Transcriptomes from the tissues of the brain-pituitary-gonad (BPG) axis of T10 samples revealed a differential gene expression ... Transcriptomes from the tissues of the brain-pituitary-gonad (BPG) axis of T10 samples revealed a differential gene expression ... Using BWA-MEM [30] to map our transcripts to our de novo transcriptome resulted in a mapping percentage range of 89 to 96%. Out ... Transcriptome analysis. Raw reads obtained from Macrogen were quality assessed using fastQC software [71] and were quantified ...

... we used a multiple k-mer approach to assemble a terminal ganglion transcriptome that included ganglia collected one, three, and ... We combined the five transcriptomes to generate a single transcriptome with a total of 2,874,823 contigs (Fig. 1). ... Trinity was used to assemble five individual transcriptomes each ato different k-mer lengths. All transcriptomes were combined ... which were combined to produce a final transcriptome of total 218,030 contigs. The number of contigs in the final transcriptome ...

This study is the first report on identifying bolting and flowering-related lncRNAs based on transcriptome sequencing in ... Herein, we used bioinformatic approaches to analyze the transcriptome datasets from two different accessions Viroflay and ... Description of transcriptome datasets. Two transcriptome datasets [13] generated from leaf tissues of two different accessions ... De novo transcriptome analysis in radish (Raphanus sativus L.) and identification of critical genes involved in bolting and ...

Transcriptome sequencing of SAMs. Pools of samples comprising 15 hand-dissected SAMs for each stage (M1-M10) were harvested in ... A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies. Nat Genet. 2009;41:258-63 ... Transcriptome analysis during cell division in plants. Proc Natl Acad Sci U S A. 2002;99:14825-30. ... As far as we are aware, this particular developmental stage has not previously been characterized by detailed transcriptome ...

Of these, six were detected as transcripts in embryo transcriptome datasets and a further four of these contained a high number ... Those with transcripts identified in tammar embryo transcriptomes are indicated, as are the miRNA genes confirmed by miRDeep2 ... and a further eight had detectable transcripts in whole embryo transcriptome datasets, indicating they are strong candidates ...

A previously performed transcriptome analysis suggests that the expression of 30 and 42 PgNACs are affected by salinity stress ... A previously performed transcriptome analysis suggests that the expression of 30 and 42 PgNACs are affected by salinity stress ... PgNAC expression levels based on a previous transcriptome analysis. The colors in the heat map reflect PgNAC expression levels ... NAC TF GO annotation and expression analysis using transcriptome data. Gene Ontology (GO) terms were assigned to PgNACs using ...

We selected a transcriptome assembly based on the features of the N50 plot over a range of k-mer lengths from 21 to 49. The ... Reference transcriptome sequence assembly. We used the Velvet short read assembly package to perform the transcript assembly ... In this study we assembled a reference transcriptome from representative natural populations of F. grandis collected from Gulf ... We used Bowtie to map the full set of filtered reads to 203,252 assembled transcriptome sequences, then determined the number ...

Correlation between transcriptome and proteome. Spearman Rank correlation was used to compare the transcriptome and proteome ... Table 1 Genes differentially expressed in the transcriptome data as a result of bldA mutation1. Full size table. ... A) Transcriptome and (B) proteome data showing the bldA-dependence of expression of the genes of unknown function SCO4251-4253 ... Correlation between transcriptome and proteome data was computed for each of the 5 time-points in each strain (a vector of 310 ...

3a). Conversely, our pollen-associated transcriptome showed a very high correlation with male transcriptomes and almost no ... SNP-based transcriptome analysis using variants between Col-0 and C24. To distinguish the parental origin of the transcripts, ... Although transcriptomes of pollinated stigmas have been recently published [16, 17], these analyses did not permit the ... Time-course Transcriptome analysis of compatible and incompatible pollen-stigma interactions in Brassica napus L. Front Plant ...

We predict 14,249 open reading frames (ORFs) of which 9,934 are validated by the transcriptome. This phytopathogen has an ... We predict 14,249 open reading frames (ORFs) of which 9,934 are validated by the transcriptome. This phytopathogen has an ... Table S3 provides the transcriptome assembly statistics. Table S4 lists the InterPro codes corresponding to the protein ... We predicted 14,249 protein-coding genes and 9,934 were validated by the transcriptome ( Additional file 1: Table S3). ...

Transcriptome microarray analysis and qRT-PCR validation. S. Typhimurium SL1344 wildtype and CMPG5624 (∆fabR) were cultured as ... Transcriptome analysis of genes controlled by luxS/autoinducer-2 in Salmonella enterica serovar Typhimurium. Foodborne Pathog ...

Transcriptome profiling of the early stages in Atlantic cod revealed the presence of transcripts involved in patterning and ... Transcriptome profiling of the oocytes and embryos of Atlantic cod with an aid of genome-wide microarray provided an insight in ... Transcriptome profiling of the early stages in Atlantic cod revealed the presence of transcripts involved in patterning and ... The UFO transcriptome encoded proteins involved in mRNA processing, some of which showed highly specific expression in oocytes ...

While acknowledging the limitations of our single tissue transcriptome, Fisher tests showed the white shark transcriptome to be ... The white shark transcriptome also contained 8,404 microsatellites (dinucleotide, trinucleotide, or tetranucleotide motifs ≥ ... The white shark heart transcriptome represents a valuable resource for future elasmobranch functional and comparative genomic ... We also compared the transcriptome to other available elasmobranch sequences, for signatures of positive selection and ...

