satijalab
bmcite donor details
Hello,
I'm interested in using the bmcite data set as a reference for a study based on human bone marrow samples; so it is important to me to understand how much this data set is representative of a general population. I searched through references provided in the help page (https://doi.org/10.1016/j.cell.2019.05.031 and GEO page), but couldn't find any detail about number of BM donors, age etc. Are those available anywhere? Thanks
It looks like it was from a single donor!
Copy and paste from https://doi.org/10.1016/j.cell.2019.05.031 (highlight my own)
Bone marrow mononuclear cells CITE-seq experiment
Bone marrow mononuclear cells from a single human donor were purchased from AllCells (cat #: ABM007F, lot #:3008803). The day of the experiment, cells were thawed according to manufacturer’s protocol. Briefly, cell vials were sprayed with ethanol and placed in a 37°C water bath for 2 min to thaw. RPMI 10% media was used to wash and resuspend cells. Cell numbers and viability were estimated using trypan blue. Cells were resuspended in CITE-seq [Stoeckius et al., 2017] staining buffer (2%BSA/0.01%Tween in PBS) and incubated with FcX blocking reagent for 10 min (BioLegend, cat #: 422302) to block nonspecific antibody binding. Following FcX blocking, cells were incubated with a pool of 25 antibodies (1 μg/antibody) for 30 min at 4°C. To ensure we could accurately identify cell doublets and distinguish empty droplets from cells with low gene counts, cells were split into 10 tubes each containing a unique hashing antibody from BioLegend [Stoeckius et al., 2018] and were incubated at 4°C for an additional 20 min. After incubation, cells were washed three times with 1 mL of staining buffer to remove any unbound antibodies. At the end of the final wash, cells were passed through a 40 μm filter to remove cell clumps (VWR, cat #: 10032-802) and resuspended in 1xPBS at the appropriate cell concentration for 10x Genomics 3′ scRNA-seq [Zheng et al., 2017].
