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Sample GSM940920 Query DataSets for GSM940920
Status Public on Jan 17, 2013
Title H3K4me3_TGFb1_4h
Sample type SRA
Source name Primary bone marrow-derived macrophages (BMDM)
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: BMDM cells (7th day of differentiation)
antibody: Anti-H3K4me3 (Active Motif #39159)
treatment: TGFb1 (1 ng/ml) for 4hrs
Treatment protocol Macrophages were subjected to different treatment (see individual samples for details)
Growth protocol Bone marrow cells isolated from C57BL/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 65ºC. DNA was then purified by Qiaquick columns (Qiagen) and quantified using PicoGreen (Invitrogen). ChIP DNA was prepared for HiSeq 2000 Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection on gel and PCR with index primers. A mixture of T4 DNA polymerase, DNA polymerase I and T4 kinase was used according to manufacturer’s instruction. Library preparation is carried out on SPRIworks Fragment Library System.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
Description Chromatin IP against H3K4me3
Data processing Reads quality filtered according to the Illumina pipeline
Reads were mapped to the mouse mm9 genome using Bowtie 0.12.7 (PMID: 19261174). All reads with a unique match to the genome with two or fewer mismatches were retained.
Peak calling was performed using MACS 1.4 (PMID 18798982) with default parameters and bw=100 (except for the pol_II for which a bw=300 was used). Each IP was compared to input DNA derived from BMDM (GSM487453).
Genome_build: mm9 (NCBI Build 37)
Supplementary_files_format_and_content: *_peaks.bed, list of the peaks called by MACS
Submission date May 31, 2012
Last update date May 15, 2019
Contact name Iros Barozzi
Organization name Medical University Vienna
Street address Borschkegasse 8a
City Vienna
ZIP/Postal code 1090
Country Austria
Platform ID GPL9250
Series (2)
GSE38377 Latent enhancers unveiled by stimulation expand and adapt the available cis-regulatory repertoire (ChIP-seq)
GSE38379 Latent enhancers unveiled by stimulation expand and adapt the available cis-regulatory repertoire
SRA SRX150869
BioSample SAMN01001301

Supplementary file Size Download File type/resource
GSM940920_MF_TGFb1_4h_input_H3K4me3_peaks.bed.gz 240.2 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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