|
| Status |
Public on Jul 22, 2015 |
| Title |
MethylCap-seq_dome |
| Sample type |
SRA |
| |
|
| Source name |
zebrafish embryo
|
| Organism |
Danio rerio |
| Characteristics |
developmental stage: dome
tissue: whole embryo
strain: mixture of AB and Tubingen strains
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples were prepared as described in (Bogdanovic et al; 2013, Methods)
Libraries were prepared as described in (Bogdanovic et al; 2013, Methods)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
kit: Diagenode (#AF-100-0048)
|
| Data processing |
Library strategy: MethylCap-seq
Basecalls performed using CASAVA version 1.8.2
Reads were aligned to the danRer7 genome using bowtie2 (version 2.2.1.) with default settings
Duplicate reads were removed using samtools rmdup (-s option)
Peaks were called using macs2 (https://github.com/taoliu/MACS/)
Genome_build: danRer7
Supplementary_files_format_and_content: ChIP-seq: BED, peak file (macs2 "broadPeak")
Supplementary_files_format_and_content: MethylCap-seq: BED, peak file (macs2 "narrowPeak")
|
| |
|
| Submission date |
Jul 13, 2015 |
| 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 |
GPL14875 |
| Series (1) |
| GSE70847 |
Genome-wide epigenetic cross-talk between DNA methylation and H3K27me3 in zebrafish embryos |
|
| Relations |
| BioSample |
SAMN03856976 |
| SRA |
SRX1092997 |
