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Sample GSM1589638 Query DataSets for GSM1589638
Status Public on Jan 23, 2015
Title BA TNBC, TUM014
Sample type RNA
 
Source name Breast tumor sample from IHC defined Triple Negative subgroup
Organism Homo sapiens
Characteristics sample_group: TNBC
array_batch: B8
hybridation batch: H4
Growth protocol Tumor samples were obtained from patients treated at the hospital of Institut Curie (Biological Resource Center, Paris, France). Healthy samples were obtained from mammary plastic surgery. Cell lines were grown from the American Type Culture Collection (ATCC),
Extracted molecule total RNA
Extraction protocol Total RNA was extracted and purified from frozen tumor samples using the RNeasy Mini Kit (Qiagen) followed by the RNA clean up kit (Macherey Nagel), according to manufacturers’ instructions.
Label biotin
Label protocol Following RNA quality and quantity control, 2 µg of total RNA were amplified and labeled according to the Affymetrix one cycle synthesis target preparation protocol to hybridize Affymetrix U133 plus 2.0 chips, as described by the company.
 
Hybridization protocol standard Affymetrix protocol
Scan protocol standard Affymetrix protocol
Description Breast tumor sample from IHC defined Triple Negative subgroup
Data processing Data were analyzed using standard AffyCDF or Brainarray HGU133Plus2_Hs_ENTREZG version 13 custom chipset definition file. Data were normalized using GC-RMA. Batch and hybridization effects were corrected using a linear model in which they were treated as fixed effects. Samples with technical replicates were subsequently averaged.
 
Submission date Jan 22, 2015
Last update date Jan 23, 2015
Contact name Thierry Dubois
E-mail(s) thierry.dubois@curie.fr
Organization name Institut Curie
Department Recherche Center
Lab Breast Cancer Biology Group
Street address 26 rue d’Ulm
City PARIS
ZIP/Postal code 75005
Country France
 
Platform ID GPL14877
Series (2)
GSE65212 Expression profiling of breast cancer samples from Institut Curie (Maire cohort) -- BrainArray CDF
GSE65216 Expression profiling of breast cancer samples from Institut Curie (Maire cohort)
Relations
Reanalysis of GSM1588988

Data table header descriptions
ID_REF
VALUE log2 GCRMA signal from Brainarray Entrez V13 custom cdf

Data table
ID_REF VALUE
100009676_at 1.999782952
10000_at 4.574311784
10001_at 7.771176823
10002_at 2.514250596
10003_at 2.44934289
100048912_at 2.09225543
100049716_at 2.762490285
10004_at 2.204108431
10005_at 6.729542419
10006_at 10.39979144
10007_at 8.478956237
10008_at 2.633207584
100093630_at 10.09513692
10009_at 8.280048335
1000_at 2.491187756
100101938_at 1.877542255
10010_at 9.866187949
100113407_at 3.582941031
10011_at 6.679552836
100124700_at 9.744494108

Total number of rows: 18123

Table truncated, full table size 367 Kbytes.




Supplementary file Size Download File type/resource
GSM1589638_BC04_ARN0034_s2h1s1_U133p2.CEL.gz 4.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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