Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proctacanthus coquilletti

ABSTRACT: Proctacanthus coquilletti de novo genome and transcriptome

PROVIDER: PRJNA343047 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	SRR4346725_1.fastq.gz	Fastqsanger.gz
	SRR4346725_2.fastq.gz	Fastqsanger.gz
	SRR4372731_1.fastq.gz	Fastqsanger.gz
	SRR4372731_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 5

Similar Datasets

Xylota coquilletti

Project description:Xylota coquilletti overview

| PRJNA759972 | ENA

Xylota coquilletti

Project description:Xylota coquilletti mitochondrion, complete genome Raw sequence reads

| PRJNA757554 | ENA

Using the Bovine SNP60k array to discover de novo copy number variations in aging bulls and fibroblasts

Project description:We have identified de novo copy number variations (CNVs) generated in ageing bulls. Blood samples from eight bulls were collected and SNP arrayed in a prospective design over 30 months allowing us to differentiate de novo CNVs from constant CNVs that are present throughout the sampling period. Quite remarkably, the total number of CNVs doubled over the 30-month period, as we observed an almost equal number of de novo and constant CNVs (107 vs. 111 or 49% vs. 51%, respectively). Twice as many de novo CNVs emerged during the second half of the sampling schedule as in the first part. It suggests a dynamic generation of de novo CNVs in the bovine genome that becomes more frequent, as the age of the animal progresses. In a second experiment de novo CNVs were detected through in vitro ageing of bovine fibroblasts by sampling passage #5, #15 and #25. De novo CNVs also became more frequent, but the proportion of them was only ~25% of the total number of CNVs (21 vs. 64). Temporal generation of de novo CNVs resulted in increasing genome coverage. Genes and quantitative trait loci overlapping de novo CNVs were further investigated for ageing related functions.

2017-03-03 | GSE95612 | GEO

Translatome and transcriptome analyses reveal novel small peptides enhance rice herbicide resistance

Project description:We combined multi-omics approaches including de novo transcriptome assembly, ribosome profiling and MS-based peptidomics to study the global role of mRNA translation and small ORFs (sORFs) in rice herbicide resistant mutant.

2021-05-11 | PXD025927 |

SRA of transcriptome of Hevea brasiliensis

Project description:We first report the use of next-generation massively parallel sequencing technologies and de novo transcriptome assembly to gain insight into the wide range of transcriptome of Hevea brasiliensis. The output of sequenced data showed that more than 12 million sequence reads with average length of 90nt were generated. Totally 48,768 unigenes (mean size = 488 bp) were assembled through transcriptome de novo assembly, which represent more than 3-fold of all the sequences of Hevea brasiliensis deposited in the GenBank. Assembled sequences were annotated with gene descriptions, gene ontology and clusters of orthologous group terms. Total 37,373 unigenes were successfully annotated and more than 10% of unigenes were aligned to known proteins of Euphorbiaceae. The unigenes contain nearly complete collection of known rubber-synthesis-related genes. Our data provides the most comprehensive sequence resource available for study rubber tree and demonstrates the availability of Illumina sequencing and de novo transcriptome assembly in a species lacking genome information. The transcriptome of latex and leaf in Hevea brasiliensis

2011-09-01 | E-GEOD-26514 | biostudies-arrayexpress

SPOCD1 is a novel executor of piRNA-directed DNA methylation that links MIWI2 to the de novo DNA methylation machinery

Project description:In mammals, the acquisition of the germline from the soma provides the germline with an essential challenge, the necessity to erase and reset genomic methylation. In the male germline RNA-directed DNA methylation silences young active transposable elements (TEs). The PIWI protein MIWI2 (PIWIL4) and its associated PIWI-interacting RNAs (piRNAs) are proposed to tether MIWI2 to nascent TE transcripts and instruct DNA methylation. The mechanism by which MIWI2 directs de novo TE methylation is poorly understood but central to the immortality of the germline. Here, we define the interactome of MIWI2 in foetal gonocytes that are undergoing de novo genome methylation and identify a novel MIWI2-associated factor, SPOCD1, that is essential for young TE methylation and silencing. The loss of Spocd1 in mice results in male specific infertility and does not impact on piRNA biogenesis nor localization of MIWI2 to the nucleus. SPOCD1 is a nuclear protein and its expression is restricted to the period of de novo genome methylation. We found SPOCD1 co-purified in vivo with DNMT3L and DNMT3A, components of the de novo methylation machinery as well as constituents of the NURD and BAF chromatin remodelling complexes. We propose a model whereby tethering of MIWI2 to a nascent TE transcript recruits repressive chromatin remodelling activities and the de novo methylation apparatus through its association with SPOCD1. In summary, we have identified a novel and essential executor of mammalian piRNA-directed DNA methylation.

2020-06-01 | E-MTAB-7997 | biostudies-arrayexpress

10x Genomics Chromium WGS of Tursiops Aduncus

Project description:This data and additional PacBio Sequel data were collected from the same individual for a de-novo genome assembly

2022-01-01 | E-MTAB-7310 | biostudies-arrayexpress

Heterocypris incongruens

Project description:Heterocypris incongruens de novo transcriptome

| PRJDB6884 | ENA

Thevenetimyia californica

Project description:Thevenetimyia sp. de novo transcriptome

| PRJNA343898 | ENA

Hyalella azteca

Project description:Hyalella azteca de novo transcriptome