Data · dataset · 2018
Data for Figures 5 A, C, D, E
Listed in Teesside University Research Data Repository
Ras activity dependent gene expression is coupled to changes in cell cycle dynamics A. RNA-seq reveals reciprocal genes expression changes in response to GefE and nutrition.
Description
RNA-seq was performed on AX3 G+, AX3 G-, and gefE- G+ cells. Ras dependent genes were identified by comparing gene expression of gefE- G+ and AX3 G+ samples.
A highly significant proportion of these 45 DEGs (80%) also show a >1.5x FC in expression between AX3 G+ and AX3 G- (hypergeometric test, p = 4 x 10-15). Comparison of log2 FCs of the 36 overlapping genes shows that stalky nutritional bias results in sporey low Ras gene activity. Candidate genes are highlighted in red.
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C. Quantification of rrgA and rigA RNA-FISH. The relative expression of each gene in each cell was calculated as an index of expression rrgA/(rrgA+rigA). Values of 1 or 0 represent only rrgA or rigA expression, respectively.
D. Ras dependent genes are maximally expressed during multicellular development. Expression profiles of RasD dependent genes were determined from RNA-seq data at different time points during development. E. rrgA and rigA mutant behaviour in stalk cell induction monolayer assays. rrgA knockout in AX3 does not significantly stalk cell differentiation, whereas the rrgA-/gefE- double mutant rescues gefE- mutant prespore bias (see Supplementary File 4 for p-values). rigA knockout in AX3 does not significantly affect stalk cell differentiation, whereas the rigA/AX3rasD(G12T) strain shows significantly reduced stalk cell differentiation compared to AX3rasD(G12T) (see Supplementary File 4 for p-values).
Plotted values are the mean of three replicates and error bars depict the standard error of the mean.
Links
Where it is published
- DOI doi.org/10.17632/k78ct68ypn.1 ↗
DOI / persistent id · from researchdata tees ac uk
Catalogue records · 1
- OAI-PMH record data.mendeley.com/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=oai%3Adata… ↗
metadata API · from researchdata tees ac uk
Topics
- From keywords
- Earth & Environmental Science · Engineering · Humanities · Life Sciences · Social Science
- Inferred from text
- Biochemistry and cell biology 71% · RNA sequencing 65%
Provenance · 1 source records, 12 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| Teesside University Research Data Repository | oai:data.mendeley.com/k78ct68ypn.1 | 11 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| concepts[field].anzsrc:group:3101 | enrichment · researchdata tees ac uk | taxonomy-embedding@1.0.0 | title+keywords+description (71%) |
| concepts[field].local:field:earth-environmental | mapping · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| concepts[field].local:field:engineering | mapping · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| concepts[field].local:field:humanities | mapping · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| concepts[field].local:field:social-science | mapping · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| concepts[modality].local:modality:rna-seq | enrichment · researchdata tees ac uk | keyword-concept-rules@1.0.0 | title+description (65%) |
| description | source · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | /metadata/dc/description |
| license | source · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | /metadata/dc/rights |
| publication_date | source · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| title | source · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | /metadata/dc/title |