|
| Status |
Public on Mar 29, 2024 |
| Title |
H1_hESC_Adaptive_Sampling |
| Sample type |
SRA |
| |
|
| Source name |
hPSC_H1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: hPSC_H1
genotype: N11_clone
|
| Growth protocol |
All differentiation experiments were performed on hESCs grown on vitronectin. hESCs were maintained in E8 medium for 2 days to reach ~80% confluence and flash frozen.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using Monarch® HMW DNA Extraction Kit for Cells & Blood (NEB, T3050), according to the manufacturer’s instructions.
Prior to ONT library preparations, DNA was sheared to ~15-20 kb fragment size using Covaris g-TUBE. Sequencing libraries were prepared from ~1–2ug of DNA, using native library preparation kit, SQK-LSK114, according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
PromethION |
| |
|
| Description |
R10.4.1
|
| Data processing |
*library strategy: Nanopore Sequencing
minimap2 (2.26) alignment
WhatsHap (2.2) variant phasing and haplotype block calling
Assembly: hg38
Supplementary files format and content: .vcf file with all variants called in phased ONECUT1 haplotype block
Supplementary files format and content: .bed file with regions selected for adaptive sampling
|
| |
|
| Submission date |
Mar 12, 2024 |
| Last update date |
Mar 29, 2024 |
| Contact name |
Samuel Joseph Kaplan |
| Organization name |
Sloan Kettering Institute
|
| Department |
Developmental Biology Program
|
| Street address |
430 E 67th St
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL26167 |
| Series (2) |
| GSE261391 |
CRISPR Screening Uncovers a Long-Range Enhancer for ONECUT1 in Pancreatic Differentiation and Links a Diabetes Risk Variant [long_read_seq] |
| GSE267330 |
CRISPR Screening Uncovers a Long-Range Enhancer for ONECUT1 in Pancreatic Differentiation and Links a Diabetes Risk Variant |
|
| Relations |
| BioSample |
SAMN40414252 |
| SRA |
SRX23908462 |
