NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7790647 Query DataSets for GSM7790647
Status Public on Dec 14, 2023
Title M-KO-MONO-Macrophages
Sample type SRA
 
Source name Brain
Organism Mus musculus
Characteristics tissue: Brain
cell line: primary cells
cell type: Macrophages
genotype: CD163KO
treatment: α-syn MONO
Treatment protocol For whole population RNA sequencing, mice (batch 1 and batch 2) received bilateral intrastriatal injection of α-syn MONO (Males WT n=7 & CD163KO n=4*; Females WT n=7 &CD163KO n=5), and α-syn PFF (Males WT n=7, & CD163KO n =5; Females WT n=7 & CD163KO n=5). Triplicates were used for sequencing. Mice were sacrificed 2 months post-surgery, their brains dissected and the immune cells (microglia & macrophages) isolated and FACS sorted for RNA purification and subsequent SMART-seq2 sequencing. *CD163KO-MONO males were excluded from the analysis due to inconsistencies in the technical replicates.
Growth protocol Adult male and female CD163KO (CD163tm1.1(KOMP)Vlcg) mice and WT (C57BL/6N) littermates (3-4 months old) (n=179 total (n=95 males (50 WT + 45 CD163KO); n=84 females (43 WT+ 41 CD163KO)) were used in this study 1. Mice weighted 20-25g (12 weeks old) at the time of the surgery and were housed maximum 4-6 per cage, with ad libitum access to food and water, in a climate-controlled facility under 12h/12h night/daylight cycle.
Extracted molecule total RNA
Extraction protocol Once sorted, microglia (200000-500000 cells) and macrophage (10000-30000 cells) cell suspensions (>90% purity after sorting) were centrifuged at 4°C and 400xg for 5 minutes, resuspended in RLT Plus Lysis buffer (QIAGEN, Germany) with 1% β-Mercaptoethanol and vortexed for 1 minute for cell lysis. The solution was further homogenized using a 1mL syringe and a 21gag needle. Total RNA was extracted using RNeasy® Mini Kit (QIAGEN) according to the manufacturer’s protocol.
Total purified RNA was sent to BGI Hong Kong where Switching Mechanism at 5’ End of RNA Template (SMART-seq2) sequencing service was requested. Samples were tested for quality control using Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit). RNA integrity (RNI) >7 was considered suitable for sequencing.
Gene expression analysis was performed through full population RNA sequencing using the SMART-seq2 method according to BGI’s standard methodology.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model DNBSEQ-G400
 
Data processing Reads mapped to rRNA were removed and raw data was obtained.
The sequencing reads which contained low-quality, adaptor-polluted and high content of unknown base (N) reads processed were removed before downstream analyses.
Clean reads were mapped to reference using Bowtie2, and then gene expression level was calculated for each sample with RSEM
DESeq2 package was used to detect the DEGs, determining at a cutoff of FDR corrected p-value≤0.05 and |log2(fold change)|≥1 as DEGs.
Principal component analysis (PCA) was performed on the Macrophage and Microglia population respectively based on the rlog of dds result from DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited text files contain counts and FPKM for each sample
 
Submission date Sep 19, 2023
Last update date Dec 14, 2023
Contact name Yonglun Luo
E-mail(s) alun@biomed.au.dk
Phone 0045-22411944
Organization name Aarhus University
Street address Wilhelm Meyers Allé 4
City aarhus
ZIP/Postal code 8000
Country Denmark
 
Platform ID GPL28457
Series (1)
GSE243536 Sex-dimorphic neuroprotective effect of CD163 in an alpha-synuclein mouse model of Parkinson’s disease
Relations
BioSample SAMN37458610
SRA SRX21827018

Supplementary file Size Download File type/resource
GSM7790647_M_KO_mono_macroph.gene.fpkm.xls.gz 1.9 Mb (ftp)(http) XLS
SRA Run SelectorHelp
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap