 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 18, 2013 |
| Title |
ChIP_R6-2_H3K4me3_12wks_ctx_rep1_rep2_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
R6/2, cortex, 12 weeks
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57Bl/6 / CBA
genotype/variation: R6/2 transgenic (Mangiarini et al., Cell 87:493-506,1996)
tissue: brain cortex
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 3 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 |
|
| Relations |
| BioSample |
SAMN02256551 |
| SRA |
SRX323780 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1187626_ChIP_R6-2_H3K4me3_12wks_ctx.bw |
463.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
