Regional differences in left ventricular shear stress contribute to heterogenity of the endocardial transcriptome

The role of shear stress, the frictional force of blood flow, on the endothelium has been well documented. Differences in shear stress can have profound effects on endothelial and blood vessel biology. Endothelial cells (ECs), termed endocardial ECs, line the heart chambers and are exposed to complex shear stress patterns. While it has been demonstrated that shear stress is important for heart development, little has been shown on the role of shear stress on adult ECs. 4D-MRI studies demonstrate regional differences in blood residence time. We sought to determine the effect of regional differences in endocardial shear stress on the endocardial transcriptome using RNA sequencing (RNA-seq) on 3 different regions (apex, mid-ventricle, outflow tract) from 8 adult pigs, for a total of 24 RNA-seq assays.

Olfactory_transcriptomics_in_dogs

In this study RNA was extracted from the olfactory mucosa of three dogs. The RNA was sequenced using the Illumina Hiseq2500 platform.

Transcriptomics_of_macaque_olfactory_mucosa___MAMMALIAN

In this study RNA was extracted from the olfactory mucosa of three macaques. The RNA was sequenced using the Illumina Hiseq2500 platform.

Transcriptome sequencing of three tissues and ten taxa related to the house mouse Mus musculus.

We sampled brain, liver and testis from populations, subspecies and species closely related to Mus musculus, spanning approximately between 3000 years and 10 million years of divergence.

RNA-seq datasets from hippocampus samples collected from 4 week old control and PRRSV infected piglets.

Environmental insults during sensitive periods can affect hippocampal development and function, but little is known about peripheral infection, especially in humans and other animals whose brain is gyrencephalic and experiences major perinatal growth. A previously published study reported increased microglial cell activity and reduced hippocampal-dependent learning and memory in neonatal piglets infected with porcine reproductive and respiratory syndrome virus (PRRSV), a virus that induces interstitial pneumonia. To investigate this further, we assessed gene expression patterns in hippocampal tissue obtained from control and PRRSV infected piglets at 4 weeks of age using RNA-seq.

Porcine hippocampal RNA-seq and RRBS datasets

RNA-seq and RRBS datasets from hippocampal tissue collected from 4 week old control and iron deficient piglets.

Post-weaning blood transcriptomic differences between Yorkshire pigs divergently selected for residual feed intake

Global gene expression profiles of peripheral blood of 35 to 42 day-old Yorkshire pigs with extremely low (more efficient) and high RFI (less efficient) values from two Iowa State University lines (the low RFI line, n = 15, and the high RFI line, n =16) that were divergently selected for RFI during the grow-finish phase were determined by Illumina RNA-seq (100 bp, paired-end) on the Hiseq2000 platform to explore the transcription biomarkers for feed efficiency in pigs.

RNA-seq of synovial membranes from a preclinical model of post-traumatic knee osteoarthritis to evaluate the effects of corticosteroid treatment

Yorkshire pigs received untreated unilateral ACL transection through a medial arthrotomy (INJ, n=6), transection with immediate injection of 20mg triamcinolone acetonide (TRI, n=6) or no surgery (CON, n=6). Synovial membranes were harvested two weeks after the injury in the lateral knee joint compartment. The whole biopsy was homogenised for RNA extraction. The objective of the experiment was to test if intraarticular corticosteroid injection mitigates injury-induced synovitis and collagen degradation after anterior cruciate ligament transection and to characterize the synovial response using the described perturbations in combination with a functional genomics approach.

RNA sequencing of the spleen / headkindey of 6 juvenile Atlantic cod (Gadus morhua) individuals.

Total RNA was isolated from the head kidney/spleen of six healthy juvenile Atlantic cod. These fish originate from the Norwegian cod breeding program and were grown out in in seawater of 3. 4 % salinity at 10 ºC, 24 hour light and fed ad libitum with commercial feed at the Aquaculture Research Station (Tromsø, Norway). The fish were reported to be healthy without any history of diseases and the use of these fish was approved by the National Animal Research authority in Norway (FOTS id 1147). The tissue was stored on RNAlater (Life Technologies) and total RNA was isolated using Trizol (Life Technologies) according to protocol but using half the amount of tissue per volume Trizol recommended by the manufacturer. Sequencing libraries were produced according to the IlluminaTruSeq protocol (Illumina, Inc., San Diego, CA). Illumina HiSeq2000 100 bp paired-end sequencing services were provided by the Norwegian Sequencing Centre (http://www. sequencing.uio. no).

RNA-Seq analysis of gene expression divergence in mammalian liver

The connection between evolution of regulatory elements and downstream gene expression is incompletely understood in mammals. We carried out a large-scale comparison of matched ChIP-seq and RNA-seq experiments across twenty species of mammals, using liver as a model somatic tissue. Herein we report the RNA-seq dataset, comprising twenty five species of mammals. When analysed alongside our previously reported ChIP-seq experiments, these data reveal a number of insights into how mammalian regulatory evolution propagates into differences in gene expression levels. Please note that all mouse RNA-seq libraries and three out of four human libraries have been previously reported in Array Express submission E-MTAB-4052 and are thus omitted here.

A splice defect in the EDA gene in dogs with an X-linked ectodermal dysplasia

X-linked hypohidrotic ectodermal dysplasia (XLHED) caused by variants in the EDA gene represents the most common ectodermal dysplasia in humans. We investigated three male mixed-breed dogs with an ectodermal dysplasia phenotype characterized by marked hypotrichosis, absence of sweat glands and altered dentition with missing and abnormally shaped teeth. Analysis of whole genome sequence data from the three affected dogs and 281 control dogs revealed that the affected dogs shared the same haplotype on a large segment of the X-chromosome, whereas they did not share any large homozygous segments elsewhere in the genome. Unexpectedly, bioinformatic analysis of the sequence data did not reveal any private non-synonymous variant in the affected dogs within the shared haplotype on the X chromosome. Furthermore, no private DNA variants were found in the EDA gene. We therefore performed an RNA-seq experiment on skin biopsies to search for changes in the transcriptome. This analysis revealed that the EDA transcript in the affected dogs lacked 103 nucleotides encoded by exon 2. We speculate that this exon skipping is caused by a genetic variant located in one of the large introns flanking this exon, which was missed by whole genome sequencing with the illumina short read technology. The altered EDA transcript splicing most likely causes the observed XLHED in the affected dogs. These dogs thus offer an excellent opportunity to gain insights into the complex splicing processes required for expression of the EDA gene and other genes with large introns.

A structural variant in the 5'-flanking region of the TWIST2 gene affects melanocyte development in belted cattle

Belted cattle have a circular belt of unpigmented hair and skin around their midsection. The belt is inherited as a monogenic autosomal dominant trait. We mapped the causative variant to a 54 kb segment on bovine chromosome 3. Whole genome sequence data o

Lake_Malawi_cichlid_RNA_sequencing

Total RNA sequencing of muscle and liver tissue in triplecates from different species of Lake Malawi cichlid fish, and total RNA sequencing of multiple tissue from Astatotilapia calliptera (Massoko yellow), brain, muscle, spleen, liver, gonad/testis, eye (whole eye ball), skin, anal fin and fry. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

Evidence of Late Pleistocene origin of Astyanax mexicanus cavefish

We found higher substitution rates in cavefish compared with surface fish, in accordance with a smaller cavefish population size which has allowed more rapid fixation of derived alleles present in the ancestral population. This result also implies that the Pachón cave population is much *younger* than previously estimated. The comparison of these data with simulations suggests that the Pachón cavefish population has probably been underground less than 30,000 years. This new time frame, together with other evidence, indicate that the evolution of cave phenotypes mainly involves the fixation of cryptic genetic variants present in surface fish populations within a short period of time.

RNA-seq of the Ileo-Caecal Valve Lymph Node of Sheep with Paratuberculosis Compared to Uninfected Controls.

Sheep total RNA was extracted from the Ileo-caecal valve lymph node (ICLN) of sheep with multibacillary paratuberculosis compared to ICLN of uninfected controls. Sequencing libaries were prepared from RNA using the Illumina TruSeq RNA Sample Preparation Kit v2. Sequencing with 101 base paired end reads was performed on an Illumina HiSeq 2500 at Edinburgh Genomics.

Transcriptional profiling of mammary gland and spleen from Mycoplasma agalactiae infected sheep

We used RNA-seq to investigate gene expression changes in sheep mammary gland and spleen tissue after experimental infection with Mycoplasma agalactiae (strain PG2). Sheep (3 per each group) were given an intra-mammary infection with 10^9 cfu infectious organisms or PBS as control. The animals were euthanized 15 days post infection to obtain the samples. Two replicates of mammary gland and spleen tissue per animal were used for Illumina RNA-sequencing.

This is an investigation into the genetic underpinnings of canine skull, morphology, with emphasis on brachycephaly.

DNA- and RNAseq of dogs to facilitate identification of putatively causal variants responsible for differences in canine skull morphology.

RNA sequencing of tissues and cell types from Texel x Scottish Blackface sheep for transcriptome annotation and expression analysis

Sheep are an important source of meat, milk and fibre globally. To support functional annotation of the sheep genome we have produced a high-resolution atlas of gene expression from a comprehensive set of tissues and cell types from Texel x Scottish Blackface crossbred individuals. RNA-Seq libraries were generated by Edinburgh Genomics from tissues and cells representing all the major organ systems from adult sheep and from several juvenile, neonatal and prenatal developmental time points. The dataset includes 352 medium depth (>25 million reads per sample) mRNA-Seq stranded libraries (125 base pairs paired-end) and 74 high depth (>100 million reads per sample) total RNA-Seq stranded libraries (125 base pairs paired-end). 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 emily.clark@roslin.ed.ac.uk, alan.archibald@roslin.ed.ac.uk, david.hume@roslin.ed.ac.uk / david.hume@uq.edu.au or faang@iastate.edu to enquire. The full guidelines can be found at http://www.faang.org/data-share-principle.

Wageningen University & Research Animal Breeding and Genomics FAANG data from three boars.

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

RNA-seq of porcine peripheral whole blood from pig divergently selected for residual feed intake and treated with lipopolysaccharide

Yorkshire pigs were divergently selected for residual feed intake (RFI) for 8 generations. Pigs with low RFI have reduced feed intake. Based on the resource allocation theory, we hypothesize that these low RFI pigs might have compromised immune response to immune stimulation. To test this hypothesis, twenty eight gilts of initial body weight (BW) of 63 +/- 4 kg from pigs selected for low RFI and high RFI were randomly selected for the ISU RFI selection project and utilized in two replicates (14 pigs/replicate) for this study. All pigs were housed in individual metabolism pens, had free access to water and were fed a corn-soy-based diet twice daily, and feed restricted (1.5 kg/day) as previously described. After a 9-day adaptation period pigs were randomly assigned within line to either a control (n = 6, three pigs per line) or lipopolysaccharide (LPS) challenge (n = 8, 4 pigs per line) group. Pigs in the challenge group were then repeatedly challenged with an intramuscular injection of 30, 36, 39, and 42 microg/kg BW of LPS from E. coli O5:B5 (sigma-Aldrich, St. Louis, MO) dissolved in saline solution at time points 0, 48, 96, and 144 hours post initial injection (hpi) to compensate for LPS tolerance after initial injection, respectively, while animals in the control group were injected with an equivalent volume of saline solution at the equivalent time points. Rectal temperatures of individual pigs were measured immediately before the initial injection (serving as baseline, called *0 hpi* for convenience), and 2, 4, 6, and 24 hpi, and 0, 4, 24 hours after each subsequent injection for all pigs. Blood samples were collected from the jugular vein into TempusTM Blood RNA tubes (Life Technologies, Grand Island, NY) for long-term storage at -80°C, EDTA tubes (BD, Franklin Lakes, NJ) for CBC tests and serum tubes for cytokine assays at 0, 2, 6, 24 and 168 hpi. At 168 hpi, all pigs were euthanized via barbiturate overdose, exsanguinated and tissue samples including the longissimus dorsi muscle, liver, spleen, and ileum were isolated, cleaned an frozen for later use. This study only focused on samples and data collected for the first 24 hours. Total RNA was extracted from the 32 blood samples of the treatment group in Replicate 2, collected at 0, 2, 6, and 24 hpi, by using preserved blood RNA purification kit I (Norgen Biotek Corp, Thorold, Ontario) per manufacturer's instruction. On-column DNA digestion was performed as described using DNase I (Qiagen, Valencia, CA). Globin transcripts (HBB and HBA) were depleted by following an RNase H-mediated method. The quantity and integrity of the RNA were monitored by using Nanodrop 2000 (Thermo Scientific, Waltham, MA) and Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) before and after globin depletion. The efficiency of globin depletion of each sample was checked by conventional RT-qPCR with beta-actin and GAPDH as the internal controls. Globin depletion efficiencies for all RNA samples were above 85%.

