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Sample GSM958904 Query DataSets for GSM958904
Status Public on Jul 12, 2012
Title Day 4.5
Sample type RNA
 
Source name 4.5 day of reprogramming
Organism Mus musculus
Characteristics cell type: Mouse Embryonic Fibroblast isolated from 13.5 day mouse embryos which carrying the Oct4-GFP transgenic allele
time: 4.5 day of reprogramming
cell passage: two passages after isolation
Treatment protocol Retrovirus containing supernant was collected 24 hr and 48 hr after Plat-E cells were transfected with pMXs-based retroviral vectors. 1) Oct4 and Klf4 containing retrovirus was delivered on day 0. 2) Oct4, Klf4 and c-Myc were delivered on Day 1.5. 3) c-Myc and Sox-2 were deivered on Day 3. 4) Sox2 were delivered on Day 4.5. 5) Vitamin C containging medium were used from Day 6.
Growth protocol MEF cells were cultured in DMEM supplemented with 10% FBS and NEAA, penicillin/streptomycin, L-glutamine
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using TRIZOL Reagent (Cat#15596-018,Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
Label Cy3
Label protocol Total RNA was amplified and labeled with Cyanine (Cy3) by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).
 
Hybridization protocol Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。
Scan protocol Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.
Description Gene expression after 4.5 day of reprogramming
Data processing Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).
 
Submission date Jul 11, 2012
Last update date Jul 12, 2012
Contact name Hui Zheng
E-mail(s) zheng_hui@gibh.ac.cn
Phone 86-20-32015334
Fax 86-20-32015231
Organization name Guangzhou Institutes of Biomedicine and Health, Chinese Academic of Science
Department Stem Cell
Street address 190 Kaiyuan Ave. Science City
City Guangzhou
State/province Guangdong
ZIP/Postal code 510530
Country China
 
Platform ID GPL7202
Series (1)
GSE39260 Gene expression analysis during reprogramming with sequential infecion of Oct4/Klf4/cMyc/Sox2

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
A_51_P135012 7.3657494
A_52_P64538 1.158164
A_51_P121031 6.1846533
A_51_P363871 3.3599024
A_52_P210011 5.401198
A_52_P459599 10.565645
A_52_P148764 6.567713
A_52_P158997 4.790527
A_52_P268355 1.3819662
A_52_P647856 1.2963444
A_52_P301261 2.422634
A_52_P332517 11.705473
A_51_P405668 11.917091
A_52_P636394 8.201793
A_51_P294970 10.508247
A_51_P324072 8.516534
A_51_P259802 9.833301
A_52_P381913 7.814146
A_52_P460037 11.641729
A_51_P200586 11.8268585

Total number of rows: 41267

Table truncated, full table size 908 Kbytes.




Supplementary file Size Download File type/resource
GSM958904_raw_data-4.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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