NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3501266 Query DataSets for GSM3501266
Status Public on Nov 24, 2019
Title Blood_MI_D30_Techn_Repl_of_hyb20783 [hyb18779]
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)
Description _Techn_Repl_of_hyb20783
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 9.226314241
TC01000002.hg.1 4.744224982
TC01000003.hg.1 3.793657554
TC01000004.hg.1 7.150402242
TC01000005.hg.1 16.62367671
TC01000006.hg.1 19.89363412
TC01000007.hg.1 19.74694455
TC01000008.hg.1 11.36903829
TC01000009.hg.1 4.575241546
TC01000010.hg.1 3.816419607
TC01000011.hg.1 7.271545008
TC01000012.hg.1 5.037484962
TC01000013.hg.1 14.52139027
TC01000014.hg.1 7.778417065
TC01000015.hg.1 7.095943572
TC01000016.hg.1 8.267827197
TC01000017.hg.1 4.922538484
TC01000018.hg.1 8.734197381
TC01000019.hg.1 5.466576062
TC01000020.hg.1 4.851187763

Total number of rows: 70523

Table truncated, full table size 1930 Kbytes.




Supplementary file Size Download File type/resource
GSM3501266_hyb18779_HTA-2_0_.CEL.gz 25.1 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap