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Effect of USB1 depletion on global miRNome in human embryonic stem cells and K562

ABSTRACT: Effect of USB1 depletion on global miRNome in human embryonic stem cells and K562

PROVIDER: PRJNA931329 | ENA |

REPOSITORIES: ENA

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Effect of USB1 depletion on global miRNome in human embryonic stem cells and K562

Project description:USB1 mutations lead to poikiloderma with neutropenia. We investigated the effect of inactivating USB1 on the global miRNome in undifferentiated hESCs and K562

2024-02-05 | GSE224501 | GEO

Effects of USB1 knockout on global miRNome in K562 cells

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Effects of USB1 knockout on global miRNome in K562 cells

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New global miRSeq analysis of “miRNome”: the example of PTC and nodal metastases

Project description:The set of expressed microRNAs in a given cell type, or “miRNome”, can be explored under many different aspects. Many studies report modulations of the miRNome in a wide variety of cancers. Papillary thyroid cancer is the most prevalent type of endocrine cancer. The presence of nodal metastases increases the risk of recurrence and mortality. In our study, we performed microRNA deep sequencing (miRSeq) of 3 PTC, their matching normal tissues and nodal metastases and designed a new bioinformatic framework to analyze variations of the different aspects of the miRNome: expression profile, isomiRs and non-templated additions distributions, mutation or A-to-I RNA-editing. Furthermore, we validated our results using qRT-PCR on independent samples from 14 patients and using the collection of miRSeq data from The Cancer Genome Atlas (up to 495 miRseq of PTC). We gave a particular attention to cell content and contamination. We showed that microRNA expression profiles of thyrocytes are altered during tumorigenesis. These alterations involve known up regulations of microRNAs such as miR-146b-5p or miR-22-3p but also down regulations such as miR-7-5p, miR-7-2-5p, miR-1179 or miR-204-5p. Furthermore, some expression modulations were increased following the nodal metastatic process such as miR-7-2-3p or miR-138-1-3p. However, we did not find variations in the other aspects of the miRNome analyzed. We used our bioinformatic frameworks on the largest PTC miRSeq data collection available, to our knowledge. It allowed us, in one study on the different aspects of the miRNome, to find modulated microRNAs that could act as biomarkers of PTC.

2015-12-01 | GSE57780 | GEO

Effect of global or hypodermal depletion of RPOA-2

Project description:Effect of global or hypodermal depletion of RPOA-2

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Healing human gingiva miRNome

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Global transcriptional response to electron acceptors AKB and pyruvate in K562 cells

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Global analysis of in vivo EGR1-binding sites in erythroleukemia cell K562 using chromatin immunoprecipitation and massively parallel sequencing

Project description:Early growth response gene 1 (EGR1) has been implicated in megakaryocyte differentiation induced by PMA (phorbol 12-myristate 13-acetate). The identification of direct EGR1 target genes in global scale is critical for our understanding of how EGR1 contributes to this process. In this study, we provide a global survey on the binding location of EGR1 in the K562 cell treated by PMA using chromatin immunoprecipitation and massively parallel sequencing (ChIP-Seq). K562 is a human erythroleukemia cell line, which is situated in the common progenitor stage of megakaryocytic and erythroid lineages of the hematopoietic stem cell differentiation and its normally following differentiation is blockaded. Upon exposure to PMA stimuli, K562 cell can be induced into megakaryocytic cell, which provides a model for the study of transcriptional control networks. Over 14 000 highly confident in vivo EGR1 binding sites were identified in PMA treated K562 cell. More than 70% of these genomic sites associated with EGR1 binding were located around annotated gene regions. This whole genome study on the EGR1 targets may help a better understanding of the EGR1 regulated genes and the downstream pathway in megakaryocyte differentiation. The in vivo binding locations of EGR1 in K562 cell treated with PMA (phorbol 12-myristate 13-acetate, 10 ng/ml for 2 hours) were identified using chromatin immunoprecipitation combing with massively parallel sequencing (ChIP-Seq) based on AB SOLiD System 2.0.

2010-09-08 | E-GEOD-21665 | biostudies-arrayexpress

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