mRNA-Seq data from the ovaries of two Finnsheep ewes collected during out-of-season breeding period

Ovarian biopsies from two Finnsheep ewes S48 and S50 were used for RNA-Seq. This data was used as a pilot study for PRJEB22101 and PRJEB32852. miRNA-Seq data from same animals are available under PRJEB34418. The publication associated with this data is available here: https://journal.fi/afs/article/view/46512

RNAseq of farmed and wild Atlantic salmon fed vegetable oil or fish oil or phospholipid diet from first feeding

10.1111/mec.15446

Farmed and wild Atlantic salmon was given either vegetable oil (low DHA and EPA) feed or fish oil (high in DHA and EPA) feed or phospholipid (high in phospholipid) feed from start of feeding. We sampled and RNAseq two tissues (pyloric caeca and liver) on day 0, day 48, day 65 and day 94 after initial feeding.

Gene expression of immune tissues and ovaries from a marine population of threespine sticklebacks from Denmark

The threespine stickleback (Gasterosteus aculeatus) has repeatedly colonized and adapted to diverse freshwater habitats since the last glaciation. To study gene expression across different populations, we sequenced transcriptomes from wild-caught sticklebacks from a marine environment to compare with data from freshwater populations published with the project accessions PRJEB8677 and PRJEB26492. Genomic data from these individuals can be found under the project accession ERP001339.

Bulk RNA-seq of the human fetal neocortex, lateral ganglionic eminence and medial ganglionic eminence at 7, 9, 11 and 20 post-conceptional weeks

Deep transcriptional profiling of the human neocortex, lateral ganglionic eminence (LGE) and medial ganglionic eminences (MGE), from 7 to 20 post-conceptional weeks (pcw), for de novo lincRNAs discovery and to establish a unique coding and non-coding gene signature for the three different regions.

RNA-seq of tissue panel samples from zebrafish (Danio rerio), medaka (Oryzias latipes), and rainbow trout (Oncorhynchus mykiss)

The aim of this sequencing experiment was to make available tissue expression panels for selected fish species for comparative expression studies between the species. Tissue samples were collected for zebrafish (Danio rerio), medaka (Oryzias latipes), and rainbow trout (Oncorhynchus mykiss). Tissue types included liver, skin, muscle, heart, gut, gill, eye, brain for all three species, with additionally pyloric caeca, kidney, head kidney, and spleen for rainbow trout. Only liver samples were taken in replicate of four or three for rainbow trout. All fish were raised under standard rearing conditions for the species. Total RNA was extracted from the tissue samples and paired‐end sequencing of sample libraries was completed on an Illumina HiSeq 2500 with 125‐bp reads. Processed count tables per species as raw counts, FPKM, or TPM, were generated from read alignment to the Ensembl genomes of the respective species using STAR and gene level counting using RSEM and Ensembl gene annotation.

Transcriptional landscape of porcine circulating immune cells

10.3389/fgene.2021.689406

Bulk RNA-seq from immune sorted cells and single cell RNA sequencing data from porcine PBMCs were generated to determine the gene expression pattern of porcine immune cells. 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 the FAANG Data Coordination Centre and FAANG consortium (email faang-dcc@ebi.ac.uk and cc faang@iastate.edu) to enquire. The full guidelines can be found at http://www.faang.org/data-share-principle."

RNAseq for Atlantic Salmon tissues

The European project AQUA-FAANG aims to improve understanding the genome function and usage of genotype-to-phenotype prediction in the six most important European farmed fish species. 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 the FAANG Data Coordination Centre and FAANG consortium (email faang-dcc@ebi.ac.uk and cc faang@iastate.edu) to enquire. The full guidelines can be found at http://www.faang.org/data-share-principle

RNA-Seq of chimpanzee (Pan troglodytes), gorilla (Gorilla gorilla), gibbon (Hylobates lar) and marmoset (Callithrix jacchus) adult testis

RNA sequencing (RNA-seq) was used to annotate chimpanzee, gorilla, gibbon, and marmoset genome and transcript isoforms in adult testis. This dataset is part of a larger evolutionary study of adult testis at the single-nucleus level (97,521 single-nuclei in total) across mammals including 10 representatives of the three main mammalian lineages: human, chimpanzee, bonobo, gorilla, gibbon, rhesus macaque, marmoset, mouse (placental mammals); grey short-tailed opossum (marsupials); and platypus (egg-laying monotremes). Corresponding data were generated for a bird (red junglefowl, the progenitor of domestic chicken), to be used as an evolutionary outgroup.

