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LncRNA DINO ChIRPseq in DNA damaged U2OS cells

ABSTRACT: Examine the chormatin localization of DINO in DNA damaged human U2OS cells using DINO ChIRP-seq.

ORGANISM(S): Homo sapiens

PROVIDER: GSE76418 | GEO | 2016/09/26

SECONDARY ACCESSION(S): PRJNA307254

REPOSITORIES: GEO

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Homo sapiens

Project description:lncRNA DINO ChIRPseq in DNA damaged U2OS cells

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ATAC-Seq on DNA damaged human fibroblasts

Project description:The goal of this experiment was to determine the role of the lncRNA DINO in the DNA damage response in regulating transcription factor occupancy of human fibroblasts. DINO, an inducible long noncoding in respose to DNA damage, is required for cell cycle arrest and induction of several p53 regulated genes. We hypothesized that ATACseq in DINO-depleted cells may uncover a role for DINO in transcription factor recruitment to p53 responsive genes following DNA damage.

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Project description:Genetically modified Dino mice were generated with loxP sites flanking the mouse Dino gene. We set out to identify the set of genes regulated by Dino in DNA damaged mouse embryonic fibroblasts using 3' sequencing. Early passage Dino+/+ or Dino loxP/loxP MEFs were treated with 0.2ug/mL doxorubicin prior to addition of Trizol and RNA isolation.

2016-09-26 | GSE76419 | GEO

Genome wide localizatoin of ORCA during G1 phase in U2OS cells and map of methyl-CpG sites in U2OS cells

Project description:ORCA is an ORC associated protein that plays important roles in replication initiation as well as heterochromatin organization. We carried out ORCA ChIP-seq in U2OS cells synchronized at different stage of G1 phase to determine its genome wide localization. To understand the genomic features of ORCA binding regions, we also carried out Methylated DNA IP (MeDIP) followed by deep sequencing in U2OS cells to determine the genome wide localizatoin of methyl-CpG sites in U2OS cells and how ORCA bidning regions co-localize with this important repressive mark.

2016-12-09 | GSE81165 | GEO

U2OS-ERa, U2OS-ERb, and U2OS-ERab cells treated with 4HT or E2

Project description:U2OS-ERa, U2OS-ERb, and U2OS-ERab cells treated with 4HT or E2 Keywords: other

2005-04-06 | GSE2292 | GEO

GRO-seq analysis of control and Myc-induced U2OS cells

Project description:We used GRO-seq to examine the effect of Myc activation on RNA transcription in U2OS cells.

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Whole-genome CRISPR screen of etoposide-treated U2OS and U2OS p53KO cells, and RNAseq of U2OS cells incubated in media conditioned by etoposide-treated U2OS or U2OS p53KO cells.

Project description:CRISPR screen: U2OS or U2OS p53KO cells expressing Cas9 were transduced with a whole-genome library of CRISPR sgRNAs, then treated with either DMSO or etoposide. Differential sgRNA abundances were calculated for each condition and used to determine the effect of each single gene knockout on fitness and the drug-induced death rate. RNA-Seq: U2OS or U2OS p53KO cells were cultured with either DMSO or etoposide for 48 hours, and then U2OS cells were incubated in this conditioned media for 8 hours. RNA was collected and use to observe differential expression changes between conditions.

2023-05-17 | GSE232592 | GEO

RNA-seq analysis of control and Myc-induced U2OS cells

Project description:We used RNA-seq to examine the effect of Myc activation on U2OS cells transcriptome. We also examined these effects in the presence of Torin-1, an inhibitor of mTOR

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GRO-seq analysis of control and Myc-induced U2OS cells

Project description:We used GRO-seq to examine the effect of Myc activation on RNA transcription in U2OS cells. We measure in duplicates gene transcription rates in U2OS cells containing an inducible Myc expression vector that were induced or mock-treated in duplicates for 5 hours.

2015-11-04 | E-GEOD-66928 | biostudies-arrayexpress

SRp20 regulates Genome-wide Alternative RNA splicing events in U2OS cells

Project description:To examine the effects of SRp20 on genome-wide RNA splicing in tumor cells, we utilized Exonhit SpliceArray to compare genome-wide changes of RNA splicing and transcription in U2OS cells with or without knockdown of SRp20 by RNAi.

2012-12-30 | GSE22149 | GEO

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