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Sample GSM2835827 Query DataSets for GSM2835827
Status Public on Mar 06, 2018
Title MEF_4H8_KO_rep2_40946
Sample type SRA
Source name primary mouse embryonic fibroblasts
Organism Mus musculus
Characteristics tissue: primary mouse embryonic fibroblasts
genotype: Supt5hFl/- Rosa26ERT2-cre/+
antibody: RNA Pol II (4H8)
Treatment protocol Primary MEFs were treated with 2 uM 4-HT for 72h and then harvested for all downstream applications.
Growth protocol Primary MEFs were prepared from d13.5 Supt5hFl/+Rosa26ERT2-cre/+ and Rosa26ERT2-cre/+ embryos and cultured in complete DMEM medium to passage 3.
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
processed data files format and content: bigWig of rpm-normalized read densities
Submission date Oct 30, 2017
Last update date May 15, 2019
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)
GSE106313 Regulation of RNA polymerase II processivity by Spt5 is restricted to a narrow window in elongation
BioSample SAMN07946553
SRA SRX3342571

Supplementary file Size Download File type/resource 339.7 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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