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Sample GSM1311269 Query DataSets for GSM1311269
Status Public on Sep 21, 2015
Title Sus_H3
Sample type SRA
 
Source name nucleus accumbens tissue
Organism Mus musculus
Characteristics strain: C57BL/6
csds and behavior group: Susceptible
cell type: nucleus accumbens cells
antibody: H3
antibody vendor: Abcam
antibody cat. #: ab1791
antibody lot #: GR81366-1
Treatment protocol For the chronic social defeat stress paradigm (CSDS), experimental C57BL/6J mouse was placed into the home cage of a CD1 mouse for 10min during which time it was physically defeated by the CD1 mouse. After the physical interaction, the CD1 and experimental mouse were maintained in sensory contact for 24?hr using a perforated plexiglass partition dividing the resident home cage in two. The experimental mice were exposed to a new CD1 mouse for 10 consecutive days. A social interaction test was performed 24 hr after the last defeat. Mice were placed in an open field which included an interaction zone and two opposing corner zones. A social target (novel CD1 mouse) was placed in a metal meshplastic box in the interaction zone, which allows sensory but not physical interaction. Ethovision XT (Noldus) tracking software was used to measure the time that the test mouse spent in the interaction zone with and without the target CD1 present (2.5 min).
Extracted molecule genomic DNA
Extraction protocol For each ChIP-seq replicate, bilateral 14-gauge NAc punches were pooled from 10 mice.
Tissue was lightly fixed to cross-link DNA with associated proteins, and the material was further sheared (ACF1 and SNF2H) or MNase digested (histone H3) and immunoprecipitated using sheep anti-rabbit magnetic beads (Invitrogen) conjugated to an antibody that specifically recognizes ACF1 (Bethyl), SNF2H, or H3 (Abcam).
Immunoprecipitated DNA and total (input) genomic DNA were prepared for ChIP-seq using an Illumina kit according to the manufacturer’s instructions. Each experimental condition was analyzed with independent biological triplicates. Briefly, each sample underwent end repair followed by addition of an A base to the 3′ end. Proprietary adapters were then ligated to the ends, followed by size selection on a 2% agarose gel. The range of excision was 200–300 bp. After DNA clean up, samples were amplified with 15 (H3) or 19 (ACF1 and SNF2H) cycles of PCR. Amplification and size selection were confirmed with a BioAnalyzer. The resulting libraries were sequenced on an Illumina HiSeq 2500 with 100 bp read length.
 
Library strategy MNase-Seq
Library source genomic
Library selection MNase
Instrument model Illumina HiSeq 2500
 
Description Sample 12
Data processing Alignemnt of ChIP-seq: CASAVA 1.8.2 aligned to mm9, and default parameters used.
Segmentation: ChromHMM 1.10, 2 states, window size 200bp, poisson p-value cutoff 1E-6.
Nucleosome events: DANPos 2.1.2, The FDR cutoff was 0.01 for both nucleosome events. For shift events, the cutoff of shifting distance was between 50 and 90 bp. For occupancy events, the FDR of difference between simulation of treatment and control was >0.01.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq wig files were generated by pyicos. The TDF files suffixed with dup2 mean that at most only 2 duplicated reads were kept at the exact same genomic position, generated by rmdup_sorted_bed.pl in diffReps package and igvtools. Segmentation bed files were generated by ChromHMM. Nucleosome events bed were generated by DANPos.
 
Submission date Jan 21, 2014
Last update date May 15, 2019
Contact name Eric Nestler
Organization name Ichan School of Medicine at Mount Sinai
Street address 1425 Madison Avenue
City New York
State/province NY
ZIP/Postal code 10029
Country USA
 
Platform ID GPL17021
Series (1)
GSE54263 ACF chromatin remodeling complex mediates stress-induced depressive-like behavior through nucleosome repositioning and transcriptional regulation.
Relations
BioSample SAMN02593675
SRA SRX445342

Supplementary file Size Download File type/resource
GSM1311269_H3.res-sus.occupancy.bed.gz 241.9 Kb (ftp)(http) BED
GSM1311269_H3.res-sus.shift.bed.gz 8.8 Kb (ftp)(http) BED
GSM1311269_danpos_susBAM.bgsub.Fnor.ajClonal.smooth.wig.gz 1.2 Gb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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