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Sample GSM838738 Query DataSets for GSM838738
Status Public on Jun 18, 2012
Title 2C::tomato+
Sample type SRA
Source name ES cells sorted by FACS
Organism Mus musculus
Characteristics genetic background: mixed strain
cell type: ES background Kdm1a FL/FL, CreERT
genotype: 2C::tomato+
crosses: LSD1 FL/FL mice (From Wang et al, Nature 446, 2007 ) were crossed with ZP3::Cre mice (Jax labs strain 003651) and backcrossed again to generate LSD1 FL/FL, ZP3Cre+ and - mice. FOr this study, only LSD1 FL/FL, ZP3::Cre negative females were used to produce oocytes. For 2C embryos, these females were crossed with wild type CB6 males
Treatment protocol Cells subject to flow cytometry to collect 2C::tomato+ and - cells
Growth protocol ES cells grown on gelatin in ES-KOSR media containing 150ug/ml hygromycin
Extracted molecule total RNA
Extraction protocol mRNA-Deq sample prep kit (Illumina)
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
Data processing 2C_tomato_+.wig; genome build: mm9
Bowtie was used to align reads, allowing 2 bp mismatchs and allowing up to 40 alignments per read
Submission date Nov 23, 2011
Last update date May 15, 2019
Contact name Todd Macfarlan
Organization name The Salk Institute
Street address 10010 North Torrey Pines
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
Platform ID GPL9250
Series (2)
GSE33920 mRNA-Seq of 2C::tomato+ vs. - ES cells
GSE33923 2C::tomato ES cells, 2-cell embryos and wild type oocytes
SRA SRX109428
BioSample SAMN00760868

Supplementary file Size Download File type/resource
GSM838738_2C_tomato_+.bed.gz 83.8 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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