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Sample GSM2339517 Query DataSets for GSM2339517
Status Public on Aug 22, 2017
Title Men1 MEFs-1
Sample type RNA
 
Source name Men1 knockout Mouse embryonic fibroblasts complemented with Men1
Organism Mus musculus
Characteristics strain: mixed FVB;129Sv background
genotype: Men1 knockout
tissue: Mouse embryonic fibroblasts
Treatment protocol Seeded cells into 10 cm2 plate at 70% density. After 24 hours incubation at 37C, detached the cells with 0.25% Tripsin and harvested the cells.
Growth protocol Cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% FBS and 1% Pen/Strep at 37C
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Total RNA was converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated the T7 promoter sequence. Second-strand cDNA synthesis was followed by in vitro transcription with T7 RNA polymerase for linear amplification of each transcript, and the resulting cRNA was converted to cDNA, fragmented, assessed by Bioanalyzer, and biotinylated by terminal transferase end labeling.
 
Hybridization protocol 15 ug labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Affymetrix Murine Genome U74Av2 GeneChips using the GeneChip Hybridization oven 640.
Scan protocol The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. A GeneChip 3000 7G scanner was used to collect fluorescence signal.
Description Gene expression data from Men1 knockout Mouse embryonic fibroblasts complemented with Men1
Data processing Affymetrix Command Console and Expression Console were used to quantitate expression levels for targeted genes using MAS 5.0
 
Submission date Oct 07, 2016
Last update date Aug 22, 2017
Contact name Xianxin Hua
E-mail(s) huax@mail.med.upenn.edu
Organization name University of Pennsylvania Perelman School of Medicine
Department Department of Cancer Biology
Lab Hua Lab
Street address 421 Curie BLVD
City philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL81
Series (1)
GSE87733 Expression data from Men1 knockout MEFs

Data table header descriptions
ID_REF
VALUE MAS5.0 signal intensity with detection flags and detection p-values
ABS_CALL
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
92180_at 666 P 0.000266
92181_at 19.6 A 0.602006
92182_at 69.6 A 0.150527
92183_at 80.4 A 0.07383
92184_at 43 A 0.089405
92185_at 270.4 P 0.001141
92186_at 2.2 A 0.994357
92188_s_at 47.7 M 0.05447
92189_at 86.7 P 0.024711
92190_at 75.3 P 0.02786
92191_at 20.6 P 0.02786
92192_s_at 3.6 A 0.749276
92193_r_at 34.9 A 0.089405
92194_at 70 A 0.098054
92195_at 101.8 P 0.003585
92196_f_at 1909.7 P 0.00418
92197_r_at 2047.2 P 0.004863
92198_s_at 0.9 A 0.97214
92199_at 64.2 P 0.021866
92200_at 20.7 A 0.438361

Total number of rows: 12488

Table truncated, full table size 315 Kbytes.




Supplementary file Size Download File type/resource
GSM2339517_Hua1_S11_1A_U74Av2.CEL.gz 2.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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