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Sample GSM1326491 Query DataSets for GSM1326491
Status Public on Dec 05, 2014
Title Blood_control 5 [NC77]
Sample type RNA
 
Source name healthy control
Organism Homo sapiens
Characteristics tissue: peripheral blood mononuclear cells
Treatment protocol Integrity and concentration of RNA were assessed after RNA extraction and prior to sample labeling.
Extracted molecule total RNA
Extraction protocol Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.
Label cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS 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 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 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).
Description Healthy controls < 18 years
Data processing Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 20 out of 30 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

note from submitter: The raw file is the most original data received from the company, containing ~17000 probes.
 
Submission date Feb 12, 2014
Last update date Dec 05, 2014
Contact name Fuquan Zhang
E-mail(s) zfq99@hotmail.com
Organization name Wuxi mental health center
Street address 156 Qianrong Rd
City Wuxi
ZIP/Postal code 214151
Country China
 
Platform ID GPL15314
Series (2)
GSE54913 mRNA expression in blood of 18 schizophrenia patients and 12 healthy controls
GSE54914 Expression in blood of schizophrenia patients and healthy controls

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
ASHG19A3A052390 10.161705
ASHG19A3A005781 8.922645
ASHG19A3A002573 5.958003
ASHG19A3A052312 6.99111
ASHG19A3A029765 11.127772
ASHG19A3A025431 11.729772
ASHG19A3A002894 5.596753
ASHG19A3A026429 8.16423
ASHG19A3A046708 6.7169266
ASHG19A3A053958 7.2153983
ASHG19A3A025127 7.603654
ASHG19A3A013697 12.97505
ASHG19A3A052259 5.990026
ASHG19A3A006787 8.300914
ASHG19A3A003996 8.335469
ASHG19A3A002220 7.3687396
ASHG19A3A035805 7.0474243
ASHG19A3A004480 15.789798
ASHG19A3A012575 9.737331
ASHG19A3A029866 9.707254

Total number of rows: 17199

Table truncated, full table size 427 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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