RNAseq of circulating neutrophils in peripartal grazing dairy cows divergent in metabolic health

In dairy cows, the transition from dry and pregnant to non-pregnant and lactating creates metabolic and immunological strain, which means many cows succumb to metabolic and infectious disease. This peripartum period, from three weeks pre-calving to three-

Ovarian transcriptome (mRNA and miRNA) profiling of Finnsheep, Texel and their F1-crosses

10.1186/s12864-017-4400-4

The aim of the project is to identify genetic markers associated with prolificacy in sheep. We have compared different reproductive tissues (ovary, corpus luteum, endometrium) between high prolific (Finnsheep, n=11) and low prolific (Texel, n=11) ewes. In order to assess the role of flushing diet, we kept half of the ewes in flushing diet during the experimental period. F1-crosses of Finnsheep and Texel (n=9) are also included in the study. mRNA- and miRNA-Seq data from all individuals are available here.

Expression of genes in different tissues of Drosophila melanogaster

The FlyAtlas 2 project is a study of the expression of the genes of Drosophila melanogaster in a range of tissues from adults and larvae. The expression data are based on RNA-Seq, with data for somatic tissues available for both male and female adult flies. Separate analysis has been performed for total RNA and microRNA.

An RNASeq normal tissue atlas for mouse and rat

The function of a gene is closely connected to its expression specificity across tissues and cell types. RNA-Seq is a powerful quantitative tool to explore genome wide expression. The aim of the present study is to provide a comprehensive RNA-Seq dataset across the same 13 tissues for mouse and rat, two of the most relevant species for biomedical research. The dataset provides the transcriptome across tissues from three male C57BL6 mice and three male Han Wistar rats. We also describe our bioinformatics pipeline to process and technically validate the data. Principal component analysis shows that tissue samples from both species cluster similarly. By comparative genomics we show that many genes with high sequence identity with respect to their human orthologues have also a highly correlated tissue distribution profile and are in agreement with manually curated literature data for human. These results make us confident that the present study provides a unique resource for comparative genomics and will facilitate the analysis of tissue specificity and cross-species conservation in higher organisms.

Goat Gene Expression Atlas

Goat mini-atlas of gene expression including 17 different tissues and two immune cell types. RNA-Seq libraries were generated by Edinburgh Genomics. This study is part of the FAANG project, promoting 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, emily.clark@roslin.ed.ac.uk, alan.archibald@roslin.ed.ac.uk and faang@iastate.edu to enquire. The full guidelines can be found at http://www.faang.org/data-share-principle.

