NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM688242 Query DataSets for GSM688242
Status Public on Nov 29, 2011
Title IL1A_KD
Sample type RNA
 
Source name HUVEC
Organism Homo sapiens
Characteristics tissue: HUVEC
sirna knocked down: IL1A siRNA knocked down
Treatment protocol HUVEC pools consisting of 10 biological isolates were transfected with siRNA smartpools from Dharmacon Inc. (Lafayette, Colorado, USA) using the siFectamine transfection reagent (ICVEC, London, UK) used according to the manufacturer’s instructions. Transfection was carried out when HUVEC pools were 60-80% confluent, with siRNA smartpools at a final concentration of 100nm per treatment and RNA was extracted 24hrs after transfection.
Growth protocol HUVECs were isolated from umbilical cords by collagenase digestion and cultured at 37ºC/5%CO2 in basal culture medium supplemented with a proprietary mixture of heparin, hydrocortisone, epidermal growth factor, 2% foetal calf serum (FCS; EGM-2, Cambrex, Workingham, UK).
Extracted molecule total RNA
Extraction protocol Cell cultures were washed with 1 x PBS and lysed using TRIzol® reagent. Total RNA was extracted using phenol chloroform, with the precipitated RNA washed in 70% ethanol and resuspended in Rnase free water. RNA concentration and quality was assess by spectrophotometer and Agilent BioAnalyser.
Label biotin
Label protocol Biotin-labelled complex cRNAs were prepared to according to the manufacturer's protocols (Applied Microarrays, formally supplied by GE Healthcare)
 
Hybridization protocol 10 µg biotin incorporated cRNA was fragmented and then denatured. The denatured cRNA was slowly loaded into the bioarray flex chamber without the introduction of air bubbles. All samples were loaded within 30 minutes of cRNA denaturation. The sealed bioarrays were left to hybridise in a 37°C shaker-incubator for 18 hours. The slides were washed and placed in a solution of Cy5-streptavidin for 30 minutes, before stringent washes were used to remove any unbound dye.
Scan protocol The arrays were scanned with Agilnet DNA Microarray Scanner model G2565BA.
Description HUVEC_KD194
Data processing The scanned images were quantified with CodeLink Expression Array Software (Applied Microarrays, formally supplied by GE Healthcare), where the intensity of each spot was divided by the spot’s signal median.
 
Submission date Mar 09, 2011
Last update date Nov 29, 2011
Contact name Hiromitsu Araki
E-mail(s) araki.hiromitsu.596@m.kyushu-u.ac.jp
Organization name Kyushu University
Street address 744 Motooka Nishi-Ku
City Fukuoka
ZIP/Postal code 819-0395
Country Japan
 
Platform ID GPL4044
Series (2)
GSE27869 Gene expression profiles of 400 siRNA knocked down on HUVEC
GSE27871 Network inference tools for the human transcriptome

Data table header descriptions
ID_REF
VALUE The median scaled intensity
Quality_Flag

Data table
ID_REF VALUE Quality_Flag
1 47.83997044 G
2 17.89214739 G
3 20.61146 G
4 474.9485801 S
5 59.44881289 G
6 8.275850781 G
7 0.475103535 G
8 426.2674964 C
9 98.53883961 G
10 293.3526023 G
11 0.040562962 L
12 42.16750283 G
13 317.7289291 G
14 17.77507113 G
15 3.449473519 G
16 65.65410863 G
17 36.29267045 G
18 59.31981838 G
19 28.12331832 G
20 39.85798511 G

Total number of rows: 20469

Table truncated, full table size 385 Kbytes.




Supplementary file Size Download File type/resource
GSM688242.txt.gz 833.9 Kb (ftp)(http) TXT
Processed data included within Sample table

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