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Analysis of microRNA transcriptome by deep sequencing of small RNA libraries of peripheral blood (seq data)

ABSTRACT: MicroRNAs are a class of small non-coding RNAs that regulate mRNA expression at the post-transcriptional level and thereby many fundamental biological processes. A number of methods, such as multiplex polymerase chain reaction, microarrays have been developed for profiling levels of known miRNAs. These methods lack ability to identify novel miRNAs and accurately determine expression at a range of concentration. Deep or massively parallel sequencing methods are providing suitable platforms for genome wide transcriptome analysis and have the ability to identify novel transcripts. The results of analysis of small RNA sequences obtained by Solexa technology of normal peripheral blood mononuclear cells, tumor cell lines K562 (chronic myelogenous leukemia) and HL60 (acute promyelogenous leukemia) are presented. Custom computation pipelines were used to generate expression profiles of known and for identification of novel miRNAs. Some of the highly expressed miRNAs in the leukocytes include several members of the let 7 family, mir-21, 103, 185, 191 and 320a. Comparison of the miRNA profiles of normal versus K562 cells or HL60 revealed a specific set of differentially expressed molecules. Correlation of the miRNA with that of mRNA expression profiles, obtained by microarray, revealed a set of target genes showing inverse correlation with miRNA levels. Our computational pipeline also predicted a number of novel miRNAs. Some of the predictions were validated by realtime RT-PCR and or RNAase protection assay.

ORGANISM(S): Homo sapiens

PROVIDER: GSE19812 | GEO | 2010/05/13

SECONDARY ACCESSION(S): PRJNA124019

REPOSITORIES: GEO

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Analysis of microRNA transcriptome by deep sequencing of small RNA libraries of peripheral blood (seq data)

Project description:MicroRNAs are a class of small non-coding RNAs that regulate mRNA expression at the post-transcriptional level and thereby many fundamental biological processes. A number of methods, such as multiplex polymerase chain reaction, microarrays have been developed for profiling levels of known miRNAs. These methods lack ability to identify novel miRNAs and accurately determine expression at a range of concentration. Deep or massively parallel sequencing methods are providing suitable platforms for genome wide transcriptome analysis and have the ability to identify novel transcripts. The results of analysis of small RNA sequences obtained by Solexa technology of normal peripheral blood mononuclear cells, tumor cell lines K562 (chronic myelogenous leukemia) and HL60 (acute promyelogenous leukemia) are presented. Custom computation pipelines were used to generate expression profiles of known and for identification of novel miRNAs. Some of the highly expressed miRNAs in the leukocytes include several members of the let 7 family, mir-21, 103, 185, 191 and 320a. Comparison of the miRNA profiles of normal versus K562 cells or HL60 revealed a specific set of differentially expressed molecules. Correlation of the miRNA with that of mRNA expression profiles, obtained by microarray, revealed a set of target genes showing inverse correlation with miRNA levels. Our computational pipeline also predicted a number of novel miRNAs. Some of the predictions were validated by realtime RT-PCR and or RNAase protection assay. The small RNA population from four samples - Two Normal Peripheral blood mononuclear cells (PBMC) samples, K562 cell line (This cell line is used as a model to study Chronic Myelogenous Leukemia), HL60 (This cell line is used to study acute promyelogenous leukemia) was sequenced using Solexa technology.

2010-05-13 | E-GEOD-19812 | biostudies-arrayexpress

Differential expression of plasma miRNAs in immune thrombocytopenia

Project description:We investigated the expression profiles of plasma miRNAs in immune thrombocytopenia (ITP) patients. Peripheral blood plasma was used for Agilent miRNA expression microarray analysis to define miRNA profiles and to identify miRNAs with discriminatory levels for ITP and healthy controls. Results were further validated using quantitative realtime PCR on a larger cohort, enabling relative quantification of plasma miRNAs and defining miRNAs with diagnostic value for the disease.

