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Sample GSM1942410 Query DataSets for GSM1942410
Status Public on Jul 31, 2016
Title 253949423925_2_4
Sample type RNA
Source name S1057-00024 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
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
Reanalyzed by GSE113533

Data table header descriptions
VALUE Normalized gMean Signal

Data table
1 13.40315271
2 5.284635626
3 5.330378014
4 11.53730319
5 6.89530111
6 5.699082692
7 11.15274319
8 5.902000323
9 14.61599532
10 6.732834005
11 8.179369955
12 10.59477855
13 7.803034678
14 9.127200114
15 5.338065635
16 5.870128701
17 10.7559667
18 8.144108491
19 12.75673155
20 10.39757463

Total number of rows: 62976

Table truncated, full table size 1089 Kbytes.

Supplementary file Size Download File type/resource
GSM1942410_US23502419_253949423925_S01_GE1_107_Sep09_2_4.txt.gz 12.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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