|
| Status |
Public on Dec 08, 2018 |
| Title |
RNA-Seq MEFs E39I 1h TNF |
| Sample type |
SRA |
| |
|
| Source name |
MEFs
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Mouse Embryonic Fibroblasts (MEFs)
genotype/variation: p65 KO, E38I p65 rescue
tnf stimulation: 1h TNF
|
| Treatment protocol |
HeLa cells and MEFs were stimulated with TNFα (20 ng/ml) for 60 min
|
| Growth protocol |
HeLa and MEF cells were cultured in DMEM (Life Technologies) supplemented with FCS and Penicillin/Streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-Seq cells were harvested and total RNA was isolated using the NucleoSpin RNA Kit (Macherey-Nagel). For ChIP-Seq samples were crosslinked using Formaldehyde, Sonicated and chromatin was extracted using the p65 Antibody. DNA was purified NucleoSpin Gel and PCR Clean UP Kit with buffer NTB (Macherey-Nagel).
RNA-Seq libraries were prepared from total RNA using the TruSeq Stranded total RNA LT kit (Illumina). ChIP-Seq libraries were prepared from purified ChIP DNA with the Microplex Library Preparation Kit (Diagenode)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
RNA-Seq data were aligned to hg38 or mm10 using RNA STAR using a gffread filtered gencode annotation file. Normalized reads were obtained using cufflinks.
|
| |
|
| Submission date |
Jun 26, 2018 |
| Last update date |
Dec 08, 2018 |
| Contact name |
Robert Liefke |
| E-mail(s) |
robert.liefke@imt.uni-marburg.de
|
| Organization name |
Philipps University of Marburg
|
| Department |
Institute of Molecular Biology and Tumor Research (IMT)
|
| Street address |
Hans-Meerwein-Str. 2
|
| City |
Marburg |
| State/province |
Hessen |
| ZIP/Postal code |
35043 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE116284 |
NF-κB p65 dimerization and DNA-binding is important for inflammatory gene expression |
|
| Relations |
| BioSample |
SAMN09497859 |
