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Sample GSM1022268 Query DataSets for GSM1022268
Status Public on Jan 17, 2013
Title H3K4me1_washout_IL4_UT
Sample type SRA
Source name Primary bone marrow-derived macrophages, no treatment, H3K4me1 ChIP
Organism Mus musculus
Characteristics strain/background: C57BL/6
cell type: bone marrow-derived macrophages (7th day of differentiation)
treatment: none
chip antibody: anti-H3K4me1
antibody vendor, catalog #: Abcam, ab8895
Treatment protocol Macrophages were subjected to different treatments (see individual samples for details).
Growth protocol Bone marrow cells isolated from 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 were reversed by incubation overnight at 65ºC. DNA was then purified by QIAquick columns (Qiagen) and quantified using PicoGreen (Invitrogen). ChIP DNA was prepared for Illumina HiSeq 2000 or Genome Analyzer II sequencing using a standard protocol consisting of 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 the manufacturer's instructions. Library preparation was carried out on SPRIworks Fragment Library System.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Description Chromatin IP against H3K4me1.
Data processing Reads were 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. Each IP was compared to input DNA derived from BMDM (GEO Sample GSM487453).
Genome_build: mm9 (NCBI Build 37)
Supplementary_files_format_and_content: *_peaks.bed: List of the peaks called by MACS.
Submission date Oct 17, 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 GPL13112
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 SRX197239
BioSample SAMN01767786

Supplementary file Size Download File type/resource
GSM1022268_WASHOUT_IL4_MF_H3K4me1_NT_input_peaks.bed.gz 1.0 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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