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Status |
Public on May 04, 2013 |
Title |
CENP-A ChIP-seq [PDNC4 cell line] |
Sample type |
SRA |
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Source name |
PDNC4 cell line
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Organism |
Homo sapiens |
Characteristics |
cell type: Fibroblast chip antibody: CENP-A (Abcam, ab13939) cell line: PDNC4
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Growth protocol |
PDNC4 fibroblasts were grown in DMEM + 10% FBS 1% P/S. Lyphoblast lines were cultured in RPMI-1640 + 10% FBS 1% P/S, 5% L-Glutamine.
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Extracted molecule |
genomic DNA |
Extraction protocol |
Histone-DNA complexes were immunopurified from clarified Mnase-digested chromatin. Sequencing libraries were generated and barcoded for multiplexing according to Illumina recommendations with minor modifications. Briefly, 2-15 ng Input or ChIP DNA was end-repaired and A-tailed. Illumina Truseq adaptors were ligated, libraries were size-selected to exclude polynucleosomes, and the libraries were PCR-amplied using Phusion polymerase. All steps in library preparation were carried out using NEB enzymes. Resulting libraries were submitted for 100 bp, paired-end Illumina sequencing on a HiSeq 2000 instrument.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
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Data processing |
Basecalling performed by CASAVA pipeline For alignments to higher order repeats, ChIP-seq reads were aligned to the ChrX or ChrY higher order repeat using Bowtie2 v2.0.0, reporting only single best alignment. Parameters: Mismatches = 0, Seed length = 50 For all other aligments, ChIP-seq reads were aligned to human genome hg19 using Bowtie2 v2.0.0, reporting only single best alignment: Parameters: Mismatches = up to 2, Seed length = 50 BED.txt and bedGraph (BDG) files were generated from SAM files using SAMtools and BAMtools Genome_build: hg19
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Submission date |
Feb 27, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Ben Black |
Organization name |
University of Pennsylvania
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Street address |
422 Curie Blvd.
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City |
Philadelphia |
ZIP/Postal code |
19103 |
Country |
USA |
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Platform ID |
GPL11154 |
Series (1) |
GSE44724 |
Genome-wide maps of CENP-A nucleosomes in three neocentromere-containing cell lines |
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Relations |
SRA |
SRX246076 |
BioSample |
SAMN01931901 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1089628_PDNC4_IMS13qregion.bedGraph.gz |
20.0 Kb |
(ftp)(http) |
BEDGRAPH |
GSM1089628_PDNC4_MS4221region.bedGraph.gz |
147.9 Kb |
(ftp)(http) |
BEDGRAPH |
GSM1089628_PDNC4_PDNC4region.bedGraph.gz |
1.1 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
Processed data provided as supplementary file |
Raw data are available in SRA |
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