|
| Status |
Public on Jun 18, 2015 |
| Title |
GR ChIP Klf15-/- MEFS 1hr vehicle 2 |
| Sample type |
SRA |
| |
|
| Source name |
Cultured Klf15-/- embryonic fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Klf15-/-
cell type: embryonic fibroblast
antibody: in-house GR antibody
|
| Growth protocol |
Mouse embryonic fibroblasts (MEFS) were generated from embryos harvested from dpc 14-17 dams. Cells were maintained in DMEM + 10% FBS and assays were performed on cells between passage 4 and 11
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitation (ChIP) was performed as described previously described (PMID: 23508109), with the following modifications: cross-linking was performed by adding methanol-free 16% formaldehyde directly to the culture media to a final concentration of 1% and incubating for 5 minutes at room temperature with gentle rocking; samples were subsequently sonicated with a Diagenode Bioruptor at high power in 30-second bursts separated by 30-second incubations in ice water for a total of 23 cycles.
A minimum of 1 ng DNA from ChIP samples were used to prepare libraries using the Nugen Ovation Ultralow System V2 1-16 Part No. 0344 according to the manufacturer’s instructions. Samples were run on an Illumina HiSeq using 1X50 bp end reads
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 2 with the default setting.
Mapped reads were compressed, sorted and indexed using Samtools
Peaks were called using MACS version 2 with the default setting
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using MACS version 2
|
| |
|
| Submission date |
Jun 17, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Tzu Lip Phang |
| E-mail(s) |
[email protected]
|
| Phone |
(303) 724-6057
|
| Organization name |
University of Colorado, Denver
|
| Department |
Medicine
|
| Street address |
12700 East 19th Avenue
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE69947 |
Comparison of glucocorticoid receptor (NR3C1) binding in wild type and Klf15-/- MEFs |
|
| Relations |
| BioSample |
SAMN03779000 |
| SRA |
SRX1060617 |
