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Sample GSM2677999 Query DataSets for GSM2677999
Status Public on Oct 19, 2017
Title N31+W20_72hr_rep1
Sample type RNA
 
Source name mouse ESC-derived neural progenitor cells
Organism Mus musculus
Characteristics treatment: W20-expressing NPCs 72 hr after initiation of cell reprogramming
Growth protocol Cells cells were maintained on a gelatin-coated culture plate in an NPC medium, RHB basal (StemCells, Inc) containing the epidermal growth factor (EGF) containing 40 ng/ml Dox for 48 hr followed by GMEM supplemented with 10% KSR, 1 μM ACTH, 1 mM sodium pyruvate, 1× nonessential amino acids, 100 μM 2-mercaptoethanol and 1000 U/ml of LIF 40 ng/ml Dox for 24 hr (Peprotech) at 10 ng/ml and the human basic fibroblast growth factor (bFGF) (Peprotech) at 10 ng/ml.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the RNeasy Kit (QIAGEN) and was assessed by Agilent 2100 Bioanalyzer and the RNA 6000 LabChip Kit (Agilent Technologies).
Label Cy3
Label protocol Microarray experiments were performed according to the manufacturer’s instruction. Twenty hundred nanograms of total RNA was labelled with cyanine 3-CTP and hybridized in Whole Mouse Genome Microarray 4x44K G4122F (Agilent Technologies).
 
Hybridization protocol 600 ng 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, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Microarray 4x44K G4122F for 17 hours at 65°C in a rotating 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 4x44K array slides.
Description W20-expressing NPCs 72 hr after initiation of cell reprogramming
Data processing The array data were analyzed using GeneSpring software (Agilent). Gene expression values were normalized by excluding low-signal intensity data and percentile shifts.
 
Submission date Jun 21, 2017
Last update date Jan 23, 2018
Contact name Takashi Ikeda
E-mail(s) tikeda@cira.kyoto-u.ac.jp
Organization name Kyoto Univ.
Street address 53 Shogoin Kawahara-cho Sakyo-ku
City Kyoto
ZIP/Postal code 6068507
Country Japan
 
Platform ID GPL7202
Series (1)
GSE96845 Artificial acceleration of mammalian cell reprogramming by bacterial proteins

Data table header descriptions
ID_REF
VALUE normalized signal

Data table
ID_REF VALUE
A_52_P616356 -7.0836954
A_52_P580582 -5.2850437
A_52_P403405 -7.0941286
A_52_P819156 -7.0995817
A_51_P331831 -0.15476084
A_51_P430630 -7.116491
A_52_P502357 -7.122622
A_52_P299964 -7.1284676
A_51_P356389 -7.1345253
A_52_P684402 -0.52919436
A_51_P414208 -7.1468606
A_51_P280918 -0.8576641
A_52_P613688 -7.159135
A_52_P258194 -6.890046
A_52_P229271 -1.5447431
A_52_P214630 1.0643516
A_52_P579519 0.40196085
A_52_P979997 -7.190709
A_52_P453864 -7.1970177
A_52_P655842 -6.3012934

Total number of rows: 41265

Table truncated, full table size 944 Kbytes.




Supplementary file Size Download File type/resource
GSM2677999_N31+W20_72hr_rep1.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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