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Sample GSM8213694 Query DataSets for GSM8213694
Status Public on Apr 20, 2024
Title SNU-449 cells transfected with vector, rep2
Sample type RNA
 
Source name SNU-449 cells transfected with vector
Organism Homo sapiens
Characteristics cell line: SNU-449
genotype: Ctrl
Treatment protocol Cells were inoculated into 24-well plates at a density of 3 × 105 cells/mL for viral infections, and cultured until cell fusion reached 20%-30%. Lenti-USP48 viruses with a MOI ≥ 90 were transduced into the cells for 24 hours in serum-free medium using HiTransG A. Subsequently, the cells were further cultured in complete medium for 4-6 days before puromycin was added for concentration screening and stable expression strain cell screening.
Growth protocol The SNU-449 cell line was grown in Roswell Park Memorial Institute (RPMI) - 1640 medium (Gibco, USA). By supplementing the medium with 10% fetal bovine serum (FBS, Gibco), penicillin, and streptomycin, we reduced microbial contamination and provided nutrition.
Extracted molecule total RNA
Extraction protocol After harvesting SNU-449 cells transfected by USP48, Trizol was used for total RNA extraction.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Data processing The conversion of image signals (.DAT files) to digital signals (.CEL files) was performed by the AGCC software, while fluorescence signal intensity at the probe level was recorded in .CEL files. The .CEL files served as the primary source files for data preprocessing, which involved background correction, integration of probe signals into probeset signals, and inter-slice normalization to eliminate non-biological inter-sample variability. Data preprocessing typically employed the RMA algorithm. Subsequently, sample correlation analysis, including cluster analysis and principal component analysis, was conducted on the data processed by the RMA algorithm to the similarity and grouping of the samples.
 
Submission date Apr 17, 2024
Last update date Apr 20, 2024
Contact name Bo Tang
Organization name The First Affiliated Hospital of Guangxi Medical University
Street address No. 6 Shuangyong Road
City Nanning
ZIP/Postal code 530021
Country China
 
Platform ID GPL570
Series (1)
GSE264186 Expression data from SNU-449 cells transfected with USP48

Data table header descriptions
ID_REF
VALUE RMA signal intensity

Data table
ID_REF VALUE
1007_s_at 8.685184833
1053_at 7.400149599
117_at 4.258142775
121_at 6.041795755
1255_g_at 1.054694307
1294_at 3.271149618
1316_at 5.835544989
1320_at 3.91820268
1405_i_at 6.395517486
1431_at 1.582153406
1438_at 3.412416574
1487_at 7.02844528
1494_f_at 4.627778474
1552256_a_at 8.404338086
1552257_a_at 7.831029373
1552258_at 3.927566657
1552261_at 3.257611987
1552263_at 6.14202444
1552264_a_at 6.325074845
1552266_at 0.857552003

Total number of rows: 54675

Table truncated, full table size 1211 Kbytes.




Supplementary file Size Download File type/resource
GSM8213694_C2.CEL.gz 4.0 Mb (ftp)(http) CEL

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