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+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