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Sample GSM2051705 Query DataSets for GSM2051705
Status Public on Jul 15, 2016
Title KO1M1, biological replicate 1
Sample type RNA
 
Source name KO1M1, biological replicate 1
Organism Mus musculus
Characteristics cell type: Bone Marrow Derived Macrophages
treatment: classically activated (M1 condition) with LPS (100 ng/ml, Sigma-Aldrich) + IFN-γ (20ng/mL, E-bioscience, San Diego, CA)
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 miRNA 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
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 Jan 31, 2016
Last update date Jul 16, 2016
Contact name Mireia Guerau
E-mail(s) mireia.guerau@osumc.edu
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)
GSE77425 Control of the inflammatory macrophage transcriptional signature by miR-155

Data table header descriptions
ID_REF
VALUE RMA normalization

Data table
ID_REF VALUE
1421025_at 390.562682
1421024_at 235.545482
1428821_at 357.317644
1433819_s_at 146.609415
1433818_at 39.089271
1433817_at 335.969447
1450504_a_at 833.511304
1436640_x_at 594.370259
1428336_at 598.660356
1434287_at 196.75381
1453257_at 832.558679
1458669_at 14.623046
1450776_at 642.794092
1422841_at 20.531519
1454799_at 25.310002
1436742_a_at 8.669818
1429421_at 223.427193
1437608_x_at 440.804898
1460621_x_at 2471.756863
1436846_x_at 1067.460866

Total number of rows: 45101

Table truncated, full table size 948 Kbytes.




Supplementary file Size Download File type/resource
GSM2051705_Sample-19-M1-1.CEL.gz 3.4 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table
Processed data are available on Series record

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