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Sample GSM2079103 Query DataSets for GSM2079103
Status Public on Mar 03, 2016
Title Primary neurons
Sample type RNA
Source name mouse embryonic primary neurons
Organism Mus musculus
Characteristics cell: primary neurons
age: E13.5
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 primary neurons
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 4.3504114
DarkCorner -8.467255
A_55_P1989846 -2.667428
A_55_P1991598 -4.1363864
A_55_P2022211 2.0336666
A_55_P1980764 -3.2740636
A_55_P1964375 -0.20751095
A_51_P128876 4.8658504
A_55_P2121042 -4.1041827
A_52_P219230 -6.3371687
A_51_P207591 -1.9969091
A_55_P2131920 -0.8453655
A_55_P2404223 -2.7096615
A_55_P2101944 7.0116673
A_52_P358860 -1.3523998
A_51_P119031 -0.21212006
A_51_P309854 -0.66989136
A_51_P343900 1.0018892
A_51_P234359 -2.7119713
A_51_P487813 3.9084272

Total number of rows: 39485

Table truncated, full table size 931 Kbytes.

Supplementary file Size Download File type/resource
GSM2079103_R001.txt.gz 1.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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