|
| Status |
Public on May 24, 2016 |
| Title |
ht10801b_input_x1_(20151015_1) |
| Sample type |
SRA |
| |
|
| Source name |
input
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: fibrosarcoma
cell line: HT1080-1b
chip antibody: none
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
the ht1080-1b fibrosarcoma cell line was grown in dmem media 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)) and digested with micrococcal nuclease (mnase, sigma, cat # n3755) at 37°c for 45 min. reactions were stopped by addition of egta to a final concentration of 20 mm and edta to 10 mm. the mnase digested chromatin was sonicated as described before (pmid: 24737864). an aliquot containing 100th of the entire chromatine solution was de-cross-linked at 65 degrees c overnight. de-cross-linked chromatin was subjected to rnase a and proeinase k treatment followed by dna extraction.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ht1080-1b cross-linked chip input, biological replicate 1
|
| Data processing |
250bp single end reads were trimmed with trim-galore version 0.3.7 with parameters --quality 20 --adapter AGATCGGAAGAGC --stringency 3 --phred33 --length 25 and then aligned with various human alpha-satellite sequences using BWA 0.7.10 aln and sampe functions saving up to 10 alignments per pair, otherwise with default options. Trimmed reads mapped to two consensus sequences representing 20 human centromere sequences are included as supplementary bed files (Cen1-like and Cen13-like).
|
| |
|
| Submission date |
Dec 23, 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 |
SAMN04364783 |
| SRA |
SRX1500121 |
