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Sample GSM2397171 Query DataSets for GSM2397171
Status Public on Nov 01, 2017
Title 2S025_F_CAU_N_1_100
Sample type RNA
 
Channel 1
Source name Stratagene UHRR reference
Organism Homo sapiens
Characteristics control type: pool of human cell line RNA
Growth protocol Blood (30 ml) was drawn early in the day from subjects fasted for at least eight hours to minimize the signals associated with nutritional and diurnal cycles from the microarray data. Blood was processed within fifteen minutes of the time of blood draw. Eight milliliters were collected into a tube containing EDTA and a proprietary mixture of proteinase inhibitors (Becton, Dickinson and Co., Cockeysville, MD) to provide a sample of plasma for fructosamine assays. The balance (22 ml) of blood was collected into 3 x 7 -ml Na-EDTA Vacutainer tubes (Becton, Dickinson and Co., Cockeysville, MD). Whole blood was treated with ten volumes of carbonate-buffered 150 mM NH4Cl to lyse red blood cells; the remaining leukocytes were washed and concentrated by centrifugation.
Extracted molecule total RNA
Extraction protocol RNA wasrecovered from leukocytes using a modified one-step acid guanidinium thiocyanate-phenol-chloroform extraction (RNA-STAT60, Tel-Test, TX). RNA was subsequently post-purified using the RNeasy Mini-kit from Qiagen in accordance with the manufacturer’s instructions. RNA quantity, purity and integrity were assessed by spectrophotometry and microcapillary electrophoresis on an Agilent BioAnalyzer 2100. RNA isolation from samples was completed within two hours, exceeding the standards of the Consortium for Expression Profiles in Sepsis.
Label Cy-3
Label protocol 500 ng of total RNA were amplified and labeled with Cy3-CTP using the Agilent Low Input RNA amplification kit exactly as described by the manufacturer.
 
Channel 2
Source name Whole blood, mononuclear cell extract
Organism Homo sapiens
Characteristics tissue: blood
cell type: mononuclear
gender: F
ancestry: CAU
obstructive_cad: N
cad class: 1
cxcl5 rank: 100
bmi: 19.2042
diabetes: N
hyperlipid: Y
hypertension: Y
scan_date_id: 11-Mar
batchid: C
Growth protocol Blood (30 ml) was drawn early in the day from subjects fasted for at least eight hours to minimize the signals associated with nutritional and diurnal cycles from the microarray data. Blood was processed within fifteen minutes of the time of blood draw. Eight milliliters were collected into a tube containing EDTA and a proprietary mixture of proteinase inhibitors (Becton, Dickinson and Co., Cockeysville, MD) to provide a sample of plasma for fructosamine assays. The balance (22 ml) of blood was collected into 3 x 7 -ml Na-EDTA Vacutainer tubes (Becton, Dickinson and Co., Cockeysville, MD). Whole blood was treated with ten volumes of carbonate-buffered 150 mM NH4Cl to lyse red blood cells; the remaining leukocytes were washed and concentrated by centrifugation.
Extracted molecule total RNA
Extraction protocol RNA wasrecovered from leukocytes using a modified one-step acid guanidinium thiocyanate-phenol-chloroform extraction (RNA-STAT60, Tel-Test, TX). RNA was subsequently post-purified using the RNeasy Mini-kit from Qiagen in accordance with the manufacturer’s instructions. RNA quantity, purity and integrity were assessed by spectrophotometry and microcapillary electrophoresis on an Agilent BioAnalyzer 2100. RNA isolation from samples was completed within two hours, exceeding the standards of the Consortium for Expression Profiles in Sepsis.
Label Cy-5
Label protocol 500 ng of total RNA were amplified and labeled with Cy3-CTP using the Agilent Low Input RNA amplification kit exactly as described by the manufacturer.
 
 
Hybridization protocol Labeled subject cRNA was co-hybridized to Agilent G4112F Whole Human Genome 4x44K oligonucleotide arrays with equimolar amounts of Cyanine-3 labeled UHRR. Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.
Scan protocol Scanned on an Axon Instruments GenePix 4000b scanner.
Data processing The data from all arrays were first subjected to background correction and LOESS within-array normalization using Agilent Feature Extraction software (v9.5.1.1 Agilent).The log expression ratios produced during the normalization step are provided.
 
Submission date Nov 18, 2016
Last update date Nov 01, 2017
Contact name Jonathan C Schisler
E-mail(s) schisler@unc.edu
Phone 919-843-8708
Organization name The University of North Carolina at Chapel Hill
Department McAllister Heart Institute
Lab Schisler Lab
Street address MBRB, Rm 2340C
City Chapel Hill
State/province NC
ZIP/Postal code 27599-7126
Country USA
 
Platform ID GPL6480
Series (2)
GSE90074 Gene expression data from Phase 2 of the SAMARA study (Supporting a Multi-disciplinary Approach to Researching Atherosclerosis)
GSE90076 Clinical Evidence Supports a Protective Role for CXCL5 in Coronary Artery Disease Progression in the Elderly

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio (Cy5/Cy3) representing test/reference

Data table
ID_REF VALUE
GE_BrightCorner -0.2210101
DarkCorner 0.36851272
A_24_P66027 3.2861214
A_32_P77178 1.9094515
A_23_P212522 1.9113808
A_24_P934473 0.6579747
A_24_P9671 0.13174237
A_32_P29551 -1.6273899
A_24_P801451 -1.7911171
A_32_P30710 -0.23559862
A_32_P89523 0.09163521
A_24_P704878 0.62691826
A_32_P86028 -0.2835885
A_24_P470079 -1.2936091
A_23_P65830 -0.793869
A_23_P109143 -0.80353177
A_24_P595567 -1.8633536
A_24_P391591 -1.1759415
A_24_P799245 0.41518688
A_24_P932757 0.41672036

Total number of rows: 41093

Table truncated, full table size 941 Kbytes.




Supplementary file Size Download File type/resource
GSM2397171_2S025.txt.gz 14.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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