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Sample GSM838740 Query DataSets for GSM838740
Status Public on Jun 18, 2012
Title 2C litter 1
Sample type SRA
Source name 2C stage embryos
Organism Mus musculus
Characteristics genetic background: mixed strain with C57/Bl6J
developmental stage: 2-cell embryo
tissue: embryo
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 Litters of 2C embryos were collected at E1.5 and lysed in Prelude direct lysis buffer
Growth protocol Mixed strain female mice were fertilized with C57/Bl6J mice
Extracted molecule total RNA
Extraction protocol Nugen Ovation RNA-Seq kit VII (for amplifying RNA) followed by Covaris fragmentation of cDNA, and library construction using Illumina mRNA sample prep kit starting with end repair
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description RNA amplified using SPIA
Data processing 2C_1.wig; genome build: mm9
Bowtie alignments, 3 mismatches per alignment, up to 20 alignments per read, for comparison with oocytes single-end (left side reads) trimmed on 3' end to 72bp
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 GPL13112
Series (2)
GSE33921 RNA-Seq from two-cell (2C) stage embryos
GSE33923 2C::tomato ES cells, 2-cell embryos and wild type oocytes
SRA SRX109430
BioSample SAMN00760870

Supplementary file Size Download File type/resource
GSM838740_2C_1.bed.gz 87.2 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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