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Sample GSM5835433 Query DataSets for GSM5835433
Status Public on Jan 25, 2025
Title KYSE150 PAFR shRNA cells (CAFs in the upper chamber)
Sample type RNA
 
Source name KYSE150 PAFR shRNA cells (CAFs in the upper chamber)
Organism Homo sapiens
Characteristics cell line: KYSE150 cells
Treatment protocol using transwell apparatus with 0.4 μm pore size to coculture KYSE150 cells and CAFs
Growth protocol cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), penicillin (100U/ml), and streptomycin (100 μg/ml).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using mirVanaTM RNA Isolation Kit (ABI, AM1561).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.
 
Hybridization protocol 1.5ug of Cy3-labelled cRNA (specific activity > 10.0 pmol Cy3/ug cRNA) was fragmented at 60 ℃ for 30 minutes in a reaction volume of 250 ml containing 1× Agilent fragmentation buffer and 2× Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2× Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Microarrays for 17 hours at 65 ℃ in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 ℃ GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned using Agilent Scanner G2505C.
Description whole gene exression
Data processing Data was extracted and normalized using Feature Extraction v10.7.1.1 software. Further Data analysis was performed using Agilent GeneSpring v13.1 software.
 
Submission date Jan 25, 2022
Last update date Jan 25, 2025
Contact name di zhao
E-mail(s) zd_0599@bjmu.edu.cn
Phone +861088196735
Organization name beijng cancer hospital
Street address 52 Fucheng Road, Haidian District, Beijing
City beijing
ZIP/Postal code 100142
Country China
 
Platform ID GPL21185
Series (1)
GSE194414 Gene expression of KYSE150 cells and CAFs in coculture system

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
GE_BrightCorner 14.821602
DarkCorner 1.8058634
A_21_P0014386 4.6750226
A_33_P3396872 7.453934
A_33_P3267760 3.246589
A_32_P194264 8.27445
A_23_P153745 13.937376
A_33_P3352837 1.7353511
A_21_P0011260 3.7570639
A_33_P3235816 1.7258964
A_21_P0014180 3.3745713
A_24_P944991 5.0620074
A_21_P0006507 1.7124915
A_23_P208706 12.195066
A_33_P3388806 1.7041363
A_33_P3324839 3.9346545
A_24_P333494 10.278284
A_22_P00006274 2.9609787
A_23_P161615 8.459895
A_33_P3384958 5.286104

Total number of rows: 58341

Table truncated, full table size 1335 Kbytes.




Supplementary file Size Download File type/resource
GSM5835433_ESCC6.txt.gz 12.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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