| Antibodies |
|
|
|
| ckit antibody |
Biolegend |
Cat # 105839, RRID:AB_2629798 |
| Sca1 antibody |
Biolegend |
Cat # 108120, RRID:AB_493273 |
| CD16/CD32 antibody |
Biolegend |
Cat # 101320, RRID:AB_1574975 |
| CD34 antibody |
BD Biosciences |
Cat # 551387, RRID:AB_394176 |
|
| Chemicals, peptides, and recombinant proteins |
|
|
|
| LPS |
Invivogen |
Cat # tlrl-pb5lps |
|
| Critical commercial assays |
|
|
|
| Vybrant Phagocytosis Assay kit |
Molecular Probes |
Cat # V6694 |
| MACS monocyte isolation kit |
Miltenyi |
Cat # 130-100-629 |
| Human Inflammatory Cytokine Cytometric Bead Array (CBA) |
BD Biosciences |
Cat # 551811 |
| XF MitoStress kit |
Seahorse Biosciences |
Cat # 101706-100 |
| PAXgene plastic 2.5 mL 16x100mm |
QIAGEN |
Cat # 762165 |
| QIAsymphony PAXgene Blood RNA Kit |
QIAGEN |
Cat # 762635 |
| Corticosterone ELISA kit |
Abcam |
Cat # ab108821 |
| TruSeq RNA Library Prep Kit v2 |
Illumina |
RS-122-2001 |
| Tagment DNA Enzyme and Buffer kit |
Illumina |
20034197 |
| Mouse IL-1β Enhanced Sensitivity Flex Set |
BD Biosciences |
Cat # 562278 |
| Mouse IL-6 Enhanced Sensitivity Flex Set |
BD Biosciences |
Cat # 562236 |
| Mouse MCP-1 Flex Set |
BD Biosciences |
Cat # 558342 |
|
| Deposited data |
|
|
|
| Raw and analyzed data |
This paper |
GEO: GSE167536
|
|
| Experimental models: Organisms/strains |
|
|
|
| C57BL/6 mice |
JAX labs |
Stock #00064 |
|
| Oligonucleotides |
|
|
|
| Primers, murine csf; for CCTTCTTCGACATGGCTGGG |
This paper |
ThermoFisher |
| Primers, murine csf; rev GTTCTGACACCTCCTTGGCA |
This paper |
ThermoFisher |
| Primers, murine kitlg; for GCGGGAATCCTGTGACTGA |
This paper |
ThermoFisher |
| Primers, murine kitlg; rev CATCCCGGCGACATAGTTGA |
This paper |
ThermoFisher |
| Primers, murine cxcl12; for GCCAACGTCAAGCATCTGAA |
This paper |
ThermoFisher |
| Primers, murine cxcl12; re TTGTTGTTCTTCAGCCGTGC |
This paper |
ThermoFisher |
|
| Software and algorithms |
|
|
|
| Basepair |
Basepair |
https://www.basepairtech.com
|
| GENEWIZ, LLC |
South Painfield, NJ, USA |
https://www.genewiz.com
|
| FastQC (v.0.11.7) |
Andrews, 2010
|
https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
|
| fastx_trimmer (v.0.0.13) |
FASTX-Toolkit |
http://hannonlab.cshl.edu/fastx_toolkit/
|
| Trimmomatic |
Bolger et al., 2014
|
http://www.usadellab.org/cms/?page=trimmomatic
|
| STAR (v.2.6.1d) |
Dobin et al., 2013
|
https://github.com/alexdobin/STAR
|
| featureCounts (v.1.6.3) |
Subread |
http://subread.sourceforge.net/
|
| DESeq2 (v.1.24.0) |
Love et al., 2014
|
https://bioconductor.org/packages/release/bioc/html/DESeq2.html
|
| pheatmap (v.1.0.12) |
Cran |
https://cran.r-project.org/web/packages/pheatmap/index.html
|
| biomaRt (v.2.40.5) |
Durinck et al., 2005, 2009
|
https://bioconductor.org/packages/release/bioc/html/biomaRt.html
|
| ggplot2 (v.3.3.3) |
Wickham, 2016
|
https://cran.r-project.org/web/packages/ggplot2/index.html
|
| Ingenuity Pathway Analysis (IPA) |
QIAGEN Redwood City, CA |
https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-ipa/
|
| ClusterProfiler |
Wu et al., 2021; Yu et al., 2012
|
https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html
|
| REVIGO |
Supek et al., 2011
|
http://revigo.irb.hr/
|
| bcl2fastq Conversion software (v.2.20) |
Illumina |
https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html
|
| Bowtie2 (v.2.3.4.1) |
Langmead and Salzberg, 2012
|
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
|
| Sambamba (v.0.6.7) |
Tarasov et al., 2015
|
https://lomereiter.github.io/sambamba/
|
| MACS (in Python v.2.7.3) |
Zhang et al., 2008
|
https://github.com/macs3-project/MACS
|
| NucleoATAC |
Schep et al., 2015
|
https://github.com/GreenleafLab/NucleoATAC
|
| deepTools (v.2.3.3) |
Ramírez et al., 2016
|
https://github.com/deeptools/deepTools
|
| DiffBind (v.3.3.0) |
Stark and Brown 2011; Ross-Innes et al., 2012
|
https://bioconductor.org/packages/release/bioc/html/DiffBind.html
|
| Genomic Regions Enrichment of Annotations Tool (GREAT) |
McLean et al., 2010
|
http://great.stanford.edu/public/html/
|
| Integrative Genomics Viewer (IGV) (v.2.5.2) |
Robinson et al., 2011; Thorvaldsdottir et al., 2013
|
https://software.broadinstitute.org/software/igv/
|
| GraphPad Prism8 (GraphPad Sofware) |
GraphPad |
https://www.graphpad.com/scientific-software/prism/
|
| Python (v.2.7.3) |
Python Software Foundation |
https://www.python.org
|
| R (v.4.0.2) |
The R Project for Statistical Computing |
https://www.r-project.org/
|
| RStudio (v.1.3.1093) |
RStudio |
https://www.rstudio.com/
|
