|
| Status |
Public on Aug 09, 2013 |
| Title |
CTCF Wapl +/delta |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
cell type: embryonic fibroblast
genotype: Wapl +/delta
genetic background: mixed C57BL/6 and 129 background
chip antibody: rabbit anti-CTCF
chip antibody manufacturer: Upstate
chip antibody catalog #: 07-729
|
| Treatment protocol |
4-OHT was added to the starvation medium to a final concentration of 500 nM
|
| Growth protocol |
MEFs were starved in OptMEM containing 2% serum for seven days
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples were sonicated for 12 x 60 second pulses with a Covaris sonicator; DNA was purified with Phase lock gel tubes (5PRIME)
Single read - Illumina
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
9147
|
| Data processing |
Alignment: Reads that passed the Illumina quality filtering were considered for alignment. The remaining reads were aligned against the mouse genome assembly version July 2007 (NCBI37/mm9) using the BOWTIE program version 12.5 [Langmead, 2009], allowing up to two mismatches, and ignoring any read that would match more than once.
Peak calling: Peaks were called using the MACS program version 1.3.6.1 [Zhang et al.] with default parameters and appropriate tag size, mm9 genome size (2654911517), sample and input read files. In cases where the read shifting model could not be build with the default mfold parameter (32), the mfold cutoff was lowered up to the point where sufficient high quality peaks could be found to build the model (100). Peaks were further filtered for p-values lower than 1e-10. This cutoff is more conservative than the default (1e-5), and worked well in removing false positive (=unique) peaks of technical replicates [data not shown].
Genome_build: mm9
Supplementary_files_format_and_content: BED files contain all uniquely aligned reads or called peaks
|
| |
|
| Submission date |
Oct 15, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Roman R Stocsits |
| E-mail(s) |
roman.stocsits@imp.ac.at
|
| Organization name |
IMP - Research Institute of Molecular Pathology
|
| Lab |
Jan-Michael Peters' Lab
|
| Street address |
Campus-Vienna-Biocenter 1
|
| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE41602 |
Wapl controls higher-order chromatin structure in interphase chromosomes (ChIP-Seq) |
| GSE41603 |
Wapl controls higher-order chromatin structure in interphase chromosomes |
|
| Relations |
| SRA |
SRX195365 |
| BioSample |
SAMN01765673 |
