|
| Status |
Public on Aug 22, 2020 |
| Title |
NfkB2-/- RelB 0h 2 |
| Sample type |
SRA |
| |
|
| Source name |
MEF_KO_RelB_0h
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: NfkB2-/-
cell type: MEF
treatment: 10ng/ml of TNF for 0h
chip antibody: RelB Antibody (sc-226, Santa Cruz)
|
| Treatment protocol |
For activation, cells were exposed to 10ng/ml of TNF (R&D) for 0 and 6 h
|
| Growth protocol |
MEF cells were cultured in DMEM medium supplemented with 10% FBS (HyClone), Penicillin-Streptomycin-Glutamine (Invitrogen)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cell nuclei were isolated and lysed. The crosslinked chromatin was subjected to fragmentation by sonication (Branson Sonicator). Chromatin immunoprecipitation (ChIP) was performed using anti-RelA antibody (Santa Cruz, sc-372) or anti-RelB antibody (sc-226) bound to 50μl Protein A Dynabeads (Invitrogen).
ChIP seq library were prepared using Nugen Ovation Ultra-low library preparation kit version 2 according to the manufacturer’s protocol (Nugen, San Carlo, CA). The libraries were sequenced on Illumina NextSeq 500 for single end reads
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
S06_KO_RelB_0h_2_S3
|
| Data processing |
Single-end reads were generated by Illumina sequencer and were demultiplexed.
Adapters, if present were removed by cutadapt and bad quality bases (Q<20) were removed.
The cleaned FASTQ files were aligned against mm9 genome using bowtie with "--best --strata" options and unique alignments were reported.
Peaks were called using cisGenome using a window size of 200 bases and a cutoff of 4 reads in total (2 reads from each strand), FDR<0.1 and Fold change >2
KO_Input was used for NfkB2-/- KO samples.
Genome_build: mm9
Supplementary_files_format_and_content: The processed data file contain the rank ordered list of peaks with enrichment values.
|
| |
|
| Submission date |
Sep 14, 2018 |
| Last update date |
Aug 24, 2020 |
| Contact name |
Supriyo De |
| Organization name |
NIA-IRP, NIH
|
| Department |
Laboratory of Genetics and Genomics
|
| Lab |
Computational Biology & Genomics Core
|
| Street address |
251 Bayview Blvd
|
| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21224 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE119961 |
Immune differentiation regulator p100 tunes NF-kB responses to TNF |
|
| Relations |
| BioSample |
SAMN10059861 |
| SRA |
SRX4680245 |
