|
| Status |
Public on Jun 23, 2011 |
| Title |
MBD_st12.5_500mM |
| Sample type |
SRA |
| |
|
| Source name |
whole embryo
|
| Organism |
Xenopus tropicalis |
| Characteristics |
tissue: whole embryo
fraction: 500mM elution
developmental stage: 12.5
bait: H6-GST-MBD fusion protein (Diagenode)
|
| Growth protocol |
Xenopus tropicalis embryos were obtained from a natural mating procedure after human chorion gonadotropin injection, dejellied in 3% cysteine and collected at Nieuwkoop-Faber stage 9 and 12.5
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was sheared by sonication to ~ 500 bp fragments. Methylated DNA was affinity purified using H6-GST-MBD fusion protein (Diagenode) following the manufacturers’ protocol with one modification. The DNA was eluted in several steps with increasing NaCl concentrations: 2 x 200mM, 1 x 300mM (washing steps 1-3), 500mM and 700mM (elutions 1 and 2)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
methylated DNA affinity capture
|
| Data processing |
Reads were mapped to the X.tropicalis genome (version JGI4.1) with ELAND, reads in identical positions were removed and peaks were called using MACS with p-value 1e-5
|
| |
|
| Submission date |
Sep 01, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Ozren Bogdanovic |
| E-mail(s) |
o.bogdanovic@gmail.com
|
| Organization name |
Garvan Institute of Medical Research
|
| Department |
Genomics and Epigenetics
|
| Street address |
384 Victoria Street
|
| City |
Darlinghurst |
| State/province |
NSW |
| ZIP/Postal code |
2010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL9405 |
| Series (1) |
| GSE23913 |
Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis |
|
| Relations |
| SRA |
SRX026884 |
| BioSample |
SAMN00113405 |
