PELICAN45 RNAseq Dataset
Ontology highlight
ABSTRACT:
PROVIDER: EGAS00001006959 | EGA |
REPOSITORIES: EGA
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Project description:The hnRNP A1 and A2 proteins regulate processes such as alternative pre-mRNA splicing and mRNA stability. Here, we report that a reduction in the levels of hnRNP A1 and A2 by RNA interference or their cytoplasmic retention by osmotic stress drastically increases the transcription of a reporter gene. Based on previous work, we propose that this effect may be linked to a decrease in the activity of the transcription elongation factor P-TEFb. Consistent with this hypothesis, the transcription of the reporter gene was stimulated when the catalytic component of P-TEFb, CDK9, was inhibited with DRB. While low levels of A1/A2 stimulated the association of RNA polymerase II with the reporter gene, they also increased the association of CDK9 with the repressor 7SK RNA, and compromised the recovery of promoter-distal transcription on the Kitlg gene after the release of pausing. Transcriptome analysis revealed that more than 50% of the genes whose expression was affected by the siRNA-mediated depletion of A1/A2 were also affected by DRB. RNA polymerase II-chromatin immunoprecipitation assays on DRB-treated and A1/A2-depleted cells identified a common set of repressed genes displaying increased occupancy of polymerases at promoter-proximal locations, consistent with pausing. Overall, our results suggest that lowering the levels of hnRNP A1/A2 elicits defective transcription elongation on a fraction of P-TEFb-dependent genes, hence favoring the transcription of P-TEFb-independent genes.
2015-04-07 | GSE67617 | GEO
Project description:The hnRNP A1 and A2 proteins regulate processes such as alternative pre-mRNA splicing and mRNA stability. Here, we report that a reduction in the levels of hnRNP A1 and A2 by RNA interference or their cytoplasmic retention by osmotic stress drastically increases the transcription of a reporter gene. Based on previous work, we propose that this effect may be linked to a decrease in the activity of the transcription elongation factor P-TEFb. Consistent with this hypothesis, the transcription of the reporter gene was stimulated when the catalytic component of P-TEFb, CDK9, was inhibited with DRB. While low levels of A1/A2 stimulated the association of RNA polymerase II with the reporter gene, they also increased the association of CDK9 with the repressor 7SK RNA, and compromised the recovery of promoter-distal transcription on the Kitlg gene after the release of pausing. Transcriptome analysis revealed that more than 50% of the genes whose expression was affected by the siRNA-mediated depletion of A1/A2 were also affected by DRB. RNA polymerase II-chromatin immunoprecipitation assays on DRB-treated and A1/A2-depleted cells identified a common set of repressed genes displaying increased occupancy of polymerases at promoter-proximal locations, consistent with pausing. Overall, our results suggest that lowering the levels of hnRNP A1/A2 elicits defective transcription elongation on a fraction of P-TEFb-dependent genes, hence favoring the transcription of P-TEFb-independent genes. two treatements and one control
2015-04-07 | E-GEOD-67617 | biostudies-arrayexpress
Project description:Transcriptional profiling of comparing human gatric cancerous tissue with noncancerous tissue. Goal was to determine the different gene expression between gastric cancer and noncancerous tissue.(reference manuscript titled"Long non-coding RNA GAPLINC regulates CD44-dependent cell invasiveness and associates with poor prognosis of gastric cancer" submitted to Cancer Research)
2014-08-19 | GSE50710 | GEO
Project description:We used NEBNext Ultra Directional RNA Library Prep Kits to prepare RNA-seq libraries of total RNA from hnRNP A2/B1 and A1 depleted A549 cells. Pro-seq libraries were prepared from A549 cells using Illumina adapters hnRNP A2/B1 and A1 depleted A549 cells were generated by lentiviral infections of shRNA constructs. RNAs were isolated using Trizol.
2016-05-17 | E-GEOD-76151 | biostudies-arrayexpress
Project description:The goal of this project was to identify the dehydrogenase enzyme that converts vitamin A1 into A2, resulting in red-shifted spectral sensitivity of the visual system. We conducted next-generation sequencing of mRNA derived from the retinal pigment epithelium (RPE) of two animal models that use vitamin A2 as a chromophore to identify this enzyme. Zebrafish switch from vitamin A1 to A2 when treated with thyroid hormone, so we profiled the RPE from TH- and vehicle-treated zebrafish (n=3). The adult American bullfrog sequesters vitamin A2 within the dorsal part of the retina, but lacks vitamin A2 in the ventral retina. We therefore also profiled dorsal and ventral American bullfrog RPE (n=3). Using this approach, we identified cytochrome p450 family member cyp27c1 as strongly enriched in both datasets, and determined through additional experiments that cyp27c1 is both necessary and sufficient for vitamin A2 production.
