|
| Status |
Public on Apr 15, 2014 |
| Title |
wt_MEFs_CATCHIT_(20121012_538386_2) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
CATCH-IT pulldown
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embryonic fibroblasts (MEFs)
genotype/variation: expressing wildtype-Chd1
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
CATCH-IT was performed as previously described (PMID: 23602475) with some modifications. Briefly, tissue culture medium was replaced with DMEM media without methionine (Invitrogen Cat# 21013-024) supplemented with 1X glutamine, 0.2 mM L-cystine, 10% FBS, and 1% penicillin-streptomycin, and cells were grown at 37C for starvation fro 30 minutes, followed by 30 minutes incubation at 37C with 4 mM azidohomoalanine (Anaspec Cat# 63669) added to the media. Cells were then harvested and washed with 1X PBS. Nuclei were isolated by hypotonic lysis of cells in ice-cold NE1 buffer (20mM HEPES-KOH (ph 7.9), 10mM KCl, 1mM MgCl2, 0.1% Triton X-100, 1mM DTT, 20% Glycerol). MNase digest, Biotin coupling, chromatin extraction, streptavidin pulldown, urea wash and DNA isolation were then performed as previously described.
|
| Label |
Cy5
|
| Label protocol |
Standard NimbleGen protocol
|
| |
|
| Channel 2 |
| Source name |
Input chromatin
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embryonic fibroblasts (MEFs)
genotype/variation: expressing wildtype-Chd1
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Same as for ch1
|
| Label |
Cy3
|
| Label protocol |
Standard NimbleGen protocol
|
| |
|
| |
| Hybridization protocol |
Standard NimbleGen protocol
|
| Scan protocol |
Standard NimbleGen protocol
|
| Description |
CATCH-IT profiling of mouse embryonic fibroblasts expressing wildtype-Chd1
|
| Data processing |
The standard deviates of the bi-weight mean adjusted log base 2 ratios of Cy5/Cy3 computedby NimbleGen were computed. The supplementary gff and wig files contain the bi-weight mean adjusted log base 2 ratios in MM9 coordinates.
|
| |
|
| Submission date |
Nov 13, 2013 |
| Last update date |
Apr 15, 2014 |
| 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 |
GPL16533 |
| Series (2) |
| GSE52347 |
The nucleosomal barrier to promoter escape by RNA Polymerase II is overcome by the chromatin remodeler Chd1 [NimbleGen] |
| GSE52349 |
The nucleosomal barrier to promoter escape by RNA Polymerase II is overcome by the chromatin remodeler Chd1 |
|
