Lung Adipose Metaplasia Shapes a Fibrogenic and Inflammatory Microenvironment in Idiopathic Pulmonary Fibrosis - raw count tables

Raw count table with metadata for the corresponding figures. Figure 2: libraries were prepared using the QuantSeq 3′ mRNA-Seq Lib Prep FWD Kit (Lexogen). Single-end 3’ sequencing (1 × 100 bp) was performed on an Illumina NextSeq 2000 platform. Metadata legend: Group (patient #); Tissue (wat: IPF lung with adipose metaplasia; lung: IPF lung without adipose metaplasia; hilum: hilar tissue with adipose tissue) -------------------- Figures 4: libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) after polyA selection. Paired-end sequencing (2 × 75 bp) was performed on a NextSeq 500 platform (Illumina) Metadata legend: Cell_Id (primary lung fibroblast #); CM_Id (condition medium #, NA = no stimulation); Treatment (cont: unstimulated, TGF: TGF-b1 stimulation; asfCM: adipocyte stromal fraction condition medium (before differentiation); adipoCM: adipocyte condition medium (after differentiation). -------------------- Figures 6: libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) after polyA selection. Paired-end sequencing (2 × 75 bp) was performed on a NextSeq 500 platform (Illumina). Metadata legend: CM (condition medium #); Treatment (cont: unstimulated, stim: stimulated with CM). ************************* Data processing:Raw sequencing reads were first processed with Trimmomatic (v0.39) to remove Illumina adapter sequences and low-quality bases, using sliding window trimming (window size = 4, quality threshold = 20) and a minimum read length cutoff of 36 nucleotides. Quality of trimmed reads was assessed using FastQC (v0.11.9), and reports were aggregated with MultiQC (v1.13). Reads were mapped to the human genome (GRCh38 primary assembly, GENCODE v44 annotation) using STAR (v2.7.9a) with default parameters in both single and paired-end modes respectively for tissue and cell samples. Resulting BAM files were sorted and indexed with Samtools (v1.14). Gene-level counts were obtained using HTSeq (v0.13.5).