|
| Status |
Public on May 30, 2018 |
| Title |
Gibbon_Hi-C |
| Sample type |
SRA |
| |
|
| Source name |
Lymphoblasts
|
| Organism |
Nomascus leucogenys |
| Characteristics |
cell type: EBV-transformed cell line
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
EBV-transformed cells were cross-linked, washed, bound to AMPure XP beads and digested with DpnII. After incorporation of biotin-dCTP, chromatin proximity ligation was carried out.
Libraries were constructed using NEBNext Ultra II DNA Library preparation Kit (NEB, E7645S).
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Raw Hi-C data was processed with the Juicer package.
TADtool was used to call TADs using the directionality index method.
Genome_build: Nleu3.0
Supplementary_files_format_and_content: Gibbon_TAD_boundaries_500kb-1Mb.bed: Bed file containing the positions of the boundaries of all TADs that range in 500kb-1Mb in size.
|
| |
|
| Submission date |
May 29, 2018 |
| Last update date |
May 30, 2018 |
| Contact name |
Lucia Carbone |
| E-mail(s) |
carbone@ohsu.edu
|
| Organization name |
Oregon Health & Science University
|
| Street address |
3303 SW Bond Ave.
|
| City |
Portland |
| State/province |
Oregon |
| ZIP/Postal code |
97239 |
| Country |
USA |
| |
|
| Platform ID |
GPL25055 |
| Series (2) |
| GSE115062 |
Epigenetic maintenance of topological domains in the rearranged gibbon genome [Hi-C] |
| GSE115065 |
Epigenetic maintenance of topological domains in the rearranged gibbon genome |
|
| Relations |
| BioSample |
SAMN09279526 |
| SRA |
SRX4138630 |
