Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Low coverage genome sequencing of the tamarind weevil Sitophilus linearis

PROVIDER: PRJNA647347 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12360587_1.fastq.gz	Fastqsanger.gz
	SRR12360587_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 2 of 2

Similar Datasets

Project description:Low coverage genome sequencing of granary weevil Sitophilus granarius

| PRJNA647520 | ENA

Project description:Low coverage genome sequencing of maize weevil Sitophilus zeamais to analyse the repeatome

| PRJNA647530 | ENA

Project description:Sitophilus linearis transcriptome

| PRJNA473923 | ENA

Project description:low-coverage Genome sequencing

| PRJNA786773 | ENA

Chromosomal microarray analysis for validation of the WGS-based CNV detection results in recurrent miscarriage couples

Project description:In order to validate of CNV detection from low-coverage whole-genome sequencing in the blood samples from recurrent miscarriage couples, we employed a customized array Comparative Genomics Hybridization (aCGH, Agilent) approach as chromosomal microarray analysis (CMA) in present study for a cohort of 78 DNA samples from blood. CMA results were compared with low-coverage whole-genome sequencing detection results. 100% consistency was obtained in pathogenic or likely pathogenic CNVs detection.

2017-11-01 | GSE83941 | GEO

Identification of driver genes in uterine leiomyosarcoma: low-coverage WGS

Project description:Low coverage whole-genome sequencing have been performed on uterine leiomyosarcoma to uncovered novel potential driver genes and recurrently affected pathways.

2018-07-02 | E-MTAB-5763 | biostudies-arrayexpress

Mosquitoes low coverage genome sequencing

Project description:Mosquitoes low coverage genome sequencing

| PRJEB22896 | ENA

Mapping meiotic crossovers in Arabidopsis using low-coverage whole-genome sequencing

Project description:Whole-genome DNA libraries were prepared from a population of just under 100 Col/Ler F1 backcrossed to Col. Low-coverage whole-genome sequencing was used to map meiotic crossovers in this population following the protocol described in Rowan et al., 2015, doi: 10.1534/g3.114.016501.

2015-10-15 | E-MTAB-3926 | biostudies-arrayexpress

Acute deletion of TET enzymes results in aneuploidy in mouse embryonic stem cells through decreased expression of Khdc3 (Whole Genome Sequencing [Low Coverage])

Project description:Low coverage whole genome sequencing (lc-WGS) from inducible Tet TKO (Tet iTKO) and control (Ctrl) mouse ESCs (mESC), as well as for germline Dnmt TKO mESCs. mESCs were sorted to isolate the Live/Dead dye and Thy1.2 negative CD326+GFP+ population representing the mESCs populations responsive to the tamoxifen treatment. The cells were resuspended in FACS buffer and filtered with a 70 µM filter before sorting. These bulk-population samples were analyzed by using low coverage Whole Genome Sequencing (lc-WGS).

2022-10-01 | GSE214402 | GEO

Evaluation of copy number variation detection between high-resolution array CGH and low-coverage short-insert and mate-pair whole-genome sequencing

Project description:In principle, whole-genome sequencing (WGS) of the human genome even at low coverage offers higher resolution for genomic copy number variation (CNV) detection compared to array-based technologies, which is currently the first-tier approach in clinical cytogenetics. There are, however, obstacles in replacing array-based CNV detection with that of low-coverage WGS such as cost, turnaround time, and lack of systematic performance comparisons. With technological advances in WGS in terms of library preparation, instrument platforms, and data analysis algorithms, obstacles imposed by cost and turnaround time are fading. However, a systematic performance comparison between array and low-coverage WGS-based CNV detection has yet to be performed. Here, we compared the CNV detection capabilities between WGS (short-insert, 3kb-, and 5kb-mate-pair libraries) at 1X, 3X, and 5X coverages and standardly used high-resolution arrays in the genome of 1000-Genomes-Project CEU genome NA12878. CNV detection was performed using standard analysis methods, and the results were then compared to a list of Gold Standard NA12878 CNVs distilled from the 1000-Genomes Project. Overall, low-coverage WGS is able to detect drastically more (approximately 5 fold more on average) Gold Standard CNVs compared to arrays and is accompanied with fewer CNV calls without secondary validation. Furthermore, we also show that WGS (at ≥1X coverage) is able to detect all seven validated deletions larger than 100 kb in the NA12878 genome whereas only one of such deletions is detected in most arrays. Finally, we show that the much larger 15 Mbp Cri-du-chat deletion can be clearly seen at even 1X coverage from short-insert WGS.

2018-06-26 | GSE105092 | 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