NEK4 suppresses cell proliferation in BT20 triple-negative breast cancer cells by diminishing expression of cell cycle genes, while its depletion mitigates proliferation in other cell lines

BT20 cells were exposed to a non-targeting siRNA (Uni) or siRNA targeting NEK4. RNA was harvested, and RNASeq followed by GSEA was completed. We note that depleting NEK4 alone caused enhancement in cell cycle genes that was consistent with the increase in cell proliferation observed in the BT20 cells following knockdown.
, RNA from BT20 cells, transfected with NT or NEK4 siRNA, was isolated and quantified as above. RNA was sequenced using Illumina HiSeq 2000 at the National Center for Genome Resources (NCGR) in Santa Fe, NM. The samples were sequenced using paired-end reads with a read length of 150 base pairs and a read depth of 20 million reads per sample. Quality control of sample reads was performed using the FastQC tool. Raw reads from sequencing were processed to remove adapter and primer sequences. Processed sequences were aligned to the Human reference genome using HISAT2. Read counts were generated using the featureCounts software. Differential gene expression was assessed using the DeSEQ2 tool. Significantly differentially expressed Q24 genes, i.e., genes with an FDR < 0.05 and fold change of > 0 for upregulated genes and < 0 for downregulated genes, were included for pathway enrichment analysis using Broad Institute’s Gene Set Enrichment Analysis (GSEA) software (http://www.broadinstit..., # Data from: NEK4 suppresses cell proliferation in BT20 triple-negative breast cancer cells by diminishing expression of cell cycle genes, while its depletion mitigates proliferation in other cell lines

Dataset DOI: [10.5061/dryad.jm63xsjps](10.5061/dryad.jm63xsjps)

## Description of the data and file structure

Cells were exposed to siRNA targeting NEK4 (NEK4) or a scrambled negative control (UNI), and RNASeq was completed followed by GSEA (Gene Set Enrichment Analysis). The results are shown here.

# Files and variables

#### File: UniPvsNEK4P.xlsx

**Description:** 

##### Variables

* Uni/NT: Cells exposed to scrambled siRNA control; universal negative control
* NEK4: Cells treated with siRNA targeting NEK4
* Gene name (Abbrv): HUGO gene name
* Fold change: Fold change in cells depleted of NEK4 versus scrambled siRNA (Uni)
* Gene Set: Set of genes enriched in our NEK4 siRNA-treated cells versus Uni control   
* Size: Number of genes in the gene set identified    
* ES: Enrichment ...,