|
| Status |
Public on Apr 19, 2011 |
| Title |
In vitro reconstituted nucleosome cores_1 |
| Sample type |
SRA |
| |
|
| Source name |
granulocytes
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Granulocytes
|
| Growth protocol |
Cells were obtained from donor buffy coat and purified using sucrose gradient and Ig-beads
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Naked genomic DNA isolated from neutrophil granulocytes from our in vivo studies was sheared by sonication using a Covaris sonicator and separated on a 1% UltraPure Agarose (Invitrogen) gel run at 100 V for 1 hour. A smear of fragments with lengths from 850-2000 base pairs (the bulk of the sheared DNA) was isolated and extracted from the gel using the QIAquick Gel Extraction Kit (Qiagen). The ends of the sheared DNA fragments were repaired as described below and then were assembled with recombinant Xenopus histones into nucleosomes as described in# at a 1.1:1 molar ratio of DNA to histone octamer such that on average one nucleosome would occupy 850 bp of DNA. Specifically 4.9ug of DNA and 0.80ug of octamer were reconstituted in a total volume of 200ul.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
AB SOLiD System 2.0 |
| |
|
| Description |
Invitrosomes_1
Nucleosome-bound DNA isolated by in vitro reconstitution of nucleosomes with human DNA, followed by micrococcal nuclease treatment, followed by gel purification
|
| Data processing |
All sequence reads were aligned using SOLiD pipeline to human hg18 reference genome using the first 25 bps and allowing for up to two mismatches. RNA-Seq data was processed using custom scripts to obtain RPKM values for each gene isoform based on hg19 RefSeq annotation.
|
| |
|
| Submission date |
Feb 20, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Anton Valouev |
| Organization name |
Stanford University
|
| Department |
Pathology
|
| Lab |
Sidow Lab
|
| Street address |
300 Pasteur Dr.
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94035 |
| Country |
USA |
| |
|
| Platform ID |
GPL9138 |
| Series (1) |
| GSE25133 |
Determinants of nucleosome organization in primary human cells |
|
| Relations |
| SRA |
SRX046680 |
| BioSample |
SAMN00217100 |
