Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of human near-haploid cell line HAP1 with CRISPR-edited frameshift mutations

ABSTRACT: The aim of the experiment is to assess the robustness of CRISPR-Cas9 based genetic engineering. Using RNA sequencing, we are able to quantify the abundance of transcripts corresponding to CRISPR-targets and thus the degree of nonsense mediated decay.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Frederik Ziebell

PROVIDER: E-MTAB-7061 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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.

2017-07-25 | E-MTAB-5865 | biostudies-arrayexpress

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

Illumina RNA-seq of polyA+ RNA from HAP1 cells

Project description:Illumina RNA-seq was performed on polyA+ RNA isolated from the human HAP1 cell line

2019-03-14 | E-MTAB-7757 | biostudies-arrayexpress

RNA-seq of human near-haploid cell line HAP1 with CRISPR-edited frameshift mutations

Project description:RNA-seq of human near-haploid cell line HAP1 with CRISPR-edited frameshift mutations

| PRJEB32841 | ENA

ChIP-seq of H3K27ac and H3K4me3 in HAP1 tRNA gene locus modified clones and control clones

Project description:This dataset contains ChIP-seq data profiling genomic binding of H3K27ac and H3K4me3 in single cell-derived control, as well as CRISPR/Cas9 induced tRNA gene deletion clones and intergenic region deletion clones in human cancer cell lines HAP1. In this study, we found a large genomic deletion of 10q23 in Cas9 modified clones and further investigate the effect of H3K27ac binding.

2023-10-24 | E-MTAB-11859 | biostudies-arrayexpress

ChIP-seq of Pol III and H3K4me3 in HAP1 and HepG2 tRNA gene deletion clones and control clones

Project description:This dataset contains ChIP-seq data of H3K4me3 and Pol III in single cell-derived control and CRISPR/Cas9 induced tRNA gene deletion clones in human cancer cell lines HAP1 and HepG2. In this study, we looked into functional Cas9-induced on-target genomic alteration in our tRNA gene deletion clones, HAP1 t72 and HepG2 t15.

2022-09-16 | E-MTAB-10651 | biostudies-arrayexpress

RNA-seq in HAP1 tRNA gene locus deleted clones and control clones

Project description:This dataset contains ploy-A tailed enriched RNA-seq data obtained from single cell-derived control and CRISPR/Cas9 induced tRNA gene deletion clones in the human cancer cell line HAP1. In this study, we found a large genomic deletion of the 10q23 locus in our Cas9 modified clones and further investigate the effect on the transcriptome.

2023-10-24 | E-MTAB-11858 | biostudies-arrayexpress

Bulk RNA-seq of cerebral organoids investigating the role of CHD8 in cortical development

Project description:We used cerebral organoids generated from wildtype and CHD8 +/- human ES cells to study the effects of CHD8, one of the top ASD risk genes, on early cortical development. CHD8 +/- hESC were generated using the CRISPR/Cas9 system to create a deletion within the helicase domain. Cerebral organoids were generated according to the protocol from Lancaster et al 2013 with minor modifications.

2022-02-01 | E-MTAB-9933 | biostudies-arrayexpress

Transcriptome profiling of MED1 wild-type and knockout human pre-B ALL cell line 697 (RNA-seq)

Project description:CRISPR/Cas9 system was used to generate mediator complex subunit 1 (MED1) knockout human pre-B ALL cell line 697. RNA-seq was performed to observe the effects of MED1 deletion on gene expression in 697.

2020-05-13 | E-MTAB-8178 | biostudies-arrayexpress

NAA80-V5 interactor screen in HeLa and HAP1 cells

Project description:Actin is N-terminally acetylated by NAA80. We aimed to characterize the NAA80 interactome.

2020-07-16 | PXD020188 | Pride