Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ena-DATASET-DCPTCUHK-17-01-2021-15:35:46:856-29 - samples

ABSTRACT: In this study, we enhanced 5mC detection using SMRT sequencing by holistically analyzing kinetic signals of a DNA polymerase and sequence context for every base within a measurement window. We employed a convolutional neural network to train a methylation classification model.

PROVIDER: EGAD00001006875 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

Genomewide detection of cytosine methylation by single molecule real-time sequencing

Project description:5-methylcytosine (5mC) is an important type of epigenetic modification. In this study, we enhanced 5mC detection using SMRT sequencing by holistically analyzing kinetic signals of a DNA polymerase and sequence context for every base within a measurement window. We employed a convolutional neural network to train a methylation classification model. This methodology has provided a system for simultaneous genome-wide genetic and epigenetic analyses.Ã‚Â

| EGAS00001004642 | EGA

Prosit: Proteome-wide prediction of peptide tandem mass spectra by deep learning

Project description:In this study, we extended the ProteomeTools peptide library (PROPEL, see PXD004732 and PXD010595) to train a deep neural network resulting in chromatographic retention time and fragment ion intensity predictions for (tryptic) peptides that exceed the quality of the experimental data.

2019-05-30 | PXD010871 | Pride

Long read sequencing of nascent RNA from S. cerevisiae and S. pombe

Project description:Long read SMRT cDNA sequencing of nascent RNA from exponentially growing S. cerevisiae and S. pombe cells was employed to obtain transcription elongation and splicing information from single transcripts. Nascent RNA was prepared from the yeast chromatin fraction (Carrillo Oesterreich, Preibisch, Neugebauer, Mol Cell 2010). The nascent 3â?? end was labeled with a 3â?? DNA adaptor through ligation. The adaptor sequence served as template for full-length reverse transcription and double-stranded cDNA was obtained in a PCR (gene-specific or transcriptome-wide). SMRT DNA sequencing libraries were prepared subsequently. Nascent RNA profiles for mainly intron-containing genes were generated with long-read SMRT cDNA sequencing.

2016-03-24 | E-GEOD-70906 | biostudies-arrayexpress

NCoR1, SMRT, Polymerase II and input ChIP-Seq

Project description:NCoR1, SMRT, Polymerase II and input ChIP-Seq

| PRJEB2940 | ENA

Prosit: Proteome-wide prediction of peptide tandem mass spectra by deep learning

2021-03-12 | MSV000087047 | MassIVE

Long-read nascent RNA sequencing from S. pombe

Project description:Long-read SMRT cDNA sequencing of nascent RNA from exponentially growing S. pombe cells was employed to obtain transcription elongation and splicing information from single transcripts. Nascent RNA was prepared from the yeast chromatin fraction (Carrillo Oesterreich, Preibisch, Neugebauer, Mol Cell 2010). The nascent 3’ end was labeled with a 3’ DNA adaptor through ligation. The adaptor sequence served as template for full-length reverse transcription and double-stranded cDNA was obtained in a transcriptome-wide PCR. SMRT DNA sequencing libraries were prepared subsequently.

2018-05-18 | GSE104679 | GEO

Long read sequencing of nascent RNA from S. cerevisiae and S. pombe

Project description:Long read SMRT cDNA sequencing of nascent RNA from exponentially growing S. cerevisiae and S. pombe cells was employed to obtain transcription elongation and splicing information from single transcripts. Nascent RNA was prepared from the yeast chromatin fraction (Carrillo Oesterreich, Preibisch, Neugebauer, Mol Cell 2010). The nascent 3’ end was labeled with a 3’ DNA adaptor through ligation. The adaptor sequence served as template for full-length reverse transcription and double-stranded cDNA was obtained in a PCR (gene-specific or transcriptome-wide). SMRT DNA sequencing libraries were prepared subsequently.

2016-03-24 | GSE70906 | GEO

RNA Polymerase II ChipSeq measurement of Pcf11 mutations in yeast

Project description:RNA Polymerase II ChipSeq measurement of Pcf11 mutations in yeast

| PRJNA785637 | ENA

A biochemical basis for toggling enhancers from the active to poised state in B cells

Project description:BCL6 is crucial for B-cell activation and lymphomagenesis. We used integrative genomics to explore BCL6 mechanism in normal and malignant B-cells. Surprisingly, BCL6 assembled distinct complexes at enhancers vs. promoters. At enhancers BCL6 preferentially recruited SMRT, which mediated H3K27 deacetylation through HDAC3, antagonized p300 activity and repressed transcription, but without decommissioning enhancers. This provides a biochemical basis for toggling enhancers from the active to poised state. Virtually all SMRT was bound with BCL6 suggesting that in B-cells BCL6 uniquely sequesters SMRT from other factors. In promoters BCL6 preferentially recruited BCOR, but most potently repressed promoters where it formed a distinctive ternary complex with SMRT and BCOR. Promoter repression was associated with decreased H3K36me3, H3K79me2 and Pol II elongation, linking BCL6 to transcriptional pausing. We identified the binding patterns of BCL6, SMRT, NCOR and BCOR corepressors in normal germinal center B cells and a DLBCL cell line (OCI-Ly1) using ChIP-seq. Additionally we treated lymphoma cells with siRNA against BCL6 and a non-targeted siRNA (NT control) and performed RNA-seq to identify the genes bound and repressed by BCL6. RNA-seq experiments were performed at 24h and 48h after siRNA treatments. Additional biological triplicate RNA-seq experiments were performed at 48h after BCL6 knockdown. Furthermore, a series of histone mark ChIP-seq and RNA polymerase ChIP-seq (total, Ser5-P and Ser2-P) were preformed to capture the chromatin states associated with the formation of BCL6 corepressor complexes.

2013-08-05 | E-GEOD-29282 | biostudies-arrayexpress

Project description:Train wastewater microbial community diversity

| PRJNA573808 | ENA