Canis lupus familiaris Transcriptome project

Transcriptomes of the heart left ventricle muscles of a normal control dog and a congestive heart failure dog.

Whole transcriptome sequencing analysis of imprinted expression in Medaka (Oryzias latipes).

Within vertebrate lineages, genomic imprinting is believed to be restricted to eutherian mammals and marsupials. However, comprehensive analysis of imprinted expression in non-mammalian vertebrates has not been done. Here we performed whole transcriptome analysis of imprinted expression in medaka (Oryzias latipes) using reciprocal crosses of inbred medaka strains, Hd-rR and Kaga.

Whole transcriptome identification of turtle

Whole transcriptome of turtle (Pelodiscus sinensis) was identified in this study by using stranded sequencing methods.

Transcriptome analysis of Tanzanian coelacanth Latimeria chalumnae

Transcriptome analysis of Tanzanian coelacanth Latimeria chalumnae

Abundant Bidirectional Transcription around Transcription Start Sites in Mammals

In mammals, more than 60% of the genome is use for transcription for mRNAs and noncoding RNAs (ncRNAs). A fraction of ncRNAs have been believed to downregulate the corresponding mRNA expression level in a pre- or post- transcriptional manner by forming RNA-RNA duplex structures.To examine the directional properties of transcription at the whole genome level, we performed directional RNA-seq analysis of mouse brain and heart samples. Our analysis revealed that there is only a small fraction of the genome where both the top and bottom strands are utilized for transcription.A significant fraction of transcription start sites (TSSs) of protein-coding genes contain borders that separate antisense- and sense-biased transcription, suggesting that head-to-head transcription at the TSS is more prevalent than previously thought.The expression of the resultant promoter-associated ncRNAs (pancRNAs) tends to occur together with that of the corresponding mRNA in a coordinated manner. A fraction of genes with tissue-specific pancRNAs show a positive correlation between their pancRNA and mRNA expression, which is in accord with the proposed role for pancRNA in facultative gene activation, whereas genes with constitutive expression lack an association with pancRNA. More than 90% of head-to-head type promoters contain CpG islands. Moreover, CCG and CGG repeats are significantly enriched in the upstream regions and downstream regions, respectively, of TSSs located in head-to-head type promoters. Here, we propose that head-to-head transcription from GC-rich sequences regulates gene expression.

Transcriptome analyses of mammalian tissues

In mammals, more than 60% of the genome is use for transcription for mRNAs and noncoding RNAs (ncRNAs). At present, little is known about the concerted expression of mRNAs and antisense transcripts located in their 5'-flanking regions, and the comprehensive transcriptome analysis focusing on the bidirectional transcription of mRNA and pancRNA has not been performed. We do not yet know the sequence characteristics of the bidirectionally transcribed regions. Here, we perform directional RNA sequencing in order to examine whether there is a correlation between the expression of sense and antisense RNAs at the genome wide level.

RNA sequencing analysis using the intestines of adult Medaka (Oryzias latipes)

To clarify the quantitative regulation of gene expression after IR irradiation, we conducted RNA sequencing using the intestine of mature fish derived from two genetically distant inbred strains of Medaka (Oryzias latipes).

Gene expression of granulosa cells and oocytes in sus scrofa

Gene expression was examined in granulosa cells and oocytes in various stage of follicle and in vitro grown oocytes and granulosa cells complexes in sus scrofa.

Transcriptome analyses of the chimpanzee tissues

In mammals, more than 60% of the genome is use for transcription for mRNAs and noncoding RNAs (ncRNAs). For the comprehensive transcriptome analysis, we perform directional RNA sequencing of the chimpanzee cerebral cortex and heart.

Medaka embryonic RNAseq

To uncover whole embryonic gene expression profiles of Medaka (O. latipes), RNAseq using Illumina paired-end library was sequenced.

EXPANDE project

EXPression AloNg Development and Evolution (EXPANDE) project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief, taking advantages of Illumina sequencing, RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates (two or more biological replicates).

Comprehensive Gene Expression Analysis of Canine Urothelial Bladder Carcinoma

Trascriptome analysis of canine normal urotherlial bladder tissue and urotherial bladder carcinoma samples were performed to compare the gene expression profiles between these tissues. The total RNA was isolated from these samples and sequenced using NextSeq 500. The differentially expressed genes between normal and tumor tissues were extracted and pathway analysis was conducted.