RNA-seq of muscle from pigs divergent in feed efficiency and product quality

Feed efficiency (FE) is an indicator of efficiency in converting energy from feed into a tissue that is of major environmental and economic significance.This study was to profile the porcine Longissimus thoracis et lumborum (LTL) muscle transcriptome, examine the product quality from pigs divergent in FE and investigate the functional networks underpinning the potential relationship between product quality and FE.

RNA-seq of adipose tissue from pigs divergent in feed efficiency reveals variations in adipose growth, extracellular matrix formation, lipid metabolism and immune response

Feed efficiency (FE) is an indicator of efficiency in converting energy, attained from macronutrient ingestion, into tissue. Adipose tissue, besides being a master regulator of systemic lipid storage, is also an active endocrine organ that communicates with skeletal muscle, liver and brain to influence appetite, lipid & glucose metabolism and energy homeostasis. Adipose tissue is hypothesised to play a vital part in regulation of FE. The objective of the present study was to sequence the subcutaneous adipose tissue transcriptome in FE-divergent pigs (n=16) and identify relevant biological processes underpinning observed differences in FE.

RNA-seq of liver from pigs divergent in feed efficiency highlights shifts in macronutrients metabolism, hepatic growth and immune response

Liver is a metabolically complex organ that influences nutrient partitioning and potentially modulates the efficiency of converting energy acquired from macronutrients ingestion into a muscle and/or adipose tissue (referred to as feed efficiency, FE). The objective of this study was to sequence the hepatic tissue transcriptome of pigs divergent for FE and identify relevant biological processes that underpin the differences in liver phenotypes and FE.

Chicken RNA-seq time-series of the development of seven major organs

This dataset covers the development of 7 organs (brain, cerebellum, heart, kidney, liver, ovary and testis) from day 10 post-conception to day 155 post-hatch.

FAANG Transcriptome Analysis of the horse

The Functional Annotation of the Animal Genome (FAANG) project aims to identify functional regulatory elements in animal genomes in both sexes and across multiple stages of development. For the horse, a biobank of tissues and cells was created, which includes 80 tissues and three cell types from two adult mares. Last year, we reported on the creation of this biobank to be used by the equine community in the functional annotation of the genome in accordance with FAANG Consortium guidelines. Since the Plant and Animal Genome conference in January of 2017, the FAANG biobank was used in the generation of 7 different datasets. In collaboration with the equine genetics community, Reduced Representation Bisulfite sequencing, Microbiome sequencing, and Chromatin Immunoprecipitation sequencing have been conducted. In addition, to date, RNA has been isolated from 34 tissues of both biobank mares using Trizol(r) chloroform phase separation and clean up via Zymo Research columns. Extracted RNA had an average RIN score of 8.2 prior to stranded library preparation. mRNA was sequenced on the Illumina HiSeq 4000. Data are publically available and linked to the phenotype information within the FAANG database. Analysis of the RNA-seq data is ongoing to determine specific signatures of each tissue type

Rabbit RNA-seq time-series of the development of seven major organs.

This dataset covers the development of 7 organs (brain, cerebellum, heart, kidney, liver, ovary and testis) from embryonic day 12 to adulthood.

Mouse RNA-seq time-series of the development of seven major organs

This dataset covers the development of 7 organs (brain, cerebellum, heart, kidney, liver, ovary and testis) from embryonic day 10.5 to adulthood.

Rat RNA-seq time-series of the development of seven major organs

This dataset covers the development of 7 organs (brain, cerebellum, heart, kidney, liver, ovary and testis) from embryonic day 11 to adulthood.

Rhesus macaque RNA-seq time-series of the development of six major organs

This dataset covers the development of 6 organs (brain, cerebellum, heart, kidney, liver and testis) from embryonic day 93 to adulthood.

Human RNA-seq time-series of the development of seven major organs

This dataset covers the development of 7 organs (brain, cerebellum, heart, kidney, liver, ovary and testis) from 4 weeks post conception to adulthood (including ageing).

