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Sample GSM1233131 Query DataSets for GSM1233131
Status Public on Jan 21, 2014
Title BreastCancer_S251
Sample type RNA
 
Source name breast cancer
Organism Homo sapiens
Characteristics centerid: 26
patid: 451
size_dissected_area: 5
percentage_tumor_cells: 60
cell_number_dissected: 1800
inflammatory_cells [%]: 20
invasive_tumor_area_size1 [mm]: 7
invasive_tumor_area_size2 [mm]: 1
invasive_tumor_cells [%]: 40
invasive_tumor_grade: 3
necrotic_cells [%]: 0
normal_epithelial_cells [%]: 0
preneoplastic_tumor_cells [%]: 0
stroma_cells [%]: 40
bgus.ct: 31.56
er.ct: 32.33
her2.ct: 26.84
pr.ct: 46.06
race: Caucasian
er: ER-
pr: PR-
her2: HER2-
arm: HER2- CT
treatment: neoadjuvant doxorubicin/paclitaxel (AT) followed by cyclophosphamide/methotrexate/fluorouracil (CMF)
age: 57
ecog: 0
inflammatory.brca: no
menopausal.status: post
pcr: RD
Extracted molecule total RNA
Extraction protocol Formalin-fixed, paraffin-embedded (FFPE) core biopsies were prospectively collected prior to treatment. The yield and purity of RNA was determined using a NanoDrop 1000 Spectrophotometer (Thermo Scientific). RNA integrity was measured using a Bioanalyzer (Agilent Technologies) with either the RNA Nano or Pico Kit, depending on sample concentration. The RNA Integrity Number (RIN) and average length of the RNA were used for sample characterization. mRNA integrity was measured using a semiquantitative reverse transcription-polymerase chain reaction assay (rtPCR). This assay is based on quantitative amplification of 5'- and 3'-end sequences of the housekeeping gene β-actin. Calculating the ratio of 3' to 5' amplicons allows for assessment of mRNA integrity: intact RNA transcripts exhibit a ratio of 1, while degraded RNA increases the ratio.
Label biotin
Label protocol A Transcriptor First Strand cDNA Synthesis Kit (Roche) was used to prepare cDNA from 100 ng of total RNA, using an anchored oligo(dT)-primer followed by a subsequent amplification step with the SYBR Green I Master on a LightCycler® 480 instrument (Roche Applied Science). Formalin-fixed paraffin-embedded tumor (FFPET)-derived RNA was amplified with the WT-Ovation™ FFPE System V2 (NuGEN). Biotin labeling of the cDNA was performed using the FL-Ovation cDNA Biotin Module V2 (NuGEN).
 
Hybridization protocol Hybridization of labeled probes on the Affymetrix GeneChip Human Genome U133 Plus 2.0 Array were conducted using the GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix).
Scan protocol For this workflow a GeneChip Fluidics Station 450 and a GeneChip Scanner 3000 7G were used
Data processing R (3.0.1) & Bioconductor (2.20.1)
 
Submission date Sep 17, 2013
Last update date Jun 06, 2022
Contact name Anton Belousov
Organization name Roche
Department NCS-TTB
Lab TTB Biostatistics
Street address Nonnenwald 2
City Penzberg
ZIP/Postal code 82377
Country Germany
 
Platform ID GPL570
Series (1)
GSE50948 Expression Data from transNOAH breast cancer trial
Relations
Reanalyzed by GSE205568

Data table header descriptions
ID_REF
VALUE RMA expression (on log2 scale)

Data table
ID_REF VALUE
1007_s_at 6.26953872
1053_at 1.523351667
117_at 5.026751782
121_at 4.716252526
1255_g_at 2.47927161
1294_at 5.764349626
1316_at 4.292973885
1320_at 3.689351536
1405_i_at 2.206018072
1431_at 2.59906682
1438_at 3.35638892
1487_at 5.52028357
1494_f_at 3.315635574
1552256_a_at 3.343445546
1552257_a_at 5.203592362
1552258_at 2.950748703
1552261_at 3.42190125
1552263_at 2.658627141
1552264_a_at 4.50462266
1552266_at 1.952259194

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM1233131_CJL251_20081021.CEL.gz 3.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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