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Deep Sequencing of the Small RNA Transcriptome of Normal and Malignant Human B cells Identifies Hundreds of Novel MicroRNAs

ABSTRACT: This SuperSeries is composed of the following subset Series: GSE15229: Massively Parallel Sequencing Identifies the MicroRNA Transcriptome of Normal and Malignant Human B cells GSE22895: Deep Sequencing of the Small RNA Transcriptome of Normal and Malignant Human B cells Identifies Hundreds of Novel MicroRNAs: microarray analysis Refer to individual Series

ORGANISM(S): Homo sapiens

SUBMITTER: Dereje Jima

PROVIDER: E-GEOD-22898 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Deep sequencing of the small RNA transcriptome of normal and malignant human B cells identifies hundreds of novel microRNAs.

Jima Dereje D DD Zhang Jenny J Jacobs Cassandra C Richards Kristy L KL Dunphy Cherie H CH Choi William W L WW Au Wing Yan WY Srivastava Gopesh G Czader Magdalena B MB Rizzieri David A DA Lagoo Anand S AS Lugar Patricia L PL Mann Karen P KP Flowers Christopher R CR Bernal-Mizrachi Leon L Naresh Kikkeri N KN Evens Andrew M AM Gordon Leo I LI Luftig Micah M Friedman Daphne R DR Weinberg J Brice JB Thompson Michael A MA Gill Javed I JI Liu Qingquan Q How Tam T Grubor Vladimir V Gao Yuan Y Patel Amee A Wu Han H Zhu Jun J Blobe Gerard C GC Lipsky Peter E PE Chadburn Amy A Dave Sandeep S SS

Blood 20100823 23

A role for microRNA (miRNA) has been recognized in nearly every biologic system examined thus far. A complete delineation of their role must be preceded by the identification of all miRNAs present in any system. We elucidated the complete small RNA transcriptome of normal and malignant B cells through deep sequencing of 31 normal and malignant human B-cell samples that comprise the spectrum of B-cell differentiation and common malignant phenotypes. We identified the expression of 333 known miRNA ...[more]

PMID: 20733160

Similar Datasets

Deep Sequencing of the Small RNA Transcriptome of Normal and Malignant Human B cells Identifies Hundreds of Novel MicroRNAs: microarray analysis

Project description:A role for microRNAs has been recognized in nearly every biological system examined thus far. A complete delineation of their role must be preceded by the identification of all microRNAs present in any system. We elucidated the complete small RNA transcriptome of normal and malignant B cells through deep sequencing of 31 normal and malignant human B cell samples that comprise the spectrum of B cell differentiation and common malignant phenotypes. We identified the expression of 333 known microRNAs, which is over twice the number previously recognized in any tissue type. We further identified the expression of 286 candidate novel microRNAs in normal and malignant B cells. These microRNAs were validated at a high rate (92%) using quantitative PCR and we demonstrated their application in the distinction of clinically relevant subgroups of lymphoma. Here, we analyzed the expression of 100 diffuse large B-cell lymphoma (DLBCL) samples using microarrays. Total RNA was extracted from frozen patient samples. The RNA was labeled, fragmented and hybridized to Human Gene 1.0 ST arrays.

2010-08-26 | E-GEOD-22895 | biostudies-arrayexpress

Massively Parallel Sequencing Identifies the MicroRNA Transcriptome of Normal and Malignant Human B cells

Project description:Profiling of miRNA transcriptome in Human mature B cells from similar populations Profiling of miRNA transcriptome in Human Normal and Malignant B cells, 8 normal samples corresponding to Naïve, Germinal Center, Plasma and Memory B cells and 23 samples derived from B cell malignancy

