 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 16, 2024 |
| Title |
HiC_tissue_DTB-022-BL |
| Sample type |
SRA |
| |
|
| Source name |
tissue
|
| Organism |
Homo sapiens |
| Characteristics |
ega: EGAS00001006604
tissue: tissue
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
As described in Hawley, J. R. et al. Reorganization of the 3D Genome Pinpoints Noncoding Drivers of Primary Prostate Tumors. Cancer Res 81, 5833-5848, doi:10.1158/0008-5472.CAN-21-2056 (2021).
The mCRPC Hi-C libraries were prepared using the SMARTer ThruPLEX DNA-seq library preparation kit (Takara Biosciences) per manufacturer’s protocol, followed by a double-size selection for 300-700 bp fragments using Ampure XP beads. The libraries were then sequenced on a NovaSeq 6000.
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Paired-end raw reads of Hi-C libraries were processed using HiC-Pro62 (version 3.0.0) Singularity container provided by HiC-Pro (https://github.com/nservant/HiC-Pro). Briefly, sequencing reads were first independently aligned to the reference human genome (hg38) using the bowtie263 end-to-end algorithm and ‘-very-sensitive’ option. To rescue the unmapped chimeric fragments spanning the ligation junction, the ligation site was detected using an exact matching procedure and the 5’ fraction of the reads was aligned back to the reference genome. Unmapped reads, multi-mapped reads, and singletons were then discarded. Each pair of aligned reads were then assigned to MboI restriction fragments. Read pairs from uncut DNA, self-circle ligation, and PCR artefacts were filtered out and the valid read pairs involving two different restriction fragments were used to build the contact matrix. Valid read pairs were then binned at 10-kb resolution. The binned contact matrix was then normalized using the iterative correction (ICED) method64 to correct for biases such as GC content, mappability, and effective fragment length in Hi-C data.
Assembly: hg38
Supplementary files format and content: Sparse matrix containing paired locus coordinates and the observed interaction frequency, after ICED normalization.
|
| |
|
| Submission date |
Dec 06, 2023 |
| Last update date |
May 16, 2024 |
| Contact name |
Felix Feng |
| Organization name |
University of California
|
| Street address |
1450 3rd Street
|
| City |
San Fransisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE249494 |
Integrated analyses highlight interactions between the 3D-genome and DNA, RNA, and epigenomic alterations in metastatic prostate cancer |
|
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7948942_DTB-022-BL_10000_iced.matrix.gz |
1.5 Gb |
(ftp)(http) |
MATRIX |
| Raw data not provided for this record |
| Processed data provided as supplementary file |
|
|
|
|
 |
