Comment[ArrayExpressAccession]	E-GEOD-70859
MAGE-TAB Version	1.1									
Public Release Date	2015-12-31
Investigation Title	The effects of TGM1 Mutations in HEK293T and HaCaT cells									
Comment[Submitted Name]	The effects of TGM1 Mutations in HEK293T and HaCaT cells
Experiment Description	Autosomal recessive congenital ichthyosis (ARCI) is a group of rare inherited skin disorders characterized by remarkable hyperkeratosis. Transglutaminase 1 (TGM1) mutations have been reported to be involved in four different phenotypes of ARCI, including lamellar ichthyosis (LI), non-bullous congenital ichthyosiform erythroderma (NBCIE), bathing suit ichthyosis (BSI), and self-improving collodion ichthyosis (SICI) according to the clinical presentation and histopathology. TGM1 has been found as a defective gene in a large amount of patients with LI and some patients with NBCIE, BSI and SICI. To further understand the effect of TGM1 mutations in epidermal cells development, we performed the transcriptome analysis of HEK293T and HaCaT cells transfected with TGM1 shRNA, TGM1 wild-type and mutant clones. The transcriptomic analysis revealed the effects of TGM1 on cell-cell interaction by suppressing genes involved in the gap junctions, tight junctions and desmosomes. These findings suggested that the TGM1 deficiency disturbed the balance of keratinocytes proliferation and differentiation processes and impaired the epithelial barrier function. The results provided the basis for further understanding on the etiology of ARCI. To explore the functional impacts on some of the TGM1mutations identified, we cloned and transfected the TGM1 wild type and mutant clones into HEK293T and HaCaT cells. R142C and R348X sequence mutations observed in ARCI (Autosomal recessive congenital ichthyosis) patients were generated. The shRNA targeting TGM1 and a scrambled negative control were obtained from Invitrogen (Carlsbad, CA). The293T and HaCaT cells were transfected with over-expression clones carry either wild-type or mutated TGM1sequence. Cells were harvested 48 hours post-transfection.									
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl								
Person Last Name	Wang	He	Wang	Zeng	Tian	Kim	Li	Lin	Wu	Zhang
Person First Name	Kai	Yuqing	Kai	Kang	Xin	Taek-Kyun	Xuemei	Juanjuan	Zhihua	Xibao
Person Email	kwang@systemsbiology.org									
Person Affiliation	Institute for Systems Biology									
Person Address	Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, USA									
Person Roles	submitter									
Protocol Name	P-GSE70859-1	P-GSE70859-3	P-GSE70859-4	P-GSE70859-2	P-GSE70859-5					
Protocol Description	The scanned images were analyzed with Agilent Feature Extraction Software X.X using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. ID_REF =  VALUE = Quantile-normalized signal intensity	Fluorescent-labeled (Cy3) probes were prepared with the single color labeling kit from Agilent (Santa Clara, CA).	Probes were then loaded on the array hybridization chambers then hybridized at 65°C for 17 h.	Total RNA was isolated with miRNeasy kit (Qiagen, Germantown, MD) according to manufacturer's instructions.	The slides were washed and scanned (Agilent, Santa Clara, CA) with Agilent DNA microarray scanner.					
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	nucleic acid extraction protocol	array scanning protocol					
Experimental Factor Name	cell line	treatment								
Experimental Factor Type	cell line	treatment								
Comment[SecondaryAccession]	GSE70859									
Comment[GEOReleaseDate]	2015-12-31									
Comment[ArrayExpressSubmissionDate]	2015-07-13									
Comment[GEOLastUpdateDate]	2016-01-01									
Comment[AEExperimentType]	transcription profiling by array									
SDRF File	E-GEOD-70859.sdrf.txt