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Sample GSM661554 Query DataSets for GSM661554
Status Public on Jan 27, 2011
Title 393m1
Sample type RNA
 
Source name metastasis derived cell line (from liver metastasis)
Organism Mus musculus
Characteristics cell type: lung adenocarcinoma metastasis derived cell line (from liver metastasis)
genotype: KrasG12D;p53-/-
Treatment protocol To determine gene expression alterations induced by Nkx2-1 knockdown in TnonMet cells Array analyses were performed on 368T1-control (bc37), 368T1-shNkx2-1 (E1), 394T4-control (bc37), and 394T4-shNkx2-1(E1) cells. The 394T4 samples were run in duplicate using either the Affymetrix GeneChip® WT Sense Target Labeling (A9242, A9244, A9245, A9247) or the Nugene Ovation® Systems Target Preparation kits (A9248 and A9249). Thus, a pairwise comparison between the three control and their corresponding shNkx2-1 datasets was used to determine the potential Nkx2-1 regulated genes
Growth protocol Tumours were initiated by intratracheal infection of KrasLSL-G12D/+;p53flox/flox mice with a lentiviral vector expressing Cre-recombinase. The MIT Institutional Animal Care and Use Committee approved all animal studies and procedures. Cell lines were created from individual lung tumours and metastases harvested from mice 8-14 months after tumour initiation. Tumours were cut into small pieces and then digested for 30 minutes at 37°C in 2ml of HBSS-free containing Trypsin, Collagenase IV, and Dispase in a 15ml conical tube. Following digestion, 4mL of Quench Solution (L15 media with 400μl of FBS and 15μl of 5mg/ml DNase) was added. Digested tumour samples were then pressed through 40μm cell strainers (BD). Finally, samples were centrifuged at 1,000 r.p.m. for 5 minutes, resuspended in culture media (DMEM, 10% FBS, pen/strep, glutamine), and plated in a 12-well plate. Cells were washed and culture media was changed every day for a week until stable cell lines were formed. In general we were able to derive cell lines from approximately 50% of tumours and metastases without a noticeable difference in the frequency of cell line generation from metastases from different site relative to the primary lung tumours.
Extracted molecule total RNA
Extraction protocol RNA was extracted using Trizol (Invitrogen)
Label biotin
Label protocol Affymetrix GeneChip® WT Sense Target Labeling
 
Hybridization protocol Performed according to manufacturer's instructions (Affymetrix) for Affymetrix Mouse Exon 1.0 ST arrays.
Scan protocol Affymetrix Gene ChIP Scanner 3000 7G; GeneChip® Command Console.
Description A8180_393m1
Data processing Data processing was done using Partek Genomics Suite 6.5 software. RMA was used to summarize and normalize the probe data into probe set expression values. The list of utilized probe sets was defined by custom .ps and .mps files. The RMA procedure used included the options adjust for GC content, probe sequence, RMA background correction, Quantile Normalization and median polish probe set summarization. Expression values for probesets were summarized to a single value per gene based on the custom file MoEx-1_0-st-v1._core+miRNA+RfSq+UCSC_.SH.2916.mps. The outlier excluded mean method was used. This procedure excludes probe set values that are more than 3 standard deviations above the mean or more and 2 standard deviations below the mean.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1._core+miRNA+RfSq+UCSC_.SH.2916.mps
 
Submission date Jan 26, 2011
Last update date Jan 27, 2011
Contact name Charles Arthur Whittaker
E-mail(s) charliew@mit.edu
Organization name Koch Institute
Street address 77 Mass Ave 76-189
City Cambridge
State/province MA
ZIP/Postal code 02152
Country USA
 
Platform ID GPL6096
Series (1)
GSE26874 Suppression of Lung Adenocarcinoma Progression by Nkx2-1

Data table header descriptions
ID_REF
VALUE Quantile normalized gene level expression values in log2 space from Partek Genomics Suite 6.5.

Data table
ID_REF VALUE
7008252 5.18237
6898252 4.23892
6823768 7.74052
6823769 3.63672
6898253 4.63435
6933677 10.7664
6958212 5.15019
6933678 9.14311
6933679 9.52594
6848296 3.04659
6958215 7.56918
6983639 3.79909
6958216 10.5013
6788351 5.09425
6788352 3.48374
6823777 6.60236
6898262 2.82712
6763829 4.04589
6823778 3.96073
6898263 3.68139

Total number of rows: 44343

Table truncated, full table size 688 Kbytes.




Supplementary file Size Download File type/resource
GSM661554.CEL.gz 21.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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