Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: deep resequencing of rice RH78 and SSI variant ERV1

PROVIDER: PRJNA657451 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12771900.fastq.gz	Fastqsanger.gz
	SRR12771901.fastq.gz	Fastqsanger.gz
	SRR12771902_1.fastq.gz	Fastqsanger.gz
	SRR12771902_2.fastq.gz	Fastqsanger.gz
	SRR12771903.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 159

Similar Datasets

Project description:Deep resequencing of rice RH78 and SSI variant ERV1 and the inbred F2 population

| PRJNA658863 | ENA

Whole genome profiling of murine lymphocytes and statistical validation of a panel of immune molecules to predict vaccine efficacy against Mycobacterium tuberculosis

Project description:Transcriptional profiling of splenic lymphocytes derived from vaccinated mice, and ex-vivo exposed to M.tb.-infected macrophages in culture. Splenocytes from mice innoculated with Mycobacterium bovis BCG Pasteur (PAS), or M. bovis BCG Copenhagen (SSI), or heat killed BCG SSI (HK), or uninfected control, were ex vivo co-cultured with mouse bone marrow macrophages previously infected with M. tb.

2021-08-06 | GSE135592 | GEO

Multi-omics resources for targeted agronomic improvement of pigmented rice

Project description:<p>Pigmented rice (<em>Oryza sativa L.</em>) is a rich source of nutrients, but pigmented lines typically have long life cycles and limited productivity. Here we generated genome assemblies of 5 pigmented rice varieties and evaluated the genetic variation among 51 pigmented rice varieties by resequencing an additional 46 varieties. Phylogenetic analyses divided the pigmented varieties into four varietal groups: Geng-japonica, Xian-indica, circum-Aus and circum-Basmati. Metabolomics and ionomics profiling revealed that black rice varieties are rich in aromatic secondary metabolites. We established a regeneration and transformation system and used CRISPR-Cas9 to knock out three flowering time repressors (Hd2, Hd4 and Hd5) in the black Indonesian rice Cempo Ireng, resulting in an early maturing variety with shorter stature. Our study thus provides a multi-omics resource for understanding and improving Asian pigmented rice.</p>

2023-03-27 | MTBLS3320 | MetaboLights

Project description:SSI EQAs

| PRJNA886874 | ENA

Project description:SSI-Acinetobacter

| PRJNA1084269 | ENA

MV-4-11 cells treated with novel SCD inhibitor SSI-4

Project description:Novel SCD inhibitor SSI-4 demonstrated good toxicity profile in experimental animals and induced cell toxicity across multiple acute myeloid leukemia models. Therefore, we treated sensitive AML cell line MV-4-11 with SSI-4 (1 µM) for 24h with or without the addition of sodium oleate (1 µM) that rescues toxicity phenotype.

2024-08-23 | E-MTAB-13174 | biostudies-arrayexpress

Project description:SSI-Gram Negative

| PRJNA1117753 | ENA

The profiling of gene expression in the roots of rice

Project description:In order to research the genetic mechanism of deep rooting in rice, we performed the transcriptomic assay of the roots in rice.

2017-07-12 | GSE84297 | GEO

Karlsson_et_al_OSA

Project description:This experiment was conducted to generate targeted resequencing data covering a region associated with osteosarcoma in greyhounds. 8 greyhounds diagnosed with osteosarcoma and 7 greyhounds without tumors were sequenced. DNA from the 15 dogs was used to prepare libraries and hybrid capture performed to enrich the region of interest prior to paired-end sequencing using Illumina Genome Analyzer II. The reads were aligned to the dog-genome CanFam2.0 using bwa and pre-processed using Picard and GATK. Variant discovery was performed using GATK. The resulting list of variants were used in the study to finemap the associated region and look for causal variants. We submit the preprocessed BAM-files that still have all reads although some reads are flagged. We also submit the resulting vcf-file with called and filtered variants in all individuals.

2013-11-16 | E-MTAB-1984 | biostudies-arrayexpress

MiRNA analysis of rice seed germination

Project description:In this study, we sequenced the sRNAs population from embryos of 0, 12, and 24 HAI rice seeds using next-generation deep sequencing technology. A series of miRNAs were identified, including both known and novel miRNAs. We also predicted the potential targets for the miRNAs. RT-PCR and 5’ RACE assay were performed to confirm some deep sequencing and target prediction results. This study provides the unique composition and expressional profiles of miRNAs and their potential regulations in the embryo at the early stages of rice seed germination.

2015-10-02 | GSE73657 | 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