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Sample GSM3834678 Query DataSets for GSM3834678
Status Public on Feb 27, 2020
Title Bcell_4H8_Spt5dep1_20454
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 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
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
BioSample SAMN11909945
SRA SRX5938661

Supplementary file Size Download File type/resource 82.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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