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Sample GSM480856 Query DataSets for GSM480856
Status Public on Dec 10, 2010
Title HBG3_Day2_r2
Sample type RNA
 
Source name ES to Motor Neuron differentiation, Day 2
Organism Mus musculus
Characteristics cell line: HBG3
Growth protocol ES cells were grown on ES Medium (DMEM, 15% FBS, Non-essential amino acids, Glutamine, Pen/Strept, 2-mercaptoethanol and LIF) on feeder cells for amplification or on Gelatin for differentiation and experiments. Motor neuron differentiation was done as described (Wichterle & Peljto, Curr Protoc Stem Cell Biol, 2009). Briefly, ES cells were tripsinized and allowed to form aggregates in ANDFK medium (Advanced DMEM/F12, Neurobasal Medium, Knockout-SR, of Pen/Strep, L-Glutamine, and 2-mercaptoethanol. Day 0 is the day of tripsinization. At Day 2, RA and Hh agonist are added.
Extracted molecule total RNA
Extraction protocol RNA was extracted with Qiagen RNAeasy at different time points following manufacturer’s instructions.
Label biotin
Label protocol RNA was amplified using NuGen Ovation amplification and labeling kit according to manufacturer’s instructions
 
Hybridization protocol RNA was hybridized to Affymetrix Mouse Genome 430 2.0 microarrays.
Scan protocol Arrays were scanned using the GeneChip Scanner 3000.
Description Gene expression data from ES to Motor Neuron differentiation, Day2 (embryoid body stage)
Data processing Data analysis was carried out using the affylmGUI BioConductor package. GCRMA normalization was performed across all arrays, followed by linear model fitting using Limma. Differentially expressed genes after 8 hours of RA treatment were defined by ranking all probesets by the moderated t-statistic-derived p-value (adjusted for multiple hypothesis testing using Benjamini & Hochberg’s method and setting thresholds of p<0.001 and a fold-change of at least 2.
 
Submission date Dec 08, 2009
Last update date Dec 10, 2010
Contact name Shaun Mahony
E-mail(s) mahony@psu.edu
Phone 814-865-3008
Organization name Penn State University
Department Biochemistry & Molecular Biology
Lab Shaun Mahony
Street address 404 South Frear Bldg
City University Park
State/province PA
ZIP/Postal code 16802
Country USA
 
Platform ID GPL1261
Series (1)
GSE19372 Expression time series during the differentiation of ventral motor neurons from embryonic stem cells

Data table header descriptions
ID_REF
VALUE GCRMA-normalized probe intensities

Data table
ID_REF VALUE
1415670_at 8.22001645
1415671_at 9.533056474
1415672_at 11.2211754
1415673_at 9.693413308
1415674_a_at 9.538899617
1415675_at 9.166613028
1415676_a_at 12.66431468
1415677_at 7.336314437
1415678_at 12.49656687
1415679_at 10.84577067
1415680_at 8.925115213
1415681_at 9.702226249
1415682_at 10.04433367
1415683_at 11.51927485
1415684_at 8.690164879
1415685_at 9.046624809
1415686_at 11.29330014
1415687_a_at 9.746854449
1415688_at 11.81787295
1415689_s_at 6.346876143

Total number of rows: 45101

Table truncated, full table size 1027 Kbytes.




Supplementary file Size Download File type/resource
GSM480856_2_r2.CEL.gz 3.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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