Global transcriptional differences between normal and heart failure left ventricle muscles of dogs.

We firstly searched heart failure-specific genes from global transcriptional differences between normal and heart failure left ventricle muscles of dogs and secondly evaluated the effects of therapeutic drugs on cardiac functional changes??and the gene expressions in failing dogs.

Analysis of gene expression differences between humans and apes

Comparison of gene expression in skin between humans and apes (chimpanzees, gorillas, orangutans) using RNA-seq

Transcriptome of Japanese medaka adult tissues

In order to investigate the regulatory properties that contribute to the stability and evolutionary conservation of gene expression, we focused on pleiotropic expression. To determine the number of tissues in which each gene was expressed, we collected transcriptome data for tissues of adult medaka fish (O. latipes). We selected a total of 25 different tissues to cover as much of the body as possible. A total of four replicates were obtained for each tissue, two from males and two from females. Each data was derived from one individual, not pooled. We found a moderate tendency that genes expressed in many tissues are less likely to fluctuate in expression levels among individuals and more likely to be evolutionarily conserved in expression levels.

RNA-seq of achilles tendon from young and old donors to study age-related changes in tendon

Tendon from young and old donors was used for RNA-Seq analysis. The aim of the study was to identify differentially expressed tendon transcripts in ageing in order to to characterize molecular mechanisms associated with age-related changes in tendon.

Early transcriptome and proteome changes in an in vivo model of post-traumatic osteoarthritis

Synovium mRNA expression data derived from a pig model of post-traumatic osteoarthritis. Samples were collected from both knees of control pigs (n=6x2=12) and injured knees of pigs that went under unilateral anterior cruciate ligament transection 1, 5, 9 and 14 days after surgery (n=6 per time-point).

RNA-seq of different tissues from Sus scrofa

10.3389/fgene.2019.01355

RNA sequencing of pig tissues for transcriptome annotation and expression analysis. Tissue specific RNA-seq data was generated to support annotation of coding and non-coding genes and to measure tissue specific expression. This study is part of the FAANG project, promoting rapid prepublication of data to support the research community. These data are released under Fort Lauderdale principles, as confirmed in the Toronto Statement (Toronto International Data Release Workshop. Birney et al. 2009. Pre-publication data sharing. Nature 461:168-170). Any use of this dataset must abide by the FAANG data sharing principles. Data producers reserve the right to make the first publication of a global analysis of this data. If you are unsure if you are allowed to publish on this dataset, please contact alan.archibald@roslin.ed.ac.uk, lel.eory@roslin.ed.ac.uk and faang@iastate.edu to enquire. The full guidelines can be found at http://www.faang.org/data-share-principle.

Sanger_zebrafish_sequencing

Abstract: Paired-end sequence data has been generated using polyA selected RNA from a range of zebrafish tissues using the Illumina Genome Analyzer. Study description: Zebrafish total RNA was extracted from adult tissue, then polyA selected. After fragmentation and reverse transcription Illumina sequencing libraries were prepared. Paired-end sequence runs were performed with 76 base reads on the Illumina Genome Analyzer.

Sexual dimorphism in mice

High-throughput sequencing of vomernasal tissues of adult male and female mice

Odom_tRNA_evolution

Homologous vertebrate tissues express a highly conserved set of transcribed genes; paradoxically, expression of tRNAs that are required to translate mRNAs into proteins have been reported to be divergent. To resolve this paradox, we mapped the genome-wide occupancy of pol III in primary tissues isolated from six mammals. We confirmed that the specific tRNA genes bound by pol III, as well as the extent and stability of binding, can vary substantially among mammalian tissues, and we discovered that this divergence is far greater between species. We combined pol III occupancy from genomically discrete tRNA loci into collective binding into isoacceptor classes and then into amino acid-based isotype classes, and at each step we found increasing conservation. At the level of amino acid isotypes, pol III binding is almost invariant among all the tissues and species profiled. Thus, the basal transcriptional machinery is constrained collectively in its synthesis of functional tRNA isotypes, despite rapid divergence of polymerase binding to specific tRNA genes.

