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Oxygen responsive lncRNAs in MCF-7 breast cancer cells

ABSTRACT: Previous studies have identified oxygen-responsive lncRNAs as having a role in the onset of several cancers. However, the lncRNAs regulated by oxygen in breast cancer have not been identified. In this study, we hypothesized that a group of lncRNAs were regulated by oxygen in breast cancer. To identify the oxygen-responsive lncRNAs, next-generation sequencing was performed

ORGANISM(S): Homo sapiens

PROVIDER: GSE84167 | GEO | 2017/12/31

REPOSITORIES: GEO

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lncRNA Mitochondrial oxygen responsive transcript 1 (MTORT1) downstream gene microarray

Project description:Long non-coding RNAs (lncRNAs) have been regarded to participate in multiple genetic pathways in cancer. Also, mitochondria-associated lncRNAs have been discovered to module mitochondrial function and metabolism. Previously, our lab identified oxygen responsive lncRNAs in breast cancer MCF-7 cells under normoxic, hypoxic and re-oxygenated conditions by using next generation sequencing technology. Among them, a novel mitochondrial lncRNA Mitochondrial Oxygen Responsive Transcript 1 (MTORT1) was chosen for further investigation. Therefore, the purpose of this study was to investigate the characterizations, function roles, and mechanisms of MTORT1 in breast cancer cells.

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Integrated analysis of sea cucumber ambient temperature and dissolved oxygen responsive lncRNAs and mRNAs

Project description:Integrated analysis of sea cucumber ambient temperature and dissolved oxygen responsive lncRNAs and mRNAs

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Upregulated mRNAs and lncRNAs in chemoresistant breast cancer

Project description:Chemoresistance is a major cause of poor prognosis of breast cancer.More and more mRNAs and lncRNAs are reported to upregulate chemoresistance in breast cancer.To explore the how mRNAs and lncRNAs involved in chemoresistance of breast cancer,we sceened upregulated mRNAs and lncRNA from parental MCF-7 , chemoresistant MCF-7 cells as well as 4 breast cancer tissue sensitive to chemotherapy and 4 resistant to chemotherapy . Total RNA was extracted using Trizol reagent. Agilent Human lncRNA Microarray V6 (4*180K) was used to analyze the global profiling of human lncRNAs and protein-coding transcripts in these samples. The microarray contains 83,835 lncRNAs and 27,233 coding genes.

2020-02-25 | E-MTAB-8787 | biostudies-arrayexpress

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Project description:We sequenced the total RNA from a tissues mixed sample (inflorescences, rosette leaves, cauline leaves and stems) of Arabidopsis thaliana. After total RNA extraction, the same amount of tissue RNA were mixed. Ribosomal RNAs were deleted from the mixed tissue total RNAs using RiboMinus™ Plant Kit repeated three times. We also sequenced 9 poly(A)- RNAs from seedlings treated with different stress conditions at different times. The poly(A)- RNAs were collected by removing poly(A)+ RNAs four times . Then rRNAs were removed from poly(A)- RNAs three times. Sequencing of total RNAs from the mixed tissues sample is taken as an example of collecting novel transcripts from high-throughput data, which could be clarified by noncoding scores derived from our integrative models. Sequencing of nonpolyA RNAs are used for identifing stress-responsive nonpolyA lncRNAs and for validation of predicted lncRNAs.

2014-09-18 | E-GEOD-49325 | biostudies-arrayexpress

Low oxygen responsive small RNAs in Arabidopsis

Project description:Low-oxygen stress associated with natural phenomena such as waterlogging, results in widespread transcriptome changes and a metabolic switch from aerobic respiration to anaerobic fermentation. High-throughput sequencing of small RNA libraries obtained from low-oxygen stressed and control root tissue identified a total of 65 unique microRNA (miRNA) sequences from 46 families, and 14 trans-acting small interfering RNA (tasiRNA) from 3 families. Low-oxygen stress resulted in changes to the abundance of 46 miRNAs from 19 families, and all 3 tasiRNA families. Chemical inhibition of mitochondrial respiration caused similar changes in expression in a majority of the low-oxygen responsive small RNAs analysed. Our data indicate that miRNAs and tasiRNAs play a role in gene regulation and possibly developmental responses to low oxygen, and that a major signal for these responses is likely to be dependent on mitochondrial function. Keywords: Small RNA transcriptome analysis

2009-10-01 | GSE16971 | GEO

Low oxygen responsive small RNAs in Arabidopsis

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Identification of glucose-regulated lncRNAs in triple-negative breast cancer cells

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Identification of glucose-regulated lncRNAs in triple-negative breast cancer cells

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2019-06-03 | GSE106729 | GEO

High-throughput sequencing technology identify the CGMMV responsive genes, lncRNAs and cirRNAs in watermelon

Project description:The DEGs, lncRNAs and cirRNAs in responsive to the CGMMV infection in watermelon leaves were obtained through deep sequencing.

2019-04-24 | GSE130223 | GEO

Investigation of androgen-regulated lncRNAs in prostate cancer cells

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