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. 2021 Sep 14;36(11):109698. doi: 10.1016/j.celrep.2021.109698
REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Viability (ef506) dye eBioscience Cat# 65-0866-18
Lineage Cocktail (FITC) eBioscience Cat# 22-7776-72; RRID:AB_2043865
CD34 (PerCP-Cy5.5) BioLegend Cat# 343522; RRID:AB_2228973
CD38 (APC) eBioscience Cat# 17-0389-42; RRID:AB_1834353
CD45RA (PE) eBioscience Cat# 12-9459-42; RRID:AB_10718238
CD90 (BV421) Biolegend Cat# 328122; RRID:AB_2561420
CD123 (PE-Cy7) eBioscience Cat# 25-1239-42; RRID:AB_1257136
Biological samples
human early fetal liver (1st trimester FL) Human Developmental Biology Resource 1_eFL, 2_eFL
Human fetal liver (2nd trimester FL) Human Developmental Biology Resource 1_FL, 2_FL
Human fetal bone marrow (matched to 2nd trimester FL) Human Developmental Biology Resource 1_FBM, 2_FBM
Pediatric bone marrow Imperial College NHS Trust 1_Paed_BM, 2_Paed_BM
Adult bone marrow StemCell Technologies, Canada (cat no. 17001). 1_Adult_BM
Chemicals, peptides, and recombinant proteins
Maxpar PBS Buffer Fluidigm Cat# 201058
10% BSA in Iscove’s MDM StemCell Technologies, Inc. Cat# 09300
Ficoll-Paque PLUS GE Healthcare Life Sciences Cat#17-5442-03
CD34 MicroBead kit and MACS system Miltenyi Biotech Cat#130-046-703
CD34 MicroBead ultra Miltenyi Biotech Cat#130-100-453
RoboSep Buffer StemCell Technologies Cat# 20104
UltraPure EDTA invitrogen Cat# 15576-028
PBS pH 7.4 GIBCO (LifeTechnologies) Cat# 10010-015
Fetal Bovine Serum (Heat inactivated) Sigma F7524
Critical commercial assays
Chromium Single Cell 3′ GEM Library with Gel Bead Kit v3 10x Genomics, Inc. Cat#1000092
Deposited data
10X scRNaseq data in this manuscript This manuscript GSE155259
10X scRNaseq data in this manuscript This manuscript Mendeley Data (https://doi.org/10.17632/phfgms85x2.1)
10X scRNaseq data in this manuscript (Louka et al., 2021) GSE111895
10X scRNaseq data in this manuscript (Psaila et al., 2020) GSE144568
Software and algorithms
R (v3.6.3, v.4.0.2, v.4.0.4) (R Core Development Team, 2013) https://cran.r-project.org/bin/macosx/
Flowjo version (10.5.3) Flowjo www.flowjo.com
RStudio (v1.1.463) Team R Studio https://www.rstudio.com/products/rstudio/download/
Cell Ranger v3.0.1 10x Genomics, Inc. https://github.com/10XGenomics/cellranger
SingCellaR (v.1.1.1, v.1.2.0) This manuscript Github: https://github.com/supatt-lab/SingCellaR
Zenodo: https://zenodo.org/record/5153387
monocle3_0.2.3.0 (Trapnell et al., 2014) https://cole-trapnell-lab.github.io/monocle3/
pyscenic_0.10.4 (Van de Sande et al., 2020) https://github.com/aertslab/pySCENIC
AUCell_1.12.0 (Aibar et al., 2017) https://www.bioconductor.org/packages/release/bioc/vignettes/AUCell/inst/doc/AUCell.html
kBET_0.99.6 (Büttner et al., 2019) https://github.com/theislab/kBET
lisi_1.0 (Korsunsky et al., 2019) https://github.com/immunogenomics/LISI
Seurat_4.0.1 (Hao et al., 2021) https://satijalab.org/seurat/
rliger_1.0.0 (Welch et al., 2019) https://github.com/welch-lab/liger
Scanorama_1.7 (Hie et al., 2019) https://github.com/brianhie/scanorama
sva_3.38.0 (Leek et al., 2012) https://bioconductor.org/packages/release/bioc/html/sva.html
harmony_1.0 (Korsunsky et al., 2019) https://github.com/immunogenomics/harmony
fgsea_1.18.0 (Korotkevich et al., 2021) https://bioconductor.org/packages/release/bioc/html/fgsea.html
DAseq_1.0.0 (Zhao et al., 2020) https://github.com/KlugerLab/DAseq
symphony_1.0 (Kang et al., 2020) https://github.com/immunogenomics/symphony
Other
BioRender Graphical abstract created with BioRender.com. https://biorender.com/