Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Next Generation Sequencing Analysis of lung and spleen tissue transcriptomes from Wild Type KrasLA2 and miR-301a-/- Kras mice

ABSTRACT: Next Generation Sequencing Analysis of lung and spleen tissue transcriptomes from Wild Type KrasLA2 and miR-301a-/- Kras mice

PROVIDER: PRJNA430230 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR6495960.fastq.gz	Fastqsanger.gz
	SRR6495961.fastq.gz	Fastqsanger.gz
	SRR6495962.fastq.gz	Fastqsanger.gz
	SRR6495953.fastq.gz	Fastqsanger.gz
	SRR6495954.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 10

Similar Datasets

Next Generation Sequencing Analysis of lung and spleen tissue transcriptomes from Wild Type KrasLA2 and miR-301a-/- Kras mice

Project description:Purpose: we used next generation sequencing to analyze gene expression profiles of lung and spleen tissues wild-type KrasLA2(WT-KrasLA2) and miR-301a knockout KrasLA2 (miR301aKO-KrasLA2) mice. The goals of this study are to compare the different gene expression profiles of lung tumorigenesis between WT-KrasLA2 and miR301aKO-KrasLA2 mice. Methods: WT-KrasLA2 and miR301aKO-KrasLA2 mice were sacrificed at 9 weeks and lung and spleen tissue were obtained and total RNA was extracted. mRNA profiles were generated by deep sequencing spleen tissue in single, lung tissue from WT and miR-301a KO mice in single, lung tissue from WT-KrasLA2 and miR301aKO-KrasLA2 mice in duplicate using High-seq 2000 Illumina sequencing platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: After quality filtering of raw sequencing data, we obtained 47,865,482 (95%) out of 50,579,239 tags of lung, 34,855,916 (96%) out of 36,426,771 tags of spleen from WT-KrasLA2 mice, and 44,632,009 (95%) out of 46,771,631 tags of lung, 44,306,242 (94%) out of 47,032,715 tags of spleen from miR301aKO-KrasLA2 mice. We then mapped these tags to the mouse genome. We identified 1,641 DEGs (1,166 upregulated and 475 downregulated) in lung between WT-KrasLA2 and miR301aKO-KrasLA2 mice with a fold change more than 2.0 (up-regulation) or less than 0.5 (down-regulation). Conclusions: We identified 1166 up-regulation and 475 down-regulation differentially expressed genes (DEGs) between WT-KrasLA2 and miR301aKO-KrasLA2 mice. Immune system response and cell cycle were major pathways involved in the protection role of miR-301a deletion in lung tumorigenesis. Runx3 activation is an early event identified in miR301aKO-KrasLA2 mice compared to WT-KrasLA2 mice.

2018-01-17 | GSE109238 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of hippocampus transcriptomes from WT and miR-301a-/- mice

Project description:Purpose: we used next generation sequencing to analyze gene expression profiles of hippocampus from WT and miR-301a-/- mice. The goals of this study are to compare the different gene expression profiles of hippocampus between WT and miR-301a-/- mice.

2022-01-28 | GSE194389 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of pancreatic tissue transcriptomes from KrasG12D;Pdx1-Cre and miR-301a-/-;KrasG12D;Pdx1-Cre mice treated with caerulein

Project description:Purpose: we used next generation sequencing to analyze gene expression profiles of pancreatic tissues from KrasG12D;Pdx1-Cre and miR-301a-/-;KrasG12D;Pdx1-Cre mice treated with caerulein. The goals of this study are to compare the different gene expression profiles of pancreatic tissue between KrasG12D;Pdx1-Cre and miR-301a-/-;KrasG12D;Pdx1-Cre mice treated with caerulein.

2021-06-11 | GSE176571 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of hippocampus transcriptomes from WT and miR-301a-/- mice

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of hippocampus transcriptomes from WT and miR-301a-/- mice

| PRJNA800430 | ENA

KRas targeting by clinically significant miR-193a-3p inhibits mutant KRas lung cancer growth, circulating tumor cells and metastasis in vivo

Project description:Ras family oncogenes are mutated in approximately 30% of human cancers and cause resistance to multiple treatment modalities. While identifying methods to directly target mutant KRas have been challenging, targeting regulators of KRas may be beneficial. Using a systems approach of integrating a genome-wide miRNA screen with patient data of a phospho-proteomic signature of the KRas downstream pathway, we identified miR-193a-3p as a potent tumor suppressor capable of reversing KRas-related signaling, whereby the 3’UTR of KRas is directly targeted via two miR-193a-3p binding sites. Mechanistic studies revealed that miR-193a-3p inhibited the KRas protein signature, KRas downstream transcriptomic network, proliferation, induced a G1 arrest, and reduced colony formation in 3D cultures through direct targeting of KRas. An ex vivo lung cancer model showed that miR-193a-3p significantly reduced the viability of circulating tumor cells as well as decreased metastasis. In vivo studies revealed that miR-193a-3p significantly reduced tumor growth as well as metastasis of a KRas-mutant lung cancer xenograft model.

