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Sample GSM879921 Query DataSets for GSM879921
Status Public on Feb 24, 2012
Title H3K36me3_ChIPSeq
Sample type SRA
 
Source name NIH-3T3_H3K36me3_ChIPSeq
Organism Mus musculus
Characteristics cell line: NIH-3T3
cell type: Mouse embryonic fibroblast cell
chip antibody: H3K36me3
chip antibody vendor: Abcam
chip antibody cat. #: ab9050
chip antibody lot/batch #: 136353
Treatment protocol Cells were cross-linked with 1% formaldehyde in cell culture medium for 10 min at 37C. After quenching with the addition of 125 mM glycine for 5 min at 37C, the cells were washed twice with ice-cold PBS containing proteinase inhibitor. Cells were collected after each wash by centrifugation at 2,500g for 3 min. Finally cells were aliquoted, frozen and kept at -80C.
Growth protocol Standard 3T3 growth conditions: 37C, .05% CO2. Medium was DMEM (Gibco) with 10% FCS (Hyclone). Cells were split 1:8 every 2-3 days.
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared as follows: 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 ~250 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 II following the manufacturer's protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
Description 31849.0
Data processing Sequence reads were mapped to the mouse genome assembly mm8 using MAQ v 0.7.1, and these alignments were converted to BED format. Read density maps were produced using IGVTools v 1.5.10 to generate a WIG file, which was then converted to BigWig format using the UCSC WigToBigWig conversion utility v 4.
Genome Build:
314G6AAXX.1.bed: mm8
3158LAAXX.5.bed: mm8
3158LAAXX.8.bed: mm8
314G6AAXX.1.bw: mm8
3158LAAXX.5.bw: mm8
3158LAAXX.8.bw: mm8
 
Submission date Feb 23, 2012
Last update date May 15, 2019
Contact name Joseph M Zullo
E-mail(s) joseph_zullo@hms.harvard.edu, jmz4@uchicago.edu
Organization name University of Chicago
Department MGCB
Lab Singh
Street address 929 E 57th Street
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
 
Platform ID GPL9250
Series (2)
GSE36048 A molecular mechanism for compartmentalization and silencing of chromatin domains at the nuclear lamina [ChIP-seq]
GSE36049 A molecular mechanism for compartmentalization and silencing of chromatin domains at the nuclear lamina
Relations
SRA SRX121864
BioSample SAMN00792228
Named Annotation GSM879921_314G6AAXX.1.bed.gz
Named Annotation GSM879921_314G6AAXX.1.bw
Named Annotation GSM879921_3158LAAXX.5.bed.gz
Named Annotation GSM879921_3158LAAXX.5.bw
Named Annotation GSM879921_3158LAAXX.8.bed.gz
Named Annotation GSM879921_3158LAAXX.8.bw

Supplementary file Size Download File type/resource
GSM879921_314G6AAXX.1.bed.gz 205.5 Mb (ftp)(http) BED
GSM879921_314G6AAXX.1.bw 230.8 Mb (ftp)(http) BW
GSM879921_3158LAAXX.5.bed.gz 245.0 Mb (ftp)(http) BED
GSM879921_3158LAAXX.5.bw 251.5 Mb (ftp)(http) BW
GSM879921_3158LAAXX.8.bed.gz 238.0 Mb (ftp)(http) BED
GSM879921_3158LAAXX.8.bw 248.3 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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