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| Status |
Public on Feb 13, 2015 |
| Title |
MeDIP_3.5hpf |
| Sample type |
SRA |
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| Source name |
embryo
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| Organism |
Danio rerio |
| Characteristics |
developmental stage: high
hours post fertilization: 3.5
strain: sjA
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Wild-type embryos were obtained through in vitro fertilization, grown in 28.5 °C egg water to develop and harvested at the desired stages. Chorions were removed with pronase and yolk was removed with ice-cold deyolking buffer (55 mM NaCl, 1.8mM KCl, 1.25 mM NaHCO3). Embryos were snap-frozen in liquid nitrogen and stored at -80 °C until time of use. The genomic DNA was isolated by incubating embryos in genomic DNA extraction uffer (50 mM Tris, 1 mM EDTA, 0.5 % SDS, 1 mg/mL Proteinase K) followed by phenol-chloroform extraction.
500 ng of DNA isolated was sonicated, end-processed, and ligated to paired-end adapters. After agarose gel size-selection, DNA was immunoprecipitated using a mouse monoclonal anti-methylcytidine antibody. Immunoprecipitated DNA was washed, amplified by 12 cycles of PCR, and size-selected by agarose gel electrophoresis.
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| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Base-calls performed using CASAVA.
Raw sequencing reads were aligned to the danRer7 genome assembly using novoalign (V2.08.02) with the following parameter: -o SAM -r random -a -H.
The aligned reads were further processed using homemade perl script. These include removing duplicated reads, bed sorting.
Genome_build: Zv9
Supplementary_files_format_and_content: bedGraph
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| Submission date |
Nov 25, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Hyung Joo Lee |
| Organization name |
Washington University School of Medicine
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| Department |
Department of Genetics
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| Lab |
Ting Wang
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| Street address |
4515 McKinley Avenue
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| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63108 |
| Country |
USA |
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| Platform ID |
GPL14875 |
| Series (2) |
| GSE52703 |
Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos (MeDIP-seq) |
| GSE52706 |
Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos |
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| Relations |
| BioSample |
SAMN02420332 |
| SRA |
SRX383002 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1274385_MeDIP_3.5hpf.bedGraph.gz |
1.3 Gb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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