{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE300nnn/GSE300462/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Other"],"species":["Homo sapiens"],"gds_type":["Other"],"full_dataset_link":["https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE300462"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"Bulk TChIC of human nucleus pulposus cells","description":"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.","dates":{"publication":"2026/09/07"},"accession":"GSE300462","cross_references":{"GSM":["GSM9060897","GSM9060898","GSM9060899","GSM9060900","GSM9060901"],"GPL":["11154"],"GSE":["300462"],"taxon":["Homo sapiens"],"PMID":["[42706237]"]}}