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Sample GSM1598138 Query DataSets for GSM1598138
Status Public on Jan 31, 2015
Title MA-345
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 13_5_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 7.7791786
DarkCorner -7.338613
A_23_P117082 3.3868256
A_33_P3246448 -5.864576
A_33_P3318220 -7.3546824
A_33_P3236322 -4.5644937
A_33_P3319925 -3.9016504
A_21_P0000509 8.900721
A_21_P0000744 0.053948402
A_24_P215804 -1.9502077
A_23_P110167 1.0487137
A_33_P3211513 -2.471075
A_23_P103349 -6.5144386
A_32_P61480 -7.352484
A_33_P3788124 -2.510027
A_33_P3414202 -2.923882
A_33_P3316686 -2.1206274
A_33_P3300975 -5.9888563
A_33_P3263061 2.7096033
A_33_P3261373 -5.6925254

Total number of rows: 50739

Table truncated, full table size 1189 Kbytes.

Supplementary file Size Download File type/resource
GSM1598138_13-5_fibro.txt.gz 3.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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