2010-08-25 | E-GEOD-15229 | biostudies-arrayexpress

The genetic landscape of mutations in Burkitt lymphoma

Project description:Burkitt lymphoma is characterized by deregulation of MYC, but the contribution of other genetic mutations to the disease is largely unknown. Here, we describe the first completely sequenced genome from a Burkitt lymphoma tumor and germline DNA from the same affected individual. We further sequenced the exomes of 59 Burkitt lymphoma tumors and compared them to sequenced exomes from 94 diffuse large B-cell lymphoma (DLBCL) tumors. We identified 70 genes that were recurrently mutated in Burkitt lymphomas, including ID3, GNA13, RET, PIK3R1 and the SWI/SNF genes ARID1A and SMARCA4. Our data implicate a number of genes in cancer for the first time, including CCT6B, SALL3, FTCD and PC. ID3 mutations occurred in 34% of Burkitt lymphomas and not in DLBCLs. We show experimentally that ID3 mutations promote cell cycle progression and proliferation. Our work thus elucidates commonly occurring gene-coding mutations in Burkitt lymphoma and implicates ID3 as a new tumor suppressor gene. Gene expression profiling on 21 Burkitt lymphomas was performed using standard Affymetrix protocols as described previously. Briefly, 1 μg of total RNA was reverse transcribed, using oligo(dT) primer to synthesize cDNA. T7 primer was used for in vitro transcription, resulting in labeled cRNA, which was fragmented and hybridized to Affymetrix Whole-Genome Gene 1.0 ST microarrays. Microarrays were washed and scanned, and the data were normalized as described previously.

2013-07-01 | E-GEOD-48435 | biostudies-arrayexpress

Genetic Heterogeneity of DLBCL

Project description:Diffuse large B-cell lymphoma (DLBCL) is the most common form of lymphoma in adults. The disease exhibits a striking heterogeneity in gene expression profiles and clinical outcomes, but its genetic causes remain to be fully defined. Through whole genome and exome sequencing, we characterized the genetic diversity of DLBCL. In all, we sequenced 73 DLBCL primary tumors (34 with matched normal DNA). Separately, we sequenced the exomes of 21 DLBCL cell lines. We identified 322 DLBCL cancer genes that were recurrently mutated in primary DLBCLs. We identified recurrent mutations implicating a number of known and not previously identified genes and pathways in DLBCL including those related to chromatin modification (ARID1A and MEF2B), NF-κB (CARD11 and TNFAIP3), PI3 kinase (PIK3CD, PIK3R1, and MTOR), B-cell lineage (IRF8, POU2F2, and GNA13), and WNT signaling (WIF1). We also experimentally validated a mutation in PIK3CD, a gene not previously implicated in lymphomas. The patterns of mutation demonstrated a classic long tail distribution with substantial variation of mutated genes from patient to patient and also between published studies. Thus, our study reveals the tremendous genetic heterogeneity that underlies lymphomas and highlights the need for personalized medicine approaches to treating these patients. 21 DLBCL cell lines and 70 DLBCL patient samples.

2013-01-23 | E-GEOD-43606 | biostudies-arrayexpress

Functional expression of membrane alanyl-aminopeptidase (CD13/APN) promotes tumor cell proliferation and neoangiogenesis in malignant gliomas.

Project description:Malignant gliomas are characterized by marked neovascularization and increased tumor cell proliferation. Recently, membrane alanyl-aminopeptidase (CD13/APN) has been identified to play a crucial role in neoangiogenesis. In this study, we show that among various central nervous system tumors, malignant astrocytomas are unique in their high expression levels of functionally active CD13/APN. CD13/APN was found in both tumor cells and tumor vessels of malignant astrocytomas, while in low-grade astrocytomas only endothelial cells of tumor vessels expressed CD13/APN. Inhibitors of the enzymatic activity of CD13/APN significantly reduced the proliferation of U87MG and U138MG malignant glioma cells. Inhibition of CD13/APN mRNA expression by siRNA in glioma cells co-cultured with human umbilical vein endothelial cells (HUVEC) effectively decreased blood vessel formation. Pro-angiogenic factors like bFGF and VEGF induced CD13/APN expression in glioma cells. Treatment of U87MG and U138MG cells with CD13/APN inhibitors resulted in an increased mRNA expression of VEGF and VEGF receptor 2 (VEGF-R2) in these cells. Taken together, these findings provide evidence that CD13/APN promotes tumor cell proliferation and blood vessel formation in malignant astrocytomas. Remarkably, inhibition of CD13/APN induces an angiogenic expression profile via an autocrine feed-back mechanism involving the VEGF/VEGF-R2 system in malignant gliomas. Experimental design includes altogether four samples with two replicate controls (U87_APN_wt_EGFP) and two replicate samples (U87_APN_L243P_EGFP). Replicates are from two independent experiments.

