GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1920187 Query DataSets for GSM1920187
Status Public on Nov 04, 2015
Title LNCaP treated with DMSO3
Sample type RNA
Source name LNCaP treated with DMSO
Organism Homo sapiens
Characteristics cell line: LNCaP (CRL-1740)
tissue: prostate cancer cells metastasized to a lymph nodes
Extracted molecule total RNA
Extraction protocol Total RNAs were isolated from the prostate cancer cell lines using an RNeasy Mini kit (Qiagen, Valencia, CA, USA) and treated with RQ1 RNase-free DNase (Promega, Madison, WI, USA) according to the manufacturer’s instructions. Reverse transcription of RNA was carried out in a final volume of 20 mL containing buffer, 0.1 M DTT, Oligo (DT)20, 10 mM dNTPs, 0.4 U/mL of RNase inhibitor, 1.25 U/mL of reverse transcriptase (Invitrogen Corp) and 1 mg of total RNA.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng RNA using the Low Input Quick Amp labeling kit, one-color (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
Hybridization protocol 480ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25 x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE Microarrays (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies), then dried immediately.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slide (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).
Description Gene expression in DMSO treated prostate cancer cell line
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent Technologies) using default parameters (protocol GE1_1010_Sep10 and Grid: 028004_D_F_20110325). Genes-screening was performed using the GeneSpring GX v12.0.0 software package (Agilent Technologies).
Submission date Oct 28, 2015
Last update date Nov 04, 2015
Contact name Shinya Sato
Organization name Nagoya City University
Street address kawasumi1, mizuho-ku
City Nagoya
ZIP/Postal code 467-8601
Country Japan
Platform ID GPL13607
Series (1)
GSE74418 Gene expression profiles of prostate cancer cell line with or without HDAC inihbitors

Data table header descriptions
VALUE Normalized signal intensity

Data table
1 9.79E+04
2 4.55E+00
3 4.59E+00
4 4.35E+02
5 2.84E+03
6 7.61E+01
7 1.83E+04
8 2.94E+03
9 3.44E+04
10 7.65E+01
11 4.80E+00
12 4.44E+03
13 2.45E+03
14 1.13E+03
15 3.18E+04
16 4.87E+00
17 4.47E+02
18 1.13E+01
19 4.88E+00
20 8.54E+03

Total number of rows: 62976

Table truncated, full table size 911 Kbytes.

Supplementary file Size Download File type/resource
GSM1920187_DMSO3.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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