2017-12-31 | GSE80401 | GEO

TEL-AML1 regulation of survivin and apoptosis via miRNA-494 and miRNA-320a

Project description:There is increasing evidence that microRNA and transcription factors interact in an instructive fashion in normal and malignant hematopoiesis. We explored the impact of TEL-AML1 (ETV6-RUNX1), the most common fusion protein in childhood leukemia, on miRNA expression and the leukemic phenotype. Using RNA interference, miRNA expression arrays, and quantitative PCR, we identified miRNA-494 and miRNA-320a to be upregulated upon TEL-AML1 silencing independently of TEL expression. Chromatin immunoprecipitation analysis identified miRNA-494 as a direct miRNA target of the fusion protein TEL-AML1. Using bioinformatic analysis as well as functional luciferase experiments we demonstrate that survivin is a target of the two miRNAs. MiRNA-494 and -320a were introduced to the cells by transfection and survivin expression determined by western blot analysis. These miRNAs blocked survivin expression and resulted in apoptosis in a similar manner as TEL-AML1 silencing by itself; this silencing was also shown to be DICER-dependent. MiRNAs-494 and -320a are expressed at lower levels in TEL-AML1+ leukemias compared to immunophenotype-matched non-TEL-AML1 ALL subtypes, and within TEL-AML1+ leukemias their expression is correlated to survivin levels. In summary our data suggest that TEL-AML1 might exert its anti-apoptotic action at least in part by suppressing miRNA-494 and miRNA-320a, lowering their expression causing enhanced survivin expression. DNAs from REH cells were pulled down using ChIP antibodies to TEL and hybridized to microRNA promoter tiling arrays.

2010-08-28 | E-GEOD-23842 | biostudies-arrayexpress

Sequencing of Argonaute-bound miRNA/mRNA hybrids reveals regulation of the unfolded protein response by microRNA-320a

Project description:MicroRNAs (miRNA) are short non-coding RNAs widely implicated in development, gene regulation, and disease progression. Most miRNAs utilize the RNase III enzymes Drosha and Dicer for biogenesis in animals. One notable exception is the RNA polymerase II transcription start sites (TSS) miRNAs whose biogenesis requires Dicer but not Drosha. The functional importance of the TSS-miRNA biogenesis pathway has remained uncertain due to their unelucidated targetomes. To better understand the function of TSS-miRNAs, we applied a modified Crosslinking, Ligation, and Sequencing of Hybrids on Argonaute (Ago-qCLASH) to identify the targets for TSS-miRNAs in HCT116 colorectal cancer cells with or without Drosha knockout (KO). We observed that miR-320a hybrids dominate in TSS-miRNA hybrids identified by Ago-qCLASH. Targets for miR-320a are enriched in the eIF2 signaling pathway, a downstream component of the unfolded protein response. Consistently, in miR-320a mimic- and inhibitor- transfected cells, differentially expressed genes are enriched in the eIF2 signaling pathway. Within the Ago-qCLASH data, we identified the endoplasmic reticulum (ER) chaperone Calnexin as a direct miR-320a target, thus connecting miR-320a to the unfolded protein response. During ER stress, but not amino acid deprivation, miR-320a up-regulates ATF4, a critical transcription factor for resolving ER stress. Our study helps to elucidate the targetome of the TSS-miRNAs in colorectal cancer cells and establishes miR-320a as a regulator of unfolded protein response.

2021-06-23 | GSE164634 | GEO

TEL-AML1 regulation of survivin and apoptosis via miRNA-494 and miRNA-320a

2010-08-28 | GSE23842 | GEO

miRNA Profiling from total blood of Multiple Sclerosis and control samples

Project description:This project aims at the detection of specific patterns of miRNAs in peripheral blood samples of MS patients. As controls, blood of donors without known affection have been tested. Using the miRNA patterns we hope to detect a diagnostic pattern for the non-invasive diagnosis of MS. In this study, we compared 20 Multiple Sclerosis samples to 21 control samples using the sanger miRBAse 12.0 miRNA biochip manufactured by febit. Samples were analyzed with the Geniom Realtime Analyzer (GRTA, febit gmbh, Heidelberg, Germany) using the Geniom Biochip miRNA homo sapiens. Each array contains 7 replicates of 866 miRNAs and miRNA star sequences as annotated in the Sanger miRBase 12.0. To benchmark the platform, we tested technical replicates using bought total RNA of brain and liver samples (ambion), achieving a correlation of 0.97.

