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Sample GSM1431142 Query DataSets for GSM1431142
Status Public on Apr 14, 2015
Title PC9 AZD9291 resistant_2
Sample type genomic
 
Channel 1
Source name PC9 cell line resistant to AZD9291
Organism Homo sapiens
Characteristics cell line: PC9
population: resistant to AZD9291
treatment: AZD9291 (160nM), dose escalation
Treatment protocol Cells were harvested when they had grown to 80% confluency. The cells were washed once in 10mls of PBS and then pelleted at 1000rpm for 5 minutes. The supernatant was removed and the cell pellet frozen at -80oC until DNA preparation was performed.
Growth protocol Resistant cell populations were cultured in RPMI, 10% FCS, 2mM L-glutamine supplemented with the indicated EGFR inhibitor. Parental cells were cultured in RPMI, 10% FCS, 2mM L-glutamine.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was prepared from the cell pellets using the Allprep DNA/RNA/miRNA Universal kit (Qiagen, Valencia, CA)
Label Cy3
Label protocol Genomic DNA extracted from experimental (cell lines) and normal control female gDNA (Promega, Madison, WI) samples was labeled using CytoSure HT Genomic DNA Labelling Kit (Oxford Gene Technology, Oxfordshire, UK) following the OGT protocol for aCGH analysis with an adjustment to the post purification step. After labelled targets were combined in one tube, an additional 2 μl of water was added and directly proceeded to hybridization.
 
Channel 2
Source name normal female gDNA, Promega
Organism Homo sapiens
Characteristics gender: female
phenotype: normal
Treatment protocol Cells were harvested when they had grown to 80% confluency. The cells were washed once in 10mls of PBS and then pelleted at 1000rpm for 5 minutes. The supernatant was removed and the cell pellet frozen at -80oC until DNA preparation was performed.
Growth protocol Resistant cell populations were cultured in RPMI, 10% FCS, 2mM L-glutamine supplemented with the indicated EGFR inhibitor. Parental cells were cultured in RPMI, 10% FCS, 2mM L-glutamine.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was prepared from the cell pellets using the Allprep DNA/RNA/miRNA Universal kit (Qiagen, Valencia, CA)
Label Cy5
Label protocol Genomic DNA extracted from experimental (cell lines) and normal control female gDNA (Promega, Madison, WI) samples was labeled using CytoSure HT Genomic DNA Labelling Kit (Oxford Gene Technology, Oxfordshire, UK) following the OGT protocol for aCGH analysis with an adjustment to the post purification step. After labelled targets were combined in one tube, an additional 2 μl of water was added and directly proceeded to hybridization.
 
 
Hybridization protocol The hybridization master mix was prepared by mixing 25 μl of Cot-1 (1mg/ml), 26 μl or Agilent 1-x Blocking Agent and 130 μl of Aligent 2x HiRPM Hybridization Buffer. The master mix was mixed with labeled experimental and control DNA and hybridized to the Agilent Human Genome CGH 2x400k Miscoarray (Agilent Technologies, Santa Clara, CA). The arrays were incubated for 40 hours at 65°C in a rotating oven at 20 rpm. After hybridization slides were washed as stated in the protocol.
Scan protocol All hybridized arrays were scanned on an Agilent G2505B scanner.
Description Populations of PC9 cells resistant to AZD9291 (160 nM)
Data processing Images were analized using Agilent Feature Extraction Software (version 10.7.3.1). Nexus Copy Number software v7.0 was used for data processing and visualization. Log2 ratio for each gene was calculated as mean of log2 values of all probes mapped to a particular gene.
 
Submission date Jul 09, 2014
Last update date Apr 15, 2015
Contact name Aleksandra Markovets
Organization name AstraZeneca
Department Oncology, iMED
Lab Bioinformatics
Street address 35 Gatehouse Dr.
City Waltham
State/province Massachusetts
ZIP/Postal code 02451
Country USA
 
Platform ID GPL9777
Series (1)
GSE59239 Acquired resistance to mutant-selective EGFR inhibitor AZD9291 is associated with increased dependence on RAS signaling

Data table header descriptions
ID_REF
VALUE Log2 ratio values represent experimental/control (Cy3/Cy5) values.

Data table
ID_REF VALUE
4 0.053709236
5 0.034337045
6 0.231291768
7 0.088553001
8 0.038378516
9 -0.007834016
10 -0.027320818
11 -0.155878247
12 -0.092835876
13 0.187860043
14 0.205737573
15 -0.183819373
16 -0.087748328
17 -0.00926588
18 0.077193062
19 -0.059578665
20 0.245868303
21 0.329945584
22 0.067229732
23 -0.016991586

Total number of rows: 415056

Table truncated, full table size 7758 Kbytes.




Supplementary file Size Download File type/resource
GSM1431142_PC9_AZDR_2.txt.gz 117.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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