|
| Status |
Public on Apr 15, 2014 |
| Title |
wt_MEFs_FLAG_ChIP_(20120817_6_4) |
| Sample type |
SRA |
| |
|
| Source name |
wildtype-Chd1 MEFs FLAG ChIP_seq
|
| Organism |
Mus musculus |
| Characteristics |
cell type: embryonic fibroblasts
transgene: wildtype-Chd1
antibody: FLAG (Sigma anti-FLAG M2 agarose beads catalog #A2220)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Mouse embryonic fibroblasts (MEFs) expressing wildtype transgenic Chd1 were crosslinked using formaldehyde for 10 minutes at room temperature. Chromatin was fragmented using MNase and then sonicated to ensure complete extraction of chromatin and associated proteins. Chromatin was immunoprecipitated using an antibody (FLAG) against the N-terminus of the transgenic Chd1. DNA was extracted from the solubilized chromatin and subjected to Illumina (Solexa) sequencing.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
FLAG-tagged Chd1 chromatin immunoprecipitation followed by sequencing from mouse embryonic fibroblasts (MEFs) expressing wildtype Chd1.
|
| Data processing |
1. We used Bowtie-0.12.7 to map paired-end 25bp reads to release MM9 of the Mus musculus genomic sequence obtained from U.C.Santa Cruz. If a read was mapped to multiple locations, one location was picked at random. 2. We extracted properly paired reads (Supplementary file .bed). 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome (Supplementary file .wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 3. and 4. for the paired-end fragments in each sub-group.
|
| |
|
| Submission date |
Nov 19, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Jorja Henikoff |
| E-mail(s) |
jorja@fhcrc.org
|
| Phone |
206-667-4850
|
| Organization name |
Fred Hutchinson Cancer Research Center
|
| Department |
Basic Sciences
|
| Lab |
Henikoff
|
| Street address |
1100 Fairview AV N, A1-162
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109-1024 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE52349 |
The nucleosomal barrier to promoter escape by RNA Polymerase II is overcome by the chromatin remodeler Chd1 |
| GSE52501 |
The nucleosomal barrier to promoter escape by RNA Polymerase II is overcome by the chromatin remodeler Chd1 [HiSeq] |
|
| Relations |
| BioSample |
SAMN02412545 |
| SRA |
SRX378985 |
