{"database": "metadata", "table": "run_metadata", "rows": [[63251, "SRR13693853", "SRX10083151", "SRS8241167", "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", null, "Tumor cells  Early stage  Ick:IRF4 fish 2 scRNA Seq", "GSM5076941", null, "source name:Zebrafish cells  transgenic|tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Early stage", "Tumor cells  Early stage  Ick:IRF4 fish 2 scRNA Seq", "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} Genome build: 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 cells  transgenic", "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. Single cell RNA Seq", "The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish.  post the development of lymphoma phenotype  tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression.  A zebrafish which was transduced only with mCherry was used as a control.", "tissue:tumors driven by overexpression of human IRF4|sorted cells:mCherry sorted cells|genotype:IRF4 overexpression|time:Early stage", "GSM5076941", "GSM5076941: Tumor cells  Early stage  Ick:IRF4 fish 2 scRNA Seq; Danio rerio; RNA Seq", "GSM5076941", null, "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. Single cell RNA Seq", "GEO Accession:GSM5076941", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP305927", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=3C I1.fastq.gz   read2PairFiles=3C R1.fastq.gz   read3PairFiles=3C R2.fastq.gz", "3C_I1.fastq.gz 3C_R1.fastq.gz 3C_R2.fastq.gz", "fastq fastq fastq", 29997585156.0, 227254433.0, "GSM5076941 r1", "0:8 1:26 2:98", "A:8572344693;C:6580024899;G:7240023287;T:7578830064;N:26362213", 8, 26, 98, null, 8572344693, 6580024899, 7240023287, 7578830064, 26362213, "SRX10083151", "SRS8241167", "SRA1195246", "GEO", "Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore", 1, 0.93097, null, 0.27389, null, 0.86318, null, 0.50798, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Singapore", "2021-02-11", "Undetermined", "Undetermined", "Cancer or Tumor", "Cancer or Tumor"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["63251"], "units": {}, "query_ms": 9.775370999705046}