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| Status |
Public on Sep 16, 2011 |
| Title |
HMEC-methylC-Seq |
| Sample type |
SRA |
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| Source name |
mammary epithelial cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HMEC
cell type: primary human mammary epithelial cells
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
5.5 µg of genomic DNA was extracted from frozen cell pellets using the DNeasy Mini Kit (Qiagen, Valencia, CA) and spiked with 25 ng unmethylated cl857 Sam7 Lambda DNA (Promega, Madison, WI). The DNA was fragmented with a Biorupter (Diagenode, Woburn, MA) to 100-300 bp, followed by end repair and addition of a 3' A base. Single-end cytosine-methylated adapters were ligated to the sonicated DNA and 150-350bp fragments were purified from a 2% agarose gel. Adapter-ligated DNA (~450 ng) was subjected to sodium bisulfite conversion using the MethylCode kit (Life Technologies, Carlsbad, CA) as per manufacturer's instructions. The bisulfite-converted, adapter-ligated DNA molecules were enriched by 5 cycles of PCR with PfuTurboCx Hotstart DNA polymerase (Stratagene). The reaction products were purified with a 2% agarose gel.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
bisulfite-converted genomic DNA
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| Data processing |
MethylC-Seq reads were mapped as previously described (Lister et al., Nature, 2009). Briefly, reads were trimmed until encountering a base with PHRED score <= 2 and bases near the 3â end were trimmed if the adapter sequence was included. For the purpose of mapping, all cytosines were computationally converted to thymines, to be reverted back to their original state after mapping. The Bowtie program(Langmead et al. 2009) was then used to align these computationally converted reads to computationally converted copies of hg18. Non-uniquely mapping reads were discarded.
Genome build: hg18
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| Submission date |
May 06, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Gary Chung Hon |
| Organization name |
UT Southwestern
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| Department |
OB/GYN
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| Street address |
5323 Harry Hines Blvd.
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| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE29069 |
Global DNA Hypomethylation Coupled to Repressive Chromatin Domain Formation and Gene Silencing in Breast Cancer |
| GSE29127 |
Genome-wide DNA methylation mapping in breast cancer cells (HCC1954) and normal breast cells (HMEC) |
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| Relations |
| SRA |
SRX062004 |
| BioSample |
SAMN00264840 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM721195_HMEC.merged.+.nodup.bam |
22.7 Gb |
(ftp)(http) |
BAM |
| GSM721195_HMEC.merged.-.nodup.bam |
22.6 Gb |
(ftp)(http) |
BAM |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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