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Sample GSM361886 Query DataSets for GSM361886
Status Public on Nov 02, 2009
Title SUSM1_ALT_1
Sample type RNA
 
Source name liver fibroblasts
Organism Homo sapiens
Characteristics cell type: liver fibroblasts
Treatment protocol None
Growth protocol SKLU, WI38-SV40, WI38 and IMR90 were cultured in MEM (10% FBS and 1% L-glutamine) and A2780 were cultured in RPMI 1640 (10% FBS and 1% L-glutamine) at 5% CO2. Bone marrow hMSC were cultured in DMEM-LG plus Glutamax supplemented with 17% Hyclone FBS (Thermo Fisher Scientific, Waltham, MA) at 5% CO2.
Extracted molecule total RNA
Extraction protocol Immortalised cell lines and normal cell strains were rinsed in PE, trypsanised and total RNA was extracted using Nucleospin II RNA extraction kit (Macherey-Nagel) as per manufacutor's instructions. Primary hMSC aspirates were isolated by centrifugation at 700 g for 15 min at 4 °C over a Ficoll-Hypaque gradient (Sigma).
Label Cy3
Label protocol 800 ng of total RNA was labelled with Cy3 using the Low RNA Input Linear Amplification Kit (Agilent technologies) as per manufacturor's instructions.
 
Hybridization protocol 100ul of purified labelled total RNA was hybridised to Agilent 4x44K whole human genome arrays for 17 hours at 65C rotating at 10 rpm and washed as as per manufacturor's instructions for one colour arrays (Agilent Technologies).
Scan protocol Slides were scanned using DNA microarray scanner model G2539A (Agilent Technologies) and Agilent Scan Control Software. Spot intensity and identity information was extracted using Agilent Feature Extraction Software.
Data processing Normalised to the 75th percentile with intensities below 0.01 being set to 0.01. Data filtered to contain only those probes with Present, Marginal or Unknown status in 26 of 28 samples.
 
Submission date Jan 21, 2009
Last update date Mar 23, 2012
Contact name W. Nicol Keith
E-mail(s) n.keith@beatson.gla.ac.uk
Organization name The University of Glasgow
Street address Center for Oncology and Applied Pharmacology, University of Glasgow, CRUK Beatson Laboratories, Garscube Estate, Switchback Road
City Glasgow
State/province Lanarkshire
ZIP/Postal code G61 1BD
Country United Kingdom
 
Platform ID GPL6480
Series (2)
GSE14487 A gene expression signature classifying telomerase and ALT immortalization I
GSE14533 A gene expression signature classifying telomerase and ALT immortalization

Data table header descriptions
ID_REF
VALUE Genespring 7.3.1 signal intensity normalised to the 75th percentile, probes with Present, Marginal or Unknown status in 26 of 28 samples

Data table
ID_REF VALUE
A_32_P70468 0.33251297
A_23_P120744 2.7476628
A_23_P420361 63.46293
A_24_P305764 14.335764
A_24_P645765 1.0408342
A_23_P428842 0.37655908
A_24_P158065 2.4305098
A_23_P43086 2.1049619
A_23_P67708 14.107961
A_23_P47135 2.2738326
A_24_P135801 14.457036
A_23_P100779 0.9288114
A_32_P136575 0.19559665
A_24_P845072 0.5258075
A_24_P128741 0.47251678
A_23_P36305 0.96376055
A_24_P196372 0.2213398
A_23_P74954 3.1727686
A_23_P259357 67.92715
A_23_P5221 0.12589854

Total number of rows: 21728

Table truncated, full table size 484 Kbytes.




Supplementary file Size Download File type/resource
GSM361886.TXT.gz 5.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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