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| Status |
Public on Sep 16, 2011 |
| Title |
HCC1954: chromatin IP against H3K9me3, bisulfite treated |
| Sample type |
SRA |
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| Source name |
breast cancer cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HCC1954
cell type: breast cancer cells
chip antibody: H3K9me3, cat #pAb-056-50, lot #a93-0041
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
To isolate chromatin, formaldehyde-cross-linked nuclei were sonicated using a Branson 450 Sonifier (Branson, Danbury, CT). Following ChIP performed with Dynal beads (Invitrogen, Carlsbad, CA), ChIP DNA was subjected to end repair, A-tailing, adaptor ligation with methylated adaptors, and gel purification. Following bisulfite conversion and PCR amplification for 20 cycles, the final library underwent gel purification.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
H3K9me3
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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 |
| GSE29120 |
Bisulfite sequencing of ChIP DNA on breast cancer cells (HCC1954) |
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| Relations |
| SRA |
SRX061999 |
| BioSample |
SAMN00264836 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM721142_H3K9me3.nodup.bam |
74.7 Mb |
(ftp)(http) |
BAM |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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