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
