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. 2024 Aug 18;27(9):110734. doi: 10.1016/j.isci.2024.110734
REAGENT or RESOURCE SOURCE IDENTIFIER
Biological samples

Mouse bone marrow Collected from long bones (femurs and tibias) of C57BL/6J and B6.Cg-Terctm1Rdp/J strains. N/A

Critical commercial assays

Chromium Single Cell 3′ V3.1 Reagent Kits 10X Genomics 1000121
Leukocyte Acid Phosphatase (TRAP) Kit Sigma-Aldrich 387A
NucleoSpin RNA II MN(Macherey-Nagel) 740955.50
REPLI-g UltraFast Mini Kit Qiagen 150035
QIAamp DNA mini kit Qiagen 51306

Deposited data

Raw single-cell DNA-seq and bulk DNA-seq data This paper PRJNA906340
Raw single-cell RNA-seq and bulk RNA-seq data This paper GSE190535; GSE169608; GSE224119
Mouse reference genome mm10 UCSC Genome Browser http://genome.ucsc.edu/cgi-bin/hgGateway?db=mm10

Experimental models: organisms/strains

C57BL/6J, mus musculus The Jackson Laboratory IMSR_JAX:000664
B6.Cg-Terctm1Rdp/J,mus musculus The Jackson Laboratory IMSR_JAX:004132

Oligonucleotides

shRNA targeting sequence: Irf8 #1: GGACATTTCTGAGCCATATAA This paper N/A
shRNA targeting sequence: Irf8 #2: GCCTATGACACACACCATTCA This paper N/A
shRNA targeting sequence: Cebpd #1: GCTGGCCTCCGGCAGTTCTTC This paper N/A
shRNA targeting sequence: Cebpd #2: GCTCCACGACTCCTGCCATGT This paper N/A
shRNA targeting sequence: Klf4 #1: GACCTAGACTTTATCCTTTC This paper N/A
shRNA targeting sequence: Klf4 #2: GGTCATCAGTGTTAGCAAAGG This paper N/A
shRNA targeting sequence: Sox4 #1: GCGACAAGATTCCGTTCATCC This paper N/A
shRNA targeting sequence: Sox4 #2: GCTCAAGGACAGCGACAAGAT This paper N/A

Recombinant DNA

pGMLV-zsGreen-vshRNA-TFs Genomeditech N/A

Software and algorithms

DESeq2 (v1.38.3) Love et al.63 https://bioconductor.org/packages/release/bioc/html/DESeq2.html
fastp (v0.21.0) Chen et al.64 https://github.com/OpenGene/fastp
CellRanger (v5.0.0) 10x Genomics https://support.10xgenomics.com/single-cell-gene-pression/software/pipelines/latest/what-is-cell-ranger
Scanpy (v1.8.2) Wolf et al.65 https://github.com/scverse/scanpy
velocyto (v.17.17) La Manno et al.66 http://velocyto.org/
SCDIFF (v2) Ding et al.38 https://github.com/phoenixding/scdiff2
CellChat (v1.5.0) Jin et al.44 https://github.com/sqjin/CellChat
HISAT2 (v2.2.0) Kim et al.67 http://daehwankimlab.github.io/hisat2/
SCcaller (v2.0.0) Dong et al.68 https://github.com/biosinodx/SCcaller
bwa (v0.7.17) Li et al.69 https://github.com/lh3/bwa
GATK (v4.1.6) McKenna et al.70 https://gatk.broadinstitute.org/hc/en-us
ToppGene Suite Chen et al.30 https://toppgene.cchmc.org/
GraphPad Prism 9 Graphpad Software https://www.graphpad.com/