Respiratory muscle gene expression of lung cancer patients

Biopsies of diaphragm, latissimus dorsi, and/or intercostal muscle were obtained from individuals during resective surgery for lung cancer. Some individuals had received respiratory muscle training as an intervention before surgery (clinical trial NCT04067830). Many had a pulmonary function test (PFT) at two time-points before surgery. Not all types of PFT could be conducted for all subjects. RNA was extracted from pulverized biopsies with miRNeasy Micro kit (Qiagen, Germantown, MD) and used for RNA sequencing in two separate batches. Some RNA samples were sequenced multiple times and/or in different amounts. TapeStation Nano assay (Agilent®, Santa Clara, CA) was used to assess RNA concentration and quality. Quality of RNA was poor for one batch because of unintended thawing of samples that occurred during failure of the -80 ºC-freezer that they were in. Sequencing libraries were prepared from 0.1 µg of RNA (or maximum available amount) using KAPA mRNA HyperPrep with RiboErase kit (Roche, Indianapolis, IN) with 15 PCR cycles for multiplexed run on NovaSeq 6000 with S2 flow-cell (Illumina, San Diego, CA). Raw paired-read sequencing data after de-multiplexing (bcl2fastq output) and detailed sample/subject information are provided here. Nine samples' sequencing data have a high rRNA content (> 20%) and these samples should be excluded from analysis. Samples with 'dupl' and/or '25ng' in names/aliases can also be excluded as they represent replicates.