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Sample GSM2079104 Query DataSets for GSM2079104
Status Public on Mar 03, 2016
Title Tet3 induced neurons 3dpi
Sample type RNA
Source name Tet3 induced neuons, 3dpi
Organism Mus musculus
Characteristics cell: induced neuons
age: E13.5
treatment: induced by Tet3 3 dpi
Treatment protocol The E13.5 ICR mouse embryos were employed to get the primary mouse embryonic fibroblasts (MEFs). MEFs were transduced with adenoviral supernatants in the presence of 4 mg/ml polybrene for 8 hours and then the clusters were refreshed by intermediate medium (low glucose with 5% FBS). And on the day 2, the same performance was repeated as that of day 1. And on the day3 and day5 after second infection, half-amount of the cell culture medium was switched to neuronal medium with 20 μM Forskolin (Sigma, F6886). After day 5, half cell culture medium was refreshed with neuronal medium every other day until the cells were ready for the sequent experiments. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.
Extracted molecule total RNA
Extraction protocol Total RNAs were obtained from the indicated samples using TRIzol Reagent (Invitrogen, 15596-018) referring to the instruction manual. RNA was quantified using a NanoDrop-1000 spectrophotometer.
Label Cy3
Label protocol Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442).RNeasy Mini Kit (Qiagen p/n 74104) NanoDrop ND-1000
Hybridization protocol Kit and Instruments:Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242):10X Blocking Agent 25X Fragmentation Buffer. 2x GEx Hybridization Buffer HI-RPM. Hybridization Chamber, stainless (Agilent p/n G2534A). Hybridization Chamber gasket slides (Agilent p/n G2534-60003) Hybridization oven (Agilent p/n G2545A). Hybridization oven rotator for Agilent Microarray Hybridization Chambers (Agilent p/n G2530-60029)
Scan protocol Instrument: Agilent Microarray Scanner (Agilent p/n G2565BA). Procedure: 1. Assemble the slides into an slide holder. 2. Place assembled slide holders into scanner carousel.3. Verify scan settings for one-color scans. Parameters Scan region Scan Area (61 x 21.6 mm) Scan resolution (μm) 5 5μm scanning mode Single Pass eXtended Dynamic range (selected) Dye channel Green Green PMT XDR Hi 100% XDR Lo 10% 4. Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.
Description Gene expression in induced neurons by Tet3 3 dpi
Data processing Agilent Feature Extraction software (version was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 2 out of 6 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed genes between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts. GO analysis and Pathway analysis were performed in the standard enrichment computation method.
Submission date Mar 02, 2016
Last update date Mar 03, 2016
Contact name Juan Zhang
Organization name Chinese Academy of Sciences
Department Institute of Zoology
Street address Beijing 100101, China
City Beijing
ZIP/Postal code 100101
Country China
Platform ID GPL11202
Series (1)
GSE78841 Time course of gene expression signatures for Tet3 induced neurons

Data table header descriptions
VALUE Normalized signal intensity

Data table
GE_BrightCorner 4.5045614
DarkCorner -8.849024
A_55_P1989846 -2.5276823
A_55_P1991598 -4.465093
A_55_P2022211 2.960164
A_55_P1980764 -3.895431
A_55_P1964375 0.26313686
A_51_P128876 6.117942
A_55_P2121042 -4.6823807
A_52_P219230 -6.397307
A_51_P207591 3.2198868
A_55_P2131920 3.2083712
A_55_P2404223 -2.2820292
A_55_P2101944 4.3735647
A_52_P358860 0.049380302
A_51_P119031 -0.88166046
A_51_P309854 -6.678584
A_51_P343900 1.3472929
A_51_P234359 -3.1499634
A_51_P487813 3.1226616

Total number of rows: 39485

Table truncated, full table size 928 Kbytes.

Supplementary file Size Download File type/resource
GSM2079104_R002.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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