Experiment Overview
| Repository ID: | FR-FCM-Z3EQ | Experiment name: | EU incorporation in Ccnc/Cdk8 WT/KO mESCs | MIFlowCyt score: | 96.42% |
| Primary researcher: | Rebecca Lloyd | PI/manager: | Steve Jackson | Uploaded by: | Rebecca Lloyd |
| Experiment dates: | 2019-07-14 - 2020-08-19 | Dataset uploaded: | Jan 2021 | Last updated: | Jan 2021 |
| Keywords: | [CCNC] [CDK8] [Ethynyl uridine] | Manuscripts: | |||
| Organizations: |
University of Cambridge, Cambridge, (UK)
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| Purpose: | To assess the impact of Ccnc or Cdk8 loss on global transcription, measured by the incorporation of the nucleotide analogue 5-ethynyl uridine into RNA. Co-incubation with the RNAPI inhibitor (10uM 3h CX5641) was used to remove nucleolar signal and specifically assess RNAPII (and RNAPIII)-mediated transcription. | ||||
| Conclusion: | No discernible impact of Ccnc or Cdk8 loss. | ||||
| Comments: | None | ||||
| Funding: | Not disclosed | ||||
| Quality control: | No EdU controls for baseline levels. Co-incubation with 3h 5uM ActD as a positive control for total transcription inhibition | ||||
Experiment variables
| Individuals | |
|---|---|
| · WT | WT 3h CX5641.fcs · WT 5uM ActD.fcs · WT DMSO.fcs · WT 5uM ActD.fcs-(1) · WT CX.fcs · WT DMSO.fcs-(1) · WT no EU.fcs · WT ActD.fcs · WT CX.fcs-(1) · WT DMSO.fcs-(2) · no EU.fcs · WT 3h 5uM ActD.fcs · WT NT.fcs · WT 3h 5uM ActD.fcs-(1) · WT NT.fcs-(1) |
| · Ccnc KO (D1) | D1 3h CX5641.fcs · D1 DMSO.fcs · D1 CX.fcs · D1 DMSO.fcs-(1) · D1 CX.fcs-(1) · D1 DMSO.fcs-(2) · D1 NT.fcs · D1 NT.fcs-(1) |
| · Ccnc KO (G2) | G2 3h CD5641.fcs · G2 DMSO.fcs · G2 CX.fcs · G2 DMSO.fcs-(1) · G2 CX.fcs-(1) · G2 DMSO.fcs-(2) · G2 NT.fcs · G2 NT.fcs-(1) |
| · Cdk8 KO (B9) | B9 3h CX5641.fcs · B9 DMSO.fcs · B9 CX.fcs · B9 DMSO.fcs-(1) · B9 CX.fcs-(1) · B9 DMSO.fcs-(2) · B9 NT.fcs · B9 NT.fcs-(1) |
| · Cdk8 KO (H4) | H4 3h CX5641.fcs · H4 DMSO.fcs · H4 CX.fcs · H4 DMSO.fcs-(1) · H4 CX.fcs-(1) · H4 DMSO.fcs-(2) · H4 NT.fcs · H4 NT.fcs-(1) |
| Conditions | |
|---|---|
| · non-treated | B9 DMSO.fcs · D1 DMSO.fcs · G2 DMSO.fcs · H4 DMSO.fcs · WT DMSO.fcs · B9 DMSO.fcs-(1) · D1 DMSO.fcs-(1) · G2 DMSO.fcs-(1) · H4 DMSO.fcs-(1) · WT DMSO.fcs-(1) · B9 DMSO.fcs-(2) · D1 DMSO.fcs-(2) · G2 DMSO.fcs-(2) · H4 DMSO.fcs-(2) · WT DMSO.fcs-(2) · B9 NT.fcs · D1 NT.fcs · G2 NT.fcs · H4 NT.fcs · WT NT.fcs · B9 NT.fcs-(1) · D1 NT.fcs-(1) · G2 NT.fcs-(1) · H4 NT.fcs-(1) · WT NT.fcs-(1) |
| · 3h 10 uM CX5641 | B9 3h CX5641.fcs · D1 3h CX5641.fcs · G2 3h CD5641.fcs · H4 3h CX5641.fcs · WT 3h CX5641.fcs · B9 CX.fcs · D1 CX.fcs · G2 CX.fcs · H4 CX.fcs · WT CX.fcs · B9 CX.fcs-(1) · D1 CX.fcs-(1) · G2 CX.fcs-(1) · H4 CX.fcs-(1) · WT CX.fcs-(1) |
| · 3h 5uM ActD | WT 5uM ActD.fcs · WT 5uM ActD.fcs-(1) · WT ActD.fcs · WT 3h 5uM ActD.fcs · WT 3h 5uM ActD.fcs-(1) |
| · no EU | WT no EU.fcs · no EU.fcs |
| Sample Type | |
|---|---|
| · Biological replicate 1 | B9 3h CX5641.fcs · B9 DMSO.fcs · D1 3h CX5641.fcs · D1 DMSO.fcs · G2 3h CD5641.fcs · G2 DMSO.fcs · H4 3h CX5641.fcs · H4 DMSO.fcs · WT 3h CX5641.fcs · WT 5uM ActD.fcs · WT DMSO.fcs |
| · Biological replicate 2 | B9 CX.fcs · B9 DMSO.fcs-(1) · D1 CX.fcs · D1 DMSO.fcs-(1) · G2 CX.fcs · G2 DMSO.fcs-(1) · H4 CX.fcs · H4 DMSO.fcs-(1) · WT 5uM ActD.fcs-(1) · WT CX.fcs · WT DMSO.fcs-(1) · WT no EU.fcs |
| · Biological replicate 3 | B9 CX.fcs-(1) · B9 DMSO.fcs-(2) · D1 CX.fcs-(1) · D1 DMSO.fcs-(2) · G2 CX.fcs-(1) · G2 DMSO.fcs-(2) · H4 CX.fcs-(1) · H4 DMSO.fcs-(2) · WT ActD.fcs · WT CX.fcs-(1) · WT DMSO.fcs-(2) · no EU.fcs |
| · Biological replicate 4 | B9 NT.fcs · D1 NT.fcs · G2 NT.fcs · H4 NT.fcs · WT 3h 5uM ActD.fcs · WT NT.fcs |
| · Biological replicate 5 | B9 NT.fcs-(1) · D1 NT.fcs-(1) · G2 NT.fcs-(1) · H4 NT.fcs-(1) · WT 3h 5uM ActD.fcs-(1) · WT NT.fcs-(1) |
