|
| Status |
Public on Mar 14, 2022 |
| Title |
Tumor cells, JQ1_day3_rep1_RNA-Seq |
| Sample type |
SRA |
| |
|
| Source name |
Zebrafish tumor cells
|
| Organism |
Danio rerio |
| Characteristics |
cell type: Zebrafish tumor cells
condition: treatment
treatment: JQ1
|
| Treatment protocol |
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.
|
| Growth protocol |
The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. After 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.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
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).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
D3_J1
|
| Data processing |
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
|
| |
|
| Submission date |
Sep 28, 2021 |
| Last update date |
Mar 14, 2022 |
| Contact name |
Tze King Tan |
| Organization name |
National University of Singapore
|
| Department |
Cancer Science Institute
|
| Lab |
Takaomi Sanda Lab
|
| Street address |
14 Medical Drive
|
| City |
Singapore |
| ZIP/Postal code |
117599 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL24776 |
| Series (2) |
| GSE166650 |
Zebrafish tumors driven by overexpression of human IRF4 |
| GSE184946 |
RNA-seq analysis for IRF4-driven zebrafish tumors after JQ1 treatment |
|
| Relations |
| BioSample |
SAMN21885847 |
| SRA |
SRX12388688 |