PIG transcriptome and gene expression

RNA sequencing of pig tissues for transcritpome annotation and expression analysis.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 the FAANG Data Coordination Centre and FAANG consortium (email faang-dcc@ebi.ac.uk and cc faang@iastate.edu) to enquire.The full guidelines can be found at http://www.faang.org/data-share-principle.

Transcriptome of wild type N2 worms at embronic stage and starved L1 stage

Non-coding RNA profiling by high throughput sequencing

Multimodal RNA-seq using single-strand, double-strand, and circligase-based capture yields a refined and extended description of the C. elegans transcriptome

Expression profiling by high throughput sequencing

The evolution of gene expression levels in mammalian organs

10.1038/nature10532

Changes in gene expression are thought to underlie many of the phenotypic differences between species. However, large-scale analyses of gene expression evolution were until recently prevented by technological limitations. Here we report the sequencing of polyadenylated RNA from six organs across ten species that represent all major mammalian lineages (placentals, marsupials and monotremes) and birds (the evolutionary outgroup), with the goal of understanding the dynamics of mammalian transcriptome evolution. We show that the rate of gene expression evolution varies among organs, lineages and chromosomes, owing to differences in selective pressures: transcriptome change was slow in nervous tissues and rapid in testes, slower in rodents than in apes and monotremes, and rapid for the X chromosome right after its formation. Although gene expression evolution in mammals was strongly shaped by purifying selection, we identify numerous potentially selectively driven expression switches, which occurred at different rates across lineages and tissues and which probably contributed to the specific organ biology of various mammals. Our transcriptome data provide a valuable resource for functional and evolutionary analyses of mammalian genomes.

[E-MTAB-445] Transcription profiling by high throughput sequencing of blackface sheep infected with the gastrointestinal helminth Teladorsagia circumcincta to analyse resistance to infection

Digital gene expression analysis of gastrointestinal helminth resistance in Scottish blackface lambs

[E-MTAB-513] Illumina Human Body Map 2.0 Project

Transcription profiling by high throughput sequencing of individual and mixture of 16 human tissues RNA.

[E-MTAB-599] Mouse Transcriptome

10.1038/nature10413

Sequencing the transcriptome of DBAxC57BL/6J mice. To study the regulation of transcription, splicing and RNA turnover we have sequenced the transcriptomes of tissues collected DBAxC57BL/6J mice.

RNA sequencing reveals diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development.

10.1101/gr.141424.112

Examination of the transcriptome of Xenopus tropicalis from a 2-cell fertilized embryo to a stage 45 feeding tapole

RNA sequencing in fly heads to examine the effect of spermidine feeding on transcription in the ageing fly brain.

10.1038/nn.3512

mRNA profiles from 3 and 10 day old Drosophila melanogaster heads were generated in duplicate by deep sequencing using Illumina GAIIx. mRNA profiles from flies that were fed food with 5mM spermidine were compared to profiles from flies that had no spermidine in thier food.

Transcriptomic analysis of zebrafish during development and homeostasis

10.1016/j.ydbio.2013.05.006

Sequencing libraries were generated from total RNA samples following the mRNAseq protocol for the generation of single end (16-36 hpf, 5 day larvae, adult head and adult tail) or paired end (24 hpf) libraries (Illumina). Single end reads of 36 nucleotides and paired end reads (2 x 76 nucleotides) were obtained with a GAIIx (Illumina). Gene expression at the different stages/tissu was assessed by cufflinks and HTseq.

The evolutionary landscape of alternative splicing in vertebrate species

10.1126/science.1230612

How species with similar repertoires of protein coding genes differ so dramatically at the phenotypic level is poorly understood. From comparing the transcriptomes of multiple organs from vertebrate species spanning ~350 million years of evolution, we observe significant differences in alternative splicing complexity between the main vertebrate lineages, with the highest complexity in the primate lineage. Moreover, within as little as six million years, the splicing profiles of physiologically-equivalent organs have diverged to the extent that they are more strongly related to the identity of a species than they are to organ type. Most vertebrate species-specific splicing patterns are governed by the highly variable use of a largely conserved cis-regulatory code. However, a smaller number of pronounced species-dependent splicing changes are predicted to remodel interactions involving factors acting at multiple steps in gene regulation. These events are expected to further contribute to the dramatic diversification of alternative splicing as well as to other gene regulatory changes that contribute to phenotypic differences among vertebrate species.

