|
| Status |
Public on Jan 07, 2016 |
| Title |
E7.5_EPC_Ascl2_WT-2 RNA-Seq |
| Sample type |
SRA |
| |
|
| Source name |
Ectoplacental cone
|
| Organism |
Mus musculus |
| Characteristics |
background strain: CD-1
developmental stage: E7.5
epc genotype: Ascl2 +/+
oocyte genotype: Ascl2 WT
tissue: trophoblast
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was DNase treated with the DNA-free kit (Life Technologies). Messenger RNA was purified using a Dynabeads mRNA Purification Kit (Life Technologies). Strand-specific libraries were generated using the ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre).
Genomic DNA and RNA were isolated from the same samples using the Allprep DNA/RNA kit (Qiagen).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Ascl2KO_expression_vsd.txt
|
| Data processing |
Raw FastQ data were trimmed with Trim Galore (v0.3.7, default parameters) and mapped to the mouse NCBIM37 genome assembly using TopHat v2.0.11, guided by gene models from Ensembl v61. Data were quantitated at mRNA level using the RNA-seq quantitation pipeline in SeqMonk software (www.bioinformatics.babraham.ac.uk)
Genome_build: NCBIM37
Genome-wide quantification files: Gene expression files were generated by normalising and transforming raw count data (variance stabilizing transformation) using DEseq.
Bismark coverage report: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count non-methylated>
|
| |
|
| Submission date |
Feb 18, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Felix Krueger |
| E-mail(s) |
fkrueger@altoslabs.com
|
| Organization name |
Altos Labs
|
| Department |
Bioinformatics
|
| Street address |
Granta Park
|
| City |
Cambridge |
| ZIP/Postal code |
CB21 6GP |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE66049 |
Maternal DNA methylation regulates early trophoblast development |
|
| Relations |
| BioSample |
SAMN03353280 |
| SRA |
SRX883252 |
