|
| Status |
Public on Sep 24, 2017 |
| Title |
MCF7_DEX_60min_1 |
| Sample type |
SRA |
| |
|
| Source name |
MCF7
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: DEX
duration: 60min
|
| Treatment protocol |
Cells were starved overnight in medium without serum and then stimulated with EGF or DEX for 60 minutes before sequencing
|
| Growth protocol |
MCF7 and IMR90 cells were grown in DME medium supplemented with 10% fetal bovine serum (FBS).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using the 5-prime kit and poly-A selected on magnetic beads using the TruSeq RNA Library Preparation Kit v2
Library were constructed using the TruSeq RNA Library Preparation Kit v2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
sixty base-pair long, single-end, RNA-Seq reads were aligned to the human genome with STAR (Dobin et al., 2013).
Reads per gene were counted using the summarizeOverlaps function from the GenomicAlignments package in R with the Refseq transcriptome as reference. Reads per gene were normalized across samples using the DESeq2 package.
Genome_build: hg19
Supplementary_files_format_and_content: Normalized (according to library size) reads for all Refseq genes
|
| |
|
| Submission date |
Feb 02, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yehoshua Enuka |
| E-mail(s) |
ys.enuka@gmail.com
|
| Phone |
+972-54-2345623
|
| Organization name |
Weizmann Institute of Science
|
| Department |
Biological Regulation
|
| Lab |
Yarden
|
| Street address |
Herzl 234
|
| City |
Rehovot |
| ZIP/Postal code |
76100 |
| Country |
Israel |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE94063 |
Epigenetic mechanisms underlie the crosstalk between growth factors and a steroid hormone |
| GSE94408 |
Epigenetic mechanisms underlie the crosstalk between growth factors and a steroid hormone [IMR90_MCF7_RNA-Seq] |
|
| Relations |
| BioSample |
SAMN06290032 |
| SRA |
SRX2533078 |