Caenorhabditis sex-specific RNAseq

Expression profiling by high throughput sequencing

Evolutionary dynamics of gene and isoform regulation in mammalian tissues

10.1126/science.1228186

Most mammalian genes produce multiple distinct mRNAs through alternative splicing, but the extent of splicing conservation is not clear. To assess tissue-specific transcriptome variation across mammals, we sequenced cDNA from 9 tissues from 4 mammals and one bird in biological triplicate, at unprecedented depth. We find that while tissue-specific gene expression programs are largely conserved, alternative splicing is well conserved in only a subset of tissues and is frequently lineage-specific. Thousands of novel, lineage-specific and conserved alternative exons were identified; widely conserved alternative exons had signatures of binding by MBNL, PTB, RBFOX, STAR and TIA family splicing factors, implicating them as ancestral mammalian splicing regulators. Our data also indicates that alternative splicing is often used to alter protein phosphorylatability, delimiting the scope of kinase signaling.

Marker gene discovery for Staphylococcus epidermidis infection in zebrafish embryos (RNA-Seq)

10.1007/s00251-014-0820-3

We use the zebrafish embryo model to study the innate immune response against Staphylococcus epidermidis. Therefore, we injected S. epidermidis into the yolk at 2 hpf and took samples at 5 days post injection.

Gene Expression Defines Natural Changes in Mammalian Lifespan

10.1111/acel.12283

RNA-seq gene expression profiling in normal liver, kidney and brain of 33 mammalian species.

The evolution of lncRNA repertoires and expression patterns in tetrapods

10.1038/nature12943

To broaden our understanding of lncRNA evolution, we used an extensive RNA-seq dataset to establish lncRNA repertoires and homologous gene families in 11 tetrapod species. We analyzed the poly- adenylated transcriptomes of 8 organs (cortex/whole brain without cerebellum, cerebellum, heart, kidney, liver, placenta, ovary and testis) and 11 species (human, chimpanzee, bonobo, gorilla, orangutan, macaque, mouse, opossum, platypus, chicken and the frog Xenopus tropicalis), which shared a common ancestor ~370 millions of years (MY) ago. Our dataset included 47 strand-specific samples, which allowed us to confirm the orientation of gene predictions and to address the evolution of sense-antisense transcripts. See also GSE43721 (Soumillon et al, Cell Reports, 2013) for three strand-specific samples for mouse brain, liver and testis.

A Genome-Wide Survey of Maternal and Embryonic Transcripts during Xenopus tropicalis Development

10.1186/1471-2164-14-762

Profiles of polyadenylated mRNA (6 stages) and ribosomal RNA-depleted total RNA (3 stages) through early Xenopus tropicalis development

Cellular source and mechanisms of high transcriptome complexity in the mammalian testis (RNA-Seq organs)

10.1016/j.celrep.2013.05.031

Understanding the extent of genomic transcription and its functional relevance is a central goal in genomics research. However, detailed genome-wide investigations of transcriptome complexities in major mammalian organs and their underlying cellular sources, transcriptional mechanisms, and functional relevance have been scarce. Here we first show, using extensive RNA-seq data, that transcription of both functional and nonfunctional genomic elements is substantially more widespread in the testis than in other organs across representative mammals. By scrutinizing the transcriptomes of all main testicular cell types in the mouse, we then reveal that meiotic spermatocytes and especially post-meiotic round spermatids have remarkably diverse transcriptomes, which explains the high transcriptome complexity of the testis as a whole. The widespread transcriptional activity in spermatocytes and spermatids encompasses protein-coding genes and long noncoding RNA genes but also poorly conserved intergenic sequences, suggesting that much of it is not of immediate functional relevance. Rather, our analyses of genome-wide epigenetic data show that this prevalent transcription, which apparently promoted the birth of new genes during evolution, results from a highly permissive chromatin state during and after meiosis that may ultimately facilitate the replacement of histones by protamines during late spermatogenesis.

