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Sample GSM1553708 Query DataSets for GSM1553708
Status Public on Nov 26, 2014
Title PS90-0074
Sample type RNA
 
Source name Bone Marrow
Organism Homo sapiens
Characteristics diagnosis: AML
tissue: bone marrow
treatment status: Pre-treatment
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the TRIzol® Plus RNA Purification Kit (Life Technologies, Grand Island NY) following the manufacturer's instructions. mRNA was purified from the total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). RNA quantity and quality were measured by NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.
Label Cy3
Label protocol Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, each mRNA sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing random priming. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.
 
Hybridization protocol 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer. The mixture was heated at 60 °C for 30 min. 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.
Scan protocol The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C). Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.
Data processing Quantile normalization and subsequent data processing were performed with using Agilent GeneSpring GX v11.5 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 2 out of 4 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs were identified through Fold Change and T-test filtering.
 
Submission date Nov 25, 2014
Last update date Nov 26, 2014
Contact name Ramiro Garzon
E-mail(s) Ramiro.Garzon@osumc.edu
Organization name Ohio State University
Street address 460 12th street
City Columbus
ZIP/Postal code 43212
Country USA
 
Platform ID GPL16956
Series (1)
GSE63614 Expression and Prognostic impact of LncRNAs in AML

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
ASHGA5P058197
ASHGA5P007773 8.627
ASHGA5P031162 7.361
ASHGA5P041796
ASHGA5P006930 8.45
ASHGA5P031496 8.485
ASHGA5P050699 9.7
ASHGA5P035298 6.353
ASHGA5P014867 4.823
ASHGA5P008172 7.486
ASHGA5P047663 5.674
ASHGA5P012016 11.079
ASHGA5P007747 7.124
ASHGA5P026943 6.339
ASHGA5P035562 5.714
ASHGA5P018786 9.034
ASHGA5P001180 7.231
ASHGA5P023786 4.87
ASHGA5P021269 6.706
ASHGA5P000239 9.087

Total number of rows: 58944

Table truncated, full table size 1121 Kbytes.




Supplementary file Size Download File type/resource
GSM1553708_PS90-0074.txt.gz 2.7 Mb (ftp)(http) TXT
Processed data included within Sample table

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