Transcriptome sequencing of leopard complex spotting in Equus caballus

Leopard complex spotting (LP) is a collection of unique white spotting patterns in several breeds of domestic horse (Equus caballus). This study undertook whole transcriptome sequencing of one LP/LP skin biopsy and one lp/lp skin biopsy.

Transcriptome sequencing of leopard complex spotting in Equus caballus

Leopard complex spotting (LP) is a collection of unique white spotting patterns in several breeds of domestic horse (Equus caballus). This study undertook whole transcriptome sequencing of one LP/LP retina, one lp/lp retina, and one LP/lp skin biopsy.

domestication_gene_expression

A comparison of brain gene expression patterns between several species pairs of domesticated and wild animals. Each pair consists of 5-6 wild and domesticated animals.

Muscle RNA-seq expression variation

Muscle RNA-seq of 89 porcine individuals from a single founder family

Transcriptome Profiling of Ten Porcine Tissues at the Gene, Isoform and TSS level

In this study we have employed RNA seq on ten different tissues including four brain tissues from two boars to gain a understanding of the differential variations in transcriptional profiles for these tissues consisting of occipital cortex, frontal cortex, hypothalamus and cerebellum along with such diverse tissues as heart, spleen, liver, kidney, lung and musculus longissimus dorsi. This has enabled us to perform comparative gene expression analysis of brain regions versus non-brain tissues along with inter-brain tissue comparisons. Hence, we have tested for differentially expressed genes and isoforms, differential splicing, transcription start sites (TSS), and differential promoter usage between all ten porcine tissues.

Phermone_detection_in_the_main_olfactory_system

Here I propose to identify transcriptional differences, by RNA sequencing using the Illumina platform, between the main olfactory epithelium from male and female mice. The transcriptome will be sequenced from 3 adult male and 3 adult female mice, and analyzed for both transcript abundance and sex-specific isoforms. The analysis will be primarily focused on the sensory receptors and molecular transduction machinery implicated in pheromone detection.

BovRNA-Seq

SNP discovery in bovine muscle: the aim of the project was to used a transcriptomic-based approach to identify coding SNPs

Genome sequencing in three primate species

We sequenced several individuals from three primate species, using paired reads, on the Illumina platform.

overview of gene expression dynamics during sheep early ovarian folliculogenesis

Separate transcription profiling of oocytes and granulosa cells for each follicle stage: primordial (PD), primary (PM), secondary (SC) follicles and the small antral stage (SA) obtained by Laser Capture Microdissection (LCM) and RNAseq. The purpose of this study was to describe global gene expression during early ovarian folliculogenesis for each follicular compartment, to identify differential and specific gene expression between the 2 follicular compartments and during follicular development, to investigate specific function and pathways and to explore bi-directional communication between oocytes and GC.

Rat_olfactory_transcriptome

The olfactory gene repertoire is largely species-specific, shaped by the nature and necessity of chemosensory information for survival in each species' niche. We are intrigued by this interspecific variation and aim to investigate the olfactory transcriptome across mammals. The rat is the best candidate species to start a comparative study because of its phylogenetic proximity to mice, because it has a similar biology, a similar but not identical olfactory receptor repertoire and a well annotated genome. Thus, analysing the olfactory transcriptome of the rat will serve both as the first step and as a proof of concept for the pan-mammalian comparative analysis we aim to do

HPA RNA-seq normal tissues

RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes.

Analysis of the canine brain transcriptome with an emphasis on the hypothalamus and cerebral cortex

The diversity of dog breeds make the domestic dog a valuable model for identifying genes responsible for many phenotypic and behavioral traits. The brain in particular, is a region of interest for the analysis of molecular changes that are involved in dog-specific behavioral phenotypes. However, such studies are handicapped due to incomplete annotation of the dog genome. We present a high coverage transcriptome of the dog brain using RNA-Seq. Two areas of the brain, hypothalamus and cerebral cortex, were selected for their roles in cognition, emotion and neuroendocrine functions.

