|
| Status |
Public on Sep 12, 2020 |
| Title |
26APR16-PacBio-HelaS3-unsyn |
| Sample type |
SRA |
| |
|
| Source name |
DpnII MC-3C on Asynchronious cells
|
| Organism |
Homo sapiens |
| Characteristics |
protocol: MC-3C
enzyme: DpnII
cell line: HelaS3
|
| Growth protocol |
Hela S3 cells were grown in DMEM media supplemented with 10% FBS and 1% Pen/Strep
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For each MC-3C library 5 Million cells were crosslinked
MC-3C was performed as described in detail in supplemental methods.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
PacBio RS II |
| |
|
| Data processing |
Library strategy: MC-3C
reads with a quality threshold over 80 were selected
reads were virtually cut at the sequence sites recognized by DpnII (GATC
cut reads were mapped using bwa-mem
cut reads had to align at least 85% to the DpnII Genomic fragment to be assigned
combined all replicates as final output
Genome_build: hg19
Supplementary_files_format_and_content: table with all interactions from c-walks represented as pairwise interactions (tab seperated)
|
| |
|
| Submission date |
Mar 13, 2020 |
| Last update date |
Sep 12, 2020 |
| Contact name |
Bastiaan Dekker |
| E-mail(s) |
bastiaan.dekker@umassmed.edu
|
| Organization name |
University of Massachusetts Medical School
|
| Department |
Systems Biology
|
| Lab |
Dekker lab
|
| Street address |
368 Plantation street
|
| City |
Worcester |
| State/province |
Massachusetts |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL21311 |
| Series (1) |
| GSE146945 |
Multi-contact 3C data reveal that the human genome is largely unentangled |
|
| Relations |
| BioSample |
SAMN14374607 |
| SRA |
SRX7909614 |
