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Sample GSM2738627 Query DataSets for GSM2738627
Status Public on Aug 01, 2018
Title microglia alone rep 3
Sample type RNA
 
Source name microglia alone
Organism Mus musculus
Characteristics strain: C57BL6
gender: male
cell type: Adult microglia
treatment: control
Treatment protocol Adult microglia and bone marrow-derived macrophges were cultured separately for 7 days, as described above; BMDMs were then re-plated on poly-L-lysine coated glass coverslips. Cells were plated at 2x10^5 per 25 mm coverslip (for insertion in 6 well plates) of 4x10^4 per 12 mm coverslip (for insertion in 24 well plates). Coverslips were pre-mounted with 3 small paraffin droplets on the same surface which the cells were plated, as previously described for neuron-astrocyte co-cultures (Jones et al., 2012). BMDMs were allowed to adhere overnight. Bilaminar culture experiments began by inserting coverslips containing BMDM and wax paraffin nodule face down, into culture plates containing adult microglia. All experiments were performed in DMEMF12 serum free media.
Growth protocol Adult microglia were re-suspended at 8x10^5 cell-mL (approximately two brains per mL) in media (DMEM F12, 10% FBS, 1% penicillin/streptomycin (P/S)) with 10% L-cell conditioned media, a source of M-CSF (or 10ng/ml recombinant mouse M-CSF [R&D cat no 416-ML-010/CF]), and 50ng/ml recombinant human TGF-β1 (Miltenyi cat no: 130-095-067)
Extracted molecule total RNA
Extraction protocol RNA was extracted using Qiagen Microkit according to manufactors instructions
Label biotin
Label protocol Sense-strand cDNA was synthesized from 100 ng of total RNA, and fragmentation and labeling were performed to produce ss DNA with the Affymetrix GeneChip® WT Terminal Labeling Kit according to manufacturer’s instructions (ThermoFisher-Affymetrix)
 
Hybridization protocol After fragmentation and labeling, 3.5µg DNA target was hybridized on Mouse Clariom™ S Assay (ThermoFisher-Affymetrix) and incubated at 45C in the Genechip® Hybridization oven 640 (ThermoFisher-Affymetrix) for 17 hours at 60 rpm.
Scan protocol The microarrays were finally scanned on a GeneChip® scanner 3000 (Affymetrix).
Description Adult mouse microglia cultured for 7 days before treatments
Data processing Microarray data sets were normalized by the robust multiarray averaging (RMA) method in Affymetrix Expression Console (Affymetrix). To assess whether there were transcripts differentially expressed between activated microglia and activated microglia in the presence of macrophages, normalized data sets were compared in Affymetrix Transcriptome Analysis Console (TAC) Software.
 
Submission date Aug 10, 2017
Last update date Aug 01, 2018
Contact name Andrew Greenhalgh
E-mail(s) adgreenhalgh@gmail.com
Organization name The Research Institute of the McGill University Health Center
Street address Montreal General Hospital, 1650 Cedar Ave
City Montreal
State/province Quebec
ZIP/Postal code H3G 1A4
Country Canada
 
Platform ID GPL23038
Series (1)
GSE102482 Effect of peripherally-derived macrophages in adult microglia (mouse cells)

Data table header descriptions
ID_REF
VALUE RMA signal

Data table
ID_REF VALUE
AFFX-BkGr-GC03_st 6.42472
AFFX-BkGr-GC04_st 5.93407
AFFX-BkGr-GC05_st 6.32566
AFFX-BkGr-GC06_st 5.95582
AFFX-BkGr-GC07_st 5.31102
AFFX-BkGr-GC08_st 4.24338
AFFX-BkGr-GC09_st 3.68855
AFFX-BkGr-GC10_st 3.35004
AFFX-BkGr-GC11_st 2.93991
AFFX-BkGr-GC12_st 2.67369
AFFX-BkGr-GC13_st 2.43007
AFFX-BkGr-GC14_st 2.35395
AFFX-BkGr-GC15_st 2.20974
AFFX-BkGr-GC16_st 2.38565
AFFX-BkGr-GC17_st 2.47496
AFFX-BkGr-GC18_st 3.05319
AFFX-BkGr-GC19_st 5.47779
AFFX-BkGr-GC20_st 5.60237
AFFX-BkGr-GC21_st 5.6513
AFFX-BkGr-GC22_st 5.75754

Total number of rows: 28846

Table truncated, full table size 749 Kbytes.




Supplementary file Size Download File type/resource
GSM2738627_3_mg_SDD111A05A05_01.CEL.gz 1.1 Mb (ftp)(http) CEL
GSM2738627_3_mg_SDD111A05A05_01.SST.sst-rma-gene-full.chp.gz 204.0 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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