scholarly journals Assessment of small RNA sorting into different extracellular fractions revealed by high-throughput sequencing of breast cell lines

2015 ◽  
Vol 43 (11) ◽  
pp. 5601-5616 ◽  
Author(s):  
J. P. Tosar ◽  
F. Gambaro ◽  
J. Sanguinetti ◽  
B. Bonilla ◽  
K. W. Witwer ◽  
...  
Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 3650-3650
Author(s):  
Michael C Wei ◽  
Elizabeth O Osborn ◽  
Michael Cleary

Abstract Abstract 3650 MicroRNAs are small, non-coding RNAs that regulate gene expression and play key roles in cancer by modulating oncogene and tumor suppressor pathways. We are investigating the clinical and prognostic roles of miRNA expression in pediatric leukemias using high-throughput sequencing as a profiling tool. To establish the methodology, we have utilized high-throughput sequencing to quantify small RNA expression from eight acute lymphoblastic leukemia cell lines and one MLL-rearranged infant ALL patient sample. We generated sequencing libraries from these cells, conducted high-throughput sequencing using the Illumina platform, and established a custom bioinformatics pipeline for data analysis. Over 50 million individual sequence reads were analyzed. These sequences were mapped against a database of human miRNAs, and the frequency of miRNA expression among samples was enumerated. Expression of hematopoietic-specific miR-142 and miR-181 cluster miRs was found in these leukemia samples, while the liver-specific miR-122 was not expressed. miR-196b, previously reported to be over-expressed in MLL-rearranged leukemias, was expressed in 3/3 MLL-rearranged leukemia cell lines and 1/5 non-MLL cell lines. Expression of individual miRNAs was validated by quantitative PCR. Additional analysis of MLL-associated miRNAs and novel small RNAs will be presented. Our results demonstrate the feasibility and potential of high-throughput sequencing to profile the expression of small RNAs from leukemia cells, and we plan to apply these methods to additional primary patient samples to examine prognostic and clinical correlations with small RNA expression patterns. Disclosures: No relevant conflicts of interest to declare.


Plants ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 954
Author(s):  
György Pasztor ◽  
Zsuzsanna Galbacs N. ◽  
Tamas Kossuth ◽  
Emese Demian ◽  
Erzsebet Nadasy ◽  
...  

Millet is a dangerous weed in crop fields. A lack of seed dormancy helps it to spread easily and be present in maize, wheat, and other crop fields. Our previous report revealed the possibility that millet can also play a role as a virus reservoir. In that study, we focused on visual symptoms and detected the presence of several viruses in millet using serological methods, which can only detect the presence of the investigated pathogen. In this current work, we used small RNA high-throughput sequencing as an unbiased virus diagnostic method to uncover presenting viruses in randomly sampled millet grown as a volunteer weed in two maize fields, showing stunting, chlorosis, and striped leaves. Our results confirmed the widespread presence of wheat streak mosaic virus at both locations. Moreover, barley yellow striate mosaic virus and barley virus G, neither of which had been previously described in Hungary, were also identified. As these viruses can cause severe diseases in wheat and other cereals, their presence in a weed implies a potential infection risk. Our study indicates that the presence of millet in fields requires special control to prevent the emergence of new viral diseases in crop fields.


2016 ◽  
Vol 44 (14) ◽  
pp. e123-e123 ◽  
Author(s):  
Yun Zheng ◽  
Bo Ji ◽  
Renhua Song ◽  
Shengpeng Wang ◽  
Ting Li ◽  
...  

PLoS ONE ◽  
2013 ◽  
Vol 8 (3) ◽  
pp. e59423 ◽  
Author(s):  
Mariana Carnavale Bottino ◽  
Sabrina Rosario ◽  
Clicia Grativol ◽  
Flávia Thiebaut ◽  
Cristian Antonio Rojas ◽  
...  

Plants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1367
Author(s):  
Edgar Baldemar Sepúlveda-García ◽  
José Francisco Pulido-Barajas ◽  
Ariana Arlene Huerta-Heredia ◽  
Julián Mario Peña-Castro ◽  
Renyi Liu ◽  
...  

Submergence and drought stresses are the main constraints to crop production worldwide. MicroRNAs (miRNAs) are known to play a major role in plant response to various stresses. In this study, we analyzed the expression of maize and teosinte miRNAs by high-throughput sequencing of small RNA libraries in maize and its ancestor teosinte (Zea mays ssp. parviglumis), under submergence, drought, and alternated stress. We found that the expression patterns of 67 miRNA sequences representing 23 miRNA families in maize and other plants were regulated by submergence or drought. miR159a, miR166b, miR167c, and miR169c were downregulated by submergence in both plants but more severely in maize. miR156k and miR164e were upregulated by drought in teosinte but downregulated in maize. Small RNA profiling of teosinte subject to alternate treatments with drought and submergence revealed that submergence as the first stress attenuated the response to drought, while drought being the first stress did not alter the response to submergence. The miRNAs identified herein, and their potential targets, indicate that control of development, growth, and response to oxidative stress could be crucial for adaptation and that there exists evolutionary divergence between these two subspecies in miRNA response to abiotic stresses.


2017 ◽  
Vol 162 (7) ◽  
pp. 1933-1942 ◽  
Author(s):  
Xiangyun Lu ◽  
Jin Yang ◽  
Haibo Wu ◽  
Zongxing Yang ◽  
Changzhong Jin ◽  
...  

2021 ◽  
Author(s):  
Oliver Lung ◽  
Rebecca Candlish ◽  
Michelle Nebroski ◽  
Peter Kruckiewicz ◽  
Cody Buchanan ◽  
...  

Abstract Cell lines are widely used in research and for diagnostic tests and are often shared between laboratories. Lack of cell line authentication can result in the use of contaminated or misidentified cell lines, potentially affecting the results from research and diagnostic activities. Cell line authentication and contamination detection based on metagenomic high-throughput sequencing (HTS) was tested on DNA and RNA from 63 cell lines available at the Canadian Food Inspection Agency’s National Centre for Foreign Animal Disease. Through sequence comparison of the cytochrome c oxidase subunit 1 (COX1) gene, the species identity of 53 cell lines was confirmed, and eight cell lines were found to show a greater pairwise nucleotide identity in the COX1 sequence of a different species within the same expected genus. Two cell lines, LFBK-αvβ6 and SCP-HS, were determined to be composed of cells from a different species and genus. Mycoplasma contamination was not detected in any cell lines. However, several expected and unexpected viral sequences were detected, including part of the classical swine fever virus genome in the IB-RS-2 Clone D10 cell line. Metagenomics-based HTS is a useful laboratory QA tool for cell line authentication and contamination detection that should be conducted regularly.


Sign in / Sign up

Export Citation Format

Share Document