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Sample GSM5470675 Query DataSets for GSM5470675
Status Public on Jul 28, 2021
Title SAMPLE 40_B64_GI_C
Sample type RNA
 
Source name breast
Organism Homo sapiens
Characteristics age: 40
Stage: IIA
tissue type: frozen tumor tissue
Extracted molecule total RNA
Extraction protocol Nucleic acids were extracted from frozen tumor tissue (pre-NAT samples) using AllPrep DNA/RNA mini kit (Qiagen France SAS, Courtaboeuf, France) according to the manufacturer’s protocol.
Label Cy3
Label protocol not provided
 
Hybridization protocol The extracted material was sent to Helixio (Saint-Beauzire, France), where it was hybridized with gene arrays (Human SurePrint, Agilent Technologies France, Les Ullis, France)
Scan protocol not provided
Data processing Limma package was applied to process Agilent microarray data and identify differentially expressed genes between progressive tumors and tumors with pathological complete response. Background correction was performed on expression intensities before normalization by the parameter of “expnorm”. Median value was taken when a gene has multiple probes. Then, “cyclicloess” method, which applies loess normalization to all possible pairs of arrays, was used to normalize corrected intensities. The probes have been filtered for those close to background and without gene name.
 
Submission date Jul 25, 2021
Last update date Jul 28, 2021
Contact name Yingjie Zhu
Organization name Memorial Sloan Kettering Cancer Center
Street address 1275 York Avenue
City New York
State/province NY
ZIP/Postal code 10065
Country USA
 
Platform ID GPL13607
Series (1)
GSE180775 Recurrence biomarkers of triple negative breast cancer treated with neoadjuvant chemotherapy combined with anti-EGFR antibodies [Agilent]

Data table header descriptions
ID_REF
VALUE normalized

Data table
ID_REF VALUE
10 5.04352051
101 9.503184799
102 4.670819382
104 6.147198853
105 7.707446222
106 4.869213351
108 5.332404594
109 8.008502105
114 8.291924635
115 6.758719487
116 5.344915316
117 7.418579547
12 10.5480657
120 8.576359121
121 11.94523465
122 6.64552855
123 8.101614116
124 9.366687029
126 5.828488956
127 9.433954835

Total number of rows: 37133

Table truncated, full table size 642 Kbytes.




Supplementary file Size Download File type/resource
GSM5470675_B64_GI_C.txt.gz 12.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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