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Sample GSM1086291 Query DataSets for GSM1086291
Status Public on Dec 17, 2013
Title THP-1 treated with PBS
Sample type RNA
Source name THP-1, PBS treated 60 min
Organism Homo sapiens
Characteristics cell line: THP-1
treatment: PBS treated 60 min
Extracted molecule total RNA
Extraction protocol Cells were dissoluved in TRIZOL, and total RNA were extracted with standerd protcol. RNA was further purified with Rnasy kit.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.
Hybridization protocol 0.60 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers 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 Gene Expression Microarray 8x60K Ver.2.0 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) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Submission date Feb 21, 2013
Last update date Dec 17, 2013
Contact name Kosuke Tanegashima
Phone +81-3-5316-3130
Organization name Tokyo Metropolitan Institute of Medical Science
Lab Stem cell project
Street address 2-1-6 Kamikitazawa
City Setagaya-ku
State/province Tokyo
ZIP/Postal code 156-8506
Country Japan
Platform ID GPL17077
Series (1)
GSE44550 THP-1 cells treated with CXCL14

Data table header descriptions
VALUE normalized signal intensity

Data table
A_23_P117082 10205.01017
A_33_P3246448 13.22999856
A_33_P3318220 13.31999836
A_33_P3236322 13.38999948
A_33_P3319925 28.74999898
A_21_P0000509 145779.9717
A_21_P0000744 15933.82484
A_24_P215804 2090.448809
A_23_P110167 16095.39096
A_33_P3211513 811.4503424
A_23_P103349 16.1106679
A_32_P61480 13.79999941
A_33_P3788124 13.81999894
A_33_P3414202 1411.219807
A_33_P3316686 1084.800475
A_33_P3300975 700.9797705
A_33_P3263061 10776.76836
A_33_P3261373 13.8599995
A_24_P278460 2139.680986
A_21_P0013109 13.84999932

Total number of rows: 50599

Table truncated, full table size 1255 Kbytes.

Supplementary file Size Download File type/resource
GSM1086291_AR0993_01raw.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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