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| Status |
Public on May 04, 2013 |
| Title |
Input DNA [MS4221 cell line] |
| Sample type |
SRA |
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| Source name |
MS4221 cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Lymphoblast
chip antibody: None
cell line: MS4221
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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 |
SRX246081 |
| BioSample |
SAMN01931906 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data not applicable for this record |
| Raw data are available in SRA |
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