|
| Status |
Public on Jan 11, 2024 |
| Title |
BM_CR_123 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow aspirates
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: T cells & HSPCs
tissue: Bone marrow aspirates
patient diagnosis: acute myeloid leukemia
disease state: complete remission (CR)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ficoll-processed primary BM samples were sorted into CD34+ and CD3+ fractions.
Library was performed according to the manufacter’s protocol CG000204 (single cell 3’ v2 protocol, 10x Genomics).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
10x Genomics
|
| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). Sample demultiplexing based on genotypes was performed using souporcell (https://www.nature.com/articles/s41592-020-0820-1)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files
|
| |
|
| Submission date |
Oct 20, 2022 |
| Last update date |
Feb 21, 2024 |
| Contact name |
Anna Mathioudaki |
| E-mail(s) |
annamathioudaki94@gmail.com
|
| Organization name |
EMBL Heidelberg
|
| Street address |
Meyerhofstraße 1, 1
|
| City |
Heidelberg |
| State/province |
None / N/A |
| ZIP/Postal code |
69126 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE216187 |
scRNAseq of bone marrow (BM) T cells and hematopoietic stem and progenitor cells (HSPCs) of acute myeloid leukemia patients post allogeneic stem cell transplantation (alloSCT). |
|
| Relations |
| BioSample |
SAMN31387014 |
| SRA |
SRX17966097 |
