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Sample GSM2822953 Query DataSets for GSM2822953
Status Public on Jul 02, 2019
Title WT Microglia biological replicate 1
Sample type RNA
 
Source name Microglia from ischemic hemisphere of WT mice
Organism Mus musculus
Characteristics genotype: WT
gender: male
strain: C57BL/6
tissue: brain
cell type: microglia
age: 8-10 weeks
Treatment protocol 8-10 week-old male C57BL/6 mice, of genotype TREM1+/+ and TREM1-/-, underwent MCAo for 45min followed by reperfusion (MCA0-RP). 48 hours after the reperfusion, mice were transcardially perfused with cold heparinized 0.9% NaCl and ischemic hemispheres were homogenized manually to filter through 70µm cell strainer. All cells in the homogenate were then purified by myelin depletion with Miltenyi Myelin removal kit according to the manufacturer’s instructions. After cell staining with CD45, CD11b and Ly6g, neutrophils (CD45Hi, CD11b+, Ly6G+), macrophages (CD45Hi, CD11b+, Ly6G-) and microglia (CD45Lo, CD11b+, Ly6G+) were sorted and RNA isolated for Affymetrix Clariom HT microarray analysis.
Extracted molecule total RNA
Extraction protocol RNA from neutrophils, macrophages and microglia from TREM1 -/- and +/+ ischemic hemispheres was extracted with Qiagen RNeasy Micro kit according to the manufacturer’s instructions.
Label biotin
Label protocol Microarray was performed at the Protein and Nucleic Acid (PAN) Facility at the Stanford University. The RNA integrity was examined on a bioanalyzer (Agilent). High-quality RNA (RNA integrity number >7.5) was used for expression microarray analysis. 0.6-0.8 ng of total RNA was used to generate double strand cDNA. 6.6 μg of ds cDNA were fragmented and labeled with biotin according to Affymetrix GeneChip Pico Reagent Kit manual (Thermo Fisher).
 
Hybridization protocol 3.0 μg of the fragmented and labeled cDNA was hybridized to Mouse Clariom S array at 60 rpm for 16 h at 45°C in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained with Streptavidin Phycoerythrin in an Affymetrix Fluidics Station 450 according to Affymetrix GeneChip Pico Reagent Kit guide (Thermo Fisher).
Scan protocol The arrays were scanned using the Affymetrix Gene Chip Scanner 3000 7G and CEL. intensity files were generated by Affymetrix GeneChip Command Console Software (AGCC, Thermo Fisher).
Description Gene expression data from microglia of ischemic hemisphere in WT mouse brain at day 2 post 45min MCAo
Data processing The Affymetric Clariom S microarrays were analyzed with RMA to detect the gene-level differential expression using the Affymetrix Transcriptome Anaylsis Console (TAC) 4.0 Software using default parameters. The significant genes (FDR<0.05) were ranked by fold-change with a cutoff of 2. TAC4.0 software output does not include data for ~6000 internal control probe sets, thus the sample tables include data for ~22K Clariom S probe sets that assay gene expression.
 
Submission date Oct 18, 2017
Last update date Jul 02, 2019
Contact name Katrin I Andreasson
E-mail(s) kandreas@stanford.edu
Organization name Stanford University
Department Neurology and neurological sciences
Lab kAT
Street address 1201 Welch Rd, MSLS P250
City Stanford
State/province California
ZIP/Postal code 94305
Country USA
 
Platform ID GPL23038
Series (1)
GSE105132 Differential gene expression in TREM1 -/- vs +/+ myeloid cells 48h after MCAo-RP

Data table header descriptions
ID_REF
VALUE RMA-normalized signal

Data table
ID_REF VALUE
TC0100000014.mm.2 941.5833505
TC0100000018.mm.2 122.5970114
TC0100000021.mm.2 570.1955619
TC0100000022.mm.2 41.13478506
TC0100000023.mm.2 12.72424367
TC0100000027.mm.2 617.527254
TC0100000038.mm.2 243.7127638
TC0100000039.mm.2 406.7614086
TC0100000041.mm.2 288.5684971
TC0100000044.mm.2 1469.072622
TC0100000045.mm.2 230.755784
TC0100000048.mm.2 812.4003213
TC0100000055.mm.2 36.8606856
TC0100000056.mm.2 63.05587983
TC0100000064.mm.2 22.3851022
TC0100000071.mm.2 64.57899123
TC0100000082.mm.2 33.69458846
TC0100000092.mm.2 650.8638605
TC0100000097.mm.2 452.0611099
TC0100000101.mm.2 68.93161923

Total number of rows: 22103

Table truncated, full table size 645 Kbytes.




Supplementary file Size Download File type/resource
GSM2822953_Microglia_WT_1.CEL.gz 1.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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