Identification of candidate genes downstream of RCO using RNA-seq
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB35497 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3675670.fastq.gz | Fastqsanger.gz | |||
| ERR3675680.fastq.gz | Fastqsanger.gz | |||
| ERR3675690.fastq.gz | Fastqsanger.gz | |||
| ERR3675700.fastq.gz | Fastqsanger.gz | |||
| ERR3675710.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 60 |
Similar Datasets
Project description:Neurospora crassa rco-1 Gene Expression Profiling - rco-1_1 transcriptome
| PRJNA580935 | ENA
Project description:Neurospora crassa rco-1 Gene Expression Profiling - rco-1_3 transcriptome
| PRJNA580937 | ENA
Project description:Neurospora crassa rco-1 Gene Expression Profiling - rco-1_2 transcriptome
| PRJNA580936 | ENA
Project description:Despite some advances in recent years, the genetic control of gonadal sex differentiation during embryogenesis is still not completely understood. To identify new candidate genes involved in ovary and testis development, RNA-seq was used to define the transcriptome of embryonic chicken gonads at the onset of sexual differentiation (day 6.0/stage 29).RNA-seq revealed more than 1000 genes that were transcribed in a sex-biased manner at this early stage of gonadal differentiation. Comparison with undifferentiated gonads revealed that sex biased expression was derived primarily from autosomal rather than sex-linked genes. Gene ontology and pathway analysis indicated that many of these genes encoded proteins involved in extracellular matrix function and cytoskeletal remodelling, as well as tubulogenesis. Several of these genes are novel candidate regulators of gonadal sex differentiation, based on sex-biased expression profiles that are altered following experimental sex reversal. We further characterised three female-biased (ovarian) genes; calpain-5 (CAPN5), G-protein coupled receptor 56 (GPR56), and FGFR3 (fibroblast growth factor receptor 3). Protein expression of these candidates in the developing ovaries suggests that they play an important role in this tissue.This study provides insight into the earliest steps of vertebrate gonad sex differentiation, and identifies novel candidate genes for ovarian and testicular development.
| S-EPMC4574023 | biostudies-literature
Project description:BackgroundBrassica napus is an important oilseed crop. Dissection of the genetic architecture underlying oil-related biological processes will greatly facilitates the genetic improvement of rapeseed. The differential gene expression during pod development offers a snapshot on the genes responsible for oil accumulation in. To identify candidate genes in the linkage peaks reported previously, we used RNA sequencing (RNA-Seq) technology to analyze the pod transcriptomes of German cultivar Sollux and Chinese inbred line Gaoyou.MethodsThe RNA samples were collected for RNA-Seq at 5-7, 15-17 and 25-27 days after flowering (DAF). Bioinformatics analysis was performed to investigate differentially expressed genes (DEGs). Gene annotation analysis was integrated with QTL mapping and Brassica napus pod transcriptome profiling to detect potential candidate genes in oilseed.ResultsFour hundred sixty five and two thousand, one hundred fourteen candidate DEGs were identified, respectively, between two varieties at the same stages and across different periods of each variety. Then, 33 DEGs between Sollux and Gaoyou were identified as the candidate genes affecting seed oil content by combining those DEGs with the quantitative trait locus (QTL) mapping results, of which, one was found to be homologous to Arabidopsis thaliana lipid-related genes.DiscussionIntervarietal DEGs of lipid pathways in QTL regions represent important candidate genes for oil-related traits. Integrated analysis of transcriptome profiling, QTL mapping and comparative genomics with other relative species leads to efficient identification of most plausible functional genes underlying oil-content related characters, offering valuable resources for bettering breeding program of Brassica napus.ConclusionsThis study provided a comprehensive overview on the pod transcriptomes of two varieties with different oil-contents at the three developmental stages.
