Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA286739 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2060090.fastq.gz | Fastqsanger.gz | |||
| SRR2060091.fastq.gz | Fastqsanger.gz | |||
| SRR2060092.fastq.gz | Fastqsanger.gz |
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Project description:The goal of this study was to compare the endogenous tRNA expression levels from cells transduced with a lentiviral vector encopding Cas9 and an sgRNA from a U6 or a Glutamine tRNA promoter. Using high-throughput sequencing methods (Illumina Hi-Seq 2000) we show that endogenous tRNA expression levels are not perturbed by expression of an sgRNA from a human tRNA. tRNA expression profiles were generated from 2 different transduced polyconal cell lines.
2015-09-09 | E-GEOD-69720 | biostudies-arrayexpress
Project description:The goal of this study was to compare the endogenous tRNA expression levels from cells transduced with a lentiviral vector encopding Cas9 and an sgRNA from a U6 or a Glutamine tRNA promoter. Using high-throughput sequencing methods (Illumina Hi-Seq 2000) we show that endogenous tRNA expression levels are not perturbed by expression of an sgRNA from a human tRNA.
2015-09-09 | GSE69720 | GEO
Project description:mRNA-seq for expression profiling of Myc and Yap1 activated mouse lung tumors and controls. 4 cohorts of lung tumors induced through nasal instillation of Cre/sgRNA(MS2)-encoding lentivirus in mice carrying conditional P53 loss (P53 F/F), oncogenic Kras (Kras LSL-G12D/+), and CRISPRa/SAM construct (Rosa26(LSL-SAM) or YFP reporter (Rosa26(LSL-YFP): 4 P53(L/L), Kras(LSL-G12D/+), Rosa26(LSL-SAM) / lenti(CMV-Cre/U6-sgRNA(Myc) (PPKS/M); 4 P53(L/L), Kras(LSL-G12D/+), Rosa26(LSL-SAM) / lenti(CMV-Cre/U6-sgRNA(Yap1) (PPKS/Y); 4 P53(L/L), Kras(LSL-G12D/+), Rosa26(LSL-SAM) / lenti(CMV-Cre/U6-sgRNA(non-targeted) (PPKS/NT); 4 P53(L/L), Kras(LSL-G12D/+), Rosa26(LSL-YFP) / lenti(CMV-Cre/U6-sgRNA(non-targeted) (PPKY/NT)
2022-08-30 | E-MTAB-11122 | biostudies-arrayexpress
Project description:To reveal the effect of U1 snRNA mutation, we performed exogenous expression analysis of U1 snRNA mutation. The pLKO.1-puro U6 sgRNA BfuAI stuffer lentiviral vector was modified by removing the internal U6 promoter. It was replaced by the U1 locus, including 393 bases of internal native U1 promoter, the U1 sequence, and 39 bases of 3’-flanking region. The r.3A>G mutation was introduced by site-directed mutagenesis. HEK-293T cells were transfected using Lipofectamine Plus with either pLKO.1-U1wt or pLKO.1-U1r.3a>g in duplicate. Messenger RNA library construction was performed based on oligo dT-based mRNA isolation using NEBNext® Poly(A) mRNA Magnetic Isolation Module. RNA Sequence was performed on NextSeq 550 using 100-bp paired-end mode.
2019-10-09 | GSE128005 | GEO
Project description:The discovery of the Clustered Regularly-Interspaced Short Palindromic Repeats (CRISPR) and its development as a genome editing tool has revolutionized the field of molecular biology. In the DNA damage field, CRISPR has brought an alternative to induce endogenous double-strand breaks (DSB) at desired genomic locations and study the DNA damage response and its consequences. Many systems for sgRNA delivery have been reported in order to efficiency generate this DSB, including lentiviral vectors. However, some of the consequences of these systems are yet not well understood. Here we report that lentiviral-based sgRNA vectors can integrate into the endogenous genomic target location, leading to undesired activation of the target gene. By generating a DSB in the regulatory region of the ABCB1 gene using a lentiviral sgRNA vector, we can induce the formation of taxol-resistant colonies. We show that these colonies upregulated ABCB1 via integration of the EEF1A1 and the U6 promoters from the sgRNA vector. We believe that this is an unreported CRISPR/Cas9 artefact that researchers need to be aware of when using lentiviral vectors for genome editing.
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Project description:LC-MS and GC-MS raw data for 13C6-glucose tracing in PDA cells expressing sgROSA or sgRNA targeting methionine sulfoxide reductase A
2022-05-21 | MSV000089514 | GNPS
Project description:TFIIB-related factor 2 (BRF2) crucially recruits RNA polymerase III (Pol III) to type III promoters containing a TATA box. These promoters encompass crucial components such as U6 spliceosomal RNA, tRNA processing enzyme RNase P, and selenocysteine tRNA. The results on cancer occurrence due to overexpression of BRF2 are known, but genetic disorders caused by mutations in BRF2 are still not well understood. Here, we first identified biallelic BRF2 variants exhibiting defective RNA Pol III activity to type III promoter in a familial patient presenting multiple anomalous features and primary immunodeficiency.
