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Sample GSM2677111 Query DataSets for GSM2677111
Status Public on Aug 16, 2018
Title Quadriceps-COPD-PC72
Sample type RNA
 
Source name Human quadriceps
Organism Homo sapiens
Characteristics disease state: COPD
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from quadriceps biopsies using the RNeasy fibrous tissue mini kit (Qiagen). RNA quality was determined by Bioanalyzer (Agilent), and samples with a RIN (RNA Integrity Number) <6 were excluded. RNA was prepared for whole transcriptome microarray analysis using the WT expression kit (Ambion).
Label biotin*
Label protocol For each sample, 200ng of total RNA was converted to cDNA using the Ambion Whole Transcript (WT) expression kit. The Affymetrix GeneChip WT Terminal Labelling Kit* was used to fragment and label 5.5µg of the prepared single-stranded cDNA.
 
Hybridization protocol Samples were hybridised to Affymetrix HuGene 1.1 ST 16- or 24-PEG array plates for 16 hours using the GeneTitan platform (Affymetrix Ltd.).
Scan protocol GeneChips were scanned using the GeneTitan platform (Affymetrix Ltd.).
Data processing Raw signal intensity data were RMA-treated, summarizing at the level of Transcript Clusters (TC) using Affymetrix Power Tools (APT, version 1.16.1). Technical batch effects were identified via Principal Variance Component Analysis (PVCA 1.6.0), and the data adjusted accordingly using ComBat (SVA 3.12.0). TC not forming part of the main array design, and universally low expressed TC were removed.
 
Submission date Jun 21, 2017
Last update date Nov 16, 2021
Contact name William Cookson
E-mail(s) w.cookson@imperial.ac.uk
Organization name Imperial College London
Street address Dovehouse Street
City London
ZIP/Postal code SW3 6LY
Country United Kingdom
 
Platform ID GPL11532
Series (1)
GSE100281 COPD is accompanied by coordinated transcriptional perturbation in the quadriceps affecting the mitochondria and ECM

Data table header descriptions
ID_REF
VALUE RMA normalised transcript cluster level expression values from Affymetrix Power Tools (APT, version 1.16.1).

Data table
ID_REF VALUE
7936596 7.91143499
8037331 5.951790989
8023672 4.644024731
8063337 4.300416773
7909064 3.255254978
8142899 4.837798801
8066925 5.000675088
8155525 4.123835282
8130916 6.937086087
7924893 5.895202859
8122933 5.016315301
7981215 3.961694816
7991296 3.398258051
8163000 4.747579553
8083223 4.881088638
8024708 4.975142875
7971653 4.780389555
7953351 5.086271775
7982574 3.885963319
8136161 2.337790703

Total number of rows: 18625

Table truncated, full table size 361 Kbytes.




Supplementary file Size Download File type/resource
GSM2677111_PC72_2.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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