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RNA-seq of coding RNA from USP14 knockout human haploid (HAP1) cells

ABSTRACT: RNA-seq of coding RNA from USP14 knockout human haploid (HAP1) cells

PROVIDER: PRJEB21723 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR2030970_1.fastq.gz	Fastqsanger.gz
	ERR2030970_2.fastq.gz	Fastqsanger.gz
	ERR2030971_1.fastq.gz	Fastqsanger.gz
	ERR2030971_2.fastq.gz	Fastqsanger.gz
	ERR2030972_1.fastq.gz	Fastqsanger.gz

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RNA-seq of coding RNA from USP14 knockout human haploid (HAP1) cells

Project description:We performed a genome-scale screen for suppressors of interferon stimulated gene (ISG) expression in human haploid cells (HAP1). Ubiquitin specific peptidase 14 (USP14) was a significant hit. In order to validate USP14 as a regulator of ISG expression, we created knockouts of USP14 in HAP1 cells using CRISPR-Cas9 and performed RNA-seq on coding RNA from USP14 KO and WT cells. This data was used to determine if ISGs were upregulated in USP14 KO HAP1 cells.

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RNA-seq of coding RNA from DDX6 knockout human haploid (HAP1) cells

Project description:We performed a genome-scale screen for suppressors of interferon stimulated gene (ISG) expression in human haploid cells (HAP1). DEAD-box helicase 6 (DDX6) was a significant hit. In order to validate DDX6 as a regulator of ISG expression, we created knockouts of DDX6 in HAP1 cells using CRISPR-Cas9 and performed RNA-seq on coding RNA from DDX6 KO and WT cells. This data was used to determine if ISGs were upregulated in DDX6 KO HAP1 cells.

2017-07-25 | E-MTAB-5867 | biostudies-arrayexpress

RNA-seq of coding RNA from DDX6 knockout human haploid (HAP1) cells

Project description:RNA-seq of coding RNA from DDX6 knockout human haploid (HAP1) cells

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Missing proteins identified from the haploid cell lines: HAP1 and KBM-7

Project description:Chromosome-centric Human Proteomic Project (C-HPP) aims at identifying and characterizing protein products encoded from all protein-coding genes of human chromosomes. As evident in the recent nature papers, it is possible that those missing proteins may be low abundant in many cell types or expressed only in a few cell types. In order to identify missing proteins, we focused on extensively unexplored cell lines(HAP1, KBM-7).

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RNA sequencing of control, DNMT1 knockout and DNMT1/L1TD1 double knockout haploid cells (HAP1)

Project description:To investigate the effects of L1TD1 ablation in DNMT1 knockout HAP-1 cells in comparison to DNMT1 knockout and control HAP1 cells

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Hap1 gene trap mutagenesis positive selection screen for HR factors

Project description:In order to identify cellular factors that influence the efficiency of AAV-HR mediated TI, we performed an unbiased genome-wide screening in a library of near haploid human cells (HAP1) mutagenized by retroviral insertions.

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Gene expression analysis of human haploid cells (HAP1) depleted of SMARCB1 and SMARCA4

Project description:The aim of this study is to analyze the change in genome wide expression levels in HAP1 cells upon loss of SMARCB1, SMARCA4 or both these genes together. The SMARCB1 and SMARCA4 genes were the hits from a genome wide screen involving genetrap mutagenesis to find new players that are involved in sensitivity to Doxorubicin (Dox). It was found that loss of SMARCB1 and SMARCA4 genes impart resistance in HAP1 cells to Dox. To validate this, the genes were knocked out in HAP1 cells with CRISPR-Cas9 technology. Gene expression levels in SMARCB1 null, SMARCA4 null and SMARCB1-SMARCA4 double null cells were compared to wildtype HAP1 cells using RNAseq. From these experiments it was found that SMARCB1 loss caused several fold increase in ABCB1 gene levels. ABCB1 is an efflux pump in cells responsible for flushing out many small-molecule drugs. Further analysis of this gene confirmed that ABCB1 was the main factor responsible for Dox resistance upon SMARCB1 loss.

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Gene expression analysis of human haploid cells (HAP1) depleted of SMARCB1 and SMARCA4

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Missing proteins identified from the haploid cell lines: HAP1 and KBM-7

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RNA-sequencing experiments to identify differentially expressed genes between Wild Type and RBM4 KO HAP1 cell line samples

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