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Sample GSM7118511 Query DataSets for GSM7118511
Status Public on Sep 27, 2023
Title As.Ctrl
Sample type RNA
 
Source name AsPC-1 cells, ctrl
Organism Homo sapiens
Characteristics cell line: AsPC1
cell type: pancreatic tumor cell
treatment: control
Treatment protocol PGR interference cells were cultured in DMEM medium supplemented with 10% fetal bovine serum. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using TRIZOL Reagent (Cat#15596-018,Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
Label biotin
Label protocol Total RNA were amplified, labeled and purified by using GeneChip 3' IVT PLUS Reagent Kit (Cat#902416, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.
 
Hybridization protocol Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.
Scan protocol Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software12.6.1 (Agilent technologies, Santa Clara, CA, US).
Description cDNA expression data from AsPC-1 cells small interference Ctrl.
Data processing The raw data (.cel files) were normalized using Gene Spring Software 12.6.1, and then the differential gene analysis between samples was performed. According to the sample conditions, Fold-change(Fold change in expression) was used to screen differential genes, and the selection conditions were as follows:
1) 2-fold difference: Fold Change (linear) =< 0.5 or Fold Change (linear) >= 2.
2) T-test p-value < 0.05 and p-value < 0.01
 
Submission date Mar 27, 2023
Last update date Sep 27, 2023
Contact name yanzhi Gai
E-mail(s) yanzhi_gai@sjtu.edu.cn
Phone 15200895615
Organization name Shanghai Jiao Tong university
Street address 800 Dongchuan Road
City Shanghai
ZIP/Postal code 200001
Country China
 
Platform ID GPL570
Series (1)
GSE228301 Progestin receptor promotes cell macropinocytosis through CDC42 in pancreatic cancer

Data table header descriptions
ID_REF
VALUE MAS 5.0 signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 983.748 P 0.000509415
AFFX-BioB-M_at 1159.36 P 4.42873e-05
AFFX-BioB-3_at 884.366 P 4.42873e-05
AFFX-BioC-5_at 2463.75 P 5.16732e-05
AFFX-BioC-3_at 2528.7 P 4.42873e-05
AFFX-BioDn-5_at 6177.87 P 4.42873e-05
AFFX-BioDn-3_at 12240.5 P 7.00668e-05
AFFX-CreX-5_at 31739.8 P 5.16732e-05
AFFX-CreX-3_at 32894.7 P 4.42873e-05
AFFX-DapX-5_at 769.244 P 5.16732e-05
AFFX-DapX-M_at 1462.96 P 0.000662269
AFFX-DapX-3_at 1535.04 P 4.42873e-05
AFFX-LysX-5_at 71.1092 P 0.0032123
AFFX-LysX-M_at 69.4436 A 0.102165
AFFX-LysX-3_at 222.338 P 0.000194887
AFFX-PheX-5_at 123.422 P 0.000224668
AFFX-PheX-M_at 147.296 P 0.00255552
AFFX-PheX-3_at 186.897 P 0.000581214
AFFX-ThrX-5_at 91.5438 P 0.00762003
AFFX-ThrX-M_at 223.101 P 0.00141043

Total number of rows: 54675

Table truncated, full table size 1636 Kbytes.




Supplementary file Size Download File type/resource
GSM7118511_AsPC1-nc.CEL.gz 4.5 Mb (ftp)(http) CEL
GSM7118511_AsPC1-nc.CHP.gz 490.4 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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