|
| Status |
Public on Jul 13, 2022 |
| Title |
MC38ishTDO2-48h-3 |
| Sample type |
SRA |
| |
|
| Source name |
MC38 cell line
|
| Organism |
Mus musculus |
| Characteristics |
derivation: MC-38 Cell Line derived from C57BL6 murine colon adenocarcinoma cells
tissue: colon adenocarcinoma cell line
|
| Treatment protocol |
Inducible shTDO2 MC38 cell lines were treated with 1 μM of Doxycycline (Sigma-Aldrich, Cat# D9891) for indicated periods to induce TDO2 knockdown.
|
| Growth protocol |
The CRC cell lines MC38 (RRID:CVCL_B288) and its isogenic cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) containing 10% Tet System Approved FBS (Clontech) and 100 U/ml ampicillin/penicillin. All cells were confirmed to be mycoplasma-free and maintained at 37 °C and 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were pelleted and RNA was isolated with RNeasy Mini Kit (Qiagen, Cat# 74104). RNA was reverse-transcribed into cDNA following SuperScriptTM III First-Strand Synthesis SuperMix (Invitrogen, Cat# 18080400). qRT-PCR was performed using SYBR Green PCR Master Mix (Thermo Fisher Scientific) in a 7500 Fast Real-Time PCR instrument (Applied Biosystems).
For RNA sequencing, RNAs were isolated from ishTDO2 APC-WT and APC-KO MC38 cells with and without Dox treatment (biological triplicates per group) using the RNeasy Mini Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 using STAR software.
The HTSeq-count program was used to generate raw read counts for each gene
Assembly: mm10
Supplementary files format and content: Raw gene counts and RPKM
|
| |
|
| Submission date |
Apr 15, 2022 |
| Last update date |
Aug 03, 2022 |
| Contact name |
Chang-Jiun Wu |
| Organization name |
University of Texas, MD Anderson Cancer Center
|
| Department |
Genomic Medicine
|
| Lab |
DePinho Lab
|
| Street address |
1515 Holcombe Blvd
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE200908 |
Synthetic Essentiality of Tryptophan 2,3-dioxygenase 2 in APC-Mutated Colorectal Cancer I |
| GSE200910 |
Synthetic Essentiality of Tryptophan 2,3-dioxygenase 2 in APC-Mutated Colorectal Cancer |
|
| Relations |
| BioSample |
SAMN27603952 |
| SRA |
SRX14871013 |
