|
| Status |
Public on Jan 21, 2014 |
| Title |
BreastCancer_S003 |
| Sample type |
RNA |
| |
|
| Source name |
breast cancer
|
| Organism |
Homo sapiens |
| Characteristics |
centerid: 40
patid: 171
size_dissected_area: 4
percentage_tumor_cells: 60
cell_number_dissected: 1500
inflammatory_cells [%]: 10
invasive_tumor_area_size1 [mm]: 2
invasive_tumor_area_size2 [mm]: 7
invasive_tumor_cells [%]: 80
invasive_tumor_grade: 2
necrotic_cells [%]: 0
normal_epithelial_cells [%]: 0
preneoplastic_tumor_cells [%]: 0
stroma_cells [%]: 10
bgus.ct: 32.3
er.ct: 34.03
her2.ct: 28.16
pr.ct: 0
race: Caucasian
er: ER-
pr: PR-
her2: HER2+
arm: HER2+ CT
treatment: neoadjuvant doxorubicin/paclitaxel (AT) followed by cyclophosphamide/methotrexate/fluorouracil (CMF)
age: 58
ecog: 1
inflammatory.brca: yes
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 |
