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Genomic maps of lnc-HLX-2-7 occupancy in human medulloblastoma cell line.

ABSTRACT: To gain more insights into the functional significance of lnc-HLX-2-7 in human medulloblastoma, genomic mapping of lnc-HLX-2-7 occupancy were analyzied by ChIRP DNA sequencing.

ORGANISM(S): Homo sapiens

PROVIDER: GSE232749 | GEO | 2023/11/01

REPOSITORIES: GEO

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RNA sequencing analysis of lnc-HLX-2-7 interacting genes and pathways in medulloblastoma

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Project description:To gain more insights into the functional significance of lnc-HLX-2-7, gene expression profiles were measured using D425, D425 lnc-HLX-2-7 KD and their intracranial xenografts by RNA sequencing. Dissociated tumor cells were used for gel bead emulsion (GEM) with chromium controler (10X genomics).

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Genes upregulated by HLX

Project description:HLX was found as a VEGF-A induced gene in HUVEC (B.Schweighofer, submitted). In order to detect genes regulated by HLX HUVEC were infected by recombinant adenovirus expressing HLX for 4, 8, 16 and 32h. RNA was isolated and subjected to microarray analysis using Affymetrix microarray. HUVEC were infected with a MOI of 40 with either HLX expressing or empty adenovirus for 4, 8, 16 or 32 hours. HUVEC without an adenovirus infection were used as control.Total RNA was isolated with Trizol according to the instructions of the manufacturer. Gene expression was analysed with Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays according to the Affymetrix protocol.

2011-02-15 | E-GEOD-13054 | biostudies-arrayexpress

Genes upregulated by HLX

2011-02-15 | GSE13054 | GEO

Identification of differentially regulated genes upon overexpression of HLX in wild-type hematopoietic stem cells

Project description:The goal was to study the role of Hlx in hematopoiesis. Sorted Lin-Kit+Sca-1+ cells from wild-type FVB/nJ bone marrow were infected with control (pCAD-IRES-GFP) or Hlx lentivirus (pCAD-IRES-GFP-Hlx) and cultured for 2 days in Iscove’s modified Dulbecco’s medium (IMDM) containing FBS, mIL-3, mIL-6 and mSCF with lentiviral supernatants in the presence of 8ug/ml polybrene. Subsequently, GFP+ cells were sorted by FACS and RNA was prepared. Three replicates of each, control vector transduced and HLX-transduced cells were used.

2012-09-14 | E-GEOD-27938 | biostudies-arrayexpress

Genomic maps of lincRNA occupancy reveal principles of RNA-chromatin interactions.

Project description:Long intergenic noncoding RNAs (lincRNAs) are key regulators of chromatin state, yet the nature and sites of RNA-chromatin interaction are mostly unknown. Here we introduce Chromatin Isolation by RNA Purification (ChIRP), where tiling oligonucleotides retrieve specific lincRNAs and bound protein and DNA sequences, which are enumerated by deep sequencing. ChIRP-seq of two lincRNAs reveal that RNA binding sites in the genome are focal, sequence-specific, and numerous. Human telomerase RNA TERC occupies telomeres and Wnt pathway genes. HOTAIR lincRNA preferentially binds a GA-rich homopurine DNA motif to nucleate broad domains of Polycomb occupancy and histone H3 lysine 27 trimethylation. HOTAIR occupancy occurs independently of EZH2, defining the order of RNA guidance of Polycomb occupancy. ChIRP-seq is readily applicable to numerous RNAs in different cell types and biological states, thus enabling the study of RNA regulation of chromatin and gene expression at a genomic scale. Examination of 3 lincRNAs in 5 cell types

2011-09-29 | E-GEOD-31332 | biostudies-arrayexpress

lnc-EAPV binding proteins in C57BL/6J BMDMs

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2018-11-07 | PXD011577 | Pride

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