NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2432204 Query DataSets for GSM2432204
Status Public on Dec 16, 2017
Title scr rep2
Sample type RNA
 
Source name pulmonary arterial endothelial cells (hPASMC)
Organism Homo sapiens
Characteristics sirna transfection: scramble
cell type: pulmonary arterial endothelial cells (hPAEC) in P2
Extracted molecule total RNA
Extraction protocol At 24h following transfection hPAEC were rinsed with PBS and the total RNA was extracted with peqGOLD TOTAL RNA Kit (VWR). RNA was frozen in liquid nitrogen and stored in -80°C prior to the shipping.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick-Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer
 
Hybridization protocol 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028004 SurePrint G3 Human GE 8x60K Microarray (GPL14550) for 18 hours at 65°C in a rotating 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 (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).
Data processing The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028004_D_F_20110819) to obtain background subtracted and spatially detrended Processed Signal intensities. Features which were not positive and significant, not above background or were population outliers were flagged as “Compromised”. If features were flagged “Compromised” in all samples, than they were excluded.
 
Submission date Dec 19, 2016
Last update date Dec 16, 2017
Contact name Rory Morty
Organization name MPI für Herz- und Lungenforschung
Department W.G. Kerckhoff-Institut
Street address Parkstr. 1
City Bad Nauheim
ZIP/Postal code 61231
Country Germany
 
Platform ID GPL17077
Series (1)
GSE92553 Gene expression analysis following 24h siRNA-mediated knockdown of transforming growth factor β receptor III (TGFBR3) in human pulmonary arterial endothelial cells (hPAEC).

Data table header descriptions
ID_REF
VALUE Quantile normalization was applied to the data set

Data table
ID_REF VALUE
GE_BrightCorner 17.009672
A_23_P117082 13.48152
A_33_P3319925 1.8449317
A_21_P0000509 14.750254
A_21_P0000744 10.684205
A_24_P215804 8.48077
A_23_P110167 13.692466
A_33_P3211513 8.535257
A_33_P3414202 7.4485664
A_33_P3316686 6.579008
A_33_P3263061 12.821957
A_24_P278460 9.482845
A_21_P0014651 5.90843
A_24_P286898 8.075984
A_23_P340890 11.040088
A_21_P0010885 11.110849
A_23_P89762 6.2429852
A_23_P109034 10.179137
A_33_P3261031 5.5173383
A_33_P3732466 7.392499

Total number of rows: 32588

Table truncated, full table size 730 Kbytes.




Supplementary file Size Download File type/resource
GSM2432204_RS-319_0002.txt.gz 12.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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