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Series GSE110184 Query DataSets for GSE110184
Status Public on Jul 18, 2019
Title Epigenetic profiling of docetaxel resistance in Breast Cancer
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary Illumina Infinium MethylationEPIC Beadchip was used to obtain DNA methylation profiles across 850000 CpGsites in nine different breast cancer PDX models. Docetaxel resistant and residual disease PDX models were also analyzed
Overall design DNA was isoleted from frozen tumors of different TNBC PDX models sensitive to docetaxel and from docetaxel resistant-derived TNBC PDX models. DNA was quanitifed by Quant-iT PicoGreen dsDNA Reagent (Invitrogen) and the integrity was analyzed in a 1.3% agarose gel. Bisulfite conversion of 600ng of each sample was performed according to the manufacturer’s recommendation for Illumina Infinium Assay. Effective bisulphite conversion was checked for the threecontrols that were converted simultaneously with the samples.4ul of bisulfite converted DNA were used to hybridize on Infinium MethylationEPIC BeadChip, following Illumina Infinium HD Methylation protocol. Chip analysis was performed using Illumina HiScan SQ fluorescent scanner. The intesities of the images were extracted with Minfi in Rstudio. Methylation score of each CpG is represented as beta value
Contributor(s) Calleja-Cervantes ME, Gómez-Miragaya J, González-Suárez E
Citation(s) 31320385
Submission date Feb 06, 2018
Last update date Jul 30, 2019
Contact name Sebastian Moran
Organization name IDIBELL
Department PEBC
Street address Av. Gran Via de l'Hospitalet, 199-203
City L'Hospitalet del Llobregat
State/province Barcelona
ZIP/Postal code 08908
Country Spain
Platforms (2)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
GPL21145 Infinium MethylationEPIC
Samples (70)
GSM2981836 tumor from IDB-01 TNBC PDX model sensitive to docetaxel (24_11_39)
GSM2981837 tumor from IDB-01 TNBC PDX model sensitive to docetaxel (24_11_40)
GSM2981838 tumor from IDB-01 TNBC PDX model resistant to docetaxel (Q24_11_39)
BioProject PRJNA433090

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE110184_AverageBeta_DetectionP-value_SignalA_SignalB_GPL13534.txt.gz 130.8 Mb (ftp)(http) TXT
GSE110184_Matrix_processed_GPL21145.csv.gz 485.7 Mb (ftp)(http) CSV
GSE110184_Matrix_signal_intensities_GPL21145.csv.gz 343.1 Mb (ftp)(http) CSV
GSE110184_RAW.tar 1.0 Gb (http)(custom) TAR (of IDAT)
SRA Run SelectorHelp
Raw data are available on Series record
Processed data included within Sample table
Processed data are available on Series record
Raw data provided as supplementary file

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