metadata: run_metadata: 14 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "10x" and tissue

14 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "10x" and tissue_curation = "Undetermined"

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.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.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.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
45061	45061	SRR6497181	SRX3586250	SRS2608613	SRP131047	PRJNA429936	10X genomics analysis of adult and larval habenula from the gng8 GFP transgenic line	GSE109158	Transcriptome Analysis	The identification of cell types and marker genes is critical for dissecting neural development and function but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly despite brain growth and functional maturation cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: For larval dataset multiple gng8 GFP labeled zebrafish brains were dissociated and habenular cells FAC sorted into PBS+1%BSA and immediately loaded into 10X chromium for cell capture. For adult dataset 5 6 habenulae were cleanly dissected out dissociated filtered in PBS+BSA and immediately captured in droplets with 10x platform. Both libraries were then constructed using standard instrutions of the 10x plaform.	parent bioproject:PRJNA414719	pubmed:29576475	larvalR2	GSM2818521	tissue:larval habenula\|developmental stage:10 dpf subtype:larval habenula	larvalR2	Raw requencing data was converted to matrizes of expression conts using cell ranger software provided by 10x genomics. Briefly raw BCL files from Illumina nExtseq were demultiplexed into compressed Fastqs for each channel using "cellranger mkfastq" FASTQ files were then provided as input to “cellranger count” which partitioned the reads into their cell of origin based on the 14bp cell barcode on the left read aligned reads to a zebrafish reference transcriptome and quantified transcript counts for each annotated gene within every cell. Here the 10bp unique molecular identifier UMI on the left read was used to collapse PCR duplicates and accurately quantify the number of transcript molecules captured for each gene in every cell. Supplementary files format and content: text file with tab delimiters	larval habenula		polyA selection based RNA capture as per the manufacturer's instructions provided by 10X genomics platform. Libraries were prepared as per manufacturer's insturctions provided by 10X genomics platform https://www.10xgenomics.com/single cell/		developmental stage:10 dpf subtype:larval habenula	GSM2818521	GSM2818521: larvalR2; Danio rerio; RNA Seq	GSM2818521 2	1	polyA selection based RNA capture as per the manufacturer's instructions provided by 10X genomics platform. Libraries were prepared as per manufacturer's insturctions provided by 10X genomics platform https://www.10xgenomics.com/single cell/	GEO Accession:GSM2818521	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP131047	dangling references:treat as unmapped	larva_possorted_genome_bam.bam	10X Genomics bam file	28345528526.0	289240087.0	GSM2818521 r11	0:98	A:8402517943;C:5487086955;G:5983229058;T:8461684002;N:11010568	98			8402517943	5487086955	5983229058	8461684002	11010568	SRX3586250	SRS2608613	SRA650466	GEO	Schier Lab, Molecular and Cellular Biology, Harvard University	1	0.89549	0.27435	0.78127	0.49496	98	B	usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United States	2017-10-18	Larval	Larval	Undetermined	Undetermined
60922	60922	SRR12658673	SRX9139731	SRS7381397	SRP282672	PRJNA663960	Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development	GSE158099	Transcriptome Analysis	We used single cell RNA sequencing to investigate the expression and the heterogeneity of wild type and runx1 mutant cd41 GFPLow cd41GFP hematopoietic stem and progenitor cells at embryonic 2.5 dpf dpf and larval stages 6 10 dpf 16 dpf. Overall design: Single cell RNA seq with FACS sorted cd41 GFPlow cells from wild type and runx1 / at 2.5 6 10 dpf 16 dpf.	parent bioproject:PRJNA663961	pubmed:34492681	cd41:GFPlow runx1 / recovered16dpf	GSM4792216	tissue:sorted cd41:GFPlow\|strain:EK\|genotype/variation:runx1 / del8 hg96 tgcd41:GFP\|age:16 dpf\|cell subset:sorted cd41:GFPlow	cd41:GFPlow runx1 / recovered16dpf	Sequences from the Chromium platform were de multiplexed and aligned using CellRanger ver. 2.0.2 from 10x Genomics using custom zebrafish reference genome GRCz10 and transcript annotation reference GRCz10.87 with default parameters. Genome build: GRCz10 Supplementary files format and content: barcodes.tsv genes.tsv features.tsv matrix.mtx	sorted cd41:GFPlow		Single cell: dissociation protocol: DOI: 10.1016/j.mex.2018.10.009. Single cells were captured using 10x Genomics Chromium. Single cell RNA seq libraries were prepared using Chromium Single Cell 3’ Library & Gel Bead Kit v3. Cell lysis cDNA preparation and library construction were prepared following the manufacturer's protocol.		