|
| Status |
Public on Nov 20, 2023 |
| Title |
dCas9_TP73_DMSO_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
TL-Om1 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: ATL
knockdown: control
treatment: DMSO
|
| Treatment protocol |
TL-Om1 cells were incubated with doxycycline for 3 days, after which total RNA were harvested.
|
| 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 2
|
| 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) |
| GSE181208 |
RNA-seq analysis after genetic overexpression or knockdown of TP73 in TL-Om1 cells |
| GSE181215 |
Requirement for TP73 in cancer cell maintenance and genetic alterations originating from its intragenic super-enhancer |
|
| Relations |
| BioSample |
SAMN20504902 |
| SRA |
SRX11611381 |