RNA_seq_Salmonella_pig

Salmonella enterica serovar Typhimurium is a gram-negative bacterium that can colonize the gut of humans and several species of food producing farm animals to cause enteric or septicaemic salmonellosis. Besides compromising public health and food safety, sub-clinical salmonellosis is also believed to be a major problem affecting the profitability of the pig industry. Distinct responses to Salmonella infection have been observed in pigs, some recovering faster and shedding lower levels of Salmonella in faeces than others (low shedders, LS versus persistent shedders, PS). This trait variation could indicate the existence of a genetic component to Salmonella shedding and resistance that may be exploited in animal breeding and disease diagnostics. The study aimed to identify porcine genes and gene co-expression networks that differentiate distinct responses to Salmonella infection with respect to faecal Salmonella shedding.

Variant in the RFWD3 Gene Associated with PATN1, a Modifier of Leopard Complex Spotting

Leopard Complex spotting (LP), the result of an incompletely dominant mutation in TRPM1, produces a collection of unique pigmentation patterns in the domestic horse. While the LP mutation allows for expression of the various patterns, other loci are responsible for modification of the extent of white. Pedigree analysis of families segregating for high levels of patterning (80-100% white hair coat) indicated a single dominant gene (PATN1) as a major effect modifier for LP. Linkage analysis identified a 16 Mbp region on ECA3p associated with PATN1. Whole transcriptome sequencing of skin samples from horses with and without the PATN1 allele was performed to identify genic SNPs for fine mapping. Two Sequenom assays were utilized to genotype 192 individuals from five LP-containing breeds. The initial panel highlighted a 1.6 Mbp region without a clear candidate gene. In the second round of fine-mapping, a SNP in the 3' UTR of RING finger and WD repeat domain 3 (RFWD3) reached a significance level of p=1.063x10-39. Sequencing of RFWD3 did not identify any coding polymorphisms specific to the PATN1 horses. Genotyping of an additional 52 LP animals increased this association to a p-value of 4.68x10-56. An additional 166 horses of breeds not segregating for LP did not contain the PATN1-associated allele. This variant is a strong candidate for PATN1 and may be used for genotyping lp/lp animals.

Sheep Tissue Atlas

Sheep total RNA was extracted from embryonic and adult tissues. Sequencing libraries were prepared from the RNA using the Illumina TruSeq stranded total RNA with the Ribo Zero gold option for the rRNA removal. The fragmentation in the standard protocol was modified to increase the average insert size in the library. Sequencing with 151 base paired end reads was performed on an Illumina HiSeq 2500 in rapid mode.

7tissues

To measure gene expression, mRNA from seven different tissues was extracted (adipose, muscle, hypothalamus, duodenum, liver, lung and kidney) from frozen tissues using TRIzol (Invitrogen). Messenger RNA from 7~14 animals was pooled equally before sequencing

RNA-seq of long non coding RNA in bovine muscle

Identification of long non coding RNA in bovine muscle

The establishment of PrV latency in the pig host (RNA-seq data)

A 2.5 kb deletion containing a cluster of nine miRNAs in the LAT locus of the pseudorabies virus affects the host response of porcine trigeminal ganglia during established latency.

RNA-seq of coding RNA from tissue samples of 127 human individuals representing 32 different tissues.

RNA-seq was performed of tissue samples from 127 human individuals representing 32 different tissues in order to study the human tissue transcriptome. This submission contains 32 samples and the remaining data is located at E-MTAB-1733.

Olfactory_transcriptomics_in_mammals

In this study RNA was extracted from the olfactory mucosa of three individuals of four mammalian species: cow, macaque, marmoset and humans. The RNA was sequenced using the Illumina Hiseq2500 platform.

Equine RNAseq Tissue pool

This dataset is comprised of RNA samples from 11 horses of various ages and sex that comprise the following tissues: Adipose Tissue, Adrenal Cortex, Adrenal Medulla, Aorta, Articular Cartilage (foal), Bladder, Bone, Bone Marrow, Cecum, Cerebrum, Cornea, Embryo (whole embryo, 34d), Endometrium (preg. day 16), Endometrium (preg. day 50), Epididymus, Hoof (germinal epithelium), Kidney, Large Intestine, Liver, Lung Lymph Node, Lymphocytes (activated), Muscle (cardiac), Muscle (skeletal, tongue), Muscle (skeletal), Muscle (smooth), Ovary, Pancreas, Pituitary (anterior), Pituitary (posterior), Placental Villous, Retina, Salivary Gland, Skin (full thickness), Spinal Cord, Spinal Root Ganglia, Spleen (red pulp), Spleen (white pulp), Stomach, Synovial Membrane, Tendon (superficial digital flexor, foal), Testes, Thymus, and Vena Cava. This study was carried out in strict accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. Tissue samples for total RNA isolation were collected under a protocol (00814A2004) reviewed and approved by the Office of Research Integrity, Institutional Animal Care and Use Committee, at the University of Kentucky (PHS Assurance Number: A3336-01). Two micrograms of mRNA from each tissue sample was used to generate the final RNA pool. The pooled sample was Illumina and 454 sequenced with the aim to improve equine gene structural annotation.

