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Sample GSM6032502 Query DataSets for GSM6032502
Status Public on Sep 30, 2023
Title The HaCaT cell lines, overexpression lentiviruses empty vectors 3
Sample type RNA
 
Source name The HaCaT cell lines were infected by overexpression lentiviruses empty vectors
Organism Homo sapiens
Characteristics cell type: HaCaT
genotype/variation: no
Treatment protocol The HaCaT cell lines were infected by overexpression lentiviruses vectors of GJB2 gene mutant p.Asp66His(D66H), and empty GV308 vector.
Growth protocol The cell lines were maintained using Gibco Roswell Park Memorial Institute (RPMI) 1640 medium supplemented with 10% FBS and 1% penicillin/streptomycin at 37°C in a humidified atmosphere containing 5% CO2.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 50-500ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, cRNA were hybridized for 16-18 hr at 45 ℃ on GeneChip PrimeView Human Gene Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450
Scan protocol GeneChips were scanned using the GeneChip Scanner 300
Data processing The gene expression profile was preprocessed using Limma package in Bioconductor and Affymetrix annotation files. The background correction, quantile normalization and probe summarization of the microarray data were performed using the Robust Multiarray average algorithm to obtain the gene expression matrix. The cut-off for the background correction was 20%, and the coefficient of variation was 25%. The Benjamini-Hochberg method was used to correct the significant difference level (FDR).
The screening criteria for significantly different genes were: |Fold Change|>1.5 and FDR<0.05.
 
Submission date Apr 07, 2022
Last update date Sep 30, 2023
Contact name Li Zhang
E-mail(s) zhangliwenzhe@medmail.com.cn
Organization name Department of Dermatology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan
Street address Department of Dermatology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China.
City Jinan
ZIP/Postal code 250021
Country China
 
Platform ID GPL15207
Series (2)
GSE200386 Gene expression and functional analysis of GJB2 mutated HaCaT cell lines [D66H]
GSE200387 Gene expression and functional analysis of GJB2 mutated HaCaT cell lines

Data table header descriptions
ID_REF
VALUE RMA

Data table
ID_REF VALUE
AFFX-BioB-5_at 8.9413
AFFX-BioB-M_at 9.26929
AFFX-BioB-3_at 9.23692
AFFX-BioC-5_at 10.19008
AFFX-BioC-3_at 10.22853
AFFX-BioDn-5_at 11.59641
AFFX-BioDn-3_at 12.52662
AFFX-CreX-5_at 13.49561
AFFX-CreX-3_at 13.66546
AFFX-DapX-5_at 9.52415
AFFX-DapX-M_at 10.41885
AFFX-DapX-3_at 10.41415
AFFX-LysX-5_at 5.58181
AFFX-LysX-M_at 6.6086
AFFX-LysX-3_at 6.67793
AFFX-PheX-5_at 7.00209
AFFX-PheX-M_at 7.24732
AFFX-PheX-3_at 7.71666
AFFX-ThrX-5_at 7.36573
AFFX-ThrX-M_at 8.15633

Total number of rows: 39254

Table truncated, full table size 828 Kbytes.




Supplementary file Size Download File type/resource
GSM6032502_E8687-3_PrimeView.CEL.gz 2.0 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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