Transcriptome data used for gene annotation

10.1038/ng.2811

To optimize the genome annotation, four tissue RNA libraries (i.e. heart, liver, lung and kidney) were constructed using the Illumina mRNA-Seq Prep Kit

Comparative Validation of the D. melanogaster Encyclopedia of DNA Elements Transcript Models

The model organism Encyclopedia of DNA Elements project (modENCODE) has produced a comprehensive annotation of D. melanogaster transcript models based on an enormous amount of high-throughput experimental data. However, some transcribed elements may not be functional, and technical artifacts may lead to erroneous inference of transcription. Inter-species comparison provides confidence to predicted annotation, since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function. We have performed RNA-Seq and CAGE-Seq experiments on more than 80 samples from multiple tissues and stages of 15 Drosophila species, including 8 previously unsequenced genomes. We have found strikingly conserved sequence, expression, and splicing for the vast majority of transcript models in modENCODE annotation (e.g. 99% exons of coding sequences (CDS), 88% exons of untranslated regions (UTR), and 87% splicing events), indicating that the transcriptome annotation is of very high quality. We also describe dynamic transcriptome evolution within the Drosophila genus, including conserved promoter structure, labile positions of transcription start sites, and rapidly evolving RNA-editing events. We demonstrate how this phylogenetic approach to DNA element validation will prove useful in the annotation of other high priority genomes, especially for genomes that are less compact than Drosophila (e.g. the vast majority of vertebrate genomes).

Developmental arrest of Drosophila survival motor neuron (Smn) mutants accounts for differences in expression of minor intron-containing genes

10.1261/rna.038919.113

RNA-seq was used to analyze mRNA levels and splicing differences between wild-type (Oregon R) and Smn null mutant larvae.

RNA-Seq Identifies Novel Myocardial Gene Expression Signatures of Heart Failure [RNA-seq]

10.1016/j.ygeno.2014.12.002

Identify the signature genes based on RNA-seq come from six Heart Failure and healthy individuals. Validation is based on Affymetrix microarray of a total of 313 individuals with/without Heart Failure.

The human skeletal muscle transcriptome - sex differences, alternative splicing and tissue homogeneity assessed with RNA sequencing

10.1096/fj.14-255000

The amount of RNA sequencing data on skeletal muscle is very limited. We have analyzed a large set of human muscle biopsy samples and provide extensive information on the baseline skeletal muscle transcriptome, including completely novel protein-coding transcripts.

The human skeletal muscle transcriptome assessed with RNA sequencing

10.1371/journal.pgen.1006294

The amount of RNA sequencing data on skeletal muscle is very limited. We have analyzed a large set of human muscle biopsy samples and provide extensive information on the baseline skeletal muscle transcriptome, including completely novel protein-coding transcripts.

RNA-Seq of the corpus callosum from 12 individuals

10.15252/msb.20145487

We performed RNA-Seq for the corpus callosum sampled from 12 individuals. The samples were dissected from the frozen postmortem brain. The 12 individuals were matched by their age, sex and ethnicity for the postmortem brain samples, but differed in their disease status with half of the subjects were diagnosed with autism spectrum disorders.

Spring Varaemia of Carp Virus (SVCV) infection of adult zebrafish

10.4049/jimmunol.1402415

During viral infection, a large number of immune response signaling molecules including the interferon regulatory (IRF) family and type I interferon (IFN) transcribe. The exact identity and expression levels of fish IRFs and type-I IFNs during viral infection remains largely unknown. Here, we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type-I IFNs during two stages of SVCV infection, i.e. 6h and 24h post-infection. For 12 zebrafish IRFs, we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV-infected tissues, but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7, which together with DrIRF3, was highly induced by SVCV infection. For type-I IFNs, zebrafish has four IFN genes, three of which, IFN1/2/3, particularly IFN 1 and IFN 3, were significantly transcribed under the same conditions.

RNA sequencing of the developing zebrafish head

10.1101/gr.176925.114

We sequenced strand-specific mRNA from the heads of 3 groups of wild type zebrafish (Danio rerio) 5 days post fertilization.

