{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Simin Wan"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15837"],"description":["To investigate the mechanism by which 25-HC restricts cytotoxic T cell differentiation, we performed RNA-seq on 25-HC-treated CD8+ T cells.Total RNA was extracted from activated CD8+ T cells, treated with 250 nM 25-HC or DMSO, using TRIzol reagent."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Growth Protocol - Naïve CD8+ T cells were purified from the spleens of C57BL/6 mice by negative selection. The cells were maintained in complete RPMI-1640 medium, supplemented with 10% FBS, 2 mM L-glutamine, 1% penicillin-streptomycin, 10 mM HEPES, and 50 μM 2-mercaptoethanol.","Sequencing - Barcoded sequencing libraries were sequenced on an Illumina NovaSeq 6000 System (Genergy Biotechnology) to generate 150 bp paired-end reads.","Sample Collection - The cells were harvested, stained at 4°C for 30 minutes for surface markers, and subsequently  sorted on a BD FACSAria IIu.","Nucleic Acid Extraction - Total RNA was extracted from the tissue sample using Trizol according to the user manual. 5’ RACE was performed for reverse transcription. The reverse transcription products were amplified by PCR with corresponding specific primers. PCR products were purified by DNA magnetic beads. PCR purified product is terminal repair (including 5 'terminal phosphorylation and 3' terminal plus' A ') by the End Prep Enzyme Mix, with sequencing adapters at both ends. Then DNA Clean Beads were purified and amplified with P5 and P7 primers. The PCR products were cleaned up using beads, validated using an Qsep100 (Bioptic, Taiwan, China), and quantified by Qubit3.0 Fluorometer  (Invitrogen, Carlsbad, CA, USA).","Library Construction - Barcoded sequencing libraries were constructed using the TruSeq Stranded mRNA Kit (Illumina)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - To activate the cells and assess the effect of 25-HC, they were seeded onto anti-CD3/CD28-coated plates and treated with either 250 nM 25-HC or an equivalent concentration of DMSO (vehicle control) for 72 hours.","Sequence Alignment - Raw sequencing data were trimmed with Skewer (v0.2.2) and quality was assessed using FastQC (v0.11.5). Clean reads were then aligned to the mm10 mouse genome using STAR (v2.7.9a) and quantified with featureCounts (v2.0.1). Differentially expressed genes were identified using DESeq2 (v1.30.1) in R software (v4.0.3), based on a log fold change (logFC) cutoff of >1 or <-1 and an adjusted P value < 0.05."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of total RNA"],"species":["Mus musculus"],"pubmed_authors":["Jianhua Li","Simin Wan"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of mouse CD8+ T cells treated with 25-HC versus DMSO control","description":"To investigate the mechanism by which 25-HC restricts cytotoxic T cell differentiation, we performed RNA-seq on 25-HC-treated CD8+ T cells.Total RNA was extracted from activated CD8+ T cells, treated with 250 nM 25-HC or DMSO, using TRIzol reagent.","dates":{"release":"2026-05-01T00:00:00Z","modification":"2026-05-01T01:03:23.83Z","creation":"2025-10-23T16:19:09.279Z"},"accession":"E-MTAB-15837","cross_references":{"ENA":["ERP182839"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"]}}