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Sample GSM3597289 Query DataSets for GSM3597289
Status Public on Mar 11, 2019
Title SW620 parental
Sample type genomic
 
Channel 1
Source name Colorectal cancer cell line SW620
Organism Homo sapiens
Characteristics cell line: SW620
cell type: Colorectal cancer
parental or resistant: Parental
selumetinib resistance concentration: N/A
Treatment protocol Cells were treated with fresh normal growth medium (with or without selumetinib as described above) for 24 hours.
Growth protocol Cells were grown in DMEM (HCT116R, HCT116R_6244R, HKH2, HKH2_6244R, LoVo, LoVo_6244R) or Leibovitz's L-15 (SW480, SW480_6244R, SW620, SW620_6244R) containing 10% FBS, penicillin (100 U mL-1), streptomycin (100 mg mL-1) and 2 mM glutamine. Liebovitz’s L-15 media was additionally supplemented with 0.75 mg mL-1 sodium bicarbonate. Cells were incubated in a humidified incubator at 37°C and 5% (v/v) CO2. For selumetinib-resistant cell lines, cells were grown in these media with added 2 µM selumetinib (HCT116R_6244R and HKH2_6244R), 4 µM selumetinib (LoVo_6244R), or 1 µM selumetinib (SW480_6244R and SW620_6244R).
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 Sex: female
disease state: normal
Treatment protocol Cells were treated with fresh normal growth medium (with or without selumetinib as described above) for 24 hours.
Growth protocol Cells were grown in DMEM (HCT116R, HCT116R_6244R, HKH2, HKH2_6244R, LoVo, LoVo_6244R) or Leibovitz's L-15 (SW480, SW480_6244R, SW620, SW620_6244R) containing 10% FBS, penicillin (100 U mL-1), streptomycin (100 mg mL-1) and 2 mM glutamine. Liebovitz’s L-15 media was additionally supplemented with 0.75 mg mL-1 sodium bicarbonate. Cells were incubated in a humidified incubator at 37°C and 5% (v/v) CO2. For selumetinib-resistant cell lines, cells were grown in these media with added 2 µM selumetinib (HCT116R_6244R and HKH2_6244R), 4 µM selumetinib (LoVo_6244R), or 1 µM selumetinib (SW480_6244R and SW620_6244R).
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 G2505C scanner.
Description Parental cell line SW620
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 Feb 11, 2019
Last update date Mar 11, 2019
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)
GSE126367 Copy number analysis of selumetinib-resistant CRC cells lines

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

Data table
ID_REF VALUE
4 5.44E-02
5 -1.55E-02
6 1.98E-01
7 1.13E-02
8 -1.11E-02
9 -2.63E-03
10 4.32E-01
11 9.67E-02
12 3.02E-01
13 1.12E-02
14 -1.01E-01
15 2.30E-01
16 2.19E-01
17 2.39E-01
18 9.36E-02
19 -5.26E-02
20 -7.22E-03
21 -8.21E-03
22 -1.80E-03
23 4.03E-02

Total number of rows: 420281

Table truncated, full table size 6665 Kbytes.




Supplementary file Size Download File type/resource
GSM3597289_0774_AZE_252185019355_S01_CGH_107_Sep09_1_2.txt.gz 117.7 Mb (ftp)(http) TXT
Processed data included within Sample table

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