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Sample GSM1942401 Query DataSets for GSM1942401
Status Public on Jul 31, 2016
Title 253949423924_1_2
Sample type RNA
 
Source name S1057-00026 R1
Organism Homo sapiens
Characteristics patientid: 18
tumor type: Breast
primary/metastatic biopsy: Primary
biopsy site: Left breast
best response: SD
rnaqc_pass: Pass
Treatment protocol 27 pre-treatment FFPE biopsy samples from 16 unique patients in our MK2206 phase 1b trial collected and sent for gene expression profiling.
Extracted molecule total RNA
Extraction protocol RNA extraction was performed by Almac Diagnostics. RNA was isolated using the Ambion RecoverAll Extraction Kit using an optimised Almac procedure.
Label Cy3
Label protocol RNA labeling and hybridization was performed by LabCorp. Extracted RNA was labeled using the Sigma WTA kit and Agilent tag labeling protocol as per manufacturer's instruction.
 
Hybridization protocol Cy3-labeled cRNA was hybridized to Agilent HD arrays containing ~60K probes (Agilent-039494) as per manufacturer's protocol.
Scan protocol Slides were scanned after washing on Agilent DNA Microarray scanner (G2505C) using one color scan setting
Description Gene expression from patient sample in MK2206 phase 1b study
Data processing For each array, the green channel mean (gMean) signal was log2-tranformed and centered within array to its 75th quantile as per manufacturer’s data processing recommendations. A fixed value of 9.5 was then added to avoid negative values
 
Submission date Nov 17, 2015
Last update date Apr 23, 2018
Contact name Christina Yau
E-mail(s) cyau@buckinstitute.org
Phone 415-209-2248
Organization name Buck Institute of Age Research
Lab Benz Lab
Street address 8001 Redwood Blvd
City Novato
State/province CA
ZIP/Postal code 94945
Country USA
 
Platform ID GPL16699
Series (1)
GSE75087 A phase 1b study of the Akt-inhibitor MK-2206 in combination with weekly paclitaxel and trastuzumab in patients with advanced HER2-overexpressing solid tumor malignancies
Relations
Reanalyzed by GSE113533

Data table header descriptions
ID_REF
VALUE Normalized gMean Signal

Data table
ID_REF VALUE
1 13.37931987
2 5.459819742
3 5.2996548
4 10.98879003
5 6.557880221
6 5.726170604
7 11.076647
8 6.036378736
9 14.93071272
10 5.652952598
11 7.793546831
12 8.739091028
13 7.547517339
14 8.627711343
15 5.404041172
16 6.53499532
17 11.1554347
18 7.699596582
19 12.56771058
20 9.642852101

Total number of rows: 62976

Table truncated, full table size 1089 Kbytes.




Supplementary file Size Download File type/resource
GSM1942401_US23502419_253949423924_S01_GE1_107_Sep09_1_2.txt.gz 12.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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