|
| Status |
Public on Aug 18, 2021 |
| Title |
K43R-R1H4HE-T2 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow aspirate
|
| Organism |
Homo sapiens |
| Characteristics |
tumor stage: refractory multiple myeloma
tissue: bone marrow
cell fraction: Tumor - bone marrow CD138+
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Bone marrow aspirate; Ficoll gradient, magnetic sorting (CD138)
10x genomics chromium scRNA-seq 3ยด (v2)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
10x genomics CellRanger 3.01
Removal of Immunoglobulin genes (n=410)
Quality filtering (mitochondrial reads/detected genes per cell)
Doublet removal (Scrublet Python tool, sim_doublet_ratio = 2; n_neighbors = 30; expected_doublet_rate = 0.1. All cells with a doublet score > 0.4 were discarded + manual curation)
Removal of low-quality clusters (high percentages of mitochondrial gene counts, low housekeeping signature scores and/or low numbers of detected genes as well as no expression of biologically relevant cell type or cell state specific genes)
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw UMI count table (cell x gene)
|
| |
|
| Submission date |
Nov 19, 2020 |
| Last update date |
Aug 18, 2021 |
| Contact name |
Karsten Rippe |
| E-mail(s) |
karsten.rippe@dkfz-heidelberg.de
|
| Organization name |
German Cancer Research Center
|
| Department |
Chromatin Networks
|
| Street address |
Im Neuenheimer Feld 280
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE161801 |
Subclone specific microenvironmental impact and drug response in refractory multiple myeloma revealed by single cell transcriptomics |
|
| Relations |
| BioSample |
SAMN16836779 |
