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Sample GSM1589022 Query DataSets for GSM1589022
Status Public on Jan 23, 2015
Title Her2, TUM038_repA
Sample type RNA
 
Source name Breast tumor sample from IHC defined Er- Her2+ subgroup
Organism Homo sapiens
Characteristics sample_group: Her2
array_batch: B3
hybridation batch: H1
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 Er- Her2+ 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 GSM1589672

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

Data table
ID_REF VALUE
1007_s_at 9.84934929500708
1053_at 8.14984464476648
117_at 6.08183320868264
121_at 2.72262599788981
1255_g_at 2.05439911296101
1294_at 7.03473359321655
1316_at 3.40733007464413
1320_at 2.57074860534317
1405_i_at 9.65579755506194
1431_at 2.66158293594429
1438_at 4.73812294937076
1487_at 6.75523131786094
1494_f_at 2.09839045192024
1552256_a_at 9.0636870152458
1552257_a_at 8.10394340281523
1552258_at 3.53876199482673
1552261_at 2.51730269376789
1552263_at 4.57407864600439
1552264_a_at 7.10967471848614
1552266_at 3.34789224830452

Total number of rows: 54673

Table truncated, full table size 1479 Kbytes.




Supplementary file Size Download File type/resource
GSM1589022_BC16_ARN0077_s1h1s1_U133p2.CEL.gz 4.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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