Ontology highlight
ABSTRACT:
PROVIDER: PRJNA897816 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22164505.fastq.gz | Fastqsanger.gz | |||
| SRR22164506.fastq.gz | Fastqsanger.gz | |||
| SRR22164507.fastq.gz | Fastqsanger.gz | |||
| SRR22164508.fastq.gz | Fastqsanger.gz | |||
| SRR22164509.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 128 |
Similar Datasets
Project description:Whole genome sequencing of 6 woolly mammoths
| PRJEB29510 | ENA
Project description:Complete genome sequences for two woolly mammoths
| PRJEB7929 | ENA
Project description:Chromosomes 8 and X from 98 woolly mammoths
| PRJEB22575 | ENA
Project description:Whole-genome sequencing of 13 Siberian woolly mammoths
| PRJEB52803 | ENA
Project description:Analyses of ancient DNA typically involve sequencing the surviving short oligonucleotides, and aligning to genome assemblies from related, modern species. Here, we report that skin from a female woolly mammoth (†Mammuthus primigenius) which died 52,000 years ago retained its ancient genome architecture. We use PaleoHi-C to map chromatin contacts and assemble its genome, yielding twenty-eight chromosome-length scaffolds. Chromosome territories, compartments, loops, Barr bodies, and inactive-X chromosome (Xi) superdomains persist. The active and inactive genome compartments in mammoth skin more closely resemble Asian elephant skin than other elephant tissues. Our analyses uncover new biology. Differences in compartmentalization reveal genes whose transcription was potentially altered in mammoths vs. elephants. Mammoth Xi has a tetradic architecture, not bipartite like human and mouse. We hypothesize that, shortly after this mammoth’s death, the sample spontaneously freeze-dried in the Siberian cold, leading to a glass transition that preserved subfossils of ancient chromosomes at nanometer scale.
2024-05-22 | GSE268050 | GEO
Project description:The investigation of archaeological samples, which are of inestimable value, requires minimally destructive or non-destructive sampling techniques. One of the most promising and recent non-invasive techniques is known under the acronym EVA, an ethylene vinyl acetate film which avoids contamination and proteins damages. The present work reports the results of the metaproteomic analysis performed on the middle part of a trunk, and on the portion of a trunk tip tissue of two different woolly mammoths some 40000 years’ old. In particular, proteins were extracted by applying EVA (Ethylene-Vinyl Acetate) films to the surface of these tissues belonging to two Mammuthus primigenus specimens, discovered in two regions located in the Russian Far East, and then investigated via a shotgun MS-based approach. This approach allowed to obtain two interesting results: i) an indirect description of the habitat of these two mammoths, and ii) an improved sequence characterization of the alpha-1 type I collagen (col1a1), the major component of type I collagen. Sequence characterization of the col1a1 highlighted some differences between M. primigenius and other Proboscidea together with the identification of two potentially diagnostic amino acidic mutations that could be used to reliably distinguish the Mammuthus primigenius respect to the other two genera of elephantids (i.e. Elephas and Loxodonta), and the extinct American mastodon (i.e. Mammut americanum). The results were validated through the level of deamidation and other diagenetic chemical modifications of the sample peptides, which were used to discriminate the “original” endogenous peptides from contaminant ones.
2022-05-19 | PXD029558 | Pride
Project description:During ripening of fruits stored under low temperatures, a number of physiological alterations which are manifested in a reduction of juice content take place, resulting in the apparition of woolly fruits. Modifications in cell wall structure during the ripening process are proposed to be key to determine the decreasing of juice content in woolly fruits. Under the assumption that changes in relative abundance of genes related to cell wall metabolism would be involved in woolliness development, in this work we present an analysis of the expression of multiple genes, which serves as an approximation to uncover the mechanisms behind this physiological alteration. The expression of 847 genes was examined using macroarrays hybridizations. Membranes were hybridized with 32P-labeled cDNAs synthesized from mRNAs of juice and woolly peaches. The results showed that 67.5% of the clones (n = 573) fulfilled all filter criteria and they were selected for sequence analysis. Our analysis indicate that 45% of transcripts which present a consistent expression level in all biological replicates are activated exclusively in juice condition, and only 15% in woolly fruits. In the resting 40% (transcripts common to both conditions,) only 5% presents an abundance increase in woolly samples. Keywords: Analysis of physiological disorder in peaches
2007-04-30 | GSE7145 | GEO
Project description:Storage at low temperatures is one of the most used methods to prolong the life of postharvest peaches (Prunus persica (L) Batch.). However, fruit quality is adversely affected by the development of woolliness, a physiological disorder that is apparent when the fruit is ripened after prolonged periods of cold storage and is mainly manifested as loss of juice in the peaches. The aim of this study was to obtain a more detailed cohort of genes that underlie the wolliness in a segregating population with contrasting phenotypes of mealiness after being exposed to cold storage at 4 °C. For this, a transcriptomics approach was applied to fruits from a progeny of individuals accounted for 6% more juicy and woolly 6% over a 2 years. Our results suggest that not only genes related to the maintenance of cell wall architecture may contribute to the development of mealy phenotype. Based on its possible physiological process and differential pattern of expression transcriptomic profiles show that genes related to maintenance (modification I) and membrane fluidity account for the differences between fruits that exhibit contrasting phenotypes of mealiness. These genes may contribute to tolerance to cold during storage. We analyzed a total of 9 woolly fruits (from 3 different trees, 3 fruits from each tree) and 12 juicy fruits (from 4 different trees, 3 fruits from each tree). An RNA pool from 9 woolly fruits was used as reference and was compared to an RNA pool of 3 juicy fruits from each individual tree. Two technical replicates were done for each comparison, thus making in total 8 hybridizations.
2011-10-25 | E-GEOD-33027 | biostudies-arrayexpress
Project description:Desmosomes are dynamic complex protein structures involved in cellular adhesion. Disruption of these structures by loss of function variants in desmosomal genes lead to a variety of skin and heart related phenotypes. Here, we report tuftelin 1 as a desmosome-associated protein, implicated in epidermal integrity. In two siblings with mild skin fragility, woolly hair and mild palmoplantar keratoderma, but without a cardiac phenotype, we identified a homozygous splice site variant in the TUFT1 gene, leading to aberrant mRNA splicing and loss of tuftelin 1 protein. Patients’ skin and keratinocytes showed acantholysis, perinuclear retraction of intermediate filaments, and reduced mechanical stress resistance. Immunolabeling and transfection studies showed that tuftelin 1 is positioned within the desmosome and its location dependent on the presence of the desmoplakin carboxy-terminal tail. A Tuft1 knock-out mouse model mimicked the patients’ phenotypes. Altogether, this study reveals tuftelin 1 as a desmosome-associated protein, whose absence causes skin fragility, woolly hair and palmoplantar keratoderma.
2023-10-30 | GSE237986 | GEO