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