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Sample GSM1233142 Query DataSets for GSM1233142
Status Public on Jan 21, 2014
Title BreastCancer_S263
Sample type RNA
 
Source name breast cancer
Organism Homo sapiens
Characteristics centerid: 26
patid: 721
size_dissected_area: 7
percentage_tumor_cells: 80
cell_number_dissected: 3400
inflammatory_cells [%]: 10
invasive_tumor_area_size1 [mm]: 8
invasive_tumor_area_size2 [mm]: 2
invasive_tumor_cells [%]: 50
invasive_tumor_grade: 3
necrotic_cells [%]: 30
normal_epithelial_cells [%]: 0
preneoplastic_tumor_cells [%]: 0
stroma_cells [%]: 10
bgus.ct: 29.62
er.ct: 32.26
her2.ct: 28.45
pr.ct: 45.63
race: Caucasian
er: ER-
pr: PR-
her2: HER2-
arm: HER2- CT
treatment: neoadjuvant doxorubicin/paclitaxel (AT) followed by cyclophosphamide/methotrexate/fluorouracil (CMF)
age: 38
ecog: 0
inflammatory.brca: no
menopausal.status: pre
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 6.546995681
1053_at 1.709130006
117_at 4.746481645
121_at 4.860366128
1255_g_at 2.106369445
1294_at 5.447744214
1316_at 4.156642239
1320_at 3.707534983
1405_i_at 2.340337094
1431_at 2.142244258
1438_at 4.167944054
1487_at 5.611381295
1494_f_at 3.022570771
1552256_a_at 3.388463267
1552257_a_at 4.611334837
1552258_at 3.051837043
1552261_at 3.320037264
1552263_at 2.775939965
1552264_a_at 4.668708945
1552266_at 1.937857142

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM1233142_CJL263_20081021.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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