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Sample GSM2677138 Query DataSets for GSM2677138
Status Public on Aug 16, 2018
Title Quadriceps-Healthy-PH8
Sample type RNA
 
Source name Human quadriceps
Organism Homo sapiens
Characteristics disease state: Healthy
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 7.72350369
8037331 5.898190084
8023672 4.539664303
8063337 4.251380996
7909064 2.749629678
8142899 5.454793161
8066925 5.533188905
8155525 4.654766964
8130916 7.074209949
7924893 4.868233169
8122933 4.47080117
7981215 4.150266678
7991296 2.832831783
8163000 4.16678087
8083223 4.61056864
8024708 4.203958557
7971653 5.039134971
7953351 5.7251225
7982574 3.844079118
8136161 2.676073518

Total number of rows: 18625

Table truncated, full table size 361 Kbytes.




Supplementary file Size Download File type/resource
GSM2677138_PH8_Healthy.CEL.gz 3.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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