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Sample GSM1121623 Query DataSets for GSM1121623
Status Public on Apr 12, 2013
Title EBF1-1
Sample type RNA
 
Source name EBF1
Organism Mus musculus
Characteristics cell type: Ebf1-/- pre-pro-B cell line
transduction: MigY-EBF1 virus
Treatment protocol High titer virus was generated using a CaPO4 transfection protocol. Cultures were supplemented with fresh medium at 12h post-infection and harvested for downstream applications at indicated time points post-infection.
Growth protocol Ebf1-/- progenitors were propagated and maintained on OP9 stromal cells in Opti-MEM, 10% FCS, primatone, L-glutamine, and Pen/Strep supplemented with 10 ng/ml each of IL-7, flt3-ligand (FL) and stem cell factor (SCF).
Extracted molecule total RNA
Extraction protocol Target preparation and hybridization protocols were conducted as described in the Ovation Pico WTA System V2 User Guide (NuGEN) and the Affymetrix GeneChip Expression Analysis Technical Manual. Briefly, [50ng] of total RNA was converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated an RNA priming region. Second-strand cDNA synthesis was followed by ribo-SPIA linear amplification of each transcript using an isothermal reaction with RNase, RNA primer and DNA polymerase, and the resulting cDNA was fragmented, assessed by Bioanalyzer, and biotinylated by terminal transferase end labeling. cDNA yields ranged from 5-9ug
Label biotin
Label protocol Protocols were conducted as described in the Affymetrix GeneChip Expression Analysis Technical Manual. Quality and quantity of extracted RNA was tested on a bioanalyser by UPENN Microarray Core Facility. the resulting cDNA was fragmented, assessed by Bioanalyzer, and biotinylated by terminal transferase end labeling. cDNA yields ranged from 5-9ug
 
Hybridization protocol Biotinylated targets were heated at 99 °C for 5 min and hybridized for 16 h at 45 °C. The microarrays were then washed at low (6× SSPE) and high (100 mM MES, 0.1 M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.
Scan protocol GeneChips were scanned using the GeneArray Scanner 3000 7G.
Data processing The data were analysed using Partek Genomics Suite, version 6.5 (Partek). Robust multichip average (RMA) with default settings was used to normalize data.
 
Submission date Apr 11, 2013
Last update date Apr 12, 2013
Contact name David Allman
E-mail(s) dallman@mail.med.upenn.edu
Phone 215 746-5547
Organization name University of Pennsylvania
Street address 36th & Hamilton Walk, 230 John Morgan Building
City Philadelphia
State/province PA
ZIP/Postal code 19104-6160
Country USA
 
Platform ID GPL6246
Series (1)
GSE46004 Expression data comparing EBF1 versus Pax5 induced genes

Data table header descriptions
ID_REF
VALUE Log2 RMA signal intensity

Data table
ID_REF VALUE
10438060 10.3399
10392142 9.45291
10434128 9.18658
10438064 9.6511
10576332 7.92362
10580752 6.96951
10527323 7.50721
10569335 7.78296
10412211 5.43045
10534638 6.18775
10558880 6.91382
10465619 6.85559
10585186 7.59699
10350173 6.12506
10429520 7.85566
10354019 7.90649
10580754 5.67965
10574166 10.0561
10551169 7.11804
10458278 6.51529

Total number of rows: 28350

Table truncated, full table size 467 Kbytes.




Supplementary file Size Download File type/resource
GSM1121623_4390_40503_MoGene-1.CEL.gz 3.6 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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