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

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

PROVIDER: PRJNA127621 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR015358.fastq.gz	Fastqsanger.gz
	SRR015359.fastq.gz	Fastqsanger.gz
	SRR015360.fastq.gz	Fastqsanger.gz
	SRR015361.fastq.gz	Fastqsanger.gz
	SRR015362.fastq.gz	Fastqsanger.gz

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

Project description: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

2010-08-25 | E-GEOD-22898 | biostudies-arrayexpress

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.

2010-08-26 | GSE22895 | GEO

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

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

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

Project description: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 miRNAs, which is more than twice the number previously recognized in any tissue type. We further identified the expression of 286 candidate novel miRNAs in normal and malignant B cells. These miRNAs were validated at a high rate (92%) using quantitative polymerase chain reaction, and we demonstrated their application in the distinction of clinically relevant subgroups of lymphoma. We further demonstrated that a novel miRNA cluster, previously annotated as a hypothetical gene LOC100130622, contains 6 novel miRNAs that regulate the transforming growth factor-? pathway. Thus, our work suggests that more than a third of the miRNAs present in most cellular types are currently unknown and that these miRNAs may regulate important cellular functions.

| S-EPMC3012600 | biostudies-literature

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

Project description:This SuperSeries is composed of the SubSeries listed below.

2010-08-26 | GSE22898 | GEO

Analysis of deregulated microRNAs in malignant mesothelioma

2012-01-11 | GSE29707 | GEO

Small RNA deep sequencing identifies viral microRNAs during malignant catarrhal fever induced by alcelaphine herpesvirus 1

Project description:Alcelaphine herpesvirus 1 (AlHV-1) is a ?-herpesvirus (?-HV) carried asymptomatically by wildebeest. Upon cross-species transmission, AlHV-1 induces an acute and fatal lymphoproliferative disease named malignant catarrhal fever (MCF) in many ruminants, including cattle and the rabbit model. Latency has been shown to be essential for MCF induction. However, the mechanisms causing the activation and proliferation of infected CD8+ T cells are unknown. Many ?-HVs express microRNAs (miRNAs). These small noncoding RNAs can suppress host or viral target genes involved in various pathways and are thought to facilitate viral infection and/or mediate activation and proliferation of infected lymphocytes. AlHV-1 genome has been predicted to encode a large number of miRNAs. However, their precise contribution in viral infection and pathogenesis in vivo remains unknown. Here, we have cloned small RNAs and sequenced 36 potential miRNAs expressed in a lymphoblastoid cell line propagated from a calf infected with AlHV-1 and developing MCF. Among the sequenced candidate miRNAs, 32 were expressed on the reverse strand of the genome in two main clusters. The expression of these 32 viral miRNAs was further validated using Northern blot and qRT-PCR in lymphoid organs of MCF-developing calves or rabbits. To determine the concerted contribution in MCF of 28 viral miRNAs clustered in the non-protein-coding region of the AlHV-1 genome, a recombinant virus was produced. The absence of these 28 miRNAs did not affect viral growth in vitro nor MCF induction in rabbits, demonstrating that AlHV-1 miRNAs clustered in the non-protein-coding genomic region are not essential for MCF induction. Small RNA sequencing from total RNA from AlHV-1-infected bovine lymphoblastoid cell line propagated with interleukin 2

2015-08-27 | E-GEOD-71056 | biostudies-arrayexpress

Small RNA deep sequencing identifies viral microRNAs during malignant catarrhal fever induced by alcelaphine herpesvirus 1

Project description:Alcelaphine herpesvirus 1 (AlHV-1) is a γ-herpesvirus (γ-HV) carried asymptomatically by wildebeest. Upon cross-species transmission, AlHV-1 induces an acute and fatal lymphoproliferative disease named malignant catarrhal fever (MCF) in many ruminants, including cattle and the rabbit model. Latency has been shown to be essential for MCF induction. However, the mechanisms causing the activation and proliferation of infected CD8+ T cells are unknown. Many γ-HVs express microRNAs (miRNAs). These small noncoding RNAs can suppress host or viral target genes involved in various pathways and are thought to facilitate viral infection and/or mediate activation and proliferation of infected lymphocytes. AlHV-1 genome has been predicted to encode a large number of miRNAs. However, their precise contribution in viral infection and pathogenesis in vivo remains unknown. Here, we have cloned small RNAs and sequenced 36 potential miRNAs expressed in a lymphoblastoid cell line propagated from a calf infected with AlHV-1 and developing MCF. Among the sequenced candidate miRNAs, 32 were expressed on the reverse strand of the genome in two main clusters. The expression of these 32 viral miRNAs was further validated using Northern blot and qRT-PCR in lymphoid organs of MCF-developing calves or rabbits. To determine the concerted contribution in MCF of 28 viral miRNAs clustered in the non-protein-coding region of the AlHV-1 genome, a recombinant virus was produced. The absence of these 28 miRNAs did not affect viral growth in vitro nor MCF induction in rabbits, demonstrating that AlHV-1 miRNAs clustered in the non-protein-coding genomic region are not essential for MCF induction.

2015-08-27 | GSE71056 | GEO

Topological screen identifies hundreds of Cp190 and CTCF dependent Drosophila chromatin insulator elements

Project description:Topological screen identifies hundreds of Cp190 and CTCF dependent Drosophila chromatin insulator elements

| PRJNA816845 | ENA

Analysis of deregulated microRNAs in malignant mesothelioma

Project description:The expression of human microRNAs in the cellular fraction of human peripheral blood of patients with diagnosed malignant mesotheliomas and asbestos-exposed controls. Altered expression of several miRNAs were observed for patients with diagnosed malignant mesotheliomas in comparison with asebstos-expsoed controls. The study group consists of 23 patients with diagnosed malignant mesothelioma (mean age 66 years, range 34 – 84 years). Patients were not treated with chemotherapy or radiation therapy before sample collection. The histological subtypes were: one sarcomatoid, seven biphasic, and twelve epithelioid cases. In three cases the histological subtype was unknown. The control group consists of 17 asbestos-exposed age-matched volunteers without any diagnosed cancer (mean age 68 years, range 47 – 80 years). Oligonucleotide microarrays were purchased from the Norwegican Microarray Consortium (www.microarray.no). The mirVana miRNA Probe Set v2.0 (Ambion) based on the miRBase Sequence Database v8.0. was used.

2012-01-11 | E-GEOD-29707 | biostudies-arrayexpress

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