metadata: run_metadata: 4 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "dropseq" and tissue

4 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "dropseq" and tissue_curation = "Brain"

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.growthprotocol	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.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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
56879	56879	SRR11164691	SRX7789375	SRS6204773	SRP250477	PRJNA608279	EPI 00649 2019 New insights into the early mechanisms of epileptogenesis in a zebrafish model of Dravet syndrome	GSE145801	Transcriptome Analysis	We report early mechanisms of epileptogenesis in a zebrafish model of Dravet syndrome caused by missense mutation in scn1lab gene. Overall design: Single cell RNA Sequencing experiments were performed on a total of 4 samples. These correspond to zebrafish brain 5 dpf and 8 dpf comparing wild type to a scn1Lab homozygous mutation.	pubmed:32096222	Zebrafish Wt brain 8 dpf	GSM4333122	tissue:Wt brain 8 dpf dpf	Zebrafish Wt brain 8 dpf	R1 contains the cell barcode 1 12 bp and UMI 13 20 bp. R2 contains the cDNA sequence. Bcl2fastq ver 2.0 was used for the base calling Paired end sequencing reads were trimmed for adaptor sequence. Based on the original Dropseq implementation Macosko et al; 2015 the reads were demultiplexed for the cell barcode and UMI. The genes mapped to GRCz11 using STAR genome aligner with default parameters Genome build: GRCz11 Supplementary files format and content: tab delimited text files include raw counts	Wt brain 8 dpf	Single cell RNA seq using Dropseq three prime bead based enrichment technique using SMART synthesis Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002 Libraries were prepared according to Drop seq methods Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002. post cDNA tagmenation PCR amplification was performed using Illumina primers N701 N702 A501. The purified cDNA fragments of 600 bp were captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSeq 500 following the manufacturer's protocols.	as described in Tiraboschi et al. EPI 00649 2019	tissue:brain\|genotype:WT\|age:8 dpf	GSM4333122	GSM4333122: Zebrafish Wt brain 8 dpf Danio rerio; RNA Seq	GSM4333122	1	Single cell RNA seq using Dropseq three prime bead based enrichment technique using SMART synthesis Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002 Libraries were prepared according to Drop seq methods Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002. post cDNA tagmenation PCR amplification was performed using Illumina primers N701 N702 A501. The purified cDNA fragments of 600 bp were captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSeq 500 following the manufacturer's protocols.	GEO Accession:GSM4333122	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP250477	8DPF4_S2_R1_001.fastq.gz 8DPF4_S2_R2_001.fastq.gz	fastq fastq	13384328000.0	167304100.0	GSM4333122 r1	0:20 1:60	A:3888292440;C:2947715560;G:3180865817;T:3366553945;N:900238	20	60	3888292440	2947715560	3180865817	3366553945	900238	SRX7789375	SRS6204773	SRA1047335	GEO	ICS, University of Luxembourg - LCSB	2	0.01406	0.88627	0.00662	0.16845	0.98768	0.79058	0.70669	0.62062	20	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	dropseq	Luxembourg	2020-02-24	Larval	Larval	Brain	Nervous System
56880	56880	SRR11164690	SRX7789374	SRS6204772	SRP250477	PRJNA608279	EPI 00649 2019 New insights into the early mechanisms of epileptogenesis in a zebrafish model of Dravet syndrome	GSE145801	Transcriptome Analysis	We report early mechanisms of epileptogenesis in a zebrafish model of Dravet syndrome caused by missense mutation in scn1lab gene. Overall design: Single cell RNA Sequencing experiments were performed on a total of 4 samples. These correspond to zebrafish brain 5 dpf and 8 dpf comparing wild type to a scn1Lab homozygous mutation.	