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Status |
Public on Jun 13, 2018 |
Title |
RNA-seq_Ssrp1-KD_rep4 (ERCC spike-in) |
Sample type |
SRA |
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Source name |
mESCs
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Organism |
Mus musculus |
Characteristics |
cell line: E14 cell line treatment: Ssrp1 knock down
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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).
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
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Description |
processed data file: RNAseq.limma.allgenes.tab processed data file: Normalized.counts.RNA-seq.Control_vs_Ssrp1KD.txt
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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
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Submission date |
Aug 24, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Peter Tessarz |
E-mail(s) |
ptessarz@age.mpg.de
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Organization name |
Max Planck Institute
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Street address |
Joseph-Stelzman-Str 9b
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City |
Cologne |
State/province |
Nordrhein-Westfalen |
ZIP/Postal code |
50931 |
Country |
Germany |
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Platform ID |
GPL21103 |
Series (1) |
GSE90906 |
Transcriptional repression by FACT is linked to regulation of chromatin accessibility at the promoter of ES cells |
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Relations |
BioSample |
SAMN07551953 |
SRA |
SRX3124472 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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