|
| Status |
Public on Feb 27, 2020 |
| Title |
Bcell_4H8_Spt5dep2_40939 |
| Sample type |
SRA |
| |
|
| Source name |
primary activated splenic B lymphocytes
|
| Organism |
Mus musculus |
| Characteristics |
antibody: RNA Pol II (4H8)
cell type: Supt5hFl/- Rosa26ERT2-cre/+ primary mature B cells
treatment: 4-hydroxy tamoxifen (4-HT)
|
| Treatment protocol |
Primary acttivated B cells were activated for 28h prior to the addition of 2 uM 4-HT for 32h (total of 60 h B cell activation with 32h 4-HT treatment) and then harvested for all downstream applications.
|
| Growth protocol |
Primary immature B cells were isolated from spleens of Supt5hFl/-Rosa26ERT2-cre/+ and Rosa26ERT2-cre/+ mice and cultured in complete RPMI medium wit IL4/LPS stimulation.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIPseq and ChIP-qPCR were performed as described without modifications (Pavri et al., 2010). In short, 20x10^6 cells were crosslinked with 1% HCHO for 10 min at 37 degree. After quenching with 0,125 M glycine, cells were sonicated with the Diagenode Bioruptor sonication machine.
After chromatin-immunprecipitation, samples were end-repaired with the Epicenter End-Repair Kit. After A-tailing the samples with Klenow (exo-) enzyme, NEXTflex adapters were ligated to the samples and then purified with AMPure XP beads. PCR amplification of the libraries was performed with the Phusion-HF enzyme and the NEXTflex primer mix.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Adapters were trimmed from the 3' ends of the reads with cutadapt v1.10.
Trimmed reads larger than 18nt were aligned to the genome using bowtie v1.0.0 (-v 2 --best --strata --tryhard -m 1)
Genome_build: NCBI mm9
Supplementary_files_format_and_content: bigWig of rpm-normalized read densities
|
| |
|
| Submission date |
May 31, 2019 |
| Last update date |
Feb 27, 2020 |
| Contact name |
Tobias Neumann |
| Organization name |
IMP
|
| Street address |
Campus-Vienna-Biocenter 1
|
| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE132029 |
Regulation of enhancer transcription by Spt5 directly couples enhancer activation with enhancer function |
|
| Relations |
| BioSample |
SAMN11909944 |
| SRA |
SRX5938662 |