pubmed:32096222	Zebrafish Mutscn1Lab brain 8 dpf	GSM4333121	tissue:Mutscn1Lab brain 8 dpf dpf	Zebrafish Mutscn1Lab brain 8 dpf	R1 contains the cell barcode 1 12 bp and UMI 13 20 bp. R2 contains the cDNA sequence. Bcl2fastq ver 2.0 was used for the base calling Paired end sequencing reads were trimmed for adaptor sequence. Based on the original Dropseq implementation Macosko et al; 2015 the reads were demultiplexed for the cell barcode and UMI. The genes mapped to GRCz11 using STAR genome aligner with default parameters Genome build: GRCz11 Supplementary files format and content: tab delimited text files include raw counts	Mutscn1Lab brain 8 dpf	Single cell RNA seq using Dropseq three prime bead based enrichment technique using SMART synthesis Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002 Libraries were prepared according to Drop seq methods Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002. post cDNA tagmenation PCR amplification was performed using Illumina primers N701 N702 A501. The purified cDNA fragments of 600 bp were captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSeq 500 following the manufacturer's protocols.	as described in Tiraboschi et al. EPI 00649 2019	tissue:brain\|genotype:scn1Lab\|age:8 dpf	GSM4333121	GSM4333121: Zebrafish Mutscn1Lab brain 8 dpf Danio rerio; RNA Seq	GSM4333121	1	Single cell RNA seq using Dropseq three prime bead based enrichment technique using SMART synthesis Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002 Libraries were prepared according to Drop seq methods Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002. post cDNA tagmenation PCR amplification was performed using Illumina primers N701 N702 A501. The purified cDNA fragments of 600 bp were captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSeq 500 following the manufacturer's protocols.	GEO Accession:GSM4333121	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP250477	8DPF3_S1_R1_001.fastq.gz 8DPF3_S1_R2_001.fastq.gz	fastq fastq	9580350080.0	119754376.0	GSM4333121 r1	0:20 1:60	A:2809490643;C:2102026943;G:2303250077;T:2364936390;N:646027	20	60	2809490643	2102026943	2303250077	2364936390	646027	SRX7789374	SRS6204772	SRA1047335	GEO	ICS, University of Luxembourg - LCSB	2	0.01149	0.9048	0.00587	0.15201	0.98979	0.79283	0.6829	0.63091	20	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	dropseq	Luxembourg	2020-02-24	Larval	Larval	Brain	Nervous System
56881	56881	SRR11164689	SRX7789373	SRS6204771	SRP250477	PRJNA608279	EPI 00649 2019 New insights into the early mechanisms of epileptogenesis in a zebrafish model of Dravet syndrome	GSE145801	Transcriptome Analysis	We report early mechanisms of epileptogenesis in a zebrafish model of Dravet syndrome caused by missense mutation in scn1lab gene. Overall design: Single cell RNA Sequencing experiments were performed on a total of 4 samples. These correspond to zebrafish brain 5 dpf and 8 dpf comparing wild type to a scn1Lab homozygous mutation.	pubmed:32096222	Zebrafish Mutscn1Lab brain 5 dpf	GSM4333120	tissue:Mutscn1Lab brain 5 dpf dpf	Zebrafish Mutscn1Lab brain 5 dpf	R1 contains the cell barcode 1 12 bp and UMI 13 20 bp. R2 contains the cDNA sequence. Bcl2fastq ver 2.0 was used for the base calling Paired end sequencing reads were trimmed for adaptor sequence. Based on the original Dropseq implementation Macosko et al; 2015 the reads were demultiplexed for the cell barcode and UMI. The genes mapped to GRCz11 using STAR genome aligner with default parameters Genome build: GRCz11 Supplementary files format and content: tab delimited text files include raw counts	Mutscn1Lab brain 5 dpf	Single cell RNA seq using Dropseq three prime bead based enrichment technique using SMART synthesis Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002 Libraries were prepared according to Drop seq methods Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002. post cDNA tagmenation PCR amplification was performed using Illumina primers N701 N702 A501. The purified cDNA fragments of 600 bp were captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSeq 500 following the manufacturer's protocols.	