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Sample GSM1589772 Query DataSets for GSM1589772
Status Public on Jan 23, 2015
Title BA Luminal B, TUM130
Sample type RNA
 
Source name Breast tumor sample from IHC defined Luminal B subgroup
Organism Homo sapiens
Characteristics sample_group: Luminal B
array_batch: B4
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 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 Jun 18, 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 GSM1589128
Reanalyzed by GSM1715286

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

Data table
ID_REF VALUE
100009676_at 2.006088836
10000_at 2.550107759
10001_at 9.342358095
10002_at 2.55748508
10003_at 2.450377874
100048912_at 2.119492761
100049716_at 2.814072089
10004_at 2.19350877
10005_at 7.494340271
10006_at 10.25773408
10007_at 10.03666215
10008_at 2.667268192
100093630_at 10.28359684
10009_at 7.826011309
1000_at 2.343216249
100101938_at 1.899682485
10010_at 8.385222773
100113407_at 4.128716263
10011_at 8.883870614
100124700_at 6.596043301

Total number of rows: 18123

Table truncated, full table size 367 Kbytes.




Supplementary file Size Download File type/resource
GSM1589772_BC16_ARN0100_s1h1s1_U133p2.CEL.gz 4.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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