title: RNA-seq of whole-blood clots from DSS-induced colitis mice treated with Shear-Labile Interaction Polymers (SLIPs)
design: RNA-seq of whole-blood clots from DSS-induced colitis mice treated with Shear-Labile Interaction Polymers (SLIPs)
library_construction_protocol: 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. 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. RNA libraries were prepared by the University of Florida Interdisciplinary Center for Biotechnology Research (ICBR).