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Sample GSM1575863 Query DataSets for GSM1575863
Status Public on Jan 03, 2015
Title PLC5 siGALNT1-2
Sample type RNA
 
Source name PLC5 siGALNT1-2
Organism Homo sapiens
Characteristics hepatocellular carcinoma cell line: PLC5
transfectant: GALNT1 siRNA
Treatment protocol HA22T and PLC5 cells were transfected with 10 nM non-targeting and GALNT1 specific siRNA (Thermo Scientific, ON-TARGET plus SMART pool L-011280-01-0005) with Lipofectamine RNAiMAX (Invitrogen) for 48 hours and extracted for total RNA
Growth protocol HA22T and PLC5 were cultured in DMEM supplemented with 10% FBS and 0.1 % penicillin and streptomycin
Extracted molecule total RNA
Extraction protocol RNA was prepared using the GeneJET RNA Purification kit (Thermo Scientific, Catelog number: K0731) following the manufacturer's recommendations. RNA was quantified using a NanoDrop spectrophotometer (Bio-Rad) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA)
Label Alexa/CyDye
Label protocol cDNA prepared from 10μg of total RNA were labeled with aa-dUTP using Invitrogen SuperScriptTM Plus Indirect cDNA Labeling System according to the manufacturer's protocol, followed by aa-cDNA column purification (QIAGEN, Valencia, CA). Alexa/CyDye was incorporated to aa-cDNA followed by column purification with Alexa/CyDye-cDNA cRNA purification (Qiagen).
 
Hybridization protocol Agilent Gene Expression Hybridization Kits was used for hybridization according to the manufacturer’s instruction. Briefly, 16 ul of dye labeled cDNA in water was fragmented at 98°C for 3 mins in a reaction volume of 40 ul containing 4 ul Agilent 10x blocking agenr and 20 ul of Agilent 2xGExHybridization Buffer HI-RPM and hybridized to Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarray (G4851B) at 65°C and rotated at 10 rpm for 17 hours. 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 (US9230696) using one color scan setting for 8x60k array slides (Scan Area 61x21.6mm, Scan resolution 2um, Dye channel is set to Green and Green PMT is set to 100%).
Description Gene expression after 48 hours transfection
Data processing The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
 
Submission date Jan 02, 2015
Last update date Jan 03, 2015
Contact name Min-Chuan Huang
E-mail(s) mchuang@ntu.edu.tw
Phone 886-223123456-88177
Organization name National Taiwan University
Department Graduate Institute of Anatomy and Cell Biology
Street address No. 1, Sec. 1, Ren-Ai RD, Taipei, Taiwan, R.O.C.
City Taipei
ZIP/Postal code 100
Country Taiwan
 
Platform ID GPL17077
Series (1)
GSE64628 siRNA knockdown of GALNT1 in hepatocellular carcinoma HA22T and PLC5 cells

Data table header descriptions
ID_REF
VALUE Normalized with percentile at 75th intensity

Data table
ID_REF VALUE
GE_BrightCorner 7.716092
DarkCorner -7.731594
A_23_P117082 0.97472954
A_33_P3246448 -4.750243
A_33_P3318220 -7.615507
A_33_P3236322 2.2280226
A_33_P3319925 -6.552598
A_21_P0000509 5.618928
A_21_P0000744 -2.8494377
A_24_P215804 -2.1203547
A_23_P110167 2.2827091
A_33_P3211513 -0.87316227
A_23_P103349 -5.5337925
A_32_P61480 -7.6415405
A_33_P3788124 -7.645059
A_33_P3414202 -0.6905422
A_33_P3316686 1.6516132
A_33_P3300975 -2.257554
A_33_P3263061 1.3776064
A_33_P3261373 -2.755128

Total number of rows: 50739

Table truncated, full table size 1191 Kbytes.




Supplementary file Size Download File type/resource
GSM1575863_7880-10-253949437955_1_2.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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