DUXC
Preface
0.1
Nomenclature
0.2
Datasets
0.3
Annotation
0.3.1
canFam3 ensembl GTF
0.4
Software
1
ChIP-seq for the canine model
1.1
ChIP-seq samples
1.2
Analysis workflow
1.3
Peaks and functional distribution
1.3.1
Number of peaks
1.3.2
Functional discribution
1.4
Overlap of peaks
1.4.1
DUXC and DUX4
1.4.2
DUXC and DUXC-ALT
1.5
Motifs analysis
2
RNA-seq to DESeq2
2.1
RNA-seq preprocessing
2.2
Reads counts
2.2.1
Define gene features
2.2.2
Read counts
2.3
DESeq2
3
DUXC transcriptome
3.1
Load datasets and settings
3.2
DESeq2
3.2.1
hypothesis settings
3.2.2
CinC: DUXC expresison in canine muscle cells
3.2.3
HinC: DUX4 expression in canine muscle cells
3.2.4
DUXC-ALT expression - CALTinC
3.3
Cross-species models: DUX4 expression in canine and murine
3.3.1
DUX4 and DUXC expression in canine
3.3.2
DUX4 and Dux expression in murine
4
DUXC and Dux transcriptome compared to that of FSHD
4.1
DUXC transcriptome compared to that of FSHD
4.1.1
Get canine-human homologs
4.1.2
GSEA: enrichment of FSHD transcriptome
4.2
Dux transcriptome compared to that of FSHD
4.2.1
Get canine-human homologs
4.2.2
GSEA: enrichment of FSHD transcriptome
5
DUXC transcriptome compared to early embryo transcriptome profile
5.1
Mouse 2C-like signature
5.2
cleavage-stage signature
5.3
iPSCs
6
Repeat elements
6.1
Takeaway
6.2
Repeat element expression
6.3
Differential analysis
6.3.1
Normalization
6.3.2
DESeq2 results
6.4
Repeat family enrichment analysis
6.4.1
Correlation between HinC and CinC transcriptome
6.4.2
Repeat family activation
6.4.3
Repeat classs activation
6.5
LTR retroelements distribution and activation
6.6
Peaks distribution in class of repeat elements
7
LTR activation
7.1
Takaway
7.2
background in murine and human
7.3
ERVL subfamily activation in canine
7.4
MaLR activation in canine
7.5
Compare to CinC and HinC to HinH
7.5.1
Copy number
7.5.2
ERVL-MaLR
7.5.3
ERVL
7.5.4
ERV1
7.6
DUXC-ALT and ERVL transcriptions
7.6.1
ERV subfamily expression
8
Non-LTR retrotrasposons and satellites
8.1
LINEs
8.1.1
L1s activation
8.1.2
LINE1 and DUXC/DUX4 binding sites
8.2
SINE
8.2.1
Distribution of SINE family
8.2.2
Expression of SINEs in HinC and CinC transcriptome
8.2.3
tRNA-Lys
8.3
Satellites
9
DUXC peaks and LINE1s
9.1
Narrow Peaks and expressed L1s
9.1.1
Motif discovery using L1-overlapped peaks
9.1.2
Match DUX4 and DUXC motif to L1-overapped peaks
9.1.3
Location of AATCA on L1-overlapped peaks
9.2
LINE1s and AATCA
References
Published with bookdown
Canine DUXC: Implications for DUX4 retrotransposition and preclinical models of FSHD
References