|
| Status |
Public on Jul 22, 2015 |
| Title |
VYS_input_DNA |
| Sample type |
SRA |
| |
|
| Source name |
VYS
|
| Organism |
Mus musculus |
| Characteristics |
tissue: visceral yolk sac
developmental stage: E12.5
genetic background: FVB
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
material from native ChIP was Phenol:Chloroform extracted
TruSeq protocol
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
RNAseq reads were aligned with GSNAP version 2012-12-12 alowing novel splicing events detection; ChIPseq reads were alined using GSNAP version 2012-12-12; WGBS reads were alined using GSNAP version 2012-12-12
read counts were summarized using RPKM_count.py from the RSeQC version 2.3.3 or using bedtools and further processed using custom scripts in R
peaks were called using MACS version 1.4.2 with the default settings
Whole genome bisulfite-seq metylation calling was done using bissnp pipeline
Genome_build: mm10
|
| |
|
| Submission date |
Mar 27, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Quanah J Hudson |
| E-mail(s) |
[email protected]
|
| Phone |
+43 1 4016070030
|
| Organization name |
CeMM - Research Center for Molecular Medicine of the Austrian Academy of Sciences
|
| Street address |
Lazarettgasse 14, AKH BT 25.3
|
| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE56276 |
Imprinted expression is different in visceral yolk sac and cystic embryoid body endoderm |
|
| Relations |
| BioSample |
SAMN02709151 |
| SRA |
SRX501926 |
