biostudies-arrayexpressLuiz RoeschMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16067This experiment investigates transcriptional changes in whole blood during the recovery phase of dextran sulfate sodium (DSS)-induced colitis in mice, with or without treatment by synthetic mucin polymers (Shear-Labile Interaction Polymers, SLIPs). DSS (2.5% w/v) was administered for four days to induce acute epithelial injury, followed by four days of recovery in which mice received either water (control) or SLIPs (6.66 mg/mL) in drinking water. Whole-blood clots were collected on day 8 and processed for RNA extraction using a modified TRIzol LS protocol adapted for frozen clots. Libraries were prepared and sequenced on an Illumina NovaSeq 6000 platform (paired-end 150 bp). Differential expression analysis compared SLIP-treated and untreated groups to identify genes involved in immune regulation, redox balance, and epithelial recovery following colitis.biostudies-arrayexpressSample Collection - Whole-blood clots were collected from DSS-treated C57BL/6J mice on day 8 of the experiment, corresponding to the recovery phase following 4 days of 2.5% (w/v) dextran sulfate sodium (DSS) administration and 4 days of treatment with either autoclaved water (control) or Shear-Labile Interaction Polymers (SLIPs, 6.66 mg/mL in drinking water). Blood was collected at euthanasia by cardiac puncture, transferred into RNase-free microcentrifuge tubes, allowed to clot at room temperature, and flash frozen in liquid nitrogen before storage at −80 °C.Sequencing - Sequencing was performed on an Illumina NovaSeq 6000 platform using paired-end 150 bp reads. Raw reads were demultiplexed by the sequencing facility. Downstream quality control and adapter trimming were performed with FastQC and Trim Galore. Sequencing depth averaged >30 million paired reads per sample, generating high-quality whole-blood transcriptome data suitable for differential expression analysis between DSS + SLIP and DSS control groups.Library Construction - RNA libraries were prepared by the University of Florida Interdisciplinary Center for Biotechnology Research (ICBR).Nucleic Acid Extraction - Total RNA was extracted from frozen blood clots using a modified TRIzol LS protocol adapted from the Genomic Medicine Biorepository method for RNA isolation from human peripheral blood. Briefly, clots were homogenized in 1× RBC lysis buffer (NH₄Cl/KHCO₃/EDTA) using a bead mill homogenizer, followed by TRIzol LS extraction and acid–phenol phase separation. After isopropanol precipitation and ethanol washing, an additional reprecipitation step with 3 M sodium acetate (pH 5.2) and 100% ethanol was performed to remove residual phenol. RNA was resuspended in nuclease-free water, quantified using the Qubit RNA HS Assay, and integrity assessed with an Agilent 4200 TapeStation.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Gene-level expression values provided in the processed data file are raw read counts obtained from featureCounts, with no additional scaling or transformation applied.UnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNAMus musculusLuiz RoeschfalseRNA-seq of whole-blood clots from DSS-induced colitis mice treated with Shear-Labile Interaction Polymers (SLIPs)This experiment investigates transcriptional changes in whole blood during the recovery phase of dextran sulfate sodium (DSS)-induced colitis in mice, with or without treatment by synthetic mucin polymers (Shear-Labile Interaction Polymers, SLIPs). DSS (2.5% w/v) was administered for four days to induce acute epithelial injury, followed by four days of recovery in which mice received either water (control) or SLIPs (6.66 mg/mL) in drinking water. Whole-blood clots were collected on day 8 and processed for RNA extraction using a modified TRIzol LS protocol adapted for frozen clots. Libraries were prepared and sequenced on an Illumina NovaSeq 6000 platform (paired-end 150 bp). Differential expression analysis compared SLIP-treated and untreated groups to identify genes involved in immune regulation, redox balance, and epithelial recovery following colitis.2026-04-01T00:00:00Z2026-04-02T01:05:03.316Z2025-11-13T15:03:56.471ZE-MTAB-16067ERP184117EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184