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Sample GSM5994515 Query DataSets for GSM5994515
Status Public on Apr 02, 2022
Title Lymphatic endothelial cells_PBS_24 hour_rep2
Sample type RNA
 
Source name Lymphatic endothelial cells, PBS, 24 hour
Organism Mus musculus
Characteristics cell type: Lymphatic endothelial cells
treatment: PBS for 24h
Treatment protocol Lymphatic endothelial cells were seeded in 6-well (15*10^4 cells/well) for 24 h at 37°C. Then the cells were treated with PBS and 300μg/ml MSU for 24h, respectively.
Growth protocol Lymphatic endothelial cells were incubated with growth medium comprising FBS (10%), streptomycin (100 μg/ml) and penicillin (100 U/ml) in a 5% CO2-humidified incubator. The cells was cultured at 37 °C with DMEM culture media.
Extracted molecule total RNA
Extraction protocol RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556) following the manufacturer's instructions.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse Gene Expression for 17 hours at 65°C 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°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).
Description Control_2
Gene expression after 24hours in PBS treated lymphatic endothelial cells.
Cell line
Data processing The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with GeneSpring 13.0 (Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.
 
Submission date Apr 01, 2022
Last update date Apr 02, 2022
Contact name Junli Chang
E-mail(s) [email protected]
Organization name Long hua Hospital
Street address Wanping South Road 725
City shanghai
ZIP/Postal code 200032
Country China
 
Platform ID GPL21163
Series (1)
GSE199950 Lymphatic vessels drain monosodium urate and activate immunity in gouty arthritis

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
(+)E1A_r60_1 17.03344272
(+)E1A_r60_3 1.793334834
(+)E1A_r60_a104 2.724299552
(+)E1A_r60_a107 4.831214279
(+)E1A_r60_a135 7.610628674
(+)E1A_r60_a20 8.951524831
(+)E1A_r60_a22 9.874468348
(+)E1A_r60_a97 12.59678079
(+)E1A_r60_n11 14.37467321
(+)E1A_r60_n9 14.82117382
3xSLv1 1.531273662
A_30_P01017428 8.495906365
A_30_P01017437 7.334996145
A_30_P01017440 2.459960189
A_30_P01017441 1.511984701
A_30_P01017444 1.561265621
A_30_P01017445 3.93191159
A_30_P01017447 6.375144359
A_30_P01017448 4.300764965
A_30_P01017453 5.500452263

Total number of rows: 56745

Table truncated, full table size 1410 Kbytes.




Supplementary data files not provided
Processed data are available on Series record
Processed data included within Sample table

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