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Sample GSM363628 Query DataSets for GSM363628
Status Public on Nov 02, 2009
Title Liposarcoma_telomerase_6
Sample type RNA
 
Source name Liposarcoma, Fresh Frozen
Organism Homo sapiens
Characteristics cell type: Liposarcoma, Fresh Frozen
Treatment protocol None
Growth protocol 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 Frozen Liposarcoma tissue was disrupted using a Hybaid Ribolyser at a setting of 5.5 for 5 x 10 second pulses with 30 second pauses in between and RNA was extracted using the RNeasy Lipid kit (Qiagen Inc, Hilden, Germany) as per manufacturers’ instructions. Primary hMSC aspirates were isolated by centrifugation at 700 g for 15 min at 4 °C over a Ficoll-Hypaque gradient (Sigma) and total RNA was extracted using Nucleospin II RNA extraction kit (Macherey-Nagel) as per manufacutor's instructions.
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 22 of 26 samples.
 
Submission date Jan 23, 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)
GSE14529 A gene expression signature classifying telomerase and ALT immortalization II
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

Data table
ID_REF VALUE
A_23_P208835 1.4554828
A_32_P30187 10.113064
A_24_P226867 1.3638492
A_23_P60472 1.350118
A_23_P98057 0.29033816
A_24_P110591 2.3421972
A_23_P105044 1.8456947
A_24_P664992 0.35578996
A_23_P129174 1.7200145
A_23_P103442 2.891597
A_32_P213103 2.438573
A_23_P31109 1.9689783
A_23_P250283 1.4949216
A_23_P93562 0.49530485
A_23_P132260 0.92310303
A_23_P400465 6.8067265
A_23_P5551 48.780495
A_23_P153489 0.2485498
A_23_P151321 104.16886
A_23_P122906 5.070623

Total number of rows: 24410

Table truncated, full table size 535 Kbytes.




Supplementary file Size Download File type/resource
GSM363628.txt.gz 1.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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