|
Status |
Public on Nov 20, 2023 |
Title |
TP73 ex2-3del_DOX_8wkcoculture_rep1 |
Sample type |
SRA |
|
|
Source name |
TL-Om1 cells
|
Organism |
Homo sapiens |
Characteristics |
cell line: ATL knockdown: deletion (8 weeks co-culture) treatment: Dox
|
Treatment protocol |
TL-Om1 cells were induced with doxycycline for 3 days to induce deletion. The cells were also cultured with control cells in the same flask for 8 weeks. In each condition, total RNA were harvested from sorted cells.
|
Growth protocol |
TL-Om1 cells were cultured in RPMI-1640 medium supplemented with 10% FBS and Pen/Strep.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was harvested using the miRNeasy Mini Kit (Qiagen). Strand-specific library construction and sequencing of paired-end, 100-bp-long reads by the DNBseq 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 |
DNBSEQ-T7 |
|
|
Description |
Replicate 1
|
Data processing |
RNA-seq reads were mapped to curated RefSeq transcripts (NM and NR transcripts) using salmon (version 1.1.0) with the options “--gcBias --seqBias –validateMappings”. The salmon index file was created with default settings. Transcript-level read counts were converted to gene-level read counts using tximport (version 1.18.0). Differentially expressed genes were estimated using DESeq2 (version 1.30.0). Supplementary_files_format_and_content: txt file for differentially expressed genes
|
|
|
Submission date |
Jul 30, 2021 |
Last update date |
Nov 20, 2023 |
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 |
GPL29480 |
Series (2) |
GSE181212 |
RNA-seq analysis after TP73 exons 2-3 deletion in TL-Om1 cells |
GSE181215 |
Requirement for TP73 in cancer cell maintenance and genetic alterations originating from its intragenic super-enhancer |
|
Relations |
BioSample |
SAMN20504912 |
SRA |
SRX11611558 |