|
| Status |
Public on Jun 03, 2022 |
| Title |
Sample 4_crispr_plustet_E2_1_S16 |
| Sample type |
SRA |
| |
|
| Source name |
Breast cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
strain: MCF7Tet-Off cell line
cell model: only ERα expression
treatment: cell cultured with tetracycline 2ug/ml, treated with E2 (10nM) for 24h
|
| Treatment protocol |
sample 1-3, 7-9 treated with ethanol, 4-6, 10-12 treated with E2 (10nM) for 24 h
|
| Growth protocol |
MCF7 cells are cultured with DMEM with 10%FBS and 1%P/S, sample 1-6 cultured with tetracycline (2ug/ml), 7-12 cultured with normal DMEM without tetracycline
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted use RNeasy Plus Mini Kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Basecall files were converted and demultiplexed to fastq files with bcl2fastq v2.20.0.422
Bcl files were converted and demultiplexed to fastq using the bcl2fastq program. STAR was used to index the human reference genome (hg38/GRCh38) and align the resulting fastq files. Mapped reads were then counted in annotated exons using featureCounts. The entrez gene annotations and reference genome were obtained from UCSC. The count table from featureCounts was imported into R/Bioconductor and differential gene expression was performed using the EdgeR package and its general linear models pipeline. For the gene expression analysis genes that had 1 count per million in 3 or more samples were used and normalized using TMM normalization. P values were adjusted for multiple hypothesis testing (FDR), and genes with and an adjusted p value under 0.05 were termed significant.
Genome_build: hg38/GRCh38
Supplementary_files_format_and_content: rawCounts
|
| |
|
| Submission date |
Aug 19, 2021 |
| Last update date |
Jun 03, 2022 |
| Contact name |
Dandan Song |
| E-mail(s) |
dandan.song@scilifelab.se
|
| Organization name |
Karolinska Institutet
|
| Department |
Biosciences and Nutrition
|
| Street address |
Tomtebodavägen 23
|
| City |
Stockholm |
| ZIP/Postal code |
171 65 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE182431 |
Overlapping and distinct functions between ERα and ERβ homodimers and corresponding transcriptomes in the same cellular context |
|
| Relations |
| BioSample |
SAMN20862129 |
| SRA |
SRX11825852 |
