|
| Status |
Public on Nov 14, 2014 |
| Title |
RNA-Seq WT-Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
E8.5 whole embryos
|
| Organism |
Mus musculus |
| Characteristics |
embryo stage: E8.5
genotype: wild type
strain: C57BL/6J
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the embryos with the RNeasy Protect Mini Kit (Qiagen).
RNA-Seq libraries were prepared from 500 ng of total RNA using ribosomal RNA depletion with the Ribo-Zero Gold kit (Epicentre) and the TruSeq Stranded Total RNA Sample preparation kit (Illumina) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
We aligned reads to the mouse mm10 genome with TopHat2 v2.0.12 using default parameters.
We calculated raw read counts in mouse RefSeq genes from the BAM files with HTseq-count v0.6.0 using default parameters.
We then used DESeq2 v1.4.5 to identify differentially expressed genes between WT and KO samples using default parameters. Normalized counts were calculated with the ‘counts’ function of DESeq2.
sample_supplementary_files_format_and_content: We provide a tab-delimited matrix table that contains raw read counts in RefSeq genes calculated by HTseq-count, as well as normalized read counts, fold change of expression and adjusted p-values calculated by DESeq2.
Genome_build: mm10
|
| |
|
| Submission date |
Nov 14, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Weber |
| Organization name |
CNRS
|
| Department |
UMR7242 Biotechnology and Cell Signalling
|
| Street address |
300 Bd Sebastien Brant
|
| City |
Illkirch |
| ZIP/Postal code |
67412 |
| Country |
France |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE60334 |
DNA methylation analysis and expression profiling during murine embryogenesis and in embryos deficient for DNMT3A or DNMT3B |
|
| Relations |
| BioSample |
SAMN03195631 |
| SRA |
SRX759712 |
