NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1525595 Query DataSets for GSM1525595
Status Public on Aug 10, 2015
Title HCAEC_si_negative_control1
Sample type RNA
 
Source name Human coronary artery endothelial cell, control siRNA, replicate1
Organism Homo sapiens
Characteristics tissue: coronary artery endothelial cell
condition: control siRNA
Treatment protocol Transfection of siRNA was conducted using Lipofectamine RNAiMAX (Invitrogen) according to the manufacturer’s protocol.
Growth protocol HCAECs were cultured in EGM-2MV (Lonza) containing 10% fetal calf serum. All cell cultures were maintained at 37˚C in normoxic environments with 5% CO2 and 100% humidity.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)
Label Cy3
Label protocol cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).
 
Hybridization protocol cRNA was hybridized to a 44K 60-mer oligomicroarray SurePrint G3 Human GE Microarray Kit 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.
Scan protocol The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).
Description Gene expression upon treatment with control siRNA
Data processing The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of four samples were normalized by the quantile algorithm with the Bioconductor.
 
Submission date Oct 15, 2014
Last update date Aug 10, 2015
Contact name Kazuhiro Ohkubo
E-mail(s) kohkubo@pediatr.med.kyushu-u.ac.jp
Organization name Graduate School of Medical Sciences, Kyushu University
Department Department of Pediatrics
Street address 3-1-1, Maidashi, Higashi-ku
City Fukuoka
State/province Fukuoka
ZIP/Postal code 812-8582
Country Japan
 
Platform ID GPL17077
Series (1)
GSE62348 Gene expression profile in HCAECs transfected with RNF213 siRNA

Data table header descriptions
ID_REF
VALUE quantile normalized signal, non-log scaled and ABS CALL.
ABS_CALL

Data table
ID_REF VALUE ABS_CALL
A_19_P00315452 578.32505 P
A_19_P00315459 87.749785 P
A_19_P00315482 6.74466075 A
A_19_P00315492 50.42113 P
A_19_P00315493 57.156875 P
A_19_P00315502 6.72573125 A
A_19_P00315506 172.60425 P
A_19_P00315518 3.19411975 A
A_19_P00315519 3.43245275 A
A_19_P00315524 37.5773975 P
A_19_P00315528 20.27949 P
A_19_P00315529 25.5277375 P
A_19_P00315538 24.453135 P
A_19_P00315541 4.049774 A
A_19_P00315543 20.0401725 P
A_19_P00315550 89.6060175 P
A_19_P00315551 117.9303525 P
A_19_P00315554 12.6022325 A
A_19_P00315581 1799.4205 P
A_19_P00315583 123.6544525 P

Total number of rows: 50599

Table truncated, full table size 1281 Kbytes.




Supplementary file Size Download File type/resource
GSM1525595_US11030397_253949414900_S01_GE1_107_Sep09_2_1.txt.gz 12.4 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap