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Sample GSM4423203 Query DataSets for GSM4423203
Status Public on Apr 06, 2020
Title Patient31_Pretreatment [FFP13.004058]
Sample type RNA
 
Source name Patientsample_brca_NCT00738777
Organism Homo sapiens
Characteristics subject status: breast cancer patient
subject id: Patient31
treatment: Pretreatment
tissue/sample type: FFPE tumor
batch: Batch TS
Treatment protocol Gene expression of primary breast cancers from patients before and after neo-adjuvant Tamoxifen treatment
FFPE sections of patient tumor material (10 x CF 5u gelcoat per sample) were sent to Agendia Inc.
Extracted molecule total RNA
Extraction protocol RNA was isolated using Qiagen RNeasy microkit according to manufacturer's specifications.
Label Cy3
Label protocol RNA was amplified and labeled using the lQuickAmp Labeling kit (Agilent).
 
Hybridization protocol 200 ng fluorescent labeled RNA was hybridized to custom Agilent arrays (4x44k arrays).
Scan protocol Agilent Technologies Scanner G2505B, Agilent Scan Control Version A.7.0.3.
Data processing Feature Extraction software v11.5.1.1 was used to quantify fluorescent intensities, custom script were used for raw data extraction and those values were normalized by 75th percentile normalisation using DataPrint software v1.15, all by Agendia Inc. Downstream data processing was subsequently done at the Netherlands Cancer Institute, by missing data impution with knn=10 and batch correction for date of RNA extraction using ComBat from the R package sva, using all available patient material from the trial (ClinicalTrials.gov Identifier: NCT00738777). Here we deposited samples used for the Tamoxifen focused analysis described in the cited paper.
 
Submission date Mar 20, 2020
Last update date Apr 07, 2020
Contact name Wilbert Zwart
E-mail(s) w.zwart@nki.nl
Organization name Netherlands Cancer Institute
Department Oncogenomics
Lab Zwart lab
Street address Plesmanlaan 121
City Amsterdam
State/province Noord-Holland
ZIP/Postal code 1066CX
Country Netherlands
 
Platform ID GPL28292
Series (1)
GSE147271 Gene expression of primary breast cancers from patients before and after neo-adjuvant Tamoxifen treatment

Data table header descriptions
ID_REF
VALUE DataPrint software (v1.15)-based normalized signal intensity

Data table
ID_REF VALUE
A_24_P685442 7.534947776
A_32_P95894 9.333618373
A_32_P76025 8.921469511
A_23_P139725 7.249125304
A_24_P316532 9.079322664
A_24_P195134 7.776906629
A_33_P3221613 8.31335486
A_24_P724989 7.609613032
A_32_P135906 7.18939274
A_33_P3333683 8.578418027
A_24_P913576 5.996803666
A_24_P877785 5.930192902
A_24_P938236 7.80671668
A_24_P705980 7.305632824
A_24_P528846 5.546669409
A_24_P937039 7.048179094
A_24_P101642 12.48126036
A_33_P3378435 7.027481042
A_24_P718223 8.05707587
A_24_P367439 8.189391357

Total number of rows: 31300

Table truncated, full table size 672 Kbytes.




Supplementary file Size Download File type/resource
GSM4423203_Agendia_FFP13-004058_32627_US22502555_253262710867_S01_1_4_SC_FullGenome+_v1.15.txt.gz 1.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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