Growth Protocol:	Human MDMs were differentiated from total blood from SSc patients and healthy donors using gradient separation (Histopaque 1077, Sigma) and adhesion purification. Following Histopaque separation, peripheral blood mononuclear cells (PBMCs) were re-suspended in RPMI (Life Technologies) and monocytes were purified by adherence for 1 h at 37 °C, 5% CO2. The monolayer was washed 3 times with HBSS to remove non-adherent cells and monocytes were matured for 5 days in RPMI containing 100 ng ml-1 M-CSF (PeproTech, UK) and 10% Fetal Calf Serum (FCS, Labtech International). Macrophage purity was confirmed by immunohistochemical assessment of CD68 and >99% cells were CD68+.
Treatment Protocol:	-
Extract Protocol:	Total RNA was extracted from hMDMs using Trizol (Invitrogen) and RNeasy mini kit (Qiagen) according to manufacturer's instructions, with an additional purification step by on-column DNase treatment using the RNase-free DNase Kit (Qiagen) to ensure elimination of any genomic DNA. The integrity and quantity of total RNA were determined using a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific) and Agilent 2100 Bioanalyzer (Agilent Technologies).
Library Construction Protocol:	In total, 500 ng of total RNA was used to generate RNA-seq libraries using TruSeq RNA sample preparation kit (Illumina) according to the manufacturer's instructions. Briefly, RNA was purified and fragmented using poly-T oligo-attached magnetic beads using two rounds of purification followed by the first and second cDNA strand synthesis. Next, cDNA 3' ends were adenylated and adapters ligated followed by 15 cycles of library amplification. Finally, the libraries were size selected using AMPure XP Beads (Beckman Coulter) purified and their quality was checked using Agilent 2100 Bioanalyzer. Samples were randomized to avoid batch effects and multiplexed libraries were run on a single lane (6 samples/lane) of the HiSeq 2500 platform (Illumina) to generate 100bp paired-end reads. An average of 64M reads coverage per samples was achieved.

Molecule Type:	poly(A)+ RNA
Library Source:
Library Layout:	PAIRED
Library Strand:	Forward
Platform:	ILLUMINA
Instrument Model:	Illumina HiSeq 2500
Strand-Specific:	Specific

Data Resource	GEN Sample ID	GEN Dataset ID	Project ID	BioProject ID	Sample ID	Sample Name	BioSample ID	Sample Accession	Experiment Accession	Release Date	Submission Date	Update Date	Species	Race	Ethnicity	Age	Age Unit	Gender	Source Name	Tissue	Cell Type	Cell Subtype	Cell Line	Disease	Disease State	Development Stage	Mutation	Phenotype	Case Detail	Control Detail	Growth Protocol	Treatment Protocol	Extract Protocol	Library Construction Protocol	Molecule Type	Library Layout	Strand-Specific	Library Strand	Spike-In	Strategy	Platform	Instrument Model	Cell Number	Reads Number	Gbases	AvgSpotLen1	AvgSpotLen2	Uniq Mapping Rate	Multiple Mapping Rate	Coverage Rate