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

QPRO-seq of mouse F1 cells

ABSTRACT: Polymerase Run-On Sequencing (PROseq) performed as previously described (cite original Kwak et al., 2013 and qPRO Judd et al., 2020) with some minor changes. Data is obtained from two F1 hybrid embryonic stem cells (ES) obtained by crossing C57BL/6NJ with CAST/EiJ and SPRET/EiJ, respectively. The resulting cell line underwent triple genetic knockout for the endogenous methyltransferase enzymes (DNMT TKO). PROseq data was obtained by permeabilizing the cells, performing a 2 biotin run-on reaction using biotin-11-UTP and biotin-11-CTP and subsequent enrichments steps for biotinylated RNA during the library preparation. This results in the enrichment of nascent transcripts, including enhancer RNA.

INSTRUMENT(S): NextSeq 500, NextSeq 2000

ORGANISM(S): Mus musculus

SUBMITTER: Charles Girardot

PROVIDER: E-MTAB-14459 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Using GRO-seq experiments to determine the mechanism of C. elegans dosage compensation's control of transcription

Project description:Dosage Compensation is required to correct for uneven gene dose between the sexes. We utilized global run-on sequencing (GRO-seq) to examine how Caenorhabditis elegans dosage compensation reduces transcription of X-linked genes. To facilitate these experiments, we required accurate 5M-bM-^@M-^Y-ends of genes that have been missing due to a co-transcriptional trans-splicing event common in nematodes. We developed a modified GRO-seq protocol to identify TSSs that are supported by transcription, and determined that TSSs lie more than 1 kb upstream of the previously annotated TSS for nearly one-quarter of all genes. We then investigated the changes that occur in transcriptionally engaged RNA Polymerase when dosage compensation is disrupted, and find that dosage compensation controls recruitment of RNA Polymerase to X-linked genes. GRO-seq experiments (two biological replicates) were performed in nuclei from many wild-type states and a dosage compensation mutant

2013-06-18 | E-GEOD-43084 | biostudies-arrayexpress

Development of GRO-cap (GRO-seq followed by 5'-cap enrichment) to map transcription start sites in C. elegans

Project description:Dosage Compensation is required to correct for uneven gene dose between the sexes. We utilized global run-on sequencing (GRO-seq) to examine how Caenorhabditis elegans dosage compensation reduces transcription of X-linked genes. To facilitate these experiments, we required accurate 5M-bM-^@M-^Y-ends of genes that have been missing due to a co-transcriptional trans-splicing event common in nematodes. We developed a modified GRO-seq protocol to identify TSSs that are supported by transcription, and determined that TSSs lie more than 1 kb upstream of the previously annotated TSS for nearly one-quarter of all genes. We then investigated the changes that occur in transcriptionally engaged RNA Polymerase when dosage compensation is disrupted, and find that dosage compensation controls recruitment of RNA Polymerase to X-linked genes. GRO-cap reactions were performed with TAP, and without TAP as a control.

2013-06-18 | E-GEOD-43085 | biostudies-arrayexpress

Condensin Controls Recruitment of RNA Polymerase II to Achieve X-Chromosome Dosage Compensation

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

2013-06-18 | E-GEOD-43087 | biostudies-arrayexpress

RIp-chip experiements with the Exo2 and Eti1 proteins

Project description:We have used RIp-chip to identify mRNAs that coprecipitae with specific proteins, and later used the protein RNA interactions to predict protein-protein associations. To test whether some of the interactions we see require intact polysomes (that is, ribosomes translating mRNAs) we treated the extracts (and, in some cases, also the cells) with different compounds. In this case, we have a standard protocol, one in which the buffers contain EDTA, and one in which it includes puromycin.

2014-05-05 | E-MTAB-1856 | biostudies-arrayexpress

Genome-wide identification of RNA polymerase, RpoD, and RpoS binding sites in Klebsiella pneumoniae MGH 78578

Project description:Genome-wide identification of RNA polymerase (RNAP) binding sites were performed in Klebsiella pneumoniae MGH 78578 (KP). Anti-RNAP is used to capture the RNAP in KP. ChIP-chip was performed on tiling array specifically made for KP. Comparison ChIP by anti-RNAP antibody vs ChIP by normal mouse IgG (control, mock IP)

2012-12-31 | E-GEOD-35927 | biostudies-arrayexpress

Pombe_polyA_mapping_NGS_v3

Project description:Regulatory elements in the 3M-^R untranslated regions (UTRs) of eukaryotic mRNAs influence mRNA localization, translation, and stability. The length of these regions is determined by the location at which mRNAs are cleaved and polyadenylated. The use of alternative polyadenylation sites is common, and can be regulated in different situations. I present here a new method to identify cleavage and polyadenylation sites (CSs) at the genome-wide level. The approach is strand-specific, avoids RNA enzymatic modification steps that can introduce sequence-specific biases, and uses molecular barcodes to ensure that every identified CS originates from an individual RNA molecule. I applied to create the first comprehensive genome-wide map of polyadenylation sites in the fission yeast Schizosaccharomyces pombe, comprising the analysis of over two million individual mRNAs that defined 10,422 major CSs. CSs were identified for 90% of coding genes and 15% of non-coding RNAs. Alternative polyadenylation was prevalent in both groups, with 61% and 49% of all detected genes, respectively, displaying more than one CS. The specificity of the cleavage reaction was gene-specific, resulting in highly variable levels of heterogeneity in the length of the 3' UTRs. Finally, I show that for both coding and non-coding genes the most common regulatory motif associated with CSs in fission yeast is the canonical human AAUAAA sequence.

2013-11-19 | E-MTAB-1642 | biostudies-arrayexpress

RNA-Seq of six mammals

Project description:Homologous vertebrate tissues express a highly conserved set of transcribed genes; paradoxically, expression of tRNAs that are required to translate mRNAs into proteins have been reported to be divergent. To resolve this paradox, we mapped the genome-wide occupancy of pol III in primary tissues isolated from six mammals. We confirmed that the specific tRNA genes bound by pol III, as well as the extent and stability of binding, can vary substantially among mammalian tissues, and we discovered that this divergence is far greater between species. We combined pol III occupancy from genomically discrete tRNA loci into collective binding into isoacceptor classes and then into amino acid-based isotype classes, and at each step we found increasing conservation. At the level of amino acid isotypes, pol III binding is almost invariant among all the tissues and species profiled. Thus, the basal transcriptional machinery is constrained collectively in its synthesis of functional tRNA isotypes, despite rapid divergence of polymerase binding to specific tRNA genes. Part of experiment series: RNA-Seq E-MTAB-424, ChIP-Seq E-MTAB-958

2011-07-29 | E-MTAB-424 | biostudies-arrayexpress

Genome-wide gene expression and identification of RNA polymerase, RpoD, and RpoS binding sites in Klebsiella pneumoniae MGH 78578

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

2012-12-31 | E-GEOD-36055 | biostudies-arrayexpress

Time course GRO-seq analysis of the human GM12878 lymphoblasts upon Sendai Virus infection.

Project description:Densely sampled time course GRO-seq analysis was performed to determine global transcriptional activities at both enhancers and promoters upon Sendai Virus infection.

2018-10-07 | E-MTAB-6047 | biostudies-arrayexpress

Comparative genomic hybridisation of Staphylococcus aureus isolates from healthy adults

Project description:Comparative genomic hybridisation of 20 Staphylococcus aureus isolates from healthy adults.

2013-11-15 | E-MTAB-1672 | biostudies-arrayexpress