2015-10-17 | GSE69219 | GEO
Project description:Transcriptome analysis of total RNA samples from heart tissue of knockout mice Alternative splicing is the main mechanism to increase protein diversity from an mRNA. Heterogeneous ribonucleoprotein (hnRNP) family members are vital regulators of alternative splicing. The hnRNP A1 is the most well-known protein in this family, but its role in embryonic development is not well understood. We generated hnRNP A1 knockout mice to study the function of hnRNP A1 in vivo. The hnRNP A1-depleted mice showed embryonic lethality because of muscle developmental defects. In a previous study, cellular hnRNP A2/B1 was reported to be capable of compensating for the expression of hnRNP A1. However, this phenomenon did not occur in the hnRNP A1 heterozygous mice in vivo. We demonstrated that hnRNP A1 regulated muscle-related genes expression and alternative splicing. In summary, our data demonstrated that hnRNP A1 plays a critical role in embryonic muscle development. Understanding the effects of hnRNP A1 in vivo may help to define the function of hnRNP A1 in alternative splicing.
2016-12-05 | GSE79076 | GEO
Project description:To determine the DGE genes upreglated and downregulated in A1,A2, A8, B5, B10 in comparison with NULL (control)
2023-01-25 | GSE221282 | GEO
Project description:A large number of oncofetal molecules were found through expression profiling of a total of lncRNAs(35923)+coding genes(24881) from 17.5-day-old embryonic livers (three independent replicate samples named A1, A2, and A3), 2-month-old adult male mouse livers (three independent replicate samples named B1, B2, and B3) and one-year-old male mouse liver cancer tissues (three independent replicate samples named C1, C2, and C3) using a microarray analysis.
2020-05-21 | GSE99157 | GEO
Project description:Peptide products from individual cleavage assays with the OOP and PreP1 enzymes were acidified by formic acid and injected into LC-MS. 2012oct12 experiment - sample labels (A1, A2, A3, B1, B2, etc...) condition: 1 - OOP 2 - PreP1 3 - ctrl peptide: A - F1beta H-1 4-15 B - F1beta H-2 43-53 C - F1beta 2-20 D - L29 E - CysD F - SytII G - Mdh oct H - Sdh oct I - P1 J - P22 K - Cox4-preseq L - Abeta28 2013jul12 experiment - sample labels (A11, A21, A31, B11, B21, etc...) condition: 1 - ctrl 2 - OOP 3 - PreP1 peptide: A - thrRS-1 B - thrRS-2 C - F1b-H2 D - L29 E - AT5G36880-11 F - F1b-53 G - AT5G36880-19 H - AT5G36880-26 I - Abeta40
2013-09-18 | PXD000444 | Pride
Project description:To gain novel molecular insights into quantitative late blight resistance, we performed a high-resolution quantitative analysis of gene expression using potato cultivars with contrasting SNP alleles at the StAOS2 locus associated with maturity corrected resistance (MCR). SuperSAGE samples were generated from uninfected and infected plants of the selected genotypes under controlled environmental conditions. Genotypes were pooled to reduce the influence of the genetic background on the transcriptome. Nine SuperSAGE samples were prepared from artificially inoculated plants in a growth chamber using total RNA of the pooled 14, 6 and 9 genotypes in groups A1, A2 and B2, respectively, at three infection time points T0, T1 and T2. Combining the tag counts of both NlaIII and DpnII libraries resulted in 1.1 to 6.2 million tags per sample. Of total 266361 unique tags (unitags), 52.6% matched to the potato genome sequence when up to three mismatches per 26 base pairs were allowed, and 23.3% matched without mismatch. Fifteen pair wise comparisons were performed between the nine SuperSAGE samples to identify transcripts that were differentially expressed in response to infection (six comparisons) or between three genotype pools at the infection time points T0, T1 and T2 (nine comparisons). The number of unitags per comparison ranged from 127 000 to 182 000 (average 158 000). Between 2100 and 11800 tags were differentially expressed in pair wise comparisons, depending on arbitrary cut-off p-values for a significant difference. The highest number of differences was observed for the comparison between genotype pools A1 and A2 one day after infection (A1-T1 vs A2-T1), and the lowest between genotype pools A2 and B2 two days after infection (B2-T2 vs A2-T2). The number of differences in response to infection and between genotype pools even before infection (T0) was in the same order of magnitude. Based on the annotations in the DFCI potato gene index, in the potato genome and in few cases by BLASTX searches against the protein database at NCBI, transcripts that showed reproducible differential expression over the infection time course or between genotype pools A1, A2 and B2 were grouped in 16 functional categories, with overlaps between categories. Genes with genotype dependent, constitutive differential expression provide excellent targets for developing novel diagnostic markers for breeding cultivars with improved quantitative resistance to late blight and possibly other biotic and abiotic stresses. Relevant in this respect appear, besides numerous genes of unknown or ill-defined function, genes with known function involved in stress responses, photosynthesis, protein biosynthesis, protein degradation via the 26S proteasome, transport of proteins, lipids, ions and other small molecules, cell wall structure and many others.
2013-10-10 | GSE48071 | GEO