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. Author manuscript; available in PMC: 2024 Oct 5.
Published in final edited form as: Cell Stem Cell. 2023 Sep 14;30(10):1368–1381.e6. doi: 10.1016/j.stem.2023.08.010

Key resources table.

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
PE anti-CD45 BioLegend Cat#103105
APC anti-CD31 Invitrogen Cat#17-0311-80
eFluor 450-conjugated Lineage (Lin) antibodies anti-CD45 ThermoFisher Scientific Cat#48-0451-82
anti-Ter-119 ThermoFisher Scientific Cat#48-5921-82
anti-CD31 BioLegend Cat#303114
anti-Tie-2 ThermoFisher Scientific Cat#13-5987-82
anti-CD326 ThermoFisher Scientific Cat#48-5791-82
anti-CD324 ThermoFisher Scientific Cat#13-3249-82
anti-CFH primary antibody LS bio Cat#LS-C819285
Alexa Fluor 488 anti-rabbit secondary antibody Invitrogen Cat#A-11008
CXCR2 antagonist AZ 10397767 Tocris Cat#5872
Critical commercial assays
SMART-Seq v4 Ultra Low Input Kit Takara Bio Cat#634894
KAPA Hyper Prep Next Generation Sequencing Roche N/A
miRNeasy Micro Kit QIAGEN Cat#217084
Fibroblast culture media (DMEM + Glutamax media) ThermoFisher Cat#10569010
Deposited data
Raw RNAseq data This paper NCBI Sequence Read Archive; BioProject PRJNA839777
Raw scRNAseq data This paper NCBI Sequence Read Archive; BioProject PRJNA839777
Allele-specific count data (MRLxCAST) This paper; Figshare doi: https://doi.org/10.6084/m9.figshare.19952513.v1
CAST/EiJ SNP calls Wellcome Trust Mouse Genome Project https://www.sanger.ac.uk/science/data/mouse-genomes-project
Ear closure QTL mapping data Cheverud et al.6 N/A
Mouse genome (GRCm38) Ensembl http://ensembl.org/
Experimental models: Organisms/strains
Mouse: CAST/EiJ The Jackson Laboratory Strain #:000928
Mouse: MRL/MpJ The Jackson Laboratory Strain #:000486
Mouse: C57BL/6J The Jackson Laboratory Strain #:000664
Software and algorithms
Bowtie2 Langmead and Salzberg58 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
DESeq2 Love et al.64 https://bioconductor.org/packages/release/bioc/html/DESeq2.html
DESeq2 analysis code This paper; Figshare doi: https://doi.org/10.6084/m9.figshare.c.6025157
Cutadapt Martin 201162 https://cutadapt.readthedocs.io/
Genome Analysis Toolkit (GATK) McKenna et al.60 https://gatk.broadinstitute.org/
BEDTools Quinlan and Hall66 https://bedtools.readthedocs.io/
Seurat Satija et al.69 https://satijalab.org/seurat/
scProportionTest Miller et al.72 https://github.com/rpolicastro/scProportionTest
CellChat Jin et al.73 http://www.cellchat.org/
Enrichr Chen et al.71 https://maayanlab.cloud/Enrichr/
PANTHER Mi et al.67 https://pantherdb.org
modPhea Weng and Liao68 https://evol.nhri.org.tw
Fiber quantification pipeline Mascharak et al.19 https://github.com/shamikmascharak/Mascharak-et-al-ENF
Other
Supplemental figures and tables This paper; Mendeley Data doi: 10.17632/9jhfh79b8d.1