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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 30, 2012 |
| Title |
fetus_4 |
| Sample type |
SRA |
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| Source name |
human cerebellum DNA
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| Organism |
Homo sapiens |
| Characteristics |
tissue: cerebellum
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| Treatment protocol |
Genomic DNA was purified by Proteinase K digestion (0.667g/l Proteinase K in 10 mM Tris-HCl, pH 8.5, 5 mM EDTA, 0.2% SDS, 200mM NaCl, overnight at 55°C) followed by extraction with equal volume 25:24:1 phenol:chloroform:isoamyl alcohol saturated with 10mM Tris, pH 8.0, 1mM EDTA. Purified genomic DNA was precipitated with an equal volume of isopropanol and resuspended in 10mM Tris-HCl, pH 8.0.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Approximately 50ng (5ul) of each 5hmC enriched DNA was used for Illumina SR library preparation by NEBNext ChIP-Seq Sample Prep Reagent Set 1(NEB) according to the manufacturer’s standard protocol.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
5hmC-chemical label pull down
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| Data processing |
Library strategy: 5hmC-capture-seq
Bowtie aligned
remove duplicate reads
To identify fetus- and adult-specific DhMRs in human brain, we employed a Poisson-based peak identification algorithm (MACS) using aligned 5-hmC-enriched tags. DhMRs were determined among all pairs of 5-hmC-enriched samples by directly comparing one sample (this submission) to another (two adult samples previous submitted in GEO with accession number: GSM794671 GSM794674) in each direction.
Genome_build: hg18/NCBI36
Supplementary_files_format_and_content: text files with adult and fetus specific DhMRs
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| Submission date |
Aug 31, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Tao Wang |
| E-mail(s) |
twang9@emory.edu
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| Phone |
4047270405
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| Organization name |
Emory University
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| Department |
Human Genetics
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| Lab |
Warren Lab
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| Street address |
615 Michael Street
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| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30322 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE40539 |
Genome-wide DNA hydroxymethylation changes are associated with neurodevelopmental genes in the developing human brain |
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| Relations |
| SRA |
SRX181814 |
| BioSample |
SAMN01141841 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM995965_adult_DhMRs.txt.gz |
303.8 Kb |
(ftp)(http) |
TXT |
| GSM995965_fetus_DhMRs.txt.gz |
259.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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