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Sample GSM665925 Query DataSets for GSM665925
Status Public on Mar 30, 2012
Title WT macrophage_SMRT_ChIPSeq
Sample type SRA
Source name wild-type primary bone marrow-derived macrophages
Organism Mus musculus
Characteristics strain: C57BL/6
age: 10 month old
gender: male
antibody: anti-SMRT
Treatment protocol Cells were fixed with 2 mM disuccinimidyl glutarate for 30 minutes, then with 1% formaldehyde for 10 minutes, then glycine-quenched and harvested.
Growth protocol Bone marrow was purified and differentiated in DMEM containing 20% fetal bovine serum, 30% L929 conditioned media, and antibiotics for 5 days, then re-plated in macrophage serum free media (Invitrogen) overnight.
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the ChIP seq sample prep kit (IP-102-1001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of 200-400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Description Chromatin IP against SMRT
Data processing Alignment: Sequence reads were obtained and mapped to the mouse (July, 2007) mm9 genome using Bowtie. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 200 bp to create summary windows.
Submission date Feb 02, 2011
Last update date May 15, 2019
Contact name Ruth T Yu
Organization name Salk Institute
Department Gene Expression Lab
Lab Ronald Evans
Street address 10010 N Torrey Pines Rd
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
Platform ID GPL11002
Series (2)
GSE27033 Genome-wide location analysis of SMRT and NCoR in wild-type and Bcl6 knockout macrophages
GSE27060 A Bcl6-Smrt/Ncor repression program controls atherosclerosis
SRA SRX040544
BioSample SAMN00205395

Supplementary file Size Download File type/resource
GSM665925_SMRT_WT.txt.gz 670.5 Mb (ftp)(http) TXT
GSM665925_SMRT_WTpeaks.txt.gz 597.4 Kb (ftp)(http) TXT
GSM665925_SMRT_macrophage.ucsc.bedGraph.gz 52.0 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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