|
| Status |
Public on May 24, 2016 |
| Title |
HuRef_CenpT_X3_(20140710_1,2_7) |
| Sample type |
SRA |
| |
|
| Source name |
Immunoprecipitated DNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell part: nuclei
cell type: Lymphoblastoid
cell line: HuRef
chip antibody: Anti-CENP-T (Abcam Ab114120)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The HuRef lymphoblastoid cell line was grown in RPMI medium using standard protocols. Cells were fixed at a density equal to 2 million/ml using formaldehyde to a final concentration of 1%. Cross-linking was quenched with 125mM glycine. Chromatin was released from cells by incubating in lysis buffer (1% SDS, 10mM EDTA and 50 mM Tris-HCl (pH 8.1)) on ice for 10 min. The resulting chromatin solution was diluted 10 times with IP dilution buffer (1% Triton X-100, 2mM EDTA, 150 mM NaCl and 20mM Tris-HCl (pH8.1)) . MNase digestion, sonication, pre-clearing and chromatin immunoprecipitation steps were performed as described previously (PMID: 24737864) using antibodies.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
HuRef cross-linked (X-ChIP) CENP-T ChIP. Replicate with Abcam antibody and pre-clearing.
|
| Data processing |
Paired reads were merged using SeqPrep (https://github.com/jstjohn/SeqPrep) with parameters -q 30 (quality) and -L 25 (minimum merged pair length). SeqPrep also removed adaptors and low-quality reads. Merged pairs were aligned with various human BACs using the aln/samse functions of BWA version 0.7.5 saving up to 10 alignments per read (-n 10), otherwise with default options. Merged pairs mapped to two consensus sequences representing 20 human centromere sequences are included as supplementary files (Cen1-like and Cen13-like).
|
| |
|
| Submission date |
Jun 12, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jorja Henikoff |
| E-mail(s) |
jorja@fhcrc.org
|
| Phone |
206-667-4850
|
| Organization name |
Fred Hutchinson Cancer Research Center
|
| Department |
Basic Sciences
|
| Lab |
Henikoff
|
| Street address |
1100 Fairview AV N, A1-162
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109-1024 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE69839 |
CENP-T and CENP-C bridge adjacent CENP-A nucleosomes on young alpha-satellite dimers |
|
| Relations |
| BioSample |
SAMN03771574 |
| SRA |
SRX1057963 |
