15	Adult	Adult	Spinal Cord	Nervous System
62940	62940	SRR13447011	SRX9860247	SRS8040678	SRP301982	PRJNA692493	Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq]	GSE164943	Transcriptome Analysis	mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue.	parent bioproject:PRJNA692492	pubmed:33609461	Z 18 gp rp 3	GSM5023600	source name:FACS sorted ctgfa:mCherry;gfap:EGFP cells\|tissue:ctgfa:mCherry;gfap:EGFP cells\|timepoint:5 xxx post injury	Z 18 gp rp 3	Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11	FACS sorted ctgfa:mCherry;gfap:EGFP cells	Adult zebrafish were subjected to complete spinal cord transection or sham injured control.	For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads	tissue:ctgfa:mCherry;gfap:EGFP cells\|timepoint:5 xxx post injury	GSM5023600	GSM5023600: Z 18 gp rp 3; Danio rerio; RNA Seq	GSM5023600	1	For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads	GEO Accession:GSM5023600	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP301982	run_2941_s_5_withindex_sequence.txt_AATGACT.fq.gz	fastq	1583531750.0	31670635.0	GSM5023600 r1	0:50 1:0	A:429031314;C:366679713;G:363462738;T:424058514;N:299471	50	429031314	366679713	363462738	424058514	299471	SRX9860247	SRS8040678	SRA1184552	GEO	Developmental Biology, Washington University	1	0.90969	0.12671	0.7458	0.57895	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2021-01-15	Adult	Adult	Spinal Cord	Nervous System
62941	62941	SRR13447010	SRX9860246	SRS8040677	SRP301982	PRJNA692493	Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq]	GSE164943	Transcriptome Analysis	mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue.	parent bioproject:PRJNA692492	pubmed:33609461	Z 15 gp rp 1	GSM5023599	source name:FACS sorted ctgfa:mCherry;gfap:EGFP cells\|tissue:ctgfa:mCherry;gfap:EGFP cells\|timepoint:5 xxx post injury	Z 15 gp rp 1	Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11	FACS sorted ctgfa:mCherry;gfap:EGFP cells	Adult zebrafish were subjected to complete spinal cord transection or sham injured control.	For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads	tissue:ctgfa:mCherry;gfap:EGFP cells\|timepoint:5 xxx post injury	GSM5023599	GSM5023599: Z 15 gp rp 1; Danio rerio; RNA Seq	GSM5023599	1	For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads	GEO Accession:GSM5023599	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP301982	run_2941_s_5_withindex_sequence.txt_TTCTTCG.fq.gz	fastq	1324698650.0	26493973.0	GSM5023599 r1	0:50 1:0	A:361437407;C:301526323;G:300125135;T:361356767;N:253018	50	361437407	301526323	300125135	361356767	253018	SRX9860246	SRS8040677	SRA1184552	GEO	Developmental Biology, Washington University	1	0.90938	0.14229	0.70869	0.50563	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2021-01-15	Adult	Adult	Spinal Cord	Nervous System

Advanced export

JSON shape: default, array, newline-delimited

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");;