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| Status |
Public on Jun 18, 2012 |
| Title |
2C::tomato- |
| Sample type |
SRA |
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| Source name |
ES cells sorted by FACS
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| 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
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| Treatment protocol |
Cells subject to flow cytometry to collect 2C::tomato+ and - cells
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| Growth protocol |
ES cells grown on gelatin in ES-KOSR media containing 150ug/ml hygromycin
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| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA-Deq sample prep kit (Illumina)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
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| 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
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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 |
GPL9250 |
| Series (2) |
| GSE33920 |
mRNA-Seq of 2C::tomato+ vs. - ES cells |
| GSE33923 |
2C::tomato ES cells, 2-cell embryos and wild type oocytes |
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| Relations |
| SRA |
SRX109429 |
| BioSample |
SAMN00760869 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM838739_2C_tomato_-.bed.gz |
73.3 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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