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| Status |
Public on Jun 09, 2015 |
| Title |
SUM159PT_H3K27me3_ChIPSeq |
| Sample type |
SRA |
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| Source name |
Breast cancer cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: SUM159PT
cell type: Basal-like cells
chip antibody: H3K27me3
chip antibody vendor: Millipore
chip antibody cat. #: 07-449
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Following cell purification, cells were immediately cross-linked with formaldehyde (final concentration is 0.5%) at room temperature for 10 minutes. Cells were washed, lysed, and sonicated using a Bioruptor (Diagenode). The sonicated lysates were incubated with a specific antibody for 8 hours. The immunoprecipitates were sequentially washed, reverse-crosslinked, and purified by phenol-chloroform extraction and ethanol precipitation. ChIP-ed DNA was end-repaired by END-It DNA End Repair Kit (Epicentre), and 'A' base was added to 3'-ends by Klenow fragment. 1:10 diluted Adaptor oligo mix (ChIP-Seq Sample Preparation Kit, Illumina) were ligated using T4 DNA ligase HC (Invitrogen), and subjected to PCR amplification (18 cycles) using specific primers provided in the kit (Illumina). Fragments ranging from 150-300 bp were isolated from 8% polyacrylamide gel, and then sequenced by Illumina Genome Analyzer.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
ChIPSeq_1
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| Data processing |
Basecalls performed using the Illumina Genome Analyzer Pipeline.
ChIP-seq reads were aligned to the hg18 (March, 2006) human genome assembly using the Illumina Genome Analyzer Pipeline with default configuration. All reads that passed quality filtering and mapped with two or fewer mismatches were retained.
peaks were called using SICER version 1.03 with the following setting: Window size (200bp), Gap size (600bp), Other parameters (default).
Genome_build: hg18
Supplementary_files_format_and_content: Bed file format for aligned chip-seq reads. ChIP-seq reads were aligned to the hg18 (March, 2006) human genome assembly using the Illumina Genome Analyzer Pipeline with default configuration. All reads that passed quality filtering and mapped with two or fewer mismatches were retained.
Supplementary_files_format_and_content: Bed file format (with appendix .probscoreisland.bed) for ChIP-Seq peaks detected by SICER. Peaks were called using SICER version 1.03 with the following setting: Window size (200bp), Gap size (600bp), Other parameters (default). Each raw represents each peak detected by SICER. Each column represents chrom, start, end and enrichment_score calculated by SICER.
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| Submission date |
Jun 18, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Kornelia Polyak |
| E-mail(s) |
[email protected]
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| Phone |
617-632-2106
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| Organization name |
Dana-Farber Cancer Institute
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| Department |
Medical Oncology
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| Lab |
Polyak
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| Street address |
450 Brookline Ave
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
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| Platform ID |
GPL9052 |
| Series (2) |
| GSE38548 |
Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer |
| GSE38788 |
Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer [ChIP-Seq 1] |
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| Relations |
| SRA |
SRX154992 |
| BioSample |
SAMN01055220 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM949575_SUM159PT_H3K27me3-W200-G600.probscoreisland.bed.gz |
484.5 Kb |
(ftp)(http) |
BED |
| GSM949575_SUM159PT_H3K27me3_ChIPSeq_aligned.bed.gz |
63.8 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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