|
| Status |
Public on Jul 06, 2023 |
| Title |
WT rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
breast
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: breast
cell line: MCF10A
cell type: epithelial cell
genotype: wild type
treatment: no
|
| Treatment protocol |
Cells were seeded in 6-well plates 1 day before RT, which was performed by a Precision X-RAD 320 Biological Irradiator. For a single high dose of RT, cells were irradiated at a single dose of 20 Gy at one time.
|
| Growth protocol |
MCF10A normal breast epithelial cells were grown in DMEM/F12 medium supplemented with 20 ng/ml epithelial growth factor (EGF; Fisher Scientific), 100 ng/ml cholera toxin (Sigma-Aldrich), 10 μg/ml insulin (Sigma-Aldrich), 0.5 mg/ml hydrocortisone (Sigma-Aldrich), and 5% horse serum (Fisher Scientific).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted (Qiagen)
An Illumina TruSeq Stranded Total RNA Library Prep Kit was used to prepare the library after rRNA depletion.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
MCF10A-v2-1_S13
|
| Data processing |
Sequence reads were trimmed for adapter content and low quality bases using Cutadapt version 1.15
Trimmed sequence reads were mapped to GRCh38 using STAR version 2.5.3a
Reads count extraction was done using HTseq-count
The raw reads were normalized using DESeq2 for which there are > 5 reads in at least one sample
Assembly: GRCh38
Supplementary files format and content: tab delimited text file include TPM values for each sample
|
| |
|
| Submission date |
Jul 03, 2023 |
| Last update date |
Jul 06, 2023 |
| Contact name |
Citu . |
| E-mail(s) |
guliasitu40@gmail.com
|
| Organization name |
University of Texas Health Science Centre
|
| Department |
McWilliams School of Biomedical Informatics
|
| Street address |
7000 Fannin Street
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE236331 |
Genome-wide CRISPR screen reveals tumor-intrinsic responses to radiotherapy |
|
| Relations |
| BioSample |
SAMN36271110 |
| SRA |
SRX20866486 |