as described in Tiraboschi et al. EPI 00649 2019	tissue:brain\|genotype:scn1Lab\|age:5 dpf	GSM4333120	GSM4333120: Zebrafish Mutscn1Lab brain 5 dpf Danio rerio; RNA Seq	GSM4333120	1	Single cell RNA seq using Dropseq three prime bead based enrichment technique using SMART synthesis Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002 Libraries were prepared according to Drop seq methods Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002. post cDNA tagmenation PCR amplification was performed using Illumina primers N701 N702 A501. The purified cDNA fragments of 600 bp were captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSeq 500 following the manufacturer's protocols.	GEO Accession:GSM4333120	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP250477	5DPF2_S2_R1_001.fastq.gz 5DPF2_S2_R2_001.fastq.gz	fastq fastq	6663274080.0	83290926.0	GSM4333120 r1	0:20 1:60	A:1851799411;C:1470225216;G:1666931688;T:1673879241;N:438524	20	60	1851799411	1470225216	1666931688	1673879241	438524	SRX7789373	SRS6204771	SRA1047335	GEO	ICS, University of Luxembourg - LCSB	2	0.01151	0.90584	0.00724	0.13592	0.99022	0.84784	0.40101	0.60276	20	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	dropseq	Luxembourg	2020-02-24	Larval	Larval	Brain	Nervous System
56882	56882	SRR11164688	SRX7789372	SRS6204770	SRP250477	PRJNA608279	EPI 00649 2019 New insights into the early mechanisms of epileptogenesis in a zebrafish model of Dravet syndrome	GSE145801	Transcriptome Analysis	We report early mechanisms of epileptogenesis in a zebrafish model of Dravet syndrome caused by missense mutation in scn1lab gene. Overall design: Single cell RNA Sequencing experiments were performed on a total of 4 samples. These correspond to zebrafish brain 5 dpf and 8 dpf comparing wild type to a scn1Lab homozygous mutation.	pubmed:32096222	Zebrafish Wt brain 5 dpf	GSM4333119	tissue:Wt brain 5 dpf dpf	Zebrafish Wt brain 5 dpf	R1 contains the cell barcode 1 12 bp and UMI 13 20 bp. R2 contains the cDNA sequence. Bcl2fastq ver 2.0 was used for the base calling Paired end sequencing reads were trimmed for adaptor sequence. Based on the original Dropseq implementation Macosko et al; 2015 the reads were demultiplexed for the cell barcode and UMI. The genes mapped to GRCz11 using STAR genome aligner with default parameters Genome build: GRCz11 Supplementary files format and content: tab delimited text files include raw counts	Wt brain 5 dpf	Single cell RNA seq using Dropseq three prime bead based enrichment technique using SMART synthesis Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002 Libraries were prepared according to Drop seq methods Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002. post cDNA tagmenation PCR amplification was performed using Illumina primers N701 N702 A501. The purified cDNA fragments of 600 bp were captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSeq 500 following the manufacturer's protocols.	as described in Tiraboschi et al. EPI 00649 2019	tissue:brain\|genotype:WT\|age:5 dpf	GSM4333119	GSM4333119: Zebrafish Wt brain 5 dpf Danio rerio; RNA Seq	GSM4333119	1	Single cell RNA seq using Dropseq three prime bead based enrichment technique using SMART synthesis Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002 Libraries were prepared according to Drop seq methods Macosko et al 2015 doi: 10.1016/j.cell.2015.05.002. post cDNA tagmenation PCR amplification was performed using Illumina primers N701 N702 A501. The purified cDNA fragments of 600 bp were captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSeq 500 following the manufacturer's protocols.	GEO Accession:GSM4333119	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP250477	5DPF1_S1_R2_001.fastq.gz 5DPF1_S1_R1_001.fastq.gz	fastq fastq	6473128320.0	80914104.0	GSM4333119 r1	0:20 1:60	A:1828609493;C:1442384903;G:1561588918;T:1640121023;N:423983	20	60	1828609493	1442384903	1561588918	1640121023	423983	SRX7789372	SRS6204770	SRA1047335	GEO	ICS, University of Luxembourg - LCSB	2	0.01235	0.90642	0.00683	0.13484	0.9892	0.83956	0.71539	0.60611	20	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	dropseq	Luxembourg	2020-02-24	Larval	Larval	Brain	Nervous 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");;