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Sample GSM1347051 Query DataSets for GSM1347051
Status Public on Dec 31, 2014
Title Cumulus Cells, Unprimed, replicate 3
Sample type RNA
 
Source name Cumulus Cells, Unprimed
Organism Mus musculus
Characteristics cell type: cumulus
pmsg-stimulation: unprimed
Treatment protocol Half of the mice were treated with 5 IU equine chorionic gonadotropin 44 hours before isolation of cumulus and mural granulosa cells
Growth protocol Fresh samples of cumulus cells and mural granulosa cells were isolated from the ovaries of 22 day old mice
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the Qiagen RNeasy Micro kit according to the manufacturers instructions.
Label biotin
Label protocol Fragmented biotinylated aRNA were produced from 20ng Total RNA according to the standard protocol using the MessageAmp II aRNA Amplification Kit from Ambion for the first round of amplification and using the MessageAmp II Biotin Enhanced Kit from Ambion for the second round of amplification.
 
Hybridization protocol Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430v2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
Data processing Average signal intensities for each probeset within arrays were calculated by the rma function provided within the affy package for R using a custom (Ensembl Transcript v13) CDF file (Dai et al., 2005; http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/13.0.0/version.html). The RMA method incorporates convolution background correction, sketch-quantile normalization, and summarization based on a multi-array model fit robustly using the median polish algorithm.
 
Submission date Mar 12, 2014
Last update date Dec 31, 2014
Contact name Timothy Michael Stearns
E-mail(s) tim.stearns@jax.org
Organization name The Jackson Laboratory
Department Computational Sciences
Lab Statistics
Street address 600 Main Street
City Bar Harbor
State/province ME
ZIP/Postal code 04609
Country USA
 
Platform ID GPL18416
Series (1)
GSE55845 Analysis of transcriptomic diversitification of developing cumulus and mural granulosa cells in mouse ovarian follicles

Data table header descriptions
ID_REF
VALUE RMA-summarized (with quantile normalization) probe set (Ensembl transcript v13 CDF; University of Michigan Brain Array) intensity values

Data table
ID_REF VALUE
AFFX-18SRNAMur/X00686_3_at 12.53301694
AFFX-18SRNAMur/X00686_5_at 13.39847609
AFFX-18SRNAMur/X00686_M_at 13.80416788
AFFX-b-ActinMur/M12481_3_at 14.28397347
AFFX-b-ActinMur/M12481_5_at 13.36422815
AFFX-b-ActinMur/M12481_M_at 13.74588025
AFFX-BioB-3_at 8.825885697
AFFX-BioB-5_at 8.54684996
AFFX-BioB-M_at 9.005881391
AFFX-BioC-3_at 10.32894082
AFFX-BioC-5_at 9.908801924
AFFX-BioDn-3_at 12.38485924
AFFX-BioDn-5_at 10.98716698
AFFX-CreX-3_at 13.97237535
AFFX-CreX-5_at 13.75454742
AFFX-DapX-3_at 10.76535527
AFFX-DapX-5_at 6.116837798
AFFX-DapX-M_at 9.678337537
AFFX-GapdhMur/M32599_3_at 14.24550867
AFFX-GapdhMur/M32599_5_at 12.41679421

Total number of rows: 41179

Table truncated, full table size 1362 Kbytes.




Supplementary file Size Download File type/resource
GSM1347051_GC_430_2_GES10_414_121210_1.CEL.gz 3.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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