Benzo[a]pyrene-induced changes in microRNA-mRNA networks
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Daneida Lizarraga
PROVIDER: E-GEOD-31252 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The microarray contains 9360 reporters, each present four times on the microarray. In our analysis 1326 human and viral reporters were used, of which 880 are unique human mature microRNAs. The other 8024 reporters represent microRNAs from other species. cDNA was generated using 1 μg of total RNA per sample. RNA was labeled only with Hy3 containing dye using the microRNACURY LNA™ microRNA Hy3 Power labeling kit (Exiqon, Denmark) according to the manufacturer’s protocol in a total volume of 25 μl. To adjust the volume to 100 μl, a hybridization buffer provided in miRCURY LNA™ microRNA Array, 5th generation kit (Exiqon, Denmark) was used.
2012-08-07 | GSE31252 | GEO
Project description:We have employed whole microRNA microarray to identify changes in microRNA expression in human bone marrow MSCs (hMSC-TERT) during adipocytic differentiation in culture on day 7 and day 13 Human MSC line (hMSC-TERT) were subjectd to adipocytic differentiation for 7 days or 13 days, subsequently, RNA was extracted. The samples were labeled using the miRCURY LNAM-bM-^DM-" microRNA Hi-Power Labeling Kit, Hy3M-bM-^DM-"/Hy5M-bM-^DM-" and hybridized on the miRCURY LNAM-bM-^DM-" microRNA Array (6'th GEN). Array product number 208400; Array version 6'th GEN, Array batch number 34014, miRBase version 17. The 'Legends_rawdata.pdf' contains the column headers (of raw data files) and their detailed description.
2014-09-09 | E-GEOD-59684 | biostudies-arrayexpress
Project description:The study aimed to identify miRNAs expression profiles associated with growth and regression of dominant-size follicles in bovine. Follicles were collected from abattoir ovaries and their status (healthy/atretic) was assessed by measuring steroid levels and aromatase expression. Total RNA was isolated from whole follicles at different developmental stages. An heterologous microarray (Exiqon, Denmark) approach followed by RT-qPCR validation (Qiagen, UK) was used to identify and compare miRNA profiles between large healthy follicles (diameter, 13M-bM-^@M-^S16 mm, n=6) and each of small (4M-bM-^@M-^S8 mm, n=6 pools of follicles) and large atretic folllicles (13-16 mm, n=6). RNA from the above groups was hybridized to the miRCURY LNAM-bM-^DM-" microRNA Hi-Power Labeling Kit,Hy3M-bM-^DM-"/Hy5M-bM-^DM-" (Exiqon) and hybridized on the miRCURY LNAM-bM-^DM-" microRNA Array (6th gen). A total of 17 and 57 microRNAs were differentially expressed (> 2 fold, adj. P-value < 0.05) between Large Healthy and each of Small and Large Atretic follicles, respectively, a fraction of which corresponded to registered bovine miRNA sequences. A subset of 5 bovine miRNAs (miR-144, miR-202,vmiR-451, miR-652, miR-873) were confirmed by qPCR to be upregulated in Large Healthy follicles, were enriched in mural granulosa cells and their predicted targets mapped to genes involved in follicular cell proliferation and differentiation, suggesting an involvemet of this subset of microRNAs in ovarian follicle development. Six biological replicates per developmental stage (total of 18 samples) were used in a double dye microRNA microarray experiment. Samples were distributed among slides so that each experimental group was represented at least once in each slide. For each gene, mean normalized intensities (n= 6 biological replicates/group) were compared between follicle stages (SF vs LHF and LHF vs LAF).
2014-06-15 | E-GEOD-54692 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2015-01-27 | E-GEOD-45802 | biostudies-arrayexpress
Project description:Cells of a human cholangiocyte cell line (H69) were exposed to 10 ng/ml of IFN-gamma for 8 h. Cells were collected and processed for miRNA array analysis carried out by EXIQON (Denmark).
2009-02-10 | E-MEXP-1906 | biostudies-arrayexpress
Project description:By employing miRCURY LNAM-bM-^DM-" microRNA Array, we have identified a subset of 21 top miRNAs that are differentially expressed between GM-BMM and M-BMM cells To know the differential expression of miRNA in mouse GM-CSF-induced bone marrow-derived macrophages (GM-BMM) vs. M-CSF-induced BMM (M-BMM)
2013-04-17 | E-GEOD-46085 | biostudies-arrayexpress
Project description:Adult aging is a complex biological process associated with altered gene expression and a decline in physiological performance. The microRNAs have been implicated in cardiac development, cardiac hypertrophy and heart failure. However, the impact of adult aging on cardiac expression of both miRNA guide strand (miR) and passenger strand (miR*), as well as miRNA clusters have not been well established. We explored the expression profile of both miR and miR* in the heart. We found that 65 miRNAs were differentially expressed in old versus young adult heart; approximately half of them were clustered miRNAs that were distributed in 11 miRNA clusters. Each miRNA cluster contains from 2 to as many as 71 miRNA genes. The majority of the clusters displayed unified expression, with most cluster members within a cluster being either increased or decreased together, suggesting that most clusters are regulated by a common signaling mechanism and that the combined expression of multiple miRNA genes in a cluster could pose an impact on a broad range of targets during aging. We also found age-related changes in the expression of miR*s. Bioinformatic analysis revealed that miR-21 and miR-21* had their own silencing targets. The expression of both miR and miR* correlated with that of pri-miRNA transcript over the time course from development and maturation through adult aging. Age-related changes in the expression of Ago1 and Ago2 proteins in the heart were also observed. Our data suggest that a concert of effects, including transcriptional regulation of pri-miRNA transcript and altered expression of Argonaut proteins, contribute to age-related changes in the expression of both miR and miR* strands during adult aging. The major changes occurred later in life, from middle to old age. It is likely that the expression of both miR and miR* is regulated by transcription and Ago1 and Ago2 proteins. Six healthy C57BL/6 mice were used in this study. Three of them were 4 months old (young adult mice: YA), and the other three were 24 months old (old mice). Total RNA samples were isolated from mouse hearts and then shipped to Exiqon Inc., where microRNA array analysis was performed. Three array slides were used for the hybridization. Each array slide hybridized with two samples labeld with either Hy3 or Hy5, with array #1 being hybridized with samples YA-1 (Hy3) and Old-1 (Hy5), array #2 with samples YA-2 (Hy3) and Old-2 (Hy5) and array #3 with samples YA-3 (Hy5) and Old-3 (Hy3). In our publication, we reveal the detail of the experiment and statistical analysis that were provided by Exiqon Inc.
