Genome Biology

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s13059-015-0732-z-s1.xlsx (14 kB)
Compiled comparison of RNAseq with new and previously published qPCR data

s13059-015-0732-z-s2.xlsx (47 kB)
Compiled list of read number for each library

s13059-015-0732-z-s3.tif (24711 kB)
P10 and P21 biological replicates clustered by principal component analysis (PCA) show expected distribution based on functional and morphological phenotypes (312 kB)
P10 (a) and P21 (b) browser shots of reads per million (RPM) normalized mapped read count for selected genes for each biological replicate show reproducibility of sequencing results between samples

s13059-015-0732-z-s5.tif (14588 kB)
Homozygous and heterozygous mutants show largely overlapping datasets

s13059-015-0732-z-s6.tif (14588 kB)
Crx mutants show little change to other non-photoreceptor phototransduction components

s13059-015-0732-z-s7.tif (14588 kB)
Heatmap showing the Z-scores comparing three biological replicates of genes determined to be enriched in either E168d2/+ (a) or E168d2neo/+ (b) retinas

s13059-015-0732-z-s8.tif (14588 kB)
Crx mutants show graded changes in gene expression of overlapping gene sets at P21

s13059-015-0732-z-s9.tif (14588 kB)
Crx mutants do not abandon the developmental program, but many genes fail to reach proper expression levels

s13059-015-0732-z-s10.xlsx (50 kB)
Compiled table of results from GO analysis on rod- or cone-enriched genes from Fig. 6a

s13059-015-0732-z-s11.xlsx (148 kB)
Compiled ordered lists of heatmap data presented in the manuscript

s13059-015-0732-z-s12.tif (14588 kB)
Groups 1, 2, 3, and 6 genes (defined in Fig. 5) presented as a heatmap with calculated FC values for each biological replicate compared with the mean age-appropriate WT value

s13059-015-0732-z-s13.tif (14576 kB)
Quantification of normal epigenetic marks near genes in groups 1, 2, 3, and 6 distinguishes up- and down-regulated genes in Crx mutants

s13059-015-0732-z-s14.tif (14588 kB)
Expanded view of areas marked with asterisks in Fig. 6

s13059-015-0732-z-s15.tif (14588 kB)
Changes in rod- and cone-enriched transcription factors are consistent with general patterns of rod and cone gene expression in Crx mutants

s13059-015-0732-z-s16.tif (3018 kB)
Retinal function is affected by light damage (LD) in E168d2neo/+ but not E168d2/+ mutant mice

s13059-015-0732-z-s17.tif (3603 kB)
E168d2/+ photoreceptor degeneration is light-independent

s13059-015-0732-z-s18.tif (14588 kB)
Increased Crx expression in mutant lines at P10

s13059-015-0732-z-s19.xlsx (54 kB)
List of primers used for qRT-PCR completed for this manuscript