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Sample GSM2677997 Query DataSets for GSM2677997
Status Public on Oct 19, 2017
Title N31+EGFP_72hr_rep1
Sample type RNA
 
Source name mouse ESC-derived neural progenitor cells
Organism Mus musculus
Characteristics treatment: control NPC cells 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 control NPC cells 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 -7.285509
A_52_P580582 -5.310234
A_52_P403405 -7.289327
A_52_P819156 -7.2918854
A_51_P331831 0.164114
A_51_P430630 -7.301425
A_52_P502357 -5.613006
A_52_P299964 -7.0824366
A_51_P356389 -7.313958
A_52_P684402 -0.51215076
A_51_P414208 -7.323312
A_51_P280918 -0.48432827
A_52_P613688 -7.333679
A_52_P258194 -7.0725336
A_52_P229271 -1.8496182
A_52_P214630 0.7048392
A_52_P579519 -0.094855785
A_52_P979997 -7.3621187
A_52_P453864 -7.368239
A_52_P655842 -6.0113983

Total number of rows: 41265

Table truncated, full table size 944 Kbytes.




Supplementary file Size Download File type/resource
GSM2677997_N31+EGFP_72hr_rep1.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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