|
| Status |
Public on Oct 10, 2011 |
| Title |
K562_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Erythroid Leukemia Cell line
|
| Organism |
Homo sapiens |
| Characteristics |
passages: 11
library strategy: Chromosome Confirmation Capture
|
| Growth protocol |
K562 cells were grown in Iscove's Modification of Dubelco's Media and were harvested at passage 8-11.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked in 2% formaldehyde, digested with Csp6I and ligated with T4 DNA ligase and lysed for 15 minutes on ice in lysis buffer (10mM Tris ph8, 10mM NacL, 0.2%NP-40, Roche EDTA free protease inhibitor tablet). Nuclei were pelleted and counted and aliquoted in microfuge tubes at 1x10^7 nuclei per tube and snap frozen in liquid nitrogen and stored at -80. Bait regions were extended using a biotin tagged primer and Illumina adapters were ligated to the 3' end. Nested PCR was used to further amplify and add a second illumina adapter to the 5' end.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
3bp tag on 5' end was trimmed and reads were aligned with bowtie, and coverage of each restriction fragment in 1 MB region of chr17 (genome build hg18) was used to identify regions interacting at greater than the expected frequency for a given linear chromosome distance.
|
| |
|
| Submission date |
Aug 01, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Jesse Raab |
| Organization name |
UC Santa Cruz
|
| Department |
MCD Biology
|
| Lab |
Rohinton Kamakaka
|
| Street address |
1156 High St
|
| City |
Santa Cruz |
| State/province |
CA |
| ZIP/Postal code |
95064 |
| Country |
USA |
| |
|
| Platform ID |
GPL9052 |
| Series (1) |
| GSE31105 |
Chromatin Conformation Capture in two biological replicates of K562 cells to identify interactions between tRNA genes in human cells. |
|
| Relations |
| SRA |
SRX087815 |
| BioSample |
SAMN00691133 |
