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Sample GSM8213693 Query DataSets for GSM8213693
Status Public on Apr 20, 2024
Title SNU-449 cells transfected with vector, rep1
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
VALUE RMA signal intensity

Data table
1007_s_at 8.688310022
1053_at 7.407866581
117_at 4.261695952
121_at 5.979003135
1255_g_at 1.269469396
1294_at 3.411643092
1316_at 5.788935773
1320_at 3.819824549
1405_i_at 6.217074954
1431_at 1.533876647
1438_at 3.426651995
1487_at 7.087018341
1494_f_at 4.515922769
1552256_a_at 8.248538084
1552257_a_at 7.71732841
1552258_at 3.927566657
1552261_at 2.93923469
1552263_at 6.450957868
1552264_a_at 6.537342269
1552266_at 0.886916261

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.

Supplementary file Size Download File type/resource
GSM8213693_C1.CEL.gz 4.0 Mb (ftp)(http) CEL

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