strain:EK\|genotype/variation:runx1 / del8 hg96 tgcd41:GFP\|age:16 dpf\|cell subset:sorted cd41:GFPlow	GSM4792216	GSM4792216: cd41:GFPlow runx1 / recovered16dpf; Danio rerio; RNA Seq	GSM4792216	1	Single cell: dissociation protocol: DOI: 10.1016/j.mex.2018.10.009. Single cells were captured using 10x Genomics Chromium. Single cell RNA seq libraries were prepared using Chromium Single Cell three prime Library & Gel Bead Kit v3. Cell lysis cDNA preparation and library construction were prepared following the manufacturer's protocol.	GEO Accession:GSM4792216	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP282672	loader:fastq load.py\|options: platform=Illumina readTypes=TBT read1PairFiles=SC9.EB200211 3.R1.fastq.gz read2PairFiles=SC9.EB200211 3.R2.fastq.gz read3PairFiles=SC9.EB200211 3.I1.fastq.gz	SC9.EB200211_3.I1.fastq.gz SC9.EB200211_3.R1.fastq.gz SC9.EB200211_3.R2.fastq.gz	fastq fastq fastq	30067491644.0	224384266.0	GSM4792216 r1	0:28 1:98 2:8	A:8170494725;C:7045853103;G:7134825989;T:7715217012;N:1100815	28	98	8	8170494725	7045853103	7134825989	7715217012	1100815	SRX9139731	SRS7381397	SRA1126726	GEO	NHGRI	1	0.9508	0.05982	0.81278	0.51138	98	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-16	Larval	Larval	Undetermined	Undetermined
60924	60924	SRR12658671	SRX9139729	SRS7381395	SRP282672	PRJNA663960	Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development	GSE158099	Transcriptome Analysis	We used single cell RNA sequencing to investigate the expression and the heterogeneity of wild type and runx1 mutant cd41 GFPLow cd41GFP hematopoietic stem and progenitor cells at embryonic 2.5 dpf dpf and larval stages 6 10 dpf 16 dpf. Overall design: Single cell RNA seq with FACS sorted cd41 GFPlow cells from wild type and runx1 / at 2.5 6 10 dpf 16 dpf.	parent bioproject:PRJNA663961	pubmed:34492681	cd41:GFPlow WT 16dpf	GSM4792214	tissue:sorted cd41:GFPlow\|strain:EK\|genotype/variation:WT tgcd41:GFP\|age:16 dpf\|cell subset:sorted cd41:GFPlow	cd41:GFPlow WT 16dpf	Sequences from the Chromium platform were de multiplexed and aligned using CellRanger ver. 2.0.2 from 10x Genomics using custom zebrafish reference genome GRCz10 and transcript annotation reference GRCz10.87 with default parameters. Genome build: GRCz10 Supplementary files format and content: barcodes.tsv genes.tsv features.tsv matrix.mtx	sorted cd41:GFPlow		Single cell: dissociation protocol: DOI: 10.1016/j.mex.2018.10.009. Single cells were captured using 10x Genomics Chromium. Single cell RNA seq libraries were prepared using Chromium Single Cell 3’ Library & Gel Bead Kit v3. Cell lysis cDNA preparation and library construction were prepared following the manufacturer's protocol.		strain:EK\|genotype/variation:WT tgcd41:GFP\|age:16 dpf\|cell subset:sorted cd41:GFPlow	GSM4792214	GSM4792214: cd41:GFPlow WT 16dpf; Danio rerio; RNA Seq	GSM4792214	1	Single cell: dissociation protocol: DOI: 10.1016/j.mex.2018.10.009. Single cells were captured using 10x Genomics Chromium. Single cell RNA seq libraries were prepared using Chromium Single Cell three prime Library & Gel Bead Kit v3. Cell lysis cDNA preparation and library construction were prepared following the manufacturer's protocol.	GEO Accession:GSM4792214	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP282672	loader:fastq load.py\|options: platform=Illumina readTypes=TBT read1PairFiles=SC7.EB200211 1.R1.fastq.gz read2PairFiles=SC7.EB200211 1.R2.fastq.gz read3PairFiles=SC7.EB200211 1.I1.fastq.gz	SC7.EB200211_1.I1.fastq.gz SC7.EB200211_1.R1.fastq.gz SC7.EB200211_1.R2.fastq.gz	fastq fastq fastq	34677745162.0	258789143.0	GSM4792214 r1	0:28 1:98 2:8	A:9669329280;C:7993628599;G:8305155445;T:8708353592;N:1278246	28	98	8	9669329280	7993628599	8305155445	8708353592	1278246	SRX9139729	SRS7381395	SRA1126726	GEO	NHGRI	1	0.94882	0.07076	0.80689	0.51887	98	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-16	Larval	Larval	Undetermined	Undetermined
60925	60925	SRR12658670	SRX9139728	SRS7381394	SRP282672	PRJNA663960	Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development	GSE158099	Transcriptome Analysis	We used single cell RNA sequencing to investigate the expression and the heterogeneity of wild type and runx1 mutant cd41 GFPLow cd41GFP hematopoietic stem and progenitor cells at embryonic 2.5 dpf dpf and larval stages 6 10 dpf 16 dpf. Overall design: Single cell RNA seq with FACS sorted cd41 GFPlow cells from wild type and runx1 / at 2.5 6 10 dpf 16 dpf.	parent bioproject:PRJNA663961	pubmed:34492681	cd41:GFPlow runx1 / 10dpf	GSM4792213	tissue:sorted cd41:GFPlow\|strain:EK\|genotype/variation:runx1 / del8 hg96 tgcd41:GFP\|age:10 dpf\|cell subset:sorted