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Sample GSM1826979 Query DataSets for GSM1826979
Status Public on Aug 31, 2015
Title ATF7_pMp_Whole_E
Sample type genomic
 
Source name Peritoneal macrophages from wild-type mice
Organism Mus musculus
Characteristics treatment: ChIP using ATF7 Ab
strain: wild-type in C57BL/6 background
cell-type: peritoneal macrophage
Treatment protocol Unterated
Growth protocol Peritoneal resident macrophages were collected by peritoneal washing, without thioglycollate injection, and were incubated in Macrophage-SFM (Life Tech.) containing 100 U/ml penicillin and 100 µg/ml streptomycin. Before and after overnight incubation, dish surfaces were washed by pipetting with PBS to remove non-adherent cells such as lymphocytes.
Extracted molecule genomic DNA
Extraction protocol Peritoneal macrophages were crosslinked with 1% formaldehyde for 8 min at RT and after washing with ice-cold PBS prepared for ChIP. Chromatin immunoprecipitation was performed using ATF7 antibody. The lysate was incubated with the antibodies over night at 4 degree, and then protein A dynabeads (Life Tech.) were added and incubated for 3 hours at 4 degree. The beads were washed several times and eluted with elution buffer (50 mM Tris, 10 mM EDTA, 1 % SDS). After reverse cross-linking by overnight incubation at 65 degree, the eluate from the beads was treated with Proteinase K. Contaminating RNA was removed by RNAse treatment. The sample was further purified by phenol-chloroform extraction and using the PCR purification kit (Qiagen).
Label biotin
Label protocol DNA was amplified by IVT (In vitro transcription) method. For the labeling, DNA was fragmented by DNaseI. DNA was end-labeled by Terminal Transferase with biotin‐N11‐ddATP.
 
Hybridization protocol Each sample was hybridized to the array in 200 ul containing 1XHybridization buffer (Affymetrix), 50pM Control oligonucleotide (oligo B2, Affymetrix), Herring Sperm DNA (0.1mg/ml), Acetylated BSA (0.5mg/ml), and 7% DMSO. Samples were denatured at 100C for 10 minutes, and then put on ice before being hybridized for 16 hours at 45C in an hybridization oven (GeneChip Hybridization Oven 640, Affymetrix). Washing and scanning protocol provided by Affymetrix was performed automatically on a fluidics station (GeneChip fluidics station 450, Affymetrix).
Scan protocol Arrays were scanned using the Genechip Scanner3000 7G following the library array description.
Description tiling_ATF7_MAT_signalNorm.bed
ATF7 distribution in whole genome of peritoneal resident macrophage. Array E of A-G
Data processing We calculated Model-Based Analysis of Tiling-Arrays (MAT) score software implementation in R (rMAT package). Signals were mapped against mouse genome assembly mm8 (NCBI Build 36), and ChIP was normalized against input for both Mouse Tiling 2.0R Arrays and Mouse Promoter 1.0R Arrays. Normalization and MAT score computations were performed using default parameters (Bandwidth = 600; MaxGap = 300; and MinProbe = 8) and the ‘pair-binned’ method for normalization. Enriched regions (peaks) were then detected using a p-value threshold set to 10-10 for both arrays. All detected peaks have a false-discovery rate, as computed by rMAT, lower than 1%.
The resulting BED files are generated by rMAT using default parameters (Bandwidth = 600; MaxGap = 300; and MinProbe = 8). Enriched regions are then detected using a p-value threshold set to 10-10 for both arrays.
 
Submission date Jul 20, 2015
Last update date Aug 31, 2015
Contact name Keisuke Yoshida
E-mail(s) keiyoshida@rtc.riken.jp
Organization name RIKEN
Lab Molecular Genetics Laboratory
Street address 3-1-1 Koyadai,
City Tsukuba
State/province Ibaraki
ZIP/Postal code 305-0074
Country Japan
 
Platform ID GPL6448
Series (2)
GSE71112 ATF7 mediates lipopolysaccharide-induced epigenetic changes in macrophages involved in innate immunological memory (ChIP)
GSE71113 ATF7 mediates lipopolysaccharide-induced epigenetic changes in macrophages involved in innate immunological memory

Supplementary file Size Download File type/resource
GSM1826979_ATF7_Mp_IP_E1.CEL.gz 29.5 Mb (ftp)(http) CEL
GSM1826979_ATF7_Mp_IP_E2.CEL.gz 28.7 Mb (ftp)(http) CEL
GSM1826979_ATF7_Mp_IP_E3.CEL.gz 27.9 Mb (ftp)(http) CEL
GSM1826979_ATF7_Mp_WCE_E1.CEL.gz 28.8 Mb (ftp)(http) CEL
GSM1826979_ATF7_Mp_WCE_E2.CEL.gz 28.1 Mb (ftp)(http) CEL
GSM1826979_ATF7_Mp_WCE_E3.CEL.gz 28.4 Mb (ftp)(http) CEL
Processed data are available on Series record

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