metadata: run_metadata: 3 rows where experiment.library_strategy = "RNA-Seq", technology = "10x" and tissue

3 rows where experiment.library_strategy = "RNA-Seq", technology = "10x" and tissue_curation = "Spleen"

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.library_name	experiment.design_description	experiment.library_construction_protocol	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
71018	71018	SRR21091734	SRX17106223	SRS14681693	SRP392539	PRJNA870096	Single cell transcriptome profiling reveals diverse immune cell populations and their responses to viral infection in the spleen of zebrafish	GSE211396	Transcriptome Analysis	Teleost fish are indispensable model organisms for comparative immunology research that should provide fundamental insights into the evolutionary history of vertebrate immunity and eventually lead to an improved understanding of the general principles of immune system design. Although numerous studies on ?sh immunology have been conducted knowledge about the cell types that orchestrate piscine immune systems remains limited. In this study we generated a comprehensive atlas of immune cell types in a zebrafish model on the basis of single cell transcriptome profiling. Overall design: Spleen leukocyte PBS administered control SVCV infected infected and SVCV vaccinated plus SVCV infected vaccinated+infected groups of the AB zebrafish were isolated byFicoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.	pubmed:37227178;pubmed:40392591	vaccinated+SVCV scRNAseq	GSM6469457	source name:Spleen\|cell type:leukocyte\|tissue:Spleen\|strain:AB\|age:5 wpf 7 wpf\|geo loc name:missing\|collection date:missing	vaccinated+SVCV scRNAseq	The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: mm10 Supplementary files format and content: Tab separated values files and matrix files	Spleen	Leukocytes were collected from the spleen samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation as previously described.[58a 62] Briefly zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The spleen was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 μg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.	cell type:leukocyte\|tissue:Spleen\|strain:AB\|age:5 wpf 7 wpf	GSM6469457	GSM6469457: vaccinated+SVCV scRNAseq; Danio rerio; RNA Seq	GSM6469457 r1	GSM6469457	1	Leukocytes were collected from the spleen samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation as previously described.[58a 62] Briefly zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The spleen was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 μg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP392539	vaccinated+SVCV_S1_L001_R1_001.fastq.gz vaccinated+SVCV_S1_L001_R2_001.fastq.gz	fastq fastq	54148439576.0	455028904.0	GSM6469457 r1	0:28 1:91	A:15899568894;C:11520113647;G:12620718617;T:14107197313;N:841105	28	91	15899568894	11520113647	12620718617	14107197313	841105	SRX17106223	SRS14681693	SRA1477254	College of Life Sciences, Zhejiang University	College of Life Sciences, Zhejiang University	2	0.01082	0.82759	0.00393	0.19284	0.99093	0.82164	0.42631	0.61086	28	91	T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x	China	2022-08-16	Juvenile	Juvenile	Spleen	Hematopoietic System
71019	71019	SRR21091735	SRX17106222	SRS14681692	SRP392539	PRJNA870096	Single cell transcriptome profiling reveals diverse immune cell populations and their responses to viral infection in the spleen of zebrafish	GSE211396	Transcriptome Analysis	Teleost fish are indispensable model organisms for comparative immunology research that should provide fundamental insights into the evolutionary history of vertebrate immunity and eventually lead to an improved understanding of the general principles of immune system design. Although numerous studies on ?sh immunology have been conducted knowledge about the cell types that orchestrate piscine immune systems remains limited. In this study we generated a comprehensive atlas of immune cell types in a zebrafish model on the basis of single cell transcriptome profiling. Overall design: Spleen leukocyte PBS administered control SVCV infected infected and SVCV vaccinated plus SVCV infected vaccinated+infected groups of the AB zebrafish were isolated byFicoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.	