NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM297809 Query DataSets for GSM297809
Status Public on Jan 01, 2009
Title A Caco2 sorted on AC133 high expression (sort #1)
Sample type RNA
 
Source name Colon carcinoma cell line (Caco2)
Organism Homo sapiens
Characteristics Caco2 Growth Properties: adherent Organism: Homo sapiens (human) Morphology: epithelial Source Organ: colon Disease: colorectal adenocarcinoma
Treatment protocol FACSort: For sorting cells expressing AC133, the cells were removed from the culture dish with 0.05% trypsin and 0.02% EDTA (Invitrogen, Carlsbad, CA), washed in PBS containing 1% FCS, stained with CD133-PE antibody (AC133, Miltenyi Biotec, Auburn, CA ) and resuspended at 106 cells per ml in the same buffer. The cells were filtered through a 35 um nylon filter prior to FACSort. Sorting was performed on a FACSDiVa flow cytometer (Becton Dickinson). Side and forward scatter profiles and propidium iodide (PI) staining were used to eliminate cell doublets and dead cells. The 10% of the cells that expressed the highest AC133 fluorescence and the AC133 negative cells were collected. Cells were recovered in 15ml conical plastic tubes containing 1ml of 100% FCS, and an aliquot was removed at the end of the sort and reanalyzed to evaluate purity.
Growth protocol Caco2: The human colon epithelial cancer cell line Caco2 was obtained from American Type Culture Collection (ATCC, Manassas, VA). Caco2 cells at passage 10 were infected with a Lentivirus reporter vectors that contain the mouse Melk promoter driving enhancer green fluorescent protein (MELK-GFP). Individual clones were isolated with the use of glass cloning rings. Two of these clones were used for further experiments. All cells were cultured in DMEM (Mediatech Inc, Manassas, VA) supplemented with 20% fetal bovine serum (Tissue Culture Biologicals, Tulare, CA) and 37 ug/ml Gentamicin (Sigma-Aldrich, St. Louis, MO).
WM115: The melanoma cell line WM115, provided by Boris Fichtman and Zeev Ronai (Burnham Institute for Medical Research, La Jolla, CA), was cultured in 10% FCS in RPMI 1640. In all experiments, cells were cultured in culture dishes (Nunc) at 37ºC in a humidified 5% CO2 incubator.
Extracted molecule total RNA
Extraction protocol Total RNA from AC133 high and negative sorted Caco2 and WM115 cells was extracted using the TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) according to the manufacturer’s protocol. Two samples each of two cell lines were analyzed as biological duplicates. Labeled cRNA was prepared from 500 ng RNA using the Illumina® RNA Amplification Kit from Ambion (Austin, TX, USA). The Biotin labeled cRNA (750 ng) was hybridized 18 hr at 58ºC to the HumanRef-8 v2 Expression BeadChip (>22,000 gene transcripts; Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.
Label Streptavidin Cy3
Label protocol As described in the illumina Human-8 chip processing protocol. Briefly, generation of biotin labelled cRNA from the product of RT cDNA synthesis and 2nd strand cDNA synthesis.
 
Hybridization protocol As recommended by illumina.
Scan protocol As suggested by illumina using the illumina scanner.
Description 1863182049_A
Data processing cubic spline
 
Submission date Jun 11, 2008
Last update date Jun 11, 2008
Contact name Roy M Williams
E-mail(s) rwillia@scripps.edu
Organization name The Scripps Research Institute
Department Regenerative Medicine
Lab Loring
Street address 3030 Science Park Road
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platform ID GPL6104
Series (1)
GSE11757 Cell cycle dependent variation of a CD133 epitope in human embryonic stem cell, colon cancer and melanoma cell lines.

Data table header descriptions
ID_REF
VALUE AVG Signal
1863182049_A.Avg_NBEADS
1863182049_A.BEAD_STDERR
1863182049_A.Detection Pval

Data table
ID_REF VALUE 1863182049_A.Avg_NBEADS 1863182049_A.BEAD_STDERR 1863182049_A.Detection Pval
ILMN_1809034 362.7433 41 17.21818 0
ILMN_1660305 237.7937 26 10.2013 0
ILMN_1792173 239.0172 43 7.950197 0
ILMN_1762337 45.20165 46 2.062729 0.1539548
ILMN_1736007 36.7278 39 1.298458 0.6666667
ILMN_1787689 48.87382 36 3.069193 0.07909604
ILMN_1731507 34.00369 29 1.782417 0.8997175
ILMN_1814316 41.78384 38 2.431402 0.2655367
ILMN_1745607 39.71838 41 1.904271 0.4110169
ILMN_1757454 44.99412 52 1.974064 0.1596045
ILMN_1735045 77.49777 38 3.980617 0.005649718
ILMN_1680754 52.67367 40 2.225244 0.0480226
ILMN_1659452 37.37086 36 2.03684 0.6016949
ILMN_1767388 71.39603 32 2.756854 0.008474576
ILMN_1673870 47.88638 27 2.972402 0.09039548
ILMN_1675204 43.82882 43 2.12104 0.1864407
ILMN_1755321 123.8908 33 6.632598 0.001412429
ILMN_1698554 128.9188 48 5.678907 0.001412429
ILMN_1805938 77.08775 48 3.111312 0.005649718
ILMN_1676336 224.4508 50 8.835155 0

Total number of rows: 22184

Table truncated, full table size 909 Kbytes.




Supplementary file Size Download File type/resource
GSM297809.txt.gz 346.8 Kb (ftp)(http) TXT
Processed data included within Sample table

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