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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 21, 2015 |
| Title |
Sus_Acf1 |
| Sample type |
SRA |
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| Source name |
nucleus accumbens tissue
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
csds and behavior group: Susceptible
cell type: nucleus accumbens cells
antibody: ACF1
antibody vendor: Bethyl Laboratories
antibody cat. #: A301-318A
antibody lot #: A301-318A-1
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| 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).
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| 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Sample 9
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| 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.
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| Submission date |
Jan 21, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Eric Nestler |
| Organization name |
Ichan School of Medicine at Mount Sinai
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| Street address |
1425 Madison Avenue
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE54263 |
ACF chromatin remodeling complex mediates stress-induced depressive-like behavior through nucleosome repositioning and transcriptional regulation. |
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| Relations |
| BioSample |
SAMN02593671 |
| SRA |
SRX445339 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1311266_Sus_2_segments.bed.gz |
12.6 Kb |
(ftp)(http) |
BED |
| GSM1311266_Sus_Acf1.wig.gz |
240.0 Mb |
(ftp)(http) |
WIG |
| GSM1311266_Sus_Acf1_2dup.tdf |
353.9 Mb |
(ftp)(http) |
TDF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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