mRNAseq_brain_(CTE long term study)

This file contains the mRNA-seq dataset that was used in the unpublished manuscript and was further analyzed with the DEGviewer online software. The dataset shows significant mRNA fold changes when comparing CTE-induced groups with the control group.Total RNA concentration was calculated using Quant-IT RiboGreen (cat no. R11490, Invitrogen). To assess the integrity of the total RNA, samples were run on a TapeStation RNA screentape (cat no. 5067-5576, Agilent Technologies, Waldbronn, Germany). Only high-quality RNA preparations (RIN greater than 7.0) were used for the RNA library construction. A library was independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit (cat no. 20020595, Illumina, Inc., San Diego, CA, USA). The first step in the workflow involves purifying the poly‐A containing mRNA molecules using poly‐T‐attached magnetic beads. Following purification, mRNA was fragmented into small pieces using divalent cations at elevated temperatures. The cleaved RNA fragments were copied into first-strand cDNA using SuperScript II reverse transcriptase (cat no. 18064014; Invitrogen) and random primers. This was followed by synthesis of second-strand cDNA using DNA Polymerase I, RNase H, and dUTP. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products were purified and enriched using PCR to create a final cDNA library. The libraries were quantified using KAPA Library Quantification kits for Illumina Sequencing platforms, according to the qPCR Quantification Protocol Guide (cat no. KK4854, Kapa Biosystems, Woburn, MA, USA) and qualified using a TapeStation D1000 ScreenTape (cat no. 5067-5582, Agilent Technologies). Indexed libraries were then submitted to an Illumina NovaSeq6000 (Illumina, Inc., San Diego, CA, USA) and paired-end (2×100 bp) sequencing was performed by Macrogen, Inc. (Daejeon, South Korea).