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| Status |
Public on Jun 13, 2018 |
| Title |
RNA-seq_Ssrp1-KD_rep1-4 |
| 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).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Fourty-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)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Data processing |
RNA-seq files were aligned using STAR (v 2.5.1b). Counts were normalised using edgeR and differential expression was performed with limma. For cryptic transcription visualisation, replicates( per condition) were merged, converted to bigwig, binned (10 bp), split by strand (forward/reverse), and RPKM normalised
Genome_build: mm10
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| Submission date |
Dec 05, 2016 |
| 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 |
GPL21493 |
| 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 |
SAMN06111828 |
| SRA |
SRX2396610 |
| 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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