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Sample GSM2143745 Query DataSets for GSM2143745
Status Public on Aug 31, 2016
Title KET6 Pre
Sample type RNA
 
Channel 1
Source name KET Pre Tx Responder
Organism Homo sapiens
Characteristics disease state: MDD
individual: KET6
treatment: KET
time: pre-treatment
response: responder
tissue: blood
Treatment protocol Patients were either treated with electroconvulsive therapy or ketamine infusions.
Growth protocol Not applicable.
Extracted molecule total RNA
Extraction protocol RNA extracted using manufacturer's intstruction.
Label Hy3
Label protocol 400 ng total RNA from both sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit (Exiqon, Denmark) following the procedure described by the manufacturer. This project was run with a dual colour setup and LOWES normalization so the reference RNA comprised a pool of RNA containing all samples in equal amounts.
 
Channel 2
Source name Reference
Organism Homo sapiens
Characteristics reference composition: a pool of RNA containing all samples in equal amounts
Treatment protocol Patients were either treated with electroconvulsive therapy or ketamine infusions.
Growth protocol Not applicable.
Extracted molecule total RNA
Extraction protocol RNA extracted using manufacturer's intstruction.
Label Hy5
Label protocol 400 ng total RNA from both sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit (Exiqon, Denmark) following the procedure described by the manufacturer. This project was run with a dual colour setup and LOWES normalization so the reference RNA comprised a pool of RNA containing all samples in equal amounts.
 
 
Hybridization protocol The hybridization was performed according to the miRCURY LNA™ microRNA Array Instruction manual using a Tecan HS4800™ hybridization station (Tecan, Austria).
Scan protocol The miRCURY LNA™ microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene® 9 (miRCURY LNA™ microRNA Array Analysis Software, Exiqon, Denmark).
Description Hy3: 1_Exiqon_K6PRE.txt
Hy5: 0_Exiqon_K6PRE.txt
Baseline Responder
Data processing The quantified signals were background corrected (Normexp with offset value 10) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.
 
Submission date May 05, 2016
Last update date Aug 31, 2016
Contact name Anand Gururajan
Organization name University College Cork
Department Anatomy & Neuroscience
Street address Western Road
City Cork
ZIP/Postal code NA
Country Ireland
 
Platform ID GPL21814
Series (1)
GSE81152 MicroRNAs as diagnostic biomarkers for major depression

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (Cy5/Cy3)

Data table
ID_REF VALUE
42638 -0.100
17519 -0.169
46507 -0.633
17928 -0.809
11134 -0.254
42812 -0.113
42918 0.294
42516 0.514
46752 0.675
46427 1.422
11052 0.037
42696 1.457
42754 0.360
42818 -0.067
42810 1.052
42591 0.307
17585 0.159
42848 0.867
17506 -0.225
42795 -0.362

Total number of rows: 2087

Table truncated, full table size 26 Kbytes.




Supplementary file Size Download File type/resource
GSM2143745_0_Exiqon_K6PRE.txt.gz 1.3 Mb (ftp)(http) TXT
GSM2143745_1_Exiqon_K6PRE.txt.gz 1.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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