|
Status |
Public on Nov 02, 2018 |
Title |
MB231_rep2 |
Sample type |
SRA |
|
|
Source name |
breast cancer cells
|
Organism |
Homo sapiens |
Characteristics |
cell line: MB231 cell type: parental
|
Treatment protocol |
Arginine deiminase (ADI, 0.3 µg/mL 48h) was added to MDA-MB-231 full growth medium.
|
Growth protocol |
DMEM (high glucose) supplemented with 10% FBS and pen/strep.
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was extracted using Trizol protocol. RNA libraries were prepared for sequencing using standard Illumina protocols
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Data processing |
Illumina Casava1.8 software used for basecalling. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie. ReadReads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using software Partek. Genome_build: hg19
|
|
|
Submission date |
Sep 21, 2017 |
Last update date |
May 15, 2019 |
Contact name |
David K. Ann |
E-mail(s) |
dAnn@coh.org
|
Organization name |
City of Hope
|
Street address |
1500 E Duarte Rd
|
City |
Duarte |
State/province |
CA |
ZIP/Postal code |
91010 |
Country |
USA |
|
|
Platform ID |
GPL16791 |
Series (1) |
GSE104105 |
Transcriptional profiling of MDA-MB-231 and its ρ0 cells (lacking mtDNA) after 48h arginine depletion by arginine deiminase (ADI). |
|
Relations |
BioSample |
SAMN07682272 |
SRA |
SRX3203778 |