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Deep sequencing of an AML cell line treated with vehicle control, BETi, MDM2i, or a drug combination

ABSTRACT: Deep sequencing of an AML cell line treated with vehicle control, BETi, MDM2i, or a drug combination

PROVIDER: PRJNA546589 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9204670_1.fastq.gz	Fastqsanger.gz
	SRR9204670_2.fastq.gz	Fastqsanger.gz
	SRR9204671_1.fastq.gz	Fastqsanger.gz
	SRR9204671_2.fastq.gz	Fastqsanger.gz
	SRR9204672_1.fastq.gz	Fastqsanger.gz

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Deep sequencing of an AML cell line treated with vehicle control, BETi, MDM2i, or a drug combination

Project description:Gene expression changes in human OCI-AML3 cells treated with DMSO (vehicle control), the BET inhibitor CPI-203, the MDM2 inhibitor Nutlin-3a, or a combination of both drugs, were compared. Method: poly-A mRNA from the OCI-AML3 cell line treated for 24 hrs with either DMSO, CPI-203, Nutlin-3a or a combination of both drugs was extracted, in triplicate, then sequenced with an Illumina NextSeq500 sequencer. Sequence reads passing the quality control filters were aligned using Tophat2 and then analysed with Cufflinks.

2020-11-04 | GSE132244 | GEO

Deep sequencing of an AML cell line, with and without p53, treated with vehicle control, BETi, MDM2i, or a drug combination

Project description:Deep sequencing of an AML cell line, with and without p53, treated with vehicle control, BETi, MDM2i, or a drug combination

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Chromatin occupancy assessment an AML cell line treated with vehicle control, BETi, MDM2i, or a drug combination (p53-bound profiles)

Project description:Chromatin occupancy assessment an AML cell line treated with vehicle control, BETi, MDM2i, or a drug combination (p53-bound profiles)

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Chromatin occupancy assessment an AML cell line treated with vehicle control, BETi, MDM2i, or a drug combination (BRD4-bound profiles)

Project description:Chromatin occupancy assessment an AML cell line treated with vehicle control, BETi, MDM2i, or a drug combination (BRD4-bound profiles)

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Deep sequencing of an AML cell line, with and without p53, treated with vehicle control, BETi, MDM2i, or a drug combination

Project description:Gene expression changes were compared in human OCI-AML3 cells, with or without p53 knock down, that were treated with DMSO (vehicle control), the BET inhibitor CPI-203, the MDM2 inhibitor Nutlin-3a, or a combination of both drugs. compared. Method: OCI-AML3 cells were transduced with either empty vector or vector expressing an shRA targeting p53. Cells were then treated for 24 hrs with either DMSO, CPI-203, Nutlin-3a or a combination of both drugs. PolyA mRNA was extracted, in triplicate, then sequenced with an Illumina NextSeq 500 sequencer. Sequence reads passing the quality control filters were aligned using Tophat2 and then analysed with Cufflinks. Keywords: Expression profiling by high throughput sequencing

2020-11-04 | GSE132245 | GEO

Chromatin occupancy assessment an AML cell line treated with vehicle control, BETi, MDM2i, or a drug combination (BRD4-bound profiles)

Project description:BRD4 chromatin occupancy changes in human OCI-AML3 cells treated with DMSO (vehicle control), the BET inhibitor CPI-203, the MDM2 inhibitor Nutlin-3a, or a combination of both drugs, were compared. Method: Genomic DNA from the OCI-AML3 cell line treated for 24 hrs with either DMSO, CPI-203, Nutlin-3a or a combination of both drugs was extracted, BRD4-bound chromatin was immunoprecipitated, then DNA was sequenced with an Illumina NextSeq 500 sequencer. Sequence reads passing the quality control filters were aligned using Bowtie2 and then analysed with SICER.

2020-11-04 | GSE132247 | GEO

Chromatin occupancy assessment an AML cell line treated with vehicle control, BETi, MDM2i, or a drug combination (p53-bound profiles)

Project description:p53 chromatin occupancy changes in human OCI-AML3 cells treated with DMSO (vehicle control), the BET inhibitor CPI-203, the MDM2 inhibitor Nutlin-3a, or a combination of both drugs, were compared. Method: Genomic DNA from the OCI-AML3 cell line treated for 24 hrs with either DMSO, CPI-203, Nutlin-3a or a combination of both drugs was extracted, p53-bound chromatin was immunoprecipitated, then DNA was sequenced with an Illumina NextSeq 500 sequencer. Sequence reads passing the quality control filters were aligned using Bowtie2 and then analysed with MACS.

2020-11-04 | GSE132246 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of the MDM2i and WIPi Combination Therapy in Intrahepatic Cholangiocarcinoma Transcriptomes

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized the systems-based analysis of cellular pathways. The purpose of this study is to compare the expression profiles of single and combination treatment of MDM2i and WIP1i in RBE cells by NGS-derived transcriptome profiling (RNA-seq). Methods: RBE mRNA profiles of HDM201 (MDM2i) and/or GSK2830371 (WIP1i) treatment for 6 or 24 hours were generated by deep sequencing, in triplicate, using Illumina NextSeq sequencer. The sequence of each read was trimmed based on the quality score (Q30), and read lengths less than 45 bp were dis-carded prior to further analysis. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: STAR aligner followed by ANOVA. Results: We mapped about 30 million sequence reads per sample to the RBE transcriptomes after HDM201 and/or GSK2830371 treatment. The differentially expressed genes were selected for more than 2-fold changes and p-values for differences in expression of less than 0.05. From four different comparisons, HDM201 alone and in combination with GSK2830371 for 6 h and 24 h, 26 consistently altered genes were identified (21 upregulated genes and 5 downregulated genes). Conclusions: Our study represents the detailed analysis of MDM2i and/or WIPi therapy in intrahepatic cholangiocarcinoma transcriptomes. Differentially expressed genes from combination treatment were enriched for genes involved in p53-dependent signal transduction pathways, involved in the DNA damage response, response to stress, and regulation of apoptotic processes. In addition, differentially expressed genes, analyzed using the KEGG pathway da-tabase, were enriched for genes involved in platinum drug resistance and the p53 signaling pathway and gene ontology database for protein-protein interaction using an adjusted p-values less than 0.01.

2021-07-09 | GSE179787 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of the MDM2i and WIPi Combination Therapy in Intrahepatic Cholangiocarcinoma Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of the MDM2i and WIPi Combination Therapy in Intrahepatic Cholangiocarcinoma Transcriptomes

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Betaproteobacteria bacterium strain:betI-A JGI_MCM16SPN007

Project description:Betaproteobacteria bacterium strain:betI-A JGI_MCM16SPN007 Genome sequencing

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