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| Status |
Public on Nov 30, 2012 |
| Title |
IMR90 Cells Methylated DNA |
| Sample type |
SRA |
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| Source name |
IMR90
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| Organism |
Homo sapiens |
| Characteristics |
cell line: IMR90
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| Growth protocol |
IMR90 DNA was donated by Ryan Lister.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
MethylMiner Methylated DNA Enrichment Kit (Invitrogen #ME10025) was used to isolate methylated DNA, as previously described (Nair, S.S., Coolen, M.W., Stirzaker, C., Song, J.Z., Statham, A.L., Strbenac, D., Robinson, M.W., and Clark, S.J. (2011). Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias. Epigenetics 6: 34-44.). The DNA was quantitated using Qubit and 10ng was used for Illumina library preparation using Illumina ChIP-Seq DNA Sample Prep Kit #IP-102-1001.
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| Library strategy |
MBD-Seq |
| Library source |
genomic |
| Library selection |
MBD2 protein methyl-CpG binding domain |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Read files of technical replicates were pooled.
Reads were mapped with bowtie 0.12.7 Only reads mapping uniquely to the genome were kept. Upto 3 mismatches to the reference sequence were allowed. When more than one read mapped to the same genomic position, only one read was kept at that position.
Genome_build: hg18
Supplementary_files_format_and_content: BigWig. Counts across the whole genome in windows 20 bases wide, per 1 million mapped reads.
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| Submission date |
Jun 13, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Aaron Statham |
| E-mail(s) |
a.statham@garvan.org.au
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| Organization name |
Garvan Institute of Medical Research
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| Department |
Cancer Department
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| Lab |
Epigenetics Research Laboratory
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| Street address |
384 Victoria St
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| City |
Darlinghurst |
| State/province |
NSW |
| ZIP/Postal code |
2010 |
| Country |
Australia |
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| Platform ID |
GPL11154 |
| Series (1) |
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| Relations |
| SRA |
SRX154493 |
| BioSample |
SAMN01048175 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM947460_IMR90_MBD2IP.bw |
457.0 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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