Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq analysis of fission yeast WT, and cbf11DBM and Pcut6MUT mutants in standard and ammonium-supplemented complex media, and upon cerulenin treatment

ABSTRACT: Transcriptome analyses of the fission yeast Schizosaccharomyces pombe cells. The following genotypes were analyzed: WT, cbf11DBM (Cbf11 mutant with compromised DNA binding), Pcut6MUT (scrambled Cbf11 binding site in the promoter of the cut6 gene). Cells were grown to exponential phase in the complex YES medium, or in YES supplemented with ammonium chloride. Also, the effects of cerulenin treatment (20 μM cerulenin or DMSO for 1 hour) on exponentially growing WT cells were determined.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Schizosaccharomyces pombe

SUBMITTER: Martin Převorovský

PROVIDER: E-MTAB-13305 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq analysis of fission yeast mga2∆ and mga2∆ cbf11∆ mutants in standard and ammonium-supplemented complex media

Project description:Transcriptome analyses of the fission yeast Schizosaccharomyces pombe cells lacking the CSL transcription factor cbf11 and/or mga2. Both genotypes were analyzed when grown to exponential phase in the complex YES medium, or in YES supplemented with ammonium chloride. The aim was to identify genes regulated by Mga2 and/or Cbf11, and how mutant phenotypes are affected by the presence of a good nitrogen source.

2024-04-05 | E-MTAB-13303 | biostudies-arrayexpress

ChIP-nexus analysis of fission yeast transcription factors Cbf11, Cbf11DBM, Cbf12, Cbf12DBM, Mga2 and Fkh2

Project description:Genome-wide identification of transcription factor (TF) binding sites in the genome of the fission yeast Schizosaccharomyces pombe. The ChIP-nexus method was used. TFs included were: Cbf11-TAP and Cbf12-TAP (and their DBM mutants with impaired DNA binding), TAP-Mga2, and Fkh2-TAP (as an irrelevant control TF). IPs from an untagged WT strain were also analyzed. Cbf11-related IPs were performed from exponential cultures, while Cbf12-related IPs were performed from stationary cultures. YES complex medium was used for all cultivations.

2024-04-05 | E-MTAB-13258 | biostudies-arrayexpress

RNA-seq analysis of fission yeast wild type and cbf11∆ mutant in standard and ammonium-supplemented complex media

Project description:Transcriptome analyses of the fission yeast Schizosaccharomyces pombe cells lacking the CSL transcription factor cbf11. Wild-type cells were used as a control. Both genotypes were analyzed when grown to exponential phase in the complex YES medium, or in YES supplemented with ammonium chloride. The aim was to identify Cbf11-regulated genes, and cbf11-associated phenotypes are affected by the presence of a good nitrogen source.

2024-04-05 | E-MTAB-13302 | biostudies-arrayexpress

ChIP-seq of histone H3 and H3K9me2 in WT and dbl2 mutant fission yeast

Project description:The aim was to compare the levels of histone H3 dimethylation at lysine 9 (H3K9me2) in wild-type and dbl2 knock-out Schizosaccharomyces pombe cells. Fission yeast cultures were grown in the complex YES medium to exponential phase and chromatin immunoprecipitation was carried out using anti-H3 and anti-H3K9me2 antibodies. Two independent biological replicates were performed. The resulting IP and input DNA samples were sequenced using Illumina sequencing (35 nt PE). H3K9me2 occupancy in each sample was normalized to the corresponding total H3 occupancy, and normalized H3K9me2 levels were compared between WT and dbl2 knock-out.

2020-10-02 | E-MTAB-9619 | biostudies-arrayexpress

Histone modification (H3, H3K9ac, H3K9me2) ChIP-seq in WT and cbf11KO strains of Schizosaccharomyces pombe

Project description:Acetylation and dimethylation of lysine 9 on histone H3 are prominent marks of euchromatin and heterochromatin, respectively. Moreover, histone acetylation has been linked to lipid metabolism. We have previously identified the transcription factor Cbf11 as a regulator of lipid metabolism and genome integrity in the fission yeast. Cut6, the acetyl-CoA carboxylase, is one of direct targets of Cbf11. To link the role of Cbf11 in lipid metabolism and chromatin regulation we have performed ChIP-seq of H3K9ac, H3K9me2 and H3 in WT and cbf11KO strains of Schizosaccharomyces pombe in three biological replicates. Strain genotypes: wild type JB32 (h+s); cbf11 knock-out MP44 (h+ cbf11::natR).