2016-09-18 | GSE73194 | GEO

KRAS-driven miR-29b Expression is Required for Tumor Suppressor Gene Silencing

Project description:KRAS activation drives DNA methylation and silencing of specific tumor suppressor genes (TSGs). We previously showed that the ERK pathway induces transcriptional repression of TET1, which results in conversion of TSG promoters from a hydroxymethylated, active state to a hypermethylated and silenced state. Here we identified miR-29b as a KRAS-induced molecule that represses TET1 expression. In KRAS-transformed cells, ectopic miR-29b inhibition restores expression of TET1, thereby reactivating TSGs by reducing methylation and restoring hydroxymethylation. Mining gene expression data of lung cancer cell lines identified additional TSGs suppressed by KRAS signaling whose expression was restored by inhibition of miR-29b and re-expression of TET1. Because KRAS changes TSG promoters from hydroxymethylated to hypermethylated with miR-29b-dependent silencing of TET1, we demonstrate a model in which DNMT1 is present on target promoters prior to KRAS transformation. We also propose miR-29b as a potential circulating biomarker and target for rational treatment of specific malignancies.

2017-07-31 | GSE100857 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and KRAS mutated lung oraganoids Transcriptomes

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare lung organoids transcriptome profiling (RNA-seq) between wild type and KRAS mutation Methods: mRNA profiles of wild-type (WT) and KRAS mutated organoids were generated by deep sequencing, in triplicate, using Illumina HiSeq. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.

2023-06-01 | GSE171728 | GEO

Spleen response following malaria infection in WT and miR-155 KO mice.

Project description:Analysis of the transcriptome pattern of spleen after maralia infection in WT and miR-155 KO mice.

2022-01-01 | GSE69931 | GEO

TTF-1-regulated miR-532-5p targets KRAS and MKL2 oncogenes and induces apoptosis in lung adenocarcinoma [pts]

Project description:Thyroid transcription factor-1 (TTF-1), also known as NKX2-1, plays a role as a lineage-survival oncogene in lung adenocarcinoma with double-edged sword characteristics. Although previous studies steadily accumulated evidence for roles of TTF-1 in the transcriptional regulation of protein-coding genes, very little is known about its regulatory relationship with miRNAs. In this study, we have identified miR-532-5p as a novel transcriptional target of TTF-1 by an integrative approach, which was designed to extract maximal information from expression profiles of both patient tumors in vivo and TTF-1-inducible cell lines in vitro. Consequently, we have found that miR-532-5p is directly regulated by TTF-1 through its binding to a genomic region 8 kb upstream of miR-532-5p, which appeared to impose transcriptional regulation independent of that of CLCN5, a protein-coding gene harboring miR-532-5p in its intron 3. Further, we have also identified KRAS and MKL2 as novel direct targets of miR-532-5p. Introduction of miR-532-5p mimics markedly induced apoptosis in KRAS-mutant as well as KRAS wildtype lung adenocarcinoma cell lines. Interestingly, miR-532-5p affected the MEK-ERK pathway signaling specifically in cell lines sensitive to siKRAS treatment, while the miR-532-5p-mediated effects were clearly phenocopied by repressing expression or inhibiting function of MKL2 regardless of KRAS mutation status. In summary, our findings demonstrate that miR-532-5p is as novel transcriptional target of TTF-1 and plays a tumor suppressive role by targeting KRAS and MKL2 in lung adenocarcinoma. Novel therapeutic strategies using miR-532-5p or an MKL2 inhibitor may prove effective against this hard-to-cure cancer irrespective of the dependence on KRAS-mediated signaling.

2017-06-21 | GSE83836 | GEO

FOSL1- and KRAS-regulated transcriptomes

Project description:RNA profiling of FOSL1- and KRAS-regulated transcriptomes in human lung cancer cells harboring KRAS mutation

2023-08-10 | GSE196596 | GEO