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Sample GSM3501417 Query DataSets for GSM3501417
Status Public on Nov 24, 2019
Title Blood_CAD_D0 [hyb21079]
Sample type RNA
 
Source name whole blood
Organism Homo sapiens
Characteristics tissue: whole blood
patient diagnosis: CAD
time point: D0
Growth protocol Whole blood RNA from peripheral blood of patients.
Extracted molecule total RNA
Extraction protocol Total RNA extraction using PAXgene Blood miRNA kit, followed by ethanol purification.
Label biotin
Label protocol 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChipTM WT PLUS Reagent Kit for GeneChipTM Whole Transcript Expression Arrays
 
Hybridization protocol A mixture of purified and fragmented biotinylated cDNA and hybridization controls (Affymetrix) was hybridized (16 hours at 45°C) on Affymetrix HTA 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s instructions.
Scan protocol Chips were scanned using a GeneChip® scanner 3000 (Affymetrix)
Data processing Raw data was preprocessed on the Affymetrix Expression Console 1.4.1.46 and normalized using Robust Multi-Array Average and Signal Space Transformation. Inter-array variability was adjusted by fitting a linear model. The normalized data was downstream analyzed using Bioconductor 3.1 for R version 3.2.2 3. A linear model was fit using the package limma 3.24.15 to determine differential expression between MI at the 2 different time points and stable controls.
 
Submission date Dec 04, 2018
Last update date Nov 26, 2019
Contact name Maarten Vanhaverbeke
E-mail(s) [email protected]
Organization name KU Leuven
Department Cardiovascular Sciences
Street address Herestraat 49 box 911
City Leuven
ZIP/Postal code 3000
Country Belgium
 
Platform ID GPL17586
Series (1)
GSE123342 Peripheral blood whole transcriptome in patients with acute myocardial infarction and at follow-up

Data table header descriptions
ID_REF
VALUE Quantile normalized gene level expression values from Affymetrix Expression Console 1.4.1.46 (RMA-SST).

Data table
ID_REF VALUE
TC01000001.hg.1 8.561507
TC01000002.hg.1 4.440625
TC01000003.hg.1 3.644421
TC01000004.hg.1 6.888317
TC01000005.hg.1 16.44756
TC01000006.hg.1 19.89325
TC01000007.hg.1 19.71406
TC01000008.hg.1 11.08108
TC01000009.hg.1 4.579463
TC01000010.hg.1 3.817069
TC01000011.hg.1 7.011175
TC01000012.hg.1 4.718987
TC01000013.hg.1 13.80418
TC01000014.hg.1 6.933007
TC01000015.hg.1 7.0973
TC01000016.hg.1 8.289421
TC01000017.hg.1 4.62499
TC01000018.hg.1 8.769156
TC01000019.hg.1 5.410207
TC01000020.hg.1 4.702932

Total number of rows: 70523

Table truncated, full table size 1724 Kbytes.




Supplementary file Size Download File type/resource
GSM3501417_hyb21079_HTA-2_0_.CEL.gz 25.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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