Comment[GEAAccession]	E-GEAD-422
MAGE-TAB Version	1.1
Investigation Title	Genetic profile of HaCaT Cells stimulated by AD skin derived Staphylococcus aureus and Cytokines
Experiment Description	The genetic profile of HaCaT cells was found to be greatly altered by S. aureus stimulation from the control, and the addition of cytokines changed the genetic profile to a different one from only S. aureus stimulation. We picked up genes that have been reported to be dominantly involved in AD, innate immunity, and other related things and checked the difference between their expression by HaCaT cells treated with cytokines and S. aureus and those without the treatments. In S. aureus stimulation, the expression of IL1a, IL8R1, TLR1, TLR6, FN1, FLG, and TSLP was increased compared with the control of HaCaT cells. In AD strain (TF3378) stimulation, the expression of IL1b, IL6, and ITGa5 was increased compared with standard strain. IFN-gamma upregulated the expression of IL12, IL8R1, and ITGa5 but suppressed the expression of IL13RA2, FN1, and FLG. While on the other hand, IL-4 stimulation upregulated IL13RA2, FLG, and TSLP, downregulated FN1, and IL33.
Experimental Design	stimulus or stress design
Experimental Factor Name	stimulus	treatment
Experimental Factor Type	stimulus	treatment
Person Last Name	Miyake
Person First Name	Ryu
Person Affiliation	Department of Dermatology Graduate school of Biomedical and Health Sciences, Hiroshima university
Person Roles	submitter
Public Release Date	2025-01-25
Protocol Name	P-GEAD-782	P-GEAD-783	P-GEAD-784	P-GEAD-785	P-GEAD-786
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	normalization data transformation protocol
Protocol Description	We prepared five samples, three each of control, NCTC8325 stimulated, TF3378 stimulated, TF3378+IFN-gamma stimulated, and TF3378+IL-4 stimulated. HaCaT cells were pretreated with or without recombinant human IFN-gamma (PeproTech), IL-4 (PeproTech) at the indicated concentration for 24 hours before S. aureus stimulation.	RNA was extracted by the RNeasy Mini Kit (Qiagen, Hilden, Germany). cDNA was prepared using the QuantiTect Reverse Transcription Kit (Qiagen).	Libraries were prepared by using the SureSelect Strand Specific RNA Reagent Kit (Agilent, Santa Clara, CA, USA).	Sequencing was performed with the Illumina HiSeq2500 (Illumina, San Diego, CA, USA; 82 cycles, single-read sequencing).	RefSeq Genes (2015.10.05) was used for gene annotation and the counts were normalized by DEseq algorithm
SDRF File	E-GEAD-422.sdrf.txt
Comment[AEExperimentType]	RNA-seq of coding RNA
Comment[BioProject]	PRJDB10904
Comment[Last Update Date]	2025-01-25