| Antibodies |
|
|
| CD45–89Y |
Fluidigm |
Cat# 3089003, RRID:AB_2661851 |
| CD235–113ln |
Biolegend |
Cat# 349102, RRID:AB_10612565 |
| CD71–115 |
Biolegend |
Cat# 334102, RRID:AB_1134247 |
| CD61–139La |
Biolegend |
Cat# 336402, RRID:AB_1227584 |
| CD3–141Pr |
BD Biosciences |
Cat# 561416, RRID:AB_10612021 |
| CD19–142Nd |
Biolegend |
Cat# 302202, RRID:AB_314232 |
| CD90–143Nd |
BD Biosciences |
Cat# 555594, RRID:AB_395968 |
| CD14–144Nd |
Biolegend |
Cat# 301802, RRID:AB_314184 |
| CD164–145Nd |
Biolegend |
Cat# 324802, RRID:AB_756020 |
| CD34–148Nd |
Biolegend |
Cat# 343502, RRID:AB_1731898 |
| CD105–150Nd |
Biolegend |
Cat# 323202, RRID:AB_755954 |
| CD123–151Eu |
Biolegend |
Cat# 306002, RRID:AB_314576 |
| CD10–152Sm |
Biolegend |
Cat# 312202, RRID:AB_314913 |
| FcER1–153Eu |
Biolegend |
Cat# 334602, RRID:AB_1227649 |
| CD84–154Sm |
Biolegend |
Cat# 326002, RRID:AB_830813 |
| CD33–158Gd |
Biolegend |
Cat# 303402, RRID:AB_314346 |
| CD11c-159Tb |
Biolegend |
Cat# 301602, RRID:AB_314172 |
| GATA-1–160Gd |
Cell Signalling |
Cat# 3535, RRID:AB_2108288 |
| CD7–162Dy |
BD Biosciences |
Cat# 555359, RRID:AB_395762 |
| CD49f-164Dy |
Biolegend |
Cat# 555734, RRID:AB_2296273 |
| CD127–165Ho |
Biolegend |
Cat# 351302, RRID:AB_10718513 |
| CD66–167Er |
BD Biosciences |
Cat# 551354, RRID:AB_394166 |
| CD38–168Er |
Biolegend |
Cat# 303502, RRID:AB_314354 |
| CD45RA-169Tm |
Biolegend |
Cat# 304102, RRID:AB_314406 |
| CD135–170Er |
Biolegend |
Cat# 313302, RRID:AB_314987 |
| CD117–171Yb |
Biolegend |
Cat# 313202, RRID:AB_314981 |
| CD133–172Yb |
Miltenyi Biotec |
Cat# 130–108-062 |
| CD172ab-173Yb |
Biolegend |
Cat# 323802, RRID:AB_830701 |
| CD2–174Yb |
Biolegend |
Cat# 309202, RRID:AB_314752 |
| HLA-DR-209Bi |
Biolegend |
Cat# 307602, RRID:AB_314680 |
| CD15-biotinylated |
Biolegend |
Cat# 301914, RRID:AB_2561326 |
| CD3-biotinylated |
Biolegend |
Cat# 300404, RRID:AB_314058 |
| CD7-biotinylated |
Thermo Fisher Scientific |
Cat# 13–0079-82, RRID:AB_891490 |
| CD56-biotinylated |
Biolegend |
Cat# 362536, RRID:AB_2565653 |
| CD34-FITC |
Myltenyi |
Cat# 130–113-178, RRID:AB_2726005 |
| CD38-BV421 |
Biolegend |
Cat# 303526, RRID:AB_10983072 |
| CD45RA-AF700 |
Biolegend |
Cat# 304120, RRID:AB_493763 |
| CD10-BV650 |
BD Biosciences |
Cat# 563734, RRID:AB_2738393 |
| CD123-PECy7 |
Biolegend |
Cat# 306010, RRID:AB_493576 |
| GATA-1-PE |
Cell Signalling |
Cat# 13353, RRID:AB_2798187 |
| CD38-APC/Cy7 |
Biolegend |
Cat# 303534, RRID:AB_2561605 |
| CD71-PE |
Biolegend |
Cat# 334108, RRID:AB_10915138 |
| CD33-PE/Cy7 |
Biolegend |
Cat# 303434, RRID:AB_2734265 |
| CD84-APC |
Biolegend |
Cat# 326010, RRID:AB_2814188 |
| GATA1 |
Abcam |
Cat# ab181544 |
| Cleaved caspase 3-PE |
BD Biosciences |
Cat# 550821, RRID:AB_393906 |
|
| Biological samples |
|
|
| Adult bone marrow |
All Cells Inc |
https://allcells.com/research-grade-tissue-products/bone-marrow/
|
|
| Deposited data |
|
|
| ATAC-seq data |
This paper |
GEO:GSE167934
|
| FACS data |
This paper |
FlowRepository:FR-FCM-Z539 |
| Mass cytometry data |
This paper |
FlowRepository:FR-FCM-Z5ZA |
|
| Experimental models: Cell lines |
|
|
| K562 |
ATCC |
Cat# CCL-243, RRID:CVCL_0004 |
| GM12878 |
Coriell Institute |
Cat# GM12878, RRID:CVCL_7526 |
|
| Software and algorithms |
|
|
| Cutadapt |
Martin, 2011
|
https://cutadapt.readthedocs.io/en/stable/
|
| Bowtie2 |
Langmead and Salzberg, 2012
|
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
|
| Picard tools |
Broad Institute |
https://broadinstitute.github.io/picard/
|
| ChrAccR |
Fabian Mueller, https://doi.org/10.5281/zenodo.6091218
|
https://github.com/GreenleafLab/ChrAccR, https://zenodo.org/record/6091218
|
| DESeq2 |
Love et al., 2014
|
https://bioconductor.org/packages/release/bioc/html/DESeq2.html
|
| SPADE |
Qiu et al., 2011
|
https://github.com/nolanlab/spade
|
| Scanpy |
Wolf et al., 2018
|
https://scanpy.readthedocs.io/en/stable/
|
| GateFinder |
Aghaeepour et al., 2018
|
https://www.bioconductor.org/packages/release/bioc/html/GateFinder.html
|
| ArchR |
Granja et al., 2020
|
https://www.archrproject.com/
|
| Harmony |
Korsunsky et al., 2019
|
https://portals.broadinstitute.org/harmony/index.html
|
| MAGIC |
Dijk et al., 2018
|
https://github.com/KrishnaswamyLab/MAGIC
|
| Seurat |
Hao et al., 2021
|
https://github.com/satijalab/seurat/
|
