|
Status |
Public on Jul 12, 2022 |
Title |
P38, 3-3 |
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: P38
|
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: 4
|
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 |
SAMN29613385 |
SRA |
SRX16101766 |