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Sample GSM1187629 Query DataSets for GSM1187629
Status Public on Jul 18, 2013
Title ChIP_WT_H3K4me3_12wks_str_rep1_rep2
Sample type SRA
Source name R6/2 wildtype littermate, striatum, 12 weeks
Organism Mus musculus
Characteristics strain/background: C57Bl/6 / CBA
genotype/variation: wild type
tissue: brain striatum
age: 12 weeks
chip antibody: H3K4me3 (Millipore, cat 17-614)
Extracted molecule genomic DNA
Extraction protocol Cortical and striatal tissues were crosslinked with 1% formaldehyde for ten minutes and the crosslinking was quenched by 0.125M final concentration of glycine. The crosslinked tissue was then homogenized, rinsed with PBS, pelleted, and frozen in liquid nitrogen for later use. Lysates were clarified from sonicated nuclei, and protein-DNA complexes were isolated with antibody (H3K4me3; Millipore, cat 17-614).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Description This Sample represents 2 replicates.
Data processing ChIP-Seq reads were aligned to the reference mouse genome (mm9) using Bowtie (v0.12.7).
Reads from biological replicates were concatenated for each condition.
Positive and negative strand reads were shifted according to a peak shift model built by the MACS algorithm (v1.4.0rc2) with parameters: effective genome size = 2.11e+09, band width = 300, p-value cutoff 1e-5.
Genome_build: MGSCv37
Supplementary_files_format_and_content: bigwig file contains peak-shifted read counts in 10 base pair windows for each chromosome.
Submission date Jul 17, 2013
Last update date May 15, 2019
Contact name Christopher Ng
Organization name Massachusetts Institute of Technology
Street address 77 Massachusetts Ave.
City Cambridge
State/province Massachusetts
ZIP/Postal code 02139
Country USA
Platform ID GPL11002
Series (2)
GSE48960 Targeting H3K4 methylation as a therapeutic strategy for Huntington's disease (ChIP-seq)
GSE48963 Targeting H3K4 methylation as a therapeutic strategy for Huntington's disease
BioSample SAMN02256553
SRA SRX323783

Supplementary file Size Download File type/resource 310.6 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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