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Sample GSM2428928 Query DataSets for GSM2428928
Status Public on Dec 14, 2016
Title Undifferentiated iPSC_donorA_rep1
Sample type RNA
Source name Undifferentiated iPSC_donorA
Organism Homo sapiens
Characteristics cell type: Undifferentiated iPSC
donor: A
Extracted molecule total RNA
Extraction protocol Total RNA was purified with an RNeasy Mini Kit (Qiagen) following the manufacturer's protocol.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low RNA Input Quick Amplification Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy 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 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE v2 8x60K Microarray (G039494) 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 (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
Description A5iPS
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 039494_D_F_20140813) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Submission date Dec 14, 2016
Last update date Apr 23, 2018
Contact name Tadahiro Shinozawa
Organization name Takeda pharmaceuticals
Street address Muraokahigashi 2chome
City Fujisawa
ZIP/Postal code 251-8555
Country Japan
Platform ID GPL17077
Series (1)
GSE92391 Global gene expression of hiPS cell derived cardiomyocytes from healthy volunteers
Reanalyzed by GSE113533

Data table header descriptions
VALUE Normalized signal intensity

Data table
(+)E1A_r60_1 0.007029548
(+)E1A_r60_3 0.076326868
(+)E1A_r60_a104 0.076603812
(+)E1A_r60_a107 0.101919301
(+)E1A_r60_a135 0.153960696
(+)E1A_r60_a20 0.183257811
(+)E1A_r60_a22 1.249738854
(+)E1A_r60_a97 0.022074057
(+)E1A_r60_n11 0.055803085
(+)E1A_r60_n9 0.027320307
3xSLv1 0.003904685
A_19_P00315452 0.130565035
A_19_P00315459 0.235726196
A_19_P00315482 0.190932368
A_19_P00315492 0.562960042
A_19_P00315493 0.027125742
A_19_P00315502 0.058604587
A_19_P00315506 1.364873893
A_19_P00315518 0.037146536
A_19_P00315519 0.003921411

Total number of rows: 50739

Table truncated, full table size 1259 Kbytes.

Supplementary file Size Download File type/resource
GSM2428928_US09503747_253949440291_S01_GE1_107_Sep09_2_1.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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