pubmed:37227178;pubmed:40392591	SVCV scRNAseq	GSM6469456	source name:Spleen\|cell type:leukocyte\|tissue:Spleen\|strain:AB\|age:5 wpf 7 wpf\|geo loc name:missing\|collection date:missing	SVCV scRNAseq	The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: mm10 Supplementary files format and content: Tab separated values files and matrix files	Spleen	Leukocytes were collected from the spleen samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation as previously described.[58a 62] Briefly zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The spleen was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 μg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.	cell type:leukocyte\|tissue:Spleen\|strain:AB\|age:5 wpf 7 wpf	GSM6469456	GSM6469456: SVCV scRNAseq; Danio rerio; RNA Seq	GSM6469456 r1	GSM6469456	1	Leukocytes were collected from the spleen samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation as previously described.[58a 62] Briefly zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The spleen was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 μg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP392539	SVCV_S1_L001_R1_001.fastq.gz SVCV_S1_L001_R2_001.fastq.gz	fastq fastq	52273900644.0	439276476.0	GSM6469456 r1	0:28 1:91	A:15161666574;C:11232538299;G:11962650688;T:13914991728;N:2053355	28	91	15161666574	11232538299	11962650688	13914991728	2053355	SRX17106222	SRS14681692	SRA1477254	College of Life Sciences, Zhejiang University	College of Life Sciences, Zhejiang University	2	0.0088	0.86697	0.00319	0.19264	0.99251	0.78289	0.46167	0.59016	28	91	T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x	China	2022-08-16	Juvenile	Juvenile	Spleen	Hematopoietic System
71020	71020	SRR21091736	SRX17106221	SRS14681691	SRP392539	PRJNA870096	Single cell transcriptome profiling reveals diverse immune cell populations and their responses to viral infection in the spleen of zebrafish	GSE211396	Transcriptome Analysis	Teleost fish are indispensable model organisms for comparative immunology research that should provide fundamental insights into the evolutionary history of vertebrate immunity and eventually lead to an improved understanding of the general principles of immune system design. Although numerous studies on ?sh immunology have been conducted knowledge about the cell types that orchestrate piscine immune systems remains limited. In this study we generated a comprehensive atlas of immune cell types in a zebrafish model on the basis of single cell transcriptome profiling. Overall design: Spleen leukocyte PBS administered control SVCV infected infected and SVCV vaccinated plus SVCV infected vaccinated+infected groups of the AB zebrafish were isolated byFicoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.	pubmed:37227178;pubmed:40392591	PBS scRNAseq	GSM6469455	source name:Spleen\|cell type:leukocyte\|tissue:Spleen\|strain:AB\|age:5 wpf 7 wpf\|geo loc name:missing\|collection date:missing	PBS scRNAseq	The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: mm10 Supplementary files format and content: Tab separated values files and matrix files	Spleen	Leukocytes were collected from the spleen samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation as previously described.[58a 62] Briefly zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The spleen was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 μg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.	cell type:leukocyte\|tissue:Spleen\|strain:AB\|age:5 wpf 7 wpf	GSM6469455	GSM6469455: PBS scRNAseq; Danio rerio; RNA Seq	GSM6469455 r1	GSM6469455	1	Leukocytes were collected from the spleen samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation as previously described.[58a 62] Briefly zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The spleen was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 μg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP392539	PBS_S1_L001_R1_001.fastq.gz PBS_S1_L001_R2_001.fastq.gz	fastq fastq	48934762310.0	411216490.0	GSM6469455 r1	0:28 1:91	A:14053810123;C:10679154471;G:11495668034;T:12705747178;N:382504	28	91	14053810123	10679154471	11495668034	12705747178	382504	SRX17106221	SRS14681691	SRA1477254	College of Life Sciences, Zhejiang University	College of Life Sciences, Zhejiang University	2	0.00845	0.84491	0.00304	0.17543	0.99212	0.78833	0.45994	0.6033	28	91	T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x	China	2022-08-16	Juvenile	Juvenile	Spleen	Hematopoietic 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");;