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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