Tissue-specific circular RNA induction during human fetal development

10.1186/s13059-015-0690-5

The pervasive expression of circular RNA from protein coding loci is a recently discovered feature of many eukaryotic gene expression programs. Computational methods to discover and quantify circular RNA are essential to the study of the mechanisms of circular RNA biogenesis and potential functional roles they may play. In this paper, we present a new statistical algorithm that increases the sensitivity and specificity of circular RNA detection.by discovering and quantifying circular and linear RNA splicing events at both annotated exon boundaries and in un-annotated regions of the genome Unlike previous approaches which rely on heuristics like read count and homology between exons predicted to be circularized to determine confidence in prediction of circular RNA expression, our algorithm is a statistical approach. We have used this algorithm to discover general induction of circular RNAs in many tissues during human fetal development. We find that some regions of the brain show marked enrichment for genes where circular RNA is the dominant isoform. Beyond this global trend, specific circular RNAs are tissue specifically induced during fetal development, including a circular isoform of NCX1 in the developing fetal heart that, by 20 weeks, is more highly expressed than the linear isoform as well as beta-actin. In addition, while the vast majority of circular RNA production occurs at canonical U2 (major spliceosome) splice sites, we find the first examples of developmentally induced circular RNAs processed by the U12 (minor) spliceosome, and an enriched propensity of U12 donors to splice into circular RNA at un-annotated, rather than annotated, exons. Together, our algorithm and its results suggest a potentially significant role for circular RNA in human development.

Transcriptional profiling of zebrafish embryos developmentally exposed to oxygenated PAHs 1,9-benz-10-anthrone and benzanthracene-7,12-dione

10.1093/toxsci/kfv139

The purpose of this study was to identify transcripts differentially expressed in zebrafish embryos exposed to two oxygenated PAHs, 1,9-benz-10-anthrone and benzanthracene-7,12-dione, which cause abnormal development.

Yap and Taz regulate retinal pigment epithelial cell fate

10.1242/dev.119008

The optic vesicle comprises a pool of bi-potential progenitor cells from which the retinal pigment epithelium (RPE) and neural retina fates segregate during ocular morphogenesis. Several transcription factors and signaling pathways have been shown to be important for RPE maintenance and differentiation, but an understanding of the initial fate specification and determination of this ocular cell type is lacking. We show that Yap/Taz-Tead activity is necessary and sufficient for optic vesicle progenitors to adopt RPE identity in zebrafish. A Teadresponsive transgene is expressed within the domain of the optic cup from which RPE arises, and Yap immunoreactivity localizes to the nuclei of prospective RPE cells. yap (yap1) mutants lack a subset of RPE cells and/or exhibit coloboma. Loss of RPE in yap mutants is exacerbated in combination with taz (wwtr1) mutant alleles such that, when Yap and Taz are both absent, optic vesicle progenitor cells completely lose their ability to form RPE. The mechanism of Yap dependent RPE cell type determination is reliant on both nuclear localization of Yap and interaction with a Tead co-factor. In contrast to loss of Yap and Taz, overexpression of either protein within optic vesicle progenitors leads to ectopic pigmentation in a dosagedependent manner. Overall, this study identifies Yap and Taz as key early regulators of RPE genesis and provides a mechanistic framework for understanding the congenital ocular defects of Sveinsson's chorioretinal atrophy and congenital retinal coloboma.

Telomerase is essential for zebrafish heart regeneration

10.1016/j.celrep.2015.07.064

Unlike human hearts, zebrafish hearts efficiently regenerate after injury. Regeneration is driven by the strong proliferation response of its cardiomyocytes to injury. In this study, we show that active telomerase is required for cardiomyocyte proliferation and full organ recovery, supporting the potential of telomerase therapy as a means of stimulating cell proliferation upon myocardial infarction.

Mapping and quantifying mouse transcriptome by RNA-Seq

Mus musculus strain:C57BL/6

Chromatin-Associated Periodicity in Genetic Variation Downstream of Transcriptional Start Sites

Might DNA sequence variation reflect germline genetic activity and underlying chromatin structure? Using two strains of medaka (Japanese killifish, Oryzias latipes), we compared genomic sequence and mapped ~37.3 million nucleosome cores from medaka Hd-rR blastulae, together with 11,654 representative transcription start sites from six embryonic stages. We observed a ~200-base pair (bp) periodic pattern of genetic variation downstream of transcription start sites; the rate of insertions and deletions longer than 1 bp peaked at positions of approximately 200, 400, and 600 bp, whereas the point mutation rate showed corresponding valleys. This ~200-bp periodicity was correlated with the chromatin structure, with nucleosome occupancy minimized at positions 0, 200, 400, and 600 bp. These data exemplify the potential for genetic activity (transcription) and chromatin structure to contribute in molding the DNA sequence on an evolutionary time scale.

