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Sample GSM948080 Query DataSets for GSM948080
Status Public on Oct 26, 2012
Title Control BXD42/TyJ-1
Sample type RNA
 
Source name macrophage
Organism Mus musculus
Characteristics gender: male
age: 16 weeks
strain: BXD42/TyJ
treatment condition: Control
cell type: macrophage
Treatment protocol Cells were washed once with PBS the day after plating and incubated for 4 hours with 1%FBS DMEM media in control-treated cells, with control media plus 2ng/mL LPS (List Biological Inc., Campbell, CA, 201), or with control media plus 50μg/mL OxPAPC. OxPAPC was prepared from PAPC (Avanti Polar Lipids, Alabaster, AL) as previously described (Watson et al., 1997). After treatment, media was removed and cells were washed once with PBS.
Growth protocol 16 week male mice maintained on 12 hr light dark cycle fed a chow diet
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from macrophage samples using RNeasy columns (Qiagen, Valencia, CA), using on-column DNase digestion (Qiagen) and according to manufacturer’s instructions.
Label biotin
Label protocol All target labeling reagents were purchased from Affymetrix (Santa Clara, CA). Double-stranded cDNAs were synthesized from 1ug total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA and used to probe Affymetrix Mouse Genome HT_MG-430A arrays.
 
Hybridization protocol The HT_MG-430A Array plate consists of 96 single MG-430A arrays arranged into standard SBS 96 well plate format. All cDNA and cRNA target preparation steps were processed on a Caliper GeneChip Array Station from Affymetrix. Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations.
Scan protocol Scanned images were subjected to visual inspection and a chip quality report was generated by the Affymetrix's GeneChip Operating System (GCOS) and Expression console (Affymetrix).
Data processing The image data was processed using the Affymetrix GCOS algorithm utilizing the Robust Multiarray method (RMA) to determine the specific hybridizing signal for each gene. To avoid detecting variation signal intensity as an artifact of SNP variation in transcripts, prior to RMA normalization we excluded individual probes in probe-sets that aligned to sequences with SNPs, and excluded entire probe-sets where at least 8 of the probes in the set aligned to a sequence with SNPs.
 
Submission date Jun 13, 2012
Last update date Oct 26, 2012
Contact name Calvin Pan
Organization name UCLA
Street address 675 Charles Young Dr South
City Los Angeles
ZIP/Postal code 90095
Country USA
 
Platform ID GPL8759
Series (1)
GSE38705 Macrophage samples from the HMDP

Data table header descriptions
ID_REF
VALUE RMA-normalized expression values (log2 scale)

Data table
ID_REF VALUE
1415670_at 7.97679639191724
1415671_at 10.3034442499809
1415672_at 8.91398963729044
1415673_at 7.23666831738172
1415674_a_at 8.12757146782711
1415675_at 8.66148018098476
1415676_a_at 10.2425746888212
1415677_at 7.68792093731827
1415678_at 8.59483555359806
1415679_at 10.6925535638298
1415680_at 7.91621199340155
1415681_at 8.27642805202861
1415682_at 6.37973042408343
1415683_at 10.0521285264521
1415684_at 7.68204308779272
1415685_at 5.7230967095212
1415686_at 8.09401366678226
1415687_a_at 13.064073731399
1415688_at 9.09675405814326
1415689_s_at 5.56380064787398

Total number of rows: 22416

Table truncated, full table size 624 Kbytes.




Supplementary file Size Download File type/resource
GSM948080_5500144064075100109605_G09.cel.gz 3.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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