biostudies-arrayexpressYang Chin-AnHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15463RNA-seq was performed to identify differences in the transcriptome between wildtype, ZNF334 +/- and ZNF334 -/- THP-1 cells with or without cold stimulation.biostudies-arrayexpressSequencing - Total RNA was subjected to high-throughput sequencing using the illumine NestSeq 2000. Raw reads were processed using CLC Genomics Workbench v25.0.1. Quality control involved trimming the first 12 bases, adapter sequences (TruSeq read1), and bases with quality scores below Q20. Filtered reads were aligned to the human reference genome (GRCh38.p14) with gene annotations from Ensembl GRCh38.113. rRNA reads were identified and filtered using the SILVA rRNA database (v138.1).Nucleic Acid Extraction - Total RNA was isolated from cultured cells using the Qiagen Total RNA Kit according to manufacturer’s instructions.Sample Collection - THP-1 cell lines (ZNF334-wild-type, ZNF334+/−, and ZNF334−/−) were seeded onto 24-well imaging plates (Greiner). For cold stimulation assays, cells were exposed to 32°C for 8 hours in the incubator.Library Construction - Library were constructed by the Qubit fluorometer with Qubit RNA BR/HS Assay Kit and sample integrity was analyzed by assay method: Agilent 4150 TapeStation system with RNA/High Sensitivity RNA ScreenTape.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Gene expression was quantified and Output files generated gene- and transcript-level expression matrices (.txt), BAM files for alignment visualization, and comprehensive QC and analysis reports (.pdf). Processed RNA sequencing count data were imported into RStudio (v2024.12.1+563) running R (v4.5.0) and processed using packages from the CRAN and Bioconductor repositories. Gene-level expression counts were read from Excel spreadsheets using the readxl package (v1.4.5), and gene symbols were assigned as row names. To reduce background noise, genes with low expression (fewer than 10 counts across all samples) were removed, except for ZNF334, which was retained due to prior biological relevance. To focus on protein-coding transcripts, gene symbols were mapped to Entrez Gene IDs and filtered using gene type annotations from the org.Hs.eg.db database (v3.21.0); only genes annotated as “protein-coding” were retained, with ambiguous or missing annotations excluded, while ZNF334 was again exempted from filtering. Filtered counts were normalized using the median-of-ratios method implemented in the DESeq2 package (v1.48.1), with sample-specific size factors estimated from the distribution of counts.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNextSeq 2000RNA-seq of coding RNAHomo sapiensYang Chin-AnfalseRNA-seq data of wildtype and ZNF334-edited THP-1 cell lines with or without cold stimulationRNA-seq was performed to identify differences in the transcriptome between wildtype, ZNF334 +/- and ZNF334 -/- THP-1 cells with or without cold stimulation.2025-12-01T00:00:00Z2025-12-01T02:01:50.594Z2025-08-08T13:44:00.334ZE-MTAB-15463ERP178563EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184