Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1101700 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Rhizophora mucronata Lam., a prevalent mangrove variety of Indo-Pacific region is reported to defy saline stress up to 40 ppt, but the genome or transcriptome behind this tolerance is yet to be investigated. As an initiative to create a reference sequence database, we have forged a set of 46,366,348 paired end RNA-Seq raw reads of Rhizophora mucronata Lam. leaf tissues from Illumina HiSeq 2500 platform (SRA study accession SRP093200 ; Bioproject accession PRJNA345155). All possible gene transcripts were then reconstructed from the RNA raw seq data and 93960 Trinity assembled, annotated transcripts that are being actively expressed at a given time is proposed (TSA accession GGEC00000000). To estimate gene transcript expression, we used Bowtie 2 programme and successfully aligned back up to 95.14% of the filtered reads to the assembled transcriptome. We allowed up to 1-mismatches in the seed region (length =31bp) and all multiple mapped position were reported. Of all filtered reads about 95.14% of reads from each sample were properly aligned back to the assembled transcriptome. Overall we found 52,153 unique transcripts which have expression >=1 FPKM.
2018-03-22 | GSE112162 | GEO
Project description:Employing Conus betulinus as a representative, we sequenced and assembled the first Conus genome. After integration of multi-omics data, we provide novel insights into the genetic central dogma of conotoxins, assuming a number ratio of ~1:1:10s for genes/transcripts/peptides.
2021-09-08 | PXD014892 | Pride
Project description:A 50-mer oligonucleotide microarray was designed for large-scale gene expression analysis in Z. viviparus. To measure the expression of the probes and the corresponding assembled transcripts, the pool of mRNA used for the sequencing was hybridized.
2009-07-24 | GSE14957 | GEO
Project description:Angiotensin II (AngII) is a polypeptide hormone that plays a pivotal role in the regulation of blood pressure. In vascular smooth muscle cells (VSMCs), AngII signaling results in hypertrophy, proliferation, contraction, and migration, which ultimately promote atherosclerosis and hypertensive cardiovascular diseases. Recent studies have shown that fundamental biological processes such as cell proliferation and differentiation are mediated in part by the activities of long non-protein-coding RNAs (lncRNAs). In this study, we sought to identify lncRNAs that are involved in the response to AngII-signaling. Genome-wide analysis of de novo assembled transcripts from rat vascular smooth muscle cells (VSMCs) identified novel lncRNA as well as protein-coding transcripts which have not been previously annotated. The majority of the genomic loci from which these novel transcripts are transcribed are enriched for histone H3 lysine 4 trimethylation and histone H3 lysine 36 trimethylation, two chromatin modifications that are closely associated with actively transcribed regions, further supporting these as bona fide transcripts. Compared with previously annotated rat transcripts, these novel lncRNA transcripts, on average, are shorter in length and are less abundant, consistent with reports from mice and humans. Expression analyses of transcripts from control and AngII-stimulated VSMCs reveal that AngII signaling affects the abundance of both protein-coding transcripts as well as lncRNAs transcripts. Altogether, these data provide new insights into the global effects of AngII signaling and reveal potential novel therapeutic targets for treatment of AngII-associated cardiovascular diseases. RNA-sequencing of control and AngII (3hrs)-stimulated rVSMSCs. ChIP-sequencing of H3K4me3 and H3K36me3 in control and AngII (3hrs)-stimulated rVSMCs.
2013-06-30 | E-GEOD-38056 | biostudies-arrayexpress
Project description:We assembled larval transcriptome of D. arcuata using RNA-seq data from both social and solitary instars, and then conducted differential gene expression analysis between the two behavioural instars. This revealed a large number of transcripts that were differential expressed between the two behavioral states, including some transcripts coding for gene products that have been previously implicated in social behaviour in other insects.
2020-06-22 | GSE146351 | GEO
Project description:To identify female sex pheromone biosynthesis genes by differential expression between males and females. Female pheromone gland tissue and male abdominal tip tissue was compared by RNA-Seq of cDNA. Transcripts were assembled using Trinity and differential expression analysis done with RSEM.
2023-12-31 | E-MTAB-12752 | biostudies-arrayexpress
Project description:The complexity of transcriptome in human liver has not been clarified quite clearly so far. Here we collect various types of liver samples, including primary tumor, relapse tumor, benign adjacent, normal liver and tumor cell lines.High-throughput RNA sequecing data was generated for each sample.We assembled transcripts from these data under the guidance of GENCODE transcript annotation (v22).After the assembly, 94,272 genes and 371,388 transcripts were identified. Furthermore, we identified alternative splicing events from these genes and transcripts.
2020-06-01 | GSE101432 | GEO