2012-08-20 | E-GEOD-32935 | biostudies-arrayexpress
Project description:We investigated the expression profiles of microRNAs (miRNA) in 27 renal cell carcinoma (RCC) FFPE tissues (3 chRCC, 5 papRCC and 18 ccRCC), 4 upper urinary tract-urothelial cell carcinomas of the renal pelvis-ureter (UUT-UCCs) and 20 normal kidneys by using the miRCURY LNAM-bM-^DM-" microRNA Array, 6th gen (Exiqon, Woburn MA), containing capture probes that target all miRNAs for all species registered in the miRBASE version 16.0. Real-time PCR (qRT-PCR) using appropriate endogenous controls was performed in order to validate the microarray results of the 27 most differentially expressed (DE) miRNAs. We identified 434 miRNAs that were significantly deregulated in all kidney tumours compared to the normal tissues. A total of 126 miRNAs (29%) had increased expression while 303 (69.8%) had decreased expression in RCC. Out of the 434 DE miRNAs, we detected 94 co-up-regulated and 218 co-down-regulated microRNAs among chRCC, papRCC and ccRCC. Of these, 89 and 203 were co-up- and co-down-regulated between RCCs and UUT-UCCs, respectively. We detected 11, 44 and 24 up-regulated miRNAs, which were specific for ccRCC, chRCC and papRCC, respectively. Moreover, 19, 18 and 8 miRNAs were uniquelly down-regulated in ccRCC, chRCC and papRCC, respectively. We also detected 89 and 203 co-up- and co-down-regulated miRNAs between kidney cancer and UUT-UCCs. Five miRNAs were up-regulated specifically in renal tumours and 49 in UUT-UCCs, whereas 15 miRNAs were down-regulated specifically in renal tumours and 89 in UUT-UCCs, respectively. Our data validicate that expression of miRNAs tends to be down-regulated renal cell carcinomas compared with normal kidney. We used 18 ccRCC, 3 chRCC, 5 papRCC, 4 UUT-UCC, 1 undifferentiated carcinoma and 19 normal tissue samples for miRNA profiling. Total RNA (0.5 M-BM-5g) from each sample and reference was labeled with Hy3M-bM-^DM-" fluorescent label, using the miRCURY LNAM-bM-^DM-" microRNA Hi-Power Labeling Kit (Exiqon, Woburn MA). The Hy3M-bM-^DM-\"-labeled samples were hybridized to the miRCURY LNAM-bM-^DM-" microRNA Array, 6th gen (Exiqon, Woburn MA), using an Agilent hybridization SureHyb chamber and gasket slide kits. After hybridization, the microarray slides were scanned at 10 M-NM-<m using the High-Resolution Microarray Scanner (Agilent Technologies) and stored in an ozone free environment. The image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA). Raw microarray data were filtered, background corrected and quantile normalizated. Normalized data were further extracted, pre-processed and sorted with Microsoft ExcelM-BM-.. MicroRNAs were considered to be significantly differentially expressed if they obtained a p-value<0.05 and a FDRM-bM-^IM-$0.05.
2013-06-18 | E-GEOD-48008 | biostudies-arrayexpress
Project description:To examine the miRNA expression profile of the profibrogenic macrophages, we compared miRNA expression in untreated versus IL-4 or IL-13-treated macrophages using miRNA microarray.IL-4 and IL-13 treatment resulted in marked changes in 18 and 19 miRNAs in macrophages, respectively.(n=3, fold changes>2, P<0.05) Total RNA from human primary macrophages (n=3) treated with or without 20 ng/ml IL-4 or 20ng/ml IL-13 for 48 hr was isolated with a mirVana miRNA Isolation kit (Ambion, Foster, CA). The miRNA expression profile of the samples were examined using miRCURY LNAM-bM-^DM-" arrays (v18.0; covering 1921 human miRNAs, Exiqon ,Vedbaek, Denmark).
2014-07-12 | E-GEOD-59348 | biostudies-arrayexpress
Project description:HepG2 cells (human liver hepatocarcinoma) were exposed for 6 different time points (6,12,18,24,36 and 48h) to Benzo[a]pyrene (BaP) in duplicate. Total RNAs were ribo-depleted and sequenced on an Illumina Hiseq2000 in pair-end 100 bp reads. One of the duplicates for BaP-treated sample at the 24 hour time point was found to have a minor fastq file integrity issue and was removed from this data set as a precaution.
2015-08-02 | E-MTAB-3292 | biostudies-arrayexpress