Supplementary Data for: Scalp Tape-Strip RNA Sequencing Captures Disease and Treatment-Responsive Signatures in Alopecia Areata

This dataset accompanies the manuscript “Scalp Tape-Strip RNA Sequencing Captures Disease and Treatment-Responsive Signatures in Alopecia Areata”.
It provides the processed transcriptomic data and analysis scripts used to characterize the molecular landscape of alopecia areata (AA) through a minimally invasive tape-strip approach.

A total of 61 RNA-seq profiles were analyzed, including scalp tape-strip and bulk biopsy samples from healthy controls and patients with AA across the clinical spectrum, before and after treatment with oral baricitinib.
Gene expression was profiled using the Ion AmpliSeq™ Transcriptome Human Gene Expression Panel v2.0, aligned to the human reference genome (hg19_AmpliSeq_Transcriptome_v1.1.04042016.Designed.bed), normalized with voom, and batch-corrected with ComBat (sva package).

The dataset includes:
1) counts_batch_corrected_ComBat_bySymbol.csv — log₂-normalized, batch-corrected expression matrix (genes × samples).
2) metadata_final.csv — clinical and experimental metadata (group, severity, treatment, sample type).
3) custom_gene_sets_AA_tapestrips.gmt — curated gene sets representing key immune (IFN/JAK–STAT, Th1/Th2/Th17/Th22, cytotoxic/NK) and epithelial (follicular, keratinization, fibrosis, proteostasis) pathways.¡
4) /scripts folder — R scripts for GSVA, DEG analysis, and figure generation.

The tape-strip RNA-seq method captured the primary immune and epithelial signatures observed in lesional biopsies—highlighting strong activation of the interferon/JAK–STAT and cytotoxic T/NK pathways, suppression of follicular and keratinization programs, and molecular normalization in post-baricitinib responders.
These data support the translational use of tape-strip transcriptomics as a noninvasive biomarker and disease-monitoring tool in alopecia areata.

All files are ready to reproduce the analyses and figures described in the publication using standard R (v4.3.2) workflows.