Transcriptomic profiling of aganglionic and ganglionic colon segments from Hirschsprung disease patients

This dataset contains bulk RNA sequencing data from paired aganglionic and ganglionic colonic tissue specimens obtained from three pediatric patients diagnosed with Hirschsprung disease (HSCR, OMIM 142623). RNA was extracted and sequenced to investigate transcriptomic alterations and signaling pathway dysregulation associated with HSCR pathogenesis. Raw paired-end FASTQ files generated by Illumina NovaSeq 6000 sequencing are provided for each sample, enabling downstream analyses of differential gene expression between diseased and unaffected intestinal segments. Overall design: Colonic tissue samples were collected from three pediatric HSCR patients during surgical resection. For each patient, paired specimens were obtained from the aganglionic segment (designated as “X”) and the ganglionic segment (designated as “K”). The paired samples from patients 1, 2, and 3 are labeled as HSCR-1 (X-1, K-1), HSCR-2 (X-2, K-2), and HSCR-3 (X-3, K-3). Total RNA was extracted using the Trizol reagent kit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol. RNA quality was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and verified using RNase-free agarose gel electrophoresis. Eukaryotic mRNA was enriched using Oligo(dT) beads, fragmented, and reverse transcribed into cDNA using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #7530, New England Biolabs, Ipswich, MA, USA). Purified double-stranded cDNA was end-repaired, A-tailed, ligated to Illumina sequencing adapters, purified with AMPure XP Beads (1.0X), and PCR-amplified. The resulting cDNA libraries from colon tissue were sequenced using the Illumina NovaSeq 6000 platform (paired-end, 150 bp) by Beijing igeneCode Biotech Co., Ltd. (Beijing, China). Raw data are provided for all six tissue samples to facilitate downstream transcriptomic analysis.