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Status |
Public on Jan 25, 2025 |
Title |
KYSE150 PAFR shRNA cells (CAFs in the upper chamber) |
Sample type |
RNA |
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Source name |
KYSE150 PAFR shRNA cells (CAFs in the upper chamber)
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Organism |
Homo sapiens |
Characteristics |
cell line: KYSE150 cells
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Treatment protocol |
using transwell apparatus with 0.4 μm pore size to coculture KYSE150 cells and CAFs
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Growth protocol |
cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), penicillin (100U/ml), and streptomycin (100 μg/ml).
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted using mirVanaTM RNA Isolation Kit (ABI, AM1561).
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Label |
Cy3
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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.
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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.
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Scan protocol |
Slides were scanned using Agilent Scanner G2505C.
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Description |
whole gene exression
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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.
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Submission date |
Jan 25, 2022 |
Last update date |
Jan 25, 2025 |
Contact name |
di zhao |
E-mail(s) |
zd_0599@bjmu.edu.cn
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Phone |
+861088196735
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Organization name |
beijng cancer hospital
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Street address |
52 Fucheng Road, Haidian District, Beijing
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City |
beijing |
ZIP/Postal code |
100142 |
Country |
China |
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Platform ID |
GPL21185 |
Series (1) |
GSE194414 |
Gene expression of KYSE150 cells and CAFs in coculture system |
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