Project description:In this study we evaluate the Swine Protein-Annotated Oligonucleotide Microarray by profiling the expression of transcripts in four porcine tissues. We validate the hybridization results by comparative analysis of expression in human orthologs, confirm expression patterns for a subset of genes by QPCR, and assess the usefulness of designed control oligonucleotides. Simple descriptive diagnostic analyses of PM/MM probe sets introduced in this paper are useful to detect non-specific hybridization. Using comparative transcriptional profiling, we found that the microarray data correlate to QPCR data for most genes detected as differentially expressed using the microarray platform. Moreover, comparison to human ortholog expression confirmed the utility of experiments based on this array in swine species as a biomedical model for human tissue specific expression. Arrays for this study contained 20,400 70-mer oligonucleotides (http://www.pigoligoarray.org/). Hybridization stringency controls included six mismatch probes (1, 2, 3, 5, 7, and 10 mismatches) designed against each of 60 contigs with the highest EST count in the database. Sixty negative controls oligonucleotides corresponded to scrambled sequence without presumed representation in either the pig or bovine genome or pig EST databases. The samples used in this study included liver, brain stem, longissimus muscle and uterine endothelium that were collected from 4 pigs (gilts at approximately 165 d of age). Tissues samples from the four gilts were evaluated in a loop design experiment. Four loops were used, one for each animal, such that loop and animal were confounded. However, the tissue sequence between loops was altered such that all tissue pairs were represented in at least one array, and tissue and dye levels were balanced.

2010-05-17 | E-GEOD-13095 | biostudies-arrayexpress

Genome-wide maps RNA Polymerase II and Histone H3 of Hydra vulgaris

Project description:Hydra have a remarkable ability to regenerate after bisection or dissociation. Thus, Hydra is a unique model for studying the mechanisms underlying stemness and self renewal biology. The regeneration of Hyrda offers unique way to investigate molecular mechanisms leading to the establishment of organizer activity during animal development. Here we have investigated the genome-wide occurrence of RNA Polymearse II and Histone H3 in Hydra vulgaris.

2020-01-01 | GSE63414 | GEO

RNA-seq of Hydra body segments and regenerated Hydra animals

Project description:Positional RNA-sequencing of isolated Hydra body pieces and RNA-sequencing of fully regenerated Hydra animal was combined with RNA-sequencing of actively regenerating spheroids (see submission E-MTAB-9672) in order to elucidate the role of tissue stretching on regeneration and body pattern formation.

2022-10-13 | E-MTAB-9676 | biostudies-arrayexpress

The Hydra magnipapillata head regeneration transcriptome

Project description:Hydra has long been studied for its remarkable ability to regenerate its head. Previous studies focusing on molecular mechanisms of axial patterning and head regeneration using a candidate gene approach have revealed a central role for the canonical Wnt pathway. We performed a global gene expression analysis during Hydra magnipapillata head regeneration using RNA-seq to identify additional genes that are transcriptionally regulated during the regeneration of the head organizer in hydra. Differential expression analysis revealed a set of 4,978 genes with significant changes during a 48-hour head regeneration time-course that includes many key genes in the Wnt, TGF-M-NM-2/BMP and MAP kinase pathways. We observed the differential regulation of several genes that are part of the epithelial-to-mesenchymal transition in bilaterians such as Snail. We assembled 806 novel putative lincRNAs with 176 of these are differentially expressed during the time course. We observed the coordinated transcriptional regulation of several factors that regulate the effective pool of free M-NM-2-catenin that together synergize to increase the amount of M-NM-2-catenin available for transcriptional regulation of downstream genes. The differential expression of Snail and some of its interacting regulators and downstream targets suggests that a partial-EMT-like response is involved in hydra head regeneration. This time-course is a valuable resource for the study of the transcriptional dynamics of head regeneration in hydra. mRNA profiling of regenerating head from 6 time points post bisection of Hydra head (H. magnipapillata), generated by deep sequencing, in duplicates, using Illumina HiSeq2500.

2014-12-13 | E-GEOD-64127 | biostudies-arrayexpress

HydRA: Deep-learning models for predicting RNA-binding capacity from protein interaction association context and protein sequence

Project description:RNA-binding proteins (RBPs) control RNA metabolism to orchestrate gene expression, and dysfunctional RBPs underlie many human diseases. Proteome-wide discovery efforts predict thousands of novel RBPs, many of which lack canonical RNA-binding domains. Here, we present a hybrid ensemble RBP classifier (HydRA) that leverages information from both intermolecular protein interactions and internal protein sequence patterns to predict RNA-binding capacity with unparalleled specificity and sensitivity using support vector machine, convolutional neural networks and transformer-based protein language models. HydRA enables Occlusion Mapping to robustly detect known RNA-binding domains and to predict hundreds of uncharacterized RNA-binding domains. Enhanced CLIP validation for a diverse collection of RBP candidates reveals genome-wide targets and confirms RNA-binding activity for HydRA-predicted domains. The HydRA computational framework accelerates construction of a comprehensive RBP catalogue and expands the set of known RNA-binding protein domains.

2023-07-10 | GSE221870 | GEO

Identification of genes involved in symbiosis of green hydra and Chlorella

Project description:Green hydra (Hydra viridissima) harbors endosymbiotic Chlorella and have established a mutual relation. To identify the host hydra genes involved in the specific symbiotic relationship, transcriptomes of intact H. viridissima colonized with symbiotic Chlorella strain A99, aposymbiotic H.viridissima and H. viridissima artificially infected with other symbiotic Chlorella were compared by microarray analysis. The results indicated that genes involved in nutrition supply to Chlorella were upregulated in the symbiotic hydra. In addition, it was induced by supply of photosynthates from the symbiont to the host, suggesting cooperative metabolic interaction between the host and the symbiotic algae.

2018-04-01 | GSE97633 | GEO

L7 vs sensory cluster (Annotated array AAA)

Project description:The marine mollusc Aplysia is a well established experimental system for cellular and systems neuroscience because of the relatively simple organization of its nervous system and the presence within it of the largest nerve cells in the animal kingdom, many of which are uniquely identifiable in every member of the species. Until now, molecular analyses of Aplysia have been seriously handicapped by lack of adequate genomic information, with only 200 sequences publicly available when this project was initiated in 2003. By sequencing cDNA libraries from the central nervous system, we have identified over 175,000 ESTs (expressed sequence tags), of which 19,814 are unique neuronal gene products and 9469 has been annotated. Through comparison with the complete genomic data available for Drosophila and C. elegans, we estimate that we have sequence information for approximately 50-70% of the total transcriptome of the Aplysia nervous system. We also identified 9,223 unique gene products in a modulatory serotonergic cell and about 1,000 unique gene products from its processes. Using gene expression oligoarrays constructed using the Aplysia EST database we also have characterized the transcript profile of sensory and motor neurons. In addition to increasing the amount of publicly available gene sequences of Aplysia by two orders of magnitude, this collection of transcripts is distinctive from a comparative biology point of view. It represents the largest database available for any member of the Lophotrochozoa clade of the animal kingdom. These molecular resources should allow the detailed study of the genomics of identified cells and circuits and provide in Aplysia a much needed bridge between genes, behavior, and learning. Keywords: Cell-type comparison

2007-01-05 | GSE4625 | GEO

Pneumocystis jirovecii TSA

Project description:Transcriptome of Pneumocystis jirovecii during human Pneumocystis pneumonia

| PRJEB370 | ENA