REAGENT or RESOURCE | SOURCE | IDENTIFIER |
---|---|---|
Biological samples | ||
Normal donor human bone marrow samples | University of Texas Lymphoma/Myeloma Department Myeloma Tissue Bank | https://www.mdanderson.org/research/departments-labs-institutes/departments-divisions/lymphoma-myeloma.html |
Myeloma precursor disease and multiple myeloma patient bone marrow samples | University of Texas Lymphoma/Myeloma Department Myeloma Tissue Bank | https://www.mdanderson.org/research/departments-labs-institutes/departments-divisions/lymphoma-myeloma.html |
Critical commercial assays | ||
Chromium Next GEM Single Cell 5’ Library and Gel Bead kit v1.1, 16 rxns. | 10x Genomics | 1000165 |
Chromium Single Cell V(D)J Enrichment Reagent Kits Human Bcells | 10x Genomics | 1000016 |
Chromium Next GEM Chip G Single Cell kit | 10X Genomics | 1000120 |
Qubit HS dsDNA Assay | ThermoFisher | Q32854 |
HS DNA Bioanalyzer | Agilent | 5067–4626 |
KAPA Biosystems KAPA Library Quantification Kit | KAPA/Roche Diagnostics | KK4835/079602040 01 |
EasySep CD138 Positive Selection Kit | StemCell Technology | Cat#: 17887A |
40-micron sterile cell strainer | VWR | Cat#: 21008–949 |
Density gradient centrifugation, LymphoPrep | StemCell Technology LymphoPrep | Cat#: 07851 |
Deposited data | ||
Aligned scRNA-seq and scBCR-seq data of myeloma and precursors | This paper | EGAS00001006694 |
Bulk mRNA-seq expression data | NCI Cancer Genomic Data Commons | MMRF-COMMPASS |
Software and algorithms | ||
Cell Ranger-5.0.0 | 10x Genomics | https://www.10xgenomics.com/ |
R-4.0.0 | R Core Team | https://www.r-project.org/ |
Seurat-4.0.3 | Stuart et al.50 | https://satijalab.org/seurat/ |
Harmony-0.1.0 | Korsunsky et al.51 | https://portals.broadinstitute.org/harmony |
inferCNV-1.5.0 | Tickle et al.53 | https://github.com/broadinstitute/inferCNV |
CytoTRACE | Gunsagar et al.40 | https://cytotrace.stanford.edu/ |
Monocle2 | Trapnell et al. (2014)41 Qiu et al. (2017)42,43 |
http://cole-trapnell-lab.github.io/monocle-release/ |
Monocle3–0.2.0 | Trapnell et al. (2014)41 Qiu et al. (2017)42,43 |
http://cole-trapnell-lab.github.io/monocle-release/ |