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Sample GSM1561521 Query DataSets for GSM1561521
Status Public on Feb 24, 2015
Title BC.3
Sample type SRA
Source name F1 Hybrid BC.3 Trophoblast stem cells
Organism Mus musculus
Characteristics data type: RNA-Seq
parent-of-origin: C57BL/6J mother X CAST/EiJ 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 (
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
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
BioSample SAMN03256363
SRA SRX836095

Supplementary file Size Download File type/resource
GSM1561521_bc.3.all.bed.gz 489.6 Mb (ftp)(http) BED
GSM1561521_bc.3.all.snpreads.txt.gz 152.6 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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