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LncRNA downregulation

ABSTRACT: lncRNA downregulation

PROVIDER: PRJEB21799 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR2122270_1.fastq.gz	Fastqsanger.gz
	ERR2122270_2.fastq.gz	Fastqsanger.gz
	ERR2122271_1.fastq.gz	Fastqsanger.gz
	ERR2122271_2.fastq.gz	Fastqsanger.gz
	ERR2122272_1.fastq.gz	Fastqsanger.gz

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Influence of the downregulation of the ARES lncRNA (AT4G14548) on gene regulation in Arabidopsis thaliana

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Downregulation of hepatic lncRNA Gm19619 improves gluconeogenesis and lipogenesis following vertical sleeve gastrectomy in mice

Project description:Downregulation of hepatic lncRNA Gm19619 improves gluconeogenesis and lipogenesis following vertical sleeve gastrectomy in mice

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cis regulated role of lncRNA in transcriptional or developmental process (ChIRP-Seq)

Project description:We report that long noncoding RNAs contribute to transcription and developmental process. Thousands of lncRNAs have been identified in the whole genome, and tend to located closely to protein-coding genes. To study position relationship between lncRNA and protein-coding genes, we classified all of lncRNA to several subgroups based on the genome position with their coding neighbors. XH, the head to head subgroup is associated with transcription and development in GO analysis. Here, we knockdown serveral XH lncRNA by shRNA in embryonic stem cells and induce nondirectional differnetiation by removing LIF or neural differnetiation by RA. Knockdown of XH lncRNAs led to uniform downregulation of nearby coding genes, and form regulatory circuits with its nearby coding genes to fine-tune embryonic lineage development. In addition, we also knockout one lncRNA-Evx1as and its nearby protein-coding gene-EVX1 by CRISPR, and get similar results as knockdown.We propose that XH lncRNA may function primarily as 'cis-regulators' of the expression of nearby protein-coding genes, and tend to participate in transcriptional or development regulations as their coding neighbors. All RNA-seq(s) were designed to reveal the differentially expressed genes between wild-type and XH lncRNA knockdown/knockout ESCs during differentiation.

2016-03-24 | E-GEOD-79541 | biostudies-arrayexpress

Downregulation of hepatic lncRNA Gm19619 improves gluconeogenesis and lipogenesis following vertical sleeve gastrectomy in mice [ChIRP-Seq]

Project description:Downregulation of hepatic lncRNA Gm19619 improves gluconeogenesis and lipogenesis following vertical sleeve gastrectomy in mice [ChIRP-Seq]

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Downregulation of hepatic lncRNA Gm19619 improves gluconeogenesis and lipogenesis following vertical sleeve gastrectomy in mice [RNA-Seq]

Project description:Downregulation of hepatic lncRNA Gm19619 improves gluconeogenesis and lipogenesis following vertical sleeve gastrectomy in mice [RNA-Seq]

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Downregulation of lncRNA XR_429159.1 could promote brain metastasis in patients with limited-stage small-cell lung cancer

Project description:Downregulation of lncRNA XR_429159.1 could promote brain metastasis in patients with limited-stage small-cell lung cancer

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Prediction of the Chronicization of Radiation-induced Acute Intestinal Injury Based on the Expression Level of lncRNA

Project description:Our team has constructed a prediction model based on the expression level of lncRNA (lncRNA-UCID、NEAT1、ciRS-7) to predict the chronicization of radiation-induced acute intestinal injury (RAII) and verified the predictive efficacy of the system in retrospective studies. This clinical study intends to further prospectively verify the accuracy of this prediction model in rectal cancer patients. In this study, we plan to enroll 200 patients diagnosed with locally advanced rectal cancer by pathology and MRI, who undergo neoadjuvant chemoradiotherapy (NCRT) and total mesorectal excision (TME) and develop RAII during NCRT or within 1 month. We will follow up the occurrence and progression of radiation-induced intestinal injury within 1 year after TME. Expression levels of lncRNA will be detected in pathological tissue after TME and applied to the prediction model to predict the chronicization of RAII. Based on the clinical diagnosis of chronic radiation-induced intestinal injury, the area under curve (AUC), accuracy, precision, specificity, and sensitivity of this prediction model in predicting the chronicization of RAII will be evaluated. The main outcome hypothesis is that the AUC of chronicization of RAII predicted by the prediction model based on the expression level of lncRNA is more than 0.8.

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Downregulation of lncRNA XR_429159.1 could promote brain metastasis in patients with limited-stage small-cell lung cancer

Project description:Purpose: To identify the aberrant long non-coding RNA (lncRNA) and explore the predictive value of lncRNA on the risk of brain metastases (BMs) for patients with limited-stage small cell lung cancer (SCLC). Patients and Methods: We executed an array of lncRNA and mRNA chip assays on peripheral blood mononuclear cells of SCLC patients with BM comparing to others without BMs to identify the lncRNAs relating to BMs. Then validation was conducted in clinical data to confirm the relationship of lncRNAs and BMs furtherly. We estimated the cumulative incidence of BMs using the Kaplan-Meier method and differences between the groups were analyzed using the log-rank test. Results: The expression of 67 lncRNAs (27 up, 40 down) and 47 mRNAs (20 up, 27 down) were different significantly in BM groups comparing to the group without BMs (fold change ≥ 2.0, p value ≤0.05) which were found by lncRNA and mRNA chip assays initially. Four lncRNAs were verified by qRT-PCR to confirm the accuracy of the microarray data and then the results of 11 pairs of patients (11 patients with BMs, while 11 patients without BMs) showed that low expression of LncRNA XR_429159.1 was the high-risk factor of BM. Further clinical data showed that the BM incidence of 25 patients with low level LncRNA XR_429159.1 was 31% at 1-year, and that was 14.3% in the 18 patients with high level LncRNA XR_429159.1, p = 0.035. Conclusion: Our present study identified that low expression of lncRNA XR_429159.1 was the high-risk factor of BM in patients with limited-stage SCLC.

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Influence of the downregulation of the MARS lncRNA (AT5G00580) of the response to Abscisic acid (ABA) in Arabidopsis

Project description:Influence of the downregulation of the MARS lncRNA (AT5G00580) of the response to Abscisic acid (ABA) in Arabidopsis

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Long non coding RNA (lncRNA) SCIRT regulates mitotic and stemness genes in breast cancer stem cells

Project description:CHART sequencing has been carried out in order to evaluate SCIRT target genes in MDA-MB-231 sphere derived cells. We discovered that lncRNA SCIRT binds promoter region of genes whose expression changes after SCIRT siRNA downregulation, suggesting that those are target SCIRT target genes.

2021-02-23 | GSE136185 | GEO

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