Journal
Nature Communications
Publication Date
2014
Volume
5
Inclusive Pages
5307
Document Type
Open Access Publication
DOI
10.1038/ncomms6307
Rights and Permissions
S.E. McGaugh, et al. 20 October 2014. The cavefish genome reveals candidate genes for eye loss. Nature communications. Art. No. 5307. DOI: 10.1038/ncomms6307. http://www.nature.com/ncomms/2014/141020/ncomms6307/full/ncomms6307.html
Recommended Citation
McGaugh, Suzanne E.; Minx, Patrick; Warren, Wesley C.; and et al, "The cavefish genome reveals candidate genes for eye loss." Nature Communications. 5, 5307. (2014).
https://digitalcommons.wustl.edu/open_access_pubs/4276
ncomms6307-s1.pdf (947 kB)
Supplementary Figures 1-2 and Supplementary References
ncomms6307-s2.xlsx (8 kB)
Reads used for assembly of the Astyanax mexicanus genome.
ncomms6307-s3.xlsx (9 kB)
Reads used for assembly of the Astyanax mexicanus transcriptome.
ncomms6307-s4.xlsx (11 kB)
Comparison of DNA transposon and retrotransposon contents in different vertebrate genomes.
ncomms6307-s5.xlsx (9 kB)
Transposable element statistics in the cavefish genome.
ncomms6307-s6.xlsx (10 kB)
Transposable element statistics in the cavefish brain transcriptome.
ncomms6307-s7.xlsx (10 kB)
Transposable element statistics in the cavefish muscle transcriptome.
ncomms6307-s8.xlsx (10 kB)
Transposable element statistics in the surface fish eye transcriptome.
ncomms6307-s9.xlsx (14 kB)
General percent statistics of the different classes, DNA, LINE, SINE and LTR summarized from transcriptomes and the genomic data.
ncomms6307-s10.xlsx (15 kB)
Detailed percent statistics of the different classes, DNA, LINE, SINE and LTR summarized from transcriptomes and the genomic data
ncomms6307-s11.xlsx (13 kB)
Genes that are implicated in congenital anomaly of the eye by Ingenuity Pathway Analysis
ncomms6307-s12.xlsx (972 kB)
All genes under eye size QTL
ncomms6307-s13.xlsx (640 kB)
Gene Expression Data from genes under eye size QTL
ncomms6307-s14.xlsx (86 kB)
IPA activation analysis for 10 hours post-fertilization
ncomms6307-s15.xlsx (90 kB)
IPA activation analysis for 24 hours post-fertilization
ncomms6307-s16.xlsx (99 kB)
IPA activation analysis for 1.5 days post-fertilization
ncomms6307-s17.xlsx (102 kB)
IPA activation analysis for 3 days post-fertilization
ncomms6307-s18.xlsx (75 kB)
Scaffolds arranged into linkage groups
ncomms6307-s19.xlsx (2797 kB)
Zebrafish homologs which are not annotated in the cavefish genome from Ensembl e74 and their presence or absence in other species
ncomms6307-s20.xlsx (241 kB)
Supplementary Figures 1-2 and Supplementary References
ncomms6307-s2.xlsx (8 kB)
Reads used for assembly of the Astyanax mexicanus genome.
ncomms6307-s3.xlsx (9 kB)
Reads used for assembly of the Astyanax mexicanus transcriptome.
ncomms6307-s4.xlsx (11 kB)
Comparison of DNA transposon and retrotransposon contents in different vertebrate genomes.
ncomms6307-s5.xlsx (9 kB)
Transposable element statistics in the cavefish genome.
ncomms6307-s6.xlsx (10 kB)
Transposable element statistics in the cavefish brain transcriptome.
ncomms6307-s7.xlsx (10 kB)
Transposable element statistics in the cavefish muscle transcriptome.
ncomms6307-s8.xlsx (10 kB)
Transposable element statistics in the surface fish eye transcriptome.
ncomms6307-s9.xlsx (14 kB)
General percent statistics of the different classes, DNA, LINE, SINE and LTR summarized from transcriptomes and the genomic data.
ncomms6307-s10.xlsx (15 kB)
Detailed percent statistics of the different classes, DNA, LINE, SINE and LTR summarized from transcriptomes and the genomic data
ncomms6307-s11.xlsx (13 kB)
Genes that are implicated in congenital anomaly of the eye by Ingenuity Pathway Analysis
ncomms6307-s12.xlsx (972 kB)
All genes under eye size QTL
ncomms6307-s13.xlsx (640 kB)
Gene Expression Data from genes under eye size QTL
ncomms6307-s14.xlsx (86 kB)
IPA activation analysis for 10 hours post-fertilization
ncomms6307-s15.xlsx (90 kB)
IPA activation analysis for 24 hours post-fertilization
ncomms6307-s16.xlsx (99 kB)
IPA activation analysis for 1.5 days post-fertilization
ncomms6307-s17.xlsx (102 kB)
IPA activation analysis for 3 days post-fertilization
ncomms6307-s18.xlsx (75 kB)
Scaffolds arranged into linkage groups
ncomms6307-s19.xlsx (2797 kB)
Zebrafish homologs which are not annotated in the cavefish genome from Ensembl e74 and their presence or absence in other species
ncomms6307-s20.xlsx (241 kB)
