|
| Status |
Public on May 04, 2023 |
| Title |
AML processed with GTAC |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: bone marrow
cell line: primary sample
cell type: CD34+
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
NGS library preparation and purification
GTAC
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
demultiplexed scATAC-seq data from a GTAC experiment
|
| Data processing |
FASTQ files were trimmed and converted to BAM. BAM files were de-duplicated using Picard. De-duplicated BAM files were merged with Samtools and the provided fragment files were generated. Fragment files were used as input for analysis in ArchR.
Assembly: hg38
Supplementary files format and content: Fragment files from merged BAM files. Each fragment is linked to the single cell where it derives from.
|
| |
|
| Submission date |
Oct 04, 2022 |
| Last update date |
May 04, 2023 |
| Contact name |
Sven Turkalj |
| E-mail(s) |
sven.turkalj@kellogg.ox.ac.uk
|
| Phone |
07307186118
|
| Organization name |
WIMM
|
| Department |
Radcliffe Department of Medicine
|
| Lab |
Vyas Lab
|
| Street address |
John Radcliffe Hospital/Headley Way, Oxford OX3 9DS
|
| City |
Oxford |
| ZIP/Postal code |
OX3 9DS |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE214812 |
GTAC enables parallel genotyping of multiple genomic loci with chromatin accessibility profiling in single cells |
|
| Relations |
| BioSample |
SAMN31155143 |
| SRA |
SRX17797471 |
