Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Prairie Rattlesnake transcriptomic sequencing

PROVIDER: PRJNA477004 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR19928811_1.fastq.gz	Fastqsanger.gz
	SRR19928811_2.fastq.gz	Fastqsanger.gz
	SRR19928812_1.fastq.gz	Fastqsanger.gz
	SRR19928812_2.fastq.gz	Fastqsanger.gz
	SRR19928813_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 84

Similar Datasets

Investigating patterns of chromatin accessibility, histone modifications, and insulation involved in rattlesnake venom gene regulation

Project description:We generated ATAC-seq data for pre- and post-extraction venom gland samples and H3K4me3, H3K27ac, and CTCF ChIP-seq from post-extraction venom gland samples from the Prairie Rattlesnake to investigate patterns of chromatin accessibility, transcription factor binding, and insulation during venom production, and to identify open promoters and active enhancer regions.

2022-04-07 | GSE169217 | GEO

Project description:Prairie Rattlesnake whole genome sequencing

| PRJNA476794 | ENA

Snakes on a Plain: Complex Biotic and Abiotic Factors Determine Venom Variation in North America's Widest Ranging Rattlesnake

Project description:Mass-spectrometric analysis of prairie rattlesnake venoms

2022-06-03 | MSV000089601 | MassIVE

Project description:Gene expression study of venom production in the Prairie Rattlesnake venom gland

| PRJNA716163 | ENA

Diverse gene regulatory mechanisms alter rattlesnake venom gene expression at fine evolutionary scales

Project description:Understanding and predicting the relationships between genotype and phenotype is often challenging, largely due to the complex nature of eukaryotic gene regulation. A step towards this goal is to map how phenotypic variation evolves through genomic changes that modify gene regulatory interactions. Using the Prairie Rattlesnake (Crotalus viridis) and related species, we integrate mRNA-seq, proteomic, ATAC-seq and whole genome resequencing data to understand how specific evolutionary modifications to gene regulatory network components produce variation in venom gene expression. Through comparisons within and between species, we find a remarkably high degree of gene expression and regulatory network variation across even a shallow level of evolutionary divergence. We use these data to test hypotheses about the roles of specific trans-factors and cis-regulatory elements, how these roles may vary across venom genes and gene families, and how variation in regulatory systems drive variation in venom phenotypes. Our results illustrate that variation in chromatin and genotype at regulatory elements plays major roles in modulating expression. However, we also find that enhancer deletions, variation in transcription-factor expression, and variation in activity of the insulator protein CTCF also impact downstream venom phenotypes. Our findings provide insight into the diversity and gene-specificity of gene regulatory features and highlight the value of comparative studies to link gene regulatory network variation to phenotypic variation.

2024-07-17 | GSE254420 | GEO

Transcriptomic regulations underlying pair-bond formation and maintenance in the socially monogamous male and female prairie vole

Project description:Background: The ability to form enduring social bonds is characteristic of human nature and as a result, impairments in social affiliation are central features of severe neuropsychiatric disorders including autism spectrum disorders and schizophrenia. Due to its ability to form long-term pair-bonds, the socially monogamous prairie vole (Microtus ochrogaster) has emerged as an excellent model to study the neurobiology of social attachment. Despite the enduring nature of the bond, however, surprisingly few genes have been implicated in the pair-bonding process in either sex. Results: Using RNA-sequencing, we aimed at identifying the transcriptomic regulations in the nucleus accumbens (NAc) underlying the formation and maintenance of a pair-bond in male and female prairie voles and found sex-specific response patterns despite similar behavioral indicators of pair-bond establishment. Indeed, 24 hrs of cohabitation with an opposite-sex partner induced widespread transcriptomic changes that remained sustained to some extent in females after 3 weeks, but returned to baseline before a second set of regulations in males. This led to a highly sexually-biased NAc transcriptome in the later phase of the bond related to processes such as neurotransmission, protein turnover, and DNA transcription. In particular, we found sex-specific alterations of mitochondrial dynamics following cohabitation, with a shift towards fission in males. Conclusions: In addition to identifying the genes, networks, and pathways involved in the pair-bonding process in the NAc, our work illustrates the vast extent of sex differences in the molecular mechanisms underlying pair-bonding in prairie voles, and paves the way to further our understanding of the complex social bonding process.

2023-04-28 | GSE150080 | GEO

Addressing the challenge of soil metaproteome complexity by improving metaproteome depth of coverage

Project description:Investigation of LC-MS/MS approaches to improve soil metaproteome depth of coverage for a Kansas prairie native soil

2018-11-21 | PXD008895 | Pride

Genome wide identification of enhancer regions in the retrosplenial cortex of the prairie vole, Microtus ochrogaster.

Project description:We use ChIP-seq targeting histone 3 lysine 4 mono-methylation (H3K4me1) to identify putative enhancer sites genome-wide, in the retrosplenial cortex of adult prairie vole males. ChIP samples were generated by targeting a known enhancer mark (H3K4me1) in chromatin extracted from the retrosplenial cortex of 8 males. Illumina libraries were prepared from ChIP and INPUT DNA and sequenced on Illimuna HiSeq 2500 platform.

2015-12-11 | E-GEOD-73670 | biostudies-arrayexpress

Becoming monogamous quickly: Adaptive evolution of a pallidal enhancer at the prairie vole Avpr1a locus

Project description:We use ChIP-seq targeting histone 3 lysine 27-acetylation (H3K27ac) to identify putative enhancer sites genome-wide in the ventral pallidum cortex of adult prairie voles

2018-01-31 | GSE85826 | GEO

Sistrurus catenatus

Project description:Sistrurus catenatus (eastern massasauga rattlesnake) genomic and transcriptomic data

| PRJNA930705 | ENA