Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Capture and sequence analysis of RNAs with 5'-hydroxyl termini in S. cerevisiae

ABSTRACT: Data from 5OH-seq experiments to map RNAs with 5'-hydroxyl termini in S. cerevisiae 17 samples of yeast RNA analyzed by 5OH-seq. 2 Replicates: +/- Xrn1,+/- Tm, +/- SAP. 1 replicate: pre-fragmented RNA

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Jay Hesselberth

PROVIDER: E-GEOD-61527 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Next Generation Sequencing Facilitates Quantitative Analysis of CNE1-mock, CNE1-BART1, CNE-BART3, CNE1-BART7 cells

Project description:By using NGS-derived retinal transcriptome profiling (RNA-seq) to compare the gene expression profiling between 4 differently treated NPC cells Examination of different gene expression in EBV-miRNA-BART1/3/7 lentivirus and their control infected nasopharyngeal carcinoma cells.

2015-06-30 | E-GEOD-43126 | biostudies-arrayexpress

RNA sequencing of bone marrow CD34+ cells from myelodysplastic syndrome patients with and without SF3B1 mutation and from healthy controls

Project description:The splicing factor SF3B1 is the most commonly mutated gene in the myelodysplastic syndromes (MDS), particularly in patients with refractory anemia with ring sideroblasts (RARS). MDS is a disorder of the hematopoietic stem cell and we thus studied the transcriptome of CD34+ cells from MDS patients with SF3B1 mutations using RNA-sequencing. Genes significantly differentially expressed at the transcript and/or exon level in SF3B1 mutant compared to wildtype cases include genes involved in MDS pathogenesis (ASXL1, CBL), iron homeostasis and mitochondrial metabolism (ALAS2, ABCB7, SLC25A37) and RNA splicing/processing (PRPF8, HNRNPD). Many genes regulated by a DNA damage-induced BRCA1-BCLAF1-SF3B1 protein complex showed differential expression/splicing in SF3B1 mutant cases. Our data indicate that SF3B1 plays a critical role in MDS by affecting the expression and splicing of genes involved in specific cellular processes/pathways, many of which are relevant to the known RARS pathophysiology, suggesting a causal link. RNA-Seq was performed to compare the transcriptome of bone marrow CD34+ cells from eight MDS patients with SF3B1 mutation, four MDS patients with no known splicing mutation and five healthy controls.

2014-11-22 | E-GEOD-63569 | biostudies-arrayexpress

Identification of non-coding RNAs expressed by Burkholderia cenocepacia during Caenorhabditis elegans infection

Project description:We investigated the transcriptome of B. cenocepacia under infection of the nematode Caenorhabditis elegans. RNAs fractions extracted from C. elegans infected with B. cenocepacia were used for Illumina high throughput sequencing using the CappableSeq method. The main objective of this work was to identify small non-coding RNAs (sRNAs) expressed by B. cenocepacia under infection conditions.

2024-01-10 | E-MTAB-12592 | biostudies-arrayexpress

Rif1 Prevents Resection of DNA Breaks and Promotes Immunoglobulin Class Switching

Project description:DNA double-strand breaks (DSBs) represent a threat to the genome because they can lead to loss of genetic information and chromosome rearrangements. The DNA repair protein p53 binding protein 1 (53BP1) protects the genome by limiting nucleolytic processing of DSBs by a mechanism that requires its phosphorylation, but whether it does so directly is not known. Here we identify Rapl-interacting factor 1 (Rif1) as an Ataxia-Telangiectasia Mutated (ATM) phosphorylation-dependent interactor of 53BP1, and show that absence of Rif1 results in 5M-bM-^@M-^Y-3M-bM-^@M-^Y DNA end resection in mice. Consistent with enhanced DNA resection, Rif1 deficiency impairs DNA repair in the G1 and S phases of the cell cycle, interferes with class switch recombination (CSR) in B lymphocytes, and leads to accumulation of chromosome DSBs. Study of Rif1 DNA-end protection activity against resection via analysis of single-stranded DNA binding protein RPA and Rad51 accumulation at sites of AID-induced DNA damage by ChIP-seq. All samples shown in Fig. 4 are included (controls and test samples, 7 samples in total).

