| Antibodies |
| Anti-Collagen 1 (mouse) |
Sigma |
Cat# C2456, RRID:AB_476836 |
| Anti-Perilipin-1 (rabbit) |
Cell Signaling Technologies |
Cat# 9349, RRID:AB_10829911
|
| Anti-CD34 (rabbit) |
Abcam |
Cat# ab81289, RRID:AB_1640331
|
| Anti-PDGFRa (goat) |
R&D Systems |
Cat# AF-307-NA, RRID:AB_354459
|
| Anti-PDGFRa (recombinant, rabbit) |
Abcam |
Cat# ab134123 RRID: N/A
|
| TE-7 (mouse) |
Merck Millipore |
Cat# CBL271, RRID:AB_93449
|
| Anti-Pax7 (mouse) |
Developmental Studies Hybridoma Bank |
Cat# pax7, RRID:AB_528428
|
| Anti-Desmin (rabbit) |
Cell Signalling Technologies |
Cat# 5332, RRID:AB_1903947
|
| Anti-Myosin Heavy Chain (mouse) |
Developmental Studies Hybridoma Bank |
Cat# MF 20, RRID:AB_2147781
|
| Anti-alpha-smooth muscle actin (mouse) |
Sigma |
Cat# A5228, RRID:AB_262054
|
| Anti-pPDGFRa (Y754) (rabbit) |
Abcam |
Cat# AB5460, RRID:AB_ 304906
|
| Anti-Collagen 1 (rabbit) |
Meridian Life Science Inc |
Cat# T40777R, RRID:AB_151099
|
| Anti-Collagen 3 (rabbit) |
Genway Biotec Inc |
Cat# GWB-7D650E, RRID:AB_10517236
|
| Anti-human-CD45-FITC |
Miltenyi Biotec |
Cat# 130-114-567, RRID:AB_2726699
|
| Anti-human-CD31-FITC |
Miltenyi Biotec |
Cat# 130-110-668, RRID:AB_2657279
|
| Anti-human-CD90-PE |
Thermo Fisher Scientific |
Cat# 12-0909-42, RRID:AB_10670624
|
| Anti-human-CD56-BV421 |
BD Bioscience |
Cat# 562751, RRID:AB_2732054
|
| Anti-human-CD82-PE-vio770 |
Miltenyi Biotec |
Cat# 130-101-302, RRID:AB_2659303
|
| Anti-mouse-CD34-APC |
BD Bioscience |
Cat# 555824, RRID:AB_398614
|
| Goat-anti-mouse IgG (H+L) Alexafluor 647 |
Thermo Fisher Scientific |
Cat# A-21235, RRID:AB_2535804
|
| Goat-anti-rabbit IgG (H+L) Alexafluor 568 |
Thermo Fisher Scientific |
Cat# A-11011, RRID:AB_143157
|
| Goat-anti-mouse IgG (H+L) Alexafluor 488 |
Thermo Fisher Scientific |
Cat# A-11001, RRID:AB_2534069
|
| Donkey-anti-goat IgG (H+L) Alexafluor 568 |
Thermo Fisher Scientific |
Cat# A-11057, RRID:AB_2534104
|
| Goat-anti-rabbit IgG (H+L) HRP |
Thermo Fisher Scientific |
Cat# 31460, RRID:AB_228341
|
| Goat-anti-mouse IgG (H+L) HRP |
Thermo Fisher Scientific |
Cat# G-21040, RRID:AB_2536527
|
| Patient characteristics presented in supplementary table 1 (study 2) |
This paper |
N/A |
| Patient characteristics from study 1 |
Kampmann, U. et al. 2011a
|
N/A |
| Patient characteristics from study 3 |
Gormsen, L.C. et al. 2018
|
N/A |
|
|
|
|
|
|
| Chemicals, peptides, and recombinant proteins |
| Propidium Iodide |
BD Bioscience |
Cat# 556463 |
| Hams F10 media incl. glutamine and bicarbonate |
Sigma |
Cat# N6908 |
| Horse serum |
Thermo Fisher Scientific |
Cat#26050088 |
| 100X Penstrep |
Thermo Fisher Scientific |
Cat#15140122 |
| Collagenase II |
Worthington |
Cat#46D16552 |
| Dispase II |
Roche Diagnostics |
Cat#04 942 078 001 |
