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Homo sapiens strain:Not applicable | isolate:U2OS | breed:Not applicable | cultivar:Not applicable

ABSTRACT: U2OS mRNA raw sequence reads

PROVIDER: PRJNA509002 | ENA |

REPOSITORIES: ENA

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Dataset's files

Source:

			Action	DRS
	SRR8293210.fastq.gz	Fastqsanger.gz
	SRR8294440.fastq.gz	Fastqsanger.gz
	SRR8293211.fastq.gz	Fastqsanger.gz
	SRR8294441.fastq.gz	Fastqsanger.gz
	SRR8293204.fastq.gz	Fastqsanger.gz

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Project description:Purpose: The goal of this study was to investigate the effect of the cytarabine treatment on the transcriptional profiles of U2OS cells retrovirally expressing DNMT3A R882C isoform, compared to DNMT3A WT and empty vector controls Methods: U2OS DNMT3A WT, R882C, and empty vector cells were treated with 10uM cytarabine or vehicle control for 24 hours. Biological triplicates were generated, ie each replicate was performed on different day using a new batch of cells. Total RNA was collected and QC'd; mRNA was enriched using Poly-T oligo attached to magnetic beads and Illumina libraries were prepared and sequenced on Novaseq6000 (PE 150). Library construction and sequencing were performed by Novogene Corporation, Inc according to standard workflow. Results: Using a custom built pipeline in PartekFlow, the reads were aligned to human (build hg38) genome with the STAR aligner 2.6.1d and low quality alignments were filtered. About 25 million sequence reads per sample were mapped to the human genome. We identified 5714 transcripts/sample and low expression genes with counts less than 10 were filtered and the raw read counts were normalized using TMM model with an offset of 1 to avoid zero counts. Unsupervised hierarchical clustering was performed on the top 2000 genes with highest variance Conclusions: The study identifies gene networks involved in cytarabine response that are deregulated by presence of mutant DNMT3A.

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Homo sapiens isolate:U2OS

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

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Mus musculus strain:CD1 | isolate:Not applicable | breed:Not applicable | cultivar:Not applicable

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U2OS osteosarcoma cells LC-MSMS

Project description:In order to identify the targets of miR-193a-5p in osteosarcoma U2OS cell line, we used a lentivirus-mediated expression system to overexpressing miR-193a precusor, miR-193a-5p target sequence and non-target sequence, respectively, in osteosarcoma cell line U2OS. A tandem mass tag (TMT)-based quantitative proteomic strategy was employed to identify the global profile of miR-193a-5p-regulated proteins. order to identify the targets of miR-193a-5p, we used a lentivirus-mediated expression system to overexpressing miR-193a precusor, miR-193a-5p target sequence and non-target sequence, respectively, in osteosarcoma cell line U2OS. A tandem mass tag (TMT)-based quantitative proteomic strategy was employed to identify the global profile of miR-193a-5p-regulated proteins.

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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.

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