Deep sequencing of the Caenorhabditis elegans transcriptome using RNA isolated from various developmental stages under various experimental conditions RW0001

The goal of this study, started as a part of the modENCODE project, is to detect and characterize previously unannotated transcripts of the C. elegans genome.

Sex-specific and lineage-specific alternative splicing in primates

Comparative studies of gene regulation suggest an important role for natural selection in shaping gene expression patterns within and between species. Most of these studies, however, estimated gene expression levels using microarray probes designed to hybridize to only a small proportion of each gene. Here we used recently-developed RNA sequencing protocols, which side-step this limitation, to assess intra- and inter-species variation in gene regulatory processes in considerably more detail than was previously possible. Specifically, we used RNAseq to study transcript levels in humans, chimpanzees, and rhesus macaques, using liver RNA samples from three males and three females from each species. Our approach allowed us to identify a large number of genes whose expression levels likely evolve under natural selection in primates. These include a subset of genes with conserved sexually dimorphic expression patterns across the three species, which we found to be enriched for genes involved in lipid metabolism. Our data also suggest that while alternative splicing is tightly regulated within and between species, sex-specific and lineage-specific changes in the expression of different splice forms are also frequent. Intriguingly, among genes in which a change in exon usage occurred exclusively in the human lineage, we found an enrichment of genes involved in anatomical structure and morphogenesis, raising the possibility that differences in the regulation of alternative splicing have been an important force in human evolution. Keywords: Gene Regulation Study Overall design: Examination of gene expression levels in livers from three primate species (human, chimpanzee, and rhesus macaque), using 3 male and 3 female samples from each species.

modENCODE D. melanogaster Developmental Total RNA-Seq

These data were produced for the modENCODE project (http://www.modencode.org/). For a description of the protocols and other experimental details please refer to the data distribution site http://www.modencode.org/Celniker.shtml. In accordance with NHGRI guidelines for community resource projects (http://www.genome.gov/), there is no restriction on the use or analysis of these data. However, the end-user is asked to respect a nine-month moratorium (from the public submission date) before submitting manuscripts describing analysis of these data. If the data producer has published any description of these data before the nine-month period, the moratorium ceases to apply and this accession page will be updated to note the appropriate citation.

Developmental Profile of the Drosophila Transcriptome by Paired-End RNA-Sequencing

In order to gain a broad sampling of the Drosophila transcriptome, RNA-Seq experiments were performed at all stages of the Drosophila life cycle, and 12 independent cDNA libraries were generated, including embryonic, larval, pupal, and adult. Some libraries were staged as specific windows: 2-4 hour embryo, 14-16 hour embryo, 3rd instar larva, 3-day pupa, and 17-day adult. Additional libraries were derived from broadly staged mixed samples: embryo, larvae, and pupa. Three-day old male and female adults were sequenced separately for discovery of sex-specific variation. Finally, one library of mixed-age pupal RNA was sequenced in replicate as a validation of the technology. A total of 272 million paired-end reads of 64-75 base pairs in length were obtained, representing greater than 690x sequence coverage of the 30Mb Drosophila melanogaster transcriptome.

A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species

A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species

Caenorhabditis angaria genome sequencing project

Whole Genome Sequencing

D. melanogaster Dissected Tissue RNASeq

ModENCODE_3445 and modENCODE_3446 and ModENCODE_4241 up to ModENCODE_4269

Oryzias latipes Project

Oryzias latipes Project

Sequencing and characterization of the guppy (Poecilia reticulata) transcriptome

Studies on the guppy (Poecilia reticulata) have advanced our general understanding of ecology and evolutionary biology but progress in that understanding has been hampered by a lack of genetic and genomic tools. Next-generation sequencing tools are providing researchers with a relatively fast and affordable option to develop genomic tools. Here we present a de novo assembly of the guppy transcriptome using 454 sequence reads. We also evaluate some of the uses of the transcriptome, including a pilot study in gene expression differences using Illumina short sequence reads.