LncRNA/mRNA expression profiling for 10 human lung samples
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE98929 | GEO | 2019/05/01
REPOSITORIES: GEO
Similar Datasets
Project description:Given the role of lncRNAs and mRNAs in tumor pathogenesis, we set out to identify transcripts that potentially drive colorectal tumorigenesis. To do this, we performed microarray analysis on matched colorectal tumor and non-tumor samples from 6 colorectal cancer patients, and determined their lncRNA and mRNA expression profiles with Agilent microarrays (Arraystar Human LncRNA Array v3.0).
2018-01-20 | GSE109454 | GEO
Project description:ArrayStar Human LncRNA/mRNA Expression Microarray Version 3.0 was used to detect lncRNA expression in CRC tissues compared with their matched non-tumoral tissues. Here we report significantly up-regulated as well as down-regulated lncRNAs in CRC tissues compared with their matched non-tumoral tissues.
2019-07-20 | GSE134525 | GEO
Project description:LncRNA expression profiles were sucessfully contructed in 370 patients with NSCLC and 198 corresponding adjacent noncancerous tissues using a custom microarray containing probes for 2412 lncRNAs and an outcome prediction of lncRNA signature was successfully identified for predicting prognosis in NSCLC.
2020-08-31 | GSE143018 | GEO
Project description:38 paires of tumor tissues and adjacent non-tumor tissues from HCC patients The number of known lncRNAs increased sharply upon the tiling microarrays and RNA-sequencing were applied to identify lncRNAs. However, only about a dozen of lncRNAs have been well characterized and demonstrated to be tightly associated with development and progression of HCC. A major challenge remains to identify functional lncRNAs associated with HCC. Previous reports mainly selected differentially expressed lncRNAs in cancer tissue or cell lines as candidates for further validation and characterizing. Here, based on mRNA and lncRNA gene expression profiles data collected from tumor and adjacent normal tissues of thirty-eight HCC patients, we adapted integrative omics strategy to identify HCC-associated lncRNAs.
2017-06-21 | GSE84004 | GEO
Project description:Using the highly sensitive lncRNA array, we screened the lncRNAs abundant in the human bladder cancer and Adjacent normal bladder tissues, and the function of differentially expressed lncRNAs were analyzed by bioinformatics. The Arraystar Human lncRNA Array (8x15K, Arraystar) and whole human mRNA Array (4x44K, Arraystar) and was used to profile differentially expressed lncRNAs and genes in bladder cancer vs. normal tissues following the manufacturerâs instructions. Briefly, extracted RNA template (1mg) was reversely transcribed into cDNA and digested into fragments with endonucleases. These fragments were labeled with DNA labeling reagent and labeled cDNAs were hybridized to the microarray via incubation at 45°C and rotated at 60 rpm for 17 h. Following washing and staining, the arrays were scanned using a GeneChip Scanner3000 with GeneChip Operating Software.
2016-07-02 | E-GEOD-83955 | biostudies-arrayexpress
Project description:Long non-coding RNAs (lncRNAs) play an important role in gene regulation and contribute to tumorigenesis. While pan-cancer studies of lncRNA expression have been performed for adult malignancies, the lncRNA landscape across pediatric cancers remains largely uncharted. Here, we curated RNA sequencing data for 1,044 pediatric leukemia and extra-cranial solid tumors and integrated paired tumor whole genome sequencing and epigenetic data in relevant cell line models to explore lncRNA expression, regulation, and association with cancer. A total of 2,657 lncRNAs were robustly expressed across six pediatric cancers, including 1,142 exhibiting histotype-elevated expression. DNA copy number alterations contributed to lncRNA dysregulation at a proportion comparable to protein coding genes. Application of a multi-dimensional framework to identify and prioritize lncRNAs impacting gene networks revealed that lncRNAs dysregulated in pediatric cancer are associated with proliferation, metabolism, and DNA damage hallmarks. Analysis of upstream regulation via cell-type specific transcription factors further implicated distinct histotype-elevated and developmental lncRNAs. Integration of these analyses prioritized lncRNAs for experimental validation, and silencing of TBX2-AS1, the top-prioritized neuroblastoma-specific lncRNA, resulted in significant growth inhibition of neuroblastoma cells, confirming the computational predictions. Taken together, these data provide a comprehensive characterization of lncRNA regulation and function in pediatric cancers and pave the way for future mechanistic studies.
