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| Status |
Public on Sep 16, 2011 |
| Title |
HCC1954: chromatin IP against H3K9me3 |
| 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 #ab8898-100, lot #699671
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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, and gel purification. Following PCR amplification for 18 cycles, the final library underwent gel purification.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
H3K9me3
Instrument models: both Illumina Genome Analyzer IIx and Illumina HiSeq 2000 were used.
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| Data processing |
We mapped ChIP-Seq reads using the Bowtie program, keeping only those reads that mapped uniquely to hg18 with at most 3 mismatches. Specifically, the parameters used were: "--solexa1.3-quals -v 3 -m 1 --best --strata -S ". PCR duplicates for each library were removed with the Picard program(Picard 2011). All biological replicates were combined and compressed/indexed by the SAMtools suite into BAM format(Li et al. 2009).
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 |
GPL10999 |
| Series (2) |
| GSE29069 |
Global DNA Hypomethylation Coupled to Repressive Chromatin Domain Formation and Gene Silencing in Breast Cancer |
| GSE29118 |
Genome-wide location analysis in breast cancer cells (HCC1954) |
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| Relations |
| SRA |
SRX061989 |
| SRA |
SRX061990 |
| BioSample |
SAMN00264829 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM721135_HCC1954.merged.H3K9me3.nodup.bam |
3.3 Gb |
(ftp)(http) |
BAM |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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