Epigrani

Once daily milking of dairy cows induces long-term effects on milk production by altering the expression of coding genes which play key roles in milk production (Boutinaud et al, 2013, Physiol Genomics, 45:973-985). These variations had been analyzed in p

RNA sequencing of marmoset embryonic development

Transcriptional profiling of common marmoset embryo stages spanning E5.0 to E7.0 was performed by RNA-seq.

RNA-Seq for EBJ-ACC affected and control

In this study, we demonstrate the use of a genome-wide association mapping together with RNA-seq in a reduced number of samples, as an efficient approach to detect the causal mutation for a Mendelian disease. Junctional epidermolysis bullosa is a recessive genodermatosis that manifests with neonatal mechanical fragility of the skin, blistering confined to the lamina lucida of the basement membrane and severe alteration of the hemidesmosomal junctions. In Spanish Churra sheep, junctional epidermolysis bullosa with aplasia cutis congenita (JEB-ACC) has been detected in two commercial flocks. The JEB-ACC locus was mapped to Ovis aries chromosome 11 by GWAS and subsequently fine-mapped to an 868-kb homozygous segment using the identical-by-descent method. The ITGB4, which is located within this region, was identified as the best positional and functional candidate gene. The RNA-seq variant analysis enabled us to discover a 4-bp deletion within exon 33 of the ITGB4 gene (c.4412_4415del). The c.4412_4415del mutation causes a frameshift resulting in a premature stop codon at position 1472 of the integrin ?4 protein. A functional analysis of this deletion revealed decreased levels of mRNA in JEB-ACC skin samples and the absence of integrin ?4 labeling in immunohistochemical assays. Genotyping of c.4412_4415del showed perfect concordance with the recessive mode of the disease phenotype. Selection against this causal mutation will now be used to solve the problem of JEB-ACC in flocks of Churra sheep. Furthermore, the identification of the ITGB4 mutation means that affected sheep can be used as a large mammal animal model for the human form of epidermolysis bullosa with aplasia cutis. Our approach evidences that RNA-seq offers cost-effective alternative to identify variants in the species in which high resolution exome-sequencing is not straightforward.

Habitat-specific gene expression in stickleback immune tissues from four parametric lake-river population pairs

The three-spined stickleback (Gasterosteus aculeatus) has repeatedly colonized and adapted to diverse freshwater habitats since the last glaciation. Among those freshwater habitats, adjacent lake and river populations harbour distinct parasite communities, a recurring ecological difference proposed to drive adaptive differentiation between lake and river stickleback ecotypes. To study the rapid adaptation of sticklebacks to lake and river habitats, we analysed gene expression profiles of 77 whole-transcriptome libraries of two immune-relevant tissues, the head kidney and the spleen, obtained from wild-caught sticklebacks of the two habitat types across multiple geographic locations. Differential expression analyses identified 189 genes showing statistically significant habitat-specific expression patterns among the three European locations. Among those genes, 15 genes are annotated with putative immune functions, and 50 have been experimentally associated with immune-responses in sticklebacks, reinforcing the hypothesis that parasites contribute to adaptive evolution of lake and river sticklebacks. Comparing expression profiles of European sticklebacks to populations in similar habitats in North America, five genes exhibited habitat-specific expression across continents.

