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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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The impact of the HSPA2 gene knockout on transcriptome profile in immortalized epidermal keratinocytes (HaCaT line) grown in standard cell culture

ABSTRACT: The specific functional features of the epidermal keratinocytes are determined by the activity of many genes. The aim of the project was to characterize the role of HSPA2, a member of the HSPA chaperone family (HSP70), in human epidermal keratinocytes. The inactivation of the HSPA2 gene in the HaCaT line of spontaneously immortalized epidermal keratinocytes was performed by CRISPR/Cas9 gene editing system. Next, the effect of modifications on the transcriptomic profile of cells growing in 2D monolayer culture was investigated. This study was supported by a Polish National Science Center grant number NCN 2017/25/B/NZ4/01550.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Dorota Scieglinska

PROVIDER: E-MTAB-13251 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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The impact of the HSPA2 gene knockout on transcriptome profile in immortalized epidermal keratinocytes (HaCaT line)

Project description:The specific functional features of the epidermal keratinocytes are determined by the activity of many genes. The aim of the project was to characterize the role of HSPA2, a member of the HSPA chaperone family (HSP70), in human epidermal keratinocytes. The inactivation of the HSPA2 gene in the HaCaT line of spontaneously immortalized epidermal keratinocytes was performed by CRISPR/Cas9 gene editing system. Next, the effect of modifications on the transcriptomic profile of cells growing in a three-dimensional model of reconstructed human epidermis in vitro was investigated. The cells were grown at air-liquid interface culture on collagen-fibroblast matrix to achieve maximal level of HaCaT differentiation in RHE system.

2023-09-25 | E-MTAB-13166 | biostudies-arrayexpress

The impact of the HSPA2 gene downregulation on transcriptome profile in immortalized epidermal keratinocytes (HaCaT line) grown in 3D cell culture

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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.

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RNA-seq data of rs2280381-containing region knock out clone in U-937 cell line

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Project description:rs2431697 is a SLE risk SNP, genetic and epigenomic analysis indicate that rs2431697-containing region is an enhancer region. To test the function and regulated genes of rs2431697-containing genes, we deleted rs2431697-containing region in U-937 cells, and performed the RNA-seq to detect the gene expression profiles.

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RNA-seq of rs2280381-containing region knock out clone in U937

Project description:rs2280381 is an autoimmune disease susceptible loci, which have be reported to be associated with SLE, RA and SSc.Genetic and epigenomic analysis indicate that rs2280381-containing region is an enhancer region in monocyte. To test the function and regulated genes of rs228381-containing region, we deleted rs2280381 ~120bp sequence in U-937 cells, and performed the RNA-seq to detect the gene expression profiles.

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2022-04-11 | E-MTAB-11597 | biostudies-arrayexpress

ChIP-seq of Stat3 with DNA binding sites mutation in human colon cancer SW480

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2020-07-06 | E-MTAB-8417 | biostudies-arrayexpress

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