Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

42 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

De novo sequencing of circulating microRNAs in locally advanced breast cancer

ABSTRACT: MicroRNAs (miRNAs) have been recently detected in the circulation of cancer patients, where they are associated with clinical parameters. Discovery profiling of circulating small RNAs has not been previously reported in breast cancer (BC), and was carried out in this study to identify blood-based small RNA markers of BC clinical outcome. The pre-treatment sera of 42 stage II–III locally advanced and inflammatory BC patients who received neoadjuvant chemotherapy (NCT) followed by surgical tumor resection were analyzed for marker identification by deep sequencing all circulating small RNAs.

ORGANISM(S): Homo sapiens

SUBMITTER: Emily Wang

PROVIDER: E-GEOD-49035 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Deep sequencing of exosomal and cellular miRNAs in MDA-MB-231 and MCF-10A cells

Project description:To identify the miRNAs that are differentially expressed and secreted between the MDA-MB-231 metastatic breast cancer cells and the MCF-10A non-cancerous human mammary epithelial cells, we profiled the cellular and exosomal small RNAs (between 17 and 52 nt) isolated from these two cell lines by Solexa deep sequencing. MiRNAs that are significantly different between the two cell lines are identified. RNA was extracted from cultured MDA-MB-231 and MCF-10A cells or purified exosomes secreted by these cells, and subjected to library construction and Solexa deep sequencing.

2013-09-01 | E-GEOD-50429 | biostudies-arrayexpress

Illumina sequencing of small RNAs from C. elegans embryos

Project description:Caenorhabditis elegans is one of the most prominent model systems to study embryogenesis. However, it has been impractical to collect large amounts of precisely staged embryos. Thus, early C. elegans embryogenesis has not been amenable to most modern high-throughput genomics or biochemistry assays. To overcome this problem, we devised a method to collect large amounts of cleanly staged C. elegans embryos by Fluorescent Activated Cell Sorting (termed eFACS). eFACS can in principle be applied to all embryonic developmental stages up to hatching. As a proof of principle we show that a single eFACS run routinely yields tens of thousands of almost perfectly staged one-cell embryos. Since in animals the earliest embryonic events are driven by post-transcriptional regulation, we combined eFACS with next-generation sequencing technology to systematically profile the embryonic expression of small, non-coding RNAs. We discovered a wealth of complex and orchestrated changes in the expression between and within almost all classes of small RNAs, including miRNAs, during embryogenesis. Our data indicate that half of all known miRNAs are already expressed in the one-cell stage embryo and we also shed light on the expression and genomic organization of the previously under-appreciated 26G-RNAs. Together, our eFACS data suggest that the complexity of small RNA expression dynamics in animals is comparable to the expression dynamics of protein encoding genes. Various C. elegans embryo samples were generated: mixed embryos by traditional bleaching (Brenner, 1974), early embryos by eFACS (Stoeckius et al., in press). RNA was extracted and length fractionated. Small RNA was subjected to a 5'-dependent ligation protocol to add sequencing adapters. The small RNA samples were sequenced using the Illumina GA I & II.

2009-09-06 | E-GEOD-17153 | biostudies-arrayexpress

Small extracellular vesicles from serum (human)

Project description:Quantitative comparison of the protein load of small extracellular vesicles circulating in serum prior and after high intensity interval training.

2022-02-15 | PXD020330 | Pride

Small RNA sequences from Schizosaccharomyces japonicus

Project description:Small interfering RNAs (siRNAs) are known to be involved in both transposon silencing and centromere function, leading us to investigate the interplay between these two roles in the Schizosaccharomyces lineage. In S. pombe, the centromeric repeats produce dicer-dependent siRNAs that are required for maintenance of centromeric structure, function and transcriptional silencing via Argonaute-dependent heterochromatin formation13. However, transposons are silenced in S. pombe by RNAi-independent mechanisms and do not produce abundant siRNAs. To investigate whether centromere-directed siRNA production is conserved within the transposon-rich centromeres of S. japonicus, we isolated and sequenced small RNAs from log-phase S. japonicus cultures. The small RNAs have a modal size of 23 nucleotides and 94% map to transposons, both telomeric and centromeric. Isolation and computational analysis of small RNAs from wild-type S. japonicus

2011-03-09 | E-GEOD-27837 | biostudies-arrayexpress

Comparison of small RNA levels in Dicer helicase mutants

Project description:Years after the discovery that Dicer is a key enzyme in gene-silencing, the role of its helicase domain remains enigmatic. Here we show that this domain is critical for accumulation of certain endogenous small interfering RNAs (endo-siRNAs) in C. elegans. The domain is required for the production of the direct products of Dicer, or primary endo-siRNAs, and consequently, affects levels of downstream intermediates, the secondary endo-siRNAs. Consistent with the role of endo-siRNAs in silencing, their loss correlates with an increase in cognate mRNA levels. We find that the helicase domain of Dicer is not required for microRNA (miRNA) processing, or RNA interference following exposure to exogenous double-stranded RNA. Comparisons of wildtype and helicase-defective strains using deep-sequencing analyses show that the helicase domain is required by a subset of annotated endo-siRNAs, in particular, those associated with the slightly longer 26 nucleotide small RNA species containing a 5M-bM-^@M-^Y guanosine. We reintroduced either wildtype Dicer, or Dicer harboring a mutation (K39A) in it's helicase domain, into dcr-1(ok247) mutant worms via transgene rescue. We then used high-throughput sequencing to compare levels of small RNAs present in each of these strains.

