|
| Status |
Public on Aug 18, 2013 |
| Title |
hippocampus_fear-conditioned_IgG |
| Sample type |
SRA |
| |
|
| Source name |
hippocampus, fear-conditioned, IgG
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57/BL6
age: 6 months
tissue: hippocampus
|
| Treatment protocol |
contextual fear-conditioning
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hippocampus from fear-conditioned and non-conditioned mice were collected, homogenized, and chromatin-immunoprecipitated with an antibody to histone H4K5 acetylation (Millipore, cat. 07-327). 200 ng of DNA from both immunoprecipitated and input control samples are sonicated at 4C to a mean fragment size of between 100 to 150 bp using the Covaris S2 System. The DNA is then end-repaired using end polishing enzymes 1 and 2 such that damaged DNA with protruding 5' or 3' ends are blunt-ended and phosphorylated. Following repair, the samples are purified using a column purification kit and the blunt ends are ligated with 1ul of multiplex adaptors P1 and P2. The ligated samples are then nick translated and amplified according to the SOLiD Fragment Library Barcoding protocol and column purified separately. The libraries are then quantitated using a Qubit Fluorometer (Invitogen). 20ul of each library is size-selected for ligation products of 170-230 bp using 2% E-gels and pooled after gel purification. Finally, equimolar amounts of each barcoded library are mixed together before ePCR followed by sequencing (ABI SOLiD System 3+).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
AB SOLiD System 3.0 |
| |
|
| Description |
IgG ChIP genomic DNA from FC group
|
| Data processing |
The color space reads were mapped to the mouse genome (mm9 obtained from USCS; http://genome.ucsc.edu/cgi-bin/hgGateway?org=mouse) using the mapping tool of the Bioscope v1.2.1 software suite (Applied Biosystems). For the mapping, only reads with maximal 4 failed color calls and quality values larger than 8 were considered. The reads were mapped allowing maximal 6 color mismatches and only uniquely mapping reads were reported in a SAM file. This file was used for subsequent identification of enriched regions.
|
| |
|
| Submission date |
Jun 30, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
C. Sehwan Park |
| E-mail(s) |
c.s.park@nlaw.northwestern.edu
|
| Organization name |
Northwestern University
|
| Department |
Pritzker School of Law
|
| Street address |
375 East Chicago Ave
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL9318 |
| Series (1) |
| GSE30325 |
Genome-wide analysis of H4K5-acetylated genes in fear memory |
|
| Relations |
| SRA |
SRX081786 |
| BioSample |
SAMN00632037 |
