NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1431146 Query DataSets for GSM1431146
Status Public on Apr 14, 2015
Title PC9 gefitinib resistant_1
Sample type genomic
 
Channel 1
Source name PC9 cell line resistant to gefitinib
Organism Homo sapiens
Characteristics cell line: PC9
population: resistant to gefitinib
treatment: Gefitinib (1.5 uM), 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 gefitinib (1.5 uM)
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 0.063124494
5 -0.016030047
6 0.203326629
7 0.082067689
8 -0.008065053
9 -0.028977927
10 -0.043307247
11 -0.227014756
12 -0.000224861
13 0.138817763
14 0.008714247
15 -0.149274979
16 -0.027765226
17 0.051714982
18 0.049802847
19 -0.03014229
20 0.057590315
21 0.130087454
22 0.011206801
23 -0.027136856

Total number of rows: 415056

Table truncated, full table size 7755 Kbytes.




Supplementary file Size Download File type/resource
GSM1431146_PC9_GR_1.txt.gz 117.3 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap