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. Author manuscript; available in PMC: 2023 Apr 7.
Published in final edited form as: Cell Stem Cell. 2022 Mar 11;29(4):577–592.e8. doi: 10.1016/j.stem.2022.02.010

Key resources table.

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
CD33-PE; clone WM53 BD cat#: 555450
CD19-BV605; clone SJ25C1 BD cat#: 562654
CD11b-APC; clone ICRF44 BD cat#: 561015
CD56-APCR700; clone NCAM16.2 BD cat#: 565140
CD66b-PE; clone G10F5 BD cat#: 561650
CD66b-BV421; clone G10F5 BD cat#: 562940
CD45-APC; clone HI30 BD cat#: 555485
CD235a-PECy7; clone 11E4B-7-6 Coulter cat#: A71564
CD3-BV786; clone SK7 BD cat#: 563800
CD34-PE; clone 581 BD cat#: 555822
CD45RA-APC; clone HI100 BD cat#: 550855
CD38-PECy7; clone HB7 BD cat#: 335790
CD10-BV786; clone HI10a BD cat#: 564960
CD90-Biotin; clone 5E10 BD cat#: 555594
Anti-LMNB1 Abcam cat#: ab16048
Anti-LBR Abcam cat#: ab32535
Anti-yH2AX ThermoFisher cat#: PA5-28778
Anti-53BP1 Cell Signaling cat#: 2675
Bacterial and virus strains
Stbl3 competent cells ThermoFisher cat#: C737303
Biological samples
Human umbilical cord blood Bloodworks Northwest https://www.bloodworksnw.org/
Human mobilized peripheral blood Primary AML samples Fred Hutch CCEH core https://www.fredhutch.org/en/research/divisions/clinical-research-division/research/co-operative-center-for-excellence-in-hematology/hematopoietic-cell-procurement-and-resource-development.html
Chemicals, peptides, and recombinant proteins
Ficoll-Paque Plus GE cat#:17-1440-02/6
Retronectin Takara cat#: T100A
Recombinant human cytokines Peprotech https://www.peprotech.com/gb/
Recombinant human BMP-4 R&D Systems cat#: 314-BP-050
Recombinant human IL-7 R&D Systems cat#: 207-IL-010
Doxycycline Sigma cat#: D9891-10G
SytoxGreen live-dead stain ThermoFisher cat#: S34860
poly-D-lysine Sigma cat#: A-003-E
Vectashield Antifade Vector labs cat#: H-1200
EdU ThermoFisher cat#: C10640
DMSO Santa Cruz cat#: 487929-M
Monastrol Sigma cat#: M8515
Nocodazole Sigma cat#: 487929-M
Trizol ThermoFisher cat#: 15596026
Critical commercial assays
CD34 Microbead kit Miltenyi cat#: 130-046-702
MethoCult Stem Cell Technologies cat#: H3434
Gateway LR clonase ThermoFisher cat#: 11791020
Anti-PE microbead kit Miltenyi cat#: 130-048-801
May-Grunwald stain Sigma cat#: MG500
Giemsa stain Sigma cat#: R03055
anti-mouse Igk beads BD cat#: 552843
Cytofix BD cat#: 554656
Trevigen neutral COMET Trevigen cat#: 4250-050-K
Chromium Next GEM Single Cell 3’ Reagents kit v.3.1 10X technologies cat#: PN-1000123
Deposited data
BeatAML patient dataset Tyner et al. 2018 www.vizome.org
TCGA LAML patient dataset TCGA www.cbioportal.org
GTEX dataset GTEX http://xena.ucsc.edu/
Atlas of human Blood Cells Xie et al., 2020 http://scrna.sklehabc.com/
The raw and processed RNA-seq, single cell RNA-seq, and Hi-C data generated in this study This paper GSE174533
Gene expression data for iPSC-MDS HPCs Hsu et al. 2019 GSE129851
Experimental models: Cell lines
TP53+/− and TP53+/−/del5q iPSC lines This paper -
293T-17 cells ATCC cat#: CRL-11268
MS-5 stromal cells Dr. Katsuhiko Itoh -
Experimental models: Organisms/strains
NOD/LtSz−scidIL2Rgnull (NSG) mice Jackson labs cat#: 005557
NOD.Cg-Prkdcscid Il2rgtm1Wjl Tg(CMV-IL3,CSF2,KITLG)1Eav/MloySzJ Jackson labs cat#: 013062
Oligonucleotides
Control Luciferase shRNA #1, 5’ACGCTGAGTACTTCGAAATGT IDT Technologies Custom order
Control Luciferase shRNA #2: 5’CTTACGCTGAGTACTTCGA IDT Technologies Custom order
LMNB1 75% knockdown shRNA: 5’-GCATGAGAATTGAGAGCCTTT Sigma TRC TRCN0000029271
LMNB1 50% knockdown shRNA: 5’-CCCAGATCAAGCTTCGAGAAT Sigma TRC TRCN0000029273
qPCR primer LMNB1 Fwd 5’-AAGAACCAGAACTCGTGGGG This paper N/A
qPCR primer LMNB1 Rev 5’-CAACCTCCTCTCCCTGAGAAT This paper N/A
qPCR primer GAPDH Fwd 5’-TCCTGCACCACCAACTGCTTA This paper N/A
qPCR primer GAPDH Rev 5’-TCTTCTGGGTGGCAGTGATGG This paper N/A
Recombinant DNA
HOAX9, ERG, RORA, SOX4, MYB (5F) plasmids Addgene https://www.addgene.org/George_Daley/
LMNB1 lentiviral overexpression plasmid Sigma TRCN0000467310
pSMAL lentiviral vector Dr. Peter van Galen Addgene
LMNB1 gateway ORF Genecopoeia cat#: GC-I3724
pLKO.1 shRNA empty vector Addgene cat#: 10878
pLKO.1 shRNA vectors for LMNB1 knockdown This paper -
Lentiviral packaging plasmids Addgene https://www.addgene.org/Didier_Trono/
Software and algorithms
FlowJo BD Biosciences https://www.flowjo.com/
Fiji/ImageJ Schindelin et al. 2012 https://imagej.nih.gov/ij/
GraphPad Prism GraphPad https://www.graphpad.com/
OpenComet software Gyori et al., 2014 cometbio.org
Cell Ranger 10X genomics https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
Monocle3 Cao et al., 2019 https://cole-trapnell-lab.github.io/monocle3/
SingleR Aran et al., 2019 https://bioconductor.org/packages/release/bioc/html/SingleR.html
DESeq2 Love et al., 2014 https://bioconductor.org/packages/release/bioc/html/DESeq2.html
GSEA Subramanian et al., 2005 https://www.broadinstitute.org/msigdb
Samtools Li et al., 2009 http://samtools.sourceforge.net/
STAR Dobin et al., 2013 https://github.com/alexdobin/STAR
Subread Liao et al., 2013 http://subread.sourceforge.net/
CytoConverter Wang and LaFramboise, 2019 https://jxw773.shinyapps.io/Cytogenetic__software/
bedtools Quinlan and Hall, 2010 https://bedtools.readthedocs.io/en/latest/
Metascape Zhou et al., 2019 https://metascape.org
Juicer Durand et al., 2016 https://github.com/aidenlab/juicer
Juicebox Robinson et al., 2018 https://github.com/aidenlab/Juicebox
deepTools Ramírez et al., 2016 https://deeptools.readthedocs.io/en/develop/
HOMER Heinz et al., 2010 http://homer.ucsd.edu/homer/
Other
X-VIVO 10 media Lonza cat#: 04-380Q
StemSpan SFEM media StemCell Technologies cat#: 9650
H5100 media StemCell Technologies cat#: 05150