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Table 2 All RNA-sequencing data used in this study

From: Quantitative analysis of cryptic splicing associated with TDP-43 depletion

  Species Cell type Protein Depletion Library type Read type Depth Citation
1 Human HeLa TDP-43 siRNA mRNA l00bp PE 97-116M Ling, 2015 [25]
2 Mouse ES TDP-43 Knockout mRNA l00bp PE 70-75M Ling, 2015 [25]
3 Human K562 TDP-43 shRNA Total RNA l00bp PE 55-62M ENCODE
4 Human K562 TDP-43 shRNA mRNA l00bp PE 25-29M ENCODE
5 Mouse Adult brain TDP-43 ASO mRNA 75bp SE 35-60M Polymenidou, 2011 [23]
6 Mouse ES TDP-43 Knockout mRNA 40bp SE 2-11M Chiang, 2010 [21]
7 Human K562 FUS shRNA mRNA l00bp SE 12-21M ENCODE
8 Mouse Adult brain FUS ASO mRNA 72bp SE 20-60M Lagier-Tourenne, 2012 [20]
9 Human HeLa hnRNP C siRNA mRNA 72bp SE 26-28M Zarnack, 2013 [12]
  1. For single end sequencing, depth is measured in millions of mapped reads whereas paired end sequencing depth is measured in millions of mapped fragments
  2. ES leukaemia cell line. siRNA small interfering RNA, shRNA short hairpin RNA, ASO antisense oligonucleotide, PE paired end sequencing, SE single end sequencing