Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq analysis of the budding yeast ctk1∆ and rad6∆ strains and prp45(1-169) ctk1∆ and prp45(1-169) rad6∆ double mutant strains

ABSTRACT: RNA-seq analysis of the budding yeast ctk1∆ and rad6∆ strains and prp45(1-169) ctk1∆ and prp45(1-169) rad6∆ double mutant strains

PROVIDER: PRJEB18556 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR1753306_1.fastq.gz	Fastqsanger.gz
	ERR1753306_2.fastq.gz	Fastqsanger.gz
	ERR1753307_1.fastq.gz	Fastqsanger.gz
	ERR1753307_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

RNA-seq analysis of the budding yeast rad6 strain and prp45(1-169) rad6 double mutant strain

Project description:Prp45 is a budding yeast NineTeen-Complex associated factor, which plays a role in pre-mRNA splicing. Because its human ortholog, SNW1/SKIP, is known to functionally and physically interact with factors involved in transcription elongation and chromatin modifications, it was suggested to be one of the coupling factors which functionally connect splicing and transcription. To determine whether the yeast Prp45 has this function as well we tested genetic interactions between prp45(1-169) allele and deletions of histone modifiers and transcription elongation regulators. RNA-seq analysis was performed to address the changes in transcription and/or splicing in strains deleted in rad6, a kinase phosphorylating serine 2 of the C-terminal domain of RNA Polymerase II and an E2 enzyme for H2BK123 monoubiquitination, respectively, and the corresponding double mutant with prp45(1-169). Total RNA was isolated by combining phenol-chlorophorm extraction with MasterPure Yeast RNA Purification Kit (Epicentre). Ribodepletion, library preparation and sequencing were performed by BGI Genomics.

2024-08-30 | E-MTAB-5336 | biostudies-arrayexpress

RNA-seq analysis of the budding yeast set1∆ strain and prp45(1-169) set1∆ double mutant strain

Project description:Prp45 is a budding yeast NineTeen-Complex associated factor, which plays a role in pre-mRNA splicing. Because its human ortholog, SNW1/SKIP, is known to functionally and physically interact with factors involved in transcription elongation and chromatin modifications, it was suggested to be one of the coupling factors which functionally connect splicing and transcription. To determine whether yeast Prp45 has this function as well we tested the genetic interactions between prp45(1-169) allele and deletions of histone modifiers and transcription elongation regulators. RNA-seq analysis was performed to address the changes in transcription and/or splicing in strains deleted in set1, a histone methyltransferase responsible for H3K4 methylation, and the corresponding prp45(1-169) set1 double mutant. Total RNA was isolated by combining phenol-chlorophorm extraction with MasterPure Yeast RNA Purification Kit (Epicentre). Ribodepletion, library preparation and sequencing were performed by BGI Genomics.

2024-08-30 | E-MTAB-5335 | biostudies-arrayexpress

RNA-seq analysis of the budding yeast prp45(1-169) strain (a scarless truncation)

Project description:Prp45 is a budding yeast NineTeen-Complex associated factor, which plays a role in pre-mRNA splicing. prp45(1-169) is a temperature-sensitive truncation allele expressing only the first 169 amino acids (the full-length protein consists of 379 amino acids). RNA-seq analysis was performed to determine changes in transcription and splicing in cells with prp45(1-169) allele prepared by the CRISPR/Cas9 method as a scarless truncation, i.e. with no tags and with preserved endogenous 3' UTR. Total RNA was isolated by combining phenol-chlorophorm extraction with MasterPure Yeast RNA Purification Kit (Epicentre). Ribodepletion, library preparation and sequencing were performed by BGI Genomics.

2024-08-30 | E-MTAB-5334 | biostudies-arrayexpress

Genomic DNA sequencing of budding yeast strains

Project description:Genomic DNA sequencing of budding yeast strains

| PRJNA470814 | ENA

RNA-seq analysis of budding yeast wild type (BY4741) and prp45(1-169) mutant

Project description:Prp45 is a budding yeast NineTeen-Complex associated factor, which plays a role in pre-mRNA splicing. In addition to its documented involvement in the second step of splicing, here we show that it is important in the early stages of co-transcriptional spliceosome assembly as well. To determine the overall splicing efficiency of prp45 mutant cells and to reveal how the efficiency depends on the sequences which define introns (whether they are consensual or non-consensual), we performed RNA-seq analysis of prp45(1-169) and corresponding wild-type cells (two biological replicates each). Total RNA was isolated by combining phenol-chlorophorm extraction with MasterPure Yeast RNA Purification Kit (Epicentre). Ribodepletion, library preparation and sequencing were performed by BGI Genomics.

2017-02-10 | E-MTAB-5149 | biostudies-arrayexpress

RNA-seq analysis of the budding yeast set1∆ strain and prp45(1-169) set1∆ double mutant strain

Project description:RNA-seq analysis of the budding yeast set1∆ strain and prp45(1-169) set1∆ double mutant strain

| PRJEB18555 | ENA

Transcription profiling of wild type and Rad6 or Rad18 knock-out yeast to identify genes regulated by Rad6/Rad18

Project description:To identify the yeast genes whose transcription is regulated by Rad6/Rad18

2008-02-20 | E-MEXP-1463 | biostudies-arrayexpress

Chromatin recruitment of Rad6 determines H3K4me3 in Saccharomyces cerevisiae

Project description:Project abstract : The trimethylation of histone H3 lysine 4 (H3K4me3) is a crucial factor in defining the promoter regions of active genes in all eukaryotes ranging from Saccharomyces cerevisiae (yeast) to humans. In budding yeast, this trimethylation process facilitated by the Set1 complex results in H3K4me3 requiring a prior mono-ubiquitination at the histone H2BK123 residue (H2Bub) by E2 enzyme Rad6 and E3 enzyme Bre1. A previous in vitro study suggested that ubiquitinated H2B directly facilitates H3K4me3. However, even low levels of global H2Bub is sufficient for the required H3K4me3 in yeast cells, thereby indicating that other factors resulting in the H2Bub-dependent H3K4me3 remain unknown. This study revealed the high level of correlation of H3K4me3 with chromatin recruitment of Rad6 at the genome-wide level. Rad6 is confirmd to interact and co-localize with Swd2/Cps35, a key factor for the H2Bub-dependent H3K4me3 in genes with high levels of H3K4me3 and intronic genes rather than non-intronic genes. This study therefore provides a mechanistic insight of the H2Bub-Rad6- Swd2/Cps35-H3K4me3 axis and its potential role in RNA biogenesis.

2022-06-07 | GSE146296 | GEO

RNA-seq analysis of the budding yeast prp45(1-169) strain (a "scarless" truncation)

Project description:RNA-seq analysis of the budding yeast prp45(1-169) strain (a "scarless" truncation)

| PRJEB18554 | ENA

RNA-seq analysis of budding yeast wild type (BY4741) and prp45(1-169) mutant

Project description:RNA-seq analysis of budding yeast wild type (BY4741) and prp45(1-169) mutant

| PRJEB16749 | ENA