biostudies-arrayexpressSOURA CHAKRABORTYMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16381LLC-OVA lung carcinoma cells were used to establish subcutaneous tumors in C57BL/6J mice. One million LLC-OVA cells were injected subcutaneously into each mouse. Tumor-bearing mice were divided into two treatment groups: three mice received mifepristone (60 mg/kg body weight) administered via oral gavage on alternate days, and four mice received vehicle control (olive oil) on the same schedule. Treatments were continued for 18 days. On day 19, mice were sacrificed and tumors were harvested for immune profiling. Tumor-infiltrating NK cells were isolated and subjected to bulk RNA-sequencing to assess transcriptional changes induced by glucocorticoid receptor antagonism within the tumor microenvironment.biostudies-arrayexpressLibrary Construction - RNA-seq libraries were prepared by Novogene using their standard mRNA-seq library preparation pipeline.Sample Collection - Tumors were excised from LLC-OVA tumor–bearing C57BL/6J mice on day 19. Each tumor was mechanically minced and enzymatically digested using IMDM supplemented with 10% FBS, collagenase D (1 mg/mL), collagenase A (1 mg/mL), and DNase I (0.4 mg/mL). Digestion was performed at 37 °C for 30–40 minutes with gentle agitation. Collagenase activity was terminated by adding EDTA (5 mM) to the samples. The resulting suspension was filtered through 70 µm cell strainers to obtain a single-cell suspension. Tumor-infiltrating NK cells were isolated by flow cytometric sorting based on CD3⁻ CD19⁻ CD56⁺ immunophenotype and collected in RNase-free tubes for downstream processing.Nucleic Acid Extraction - Total RNA was extracted from sorted NK cells using the Qiagen RNA extraction kit according to the manufacturer’s instructions, including optional on-column DNase digestion. RNA concentration and purity were determined using a NanoDrop spectrophotometer, and RNA integrity was assessed using Bioanalyzer. Only high-quality RNA samples were used for library construction.Sequencing - Libraries were sequenced by Novogene on an Illumina NovaSeq platform using paired-end sequencing (typically 150 bp). Base calling, demultiplexing, adapter trimming, and primary quality filtering were performed using standard Illumina pipelines. Clean FASTQ files were delivered for downstream analysis.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesData Transformation - Raw RNA-seq FASTQ files were pre-processed and aligned to the mouse reference genome GRCm39 (Gencode M32 annotation) using HISAT2 (v2.2.1). The resulting SAM files were inspected, filtered, and converted to sorted BAM files using SAMtools (v1.13). Gene-level read counts were generated from the BAM files using HTSeq-count. Count matrices were imported into DESeq2 (v1.34.0) in R (v4.1.1) for normalization and differential expression analysis. DESeq2’s internal size-factor estimation was used for normalization. For each gene, log₂ fold changes were computed and statistical significance was assessed using the Wald test, including calculation of P values and Benjamini–Hochberg adjusted P values.UnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000Novogene in-house automated library preparation systemRNA-seq of coding RNAMus musculusSOURA CHAKRABORTYfalseTranscriptomic analysis of tumor-infiltrating NK cells from mifepristone-treated and vehicle-treated LLC-OVA tumor–bearing miceLLC-OVA lung carcinoma cells were used to establish subcutaneous tumors in C57BL/6J mice. One million LLC-OVA cells were injected subcutaneously into each mouse. Tumor-bearing mice were divided into two treatment groups: three mice received mifepristone (60 mg/kg body weight) administered via oral gavage on alternate days, and four mice received vehicle control (olive oil) on the same schedule. Treatments were continued for 18 days. On day 19, mice were sacrificed and tumors were harvested for immune profiling. Tumor-infiltrating NK cells were isolated and subjected to bulk RNA-sequencing to assess transcriptional changes induced by glucocorticoid receptor antagonism within the tumor microenvironment.2025-12-18T00:00:00Z2025-12-18T16:41:14.243Z2025-12-11T13:53:13.906ZE-MTAB-16381ERP186431EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184