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Status |
Public on Oct 02, 2015 |
Title |
MCF10a A66_t=300_replicate2 |
Sample type |
SRA |
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Source name |
MCF10a Breast Epithelium Cell line
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Organism |
Homo sapiens |
Characteristics |
genotype: WT cell line: MCF10a condition: EGF Stimulation + A66 (20min preincubation) timepoint: 180 min
|
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).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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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.
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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.
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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 |
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Relations |
BioSample |
SAMN03771283 |
SRA |
SRX1057398 |