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Sample GSM1589079 Query DataSets for GSM1589079
Status Public on Jan 23, 2015
Title Luminal A, TUM087
Sample type RNA
 
Source name Breast tumor sample from IHC defined Luminal A subgroup
Organism Homo sapiens
Characteristics sample_group: Luminal A
array_batch: B3
hybridation batch: H2
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 Luminal A 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 GPL570
Series (2)
GSE65194 Expression profiling of breast cancer samples from Institut Curie (Maire cohort) --Affy CDF
GSE65216 Expression profiling of breast cancer samples from Institut Curie (Maire cohort)
Relations
Reanalyzed by GSM1589729

Data table header descriptions
ID_REF
VALUE log2 GCRMA signal from Affy cdf

Data table
ID_REF VALUE
1007_s_at 9.83566855341631
1053_at 6.67888852850431
117_at 6.13448759973189
121_at 2.62262576508358
1255_g_at 2.04190236889784
1294_at 7.39462317135212
1316_at 3.20680467718279
1320_at 2.62957654712843
1405_i_at 8.75712337928006
1431_at 2.81284032043818
1438_at 4.73809409160379
1487_at 6.07702713828459
1494_f_at 2.0648064005981
1552256_a_at 8.89606612418024
1552257_a_at 9.44551770376849
1552258_at 3.3524991187088
1552261_at 2.50874329461654
1552263_at 4.13482929862244
1552264_a_at 6.38114080882452
1552266_at 3.37861559296528

Total number of rows: 54673

Table truncated, full table size 1479 Kbytes.




Supplementary file Size Download File type/resource
GSM1589079_BC16_ARN0086_s1h1s1_U133p2.CEL.gz 4.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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