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Sample GSM622871 Query DataSets for GSM622871
Status Public on Nov 28, 2011
Title F2-2313-F
Sample type RNA
 
Source name liver, F2, female
Organism Mus musculus
Characteristics strain: MRL/MpJ x SM/J
generation: F2
Sex: female
age: 13 weeks
tissue: liver
hyb_date: 10-07-08
batch: 1
Treatment protocol The mice were housed individually for 3 days prior to the tissue collection and fasted for 4-5 hours on the day of the collection. There was no treatment group, all mice were in the same conditions.
Growth protocol Mice were housed in a climate-controlled facility with a 14-hour:10-hour light-dark cycle with free access to food and water throughout the experiment. After weaning, mice were maintained on a chow diet (5K52 LabDiet, St. Louis, MO). F2 mice were tail-tipped at 2 weeks of age.
Extracted molecule total RNA
Extraction protocol Tissue samples were stored in RNAlater (Ambion, Austin TX) following dissection and later homogenized in TRIzolTM (Invitrogen, Carlsbad, CA). Total RNA was isolated by TRIzolPlus TM methods according to the manufacturer’s protocols, and quality was assessed using an Agilent 2100 Bioanalyzer instrument and RNA 6000 Nano LabChip assay (Agilent Technologies, Palo Alto, CA).
Label biotin
Label protocol Following reverse transcription with random primers-T7 primers (Affymetrix, Santa Clara, Ca), double stranded cDNA was synthesized with the GeneChip WT cDNA Synthesis and Amplification Kit (Affymetrix, Santa Clara, Ca). In an in vitro trancription (IVT) reaction with T7 RNA polymerase, the cDNA was linearly amplified to generate cRNA. In the second cycle of cDNA synthesis, random primers are used to generate single-stranded DNA in the sense orientation. Incorporation of dUTP in the cDNA synthesis step allows for the fragmentation of the cDNA strand utilizing uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) that specifically recognizes the dUTP and allows for breakage at these residues. Labeling occurs by terminal deoxynucleotidyl transferase (TdT) where biotin is added by a Affymetrix Labeling Reagent.
 
Hybridization protocol 2.3µg of biotin-labeled and fragmented cDNA was then hybridized onto GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix) for 16 hours at 45°C. Post-hybridization staining and washing were performed according to manufacturer’s protocols using the Fludics Station 450 instrument (Affymetrix).
Scan protocol Arrays were scanned with a GeneChipTM Scanner 3000 laser confocal slide scanner.
Description Transcript expression data from a female (MRL/MpJ x SM/J)F2 mouse.
Data processing Data were imported into R (v2.11) and processed using the affy package from Bioconductor (v2.6). The data were normalized using robust multi-array average (rma) expression with no background correction. A custom cdf file MoGene10stvMmENST cdf V11.0.1 was obtained from Brainarray (http://brainarray.mbni.med.umich.edu).
 
Submission date Nov 12, 2010
Last update date Nov 28, 2011
Contact name Ricardo Alejandro Verdugo
E-mail(s) ricardo.a.verdugo@gmail.com
Organization name The Jackson Laboratory
Department Research
Lab Gary A. Churchill
Street address 600 Main Street
City Bar Harbor
State/province ME
ZIP/Postal code 04609
Country USA
 
Platform ID GPL11204
Series (1)
GSE25322 MRLxSM eQTL in Liver by RMA on Ensembl transcripts

Data table header descriptions
ID_REF
VALUE Log2 RMA signal (not background corrected)

Data table
ID_REF VALUE
ENSMUST00000000001_at 9.6432
ENSMUST00000000003_at 5.2439
ENSMUST00000000010_at 6.6413
ENSMUST00000000028_at 6.4726
ENSMUST00000000031_at 6.3099
ENSMUST00000000033_at 6.2773
ENSMUST00000000049_at 12.3166
ENSMUST00000000058_at 6.3667
ENSMUST00000000080_at 6.7962
ENSMUST00000000087_at 7.0668
ENSMUST00000000090_at 8.9687
ENSMUST00000000094_at 6.745
ENSMUST00000000095_at 7.0153
ENSMUST00000000096_at 6.0518
ENSMUST00000000102_at 6.2613
ENSMUST00000000109_at 5.8567
ENSMUST00000000122_at 6.9291
ENSMUST00000000127_at 6.2817
ENSMUST00000000128_at 7.1651
ENSMUST00000000129_at 7.5689

Total number of rows: 34406

Table truncated, full table size 971 Kbytes.




Supplementary file Size Download File type/resource
GSM622871.CEL.gz 3.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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