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Status |
Public on Sep 16, 2011 |
Title |
HCC1954: input DNA |
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: input
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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 |
input
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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 |
SRX061996 |
BioSample |
SAMN00264833 |
Supplementary file |
Size |
Download |
File type/resource |
GSM721139_HCC1954.merged.input.nodup.bam |
1.1 Gb |
(ftp)(http) |
BAM |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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