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Sample GSM2752816 Query DataSets for GSM2752816
Status Public on Jun 13, 2018
Title RNA-seq_Control_rep1 (ERCC spike-in)
Sample type SRA
Source name mESCs
Organism Mus musculus
Characteristics cell line: E14 cell line
treatment: control
Growth protocol The E14 cell line (mESCs) was cultured at 37 °C, 7.5% CO2, on 0.1% gelatin coated plates, in DMEM + GlutaMax™ (Gibco) with 15% fetal bovine serum (Gibco), MEM non- essential amino acids (Gibco), penicillin/streptomycin (Gibco), 550 µM 2-mercaptoethanol (Gibco), and 10 ng/ml of leukaemia inhibitory factor (LIF) (eBioscience). 293T (HEK), N2a, and B16 cell lines were cultured at 37 °C, 5% CO2 in DMEM + GlutaMax™ (Gibco) with 10% fetal bovine serum (Gibco), and penicillin/streptomycin (Gibco).
Extracted molecule total RNA
Extraction protocol Forty-eight hours (48h) after transfection, puromycin (2 µg /ml) selection was applied for an additional 24h period, before cell collection and RNA preparation. Total RNA was obtained via phenol-chloroform extraction (QIAzol Lysis Reagent – QIAGEN) followed by purification via Quick-RNA™ MicroPrep (Zymo Research). ERCC spike-in controls were added according to the manufacturer instructions
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
Description processed data file:
processed data file: Normalized.counts.RNA-seq.Control_vs_Ssrp1KD.txt
Data processing RNA-seq files were aligned using STAR (v 2.5.1b). Counts were normalized using edgeR and differential expression was performed with limma.
Genome_build: mm10
Submission date Aug 24, 2017
Last update date May 15, 2019
Contact name Peter Tessarz
Organization name Max Planck Institute
Street address Joseph-Stelzman-Str 9b
City Cologne
State/province Nordrhein-Westfalen
ZIP/Postal code 50931
Country Germany
Platform ID GPL21103
Series (1)
GSE90906 Transcriptional repression by FACT is linked to regulation of chromatin accessibility at the promoter of ES cells
BioSample SAMN07551951
SRA SRX3124465

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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