2024-11-06 | GSE280098 | GEO
Project description:Purpose: Cancer immunotherapy has shown promising results in both mouse models and clinical trials. However, to specifically reprogram the immune microenvironment of advanced tumor lesions remains a huge challenge. Therefore, we assembled a synthetic gene circuit aimed at specifically targeting p53-negative LLC cells, but not their p53+ derivatives, for immune activation. Methods: Firstly, we established an LLC-derived knock-in line (p53+), where the WT p53 coding region was re-introduced into the endogenous locus to rescue the bi-allelic point mutations (a nonsense mutation at E32, and a R334P mutation) in the parental LLC cells. Next, both the parental LLC cells and p53+ LLC cells were introduced with the AND-NOT gene circuits which contains the tumor-specific survivin promoter-driven dCas9 (Psuv-dCas9), U6 promoter-driven Ifng-activating sgRNA (or control sgRNA), and p53-responsive promoter PM2-driven AcrIIA4max. 48 hours after transfection, the total RNA was isolated and subjected to RNAseq services. Results: The p53+ LLC cell showed differences of hundreds of genes compared with the parental LLC cells. This group of genes contain a number of classical p53 targets. Notably, the logic circuit drove selective induction of a different gene set in the parental, but not the p53+ cells. Importantly, the vast majority of the circuit-induced genes are known downstream targets of IFN, confirming the specificity of a CRISPRa-driven transcriptional rewiring. Conclusion: Overall, this dataset provides evidence that the AND-NOT gene circuit selectively targets p53-negative LLC cells, but not their p53+ derivatives, and subsequently programs a highly specific immune-rewiring output.
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Project description:During transcription the nascent RNA can invade the DNA template, forming extended RNA-DNA duplexes (R-loops). Here we employ ChIP-seq in strains expressing or lacking RNase H to map targets of RNase H activity throughout budding yeast genome. In wild-type strains, R-loops were readily detected over the 35S rDNA region transcribed by Pol I and over the 5S rDNA transcribed by Pol III. In strains lacking RNase H activity, R-loops were elevated over other Pol III genes notably tRNAs, SCR1 and U6 snRNA, and were also associated with the cDNAs of endogenous TY1 retrotransposons, which showed increased rates of mobility to the 5?-flanking regions of tRNA genes. Unexpectedly, R-loops were also associated with mitochondrial genes in the absence of RNase H1, but not of RNase H2. Finally, R-loops were detected on highly expressed protein-coding genes in the wild-type, notably over the second exon of spliced ribosomal protein genes. ChIP-seq of RNA-DNA hybrids using antibody S9.6
2014-11-03 | E-GEOD-53420 | biostudies-arrayexpress
Project description:Huntington’s disease is a devastating, incurable neurodegenerative disease affecting up to 12 per 100,000 patients worldwide. The disease is caused by a mutation in the Huntingtin (Htt) gene. There is interest in reducing mutant Huntingtin by targeting it at the mRNA level but the maximum tolerable dose and long-term effects of such a treatment are unknown. Using a self-complementary AAV9 vector, we delivered a mir-155 based artificial miRNA under the control of the chicken ß-actin or human U6 promoter. In mouse brain, the artificial miRNA reduced the human huntingtin mRNA by 50%. The U6, but not the CßA promoter, produced the artificial miRNA at supraphysiologic levels. Embedding the antisense strand in a U6-mir-30 scaffold reduced expression of the antisense strand but increased the sense strand. In mice treated with scAAV9-U6-mir-155-HTT or scAAV9-CßA-mir-155-HTT, activated microglia were present around the injection site one-month post-injection. Six-months post-injection, mice treated with scAAV9-CßA-mir-155-HTT were indistinguishable from controls. Those that received scAAV9-U6-mir-155-HTT showed behavioural abnormalities and striatal damage. In conclusion, miRNA backbone and promoter can be used together to modulate expression levels and strand selection of artificial miRNAs and in brain the CßA promoter can provide an effective and safe dose of a human huntingtin. We also performed RNAseq on total RNA. In the mice injected with AAV9-U6-anti-HTT-6433, 44 transcripts were significantly downregulated while 30 were significantly upregulated when compared to the naïve control. In the AAV-CßA-anti-HTT-6433 group, 12 transcripts were downregulated and 4 were upregulated. Overall, transcripts containing a seed sequence target are downregulated in the scAAV-U6-anti-HTT-6433 group but not the scAAV9-CßA-anti-HTT-6433 group.
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