|
| Status |
Public on Feb 24, 2015 |
| Title |
CB.3 |
| Sample type |
SRA |
| |
|
| Source name |
F1 Hybrid CB.3 Trophoblast stem cells
|
| Organism |
Mus musculus |
| Characteristics |
data type: RNA-Seq
parent-of-origin: CAST/EiJ mother X C57BL/6J father
passage number: 9-15
|
| 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 1x before harvesting.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol
Strand-specific RNA-Seq prepped with mRNA-Seq kit from KAPA Biosciences
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Strand-specific RNA-Seq prepped with mRNA-Seq kit from KAPA Biosciences
|
| Data processing |
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: BED files were generated from mm9 alignments, and reported read ends reflect an average fragment size of 100bp for corresponding libraries. Snp files contain snp-overlapping read locations, snp-overlapping base, and snp-overlapping read allele.
|
| |
|
| Submission date |
Dec 08, 2014 |
| 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 |
GPL19057 |
| Series (1) |
| GSE63968 |
A survey of imprinted gene expression in mouse trophoblast stem cells |
|
| Relations |
| BioSample |
SAMN03256361 |
| SRA |
SRX836093 |
