title: GSM9294193: 3-week Vehicle-Recovery Replicate 1 Liver; Mus musculus; RNA-Seq
library_construction_protocol: Total RNA was extracted from frozen liver and kidney samples using TRIzol Reagent (Thermo Fisher Scientific, 15596018) following the TREx RNA Extraction Protocol v1.8 (Cornell University Transcription Regulation and Expression Facility). After tissue homogenization, chloroform was added to promote phase separation of RNA from DNA and protein, and the aqueous phase was transferred to Phaselock Gel tubes (VWR 01847‐802) for clean extraction. The RNA was precipitated with isopropanol (molecular biology grade), using GlycoBlue (Thermo AM9515) to enhance recovery. Pellets were washed twice with 75% ethanol, air-dried, and resuspended in RNase-free water. RNA concentration was quantified using a NanoPhotometer N50 (Implen) and RNA integrity assessed with an Agilent 2100 Bioanalyzer. Libraries were generated using the NEBNext UltraExpress RNA Library Prep Kit (NEB #E3330), incorporating poly(A) enrichment to select mRNA. Sequencing was performed across one lane of an Illumina NextSeq 2000 using single-end 75 bp reads, targeting ~20-25 million reads per sample. Each experimental group included 3 Treatment samples, 3 Recovery samples, and 4 Control samples per organ (3 Control from the treatment timepoint, 1 from the recovery timepoint). NEBNext UltraExpress RNA Library Prep Kit (NEB #E3330)