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Sample GSM1054216 Query DataSets for GSM1054216
Status Public on Dec 09, 2015
Title 253G1_p37
Sample type RNA
Source name 253G1, passage 37, untreated
Organism Homo sapiens
Characteristics cell type: human HDF-derived iPS cell
cell line: 253G1
passage number: 37
lectin treatment: none
treatment period: 0
Growth protocol Human iPSCs and ESCs were maintained in an undifferentiated state in the presence of bFGF. The cultures were incubated at 37 ºC in a humidified incubator with 3 or 5% CO2.
Extracted molecule total RNA
Extraction protocol Total RNA was prepared using ISOGEN (Nippon Gene) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng of total RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
Hybridization protocol 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug 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, 55 ul of 2x HiRPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K Microarray Kit (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) 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 (G2505C) using one color scan setting for 8x60k array slides.
Description Gene expression in human iPS cell
Data processing The scanned images were analyzed with Feature Extraction Software GX12.0 (Agilent) using default parameters.
Submission date Dec 18, 2012
Last update date Dec 09, 2015
Contact name Yuzuru Ito
Organization name National Institute of Advanced Industrial Science and Technology (AIST)
Department Biotechnology Research Institute for Drug Discovery
Street address Central 6, Higashi 1-1-1
City Tsukuba
State/province Ibaraki
ZIP/Postal code 3058566
Country Japan
Platform ID GPL13607
Series (1)
GSE42976 Effect of rBC2LCN on human embryonic stem cells

Data table header descriptions
VALUE processed Cy3 signal intensity (Agilent gProcessedSignal)

Data table
1 7.642225e+004
2 4.290142e+000
3 4.302961e+000
4 2.767178e+002
5 9.012998e+002
6 1.412984e+002
7 3.225643e+003
8 1.271800e+003
9 4.350892e+000
10 6.970951e+001
11 4.357766e+000
12 1.476370e+002
13 2.017185e+003
14 7.075628e+002
15 7.813977e+003
16 4.357066e+000
17 3.286501e+002
18 3.840369e+001
19 4.345958e+000
20 1.813349e+003

Total number of rows: 62976

Table truncated, full table size 1219 Kbytes.

Supplementary file Size Download File type/resource
GSM1054216_US91703677_252800415361_S01_GE1_107_Sep09_1_1.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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