|
| Status |
Public on Oct 02, 2015 |
| Title |
MCF10a WT_t=0_replicate1 |
| Sample type |
SRA |
| |
|
| Source name |
MCF10a Breast Epithelium Cell line
|
| Organism |
Homo sapiens |
| Characteristics |
genotype: WT
cell line: MCF10a
condition: no EGF + DMSO
timepoint: 0
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cells using the Qiagen RNeasy kit.
RNA-seq libraries are produced using the Truseq RNA sample prpeparaion kit from Illumina. Amplified libraries were assessed for quality and quantity using High-Sensitivity DNA chips on the Agilent Bioanalyzer, and the KAPA Library Quantification Kit for Illumina (KAPA Biosystems).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Preparation / starvation: Day1: cells were seeded at 320000 cells in 60mm dish in growth medium. Day2: cells are starved in serum-EGF-Insulin for 18h.
Stimulation: Day3: Cells were pre-incubated for 20 min with A66 (2uM) or DMSO (vehicule for A66), then stimulated with EGF (10ng/ml) +/- A66 or DMSO for 15, 40, 90, 180, 300 min or not stimulated (t=0). Except for A66 no EGF where cells are left in A66 for 300 min without EGF.
|
| Data processing |
Raw FastQ data were trimmed with Trim Galore (v0.3.8, default parameters; www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and mapped to the human GRCh37 genome assembly using TopHat v2.0.10, with a Bowtie2 index file from Illumina iGenomes. Raw counts for DESeq2 analysis were generated at gene level using HTSeq v0.6.1 (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html). The 1.4.5 version of DESeq2 was used to perform differential expression analysis.
Genome_build: human GRCh37
Supplementary_files_format_and_content: Raw counts RNA-Seq data files are tab delimited and contain the following columns: (1) Gene ID (Ensembl); (2-76) Sample Raw Counts.
Supplementary_files_format_and_content: The RNA-Seq_RPKMs.txt file is tab delimited and includes the gene expression in RPKM units.
|
| |
|
| Submission date |
Jun 12, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Felix Krueger |
| E-mail(s) |
fkrueger@altoslabs.com
|
| Organization name |
Altos Labs
|
| Department |
Bioinformatics
|
| Street address |
Granta Park
|
| City |
Cambridge |
| ZIP/Postal code |
CB21 6GP |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE69822 |
Perturbations of PIP3 signaling trigger a global remodeling of mRNA landscape and reveal a transcriptional feedback loop |
|
| Relations |
| BioSample |
SAMN03771337 |
| SRA |
SRX1057364 |
