run_metadata: 66220
This data as json
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| 66220 | SRR16102692 | SRX12388680 | SRS10358682 | SRP339154 | PRJNA767083 | RNA seq analysis for IRF4 driven zebrafish tumors post JQ1 treatment | GSE184946 | Transcriptome Analysis | RNA seq analysis was performed using tumor cells driven by IRF4 to analyze gene expression changes post JQ1 treatment Overall design: The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype animals were treated with JQ1 or control DMSO for 1 or 3 days. Tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Total RNAs were harvested from each sample and then applied for RNA seq analysis. | parent bioproject:PRJNA701471 | pubmed:35504924 | Tumor cells DMSO day1 rep2 RNA Seq | GSM5602241 | tissue:Zebrafish tumor cells|cell type:Zebrafish tumor cells|condition:control|treatment:DMSO | Tumor cells DMSO day1 rep2 RNA Seq | RNA seq datasets of DMSO treated control samples and JQ1 treated samples were aligned to the GRCz11 zebrafish genome Ensembl annotation with ERCC spike in information using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1. featureCount was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation and ERCC annotation. Bioconductor package DESeq2 v1.12.4 was used to analyze differential gene expression using 3 DMSO vs 3 JQ1 treated samples. Genome build: danRer11 Supplementary files format and content: featureCount read count for all sample DESeq2 files for differentially expressed genes | Zebrafish tumor cells | JQ1 was dissolved in DMSO. Animals were treated with JQ1 at 4microM or the same amount of DMSO in individual tanks for 1 or 3 days. Experiments were done using 3 independent animals. | Total RNA was harvested using the miRNeasy Mini Kit Qiagen. ERCC spike in was added based on the total cell number. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong. | The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype animals were treated with JQ1. Tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Total RNAs were harvested from each sample and then applied for RNA seq analysis. | cell type:Zebrafish tumor cells|condition:control|treatment:DMSO | GSM5602241 | GSM5602241: Tumor cells DMSO day1 rep2 RNA Seq; Danio rerio; RNA Seq | GSM5602241 | 1 | Total RNA was harvested using the miRNeasy Mini Kit Qiagen. ERCC spike in was added based on the total cell number. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong. | GEO Accession:GSM5602241 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP339154 | D1_D2_1.fq.gz D1_D2_2.fq.gz | fastq fastq | 4464096200.0 | 44640962.0 | GSM5602241 r1 | 0:100 1:100 | A:1185692334;C:1031585570;G:1050205768;T:1196612528;N:0 | 100 | 100 | 1185692334 | 1031585570 | 1050205768 | 1196612528 | 0 | SRX12388680 | SRS10358682 | SRA1302013 | GEO | Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore | 1 | 0.94785 | 0.24425 | 0.78165 | 0.4975 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Singapore | 2021-09-28 | Undetermined | Undetermined | Cancer or Tumor | Cancer or Tumor |