cd41:GFPlow	cd41:GFPlow runx1 / 10dpf	Sequences from the Chromium platform were de multiplexed and aligned using CellRanger ver. 2.0.2 from 10x Genomics using custom zebrafish reference genome GRCz10 and transcript annotation reference GRCz10.87 with default parameters. Genome build: GRCz10 Supplementary files format and content: barcodes.tsv genes.tsv features.tsv matrix.mtx	sorted cd41:GFPlow		Single cell: dissociation protocol: DOI: 10.1016/j.mex.2018.10.009. Single cells were captured using 10x Genomics Chromium. Single cell RNA seq libraries were prepared using Chromium Single Cell 3’ Library & Gel Bead Kit v3. Cell lysis cDNA preparation and library construction were prepared following the manufacturer's protocol.		strain:EK\|genotype/variation:runx1 / del8 hg96 tgcd41:GFP\|age:10 dpf\|cell subset:sorted cd41:GFPlow	GSM4792213	GSM4792213: cd41:GFPlow runx1 / 10dpf; Danio rerio; RNA Seq	GSM4792213	1	Single cell: dissociation protocol: DOI: 10.1016/j.mex.2018.10.009. Single cells were captured using 10x Genomics Chromium. Single cell RNA seq libraries were prepared using Chromium Single Cell three prime Library & Gel Bead Kit v3. Cell lysis cDNA preparation and library construction were prepared following the manufacturer's protocol.	GEO Accession:GSM4792213	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP282672	loader:fastq load.py\|options: platform=Illumina readTypes=TBT read1PairFiles=SC6.zf rx1 10dpf cd41.R1.fastq.gz read2PairFiles=SC6.zf rx1 10dpf cd41.R2.fastq.gz read3PairFiles=SC6.zf rx1 10dpf cd41.I1.fastq.gz	SC6.zf_rx1_10dpf_cd41.I1.fastq.gz SC6.zf_rx1_10dpf_cd41.R1.fastq.gz SC6.zf_rx1_10dpf_cd41.R2.fastq.gz	fastq fastq fastq	14974412901.0	117908763.0	GSM4792213 r1	0:28 1:91 2:8	A:3982657699;C:3492784275;G:3627405921;T:3870769189;N:795817	28	91	8	3982657699	3492784275	3627405921	3870769189	795817	SRX9139728	SRS7381394	SRA1126726	GEO	NHGRI	1	0.94556	0.09828	0.81566	0.51593	91	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-16	Larval	Larval	Undetermined	Undetermined
60926	60926	SRR12658669	SRX9139727	SRS7381393	SRP282672	PRJNA663960	Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development	GSE158099	Transcriptome Analysis	We used single cell RNA sequencing to investigate the expression and the heterogeneity of wild type and runx1 mutant cd41 GFPLow cd41GFP hematopoietic stem and progenitor cells at embryonic 2.5 dpf dpf and larval stages 6 10 dpf 16 dpf. Overall design: Single cell RNA seq with FACS sorted cd41 GFPlow cells from wild type and runx1 / at 2.5 6 10 dpf 16 dpf.	parent bioproject:PRJNA663961	pubmed:34492681	cd41:GFPlow WT 10dpf	GSM4792212	tissue:sorted cd41:GFPlow\|strain:EK\|genotype/variation:WT tgcd41:GFP\|age:10 dpf\|cell subset:sorted cd41:GFPlow	cd41:GFPlow WT 10dpf	Sequences from the Chromium platform were de multiplexed and aligned using CellRanger ver. 2.0.2 from 10x Genomics using custom zebrafish reference genome GRCz10 and transcript annotation reference GRCz10.87 with default parameters. Genome build: GRCz10 Supplementary files format and content: barcodes.tsv genes.tsv features.tsv matrix.mtx	sorted cd41:GFPlow		Single cell: dissociation protocol: DOI: 10.1016/j.mex.2018.10.009. Single cells were captured using 10x Genomics Chromium. Single cell RNA seq libraries were prepared using Chromium Single Cell 3’ Library & Gel Bead Kit v3. Cell lysis cDNA preparation and library construction were prepared following the manufacturer's protocol.		strain:EK\|genotype/variation:WT tgcd41:GFP\|age:10 dpf\|cell subset:sorted cd41:GFPlow	GSM4792212	GSM4792212: cd41:GFPlow WT 10dpf; Danio rerio; RNA Seq	GSM4792212	1	Single cell: dissociation protocol: DOI: 10.1016/j.mex.2018.10.009. Single cells were captured using 10x Genomics Chromium. Single cell RNA seq libraries were prepared using Chromium Single Cell three prime Library & Gel Bead Kit v3. Cell lysis cDNA preparation and library construction were prepared following the manufacturer's protocol.	GEO Accession:GSM4792212	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP282672	loader:fastq load.py\|options: platform=Illumina readTypes=TBT read1PairFiles=SC5.zf wt 10dpf cd41.R1.fastq.gz read2PairFiles=SC5.zf wt 10dpf cd41.R2.fastq.gz read3PairFiles=SC5.zf wt 10dpf cd41.I1.fastq.gz	SC5.zf_wt_10dpf_cd41.I1.fastq.gz SC5.zf_wt_10dpf_cd41.R1.fastq.gz SC5.zf_wt_10dpf_cd41.R2.fastq.gz	fastq fastq fastq	12709489567.0	100074721.0	GSM4792212 r1	0:28 1:91 2:8	A:3437201292;C:2934750461;G:3075955007;T:3260906593;N:676214	28	91	8	3437201292	2934750461	3075955007	3260906593	676214	SRX9139727	SRS7381393	SRA1126726	GEO	NHGRI	1	0.93877	0.12223	0.81657	0.51571	91	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-16	Larval	Larval	Undetermined	Undetermined
