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| Status |
Public on Jun 18, 2012 |
| Title |
2C litter 3 |
| Sample type |
SRA |
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| Source name |
2C stage embryos
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| 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
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| Treatment protocol |
Litters of 2C embryos were collected at E1.5 and lysed in Prelude direct lysis buffer
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| Growth protocol |
Mixed strain female mice were fertilized with C57/Bl6J mice
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
RNA amplified using SPIA
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| Data processing |
2C_3.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
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| Submission date |
Nov 23, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Todd Macfarlan |
| E-mail(s) |
macfarlan@salk.edu
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| Organization name |
The Salk Institute
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| Street address |
10010 North Torrey Pines
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
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| 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 |
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| Relations |
| SRA |
SRX109432 |
| BioSample |
SAMN00760872 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM838742_2C_3.bed.gz |
94.4 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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