The details of RNA extraction, RNA-sequencing, quality control, and transcriptome profiling are described in the Supplemental Methods . Briefly, after total RNA extraction, DNase treatment, and ribosomal RNA reduction, we performed RNA-sequencing with NovaSeq6000 (Illumina, San Diego, CA, USA) using an S4 100PE Flowcell (Illumina, San Diego, CA, USA). All RNA-sequencing samples had high sequence coverage after quality control. The transcript abundances were estimated with Salmon using the human genome hg38 and the mapping-based mode [28 (link)].
Protocol detail
Comprehensive RNA-seq Transcriptome Profiling
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Corresponding Organization :
Other organizations : Massachusetts General Hospital, Pulmonary Associates, University of Pittsburgh, National Research Institute, George Washington University
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Variable analysis
independent variables
- RNA extraction
- RNA-sequencing
- Transcriptome profiling
- Transcript abundances
- DNase treatment
- Ribosomal RNA reduction
- Quality control of RNA-sequencing samples
- Positive control: None specified
- Negative control: None specified
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