60927	60927	SRR12658668	SRX9139726	SRS7381392	SRP282672	PRJNA663960	Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development	GSE158099	Transcriptome Analysis	We used single cell RNA sequencing to investigate the expression and the heterogeneity of wild type and runx1 mutant cd41 GFPLow cd41GFP hematopoietic stem and progenitor cells at embryonic 2.5 dpf dpf and larval stages 6 10 dpf 16 dpf. Overall design: Single cell RNA seq with FACS sorted cd41 GFPlow cells from wild type and runx1 / at 2.5 6 10 dpf 16 dpf.	parent bioproject:PRJNA663961	pubmed:34492681	cd41:GFPlow runx1 / 6dpf	GSM4792211	tissue:sorted cd41:GFPlow\|strain:EK\|genotype/variation:runx1 / del8 hg96 tgcd41:GFP\|age:6 dpf\|cell subset:sorted cd41:GFPlow	cd41:GFPlow runx1 / 6dpf	Sequences from the Chromium platform were de multiplexed and aligned using CellRanger ver. 2.0.2 from 10x Genomics using custom zebrafish reference genome GRCz10 and transcript annotation reference GRCz10.87 with default parameters. Genome build: GRCz10 Supplementary files format and content: barcodes.tsv genes.tsv features.tsv matrix.mtx	sorted cd41:GFPlow		Single cell: dissociation protocol: DOI: 10.1016/j.mex.2018.10.009. Single cells were captured using 10x Genomics Chromium. Single cell RNA seq libraries were prepared using Chromium Single Cell 3’ Library & Gel Bead Kit v3. Cell lysis cDNA preparation and library construction were prepared following the manufacturer's protocol.		strain:EK\|genotype/variation:runx1 / del8 hg96 tgcd41:GFP\|age:6 dpf\|cell subset:sorted cd41:GFPlow	GSM4792211	GSM4792211: cd41:GFPlow runx1 / 6dpf; Danio rerio; RNA Seq	GSM4792211	1	Single cell: dissociation protocol: DOI: 10.1016/j.mex.2018.10.009. Single cells were captured using 10x Genomics Chromium. Single cell RNA seq libraries were prepared using Chromium Single Cell three prime Library & Gel Bead Kit v3. Cell lysis cDNA preparation and library construction were prepared following the manufacturer's protocol.	GEO Accession:GSM4792211	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP282672	loader:fastq load.py\|options: platform=Illumina readTypes=TBT read1PairFiles=SC4.G10 rx1null 6dpf.R1.fastq.gz read2PairFiles=SC4.G10 rx1null 6dpf.R2.fastq.gz read3PairFiles=SC4.G10 rx1null 6dpf.I1.fastq.gz	SC4.G10_rx1null_6dpf.I1.fastq.gz SC4.G10_rx1null_6dpf.R1.fastq.gz SC4.G10_rx1null_6dpf.R2.fastq.gz	fastq fastq fastq	24249596626.0	180967139.0	GSM4792211 r1	0:28 1:98 2:8	A:6500438445;C:5732773450;G:5845760006;T:6155899149;N:14725576	28	98	8	6500438445	5732773450	5845760006	6155899149	14725576	SRX9139726	SRS7381392	SRA1126726	GEO	NHGRI	1	0.94347	0.12579	0.80158	0.53123	98	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-16	Larval	Larval	Undetermined	Undetermined
60928	60928	SRR12658667	SRX9139725	SRS7381391	SRP282672	PRJNA663960	Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development	GSE158099	Transcriptome Analysis	We used single cell RNA sequencing to investigate the expression and the heterogeneity of wild type and runx1 mutant cd41 GFPLow cd41GFP hematopoietic stem and progenitor cells at embryonic 2.5 dpf dpf and larval stages 6 10 dpf 16 dpf. Overall design: Single cell RNA seq with FACS sorted cd41 GFPlow cells from wild type and runx1 / at 2.5 6 10 dpf 16 dpf.	parent bioproject:PRJNA663961	pubmed:34492681	cd41:GFPlow WT 6dpf	GSM4792210	tissue:sorted cd41:GFPlow\|strain:EK\|genotype/variation:WT tgcd41:GFP\|age:6 dpf\|cell subset:sorted cd41:GFPlow	cd41:GFPlow WT 6dpf	Sequences from the Chromium platform were de multiplexed and aligned using CellRanger ver. 2.0.2 from 10x Genomics using custom zebrafish reference genome GRCz10 and transcript annotation reference GRCz10.87 with default parameters. Genome build: GRCz10 Supplementary files format and content: barcodes.tsv genes.tsv features.tsv matrix.mtx	sorted cd41:GFPlow		Single cell: dissociation protocol: DOI: 10.1016/j.mex.2018.10.009. Single cells were captured using 10x Genomics Chromium. Single cell RNA seq libraries were prepared using Chromium Single Cell 3’ Library & Gel Bead Kit v3. Cell lysis cDNA preparation and library construction were prepared following the manufacturer's protocol.		strain:EK\|genotype/variation:WT tgcd41:GFP\|age:6 dpf\|cell subset:sorted cd41:GFPlow	GSM4792210	GSM4792210: cd41:GFPlow WT 6dpf; Danio rerio; RNA Seq	GSM4792210	1	Single cell: dissociation protocol: DOI: 10.1016/j.mex.2018.10.009. Single cells were captured using 10x Genomics Chromium. Single cell RNA seq libraries were prepared using Chromium Single Cell three prime Library & Gel Bead Kit v3. Cell lysis cDNA preparation and library construction were prepared following the manufacturer's protocol.	GEO Accession:GSM4792210	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP282672	loader:fastq load.py\|options: platform=Illumina readTypes=TBT read1PairFiles=SC3.F10 WT 6dpf.R1.fastq.gz read2PairFiles=SC3.F10 WT 6dpf.R2.fastq.gz read3PairFiles=SC3.F10 WT 6dpf.I1.fastq.gz	SC3.F10_WT_6dpf.I1.fastq.gz SC3.F10_WT_6dpf.R1.fastq.gz SC3.F10_WT_6dpf.R2.fastq.gz	fastq fastq fastq	21899129292.0	163426338.0	GSM4792210 r1	0:28 1:98 2:8	A:5782561921;C:5266812318;G:5476022470;T:5360450075;N:13282508	28	98	8	5782561921	5266812318	5476022470	5360450075	13282508	SRX9139725	SRS7381391	SRA1126726	GEO	NHGRI	1	0.96289	0.06305	0.85387	0.53032	98	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-16	Larval	Larval	Undetermined	Undetermined
