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Sample GSM5470650 Query DataSets for GSM5470650
Status Public on Jul 28, 2021
Title SAMPLE 15_E55_CON_BE
Sample type RNA
 
Source name breast
Organism Homo sapiens
Characteristics age: 53
Stage: IIB
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 5.140013979
101 8.693568048
102 5.056983869
104 7.11586538
105 7.445090485
106 4.691302762
108 4.580721867
109 9.070548365
114 8.347209408
115 7.323749163
116 5.220592173
117 7.526840579
12 9.059309134
120 7.650058525
121 11.32334551
122 4.433234817
123 8.030334934
124 10.10683341
126 5.731350297
127 10.40059211

Total number of rows: 37133

Table truncated, full table size 642 Kbytes.




Supplementary file Size Download File type/resource
GSM5470650_E55_CON_BE.txt.gz 12.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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