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Sample GSM1304836 Query DataSets for GSM1304836
Status Public on Mar 31, 2014
Title BMDM, untreated, 1
Sample type RNA
Source name Bone marrow derived macrophages, untreated
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: bone marrow
cell type: macrophages
treatment: Untreated
Treatment protocol Bone marrow derived macrophages from C56BL/6J mice were either untreated or treated with 10 ng/ml of IFNg , LPS or 10 ng/ml of IFNg+10 ng/ml of LPS.
Extracted molecule total RNA
Extraction protocol The samples were harvested after 24h and RNA was isolated using Qiagen RNeasy mini kit.
Label Biotin
Label protocol Preparation of cRNA was done using Affymetrix 3'IVT Express kit and protocol provided by Affymetrix. Briefly, 0.5 ug of total RNA was converted into double-stranded cDNA and used to generate biotin labeled cRNA which was then purified.
Hybridization protocol 12.5 micrograms of cRNA was fragmented and hybridized to Mouse Genome 430 2.0 arrays at 45°C for 19 hours in a rotisserie oven set at 60 rpm.
Scan protocol Arrays were washed and stained using Affymrtrix HWS kit using their Fluidics station and then scanned on GeneChip scanner 3000.
Description Gene expression data from untreated bone marrow derived macrophages
Data processing Command Console/Expression Console/ExpressionStat5.0
Submission date Jan 10, 2014
Last update date Mar 31, 2014
Contact name Jason A Hackney
Organization name Genentech, Inc.
Department Department of Bioinformatics and Computational Biology
Street address 1 DNA Way
City South San Francisco
State/province CA
ZIP/Postal code 94080
Country USA
Platform ID GPL1261
Series (1)
GSE53986 NRROS negatively regulates ROS in phagocytes during host defense and autoimmunity

Data table header descriptions
VALUE Signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)

Data table
AFFX-BioB-5_at 744.401 P 5.16732e-05
AFFX-BioB-M_at 1247.41 P 4.42873e-05
AFFX-BioB-3_at 865.81 P 4.42873e-05
AFFX-BioC-5_at 2015.67 P 4.42873e-05
AFFX-BioC-3_at 3064 P 4.42873e-05
AFFX-BioDn-5_at 5122.63 P 4.42873e-05
AFFX-BioDn-3_at 10423.6 P 5.16732e-05
AFFX-CreX-5_at 21395 P 5.16732e-05
AFFX-CreX-3_at 23956 P 4.42873e-05
AFFX-DapX-5_at 1522.83 P 4.42873e-05
AFFX-DapX-M_at 3071.93 P 7.00668e-05
AFFX-DapX-3_at 3965.54 P 4.42873e-05
AFFX-LysX-5_at 201.205 P 6.02111e-05
AFFX-LysX-M_at 340.813 P 0.000169227
AFFX-LysX-3_at 605.888 P 6.02111e-05
AFFX-PheX-5_at 260.77 P 9.4506e-05
AFFX-PheX-M_at 337.296 P 4.42873e-05
AFFX-PheX-3_at 410.771 P 4.42873e-05
AFFX-ThrX-5_at 234.619 P 0.000195116
AFFX-ThrX-M_at 373.368 P 7.00668e-05

Total number of rows: 45101

Table truncated, full table size 1380 Kbytes.

Supplementary file Size Download File type/resource
GSM1304836_39142_BM_Untreated_SPR1090_Mouse430v2.CEL.gz 3.4 Mb (ftp)(http) CEL
GSM1304836_39142_BM_Untreated_SPR1090_Mouse430v2.mas5.CHP.gz 398.3 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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