60929	60929	SRR12658666	SRX9139724	SRS7381390	SRP282672	PRJNA663960	Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development	GSE158099	Transcriptome Analysis	We used single cell RNA sequencing to investigate the expression and the heterogeneity of wild type and runx1 mutant cd41 GFPLow cd41GFP hematopoietic stem and progenitor cells at embryonic 2.5 dpf dpf and larval stages 6 10 dpf 16 dpf. Overall design: Single cell RNA seq with FACS sorted cd41 GFPlow cells from wild type and runx1 / at 2.5 6 10 dpf 16 dpf.	parent bioproject:PRJNA663961	pubmed:34492681	cd41:GFPlow runx1 / 2.5dpf	GSM4792209	tissue:sorted cd41:GFPlow\|strain:EK\|genotype/variation:runx1 / del8 hg96 tgcd41:GFP\|age:2.5 dpf\|cell subset:sorted cd41:GFPlow	cd41:GFPlow runx1 / 2.5dpf	Sequences from the Chromium platform were de multiplexed and aligned using CellRanger ver. 2.0.2 from 10x Genomics using custom zebrafish reference genome GRCz10 and transcript annotation reference GRCz10.87 with default parameters. Genome build: GRCz10 Supplementary files format and content: barcodes.tsv genes.tsv features.tsv matrix.mtx	sorted cd41:GFPlow		Single cell: dissociation protocol: DOI: 10.1016/j.mex.2018.10.009. Single cells were captured using 10x Genomics Chromium. Single cell RNA seq libraries were prepared using Chromium Single Cell 3’ Library & Gel Bead Kit v3. Cell lysis cDNA preparation and library construction were prepared following the manufacturer's protocol.		strain:EK\|genotype/variation:runx1 / del8 hg96 tgcd41:GFP\|age:2.5 dpf\|cell subset:sorted cd41:GFPlow	GSM4792209	GSM4792209: cd41:GFPlow runx1 / 2.5dpf; Danio rerio; RNA Seq	GSM4792209	1	Single cell: dissociation protocol: DOI: 10.1016/j.mex.2018.10.009. Single cells were captured using 10x Genomics Chromium. Single cell RNA seq libraries were prepared using Chromium Single Cell three prime Library & Gel Bead Kit v3. Cell lysis cDNA preparation and library construction were prepared following the manufacturer's protocol.	GEO Accession:GSM4792209	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP282672	loader:fastq load.py\|options: platform=Illumina readTypes=TBT read1PairFiles=SC2.A8 runx1 nulls.1.R1.fastq.gz read2PairFiles=SC2.A8 runx1 nulls.1.R2.fastq.gz read3PairFiles=SC2.A8 runx1 nulls.1.I1.fastq.gz	SC2.A8-runx1_nulls.1.I1.fastq.gz SC2.A8-runx1_nulls.1.R1.fastq.gz SC2.A8-runx1_nulls.1.R2.fastq.gz	fastq fastq fastq	38938658748.0	294989839.0	GSM4792209 r1	0:26 1:98 2:8	A:10648313958;C:9159222906;G:9191746077;T:9913634426;N:25741381	26	98	8	10648313958	9159222906	9191746077	9913634426	25741381	SRX9139724	SRS7381390	SRA1126726	GEO	NHGRI	1	0.93897	0.09737	0.87271	0.49815	98	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-16	Hatching	Embryo	Undetermined	Embryo Imprecise
60930	60930	SRR12658665	SRX9139723	SRS7381389	SRP282672	PRJNA663960	Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development	GSE158099	Transcriptome Analysis	We used single cell RNA sequencing to investigate the expression and the heterogeneity of wild type and runx1 mutant cd41 GFPLow cd41GFP hematopoietic stem and progenitor cells at embryonic 2.5 dpf dpf and larval stages 6 10 dpf 16 dpf. Overall design: Single cell RNA seq with FACS sorted cd41 GFPlow cells from wild type and runx1 / at 2.5 6 10 dpf 16 dpf.	parent bioproject:PRJNA663961	pubmed:34492681	cd41:GFPlow WT 2.5dpf	GSM4792208	tissue:sorted cd41:GFPlow\|strain:EK\|genotype/variation:WT tgcd41:GFP\|age:2.5 dpf\|cell subset:sorted cd41:GFPlow	cd41:GFPlow WT 2.5dpf	Sequences from the Chromium platform were de multiplexed and aligned using CellRanger ver. 2.0.2 from 10x Genomics using custom zebrafish reference genome GRCz10 and transcript annotation reference GRCz10.87 with default parameters. Genome build: GRCz10 Supplementary files format and content: barcodes.tsv genes.tsv features.tsv matrix.mtx	sorted cd41:GFPlow		Single cell: dissociation protocol: DOI: 10.1016/j.mex.2018.10.009. Single cells were captured using 10x Genomics Chromium. Single cell RNA seq libraries were prepared using Chromium Single Cell 3’ Library & Gel Bead Kit v3. Cell lysis cDNA preparation and library construction were prepared following the manufacturer's protocol.		