run_metadata: 63237

This data as json

rowid	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	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.spot_descriptor	experiment.study_ref	run.title	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.r4_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	tech_variant	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
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