2023-07-31 | GSE238166 | GEO
Project description:Many long non-coding RNA (lncRNA) species have been identified in mammalian cells, but the genomic origin, regulation and function of these molecules in individual cell types is poorly understood. We have generated comprehensive catalogs of lncRNA species expressed in human and murine embryonic stem cells (ESCs) and mapped their genomic origin. A surprisingly large fraction of these transcripts (>60%) originate from divergent transcription at promoters of active protein-coding genes. The divergently transcribed lncRNA/mRNA gene pairs exhibit coordinated changes in transcription when ESCs are differentiated into endoderm. A significant number of the divergently transcribed lncRNAs/mRNA pairs are conserved between human and mouse ESCs. Disruption of promoter-associated lncRNA orthologs in a zebrafish model of early development causes gross developmental defects. Our results reveal that transcription of most lncRNA genes is coordinated with transcription of protein-coding genes and that these lncRNAs have roles in early development. Analysis of genome-wide lncRNA transcription in human embryonic stem cells and early differentiation using RNA-seq, GRO-seq and ChIP-seq
2013-01-02 | E-GEOD-41009 | biostudies-arrayexpress
Project description:Once thought to be transcriptional noise, large non-coding RNAs (lncRNAs) have recently been demonstrated to be functional molecules. Cell type-specific expression patterns of lncRNAs suggest that their transcription may be regulated epigenetically. Using a custom-designed microarray, here we examine the expression profile of lncRNAs in embryonic stem (ES) cells, lineage-restricted neuronal progenitor cells (NPC), and terminally differentiated fibroblasts. In addition, we also analyze the relationship between their expression and their promoter H3K4 and H3K27 methylation patterns. We find that numerous lncRNAs in these cell types undergo changes in the levels of expression and promoter H3K4me3 and H3K27me3. Interestingly, lncRNAs that are expressed at lower levels in ES cells exhibit higher levels of H3K27me3 at their promoters. Consistent with this result, knockdown of the H3K27me3 methyltransferase Ezh2 results in derepression of these lncRNAs in ES cells. Thus, our results establish a role for Ezh2-mediated H3K27 methylation in lncRNA silencing in ES cells and reveal that lncRNAs are subject to epigenetic regulation in a similar manner to that of protein-coding genes. lncRNA expression analysis was performed in 5 different cell types: (1) ES cells, (2) neuroprogenitors, (3) tail tip fibroblasts, (4) Ezh2 knockdown #1 ES cells, and (5) Ezh2 knockdown #2 ES cells. Total RNA was extracted and RNA quality was assessed via Agilent Bioanlayzer. mRNA was amplified using the Low RNA Linear Amplification Kit (Agilent Technologies) by standard manufacturer's protocol. Hybridization of experimental RNA labeled with Cy5 and Cy3-labeled Universal Reference RNA (Ambion) was carried out by standard protocol on a custom-designed array manufactured by Agilent Technologies. Briefly, three unique 60nt probes were designed for each entry in the Fantom3 database and were synthesized along with lineage marker control probes on a 2x105K format array. Upon array scanning, data was quality filtered, normalized by the Lowess method, and all probes corresponding to a given lncRNA were averaged using the UNC Microarray Database (UNCMD). Intraclass correlation analysis was carried out in the UNCMD.
2010-08-05 | E-GEOD-22451 | biostudies-arrayexpress
Project description:CapitalBio Technology Human LncRNA Array v4, 4x180K was used to detect lncRNA expression in CRC tissues compared with their matched non-tumoral tissues. Here we report significantly up-regulated as well as down-regulated lncRNAs in CRC tissues compared with their matched non-tumoral tissues.
2022-07-25 | GSE134834 | GEO
Project description:Given the role of lncRNAs and mRNAs in tumor pathogenesis, we set out to identify transcripts that potentially drive colorectal tumorigenesis. In this study, we will use the microarray analysis to study the differences of the expression profiles of lncRNA and mRNA in colorectal cancer tissues, analyzing the differentially expressed genes by GO/KEGG enrichment, and predicting the new lncRNAs’ function.
2019-02-06 | GSE126092 | GEO