|
| Status |
Public on Mar 18, 2024 |
| Title |
G390-HiC |
| Sample type |
SRA |
| |
|
| Source name |
glioblastoma stem-like cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: glioblastoma stem-like cells
assay: Hi-C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hi-C was performed on 0.5-1 million cells from each GSC line using the Hi-C+ kit (Arima Genomics) according to the manufacturer’s instructions.
Arima-HiC Kit, Library Preparation using KAPA Hyper Prep Kit
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
CNV-balanced
|
| Data processing |
Hi-C reads were aligned to the reference genome GRCh38 using bwa mem (v0.7.17) with “-SP5M”
Invalid data, including PCR duplicates and read pairs mapping to the same restriction fragment, were removed using pairtools (v0.3.0).
The runHiC (v0.8.4-r1; https://zenodo.org/badge/doi/10.5281/zenodo) and cooler (v0.8.6) packages were used to construct contact matrices at various resolutions.
Raw Hi-C matrices were corrected using a modified matrix balancing method to account for CNV effects and other systematic biases including mappability, GC content, and restriction enzyme sites, all processed via Neoloopfinder (v0.3.0.post4).
Assembly: GRCh38
Supplementary files format and content: .mcool file contains Hi-C contact matrices in a sparse format, storing the non-zero values of the upper triangular matrix in the HDF file.mcoolfiles can include multiple normalisations and resolutions within the same file.
|
| |
|
| Submission date |
Apr 18, 2023 |
| Last update date |
Mar 18, 2024 |
| Contact name |
Argyris Papantonis |
| E-mail(s) |
argyris.papantonis@med.uni-goettingen.de
|
| Organization name |
University Medical Center Göttingen
|
| Department |
Institute of Pathology
|
| Street address |
Robert-Koch-Str. 40
|
| City |
Göttingen |
| State/province |
Goettingen |
| ZIP/Postal code |
37075 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE229962 |
Extreme structural heterogeneity rewires glioblastoma chromosomes to sustain patient-specific transcriptional programs [Hi-C] |
| GSE229966 |
Extreme structural heterogeneity rewires glioblastoma chromosomes to sustain patient-specific transcriptional programs |
|