2021-11-03 | E-MTAB-11081 | biostudies-arrayexpress

RIP-seq identification of RNAs enriched on RNA polymerase and the primary sigma factor (sigma A) in Corynebacterium glutamicum

Project description:6S RNA is a small RNA with specific secondary structure that associates with the complex of RNA polymerase (RNAP) and the primary sigma factor in majority of bacteria. In mycobacteria, Ms1 interacts with the RNAP core without the sigma factor and probably replaces 6S RNA. Ms1 has been predicted in many actinobacterial species, except of corynebacteria. To identify RNAs that have a similar function as Ms1 or 6S RNA in Corynebacterium glutamicum, we sequenced RNAs that co-immunoprecipitated with RNAP or the primary sigma factor sigma A. We also sequenced total RNA isolated from the lysate (input sample). We expect that Ms1 or 6S RNA homologs are enriched in RNA polymerase or sigma A samples compared to the inputs. The experiment was performed in exponential and stationary phase of growth.

2024-02-09 | E-MTAB-13608 | biostudies-arrayexpress

Histone modification (H3, H3K9ac, H3K9me2) ChIP-seq in Pcut6MUT strain of Schizosaccharomyces pombe

Project description:Acetylation and dimethylation of lysine 9 on histone H3 are prominent marks of euchromatin and heterochromatin, respectively. Moreover, histone acetylation has been linked to lipid metabolism. Cut6, the acetyl-CoA carboxylase, is one of direct targets of Cbf11 which we have previously identified as a regulator of lipid metabolism. Here we have performed ChIP-seq of H3K9ac, H3K9me2 and H3 in Pcut6MUT strain (promoter mutant of cut6 with abolished Cbf11 binding) of Schizosaccharomyces pombe in three biological replicates. Strain genotypes: cut6 promoter mutant MP636 (h- Pcut6MUT).

2023-05-24 | E-MTAB-11082 | biostudies-arrayexpress

RIP-seq identification of RNAs enriched on RNA polymerase and the primary sigma factor (sigma A) in Mycobacterium tuberculosis

Project description:6S RNA is a small RNA with specific secondary structure that associates with the complex of RNA polymerase (RNAP) and the primary sigma factor in majority of bacteria. In Mycobacterium smegmatis, Ms1 interacts with the RNAP core without the sigma factor and probably replaces 6S RNA. It is currently unknown if Ms1 homolog (MTS2823) in M. tuberculosis also binds to RNAP core. We sequenced RNAs that co-immunoprecipitated with RNAP or the primary sigma factor sigma A and total RNA isolated from the lysate (input sample). We expect that putative Ms1 or 6S RNA homologs are enriched in RNA polymerase or sigma A sample compared to the input.

2024-02-09 | E-MTAB-13584 | biostudies-arrayexpress

Eic1 links Mis18 with the CCAN/Mis6/Ctf19 complex to promote CENP-A assembly

Project description:CENP-A chromatin the foundation for kinetochore assembly in all eukaryotes. CENP-A is incorporated outside of S phase and depends on its chaperone HJURPScm3, and Mis18 in vertebrates and fission yeast. The recruitment of Mis18 and HJURPScm3 to centromeres is cell cycle regulated. Vertebrate Mis18 associates with Mis18BP1KNL2 and RbAp46/48Mis16/Hat2. Mis18BP1KNL2 is critical for the recruitment of Mis18 and HJURPScm3 to vertebrate centromeres. However, no ortholog of Mis18BP1KNL2 has been identified in fission yeast, consequently it remains unknown how the key Cnp1CENP-A loading factor Mis18 is recruited. We identify two novel Mis18-interacting proteins (Eic1 and Eic2) in fission yeast. Our analyses show that Eic1 and Eic2 are components of a Mis18 complex. Eic1 is essential to maintain normal Cnp1CENP-A levels at centromeres and therefore is crucial for kinetochore integrity whereas Eic2 is dispensable. Eic1 also associates with components of the large constitutive CCAN/Sim4/Ctf19 complex. Our findings suggest that Eic1 is the functional counterpart of Mis18BP1KNL2 and acts as a link with constitutive kinetochore components to allow the temporally regulated recruitment of the Mis18 Cnp1CENP-A loader. 100bp paired end ChIP-Seq analysis of GFP tagged Eic1, Eic2, Scm3, and Mis18 with sonicated whole cell extract input DNA in asynchornous Schizosaccharomyces pombe cells.

2014-05-19 | E-GEOD-54685 | biostudies-arrayexpress

Transcriptome analysis (Agilent microarrays) of WT, cbf11 and cbf12 Schizosaccharomyces pombe strains treated with camptothecin

Project description:The aim was to determine expression levels in untreated cells and cells treated with 20 micromolar camptothecin (CPT) for 2 hours. And the to compare the cbf11 and cbf12 deletion mutants with WT. Cells were grown to exponential phase in YES at 32°C, aliquots of cultures were collected (sample \\"control\\"), remaining cells were treated with CPT (dissolved in DMSO) and harvested 2 hours later. Two independent biological experiments were performed. A pooled RNA sample was prepared for each independent run that contained aliquots of all 6 individual RNA samples. RNA was hybridized on 2-colour Agilent microarrays against the corresponding pooled sample (with dye swap).

2024-04-05 | E-MTAB-13621 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data