Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA129159 | ENA |
REPOSITORIES: ENA
Similar Datasets
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
Project description:Deep Sequencing of the Small RNA Transcriptome of Normal and Malignant Human B cells Identifies Hundreds of Novel MicroRNAs
| PRJNA127621 | ENA
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
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
Project description:Small RNA deep sequencing identifies viral microRNAs during malignant catarrhal fever induced by alcelaphine herpesvirus 1
| PRJNA290200 | ENA
Project description:In cell senescence, cultured cells cease proliferating and acquire aberrant gene expression patterns. MicroRNAs (miRNAs) modulate gene expression through translational repression or mRNA degradation, and have been implicated in senescence. We have used deep sequencing to carry out a comprehensive survey of miRNA expression and its involvement in cell senescence. Informatic analysis of small RNA sequence datasets from young and senescent IMR90 human fibroblasts identifies many known miRNAs, and a small number of novel miRNAs, that are regulated (either up or down) with cell senescence. Comparison with mRNA expression profiles revealed potential mRNA targets of the senescence-regulated miRNAs. The target mRNAs are enriched for genes involved in biological processes associated with cell senescence. This result greatly extends existing information on the role of miRNAs in cell senescence, and is consistent with miRNAs having a causal role in the process. Comprehensive survey of miRNA from young and senescent IMR90 fibroblasts using deep sequencing
2011-08-09 | E-GEOD-27404 | biostudies-arrayexpress
Project description:Most human pre-mRNAs are spliced into linear molecules that retain the exon order defined by the genomic sequence. By deep sequencing of RNA from a variety of normal and malignant human cells, we found RNA transcripts from many human genes in which the exons were arranged in a non-canonical order. Statistical estimates and biochemical assays provided strong evidence that a substantial fraction of the spliced transcripts from hundreds of genes are circular RNAs. Our results suggest that a non-canonical mode of RNA splicing, resulting in a circular RNA isoform, is a widespread and perhaps general feature of the gene expression program in human cells. 3 samples of non-malignant primary human leukocytes, one replicate each
2012-02-10 | E-GEOD-33772 | biostudies-arrayexpress
Project description:The aim of this study was to identify and quantify microRNAs and other small regulatory RNAs expressed in primary retinal microvascular endothelial cells (RMECs) using deep sequencing. RMECs were isolated, RNA extracted, a small RNA library prepared and deep sequencing performed. A total of 6.8 million reads were mapped to 250 known microRNAs in miRBase (release 16). Several novel microRNAs and multiple new members of the miR-2284/2285 family were detected. Several ~30 nucleotide sno-miRNAs were identified, with the most highly expressed being derived from snoRNA U78. Highly expressed microRNAs previously associated with endothelial cells included miR-126 and miR-378, but the most highly expressed was miR-21, comprising more than one third of all mapped reads. The independence from prior sequence knowledge provided by deep sequencing facilitates analysis of novel microRNAs and other small RNAs. This approach also enables quantitative evaluation of microRNA expression, which has highlighted the predominance of a small number of microRNAs in RMECs. Further characterisation of the functions of the highly expressed microRNAs will provide insights into endothelial biology. Single sample of primary cell culture
2012-02-13 | E-GEOD-31340 | biostudies-arrayexpress
Project description:The aim of this study was to identify and quantify microRNAs and other small regulatory RNAs expressed in primary retinal microvascular endothelial cells (RMECs) using deep sequencing. RMECs were isolated, RNA extracted, a small RNA library prepared and deep sequencing performed. A total of 6.8 million reads were mapped to 250 known microRNAs in miRBase (release 16). Several novel microRNAs and multiple new members of the miR-2284/2285 family were detected. Several ~30 nucleotide sno-miRNAs were identified, with the most highly expressed being derived from snoRNA U78. Highly expressed microRNAs previously associated with endothelial cells included miR-126 and miR-378, but the most highly expressed was miR-21, comprising more than one third of all mapped reads. The independence from prior sequence knowledge provided by deep sequencing facilitates analysis of novel microRNAs and other small RNAs. This approach also enables quantitative evaluation of microRNA expression, which has highlighted the predominance of a small number of microRNAs in RMECs. Further characterisation of the functions of the highly expressed microRNAs will provide insights into endothelial biology.
2012-02-13 | GSE31340 | GEO
Project description:microRNAs (miRNAs) are a large class of small non-coding RNAs which post-transcriptionally regulate the expression of a large fraction of all animal genes and are important in a wide range of biological processes. Recent advances in high-throughput sequencing allow miRNA detection at unprecedented sensitivity, but the computational task of accurately identifying the miRNAs in the background of sequenced RNAs remains challenging. For this purpose we have designed miRDeep2, a substantially improved algorithm which identifies canonical and non-canonical miRNAs such as those derived from transposable elements and informs on high-confidence candidates that are detected in multiple independent samples. Analyzing data from seven animal species representing the major animal clades, miRDeep2 identified miRNAs with an accuracy of 98.6-99.9% and reported hundreds of novel miRNAs. To test the accuracy of miRDeep2, we knocked down the miRNA biogenesis pathway in a human cell line and sequenced small RNAs before and after. The vast majority of the >100 novel miRNAs expressed in this cell line were indeed specifically down-regulated, validating most miRDeep2 predictions. Last, a new miRNA expression profiling routine, low time and memory usage and user-friendly interactive graphic output can make miRDeep2 useful to a wide range of researchers." high-throughput sequencing was used to profile small RNA expression in a human MCF-7 cell line before and after Dicer knock-down
2011-09-12 | E-GEOD-31069 | biostudies-arrayexpress