Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1097370 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Here we studied Vanessa cardui, the species with the widest diet breadth among butterflies and a potential insect pest, by comparing tissue-specific transcriptomes from caterpillars that were fed six different host plants. We tested whether the similarities of gene-expression response reflect the evolutionary history of adaptation to these plants in the Vanessa and related genera, against the null hypothesis of transcriptional profiles reflecting plant phylogenetic relatedness. Science for Life Laboratory (SciLifeLab, Sweden) conducted the sequencing of RNA samples. The cDNA libraries (Illumina TruSeq RNA) were sequenced using the Illumina HiSeq 2000 platform using 100-bp paired-end sequencing. We obtained more than 9 million read-pairs from seventy one cDNA libraries sequenced and the transcriptome assembly (TA) of these sequences resulted in 213, 237 transcripts (162,189 components) with a contig N50 of 2,193 bp. Thus, we covered approximately 300x the transcriptome of caterpillars of the species V. cardui.
2015-11-18 | E-MTAB-3861 | biostudies-arrayexpress
Project description:The phytochromes (PHYs) are a family of photoreceptors which absorb light of red and far-red wavelengths to modulate developmental responses in photosynthetic organisms. We developed knockout mutants of PHYB and PHYC in wheat and performed replicated RNA-seq studies to analyze and compare the regulons of each phytochrome under long day photoperiods. Illumina Truseq v2 RNA-seq libraries were constructed from four biological replicates of phyBnull mutants and their wild-type sister lines and of phyCnull mutants and their wild-type sister lines. Subsequently, the entire experiment was replicated. Reads were mapped to the draft assembly (v2.2) of the wheat genome provided by the International Wheat Genome Sequencing Consortium (IWGSC) and transcribed regions were identifed by mapping a non-redundant set of transcripts to this genomic assembly. Sequencing reads mapping uniquely within these identified transcribed regions were used to determine relative expression profiles. Loci which were differentially expressed in both experimental replicates were designated high-confidence PHYB-regulated and PHYC-regulated genes, respectively. A GTF file is provided detailing the location of the 150,754 loci within the IWGSC pseduomolecules and contig scaffold followed by the longest transcribed sequence mapping to this region. Most, but not all, transcribed sequences are annotated through Ensembl.
2016-06-29 | E-GEOD-79049 | biostudies-arrayexpress
Project description:Salvia is an important genus from the Lamiaceae with approximately 1000 species distributed globally. Several Salvia species are commercially important because of their medicinal and culinary properties. We report the construction of the first fingerprinting array for Salvia species enriched with polymorphic and divergent DNA sequences and demonstrate the potential of this array for fingerprinting several economically important members of this genus.
2013-07-31 | GSE39403 | GEO
Project description:TaGPC1 and TaGPC2 are NAC-domain transcription factors which accelerate the onset of senescence and facilitate nutrient translocation in wheat. We developed knockout mutants of these genes in tetraploid wheat and used RNA-seq to identify the effect of these mutations on the wheat flag leaf transcriptome during monocarpic senescence. Several transporter-related genes were identified which were upregulated during senescence and differentially expressed between genotypes. Illumina cDNA libraries were constructed from four biological replicates of three genotypes (WT, gpc-a1 and gpc-a1/gpc-b2) at three timepoints (Heading date, 12 days after anthesis and 22 days after anthesis). Reads were aligned to a collection of assembled genomic contigs from flow-sorted chromosome arms (A and B genomes only) provided by the International Wheat Genome Sequencing Consortium. A custom GTF file was generated to identify 139828 gene loci corresponding to transcribed regions of this reference sequence. Please note that the contig names provided by URGI (http://wheat-urgi.versailles.inra.fr/Seq-Repository) were used in the analysis. Most, but not all, of these loci are present in Ensembl (With a modified name, but the same basic information, chromosome arm and unique contig ID) at ftp://ftp.ensemblgenomes.org/pub/plants/release-22/fasta/triticum_aestivum/dna/ Therefore, the contig IDs from URGI (which are available for all our sequences) were used in the processed data file (i.e. the count table and GFF file) and an additional file describing the corresponding Ensembl names for these was provided (Additional_file_2.xlsx).
2014-12-23 | E-GEOD-60635 | biostudies-arrayexpress
Project description:Purpose: The goal of this study was to identify the differentially expressed genes (DEGs) in the fluoride susceptible indica rice cultivar IR-64 in response to prolonged fluoride stress. The genes exhibiting high significance of relative expression were further analyzed by RT-PCR. Results: De novo transcriptome assembly by Trinity v2.8.3 led to the identification of 158411 transcripts. The Percent GC was 49.67, contig N50 was 1327, Median contig length was 422, average contig was 768.66 and total assembled bases were 121764099. After refinement and open reading frame detection with TransDecoder 70578 transcripts were retained. Among them, 68009 transcripts had at least one hit from Uniref100, Uniprot or Pfam. Differential expression analysis identified 1303 genes to be overexpressed and 93 genes to be down regulated in response to fluoride stress. After filtering, the transcripts with absolute log2 fold change 2 or more and p-value < 0.05 were considered as significantly differentially expressed. A total of 1396 transcripts with differential expression (majority overexpressed and some down regulated) were considered for further analysis. Next, PCR analysis with gene-specific primers was performed with some of the significant DEGs associated with transport, cytoskeletal organization and signaling to identify the genes/transcripts that are involved in stress
2020-08-18 | GSE131517 | GEO
Project description:In a field study, trees from two sites in Lower Saxony, Germany, were compared. RNA-seq (performed on an Illumina HiSeq 2000) was conducted on RNA from developing xylem tissue from 4 different harvests throughout the growth season to analyze transcriptional changes related to variations in wood formation and development. A transcriptome contig database was created from the combined raw reads using ABySS. Mapping of reads from distinct samples to the contig database was performed using Bowtie.
2016-07-03 | E-MTAB-3615 | biostudies-arrayexpress
Project description:De novo DNA methylation (DNAme) occurs coincident with transcription during mouse oogenesis. As many oocyte transcripts originate in Long Terminal Repeats (LTRs), which are divergent across species, we examined whether polymorphic LTR-initiated transcription units (LITs) shape the oocyte methylome. We identified thousands of syntenic regions in mouse, rat and human, including CpG islands (CGIs), that show divergent DNAme associated with polymorphic LITs. Notably, many CGI promoters methylated exclusively in mouse and/or rat are embedded within rodent-specific LITs, and show persistent maternal methylation in the blastocyst. Polymorphic LITs are also responsible for divergent methylation of CGI promoters in distantly related mouse strains, revealing that LITs also promote intra-species diversification of promoter DNAme.
2018-07-06 | GSE112622 | GEO