| S-EPMC4619414 | biostudies-literature
Project description:BACKGROUND AND OBJECTIVE:Lung adenocarcinoma (AC) is the most common type of lung cancer, however, its mechanism of oncongenesis is still unknown. The aim of this study is to screen candidate genes of lung adenocarcinoma using bioinformatics strategy and elucidate the mechanism of lung adenocarcinoma. METHODS:Two published microarray data (GSE7670 and GSE10072) was obtained from Gene Expression Omnibus (GEO). Significance analysis of microarrays was performed with the software dchip, and differential expression genes from dchip analysis were defined as "test gene set". Genes correlated with lung adenocarcinoma, obtained by data mining tools genecard and Fable were regarded as "train gene set". Finally, candidate genes of lung adenocarcinoma were screened by the tool "Toppgene". RESULTS:Three hundred and forty-four differential genes were defined as "test gene set", and 277 genes correlated with lung adenocarcinoma were regarded as "train gene set". Thirty-six candidate genes were screened out by Toppgene, among them, 21 genes had nearly no report in cancer. In the following QRT-PCR experiment, CD36, PMAIP1 and FABP4 were down-regulated expression in A549, which coincided with the gene chip. CONCLUSION:It is demonstrated that Toppgene is useful in identification of the candidate genes of lung adenocacinoma, which provides the proof for the discovery of the specific disease genes.
| S-EPMC6000438 | biostudies-literature
Project description:To understand the transcriptional program controlled by AGL24, we took advantage of a functional estradiol-inducible AGL24 expression system in combination with microarray analysis to identify AGL24 target genes. Keywords: inducible system
2008-04-30 | GSE6954 | GEO
Project description:To understand the transcriptional program controlled by RGA, we took advantage of a functional steroid-inducible RGA proteins system in combination with microarray analysis to identify RGA target genes. Keywords: steroid-inducible system
2008-05-28 | GSE10019 | GEO
Project description:Toll-like receptor 4 (TLR4) is involved in ozone (O3)-induced pulmonary hyperpermeability and inflammation, although the downstream signaling events are unknown.The aims of our study were to determine the mechanism through which TLR4 modulates O3-induced pulmonary responses and to use transcriptomics to determine potential TLR4 effector molecules.C3H/HeJ (HeJ; Tlr4 mutant) and C3H/HeOuJ (OuJ; Tlr4 normal) mice were exposed continuously to 0.3 ppm O3 or filtered air for 6, 24, 48, or 72 hr. We assessed inflammation using bronchoalveolar lavage and molecular analysis by mRNA microarray, quantitative RT-PCR (real-time polymerase chain reaction), immunoblots, immunostaining, and ELISAs (enzyme-linked immunosorbent assays). B6-Hspa1a/Hspa1btm1Dix/NIEHS (Hsp70-/-) and C57BL/6 (B6; Hsp70+/+ wild-type control) mice were used for candidate gene validation studies.O3-induced TLR4 signaling occurred through myeloid differentiation protein 88 (MyD88)-dependent and -independent pathways in OuJ mice and involved multiple downstream pathways. Genomewide transcript analyses of lungs from air- and O3-exposed HeJ and OuJ mice identified a cluster of genes that were significantly up-regulated in O3-exposed OuJ mice compared with O3-exposed HeJ mice or air-exposed controls of both strains; this cluster included genes for heat-shock proteins (e.g., Hspa1b, Hsp70). Moreover, O3-induced inflammation, MyD88 up-regulation, extracellular-signal-related kinase-1/2 (ERK1/2) and activator protein-1 (AP-1) activation, and kerotinocyte-derived chemokine (KC) protein content were significantly reduced in Hspa1a/Hspa1btm1Dix (Hsp70-/-) compared with Hsp70+/+ mice (p < 0.05).These studies suggest that HSP70 is an effector molecule downstream of TLR4 and is involved in the regulation of O3-induced lung inflammation by triggering similar pathways to TLR4. These novel findings may have therapeutic and preventive implications for inflammatory diseases resulting from environmental exposures.
| S-EPMC3237361 | biostudies-other