2010-04-01 | E-GEOD-20336 | biostudies-arrayexpress

De novo sequencing of circulating microRNAs in locally advanced breast cancer

Project description:MicroRNAs (miRNAs) have been recently detected in the circulation of cancer patients, where they are associated with clinical parameters. Discovery profiling of circulating small RNAs has not been previously reported in breast cancer (BC), and was carried out in this study to identify blood-based small RNA markers of BC clinical outcome.

2013-07-20 | GSE49035 | GEO

High-throughput sequencing of endogenous small RNAs from rat vascular smooth muscle cells with and without Angiotensin II stimulation

Project description:Angiotensin II (Ang II)-mediated vascular smooth muscle cells (VSMC) dysfunction plays a critical role in cardiovascular diseases. However, the role of microRNAs (miRNAs) in this process is unclear. We used small RNA deep sequencing to profile Ang II-regulated miRNAs in rat VSMC and evaluated their role in VSMC dysfunction. Sequencing results revealed several Ang II-responsive miRNAs and bioinformatics analysis showed that their predicted targets can modulate biological processes relevant to cardiovascular diseases. Examined 4 samples of Rat VSMC. Control (without Ang II treatment) and 3 samples treated with Ang II for 1h, 3h, and 24h. Compared the changes in gene expression in Ang II treated samples relative to control samples.

2012-03-23 | E-GEOD-35664 | biostudies-arrayexpress

Changes in the expression of miR-381 and miR-495 are inversely associated with the expression of the MDR1 gene and development of multi-drug resistance

Project description:Multidrug resistance (MDR) frequently develops in cancer patients exposed to chemotherapeutic agents and is usually brought about by over-expression of P-glycoprotein (P-gp) which acts as a drug efflux pump. MiRNAome profiling using next-generation sequencing identified differentially expressed microRNAs (miRs) between parental K562 cells and MDR K562 cells (K562/ADM) induced by chronic adriamycin treatment. MiRNAome profiling in untreated K562 cells and K562 cells exposed to long-term adriamycin treatment

2013-10-29 | E-GEOD-51774 | biostudies-arrayexpress

Cross platform standardization of an experimental pipeline for use in the identification of dysregulated human circulating miRNAs

Project description:In this study we present an experimental pipeline that takes into consideration sample collection, processing, enrichment, and the subsequent comparative analysis of circulating small ribonucleic acids using small RNA sequencing and RT-qPCR. Initially, a panel of miRNAs dysregulated in circulating blood from breast cancer patients compared to healthy women were identified using small RNA sequencing. MiR-320a was identified as the most dysregulated miRNA between the two female cohorts. Total RNA and enriched small RNA populations (<30 bp) isolated from peripheral blood from the same female cohort samples were then tested using a miR-320a RT-qPCR assay. When total RNA was analyzed with this miR-320a RT-qPCR assay, a 2.3-fold decrease in expression levels was observed between blood samples from healthy controls and breast cancer patients. However, upon enrichment for the small RNA population and subsequent analysis of miR-320a using RT-qPCR, its dysregulation in breast cancer patients was more pronounced with an 8.89-fold decrease in miR-320a expression. miRNAseq with Illumina 2000 of human females n=23 controls and n=14 cases [Ethics Statement] Written informed consent was received from all participants in the study. Ethical approval was granted by the Clinical Research Ethics Committee, Galway University Hospital.

2015-08-30 | E-GEOD-72080 | biostudies-arrayexpress

Next generation sequencing profiling identifies miR-574-3p and miR-660-5p as potential novel prognostic markers for breast cancer

Project description:Prognostication of Breast Cancer (BC) relies largely on traditional markers such as hormone or growth factors but due to their suboptimal specificities, it is challenging to identify the subset of patients who are likely to undergo recurrence and markers of higher specificity are sought to guide therapies. MicroRNAs (miRNAs) are small non-coding RNAs which function as post-transcriptional regulators of gene expression and have shown promise as potential prognostic markers in several cancer types including BC. In our study, we sequenced 104 breast tumor tissue samples and 11 apparently healthy normal breast tissues for miRNAs. Two widely used approaches were adopted to identify prognostic markers â Case-control and Case-only. For both the approaches, Cox-proportional hazards regression model and risk score analysis was performed to identify miRNA signature independent of potential confounders. Representative miRNAs were validated using qRT-PCR. Gene ontology terms were identified for miRNAs significant in survival analysis. A total of 1,423 miRNAs were captured from the tissues, of which 126 were retained with predetermined criteria for good read counts. In the case-control approach, 80 miRNAs were differentially expressed, from which four and two miRNAs were significant for OS and RFS respectively. In the case-only approach, from 147 miRNAs, 11 and four miRNAs were significant for OS and RFS respectively, in which miR-574-3p and miR-660-5p were novel and were not previously found to be associated with BC prognosis. Multivariate Cox analysis indicated that the risk scores calculated in both the approaches were potential independent prognostic factors for BC. Targets for the identified miRNAs were enriched for cell proliferation, invasion and migration. Identification of miRNAs as prognostic markers for breast cancer

2016-03-02 | E-GEOD-68085 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data