Porcine Transcriptome and Methylome Map

This study is part of the FAANG project, promoting rapid prepublication of data to support the research community. These data are released under Fort Lauderdale principles, as confirmed in the Toronto Statement (Toronto International Data Release Workshop. Birney et al. 2009. Pre-publication data sharing. Nature 461:168-170). Any use of this dataset must abide by the FAANG data sharing principles. Data producers reserve the right to make the first publication of a global analysis of this data. If you are unsure if you are allowed to publish on this dataset, please contact faang@iastate.edu to enquire. The full guidelines can be found at http://www.faang.org/data-share-principle. Pigs (Sus scrofa) provide relevant biomedical models to dissect complex diseases due to their anatomical, genetic, and physiological similarities with humans. Aberrant DNA methylation has been linked to many of these diseases and is associated with gene expression; however, the functional similarities and differences between porcine and human DNA methylation patterns are largely unknown. DNA and RNA was isolated from eight tissue samples (fat, heart, kidney, liver, lung, lymph node, muscle, and spleen) from the adult female Duroc utilized for the pig genome sequencing project. Reduced representation bisulfite sequencing (RRBS) and RNA-seq were performed on an Illumina HiSeq2000. RRBS reads were aligned using BSseeker2, and only sites with a minimum depth of 10 reads were used for methylation analysis. RNA-seq reads were aligned using Tophat, and expression analysis was performed using Cufflinks. In addition, SNP calling was performed using GATK for targeted control and whole genome sequencing reads for CpG site validation and allelic expression analysis, respectively. These results provide transcriptional and DNA methylation datasets for the biomedical community that are directly relatable to current genomic resources. In addition, the correlation between TSS CpG density and expression suggests increased mutation rates at CpG sites play a significant role in adaptive evolution by reducing CpG density at TSS over time, resulting in higher methylation levels in these regions and more permanent changes to lower gene expression. This is proposed to occur predominantly through deamination of 5-methylcytosine to thymidine, resulting in the replacement of CpG with TpG sites in these regions, as indicated by the increased TSS TpG density observed in non-expressed genes, resulting in a negative correlation between expression and TSS TpG density. This study provides baseline methylation and gene transcription profiles for a healthy adult pig, reports similar patterns to those observed in humans, and supports future porcine studies related to human disease and development. Additionally, the observed reduced CpG and increased TpG density at TSS of lowly expressed genes suggests DNA methylation plays a significant role in adaptive evolution through more permanent changes to lower gene expression.

Rabbit Lung_DH_TO_Control

Investigation into the effects of Congenital Diaphragmatic Hernia (CDH) and subsequent treatment with tracheal occlusion (TO) on the pulmonary transcriptome. A diaphragm defect was created by surgical means in fetal rabbits. The surgical creation of diaphragmatic hernia (DH) allows for direct analysis of changes in pulmonary gene expression due to pulmonary hypoplasia, without the need for gene knockdown (as for KO mice) or use of teratogens (such as nitrofen). The subsequent treatment with tracheal occlusion (TO) was also investigated to determine the changes in gene expression due to forced lung growth in the prenatal phase. RNA-Seq analysis was performed on left lung samples from fetal rabbits. Samples were generated and analysed for DH (n=4), TO (n=6), and control lungs (n=4)

Medaka_Reciprocal_cross_RNAseq

Medaka fish is a long standing genetic model organism from the 1930s. Uniquely amongst vertebrates Medaka fish can be routinely inbred from the wild (laboratory mice are inbred, but this does not happen as a routine process from wild individuals), leading to a large number of fully inbred wild-derived strains. As part of a broader collaboration I am part of a project to inbred over 100 wild derived strains of Medaka and use them in a similar manner to Arabidopsis and Drosophila wild derived lines. To help explore the phenotyping possibilities in this context, we have taken already established wild Medaka lines and done reciprocal F1 crosses between 3 strains, and have 4 tissues, and a number of parental tissues, giving a total of 40 samples. By doing RNA-seq on these tissues we do a number of things: (a) assess the level of allele specific expression in Medaka (b) test whether there is any imprinting (parent of origin) in fish. This is thought to not be the case, but in fact has not been well tested (not least because getting truly inbred fish is hard) (c) assess the level of random allelic activation in brain (d) assess the feasibility for RNAseq based phenotyping in Medaka, providing preliminary data for future proposals.

Medaka_F1_Expression_survey

We generated reciprocal crosses between 3 inbred strains of Medaka; HdR (the reference strain), Kaga and Cab, and sequenced a number of tissues to look at allele specific differences in expression between these F1 individuals.