|
| Status |
Public on May 23, 2017 |
| Title |
GB238 |
| Sample type |
SRA |
| |
|
| Source name |
Glioblastoma clinical tumour sample
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Glioblastoma clinical tumour sample
|
| Growth protocol |
The transformed mouse cell line was grown in Dulbecco's modified eagle medium (DMEM) with 10% fetal calf serum (FCS) and 1% Penicillin/Streptomycin supplemented with puromycin. Human lymphoblastoid cell lines (FY1199 and DD1618 - European Collection of Cell Cultures (ECACC)) were grown in RPMI-1640 medium with 10% fetal calf serum (FCS) and 1% Penicillin/Streptomycin. Tumors were received from Prof. V. Peter Collins (Department of Pathology, Addenbrooke’s Hospital, Cambridge, UK), with accompanying full ethical approval, as fresh frozen pieces consisting of between 75% and 90% tumor content, as determined by the pathologist. Approximately 160 mg of frozen tumor was finely chopped before being fixed and taken through the Hi-C protocol.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from tumor tissue using the Qiagen QIAamp DNA Micro Kit, according to manufacturer’s instructions. Sequencing libraries were then prepared according to Scheinin, I., et al. Genome research 24, 2022-2032 (2014).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Data processing |
Library strategy: QDNAseq
Standard Illumina Sequencing Pipeline
Hi-C Processing: HiCUP (Wingett S, Ewels P, Furlan-Magaril M et al. HiCUP: pipeline for mapping and processing Hi-C data (doi: 10.12688)
QDNAseq package with default parameters an 100kb bin size
Genome_build: Human: GRCh37;Mouse: NCBIM37
Supplementary_files_format_and_content: Hi-C interaction files lists interacting restriction fragments
|
| |
|
| Submission date |
May 25, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Steven William Wingett |
| E-mail(s) |
steven.wingett@mrc-lmb.cam.ac.uk
|
| Organization name |
MRC Laboratory of Molecular Biology
|
| Department |
Cell Biology
|
| Street address |
Francis Crick Avenue, Cambridge Biomedical Campus
|
| City |
Cambridge |
| State/province |
Cambs |
| ZIP/Postal code |
CB2 0QH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL15433 |
| Series (1) |
| GSE81879 |
Hi-C As A New Tool For Precise Detection And Characterization Of Chromosomal Rearrangements And Copy Number Variation In Human Tumors |
|
| Relations |
| BioSample |
SAMN05173322 |
| SRA |
SRX1799563 |
