biostudies-arrayexpressJamie BlumMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16143We identified alpha-zein as a novel antigen recognized by intestinal Tregs. This experiment was designed to compare Zein-reactive intestinal Tregs to either OVA-specific Tregs (OTII) or bulk population of Tregs from chow fed, amino acid diet fed, or germ-free mice.biostudies-arrayexpressSequencing - Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 Software. One mis-match was allowed for index sequence identification.Sample Collection - Samples were sorted into Trizol reagent, frozen at -80, and sent to Genewiz/Azenta Life Sciences for Ultra-low input RNA-seq.Library Construction - The SMARTSeq HT Ultra Low Input Kit was used for full-length cDNA synthesis and amplification (Clontech, Mountain View, CA), and Illumina Nextera XT library was used for sequencing library preparation.Nucleic Acid Extraction - Total RNA was extracted from cells following the Trizol Reagent User Guide (Thermo Fisher Scientific). Extracted RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Fastq files were quality checked using FastQC. Next, low-quality reads and adapter sequences were trimmed with Trimmomatic and FastQC was re-run to evaluate the quality. Reads were aligned to the mouse reference genome using STAR and resulting data were analyzed in DESeq2 (Version 1.42.0).MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNAMus musculusJamie BlumfalseBulk RNA-seq Comparison of Populations of Intestinal TregsWe identified alpha-zein as a novel antigen recognized by intestinal Tregs. This experiment was designed to compare Zein-reactive intestinal Tregs to either OVA-specific Tregs (OTII) or bulk population of Tregs from chow fed, amino acid diet fed, or germ-free mice.2025-12-10T00:00:00Z2026-05-27T17:34:21.31Z2025-11-16T12:53:58.802ZE-MTAB-16143ERP185122EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184