|
| Status |
Public on Aug 21, 2023 |
| Title |
HiC_HSC_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Bone Marrow
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Bone Marrow
cell type: CD34+ HSPC
cell subset: HSC
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching, cells were lysed and nuclei frozen. Nuclei were sonicated using a Bioruptor Pico to generate chromatin fragments.
Libraries were generated using the Arima Genomics HiC kit (Arima cat#A101020) Biotinylated fragments were enriched and sheared prior to library preparation which was performed using Accel NGS 2S Plus DNA Library kit (Swift Biosciences)
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
HSC_40000.matrix
40000_abs.bed
|
| Data processing |
HiC fastq files were processed and mapped to GRCh38, then PCR duplicates removed and contact matrices generated from the merged valid-pairs files
HOMER was used to identify compartments and TADs from balanced HiC-Pro contact matrice
Assembly: hg38
Supplementary files format and content: .matrix, .bed
|
| |
|
| Submission date |
May 02, 2023 |
| Last update date |
Aug 21, 2023 |
| Contact name |
Julie Thoms |
| E-mail(s) |
j.thoms@unsw.edu.au
|
| Organization name |
UNSW Sydney
|
| Department |
Adult Cancer Program
|
| Street address |
Level 2, C25 Lowy Cancer Research Centre, UNSW Sydney, High St
|
| City |
Randwick |
| State/province |
NSW |
| ZIP/Postal code |
2052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE231485 |
Genome-wide Transcription Factor binding maps reveal cell-specific changes in the regulatory architecture of human HSPC [HiC] |
| GSE231486 |
Genome-wide Transcription Factor binding maps reveal cell-specific changes in the regulatory architecture of human HSPC |
|
| Relations |
| BioSample |
SAMN34535690 |
| SRA |
SRX20189764 |