To address this, we sequenced the genome and transcriptome of the widely grown Macadamia integrifolia cultivar 741. Over 95 ... From: Genome and transcriptome sequencing characterises the gene space of Macadamia integrifolia (Proteaceae) ...

Comparative analysis of transcriptomes revealed that 5179 unigenes were differentially expressed (with at least 2-fold changes ... This is the first study to assess the cold-responsive transcriptome in an Ocimum species. Our results suggest that cold ... To increase our understanding of cold stress responses in this species, we performed de novo transcriptome assembly for O. ... pilosum and compared the transcriptomes of plants grown under normal and low temperatures. A total of 115,022,842 high quality ...

Xu Q, Modrek B, Lee C. Genome-wide detection of tissue-specific alternative splicing in the human transcriptome. Nucleic Acids ... Minor class splicing shapes the zebrafish transcriptome during development. Proc Natl Acad Sci U S A. 2014;111(8):3062-7. ... Widespread intron retention in mammals functionally tunes transcriptomes. Genome Res. 2014;24(11):1774-86. ...

This study characterized the canopy-layer specific transcriptome of five sorghum genotypes using RNA sequencing. A set of 284 ... We have conducted a transcriptome analysis to identify genes controlling leaf angle at specific canopy layers and generated new ... Leaf angle phenotypes and canopy layer-specific transcriptome analysis. Leaf angle gradually increased from lower to upper ... The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome ...

By analyzing the methylomes and transcriptomes of 14 fetal and 181 adult livers, we identified 657 differentially methylated ... The transcriptome of the developing liver. Comparison of gene expression levels between the fetal and adult liver samples ... This has been described in the transcriptome of fetal livers at different stages of development in mice [23-25]. ... Comparison of the fetal and adult liver methylomes and transcriptomes revealed that hypomethylated CpG sites and up-regulated ...

The draft genome and transcriptome of Cannabis sativa. Genome Biol. 2011; 12(10):102. doi:10.1186/gb-2011-12-10-r102. ...

Therefore, a global transcriptome analysis on A. mongolicus tissues was performed to identify the genes essential for the ... A transcriptome study was performed for A. mongolicus tissues to construct and profile their metabolic pathways, especially for ... Table 1 Overview of the sequencing and assembly of transcriptome of A. mongolicus.. Full size table. ... Additional file 4: Transcription factors (TFs) identified from A. mongolicus transcriptome. List of total TFs identified in A. ...

... the larval transcriptome profile was analyzed using a short-read deep sequencing method (Illumina). Symbiotic polydnaviruses ( ... From: Deep sequencing-based transcriptome analysis of Plutella xylostella larvae parasitized by Diadegma semiclausum ...

The transcriptome was assembled using the genome-guided method of StringTie v1.3.3 with de novo annotation [47]. Transcriptome ... Transcriptome profiling of the rice blast fungus Magnaporthe oryzae and its host Oryza sativa during infection. Mol Plant ... Then, in planta RNA-seq data and the updated transcriptome annotation from the first step were used in the second step. We used ... This study expands the transcriptome-level knowledge of M. oryzae, from protein-coding genes to long non-coding transcripts; it ...

With the transcriptome sequence data combined with publicly available expressed sequence tags evidences, 18,121 genes were ... We hereby provide a reconstructed transcriptome from deep sequencing of juvenile (glass eels) whole body samples. The provided ... This annotation provide information of the coding regions of the genes supported by transcriptome based evidence. The derived ... From: Transcriptome sequencing based annotation and homologous evidence based scaffolding of Anguilla japonica draft genome ...

A third of the transcriptome showed similarity with previously characterized immune-related genes that included both the known ... In the present study we constructed and analysed the immune transcriptome of the lepidopteran Antheraea mylitta, an ... The current transcriptome represents genes likely expressed upon E. coli infection in the A. mylitta fat body at 24 hrs post ... The transcriptome under study most likely represents a plethora of E. coli-induced genes in the fat body of the tasar silkmoth ...

Mb shoot transcriptome consisting of 28,621 contigs for P. tecunumanii and a 72 Mb shoot transcriptome consisting of ... The P. tecunumanii transcriptome is the first gene catalogue for the species, representing an important resource for studying ... Eight reference based and 12 de novo assembled transcriptomes were produced, for juvenile shoot tissue from both species. ... Predicted protein sequences encoded by the assembled transcriptomes were clustered with reference proteomes from 92 other ...

A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA. 2004, 101: 6062-6067. 10.1073/pnas ...

These miRNAs are also among the best expressed of larval transcriptomes in D. virilis [16]. The most well-known is bantam, ...

The transcriptome assembly and expression value estimation were done as described in Clevenger et al. [62]. Briefly, de novo ... Clevenger J, Chu Y, Scheffler B, Ozias-Akins P. A developmental transcriptome map for allotetraploid Arachis hypogaea. Front ... Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29:644. ...

... and a partial transcriptome of the virus. We then tested for differential gene expression between moths that were exposed to ... We sequenced, assembled and annotated the complete transcriptome of the moth, ... Nucleotide sequence similarity dot plot of the de novo transcriptome of Plodia interpunctella granulovirus (this study) versus ... This analysis suggests that the current P. interpunctella granulovirus transcriptome assembly is approximately 44% complete. ...

Extrapolated to the transcriptome of soybean, an intron of approximately 220 bp will be encountered every 350 bp of coding ... Secondly, the EST libraries could represent a very shallow sampling of the transcriptome of soybeans. While formally a ... were sampled indicating that it is a broad sampling of the transcriptome in terms of tissues and developmental stages sampled. ... which the ESTs were derived were not normalized thus the libraries are expected to be a biased sampling of the transcriptome. ...