{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Ying Shiang Lim"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15754"],"description":["Inflammasomes are multicomplex proteins which drive pro-inflammatory cytokine responses and pyroptosis in innate immunity. Of which, the NLRP3 inflammasome is the most extensively studied, especially in myeloid immune cells such as macrophages. Conversely, the regulation of NLRP3 in non-immune cell types such as keratinocytes remains elusive. To understand this under specific immune environments, immortalized N/TERT keratinocytes were stimulated overnight with or without 50ng/ml IFNγ (technical triplicates per group ,Untreated (UNT) vs stimulated (IFNy), 6 samples in total). Total RNA was extracted from the cells by TRIzol-based RNA extraction for quantification and quality check,  library construction and RNA-seq (paired-end sequencing) was performed according to standard protocols from Macrogen (South Korea) on the NovaSeq 6000 platform."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Total RNA extraction was performed using TRIzol reagent. Isopropyl alcohol is added to the the cells homogenized in TRIzol, followed by centrifugation.","Sample Treatment - Immortalized N/TERT keratinocytes are seeded on a 6-well plate and treated at 80% confluency with 50ng/ml of IFN-gamma (or untreated) overnight.","Sample Collection - TRIzol is added directly to the cells in a 6-well plate after overnight stimulation.","Sequencing - The sequencing libraries were multiplexed and loaded on the flowcell on the Illumina NovaSeq 6000 instrument according to manufacturer’s instructions. The samples were sequenced using a Pair-End (PE) configuration.","Library Construction - Library construction was conducted via standard protocol  with Macrogen (South Korea)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Sequencing reads were mapped to the reference genome (Homo sapiens, GRCh38) using HISAT2. Transcripts were assembled from the aligned reads using StringTie, and expression profiles were quantified as read counts and normalized values, represented as transcripts per kilobase million (TPM) for each sample, taking into account transcript length and coverage depth"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_title":["Clarifying the priming requirement and activator specificity for the NLRP3 inflammasome in human keratinocytes in vitro","IFNγ priming enables NLRP3 inflammasome activation in human keratinocytes in vitro"],"pubmed_authors":["Pritisha Rozario, Ying Shiang Lim, Shirley Suet Lee Ding, Muhammad Jasrie Firdaus, Stephen Wearne, Wong Han Siang Brandon, Rae Chua, Kim S Robinson, Julie Tung Sem Chu, Liu Meng, Shan Sophie Carrie CAI, Sern Ting Eugene TAN, Soon Keong Wee, Mart Matthias Lamers, Navin Kumar Verma, Xia Yun, Eric Peng Huat Yap, John E. A  Common, Franklin Zhong","Franklin Zhong","Ying Shiang Lim"],"additional_accession":[]},"is_claimable":false,"name":"Bulk RNA-seq of immortalized N/TERT keratinocytes stimulated with IFNγ","description":"Inflammasomes are multicomplex proteins which drive pro-inflammatory cytokine responses and pyroptosis in innate immunity. Of which, the NLRP3 inflammasome is the most extensively studied, especially in myeloid immune cells such as macrophages. Conversely, the regulation of NLRP3 in non-immune cell types such as keratinocytes remains elusive. To understand this under specific immune environments, immortalized N/TERT keratinocytes were stimulated overnight with or without 50ng/ml IFNγ (technical triplicates per group ,Untreated (UNT) vs stimulated (IFNy), 6 samples in total). Total RNA was extracted from the cells by TRIzol-based RNA extraction for quantification and quality check,  library construction and RNA-seq (paired-end sequencing) was performed according to standard protocols from Macrogen (South Korea) on the NovaSeq 6000 platform.","dates":{"release":"2025-10-30T00:00:00Z","modification":"2026-05-27T17:00:25.054Z","creation":"2025-10-16T11:25:47.698Z"},"accession":"E-MTAB-15754","cross_references":{"ENA":["ERP182296"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"],"doi":["10.1101/2025.08.13.669639"]}}