Project description:Baz2B protein was shown to form a chromatin remodelig complex mit Snf2H or Snf2L catalytic subunits. It is known that chromatin remodeling proteins regulate diffferent DNA-templated processes, therefore we wanted to know whether Baz2B plays a role in transcription regulation. We used microarrays to detail the global expression of transcripts in Hap1 parental cell line and compare them to Baz2B-KO. We found up- and down-regulated trasncripts that could be associated with the decreased cellular proliferation in Baz2B-KO cell line
Project description:We analysed the global effect of CHD3-KO and SENP1-KO HAP1 cell lines compared to control cell line, on chromatin accessibility using ATAC-seq.
Project description:In this study, we aimed at determining RNA interactors of L1TD1 RNPs. To achieve this, DNMT1 KO and DNMT1 L1TD1 DKO HAP1 cells were generated by Crispr/Cas9 gene editing tool and L1TD1 RIP was performed by using these cell lines. Our study reveals a comprehensive analysis of differentially enriched transcripts in L1TD1 containing RNPs.
Project description:The impact of NatC subunits NAA30, NAA35 and NAA38 on the human proteome (protein abundance). Analysis of HAP1 WT, NAA30 KO, NAA35 KO and NAA38 KO cells
Project description:Purpose: The aim of the experiment was to eludicate differentialy expressed genes (DEGs) upon treatment with alkylating agent MMS between WT and MED13 deficient HAP1 cells. Results: After bioinformatic processing, at ≥2-fold change and an FDR≤0.1, 446 DEGs were identified in MED13 KO cells when compared to WT. Upon the MMS treatment 394 DEGs were identified in MED13 KO cells, of which 229 were common with untreated MED13 KO cells. Conclusions: Common DEGs represented genes directly regulated by MED13.
Project description:In this study, we aimed at analyzing gene expression profile of DNMT1 KO and DNMT1 L1TD1 DKO HAP1 cells using high throughput sequencing. Our study reveals a comprehensive analysis of differentially expressed transcripts in the absence of L1D1.
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.
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.