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Sample GSM1704688 Query DataSets for GSM1704688
Status Public on Dec 08, 2015
Title WT3M1, biological replicate 3
Sample type RNA
Source name Bone Marrow Derived Macrophages
Organism Mus musculus
Characteristics cell type: BMDM
treatment: classically activated (M1 condition) with LPS + IFN-gamma
Treatment protocol On day 7 in culture the cells were washed, counted and replated in DMEM media (without L929 supernatant) at a density of 6-8^6 cells/well (6-well plate, Falcon polystyrene). Cells were classically activated (M1 condition) with LPS (100 ng/ml, Sigma-Aldrich) + IFN-γ (20ng/mL, E-bioscience, San Diego, CA) or alternatively activated (M2 condition) with IL-4 (20ng/mL, E-bioscience) or received media alone (M0 condition). Cells were harvested at 24 hours post-stimulation, by washing in phosphate buffered saline (PBS) before cell lysis in miRVana Lysis buffer (Life Technologies) for total RNA isolation.
Growth protocol To generate BMDM, the bone marrow cells from femurs and tibias from mice were harvested and cultured. Briefly, isolated cells were incubated in Dulbecco’s Modified Eagle Media (DMEM, Mediatech, Herndon, VA) supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Life Technologies, Grand Island, NY)), 1% penicillin/streptomycin, 1% glutamine, and 20% L929 cell supernatant (containing macrophage colony stimulating factor).
Extracted molecule total RNA
Extraction protocol To examine mRNA expression, cells were isolated using the miRVana isolation kit (Life Technologies) according to manufacturer specifications.
Label biotin
Label protocol Samples were enzymatically labeled using BioArray HighYield RNA Transcript Labeling kit (Enzo)
Hybridization protocol Samples were hybridized to Affymetric 430_2 array using Herring sperm DNA, acetlylated BSA (50 mg/ml) and, Bioarray Eukaryotic Hybridization controls (Enzo Life Sciences), heated 650C 5 minutes, 990C 5 minutes, 450C 5 minutes, centrifuge top speed for 5 minutes, hybridize 16 hours at 450C at 60 rpm; Fluidics script EukGE-WS2v4_450
Scan protocol Affymetrix Gene ChIP scanner 30007G using Command Console
Description Sample Expr WT3M1
Data processing Raw data were normalized with the RMA algorithm implemented in the ‘‘Expression File Creator’’ module from the GenePattern software package. Data were visualized with the Multiplot modules from GenePattern.
Submission date Jun 05, 2015
Last update date Dec 08, 2015
Contact name Mireia Guerau
Phone 614 293 4176
Organization name The Ohio State University
Department HRS-Medical Laboratory Science
Street address 453 W 10th Ave
City Columbus
State/province OH
ZIP/Postal code 43220
Country USA
Platform ID GPL1261
Series (1)
GSE69607 Novel transcriptome signatures and markers defining murine macrophages at the extremes of the canonical M1 and M2 polarization spectrum

Data table header descriptions
VALUE RMA normalized signal

Data table
1421025_at 424.026996
1421024_at 253.723225
1428821_at 331.716067
1433819_s_at 87.254287
1433818_at 36.234299
1433817_at 267.830838
1450504_a_at 885.759997
1436640_x_at 733.791542
1428336_at 778.407566
1434287_at 193.315391
1453257_at 877.640255
1458669_at 12.940795
1450776_at 702.213625
1422841_at 22.024593
1454799_at 60.499595
1436742_a_at 10.806487
1429421_at 190.585782
1437608_x_at 463.745061
1460621_x_at 2384.894445
1436846_x_at 1084.16804

Total number of rows: 45101

Table truncated, full table size 949 Kbytes.

Supplementary file Size Download File type/resource
GSM1704688_Sample-8-M1-3.CEL.gz 3.4 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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