Opossum RNA-seq time-series of the development of seven major organs

This dataset covers the development of 7 organs (brain, cerebellum, heart, kidney, liver, ovary and testis) from embryonic day 13.5 to adulthood.

Transcriptome profiling of liver and T cells in 4 livestock species by the FAANG pilot project FR-AgENCODE

10.1186/s12915-019-0726-5

RNA sequencing of liver and T cells for transcriptome characterization in the 4 livestock species of the FAANG pilot project FR-AgENCODE at the INRA. RNA-seq profiling was performed in liver-dissociated cells, PBMC-sorted CD4+ primary T cells and PBMC-sorted CD8+ primary T cells from 4 biological replicates (2 males and 2 females) of the 4 target species of the FR-AgENCODE project: pig (Sus scrofa), cattle (Bos taurus), goat (Capra hircus) and chicken (Gallus gallus) in order to contribute to the functional annotation of these genomes. 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".

Ovine pulmonary adenocarcinoma (OPA) is a chronic respiratory disease of sheep caused by jaagsiekte sheep retrovirus (JSRV). JSRV infects respiratory epithelial cells and initiates tumor growth. OPA is an important economic and welfare issue for sheep far

Ovine pulmonary adenocarcinoma (OPA) is a chronic respiratory disease of sheep caused by jaagsiekte sheep retrovirus (JSRV). JSRV infects respiratory epithelial cells and initiates tumor growth. OPA is an important economic and welfare issue for sheep farmers but is also considered to be a valuable animal model for human lung adenocarcinoma. In this study, we investigated the pathogenesis of OPA at the gene expression level and used the deregulated gene list to tp compare to transcriptional changes occurring in human lung cancer. Whole transcriptome profiling was performed on lung samples derived from JSRV-infected and uninfected lambs using RNA-seq. Following mapping of sequence reads to the sheep genome, differentially expressed genes were identified. A list of 1,971 differentially expressed transcripts was identified between the two groups. The main differentially expressed pathways of the upregulated genes were related to immune response to wound healing, tumorigenesis, epithelial cell differentiation and tissue development. Several genes involved in these biological processes were confirmed with immunohistochemistry and RT-qPCR. Important novel insights include the activation of Hippo signaling in OPA and the upregulation of a family of tyrosine kinase receptor ligands, both of which may have important contributions to oncogenesis in this disease. In addition, a variety of myeloid cell markers were upregulated, reflecting a role for tumor associated macrophgaes in this disease. Pathway and functional annotation analysis was performed using Ingenuity pathway analysis and DAVID annotation software and sheep data were compared with already published data derived from non-small cell lung cancer cases in humans. Many of the upregulated gene have also been shown to play an important role in human lung adenocarcinoma and ??? analysis confirmed the closer similarity of experimental OPA with early stage human lung adenocarcinoma. Sheep lung adenocarcinoma shares important similarities with human lung adenocarcinoma. This analysis provides a great deal of new information regarding the pathogenesis of OPA at a transcriptional level and strengthens the use of this naturally occurring animal model for human lung adenocarcinoma.

RNA-seq reveals extremely low levels of reticulocyte-derived globin gene transcripts in peripheral blood from cattle (Bos taurus)

RNA-seq has emerged as an important technology for measuring gene expression in peripheral blood samples collected from humans and other vertebrate species. However, an obstacle to these methods in many mammalian species is the presence of reticulocyte-derived globin mRNAs in large quantities, which can complicate RNA-seq library sequencing and impede detection of other mRNA transcripts. Here, we use comparative analyses of published RNA-seq data sets from human, porcine, and equine peripheral blood, in addition to bovine data generated by us, to systematically assess the impact of globin mRNA on routine transcriptome profiling of whole blood in cattle and horses. Bovine peripheral blood was collected into Tempus blood RNA tubes and total RNA was subsequent extracted. Ten paired-end 2 x 100 bp RNA-seq libraries were generated and then sequenced in an Illumina HiSeq 2000 platform over five lanes.The results of these analyses demonstrate that total RNA isolated from equine and bovine peripheral blood contains very low levels of globin mRNA transcripts, thereby negating the need for globin depletion and greatly simplifying blood-based transcriptomics studies in these two domestic species.

