|
| Status |
Public on Nov 21, 2012 |
| Title |
CTCF |
| Sample type |
SRA |
| |
|
| Source name |
F1 C/B trophoblast stem cells
|
| Organism |
Mus musculus |
| Characteristics |
antibody: CTCF (Pugacheva et. al. 2005 Hum Mol Genet 14, 953-965)
cell type: F1 C/B trophoblast stem cells
data type: ChIP-Seq
parent of origin: CAST/EiJ mother X C57BL/6J father
tsc passage number: 10-15
total obtained reads: 89942473
|
| Growth protocol |
TSCs were grown under standard conditions (Quinn J, Kunath T, Rossant J. Methods Mol Med. 2006). To eliminate feeder cell contamination of TSC RNA and chromatin preparations, TSC cultures grown on sub-lethally irradiated feeders were trypsinized and pre-plated for 40 minutes before transferring to new plates. TSC cultures were then split an additional 2x or 4x before harvesting cells for chromatin and RNA, respectively.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Strand-specific RNA-Seq libraries were prepared according to (Ingolia NT, et al. Science. 2009; PMID 19213877). ChIP-Seq libraries were prepared according to Illumina instructions. FAIRE-Seq libraries were prepared according to (Giresi PG, Lieb JD. Methods. 2009; PMID 19303047). DNase-Seq libraries were prepared according to (Song L, et al. Genome Res. 2011; PMID 21750106).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Variant sequence data was obtained from the Sanger Institute (http://www.sanger.ac.uk/resources/mouse/genomes/) on 1/15/10.
Reads were aligned to mm9 or an in silico constructed version of the Cast genome using Bowtie.
SNP-containing reads were extracted using custom scripts.
Genome_build: mm9
Supplementary_files_format_and_content: WIG and BED files were generated from mm9 alignments, and reported read ends reflect average fragment size of corresponding libraries. Snp files contain snp-overlapping read locations, snp-overlapping base, and snp-overlapping read allele.
|
| |
|
| Submission date |
Jul 17, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
J Mauro Calabrese |
| E-mail(s) |
jmcalabr@med.unc.edu
|
| Phone |
919-843-3257
|
| Organization name |
UNC-Chapel Hill
|
| Department |
Pharmacology
|
| Street address |
120 Mason Farm Road
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27516 |
| Country |
USA |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE39406 |
Site-specific silencing of regulatory elements as a mechanism of X-inactivation |
|
| Relations |
| Alternative to |
GSM998993 |
| SRA |
SRX160416 |
| BioSample |
SAMN01090641 |