strain:EK\|genotype/variation:WT tgcd41:GFP\|age:2.5 dpf\|cell subset:sorted cd41:GFPlow	GSM4792208	GSM4792208: cd41:GFPlow WT 2.5dpf; Danio rerio; RNA Seq	GSM4792208	1	Single cell: dissociation protocol: DOI: 10.1016/j.mex.2018.10.009. Single cells were captured using 10x Genomics Chromium. Single cell RNA seq libraries were prepared using Chromium Single Cell three prime Library & Gel Bead Kit v3. Cell lysis cDNA preparation and library construction were prepared following the manufacturer's protocol.	GEO Accession:GSM4792208	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP282672	loader:fastq load.py\|options: platform=Illumina readTypes=TBT read1PairFiles=SC1.A7 WT.1.R1.fastq.gz read2PairFiles=SC1.A7 WT.1.R2.fastq.gz read3PairFiles=SC1.A7 WT.1.I1.fastq.gz	SC1.A7-WT.1.I1.fastq.gz SC1.A7-WT.1.R1.fastq.gz SC1.A7-WT.1.R2.fastq.gz	fastq fastq fastq	32778402756.0	248321233.0	GSM4792208 r1	0:26 1:98 2:8	A:9066035393;C:7671732666;G:7865454744;T:8153280795;N:21899158	26	98	8	9066035393	7671732666	7865454744	8153280795	21899158	SRX9139723	SRS7381389	SRA1126726	GEO	NHGRI	1	0.95064	0.07069	0.86634	0.53298	98	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-16	Hatching	Embryo	Undetermined	Embryo Imprecise
63234	63234	SRR18508141	SRX14639419	SRS12405515	SRP305927	PRJNA701473	Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors	GSE166646	Transcriptome Analysis	Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4. Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter. Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry. Normal cells was prepared from a control zebrafish which overexpresses only mCherry. Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique.	parent bioproject:PRJNA701471	pubmed:35504924	Preleukemic stage Ick:IRF4 fish 5	GSM5976296	tissue:Zebrafish\|cells:mCherry sorted cells\|transgenic:IRF4 overexpression	Preleukemic stage Ick:IRF4 fish 5	Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information. Single cell data were generated using mkref from cellranger package. Alignment barcode assignation and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count id zv11 {sampleID} fastqs={directory scSeq} sample={sampleID} transcriptome={mkgtf generated STAR library} Assembly: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells. The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze	Zebrafish	No treatment	post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis.	The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. The cells were harvested at different stages and sorted by flow cytometry based on mCherry fluorescence expression. A zebrafish which was transduced only with mCherry was used as a control.	cells:mCherry sorted cells\|transgenic:IRF4 overexpression	GSM5976296	GSM5976296: Preleukemic stage Ick:IRF4 fish 5; Danio rerio; RNA Seq	GSM5976296	1	post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis.	GEO Accession:GSM5976296	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP305927	loader:fastq load.py\|options: readTypes=TTB read1PairFiles=22 PS5 I1.fastq.gz read2PairFiles=22 PS5 R1.fastq.gz read3PairFiles=22 PS5 R2.fastq.gz	22_PS5_I1.fastq.gz 22_PS5_R1.fastq.gz 22_PS5_R2.fastq.gz	fastq fastq fastq	29499386664.0	223480202.0	GSM5976296 r1	0:8 1:26 2:98	A:5916946346;C:5161367423;G:5141267981;T:5676847603;N:4630443	8	26	98	5916946346	5161367423	5141267981	5676847603	4630443	SRX14639419	SRS12405515	SRA1195246	GEO	Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore	1	0.80645	0.12105	0.84185	0.60542	98	B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Singapore	2022-03-28	Undetermined	Undetermined	Undetermined	Undetermined
63235	63235	SRR18508140	SRX14639418	SRS12405514	SRP305927	PRJNA701473	Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors	GSE166646	Transcriptome Analysis	Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4. Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter. Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry. Normal cells was prepared from a control zebrafish which overexpresses only mCherry. Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique.	parent bioproject:PRJNA701471	pubmed:35504924	Preleukemic stage Ick:IRF4 fish 4	GSM5976295	tissue:Zebrafish\|cells:mCherry sorted cells\|transgenic:IRF4 overexpression	Preleukemic stage Ick:IRF4 fish 4	Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information. Single cell data were generated using mkref from cellranger package. Alignment barcode assignation and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count id zv11 {sampleID} fastqs={directory scSeq} sample={sampleID} transcriptome={mkgtf generated STAR library} Assembly: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells. The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze	Zebrafish	No treatment	post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis.	