| StemMACS cryopreservation buffer |
Miltenyi Biotec |
Cat#130-109-558 |
| Human FcR blocking solution |
Miltenyi Biotec |
Cat#130-059-901 |
| Compensation beads |
Thermo Fisher Scientific |
Cat#01-2222-41 |
| Collagen |
Sigma |
Cat#C8919 |
| Laminin |
Thermo Fisher Scientific |
Cat#23017-015 |
| Fetal Bovine serum |
Thermo Fisher Scientific |
Cat#16000044 |
| Recombinant human bFGF |
Sigma |
Cat# F0291 |
| DMEM (4.5 g/L glucose) incl glutamine and bicarbonate |
Thermo Fisher Scientific |
Cat#11965092 |
| Adipogenic differentiation media |
Miltenyi Biotec |
Cat#130-091-677 |
| Extra-cellular matrix coating gel |
Sigma |
Cat# E1270 |
| Poly-D-Lysine |
Merck Millipore |
Cat#A-003-E |
| Bio-AMF 2 growth media |
Biological Industries |
Cat#01-194-1A |
| Recombinant human Insulin |
Sigma |
Cat#91077C |
| Dexamethasone |
Sigma |
Cat# D4902 |
| 3-isobutyl-1-methylxanthine (IBMX) |
Sigma |
Cat# I7018 |
| Rosaglitazone |
Sigma |
Cat# R2408 |
| Recombinant human TGFb |
Sigma |
Cat# T7039 |
| Recombinant human PDGF-AA |
Miltenyi Biotec |
Cat#130-108-983 |
| Metformin |
Sigma |
Cat#D150959 |
| Imatinib |
Sigma |
Cat#SML1027 |
| Osteogenic differentiation media |
Miltenyi Biotec |
Cat#130-091-678 |
| Histofix |
Histolabs |
Cat#01000 |
| Normal Goat serum |
Thermo Fisher Scientific |
Cat31873 |
| Wheat-germ-agglutinin |
Thermo Fisher Scientific |
Cat# W1126 |
| Alzirian red staining solution |
Sigma |
Cat# A5533 |
| Phenol red and bicarbonate free DMEM Seahorse Media |
Agilent |
Cat#103575-100 |
| Glucose |
Sigma |
Cat#G8769 |
| Sodium-pyruvate |
Thermo Fisher Scientific |
Cat#11360-039 |
| L-glutamine |
Sigma |
Cat# G7513 |
| Hoechst 33342 |
Thermo Fisher Scientific |
Cat# H3570 |
| 2-Deoxy-glucose |
Sigma |
Cat# D8375
|
| Oligomycin |
Sigma |
Cat#75351 |
| Carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone (FCCP) |
Sigma |
Cat#C2920 |
| Antimycin |
Sigma |
Cat#A8674 |
| Rotenone |
Sigma |
Cat#R8875 |
|
|
|
|
|
|
| Critical commercial assays |
| Click-iT™ EdU cell proliferation kit for imaging |
Thermo Fisher Scientific |
Cat#C10337
|
| Click-iT™ EdU cell proliferation kit for imaging |
Thermo Fisher Scientific |
Cat#C10340
|
| PrimeFlow™ RNA assay kit |
Thermo Fisher Scientific |
Cat#88-18005-210 |
| QiaSymphony RNA Mini kit |
Qiagen |
Cat#931636 |
| Seahorse Mito-stress test kit |
Agilent |
Cat#103015-100 |
| Takara SMARTer Stranded Total RNA-Seq Kit v2 pico kit |
Takara Bio |
Cat#634411 |
| TruSeq. Stranded mRNA Sample preparation kit |
Illumina Inc |
Cat#20020594 |
| Chromium Single Cell 3’ Reagent Kits (v3 Chemistry) |
10X Genomics |
Cat#1000075 |
|
|
|
|
|
|
| Deposited data |
| Population-based RNA-sequencing data |
This paper www.ega-archive.org
|
EGAS00001005599 |
| Single cell RNA-sequencing data |
This paper www.ega-archive.org