2012-05-27 | E-GEOD-37923 | biostudies-arrayexpress

Identification and Correction of Amplification Protocol Bias in Microarray Studies

Project description:mRNA abundance microarrays are the most widely used high-throughput technology for functional genomics. But despite this extensive characterization, and despite their wide-spread adoption in discovery research, the uptake of microarrays as clinical diagnostic tools remains relatively limited due to sample degradation. Recently, the NuGEN WT-Ovation Pico kit was developed to resolve this problem. Here, we comprehensively evaluate its utility on two separate biological problems. First, we evaluate its effect on 12 malignant and 2 normal cervix samples. Second, we evaluate its effect on 2 normal kidney samples. In each case, we directly compare aliquots of the same RNA sample that are prepared by standard and low-input/low-RIN protocols to address three key questions. First, does the use of a low-input/degraded-sample protocol alter transcriptional profiles either globally or of specific genes? Second, do these changes alter biological conclusions drawn from the dataset? Third, are these changes biased towards specific classes of genes, either in terms of their sequence characteristics (e.g. length, GC-content) or their biological function? To achieve these goals, we selected 12 frozen cervix cancers and 2 unmatched normal samples. RNA was extracted and was split into two aliquots: one was prepared using the Nugen WT-Ovation Pico kit and the other using the standard Affymetrix Express array method. This approach allows us to directly assess the effect of sample preparation, in isolation of any other effects. These data were then pre-processed and the filtered genes were subject to linear-modeling to evaluate technical and biological variability. The resulting gene sets were then subject to pathway and sequence analysis, and LTR analysis. Lastly, to generalize these conclusions we repeated this experimental approach identically in two normal kidney samples and one RNA mixture control sample.

2014-01-01 | E-GEOD-42764 | biostudies-arrayexpress

Illumina methylation EPIC arrays of human blood at baseline and after 18 months of dietary interventions

Project description:To highlight molecular mechanisms underlying the beneficial metabolic effects of a Mediterranean (MED) diet, a MED diet enriched in polyphenols and reduced in red/processed meat (greenMED), and a diet with healthy dietary guidelines (HDG), we analyzed their effects on the methylome in the 18-month DIRECT PLUS randomized controlled trial. The methylation arrays contains individuals from the three intervention arms (MED, greenMED, HDG) for baseline (T0). We will gladly provide further metadata upon request.

2023-07-26 | E-MTAB-12527 | biostudies-arrayexpress

Location of indigenous human HSCs reveals functional properties of HSCs that are dictated by anatomic and cellular architecture of bone marrow

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-08-01 | E-GEOD-47936 | biostudies-arrayexpress

miRNA array of patients with Pulmonary Arterial Hypertension

Project description:Comparison of miRNA expression between patients with idiopathic and systemic sclerosis PAH and healthy controls and systemic sclerosis without PAH

2021-06-01 | E-MTAB-10425 | biostudies-arrayexpress

Multigene panel test in 44 Homo sapiens patients with either digestive system neuroendocrine Neoplasm (NEN) or medullary thryoid gland carcinoma samples

Project description:The DNA isolated from 44 either frozen or FFPE Neuroendocrine Neoplasm (NEN) was analysed by NGS, to identify genes more likely to be subject to sequence variations among 523 cancer-related ones.

2022-06-30 | E-MTAB-11529 | biostudies-arrayexpress

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