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Status |
Public on Feb 27, 2020 |
Title |
Bcell_4H8_Spt5dep1_20454 |
Sample type |
SRA |
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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)
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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.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
|
|
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
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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 |
GPL13112 |
Series (1) |
GSE132029 |
Regulation of enhancer transcription by Spt5 directly couples enhancer activation with enhancer function |
|
Relations |
BioSample |
SAMN11909945 |
SRA |
SRX5938661 |