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Sample GSM5835439 Query DataSets for GSM5835439
Status Public on Jan 25, 2025
Title PAFR shRNA CAFs
Sample type RNA
 
Source name PAFR shRNA CAFs
Organism Homo sapiens
Characteristics cell line: CAF 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 16.056265
DarkCorner 2.2536197
A_21_P0014386 3.395438
A_33_P3396872 8.162959
A_33_P3267760 2.458189
A_32_P194264 4.923265
A_23_P153745 11.976483
A_33_P3352837 2.4350686
A_21_P0011260 8.824699
A_33_P3235816 2.4198315
A_21_P0014180 2.41068
A_24_P944991 5.8448715
A_21_P0006507 2.3936863
A_23_P208706 13.221395
A_33_P3388806 2.3702414
A_33_P3324839 4.170307
A_24_P333494 11.345223
A_22_P00006274 2.33447
A_23_P161615 6.6532965
A_33_P3384958 5.175092

Total number of rows: 58341

Table truncated, full table size 1335 Kbytes.




Supplementary file Size Download File type/resource
GSM5835439_NF4.txt.gz 12.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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