2013-03-01 | E-GEOD-42298 | biostudies-arrayexpress

Genome-wide distribution of histones modifications in mouse ESC Rif1+/+ and Rif1-/-

Project description:Analyzed histones modifications: H3K9 H3K4 H3K27 H4K20

2015-12-24 | E-MTAB-3743 | biostudies-arrayexpress

Tissue-specific changes in Tcrb conformation

Project description:We report the changes in Tcrb interactome upon transitioning from DN to DP stage of thymocyte development Examination of the interactomes of Eb and Trbv5 viewpoints in RAG-deficient DN and DP thymocytes

2015-07-08 | E-GEOD-68955 | biostudies-arrayexpress

Drosophila melanogaster S2 cells nucleosome occupancy data after simulation by heat killed Staphylococcus aureus

Project description:The innate immune response is among the strongest genomic responses and is conserved across all metazoa. Although transcription during the innate immune response has been well studied, the associated chromatin reorganizations are largely uncharacterized. Here we show that Drosophila S2 cells stimulated with Staphylococcus aureus display a dynamic change in genome-wide nucleosome occupancy and sensitivity. We found a widespread and transient nucleosomal loss peaking at 30 minutes post stimulation, and we demonstrated that the regulatory potentials of nucleosomes differ following stimulation. In addition, we identified differentially sensitive nucleosomes with response-specific potentials. Our results provide high-resolution nucleosome-distribution maps of the fly genome, revealing chromatin's role in: the innate immune response to Gram-positive bacteria, response-specific regulatory-factor binding, and nucleosome sensitivity. We identify functional chromatin regulatory features associated with immune response, and lay a foundation for a framework linking general and locus-specific roles for nucleosomes in immune regulation. Drsophila S2 cells at 0hr, 30minutes, 1hr and 4hr post heat-killed Staphylococcus aureus stimulation

2015-02-28 | E-GEOD-66367 | biostudies-arrayexpress

An alternative pluripotent state confers interspecies chimaeric competency [ChIP-seq]

Project description:Here we show that by simple modulation of extrinsic signaling pathways, a new class of pluripotent stem cells, referred to as region selective epiblast stem cells (rsEpiSCs), could be efficiently derived from different stages of the early embryo. rsEpiSCs share features of primed pluripotency yet are distinct from EpiSCs in their molecular characteristics and ability to colonize post-implantation embryos. We performed ChIP-seqencing experiments using antibodies against H3K4me3 and H3K27me3, comparing conventional EpiSCs and rsEpiSCs, as well as comparing conventional human H1 ESCs and human H1 ESCs cultured in mouse rsEpiSCs based culture conditions (H1 rsESCs). Examination of 2 different histone modifications (H3K4me3, H3K27me3) in 2 pluripotent stem cell types in mouse and human.

2015-05-06 | E-GEOD-60604 | biostudies-arrayexpress

Genome wide maps of replicative polymerase contributions to the fully replicated yeast genome

Project description:We report the application of high through-put tag sequencing to measure the location and strand of DNA embedded ribonucleotides in the yeast genome. Mutations in the catalytic subunits of the polymerases (pol1-L868M, pol2-M644G and pol3-L612M) lead to the increased incorporation of ribonucleotides during DNA replication, providing an in vivo label with which to track the contribution of each polymerase to the fully replicated genome. Yeast strains used in this study are deleted for rnh201, encoding the catalytic subunit of the RNase H2 gene so that embedded ribonucleotides are not rapidly removed by ribonucleotide excision repair following DNA replication. Analysis of this data demonstrates that polymerase alpha contributes to the fully replicated genome. Sequencing of DNA embedded ribonucleotides in S. cerevisiae strains to map the contribution of replicative polymerases to the fully replicated genome.

2015-01-26 | E-GEOD-64521 | biostudies-arrayexpress

Parsing the interferon transcriptional network and its disease associations

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-11-24 | E-GEOD-75306 | biostudies-arrayexpress