|
| Status |
Public on Mar 01, 2013 |
| Title |
Dnmt1-/- MEF |
| Sample type |
SRA |
| |
|
| Source name |
Dnmt1-/- mouse embryonic fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Mouse embryonic fibroblasts
strain: unknown [see Lande-Diner 2007 (PMID: 17311920)]
genotype/variation: Dnmt1-/-
|
| Growth protocol |
Mouse embryonic fibroblasts were cultured under standard conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Trizol (Invitrogen) according to manufacturer's instructions and was treated with Dnase
Illumina's strand-specific mRNA library preparation was performed according to Illumina's instructions by Ambry Genetics (Aliso Viejo, CA, USA)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
the raw sequence data contains 18 files
|
| Data processing |
Base calling was performed as standard by Ambry Genetics (Aliso Viejo, CA, USA)
Reads were mapped to the mm9 build of the mouse genome using Tophat
Transcript abundance in the form of RPKM was calculated using Cufflinks/Cuffdiff
Genome_build: mm9
Supplementary_files_format_and_content: Output file from Cuffdiff giving the RPKM for each measured transcript in each sample
|
| |
|
| Submission date |
Feb 27, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
James P Reddington |
| Organization name |
EMBL
|
| Street address |
Meyerhofstrasse 1
|
| City |
Heidelberg |
| ZIP/Postal code |
69115 Heidelberg |
| Country |
Germany |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE44278 |
Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of polycomb-target genes |
| GSE44733 |
mRNA-seq in DNA methylation deficient mouse embryonic fibroblasts |
|
| Relations |
| SRA |
SRX246875 |
| BioSample |
SAMN01933050 |