2010-06-25 | E-GEOD-17846 | biostudies-arrayexpress

miRNA Profiling from total blood of lung cancer and control samples

Project description:This project aims at the detection of specific patterns of miRNAs in peripheral blood samples of lung cancer patients. As controls, blood of donors without known affection have been tested. Using the miRNA patterns we hope to detect a diagnostic pattern for the non-invasive diagnosis of non-small cell lung carcinoma. In this study, we compared 17 lung cancer samples to 19 control samples using the sanger miRBAse 12.0 miRNA biochip manufactured by febit. Samples were analyzed with the Geniom Realtime Analyzer (GRTA, febit gmbh, Heidelberg, Germany) using the Geniom Biochip miRNA Homo sapiens. Each array contains 7 replicates of 866 miRNAs and miRNA star sequences as annotated in the Sanger miRBase 12.0. To benchmark the platform, we tested technical replicates using bought total RNA of brain and liver samples (ambion), achieving a correlation of 0.97.

2010-06-25 | E-GEOD-17681 | biostudies-arrayexpress

Regulatory networks in prenatal porcine skeletal muscle development under nutrient restriction

Project description:We generated transcriptome profiles of skeletal muscles from Largewhite pigs at 35, 55, and 90 days of gestation (dg), using high-throughput deep sequencing methods. A large number of differentially expressed (DE) genes and miRNAs were identified between stages and dietary treatments. Interestingly, reduced maternal calorie supply led to significant changes in mRNA and miRNA expression patterns. Down-regulation of critical genes and miRNAs associated with increased cell growth and myoblast differentiation at certain stages was found to be responsible for repressed myofiber formation in calorie-restricted pigs. Moreover, an integrative analysis of the miRNA and mRNA using sequence-based target prediction and negative correlation of miRNA-mRNA profiles identified a number of novel miRNA-mRNA interactions that are potentially involved in prenatal myogenesis regulation. Importantly, some critical miRNA-mRNA interactions were validated. And we first proposed a miRNA-TF-mRNA regulatory loop, which significantly increased the number of biologically relevant targets of miRNAs and introduced new mechanisms underlying the nutrient-modulated myogenesis.

2020-07-14 | GSE81751 | GEO

Identification of potential miRNA–mRNA regulatory network contributing to cytarabine resistance HL60 cells [array]

Project description:Cytarabine is the main drug for acute myeloid leukemia (AML) treatment; however, drug resistance hinders the treatment of AML. Although microRNA (miRNA) alteration is one of the well-recognized mechanisms underlying drug resistance in AML, few studies have investigated the role and function of miRNAs in the development of cytarabine resistance. In this study, total RNA was isolated from parental HL60 and cytarabine resistant HL60 (R-HL60) cells. Subsequently, miRNAs and mRNAs were detected using small RNA sequencing and gene expression array, respectively. The miRNAs and genes with ≥ 2-fold difference in expression between HL60 and R-HL60 cells were screened out. Negatively correlated miRNA–mRNA pairs were selected as candidate miRNA–mRNA target pairs by using the miRDB, Targetscan or miRTar databases. Functional enrichment analysis of differentially expressed genes (DEGs) included in the candidate miRNA–mRNA network was performed. The results revealed that CCL2, SOX9, SLC8A1, ICAM1, CXCL10, SIPR2, FGFR1, OVOL2, MITF, and CARD10 were simultaneously involved in seven GO pathways, namely the regulation of cell migration, regulation of locomotion, regulation of cellular component movement, cell migration, locomotion, cell motility, localization of cell. These genes were negatively correlated with the altered miRNAs (miR-1-3p, miR-155-5p, miR-1255b-5p, miR-200c-5p, miR-3609, miR-1285-3p, miR-124-3p, miR-146a-5p, miR-497a-5p, and miR-3150a-5p), suggesting that they are the potential targets of the miRNAs to regulate cell migration behavior or ability. Therefore, our results advance our understanding of the regulatory mechanism underlying cytarabine resistance development, specifically related to miRNAs.

2023-12-03 | GSE221718 | GEO

Identification of potential miRNA–mRNA regulatory network contributing to cytarabine resistance HL60 cells [miRNA-seq]

2023-12-03 | GSE221717 | GEO

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