|
| Status |
Public on Jul 12, 2022 |
| Title |
COMBO, 8-1 |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MB-231
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
cell type: triple-negative breast cancer (TNBC) cell
treatment: Combo (EPZ + P38i)
|
| Treatment protocol |
When tumors reached 100 mm3 mice were treated 5 days/weeks by intraperitoneal (i.p.) injection with 4% DMSO-30% PEG 300-5% Tween 80 (control), P38i, SB202190 (1mg/kg/day), EZH2i, EPZ-6428 (10mg/kg/day) or a combination of SB202190 and EPZ-6438
|
| Growth protocol |
MDA-MB-231 cells were orthotopically injected into the right inguinal mammary fat pad of anesthetized mice at a concentration of 2 x10^6 cells resuspended in 50 μl of Matrigel (n = 10 mice per group)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
QuantSeq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
counts_raw.txt column: 10
|
| Data processing |
Trimmed using Trim_Galore (v 0.5.0)
Aligned using STAR (v 2.6.0)
UMI collapsed using Lexogen’s supplied collapse_UMI_bam binary
Assembly: hg19
Supplementary files format and content: tab-delimited text of raw counts
|
| |
|
| Submission date |
Jul 08, 2022 |
| Last update date |
Jul 12, 2022 |
| Contact name |
Bioinformatics Core |
| E-mail(s) |
bioinformatics@umich.edu
|
| Organization name |
University of Michigan
|
| Street address |
BRCF Bioinformatics Core, 2800 Plymouth Rd
|
| City |
Ann Arbor |
| State/province |
Mi |
| ZIP/Postal code |
48109-2800 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE207795 |
EZH2 T367 phosphorylation activates p38 signaling through lysine methylation to promote breast cancer progression [RNA-seq] |
| GSE207796 |
EZH2 T367 phosphorylation activates p38 signaling through lysine methylation to promote breast cancer progression |
|
| Relations |
| BioSample |
SAMN29613391 |
| SRA |
SRX16101760 |
