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Sample GSM767736 Query DataSets for GSM767736
Status Public on Apr 09, 2012
Title H3K4me3_MLL2_KO_UT
Sample type SRA
 
Source name ChIP_H3K4me3_MLL4_KO_Untreated
Organism Mus musculus
Characteristics strain background: mixed C57BL/6 (94%) and 129/Ola (6%)
genotype/variation: Wbp7-/-
cell type: Primary BMDM cells (7th day of differentiation)
chip antibody: Anti- Histone H3 trimethyl Lys4 (Active Motif, Catolog # 39159)
treatment: No treatment
Treatment protocol Macrophages were stimulated with lipopolysaccharide (LPS, 10 ug/ml)
Growth protocol Bone marrow cells isolated from mixed C57BL/6 (94%) and 129/Ola (6%) mice were plated in 10 cm plates in 5ml of BM-medium (high glucose DMEM supplemented with 20% low endotoxin fetal bovine serum, 30% L929-conditioned medium, 1% glutamine, 1%, Pen/Strep, 0.5% Sodium Pyruvate, 0.1% β-mercaptoethanol). Cultures were fed with 2.5 ml of fresh medium every two days.
Extracted molecule genomic DNA
Extraction protocol ChIP lysates were generated from 2x10^8 cells. Cells were fixed in 1% formaldehyde for 10min. Lysate was immunoprecipitated with 10ug of antibody. Antibodies were pre-bound overnight to 100ul of G protein-coupled paramagnetic beads in PBS/BSA 0.5%. Beads were then added to lysates (the preclearing step was omitted) and incubation was let to proceed overnight. Beads were washed 6 times in a modified RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and once in TE containing 50mM NaCl. DNA was eluted in TE containing 2% SDS and crosslinks reversed by incubation overnight at 65C. DNA was then purified by Qiaquick columns (Qiagen) and quantified using PicoGreen (Invitrogen). ChIP DNA was prepared for Solexa 2G sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection on gel and PCR. A mixture of T4 DNA polymerase, DNA polymerase I and T4 kinase was used according to manufacturer’s instruction.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
Description Chromatin IP against H3K4me3
Data processing Alignment: sequence reads were mapped to the mouse mm9 genome using Bowtie (PMID: 19261174). All reads with a unique match to the genome with two or fewer mismatches were retained.
 
Submission date Jul 27, 2011
Last update date May 15, 2019
Contact name Iros Barozzi
E-mail(s) iros.barozzi@meduniwien.ac.at
Organization name Medical University Vienna
Street address Borschkegasse 8a
City Vienna
ZIP/Postal code 1090
Country Austria
 
Platform ID GPL9250
Series (2)
GSE30972 The Histone Methyltransferase Wbp7 Controls Macrophage Function through GPI Glycolipid Anchor Synthesis. [ChIP_seq]
GSE30973 The Histone Methyltransferase Wbp7 Controls Macrophage Function through GPI Glycolipid Anchor Synthesis
Relations
SRA SRX085352
BioSample SAMN00690260

Supplementary file Size Download File type/resource
GSM767736_H3K4me3_MLL2_KO_UT.SAM.gz 1.3 Gb (ftp)(http) SAM
GSM767736_H3K4me3_MLL2_KO_UT_input_peaks.bed.gz 193.1 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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