Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Whole-genome bisulfite sequencing of two silkworm strains

PROVIDER: PRJNA639002 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12001100_1.fastq.gz	Fastqsanger.gz
	SRR12001100_2.fastq.gz	Fastqsanger.gz
	SRR12001101_1.fastq.gz	Fastqsanger.gz
	SRR12001101_2.fastq.gz	Fastqsanger.gz
	SRR12001102_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 16

Similar Datasets

A multicenter translational biomarker phase II trial of regorafenib in patients with non-resectable pretreated colorectal cancer.

Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS). Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).

| 2533916 | ecrin-mdr-crc

MicroRNAs of Bombyx mori identified by Solexa sequencing

Project description:Background: MicroRNA (miRNA) and other small regulatory RNAs contribute to the modulation of a large number of cellular processes. We sequenced three total RNA libraries prepared from the whole body, and the anterior and posterior silk glands of Bombyx mori, with a view to expanding the repertoire of silkworm miRNAs and exploring transcriptional differences in miRNAs between segments of the silk gland. Results: With the aid of large-scale Solexa sequencing technology, we validated 244 unique miRNA genes, including 191 novel and 53 previously reported genes, corresponding to 309 loci in the silkworm genome. Interestingly, 24 unique miRNAs were widely conserved from invertebrates to vertebrates; 12 unique ones were limited to invertebrates and 33 were confined to insects; whereas the majority of the newly identified miRNAs were silkworm-specific. We identified 21 clusters and 42 paralogs of miRNAs in the silkworm genome. However, sequence tags showed that paralogs or clusters are not prerequisites for coordinated transcription and accumulation. The majority of silkworm-specific miRNAs are located in transposable elements, and display significant differences in abundance between the anterior and posterior silk glands. Conclusions: Conservative analysis revealed that miRNAs serve as phylogenetic markers and function in evolutionary signaling. The newly identified miRNAs greatly enriched the repertoire of insect miRNAs, and provide insights into miRNA evolution, biogenesis, and expression in insects. The differential expression of miRNAs in the anterior and posterior silk glands supports their involvement as new layers in the regulation of the silkworm silk gland. Sequencing three total RNA pools of the whole silkworm body from 5th-instar day-3 larvae, and anterior and posterior silkworm silk glands, using the latest sequencing Solexa technology

2010-02-01 | E-GEOD-17965 | biostudies-arrayexpress

BN and SHR rat expression profiling left ventricle

Project description:Gene expression data was generated in BN and SHR rats to correlate gene expression differences with CpG methylation differences detected between the strains by whole-genome bisulfite sequencing.

2013-07-19 | E-MTAB-1702 | biostudies-arrayexpress

MicroRNAs of Bombyx mori identified by Solexa sequencing

2010-02-01 | GSE17965 | GEO

Whole genome bisulfite sequencing of MDCK cells, before and after TGFB-induced epithelial-mesenchymal transition

Project description:Whole genome bisulfite sequencing of MDCK cells, before and after TGFB-induced epithelial-mesenchymal transition Sequencing of bisulfite converted DNA from MDCK cells untreated, and after a 30 days treatment with TGF beta

2014-08-14 | E-GEOD-43697 | biostudies-arrayexpress

Effect of Chromomethylase-2 and Dicer-like-3 knockouts on DNA methylation

Project description:Whole genome bisulfite sequencing was performed on Chromomethylase-2 and Dicer-like-3 knockout mutants in order to confirm the results from genome wide association mapping and to identify the respective genomic regions that they target. Bisulfite sequencing of knockout mutants and WT controls

2015-03-28 | E-GEOD-66017 | biostudies-arrayexpress

WGBS

Project description:Whole genome bisulfite sequencing

| OEX00003766 | NODE

Amino acid substitutions in ribosomal protein RpsU enable switching between high fitness and multiple-stress resistance in Listeria monocytogenes

Project description:A previously described low-fitness, high stress-resistant, variant of Listeria monocytogenes LO28 WT was subjected to an experimental evolution regime, selecting (in two parallel lines) for increased fitness in unstressed conditions. Evolved variants with increased fitness reverted to WT-like stress resistance. Whole genome sequencing and proteomics were used to identify differences between the ancestral and evolved strains.

2023-10-03 | PXD022732 | Pride

Highly integrated epigenome maps in Arabidopsis - whole genome shotgun bisulfite sequencing

Project description:Part of a set of highly integrated epigenome maps for Arabidopsis thaliana. Keywords: Illumina high-throughput bisulfite sequencing Whole genome shotgun bisulfite sequencing of wildtype Arabidopsis plants (Columbia-0), and met1, drm1 drm2 cmt3, and ros1 dml2 dml3 null mutants using the Illumina Genetic Analyzer.

2008-04-21 | E-GEOD-10966 | biostudies-arrayexpress

Population-based whole-genome bisulfite sequencing in multiple human tissues

Project description:Analysis of human population methylome variation in adipose tissue and whole blood at single-site resolution by whole genome bisulfite sequencing.

2015-10-26 | E-MTAB-3549 | biostudies-arrayexpress

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