Hap1 gene trap mutagenesis positive selection screen for HR factors
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB39032 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR4289983.fastq.gz | Fastqsanger.gz | |||
| ERR4289984.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 2 of 2 |
Similar Datasets
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.
2020-08-25 | E-MTAB-9247 | biostudies-arrayexpress
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. In total there are four different cell types with two replicates for each cell type. Therefore, 8 samples in total.
2016-08-22 | E-GEOD-75515 | biostudies-arrayexpress
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.
2016-08-22 | GSE75515 | GEO
Project description:One hundred million HAP1 Tet-On-MLKLTE/SD cells were mutagenized with the GFP gene trap retrovirus, as described (PMID: 21623355). The selection experiment was performed by inducing MLKLTE/SD expression with 200 ng/mL DOX over five days and subsequently allowing resistant colonies to grow for four days after withdrawing DOX. Resistant colonies were then pooled together and genomic DNA was extracted from the pool (Qiagen, 51306). Retroviral gene trap insertion sites were amplified using a linear amplification (LAM) PCR protocol as described previously (PMID: 21623355), sequenced using the Genome Analyzer (Illumina).
2018-05-16 | E-MTAB-6777 | biostudies-arrayexpress
Project description:Recently, gene-trap mutagenesis in near haploid human cells has been used to disrupt genes and identify novel host-pathogen interactions and elucidate mechanisms of drug action. Building on this technology, we here report the generation of a human gene-trap mutant collection of individual clones, which currently covers over a quarter of the expressed genome. Strand specific RNA-Seq of ribosomal RNA depleted total cellular RNA to measure transcript abundance and to detect fusion transcripts in KBM7 cells at standard culture conditions.
2013-12-31 | E-GEOD-47428 | biostudies-arrayexpress
Project description:Recently, gene-trap mutagenesis in near haploid human cells has been used to disrupt genes and identify novel host-pathogen interactions and elucidate mechanisms of drug action. Building on this technology, we here report the generation of a human gene-trap mutant collection of individual clones, which currently covers over a quarter of the expressed genome.
2013-12-31 | GSE47428 | GEO
Project description:Rattus norvegicus Hr, HR, lysine demethylase and nuclear receptor corepressor [Source:RGD Symbol;Acc:620634], is expressed in 5 baseline experiment(s);
| ENSRNOG00000011427 | ExpressionAtlas
Project description:Monodelphis domestica HR, HR lysine demethylase and nuclear receptor corepressor [Source:NCBI gene;Acc:100033094], is expressed in 1 baseline experiment(s);
| ENSMODG00000009614 | ExpressionAtlas
Project description:Rattus norvegicus Hr, HR, lysine demethylase and nuclear receptor corepressor [Source:RGD Symbol;Acc:620634], is differentially expressed in 23 experiment(s);
| ENSRNOG00000011427 | ExpressionAtlas
Project description:Sus scrofa HR, HR lysine demethylase and nuclear receptor corepressor [Source:VGNC Symbol;Acc:VGNC:88969], is differentially expressed in 4 experiment(s);
| ENSSSCG00000009616 | ExpressionAtlas