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Architectural Mediator subunits are differentially essential for global transcription in yeast (RNA-seq/4tU-seq ; Sua7-AID)

ABSTRACT: Architectural Mediator subunits are differentially essential for global transcription in yeast (RNA-seq/4tU-seq ; Sua7-AID)

PROVIDER: PRJNA610076 | ENA |

REPOSITORIES: ENA

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Architectural Mediator subunits are differentially essential for global transcription in yeast (RNA-seq/4tU-seq ; Med14-AID, Med17-AID)

Project description:Architectural Mediator subunits are differentially essential for global transcription in yeast (RNA-seq/4tU-seq ; Med14-AID, Med17-AID)

| PRJNA610054 | ENA

Architectural Mediator subunits are differentially essential for global transcription in yeast (RNA-seq/4tU-seq ; Med14-AID, Med17-AID)

Project description:This project aims to understand the function of different mediator subunits (Med14 and Med17) in transcription in S. cerevisiae. Thus we analyzed total and newly synthesized RNA levels in conditional Med14 and Med17 depletion strains. For this purpose we used an auxin inducible degron system system to specifically induce the degradation Mediator subunits by addition of auxin into the culture medium. We measured transcript levels after 30 min auxin or DMSO (control) treatment induction of degradation of Med14 or Med17 by the addition of auxin (30 min) or with the carrier DMSO (control) followed by a 6 min labelling of newly synthesized RNA with 4-thiouracil (4tU). In parallel wiltype S.pombe cells were labelled with 4tU for 6min during midlog growth phase. Prior to RNA extraction (Ribopure Yeast Kit, Ambion) our labelled S.cerevisiae cells of interest were mixed with labelled S.pombe cells as a spike to allow normalization against an exogenous reference (ratio 3 S .cerevisiae for 1 S.pombe cell. From the total RNA we purified the 4tU labelled fraction of RNAs containing 4tU. Both the total RNA and the purified newly synthesized RNAs will then be subject to RNA-sequencing after ribosomal RNA depletion. In summary, we will provide 16 samples for this project containing RNA from both S.cerevisiae and S.pombe. The sample read counts were normalized with size factors computed by the median-of-ratios method proposed by Anders and Huber (Anders et al. 2010) on S. pombe genes to make these counts comparable between samples.

2020-03-04 | GSE146300 | GEO

Architectural Mediator subunits are differentially essential for global transcription in yeast (RNA-seq/4tU-seq ; Sua7-AID)

Project description:This project aims to understand the function of general transcription factor TFIIB in transcription in S. cerevisiae. Thus, we analyzed total and newly synthesized RNA levels in a conditional Sua7 (TFIIB) depletion strain. For this purpose we used an auxin inducible degron system system to specifically induce the degradation Sua7 by addition of auxin into the culture medium. We measured transcript levels after 30 min auxin or DMSO (control) treatment induction of degradation of Sua7 by the addition of auxin (30 min) or with the carrier DMSO (control) followed by a 6 min labelling of newly synthesized RNA with 4-thiouracil (4tU). In parallel wiltype S.pombe cells were labelled with 4tU for 6min during midlog growth phase. Prior to RNA extraction (Ribopure Yeast Kit, Ambion) our labelled S.cerevisiae cells of interest were mixed with labelled S.pombe cells as a spike to allow normalization against an exogenous reference (ratio 3 S .cerevisiae for 1 S.pombe cell. From the total RNA we purified the 4tU labelled fraction of RNAs containing 4tU. Both the total RNA and the purified newly synthesized RNAs will then be subject to RNA-sequencing after ribosomal RNA depletion. In summary, we will provide 8 samples for this project containing RNA from both S.cerevisiae and S.pombe. The sample read counts were normalized with size factors computed by the median-of-ratios method proposed by Anders and Huber (Anders et al. 2010) on S. pombe genes to make these counts comparable between samples.

