This file describes the files for the single-nucleus RNA sequencing analysis of human chronic traumatic encephalopathy (CTE) tissue and matched control tissue. Sixteen samples were collected via the inDrops single cell method, 8 CTE and 8 controls. The inDrops method separates samples into groups of ~3,000 nuclei, which is why each samples is further divided, e.g. Control1.1, Control1.2, Control1.3. Complementary DNA produced by the inDrops facility was sequenced over eight NextSeq500 runs: Run1, Run2, Run3.1, Run3.2, Run4.1, Run4.2, Run5.1, Run5.2. Each run produced several count matrices comprising both control and CTE data. Count matrices are combined for each run and named Sample1.tsv Sample2.tsv, Sample3.tsv, Sample4.tsv, Sample5.tsv, Sample6.tsv, Sample7.tsv, Sample 8.tsv. Data are organized as follows: Run1 produced data in Sample1 Sample 1 contains: control.5.1 control.5.2 control.5.3 CTE.1.1 CTE.1.2 CTE.1.3 Run2 produced data in Sample2 Sample 2 contains: control.4.1 control.4.2 control.6.1 control.6.2 control.6.3 control.7.1 control.7.2 control.7.3 CTE.2.1 CTE.2.2 CTE.3.1 CTE.3.2 CTE.4.1 CTE.4.2 CTE.4.3 Run3.1 produced data in Sample3 Sample3 contains: control.5.4 control.5.5 control.5.6 control.6.4 control.6.5 control.6.6 CTE.2.3 CTE.2.4 CTE.2.5 CTE.3.3 CTE.3.4 CTE.3.5 Run3.2 produced data in Sample4 Sample4 contains: control.4.3 control.4.4 control.4.5 control.7.4 control.7.5 control.7.6 CTE.1.4 CTE.1.5 CTE.1.6 CTE.4.4 CTE.4.5 CTE.4.6 Run4.1 produced data in Sample5 Sample5 contains: control.2.1 control.2.2 control.2.3 control.8.1 control.8.2 control.8.3 CTE.5.1 CTE.5.2 CTE.5.3 CTE.6.1 CTE.6.2 CTE.6.3 Run4.2 produced data in Sample6 Sample6 contains: control.1.1 control.1.2 control.1.3 control.3.1 control.3.2 control.3.3 CTE.7.1 CTE.7.2 CTE.7.3 CTE.8.1 CTE.8.2 CTE.8.3 Run5.1 produced data in Sample7 Sample7 contains: control.5.7 control.5.8 control.5.9 control.7.7 control.7.8 control.7.9 Run5.2 produced data in Sample9 Sample9 contains: control.2.4 control.2.5 control.2.6 control.8.4 control.8.5 control.8.6 Fastq files can be de-multiplexed to reproduce count matrices following the inDrops processing pipeline: https://github.com/indrops/indrops Below are the library indices needed as input in the inDrops processing pipeline for each sample. Sample1 control.5.1 TCGCATAA control.5.2 TTACCTCC control.5.3 CAGTTATG CTE.1.1 CTTAATAG CTE.1.2 ATAGCCTT CTE.1.3 TAAGGCTC Sample2 control.4.1 AGAGGATA control.4.2 CTCCTTAC control.4.3 TATGCAGT control.6.1 TACTCCTT control.6.2 AGGCTTAG control.6.3 ATTAGACG control.7.1 ACGCTCTT control.7.2 CGCATTCT control.7.3 ATAGAGAG CTE.2.1 CGGAGAGA CTE.2.2 AGCTAGAA CTE.3.1 TCTTACGC CTE.3.2 CTTAATAG CTE.4.1 CCTTTACT CTE.4.2 GAGACGGA CTE.4.3 AGAAAGCT Sample3 control.5.4 ATAGAGAG control.5.5 AGAGGATA control.5.6 CTCCTTAC control.6.4 AGCTAGAA control.6.5 ACTCTAGG control.6.6 TCTTACGC CTE.2.3 ATTAGACG CTE.2.4 CGGAGAGA CTE.2.5 CTAGTCGA CTE.3.3 TATGCAGT CTE.3.4 TACTCCTT CTE.3.5 AGGCTTAG Sample4 control.4.4 ACGCTCTT control.4.5 CGCATTCT control.7.4 CCTTTACT control.7.5 GAGACGGA control.7.6 AGAAAGCT CTE.1.4 TCGCATAA CTE.1.5 TTACCTCC CTE.1.6 CAGTTATG CTE.4.4 CTTAATAG CTE.4.5 ATAGCCTT CTE.4.6 TAAGGCTC Sample5 control.2.1 TATGCAGT control.2.2 TACTCCTT control.2.3 AGGCTTAG control.8.1 ATAGAGAG control.8.2 AGAGGATA control.8.3 CTCCTTAC CTE.5.1 ATTAGACG CTE.5.2 CGGAGAGA CTE.5.3 CTAGTCGA CTE.6.1 AGCTAGAA CTE.6.2 ACTCTAGG CTE.6.3 TCTTACGC Sample6 control.1.1 CTTAATAG control.1.2 ATAGCCTT control.1.3 TAAGGCTC control.3.1 TCGCATAA control.3.2 TTACCTCC control.3.3 CAGTTATG CTE.7.1 CCTTTACT CTE.7.2 GAGACGGA CTE.7.3 AGAAAGCT CTE.8.1 ACGCTCTT CTE.8.2 CGCATTCT CTE.8.3 GGTACTCA Sample7 control.5.7 ATAGAGAG control.5.8 AGAGGATA control.5.9 CTCCTTAC control.7.7 TATGCAGT control.7.8 TACTCCTT control.7.9 AGGCTTAG Sample8 control.2.4 ACGCTCTT control.2.5 CGCATTCT control.2.6 GGTACTCA control.8.4 CCTTTACT control.8.5 GAGACGGA control.8.6 AGAAAGCT