Derek L. Stemple
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View article: Zebrafish Developmental Stage 3' end data (GRCz11/e92)
Zebrafish Developmental Stage 3' end data (GRCz11/e92) Open
This contains the DeTCT data presented in White et al. 2017 (https://doi.org/10.7554/eLife.30860) mapped to the GRCz11 assembly and counted against the Ensembl version 92 annotation.Descriptions of each file are in the README.md file
View article: A Comparative Survey of the Frequency and Distribution of Polymorphism in the Genome of Xenopus tropicalis
A Comparative Survey of the Frequency and Distribution of Polymorphism in the Genome of Xenopus tropicalis Open
Naturally occurring DNA sequence variation within a species underlies evolutionary adaptation and can give rise to phenotypic changes that provide novel insight into biological questions. This variation exists in laboratory populations jus…
View article: Identification of slit3 as a locus affecting nicotine preference in zebrafish and human smoking behaviour
Identification of slit3 as a locus affecting nicotine preference in zebrafish and human smoking behaviour Open
To facilitate smoking genetics research we determined whether a screen of mutagenized zebrafish for nicotine preference could predict loci affecting smoking behaviour. From 30 screened F3 sibling groups, where each was derived from an indi…
View article: Zebrafish Developmental Stages RNA-seq count data (GRCZ11)
Zebrafish Developmental Stages RNA-seq count data (GRCZ11) Open
Count data generated from RNA-seq from zebrafish embryos from 18 developmental stages from 1-cell to 5 dpf (White et al. 2017, http://dx.doi.org/10.7554/eLife.30860) mapped to the GRCz11 assembly.
View article: The gene regulatory basis of genetic compensation during neural crest induction
The gene regulatory basis of genetic compensation during neural crest induction Open
The neural crest (NC) is a vertebrate-specific cell type that contributes to a wide range of different tissues across all three germ layers. The gene regulatory network (GRN) responsible for the formation of neural crest is conserved acros…
View article: Endothelin receptor Aa regulates proliferation and differentiation of Erb-dependent pigment progenitors in zebrafish
Endothelin receptor Aa regulates proliferation and differentiation of Erb-dependent pigment progenitors in zebrafish Open
Skin pigment patterns are important, being under strong selection for multiple roles including camouflage and UV protection. Pigment cells underlying these patterns form from adult pigment stem cells (APSCs). In zebrafish, APSCs derive fro…
View article: Supplemental gene list to accompany Figure 2f. 15 individual subset gene lists and full ZFA enrichment.
Supplemental gene list to accompany Figure 2f. 15 individual subset gene lists and full ZFA enrichment. Open
15 gene lists which are derived from the 15 different subsets found in Figure 2f. An UpSet comparison of tfap2a;tfap2c knockouts at 4 somites, 15 somites, 24 hpf and a neural crest gene enriched set from 22 hpf FACSed and RNA-Seq sequenced…
View article: Intron Retention data (using iDiffIR)
Intron Retention data (using iDiffIR) Open
Intron retention data for Collins et al. 2019This contains data for 3 mutant lines from the mouse DMDD project (Dhx35, Morc2a and Hmgxb3).Repeat annotation identified by RepeatMasker was downloaded (http://www.repeatmasker.org/genomes/mm10…
View article: Differentially expressed gene lists - Repeats
Differentially expressed gene lists - Repeats Open
Files for 13 mutant lines, investigated for differentially expressed repeats, containing the repeat instances determined to be differentially expressed (using DESeq2).see the README for more detail.
View article: Differentially expressed gene lists - Repeats
Differentially expressed gene lists - Repeats Open
Files for 13 mutant lines, investigated for differentially expressed repeats, containing the repeat instances determined to be differentially expressed (using DESeq2).see the README for more detail.
View article: Differentially expressed gene lists - Repeats (mapped with a transcriptome reference)
Differentially expressed gene lists - Repeats (mapped with a transcriptome reference) Open
Differentially expressed gene lists - Repeats (mapped with a transcriptome reference)Data for Collins et al. 2019 (doi: 10.7554/eLife.30860) p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica} These are files of differentially e…
View article: Identification of<i>Slit3</i>as a locus affecting nicotine preference in zebrafish and human smoking behaviour
Identification of<i>Slit3</i>as a locus affecting nicotine preference in zebrafish and human smoking behaviour Open
To facilitate smoking genetics research we determined whether a screen of mutagenized zebrafish for nicotine preference could predict loci affecting smoking behaviour. Of 30 ENU mutagenized families screened, two showed increased or decrea…
View article: Collins et al. 2019 - Processed Counts
Collins et al. 2019 - Processed Counts Open
Collins et al. 2019 - Processed count files for mutant lines. These files contain counts for each gene in the Ensembl version 88 annotation for the samples in each mutant line.The README file has more details.
View article: EMAPA Enrichment - Mutant Response
EMAPA Enrichment - Mutant Response Open
EMAPA Enrichment results based on differentially expressed gene lists for the Mutant Response set.see README.md for more details.
View article: EMAPA Enrichment - Discard
EMAPA Enrichment - Discard Open
EMAPA Enrichment results based on differentially expressed gene lists for the Discard set.see README.md for more details.
View article: EMAPA Enrichment - unfiltered
EMAPA Enrichment - unfiltered Open
EMAPA Enrichment results based on differentially expressed gene lists.see README.md for more details.
View article: EMAPA Enrichment - Delay
EMAPA Enrichment - Delay Open
EMAPA Enrichment results based on differentially expressed gene lists for the Delay set.see README.md for more details.
View article: EMAPA Enrichment - No Delay
EMAPA Enrichment - No Delay Open
EMAPA Enrichment results based on differentially expressed gene lists for the No Delay set.see README.md for more details.
View article: Differentially expressed gene lists - No Delay
Differentially expressed gene lists - No Delay Open
Files of differentially expressed genes (using DESeq2) from different mutant lines. No Delay set.see the README for more detail.
View article: Differentially expressed gene lists - Mutant response
Differentially expressed gene lists - Mutant response Open
Files of differentially expressed genes (using DESeq2) from different mutant lines. Mutant response.see the README for more detail.
View article: Differentially expressed gene lists - Discard
Differentially expressed gene lists - Discard Open
Files of differentially expressed genes (using DESeq2) from different mutant lines. Discard set.see the README for more detail.
View article: Differentially expressed gene lists - Delay
Differentially expressed gene lists - Delay Open
Files of differentially expressed genes (using DESeq2) from different mutant lines. Delay.see the README for more detail.
View article: Gene Ontology Enrichment - Mutant Response
Gene Ontology Enrichment - Mutant Response Open
GO enrichment results using differentially expressed gene lists for the Mutant Response set.see README.md for more details.
View article: Gene Ontology Enrichment - Discard
Gene Ontology Enrichment - Discard Open
GO enrichment results using differentially expressed gene lists for the Discard set.see README.md for more details.
View article: Gene Ontology Enrichment - Delay
Gene Ontology Enrichment - Delay Open
GO enrichment results using differentially expressed gene lists for the Delay set.see README.md for more details.
View article: Gene Ontology Enrichment - unfiltered
Gene Ontology Enrichment - unfiltered Open
Gene Ontology Enrichment results based on differentially expressed gene lists.see README.md for more details.
View article: Gene Ontology Enrichment - No Delay
Gene Ontology Enrichment - No Delay Open
GO enrichment results using differentially expressed gene lists for the No Delay set.see README.md for more details.