Transcriptome diversity and differential expression of supporting limb laminitis

To date, very few studies have examined laminitis from the transcriptome perspective. Our objective was to identify genes and pathways involved in the pathogenesis of equine supporting limb laminitis to further understanding of the disease etiology. We generated an updated lamellar transcriptome using PacBio Iso-Seq to supplement current equine annotation for differential expression analysis using Illumina RNA-seq.

Using ribosome profiling and matched RNA sequencing to study the evolution of gene expression levels in mammalian organs across two major gene expression layers

Ribosome profiling (Ribo-seq) and matched RNA sequencing (RNA-seq) data for three major mammalian organs (brain (cerebrum), liver, and testis) from five representatives of the three main mammalian lineages: human, macaque, mouse (placental mammals); grey short-tailed opossum (marsupials); and platypus (egg-laying monotremes).

Comprehensive RNA-Seq Profiling of the Lung Transcriptome of Bashbay Sheep in Response to Experimental Mycoplasma ovipneumoniae Infection

Bashbay sheep (Ovis aries), an indigenous breed of Xinjiang, China, has many excellent characters. It is resistant to Mycoplasma ovipneumoniae (MO) infection, the causative agent of Mycoplasma ovipneumonia, a chronic respiratory disease, which is harmful to the sheep industry. As of date, knowledge regarding the mechanisms responsible for MO pathogenesis in scant. Herein, we report the results of transcriptome profiling of the lung tissue of Bashbay sheep experimentally infected with M. ovipneumoniae strain at 4days post-infection(DPI) and 14DPI in comparison to the mock-infected animals (0d), which was performed by Illumina deep sequencing (RNASeq). The analysis of differentially expressed genes (DEGs) was performed to determine the concomitant gene-specific temporal patterns of mRNA expression in the lung after MO infection. The results showed 1048 DEGs (up-regulated: 575; down-regulated: 473) were screened at 4DPI compared to 0d, and 2823 DEGs (up-regulated: 1362; down-regulated: 1461) were screened at 14DPI compared to 0d. KEGG analysis found that the DEGs at 4DPI and 14DPI compared to 0d were enriched in 245 and 287 pathways respectively, the most closely related to MO infection of which was TLR signaling pathway (p<0.01). Two pathways (First: LAMP-TLR2/TLR6-MyD88-MKK6-AP1-IL1B; Second: LAMP-TLR8- MyD88-IRF5-RANTES) were obtained from the figure of TLR signaling pathway that DEGs related with MO infection were mapped to. GO analysis found that the DEGs in different groups were enriched to 1580 and 4561 terms, the most closely releted to MO infection of which was positive regulation of inflammatory response (p<0.01).Our study shouldpave the road for the further analysis of Mycoplasma ovipneumonia.

RNA-seq of liver and pyloric caeca in salmon fry before and after initial feeding

10.1016/j.aquaculture.2018.12.089

The salmon fry was sampled at day 0 (before initial feeding) and day 1 (20h after initial feeding). The fish was about 0.2g, liver and pyloric caeca were dissected and used for RNA-seq. Fish was given standard commercial diets with high PUFA.

Abnormal keratinocyte differentiation in the nasal planum of Labrador Retrievers with hereditary nasal parakeratosis (HNPK)

Formalin-fixed biopsies of the nasal planum of Labrador Retrievers were screened by immunofluorescence microscopy for the presence and distribution of epidermal proliferation and differentiation markers. Gene expression of these markers was further analysed using RNA sequencing (RNA-seq) and ultrastructural epidermal differences were investigated by electron microscopy.