The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. The cells were harvested at different stages and sorted by flow cytometry based on mCherry fluorescence expression. A zebrafish which was transduced only with mCherry was used as a control.	cells:mCherry sorted cells\|transgenic:IRF4 overexpression	GSM5976295	GSM5976295: Preleukemic stage Ick:IRF4 fish 4; Danio rerio; RNA Seq	GSM5976295	1	post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis.	GEO Accession:GSM5976295	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP305927	loader:fastq load.py\|options: readTypes=TTB read1PairFiles=21 PS4 I1.fastq.gz read2PairFiles=21 PS4 R1.fastq.gz read3PairFiles=21 PS4 R2.fastq.gz	21_PS4_I1.fastq.gz 21_PS4_R1.fastq.gz 21_PS4_R2.fastq.gz	fastq fastq fastq	27210025260.0	206136555.0	GSM5976295 r1	0:8 1:26 2:98	A:6014697783;C:4212623706;G:4664602896;T:5305183874;N:4274131	8	26	98	6014697783	4212623706	4664602896	5305183874	4274131	SRX14639418	SRS12405514	SRA1195246	GEO	Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore	1	0.90833	0.21102	0.81292	0.52636	98	B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Singapore	2022-03-28	Undetermined	Undetermined	Undetermined	Undetermined
63236	63236	SRR18508139	SRX14639417	SRS12405513	SRP305927	PRJNA701473	Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors	GSE166646	Transcriptome Analysis	Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4. Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter. Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry. Normal cells was prepared from a control zebrafish which overexpresses only mCherry. Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique.	parent bioproject:PRJNA701471	pubmed:35504924	Preleukemic stage Ick:IRF4 fish 3	GSM5976294	tissue:Zebrafish\|cells:mCherry sorted cells\|transgenic:IRF4 overexpression	Preleukemic stage Ick:IRF4 fish 3	Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information. Single cell data were generated using mkref from cellranger package. Alignment barcode assignation and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count id zv11 {sampleID} fastqs={directory scSeq} sample={sampleID} transcriptome={mkgtf generated STAR library} Assembly: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells. The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze	Zebrafish	No treatment	post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis.	The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. The cells were harvested at different stages and sorted by flow cytometry based on mCherry fluorescence expression. A zebrafish which was transduced only with mCherry was used as a control.	cells:mCherry sorted cells\|transgenic:IRF4 overexpression	GSM5976294	GSM5976294: Preleukemic stage Ick:IRF4 fish 3; Danio rerio; RNA Seq	GSM5976294	1	post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis.	GEO Accession:GSM5976294	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP305927	loader:fastq load.py\|options: readTypes=TTB read1PairFiles=20 PS3 I1.fastq.gz read2PairFiles=20 PS3 R1.fastq.gz read3PairFiles=20 PS3 R2.fastq.gz	20_PS3_I1.fastq.gz 20_PS3_R1.fastq.gz 20_PS3_R2.fastq.gz	fastq fastq fastq	27905597412.0	211406041.0	GSM5976294 r1	0:8 1:26 2:98	A:5697185546;C:4728899722;G:4759285311;T:5528101272;N:4320167	8	26	98	5697185546	4728899722	4759285311	5528101272	4320167	SRX14639417	SRS12405513	SRA1195246	GEO	Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore	1	0.86766	0.13828	0.81099	0.56202	98	B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Singapore	2022-03-28	Undetermined	Undetermined	Undetermined	Undetermined
63237	63237	SRR18508138	SRX14639416	SRS12405512	SRP305927	PRJNA701473	Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors	GSE166646	Transcriptome Analysis	Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4. Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter. Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry. Normal cells was prepared from a control zebrafish which overexpresses only mCherry. Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique.	parent bioproject:PRJNA701471	pubmed:35504924	Preleukemic stage Ick:IRF4 fish 2	GSM5976293	tissue:Zebrafish\|cells:mCherry sorted cells\|transgenic:IRF4 overexpression	Preleukemic stage Ick:IRF4 fish 2	Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information. Single cell data were generated using mkref from cellranger package. Alignment barcode assignation and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count id zv11 {sampleID} fastqs={directory scSeq} sample={sampleID} transcriptome={mkgtf generated STAR library} Assembly: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells. The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze	Zebrafish	No treatment	post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis.	