Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

4e770c42-cbe9-472c-976c-46298b50acaa - samples

ABSTRACT: 10x Genomics linked read data used in variant phasing and de novo assembly scaffolding for the EGYPT individual (mapped against GRCh38).

PROVIDER: EGAD00001006035 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

c0960a1a-7f29-4c8e-bf11-177f7445ed4d - samples

Project description:This is the PacBio long read data used for performing de novo assembly of the EGYPT individual (mapped against GRCh38).

| EGAD00001006034 | EGA

De novo assembly of siRNA immunity in wild plants

Project description:We describe an application of deep sequencing and de novo assembly of short RNA reads to investigate small interfering (si)RNAs mediated immunity in leaf samples from eight tree taxa naturally occurring in Wytham Woods, Oxfordshire, UK. BLAST search for homologues of contigs in the GenBank identified siRNA populations against a number of RNA viruses and a Ty1-copia retrotransposons in these tree species. Small RNA sequencing and de novo assembly

2012-06-01 | E-GEOD-22079 | biostudies-arrayexpress

Xdrop - Oxford Nanopore long read seqeuncing of HAP1 and HepG2 tRNA gene deletion clones

Project description:This dataset contains Xdrop followed by oxford nanopore long read sequencing performed in target tRNA gene deletion clones in HAP1 (t72) and HepG2 (t15). By applying de novo assembly based approach to Xdrop-LRS data, we identified Cas9-induced on-target genomic alteration.

2022-09-16 | E-MTAB-10652 | biostudies-arrayexpress

Xdrop - Oxford Nanopore long read seqeuncing of HepG2 genetic modified clones

Project description:This dataset contains Xdrop followed by oxford nanopore long read sequencing performed in target tRNA gene deletion (t8) and intergenic region deletion (i50) clones in HepG2 . By applying de novo assembly based approach to Xdrop-LRS data, we identified Cas9-induced on-target genomic alteration.

2022-09-16 | E-MTAB-11327 | biostudies-arrayexpress

De novo assembly of transcripts from RNAseq study to examine developmental regulation of Strongyloides stercoralis transcripts with a focus on infectious third-stage larvae

Project description:De novo assembly of transcripts from RNAseq study to examine developmental regulation of S. stercoralis transcripts with a focus on infectious third-stage larvae. Raw read files are part of the submission 'RNAseq of S. stercoralis PV001 strain developmental stages' accession E-MTAB-1164, associated ENA accessions are included where appropriate .

2012-06-30 | E-MTAB-1184 | biostudies-arrayexpress

The brain transcriptome of the wolf spider, Schizocosa ocreata

Project description:The goal of this study was to lay the groundwork for comparative transcriptomics of sex differences in the brain of wolf spiders, a non-model organism of the pyhlum Euarthropoda, by generating transcriptomes and analyzing gene expression. To examine differences in sex-differential gene expression, short read transcript sequencing and de novo transcriptome assembly were performed. Messenger RNA (mRNA) was isolated from dissected brain tissue of male and female subadult and mature wolf spiders (Schizocosa ocreata). The data consist of short read sequences for the two different life stages in each sex. Computational analyses on these data include de novo transcriptome assembly, using Trinity and CAP3 assembly suites, and differential expression analysis using the edgeR package. Sample-specific and combined transcriptomes, gene annotations, and differential expression results are described in this data note and are available from associated database submissions.

2021-03-12 | GSE168766 | GEO

Helianthemum almeriense mycorrhizal symbiosis

Project description:Illumina HiSeq technology was used to generate mRNA profiles from Helianthemum almeriense in three different conditions: non-mycorrhizal plant, well-watered mycorrhizal plant and drought-stressed mycorrhizal plant. Paired-end reads of 75 bp were generated and aligned to a de novo transcriptome assembly from H. almeriense, which was performed using Megahit version 1.1.3 and transcripts from each condition were mapped onto the de novo transcriptome with Bowtie2 version 2.3.0.

2020-10-21 | GSE155042 | GEO

Transcriptome Analysis of Immunity- and Reproduction-related Differential Gene Expression in Parasitized Locusta migratoria

Project description:The transcriptome and DGE analysis of the fat body and ovary of L. migratoria based on the Illumina short-read sequencing technology and De novo assembly. Research on the trade-offs between immunity and reproduction is contributing significantly to the understanding of the fitness of organisms in nature.

2017-05-01 | GSE57437 | GEO

Catharanthus Transcriptome and Gene Expression

Project description:In this study, we aim to present a global transcriptome analysis of medicinal plant, Catharanthus roseus. We generated about 343 million high-quality reads from three tissues (leaf, root and flower) using Illumina platform. We performed an optimized de novo assembly of the reads and estimated transcript abundance in different tissue samples. The transcriptome dynamics was studied by differential gene expression analyses among tissue samples. We collected different tissue samples from the mature plants. Total RNA isolated from these tissue samples was subjected to Illumina sequencing. The sequence data was further filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were used for de novo assembly optimization. The reads were further mapped to the Catharanthus transcripts via CLC Genomics Workbench and differential gene expression analysis was performed using DESeq software.

2014-07-29 | E-GEOD-57326 | biostudies-arrayexpress

Zhang2020 - Draft metabolic reconstruction model of Atlantic cod liver generated from gadMorTrinity and iHepatocyte2322

Project description:This is an auto-generated model with COBRA Matlab toolbox. The gadMorTrinigy de novo Trinity transcript assembly and peptide sequences are available at https://doi.org/10.6084/m9.figshare.c.5168303.v2

2020-10-26 | MODEL2010090002 | BioModels

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