|
| Status |
Public on Jan 01, 2016 |
| Title |
F1 TSC Dnase-Seq |
| Sample type |
SRA |
| |
|
| Source name |
F1 BC.1 trophoblast stem cells
|
| Organism |
Mus musculus |
| Characteristics |
parent_of_origin: C57BL/6J mother X CAST/EiJ father
tsc_passage_number: 12-16
total_obtained_reads: 293159308
antibody: None
|
| Growth protocol |
TSCs were grown under standard conditions (Quinn J, Kunath T, Rossant J. Methods Mol Med. 2006; PMID: 16251740). 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 before harvesting.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNase-Seq libraries were prepared according to (Song L, et al. Genome Res. 2011; PMID 21750106)
|
| |
|
| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
DNase-Seq reads were trimmed prior to all analyses to include only the first 20 bases; the remainder were linker derived (see Song L, et al. Genome Res. 2011; PMID 21750106).
Variant sequence data was obtained from the Sanger Institute (http://www.sanger.ac.uk/resources/mouse/genomes/).
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 |
Oct 23, 2013 |
| 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 |
GPL13112 |
| Series (1) |
| GSE51610 |
Defining principles of gene and regulatory element imprinting in mouse trophoblast stem cells |
|
| Relations |
| BioSample |
SAMN02381823 |
| SRA |
SRX367112 |