The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. The cells were harvested at different stages and sorted by flow cytometry based on mCherry fluorescence expression. A zebrafish which was transduced only with mCherry was used as a control.	cells:mCherry sorted cells\|transgenic:IRF4 overexpression	GSM5976293	GSM5976293: Preleukemic stage Ick:IRF4 fish 2; Danio rerio; RNA Seq	GSM5976293	1	post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis.	GEO Accession:GSM5976293	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP305927	loader:fastq load.py\|options: readTypes=TTB read1PairFiles=19 PS2 I1.fastq.gz read2PairFiles=19 PS2 R1.fastq.gz read3PairFiles=19 PS2 R2.fastq.gz	19_PS2_I1.fastq.gz 19_PS2_R1.fastq.gz 19_PS2_R2.fastq.gz	fastq fastq fastq	24632876400.0	186612700.0	GSM5976293 r1	0:8 1:26 2:98	A:4778279544;C:4417666940;G:4309561799;T:4778714812;N:3821505	8	26	98	4778279544	4417666940	4309561799	4778714812	3821505	SRX14639416	SRS12405512	SRA1195246	GEO	Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore	1	0.8543	0.09898	0.8521	0.57296	98	B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Singapore	2022-03-28	Undetermined	Undetermined	Undetermined	Undetermined
63238	63238	SRR18508137	SRX14639415	SRS12405511	SRP305927	PRJNA701473	Single cell RNA seq analysis for normal lymphocytes and IRF4 driven zebrafish tumors	GSE166646	Transcriptome Analysis	Single cell RNA seq analysis was carried out for 1 normal sample from a control zebrafish line lck mCherry and 5 non tumor and 14 tumor samples from the IRF4 transgenic line lck IRF4. Tumor cells were harvested from the animals with or without xxx p53 mutation at different time points of tumor development. Overall design: Human IRF4 gene was overexpressed together with mCherry under the zebrafish lck promoter. Samples were harvested from control or IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. mCherry positive cells sorted by flow cytometry. Normal cells was prepared from a control zebrafish which overexpresses only mCherry. Single cell RNA seq analysis was performed by 10X Genomics using three prime Chromium Single Cell Technique.	parent bioproject:PRJNA701471	pubmed:35504924	Preleukemic stage Ick:IRF4 fish 1	GSM5976292	tissue:Zebrafish\|cells:mCherry sorted cells\|transgenic:IRF4 overexpression	Preleukemic stage Ick:IRF4 fish 1	Annotations from Ensembl GRCz11 for zebrafish genes and transcripts were used and concatenated with mCherry and human IRF4 ENSG00000137265 gene information. Single cell data were generated using mkref from cellranger package. Alignment barcode assignation and generation of cell gene count matrices were all performed using cellranger count from 10x genomics version 3.1.0 cellranger count id zv11 {sampleID} fastqs={directory scSeq} sample={sampleID} transcriptome={mkgtf generated STAR library} Assembly: GRCz11 Danio Rerio + mCherry + Human IRF4 ENSG00000137265 Supplementary files format and content: HDF5 Gene Barcode Matrix format containing UMI counts of each gene for individual cells. The data files can be deconvoluted to tsv and mtx files using cellranger reanalyze	Zebrafish	No treatment	post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis.	The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. The cells were harvested at different stages and sorted by flow cytometry based on mCherry fluorescence expression. A zebrafish which was transduced only with mCherry was used as a control.	cells:mCherry sorted cells\|transgenic:IRF4 overexpression	GSM5976292	GSM5976292: Preleukemic stage Ick:IRF4 fish 1; Danio rerio; RNA Seq	GSM5976292	1	post sorting the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell three prime Solution v2 kit following manufacturer's instructions. Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5 P7 Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally each fragment contains the 10x Barcode UMI and cDNA insert sequence used in data analysis.	GEO Accession:GSM5976292	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP305927	loader:fastq load.py\|options: readTypes=TTB read1PairFiles=18 PS1 I1.fastq.gz read2PairFiles=18 PS1 R1.fastq.gz read3PairFiles=18 PS1 R2.fastq.gz	18_PS1_I1.fastq.gz 18_PS1_R1.fastq.gz 18_PS1_R2.fastq.gz	fastq fastq fastq	32112448896.0	243276128.0	GSM5976292 r1	0:8 1:26 2:98	A:7019250955;C:4996601756;G:5458243501;T:6361897622;N:5066710	8	26	98	7019250955	4996601756	5458243501	6361897622	5066710	SRX14639415	SRS12405511	SRA1195246	GEO	Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore	1	0.90268	0.1795	0.79371	0.53243	98	B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Singapore	2022-03-28	Undetermined	Undetermined	Undetermined	Undetermined

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");;