|
| Status |
Public on May 01, 2024 |
| Title |
PANGUA-D Hi-C |
| Sample type |
SRA |
| |
|
| Source name |
primary bone marrow
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: B-ALL
cell type: primary bone marrow
genotype: Diagnosis
|
| Growth protocol |
Cryopreserved paired diagnosis/relapse primary patient bone marrow samples from individual patients were obtained from the Children’s Oncology group (COG) ALL biorepository or St. Jude Children’s Research Hospital.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Following FACS, leukemic cells were immediately fixed and crosslinked with 2% formaldehyde at room temperature for 10 minutes. Glycine was added to stop the reaction. Crosslinked cells were washed with PBS and then frozen on dry ice. Crosslinked cell pellets were stored at -80 until ready for processing.
Hi-C libraries were generated using the Arima-HiC kit (A410110) with Swift Biosciences® Accel-NGS® 2S Plus DNA Library Kit (Cat # 21024) and Indexing kit (Cat #) according to manufacturer’s protocol.
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
hic-bench platform
Reads filtered for accepted intra-chromosomal read-pairs by the GenomicTools tools-hic filter command in the hic-bench platform
Interaction matrices for each chromosome separately were created by the hic-bench platform at 40kb resolution
Filtered read counts were normalized by iterative correction and eigenvector decomposition
To account for variances in read counts of more distant loci, distance normalization for each chromosome matrix was performed.
Assembly: hg19
Supplementary files format and content: .hic files consisting of hic signal and compartment bedgraphs consisting of A/B compartment tracks for each patient
|
| |
|
| Submission date |
Jan 11, 2023 |
| Last update date |
May 01, 2024 |
| Contact name |
Sonali Narang |
| E-mail(s) |
sonali.narang@nyulangone.org
|
| Phone |
5169652665
|
| Organization name |
NYU Langone
|
| Street address |
435 east 30th street
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE222679 |
Clonal evolution of the 3D chromatin landscape of relapsed ALL [Hi-C] |
| GSE222687 |
Clonal evolution of the 3D chromatin landscape of relapsed ALL |
|
| Relations |
| BioSample |
SAMN32682103 |
| SRA |
SRX19007836 |
