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Sample GSM345285 Query DataSets for GSM345285
Status Public on Jun 15, 2010
Title C57_control_rep 1
Sample type RNA
Source name C57BL/6 mice, control treated, 2 h
Organism Mus musculus
Characteristics Cell type: peritoneal macrophages
Strain: C57BL/6
Gender: female
Age: 10 weeks
Extracted molecule total RNA
Extraction protocol The RNeasy RNA extraction kit, with on column DNAse digestion (Qiagen) was used, according to manufacturer's protocol.
Label Cy3
Label protocol Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.
Hybridization protocol For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.
Scan protocol Slides were washed and then scanned with an Agilent Scanner.
Description Intra-peritoneally inject 2 ml of 4% Brewer’s thioglycolate to mouse (5.8 mg thioglycolate/150 mg agar/200cc H20) and euthanize mouse 96 h later. Wash abdominal cavity with 10 ml of ice cold sterile PBS (endotoxin free) twice to remove cells from peritoneum. Keep cells on ice. 2. Spin down cells 1,000 RPM, 6 min, 4°C. Wash two times with sterile cold PBS-CMF (10-30 mls), decanting. Resuspend in DMEM+pen/strep+0.1% FBS. Count cells, and plate 1.5 million cells/well in 1 ml in a 12 well plate (can plate as low as 1.1 million if necessary, but keep consistent between cell types). Let settle for at least 2 h before changing media to cholesterol-loading media (1ml/well). Make fresh cholesterol-loading media every time: DMEM (0.1% FBS)/2mg/ml BSA (low LPS)/10ug/ml cholesterol, adding cholesterol at the end (after the FBS and BSA) while swirling. Let media swirl on rocker for 5 min. before using to ensure cholesterol is completely in solution. Incubate overnight. Next day: Wash 2x with warm sterile 1x PBS-CMF. Change media to DMEM/penstrep/2mg/ml BSA (low LPS)/25µg/ml polymyxin B (1ml/well).
Data processing Data were obtained and processed with the Agilent Feature Extraction Software (v9.5). The resulting data were imported into Rosetta Resolver (v7.1) and log10 intensities were exported.
Submission date Nov 25, 2008
Last update date Jan 04, 2012
Contact name NIEHS Microarray Core
Organization name NIEHS
Department DIR
Lab Microarray Core
Street address 111 T.W. Alexander Drive
City RTP
State/province NC
ZIP/Postal code 27709
Country USA
Platform ID GPL7202
Series (1)
GSE13772 The apoA-I induced transcriptome and dependence on MyD88

Data table header descriptions
ID_REF probe IDs from the Agilent-014868 Whole Mouse Genome 4x44K array
VALUE Rosetta Resolver Error Model, log10 Intensity

Data table
A_52_P305654 1.97979
A_52_P891296 1.35624
A_51_P243283 4.50011
A_52_P62270 2.14856
A_51_P362627 2.30936
A_52_P229709 3.84069
A_52_P662142 2.12332
A_52_P112017 4.26629
A_51_P163444 3.3432
A_51_P270605 1.22021
A_51_P239367 1.05239
A_51_P442759 1.89028
A_51_P106443 1.88888
A_51_P275658 2.55265
A_51_P460247 0.83419
A_52_P1044206 0.81014
A_52_P473542 3.19669
A_51_P145507 1.35938
A_52_P441355 0.84438
A_52_P219216 1.91197

Total number of rows: 41174

Table truncated, full table size 838 Kbytes.

Supplementary file Size Download File type/resource
GSM345285_US22502532_251486814024_S01_GE1-v5_95_Feb07_1_4.txt 25.0 Mb (ftp)(http) TXT
GSM345285_US22502532_251486814024_S01_H.tif 100.6 Mb (ftp)(http) TIFF
GSM345285_US22502532_251486814024_S01_L.tif 100.6 Mb (ftp)(http) TIFF
Processed data included within Sample table

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