2020-03-04 | GSE146318 | GEO

Architectural Mediator subunits are differentially essential for global transcription in yeast (RNA-seq/4tU-seq)

Project description:Architectural Mediator subunits are differentially essential for global transcription in yeast (RNA-seq/4tU-seq)

| PRJNA610215 | ENA

Architectural Mediator subunits are differentially essential for global transcription in yeast (RNA-seq/4tU-seq ; Med14-Med17-doubleAID)

Project description:Architectural Mediator subunits are differentially essential for global transcription in yeast (RNA-seq/4tU-seq ; Med14-Med17-doubleAID)

| PRJNA610077 | ENA

Architectural Mediator subunits are differentially essential for global transcription in yeast (RNA-seq/4tU-seq ; Med14-Med17-doubleAID)

Project description:This project aims to understand the function of Mediator and the interplay in transcription in S. cerevisiae. Thus we analyzed total and newly synthesized RNA levels in a conditional Med14 and Med17 depletion strain. For this purpose we used an auxin inducible degron system system to specifically induce the degradation Med14 and Med17 by addition of auxin into the culture medium. We measured transcript levels after 30 min auxin or DMSO (control) treatment induction of degradation of Med14 and Med17 by the addition of auxin (30 min) or with the carrier DMSO (control) followed by a 6 min labelling of newly synthesized RNA with 4-thiouracil (4tU). In parallel wiltype S.pombe cells were labelled with 4tU for 6min during midlog growth phase. Prior to RNA extraction (Ribopure Yeast Kit, Ambion) our labelled S.cerevisiae cells of interest were mixed with labelled S.pombe cells as a spike to allow normalization against an exogenous reference (ratio 3 S .cerevisiae for 1 S.pombe cell. From the total RNA we purified the 4tU labelled fraction of RNAs containing 4tU. Both the total RNA and the purified newly synthesized RNAs will then be subject to RNA-sequencing after ribosomal RNA depletion. In summary, we will provide 8 samples for this project containing RNA from both S.cerevisiae and S.pombe. The sample read counts were normalized with size factors computed by the median-of-ratios method proposed by Anders and Huber (Anders et al. 2010) on S. pombe genes to make these counts comparable between samples.

2020-03-04 | GSE146321 | GEO

Architectural Mediator subunits are differentially essential for global transcription in yeast (ChIP-seq)

Project description:Architectural Mediator subunits are differentially essential for global transcription in yeast (ChIP-seq)

| PRJNA607312 | ENA

Architectural Mediator subunits are differentially essential for global transcription in yeast (RNA-seq/4tU-seq)

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-03-04 | GSE146346 | GEO

4tU RNA-seq from wild-type and Rpb7-QHF cells

Project description:Our structural and biochemical studies show that S. cerevisiae RNA Polymerase II (RNAPII) homodimerizes through the stalk domain (formed by the Rpb4-Rpb7 subunits). To explore the biological impact of disrupting this interaction we introduced a triple point mutation at the RNAPII dimerization interface in Rpb7 (Q96A, H97A, F109K). To test the impact of the dimerization mutant on RNA synthesis and 3' end processing in WT and Rpb7-QHF cells, we labelled nascent transcripts with 4tU which enabled subsequent biotinylation and purification of newly-synthesized transcripts. Nascent transcripts were then used to prepare strand-specific RNA-seq libraries.

2023-12-31 | E-MTAB-13370 | biostudies-arrayexpress

Total and 4-thiouracil (4tU) labeled RNA samples of wild-type Schizosaccharomyces pombe strain ED666 (BIONEER)

Project description:RNA-seq of S.pombe total and metabolically labeled (4tU) RNA fractions with independent biological replicates. 4tU-labeling allows the isolation of newly transcribed RNAs. Samples differ in the duration of exposure with 4tU (2,4,6,8,10 minutes). For a detailed description of the labeling protocol see Miller et al. (MSB, 2011) and Schulz et al. (Cell, 2014).

2016-05-11 | E-MTAB-3653 | biostudies-arrayexpress

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