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Sample GSM3501373 Query DataSets for GSM3501373
Status Public on Nov 24, 2019
Title Blood_MI_D30 [hyb20835]
Sample type RNA
 
Source name whole blood
Organism Homo sapiens
Characteristics tissue: whole blood
patient diagnosis: MI
time point: D30
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 6.717653
TC01000002.hg.1 4.665569
TC01000003.hg.1 3.810682
TC01000004.hg.1 6.330074
TC01000005.hg.1 15.97069
TC01000006.hg.1 19.87094
TC01000007.hg.1 19.42079
TC01000008.hg.1 11.58028
TC01000009.hg.1 4.274693
TC01000010.hg.1 4.022885
TC01000011.hg.1 7.561451
TC01000012.hg.1 5.355019
TC01000013.hg.1 15.63182
TC01000014.hg.1 6.661447
TC01000015.hg.1 6.858894
TC01000016.hg.1 7.782972
TC01000017.hg.1 4.697192
TC01000018.hg.1 9.246965
TC01000019.hg.1 5.463306
TC01000020.hg.1 4.821276

Total number of rows: 70523

Table truncated, full table size 1724 Kbytes.




Supplementary file Size Download File type/resource
GSM3501373_hyb20835_HTA-2_0_.CEL.gz 23.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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