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/ |