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| Status |
Public on Jan 30, 2017 |
| Title |
H3K27me3 ChIP-Seq |
| Sample type |
SRA |
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| Source name |
G401 (rhabdoid tumor of the kidney)
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| Organism |
Homo sapiens |
| Characteristics |
tissue: kidney
tumor type: rhabdoid tumor of the kidney
chip antibody: Active Motif
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| Growth protocol |
Cells were grown in RPMI +15% FBS and grown to 80% confluency
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Lysates were sonicated with a microtip sonicator to shear the DNA. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. For each ChIP reaction, 30 ug of chromatin was precleared with protein A agarose beads (Invitrogen). ChIP reaction was set up using precleared chromatin and antibody and incubated overnight at 4 C. Protein A agarose beads were added and incubation at 4 C was continued for another 3 hr. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on HiSeq 2500.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Sequences: Standard Illumina software base-calling and quality-control filtering was applied
Sequences (50 nt reads, single end) were aligned to the human genome (hg19) using the BWA algorithm (default parameters).
Aligns were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWIG files.
Peak locations were determined using the MACS algorithm (v1.4.2) with a cutoff of pvalue = 1E-7.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations
Genome_build: hg19
Supplementary_files_format_and_content: BAM = standard BAM alignment format
Supplementary_files_format_and_content: BW = signal map in bigWIG format (UCSC)
Supplementary_files_format_and_content: BED = standard BED file containing MACS peaks
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| Submission date |
Jul 16, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Paul-Joseph P Aspuria |
| Organization name |
Cedars-Sinai Medical Center
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| Department |
Women's Cancer Program
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| Lab |
Sandra Orsulic
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| Street address |
8400 Beverly Blvd.
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| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90048 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
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| Relations |
| BioSample |
SAMN03863191 |
| SRA |
SRX1098822 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1824915_2_2839Cedars_G401_H3K27me3_i88_uniq_signal.bw |
80.0 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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