|
| Status |
Public on May 11, 2016 |
| Title |
F2T MeDIP |
| Sample type |
SRA |
| |
|
| Source name |
F2T
|
| Organism |
Oryzias melastigma |
| Characteristics |
group: Transgenerational group in F2 generation
cell type: sperm
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For each group, sperm from 10 male fish were collected by gently pressing the harvested testis and pooled. Sperm genomic DNA was extracted using a DNA extraction kit (MO BIO Ultraclean® Tissue & Cells DNA Isolation Kit, USA).
Extracted DNA was prepared by the Paired-End DNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions. Briefly, DNA was sonicated to fragments of 100-500 bp before the addition of dAs and adaptor ligation. Methylated DNA was then pulled down by an antibody specifically recognizing 5-methylcytosine. The pull-down fraction containing the antibody-5-methylcytosine complex was subjected to column purification (Zymo Research). The purified DNA was next enriched by an adaptor-mediated PCR process. Fragments of 220-232 bp were gel purified with a Gel Extraction Kit (Qiagen).
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The genome sequence of freshwater medaka was used as the reference genome for bowtie alignment.
DiffReps software was employed to identify the differentially methylated regions with a FDR cut-off of 0.01.
Genome_build: Oryzias_latipes release 73 downloaded from ensembl
Supplementary_files_format_and_content: .wig files report peaks
|
| |
|
| Submission date |
May 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Eric Greer |
| E-mail(s) |
Eric.Greer@childrens.harvard.edu
|
| Organization name |
Boston Children's Hospital/Harvard Medical School
|
| Department |
Newborn Medicine/Department of Pediatrics
|
| Lab |
Greer Lab
|
| Street address |
320 Longwood Avenue
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL21858 |
| Series (1) |
| GSE81312 |
MeDIP on the marine medaka sperm (Oryzias melastigma) |
|
| Relations |
| BioSample |
SAMN04987095 |
| SRA |
SRX1756770 |
