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Sample GSM357121 Query DataSets for GSM357121
Status Public on Dec 31, 2009
Title ZNF191 siRNA cells vs Control
Sample type RNA
 
Channel 1
Source name human embryo kidney cells transfected with ZNF191 siRNA vectors
Organism Homo sapiens
Characteristics ZNF191 siRNA
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the NucleoSpin RNAII Kit (Macherey-Nagel, Düren, DE) and quantified via spectrophotometry (Nanodrop, Labtech). RNA integrity was confirmed using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).
Label cy3
Label protocol Total RNA was isolated using the NucleoSpin RNAII Kit (Macherey-Nagel, Düren, DE) and quantified via spectrophotometry (Nanodrop, Labtech). RNA integrity was confirmed using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).
 
Channel 2
Source name human embryo kidney cells transfected with empty vectors
Organism Homo sapiens
Characteristics HEK293 cell line
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the NucleoSpin RNAII Kit (Macherey-Nagel, Düren, DE) and quantified via spectrophotometry (Nanodrop, Labtech). RNA integrity was confirmed using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).
Label cy5
Label protocol Agilent’s recommended procedures for microarray-based one-color gene expression analysis were followed. Briefly, 350ng of total RNA with control RNA Spike In were amplified and labeled with Cy5-CTP using the T7-based Low RNA Input Linear Amplification Kit, PLUS, One-Color (Agilent Technologies, Santa Clara, CA). After purification (RNeasy Mini Kit, QIAGEN), labeled cRNAs were quantified for yield and dye incorporation using a Nanodrop spectrophotometer.
 
 
Hybridization protocol 1.65microg of Cy3-labeled RNA and Cy5-labeled RNA were hybridized to each array in a 110microl total volume of hybridization buffer (Agilent Technologies) for 17 hours at 65°C. Washing was performed according to the Agilent protocol.
Scan protocol Arrays were analyzed using the dynamic autofocus Agilent G2565BA microarray scanner and the Agilent Feature Extraction software (FE v9.4.1, GE1-v5_91_0806 protocol).
Description Poor quality spots were flagged according to default FE criteria and corresponding values were removed.
Data processing GeneSpring 10.0 quantile normalization
 
Submission date Jan 03, 2009
Last update date Jan 05, 2009
Contact name Jianzhong Li
E-mail(s) lijianzhong1234@yahoo.com
Organization name Second Military Medical University
Department Department of Biochemical Pharmacy
Street address GuoHe Road 325#
City ShangHai
ZIP/Postal code 200433
Country China
 
Platform ID GPL6480
Series (1)
GSE14273 The target genes of transcript factor ZNF191

Data table header descriptions
ID_REF
VALUE log2 of PRE_VALUE, ie, log2(test/ref)
PRE_VALUE normalized Cy3/Cy5 ratio (no log transform)

Data table
ID_REF VALUE PRE_VALUE
A_23_P100001 -0.1523 0.899792
A_23_P100011 0.0916 1.065586
A_23_P100022 -0.0114 0.992123
A_23_P100056 0.3334 1.259947
A_23_P100074 0.0637 1.045157
A_23_P100092 -0.1506 0.900851
A_23_P100103 -0.1726 0.887223
A_23_P100111 -0.1482 0.902364
A_23_P100127 0.2917 1.224046
A_23_P100133 0.1208 1.087325
A_23_P100141 0.0024 1.001695
A_23_P100156 -0.0717 0.95154
A_23_P100177 0.0635 1.045023
A_23_P100189 0.1634 1.119953
A_23_P100196 -0.1285 0.914766
A_23_P100203 0.3962 1.316081
A_23_P100220 -0.2325 0.85114
A_23_P100240 0.5472 1.461276
A_23_P10025 0.4534 1.369308
A_23_P100263 0.0163 1.011376

Total number of rows: 41000

Table truncated, full table size 1138 Kbytes.




Supplementary file Size Download File type/resource
GSM357121_raw.txt.gz 13.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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