|
| Status |
Public on Oct 25, 2016 |
| Title |
MCF7 E2_7 |
| Sample type |
SRA |
| |
|
| Source name |
MCF7-Luc cells
|
| Organism |
Homo sapiens |
| Characteristics |
mutation status (esr1): WT
treatment: 10nM E2
|
| Treatment protocol |
17ß-estradiol (E2), purchased from Sigma-Aldrich, was prepared in ethanol. Cells were treated with either E2 or ethanol, as vehicle control, for 8 hours before RNA extraction.
|
| Growth protocol |
Cell lines were routinely cultured in DMEM containing 10% FCS. For estrogen depletion experiments, the cells were transferred to DMEM lacking phenol red and containing 5% dextran-coated charcoal-stripped FCS (DSS) for 72 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using RNeasy Mini Kit (Qiagen), with DNase treatment to remove genomic DNA.
cDNA libraries were prepared using TruSeq® RNA Sample Preparation Kit v2 (Illumina, UK), according to manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample_7
|
| Data processing |
Illumina CASAVA 1.8.4 software used for basecalling
Quality control checks were performed on raw sequence reads using FastQC 0.11.3 and then reads were trimmed using FASTX trimmer 0.0.13 to remove biased sequence composition in the first 15 bases. All samples, except one Y537S E2 sample, passed quality control. This sample was removed from subsequent analysis.
Reads were aligned to the human genome (Homo sapiens UCSC hg19) using TopHat 2.0.14.
Aligned reads were counted by HTSeq 0.6.1.
Total read counts for each sample were obtained by adding together the read counts resulting from both sequencing lanes (5 and 6)
The R package ‘DESeq2’ was used to normalize counts using a regularized log transformation (rlog). Shrunken log2 fold changes were also calculated to determine DEGs (differentially expressed genes) between conditions, while minimizing the fold change variation of low expressed genes. For more information on DESeq2, see Love et al., 2014.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Excel files include output from DESeq2 for DEGs between conditions (log2 fold changes, p-adjusted values)
|
| |
|
| Submission date |
Feb 24, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Van Thuy Mai Nguyen |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute of cancer research
|
| Department |
Cancer Biology
|
| Street address |
237 Fulham Rd, Chester Beatty Laboratories, third floor
|
| City |
London |
| ZIP/Postal code |
SW3 6JB |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE78285 |
Modeling the ESR1 tyrosine 537 mutation with CRISPR-Cas9 for mechanistic studies and evaluation of therapeutic approaches for metastatic breast cancer [RNA-Seq] |
| GSE78286 |
Modeling the ESR1 tyrosine 537 mutation with CRISPR-Cas9 for mechanistic studies and evaluation of therapeutic approaches for metastatic breast cancer |
|
| Relations |
| BioSample |
SAMN04515283 |
| SRA |
SRX1599025 |