Comprehensive RNA-Seq profiling of the lung transcriptome of Argali hybrid sheep in response to experimental Mycoplasma ovipneumoniae infection

The Bashbay sheep (Ovis aries), an indigenous breed of Xinjiang, China, has many excellent characteristics. However, hybrids of Argali sheep and Bashbay sheep are susceptible to Mycoplasma ovipneumoniae infection, the causative agent of mycoplasma ovipneumonia, a chronic respiratory disease that is harmful to the sheep industry. To date, knowledge regarding the mechanisms responsible for M. ovipneumoniae pathogenesis is in scant. Herein, we report the results of transcriptome profiling of lung tissues from Argali hybrid sheep experimentally infected with an M. ovipneumoniae strain at 4 and 14 days post-infection, in comparison to mock-infected animals (0 d). Transcriptome profiling was performed by deep RNA sequencing, using the Illumina platform. The analysis of differentially expressed genes was performed to determine concomitant gene-specific temporal patterns of mRNA expression in the lungs after M. ovipneumoniae infection. We found 156 differentially expressed genes (44 up-regulated, 112 down-regulated) when comparing transcriptomic data at 4 and 0 days post-infection, and 367 (35 up-regulated, 332 down-regulated) when comparing 14 versus 0 days post-infection. Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that the differentially expressed genes at 4 and 14 versus 0 days post-infection were enriched in 109 and 150 pathways, respectively, and the Primary immunodeficiency pathway was considered most closely related to MO infection (p < 0.01). Hyper-IgM syndrome was identified based on the B-cell immunodeficiency signaling pathway from differentially expressed genes related M. ovipneumoniae infection. Gene Ontology analysis showed that differentially expressed genes in different groups were enriched for 497 and 928 terms, where those most closely related to M. ovipneumoniae infection are ciliated motor damage (p < 0.01). These results could aid in understanding why the Argali hybrid sheep are susceptible to MO as well as how M. ovipneumoniae infection progresses in the lungs and may provide useful information regarding key regulatory pathways.

RNA-seq of healthy brain, liver and muscle in 5 mammals

RNA-seq of total RNA was produced to aid in re-annotation of genes in horse, mouse, opossum, macaque, rat and pig. The RNA-seq was isolated from brain, liver and/or muscle.

RNA-seq in 4 tissues of 10 mammals

To study the tissue-specific evolution of regulatory elements and gene expression in the mammalian lineage, we created a comprehensive map of promoters and enhancers in 4 tissues of 10 mammalian species. To assay tissue-specific gene expression we performed RNA-seq experiments in adult liver, muscle, brain and testis of all 10 species. The species included in the study are: macaque, marmoset, mouse, rat, rabbit, pig, dog, cat, horse and opossum. To map in-vivo promoters and enhancers, we performed ChIP-seq experiments for H3K4me3, H3K27ac and H3K4me1 in all tissues and species and submitted these separately to ArrayExpress.

This is a repository for goat transcriptomes

We would depositing all goat transcriptomes (RNA-seq) from various tissues.

Comparison of the myometrial transcriptome from singleton and twin pregnancies by high throughput RNA-Seq

We performed high-throughput RNA sequencing (RNA-Seq) of human myometrium from singleton and twin pregnancies at term (> 37+0 weeks) and preterm (< 37+0 weeks), collected during pre-labour Caesarean Section. We performed high-throughput RNA sequencing (RNA-Seq) of human myometrium from singleton and twin pregnancies at term (> 37+0 weeks) and preterm (< 37+0 weeks), collected during pre-labour Caesarean Section.

RNA-seq of prefrontal cortex in adult human, chimp and macaque

The human brain has changed dramatically since humans diverged from our closest living relatives, chimpanzees and the other great apes. However, the genetic and developmental programs underlying this divergence are not fully understood. Here, we generate single-nucleus RNA-seq data of human, chimpanzee and macaque adult prefrontal cortex. Spatial information is obtained by isolating nuclei from sequential sections sliced from basal to apical positions. Bulk RNA-seq is performed for the same sections to determine positional information of the sections, by comparing the section transcriptome with published transcriptome data of cortical layers in human, chimpanzee and macaque.