Bulk TChIC of human nucleus pulposus cells

ABSTRACT: Cryopreserved P1 cells were used directly for the TCHiC as detailed in the corresponding manuscript. Final DNA libraries were sequenced using paired-end 100 bp reads on a NextSeq2000. For transcript and ChIC analysis, Fastq files were processed into count tables using the T-ChIC Snakemake (see https://github.com/marloes3105/tchic/tree/main/workflows/1.snakemake-workflow/, v1.0). Following demultiplexing, for the transcript, reads were mapped to the human (hg38) genome using STAR (version 2.5.3a). For ChIC, reads were mapped paired-end to the human (hg38) genome using bwa mem (version 0.7.16a) with parameters -M -I 1000. Gene specific H3K27me3 enrichment was quantified using the bamCountRegions.py script, which generated a count table based on reads within 10 kb window around the transcription start sites (TSS) of annotated genes. Gene-level RNA counts and TSS-level H3K27me3 counts were aggregated per sample and normalised using median ratio normalisation for downstream visualisation.

ORGANISM(S): Homo sapiens

PROVIDER: GSE300462 | GEO | 2026/09/07

REPOSITORIES: GEO