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Sample GSM4635322 Query DataSets for GSM4635322
Status Public on Dec 22, 2020
Title scribKD_Tet(–)_30hr
Sample type RNA
 
Source name scribKD, 30hr, without Tet
Organism Canis lupus familiaris
Characteristics cell line: Madin-Darby Canine Kidney (MDCK) cellls
treatment condition: cultured without tetracycline for 30 hours
Treatment protocol The cells were treated with tetracycline at a final concentration of 5 µg/ml at 6 hours after plating.
Growth protocol MDCK-II scribKD cells were plated in a 12-well plate at a density of 154,000 cells/wel. The cells were cultured in DMEM high glucose supplemented with 10% FBS and 100 units/ml penicillin G in a 5% CO2 atmosphere at 37℃.
Extracted molecule total RNA
Extraction protocol At the indicated time after tetracycline addtion, total RNA was extracted from three independent wells of the same condition and mixed using Isogen (Wako) according to the manufacturer's instructions.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared using the Low Input Quick Amp Labeling 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-2000 Spectrophotometer.
 
Hybridization protocol Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Canine (V2) Gene Expression Microarray (Agilent, G2519F-021193) 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).
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides. Dye channel is set to Green and Green PMT is set to 100%.
Description Gene expression at 30 hours after cultured without tetracycline
Data processing The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
 
Submission date Jun 24, 2020
Last update date Dec 22, 2020
Contact name Motoyuki Ogawa
Organization name The University of Tokyo
Department Graduate School of Pharmaceutical Sciences
Lab Cell Signaling
Street address 7-3-1, Hongo
City Bunkyo-ku
State/province Tokyo
ZIP/Postal code 113-0033
Country Japan
 
Platform ID GPL13605
Series (1)
GSE153186 Gene expression change of MDCK cells expressing scribble shRNA in a tetracycline-inducible manner (scribKD cells)

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
12 278.6
13 9
14 525.9
15 9
16 10.4
17 12119.9
18 9
19 5203.1
20 15.6
21 40.1
22 2026.3
23 2021.6
24 889.2
25 920.6
26 429.8
27 1647
28 9.1
29 9.1
30 160.8
31 1713

Total number of rows: 43803

Table truncated, full table size 481 Kbytes.




Supplementary file Size Download File type/resource
GSM4635322_AR2488_01raw.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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