Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Artificial sequences

ABSTRACT: Simulated high-throughput genome sequencing on synthetic genomes (VarSim)

PROVIDER: PRJNA263417 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR1732000_1.fastq.gz	Fastqsanger.gz
	SRR1732000_2.fastq.gz	Fastqsanger.gz
	SRR1732001_1.fastq.gz	Fastqsanger.gz
	SRR1732001_2.fastq.gz	Fastqsanger.gz
	SRR1732002_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 26

Similar Datasets

Arabidopsis thaliana small RNAs sequences identified using high-throughput 454 sequencing technology

2007-02-01 | GSE6682 | GEO

Synthetic reversed sequences reveal default genomic states

Project description:Pervasive transcriptional activity is observed across diverse species. The genomes of extant organisms have undergone billions of years of evolution, making it unclear whether these genomic activities represent effects of selection or ‘noise’1,2,3,4. Characterizing default genome states could help understand whether pervasive transcriptional activity has biological meaning. Here we addressed this question by introducing a synthetic 101-kb locus into the genomes of Saccharomyces cerevisiae and Mus musculus and characterizing genomic activity. The locus was designed by reversing but not complementing human HPRT1, including its flanking regions, thus retaining basic features of the natural sequence but ablating evolved coding or regulatory information. We observed widespread activity of both reversed and native HPRT1 loci in yeast, despite the lack of evolved yeast promoters. By contrast, the reversed locus displayed no activity at all in mouse embryonic stem cells, and instead exhibited repressive chromatin signatures. The repressive signature was alleviated in a locus variant lacking CpG dinucleotides; nevertheless, this variant was also transcriptionally inactive. These results show that synthetic genomic sequences that lack coding information are active in yeast, but inactive in mouse embryonic stem cells, consistent with a major difference in ‘default genomic states’ between these two divergent eukaryotic cell types, with implications for understanding pervasive transcription, horizontal transfer of genetic information and the birth of new genes.

2024-01-16 | GSE252482 | GEO

marine metagenome

Project description:Synthetic marine metagenome high-throughput sequencing

| PRJNA182065 | ENA

To explore the relationship between new gene expression / mutation and survival of patients in colorectal cancer

Project description:Interventions: Case vs control:No Primary outcome(s): High-throughput sequencing Study Design: Case-Control study

| 2676067 | ecrin-mdr-crc

The mutation spectrum revealed by paired genome sequences from a lung cancer patient

Project description:This SuperSeries is composed of the following subset Series: GSE20574: Agilent 244A aCGH array for comparison of lung tumor CNA to high-throughput sequencing data GSE20578: Assessment of mutation on expression levels GSE20584: Affymetrix SNP6.0 array for comparison of lung tumor and adjacent normal to high-throughput sequencing data Refer to individual Series

2010-05-27 | E-GEOD-20585 | biostudies-arrayexpress

POEMS syndrome Immunoglobulin sequences

Project description:Full-length immunoglobulin high-throughput sequencing in POEMS syndrome

| PRJEB35157 | ENA

Identification of variant distribution in ethanol-selected sRNA libraries

Project description:In this study we subjected a library of synthetic sRNAs to multiple rounds of ethanol selection and analyzed changes in sRNA variant abundance by high-throughput sequencing.

2019-01-22 | GSE125161 | GEO

Systematic discovery of cap-independent translation sequences in human and viral genomesÂ

Project description:To investigate gene specificity at the level of translation in both the human genome and viruses we devised a high-throughput bicistronic assay to quantify cap-independent translation. We uncover thousands of novel cap-independent translation sequences and provide insights on the landscape of translational regulation in both human and viruses. We find extensive translational elements in the 3â untranslated region (3âUTR) of human transcripts and the polyprotein region of un-capped RNA viruses. Through the characterization of regulatory elements underlying cap-independent translation activity we identify potential mechanisms of secondary structure, short sequence motif and base-pairing with the 18S rRNA. Furthermore, we systematically map the 18S rRNA regions for which reverse complementary enhance translation. Thus we provide insights into the mechanisms of translational control in humans and viruses. high-throughput bicistronic assay for obtaining cap-independent translation measurements of 55,000 fully designed sequences in parallel using fluorescence-activated cell sorting and high-throughput DNA sequencing (FACS-seq).

2015-10-23 | E-GEOD-74277 | biostudies-arrayexpress

Arabidopsis thaliana small RNAs sequences identified using high-throughput 454 sequencing technology

Project description:To determine the extent to which the major small RNA pathways functions across the Arabidopsis thaliana genome, small RNA populations from several tissues of wild-type (wt) and mutant plants were amplified by RT-PCR and sequenced using high-throughput 454 sequencing technology. Keywords: small RNAs, high-throughput sequencing Amplicons were prepared by 5' and 3' adaptor ligation and RT-PCR using small RNA fractions from inflorescence tissue (containing stage 1-12 flowers) of wt Col-0 plants, mutants with defects in each DCL gene (dcl1-7, dcl2-1, dcl3-1, dcl4-2), and mutants with defects in each RDR gene for which a function has been established (rdr1-1, rdr2-1, rdr6-15). Amplicons from whole seedlings (3 day post-germinations) were prepared from Col-0 and rdr6-15 plants. Small RNA preparations from leaf samples of Col-O that were either uninoculated or inoculated by Pseudomonas syringae pv tomato (DC3000hrcC) for 1 hr and 3 hr were also sequenced.

2007-02-01 | E-GEOD-6682 | biostudies-arrayexpress

Computational and Analytical Framework for Small RNA Profiling by High-Throughput Sequencing (standards)

Project description:The purpose of this work was to describe a computational and analytical methodology for profiling small RNA by high-throughput sequencing. The datasets here were used to develop synthetic oligoribonucleotides as spike-in standards.

2009-06-03 | GSE14695 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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