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Sample GSM1598136 Query DataSets for GSM1598136
Status Public on Jan 31, 2015
Title MA-343
Sample type RNA
Source name iPSC
Organism Homo sapiens
Characteristics cell type: iPSC
Treatment protocol No treatment applied.
Growth protocol Episomal vectors encoding reprogramming factors (OCT3/4, SOX2, KLF4, L-MYC, LIN28 and p53 shRNA) were transduced into fibroblasts on day 0 as described previously (Okita et al., 2011). The transfected cells were reseeded onto feeder layers on day 7, and maintained in embryonic stem cell medium (ReproCELL). Around day 30, the iPSC colonies were picked up and expanded. Cell culture was performed under 37°C , with 5% CO2 and 21% O2.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted and purified using RNA mini kit (QIAGEN) according to manufacturer’s instruction.
Label Cy3
Label protocol 100 ng of total RNA was first amplified with WT-OvationTM Pico System (Nugen). The RNA was labelled with Cy3 using Genomic DNA Enzymatic Labeling Kit (Agilent Technologies).
Hybridization protocol Labelled cDNA was fragmented with Gene Expression Hybridization Kit (Agilent Technologies), followed by hybridization at 65˚C for 17 hrs.
Scan protocol Images were acquired by DNA Microarray Scanner (Agilent Technologies)
Description 409B2_iPSC
Data processing Raw data were processed with FeatureExtraction version Normalization among samples were performed by GeneSpring GX 12.6.1. Signal were normalized to 75% percentile.
Submission date Jan 30, 2015
Last update date Apr 23, 2018
Contact name Megumu Saito
Organization name Kyoto University
Street address 53, Shogoin-Kawahara
City Kyoto
ZIP/Postal code 6068507
Country Japan
Platform ID GPL17077
Series (1)
GSE65470 Modeling the early phenotype at the neuromuscular junction of spinal muscular atrophy using patient-derived iPSCs
Reanalyzed by GSE113533

Data table header descriptions
VALUE Normalized signal intensity

Data table
GE_BrightCorner 7.439168
DarkCorner -7.6131525
A_23_P117082 3.2883902
A_33_P3246448 -4.7174544
A_33_P3318220 -7.634651
A_33_P3236322 -6.8704014
A_33_P3319925 -3.7525387
A_21_P0000509 8.774713
A_21_P0000744 -0.59955406
A_24_P215804 -2.275322
A_23_P110167 1.2911711
A_33_P3211513 -2.2917333
A_23_P103349 -6.8130445
A_32_P61480 -7.640155
A_33_P3788124 -2.273417
A_33_P3414202 -2.1806736
A_33_P3316686 -0.93378067
A_33_P3300975 -6.0859017
A_33_P3263061 3.435194
A_33_P3261373 -6.387821

Total number of rows: 50739

Table truncated, full table size 1190 Kbytes.

Supplementary file Size Download File type/resource
GSM1598136_409B2_iPSC.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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