NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1589113 Query DataSets for GSM1589113
Status Public on Jan 23, 2015
Title Luminal B, TUM115
Sample type RNA
 
Source name Breast tumor sample from IHC defined Luminal B subgroup
Organism Homo sapiens
Characteristics sample_group: Luminal B
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 B 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 GSM1589757

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

Data table
ID_REF VALUE
1007_s_at 9.66703752154192
1053_at 7.62965286515934
117_at 7.89240879444536
121_at 2.59424898395986
1255_g_at 2.04639606892669
1294_at 7.93732336729213
1316_at 3.2859085275513
1320_at 2.59025016791557
1405_i_at 11.0851825723758
1431_at 2.68572368794558
1438_at 2.78137965696358
1487_at 6.34941902719978
1494_f_at 2.06941505379247
1552256_a_at 8.49903751537409
1552257_a_at 9.72132443112874
1552258_at 3.51727645437604
1552261_at 2.51296642484675
1552263_at 4.20706677566516
1552264_a_at 5.96973224966055
1552266_at 3.40842277220167

Total number of rows: 54673

Table truncated, full table size 1479 Kbytes.




Supplementary file Size Download File type/resource
GSM1589113_BC16_ARN0088_s1h1s1_U133p2.CEL.gz 4.6 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap