NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM188634 Query DataSets for GSM188634
Status Public on May 15, 2007
Title PANC-1_BiolRep1_TechRep1_2
Sample type RNA
 
Channel 1
Source name PANC-1 cell line grown in serum-containing media
Organism Homo sapiens
Characteristics Human pancreatic carcinoma, epithelial-like cell line
Gender: Male
Biomaterial provider ATCC
Treatment protocol To induce ICA formation, Serum-containing medium (SCM) was removed, cells were exposed for 60–120 s to 0.05% trypsin (CellgroMediatech) at 25°C, to loosen but not detach the cells from their extracellular matrix (ECM) and then cultured in Serum Free Medium (SFM). SFM was DME/F12 medium containing 17.5 mM glucose, 1% BSA (no. 152401, ICN) and insulin— transferrin—selenium (GIBCO).
Growth protocol PANC-1 cells (American Type Culture Collection, Manassas, VA) were started as passage 1 (passages 3–6 were used for all experiments). Cells were cultured in serum-containing media (SCM), a mixture of DMEM (Cellgro, Mediatech, Herndon, VA) containing 10% FBS.
Extracted molecule total RNA
Extraction protocol TRIzol to isolate total RNA, followed by cleanup using QIAGEN RNeasy Mini Kit.
Label Cy5
Label protocol 10 ug of RNA was labeled using the Agilent Fluorescent Direct Label Kit
 
Channel 2
Source name PANC-1 cell line 24 hours after serum withdrawal
Organism Homo sapiens
Characteristics Human pancreatic carcinoma, epithelial-like cell line
Gender: Male
Biomaterial provider ATCC
Treatment protocol To induce ICA formation, Serum-containing medium (SCM) was removed, cells were exposed for 60–120 s to 0.05% trypsin (CellgroMediatech) at 25°C, to loosen but not detach the cells from their extracellular matrix (ECM) and then cultured in Serum Free Medium (SFM). SFM was DME/F12 medium containing 17.5 mM glucose, 1% BSA (no. 152401, ICN) and insulin— transferrin—selenium (GIBCO).
Growth protocol PANC-1 cells (American Type Culture Collection, Manassas, VA) were started as passage 1 (passages 3–6 were used for all experiments). Cells were cultured in serum-containing media (SCM), a mixture of DMEM (Cellgro, Mediatech, Herndon, VA) containing 10% FBS.
Extracted molecule total RNA
Extraction protocol TRIzol to isolate total RNA, followed by cleanup using QIAGEN RNeasy Mini Kit.
Label Cy3
Label protocol 10 ug of RNA was labeled using the Agilent Fluorescent Direct Label Kit
 
 
Hybridization protocol Each Agilent slide contained two sets of coordinate arrays, where samples labeled with the opposite dye (Cy5 and Cy3) configurations were hybridized using the Agilent cDNA Microarray Kit Hybridization Protocol
Scan protocol Slides were scanned using the Agilent G2566AA scanner
Description RNA extracted from the first biological replicate was derived from 3 culture dishes producing enough sample for three technical replicates, whereas RNA from the second and third biological replicates were derived from one culture dish each.
Data processing For the Agilent cDNA arrays, the default settings of the Agilent G2566AA Feature Extraction Software (v.A.5.1.1) were used, which selects the LOWESS (locally weighted linear regression curve fit) normalization method. A second round of normalization included median scaling followed by batch (including dye, RNA extraction batch, slide configuration and array) effect removal using Partek Genomics Solution software.
 
Submission date May 13, 2007
Last update date May 14, 2007
Contact name Margaret C Cam
E-mail(s) maggie.cam@nih.gov
Phone 240-760-7179
Organization name NIH
Street address Bldg 37/3041C
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL875
Series (1)
GSE7785 PANC-1 cell differentiation

Data table header descriptions
ID_REF
VALUE Log2 Ratio of (D11-Cy3)/(C11-Cy5)
D11-Cy3 Day 1 treated, Median normalized, batch removed signal
Lowess Normalized D11-Cy3 Day 1 treated, Lowess normalized
C11-Cy5 Control, Median normalized, batch removed signal
Lowess Normalized C11-Cy5 Control, Lowess normalized
Ratio Ratio of (D11-Cy3)/(C11-Cy5)

Data table
ID_REF VALUE D11-Cy3 Lowess Normalized D11-Cy3 C11-Cy5 Lowess Normalized C11-Cy5 Ratio
2 -2.1203 80.71 74.05 343.34 742.33 0.23
3 0.7740 55145.22 67352.60 32144.89 34730.10 1.71
5 -1.3219 47.15 63.64 115.59 248.38 0.40
6 -0.2688 2676.56 2792.87 3200.97 3137.04 0.83
7 -0.1844 345.91 440.28 392.29 598.11 0.88
8 0.0841 989.25 1184.46 930.23 1097.33 1.06
9 -0.1047 163.97 188.50 176.22 257.38 0.93
10 -1.0291 1313.59 1722.10 2660.35 3415.15 0.49
11 -0.1047 323.81 357.01 346.49 392.76 0.93
12 1.1699 3260.86 4083.60 1446.74 1940.77 2.25
13 -0.2345 7364.00 9219.60 8612.03 10755.00 0.85
14 -0.5778 76.99 87.20 113.80 149.33 0.67
15 -0.4540 3236.58 3798.94 4402.23 5107.74 0.73
17 0.3561 2515.93 3229.64 1952.16 3026.84 1.28
18 -0.7370 109.37 141.89 180.41 221.92 0.60
19 0.1375 46.37 40.82 41.83 41.56 1.10
20 1.2388 1212.21 1471.32 513.24 773.98 2.36
22 0.5059 286.71 372.36 201.82 341.97 1.42
25 0.1375 2522.06 3347.64 2278.73 2942.94 1.10
26 0.0144 3173.71 3115.12 3115.96 3394.06 1.01

Total number of rows: 13675

Table truncated, full table size 638 Kbytes.




Supplementary file Size Download File type/resource
GSM188634.txt.gz 2.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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