|
| Status |
Public on Mar 14, 2022 |
| Title |
Tumor cells, Late stage, IRF4;p53+/- fish 5_scRNA-Seq |
| Sample type |
SRA |
| |
|
| Source name |
Zebrafish cells, transgenic
|
| Organism |
Danio rerio |
| Characteristics |
tissue: tumors driven by overexpression of human IRF4
sorted cells: mCherry sorted cells
genotype: IRF4 overexpression and p53 mutation
time: Late stage
|
| Treatment protocol |
No treatment
|
| 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, 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.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After sorting, the cells were washed and processed for barcoding using the 10x Genomics Chromium Single Cell 3' 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
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
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
|
| |
|
| Submission date |
Feb 11, 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 |
GPL23085 |
| Series (2) |
| GSE166646 |
Single cell RNA-seq analysis for normal lymphocytes and IRF4-driven zebrafish tumors |
| GSE166650 |
Zebrafish tumors driven by overexpression of human IRF4 |
|
| Relations |
| BioSample |
SAMN17882782 |
| SRA |
SRX10083163 |