|
EGAS00001005599 |
| Whole muscle RNA-sequencing data |
This paper www.ega-archive.org
|
EGAS00001005599 |
|
|
|
|
|
|
| Oligonucleotides |
| B2M: Sense AATGTCGGATGGATGAAACC, Antisense TCTCTCTTTCTGGCCTGGAG |
HotStar Taq, Qiagen |
N/A |
| TGFB1: Sense GGACACCAACTATTGCTTCAGCTC, Antisense AAGTTGGCATGGTAGCCCTTGG |
HotStar Taq, Qiagen |
N/A |
| COL1A1: Sense TGCGATGACGTGATCTGTGACG, Antisense TTTCTTGGTCGGTGGGTGACTCTG |
HotStar Taq, Qiagen |
N/A |
| COL3A1: Sense ATTGCTGGGATCACTGGAGCAC, Antisense CCTGGTTTCCCACTTTCACCCTTG |
HotStar Taq, Qiagen |
N/A |
| COL6A1: Sense ATCAGCCAGACCATCGACACCATC, Antisense TTCGAAGGAGCAGCACACTTGC |
HotStar Taq, Qiagen |
N/A |
| COL1A1 (PrimeFlow type 4 probe) |
Thermo Fisher Scientific |
NM_000088.3 |
| RPL13A (PrimeFlow type 1 probe) |
Thermo Fisher Scientific |
NM_001270491.1 |
|
|
|
|
|
|
| Software and algorithms |
| ImageJ (for fluoresent image analysis) |
NIH |
https://imagej.nih.gov/ij/
|
| FlowJo (10.6.1) for FACS and flow cytometry analysis |
BD Bioscience |
https://www.flowjo.com/
|
| Prism 8 (version 9.0) for data presentation and statistics |
GraphPad Software |
https://www.graphpad.com/scientific-software/prism/
|
| Limiting dilution Analysis |
Walter and Eliza Hall Institute of Medical Research |
http://bioinf.wehi.edu.au/software/limdil/
|
| Trimgalore (v 0.4.1) for adapter and quality trimming of RNA sequencing reads |
Babraham Bioinformatics, Babraham Institute |
https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
|
| Hisat2 (v 2.1.0) for alignment of RNA sequencing reads to the reference genome |
Kim D et al., 2015
|
http://daehwankimlab.github.io/hisat2/
|
| Samtools (v 1.9) for sorting the alignment files |
Li H et al., 2009
|
http://www.htslib.org/
|
| htseq-count (v 0.6.1) for feature number estimation (gene counts) |
Anders S et al., 2014
|
https://htseq.readthedocs.io/en/master/count.html
|
| R (v 4.0.3) for bioinformatics and statistical analysis |
The R project for statistical computing |
https://www.r-project.org/
|
| R package DESeq2 (v 1.26.0) for differential expression analysis of RNAseq data |
Love MI., 2014
|
https://bioconductor.org/packages/release/bioc/html/DESeq2.html
|
| R package Seurat (v 4.0.1) for scRNAseq analysis |
Hao et al., 2020 |
https://satijalab.org/seurat/index.html
|
| R package Doubletfinder (v 2.0.3) for doublet removal in the scRNAseq dataset |
McGinnis CS et al., 2019
|
https://github.com/chris-mcginnis-ucsf/DoubletFinder
|
| R package XGR (v 1.1.7) for gene set and pathway enrichment analysis of differentially expressed genes |
Fang et al., 2016
|
http://galahad.well.ox.ac.uk:3030/
|
| R package Slingshot (v. 1.8.0) for pseudotime inference analysis |
Street et al., 2018
|
https://bustools.github.io/BUS_notebooks_R/slingshot.html
|
|
|
|
|
