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Sample GSM699320 Query DataSets for GSM699320
Status Public on Dec 11, 2011
Title ALS11
Sample type RNA
 
Channel 1
Source name Lymphocytes definite sALS
Organism Homo sapiens
Characteristics de-identified research code: 03070801
age: 58
gender: Female
Treatment protocol Presence of disease (amyotrophic lateral sclerosis) compared to absence of disease (healthy control subjects with no presence of cancer, autoimmune disease or neurological disease)
Extracted molecule total RNA
Extraction protocol RNA isolation, quality control evaluation and microarray experiments were performed at Cogenics Inc. (Morrisville, NC). Total RNA was extracted from the cell samples at Cogenics Inc. (Morrisville, NC) using standard procedures: TRIzol extraction following manufacturer's instructions (Invitrogen Life Technologies Carlsbad, CA) and RNA purification using Rneasy Mini-kit (Qiagen, Valencia, CA).
quality control: The quantity of each of the total RNA samples (A260/280 ratio and yield) was determined by spectrophotometry and the size distribution (RIN) was assessed using an Agilent Bioanalyzer 2100.
Label Cy5
Label protocol Fifty nanograms of total RNA was converted into labeled cRNA with nucleotides coupled to a fluorescent dye (either Cy3 or Cy5) using the Quick Amp Kit (Agilent Technologies, Palo Alto, CA) following the manufacturer’s protocol.
 
Channel 2
Source name HC Reference pool HC1 to HC11
Organism Homo sapiens
Characteristics reference: HC Reference pool
Treatment protocol Presence of disease (amyotrophic lateral sclerosis) compared to absence of disease (healthy control subjects with no presence of cancer, autoimmune disease or neurological disease)
Extracted molecule total RNA
Extraction protocol RNA isolation, quality control evaluation and microarray experiments were performed at Cogenics Inc. (Morrisville, NC). Total RNA was extracted from the cell samples at Cogenics Inc. (Morrisville, NC) using standard procedures: TRIzol extraction following manufacturer's instructions (Invitrogen Life Technologies Carlsbad, CA) and RNA purification using Rneasy Mini-kit (Qiagen, Valencia, CA).
quality control: The quantity of each of the total RNA samples (A260/280 ratio and yield) was determined by spectrophotometry and the size distribution (RIN) was assessed using an Agilent Bioanalyzer 2100.
Label Cy3
Label protocol Fifty nanograms of total RNA was converted into labeled cRNA with nucleotides coupled to a fluorescent dye (either Cy3 or Cy5) using the Quick Amp Kit (Agilent Technologies, Palo Alto, CA) following the manufacturer’s protocol.
 
 
Hybridization protocol Equal amounts of Cy3 and Cy5-labeled cRNA (825 ng) from two different samples (test and reference pool) were hybridized to Agilent Human Whole Genome 4x44k Microarrays.
Scan protocol The hybridized arrays were washed and scanned using Agilent G2565BA scanner and data were extracted from the scanned image using Feature Extraction version 10.2 (Agilent Technologies).
Description Pooled RNA from HC1 to HC11 for cohybridization with Cy5 labelled RNA
patient samples: Lymphocytes were isolated from whole blood drawn by venipuncture into BD ACD tubes using the method described by Repnik et al. (2003) [PMID:12957415].
Data processing Conversion of raw data .txt files to .mev files, data normalization and filtering using the TM4 (MIDAS pipeline) were performed by the PI Jean-Luc Mougeot. Raw data .txt files in Agilent format were converted to .mev files using ExpressConverterTM v2.1 of the TM4 Microarray Suite (TIGR Genomics, Rockville, CA). Background-subtracted raw data were normalized using the MIDAS pipeline (TM4, TIGR Genomics, Rockville, MD) according to Sioson et al. (2006) [PMID: 16626497] with the following steps: total intensity normalization, LocFit (LOWESS), standard deviation regularization and low intensity trim. We generated two datasets for further analysis, DS3500 and DS7000 where both Cy3 and Cy5 integrated intensities (ISI) were above one (ISI=3500) or two (ISI=7000) standard deviation(s) of their respective background.
 
Submission date Mar 29, 2011
Last update date Dec 11, 2011
Contact name Jean-Luc C Mougeot
E-mail(s) jean-luc.mougeot@carolinas.org
Organization name Carolinas Medical Center
Department Internal Medicine
Street address 1542 Garden Terrace
City Charlotte
State/province NC
ZIP/Postal code 28232-2861
Country USA
 
Platform ID GPL4133
Series (1)
GSE28253 Peripheral blood lymphocytes: ALS patients vs. healthy controls

Data table header descriptions
ID_REF
VALUE normalized log10 ratio Cy5/Cy3

Data table
ID_REF VALUE
1 -5.402640109e-001
2 0.000000000e+000
3 0.000000000e+000
4 0.000000000e+000
5 0.000000000e+000
6 0.000000000e+000
7 4.250404888e-001
8 0.000000000e+000
9 0.000000000e+000
10 0.000000000e+000
11 0.000000000e+000
12 -5.265537701e-001
13 0.000000000e+000
14 -1.458731416e-001
15 0.000000000e+000
16 -1.319621220e-001
17 0.000000000e+000
18 -2.033316002e-001
19 1.877519816e-001
20 -5.520355254e-002

Total number of rows: 45015

Table truncated, full table size 1019 Kbytes.




Supplementary file Size Download File type/resource
GSM699320.txt.gz 15.4 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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