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Sample GSM4355786 Query DataSets for GSM4355786
Status Public on Mar 01, 2020
Title MP3: Monocyte RFP+ 6
Sample type RNA
 
Source name infected (RFP+) monocytes
Organism Mus musculus
Characteristics strain: C57Bl/6
Sex: Female
age: 8 weeks
time post-infection: 2 weeks
parasite: Leishmania amazonensis
tissue: skin
Extracted molecule total RNA
Extraction protocol Monocytes were sorted out of the skin mice using FACSAria II and RNA was extracted using Qiagen Rneasy mini kit according to the manufacture's protocol.
Label n/a
Label protocol RNA was not labeled. 30ng/ul of RNA was converted to cDNA to follow the NanoString manufacture's protocol for the hybridization
 
Hybridization protocol cDNA samples were hybridized to capture the reporter CodeSet and the capture ProbeSet provided by NanoString forming the target-probe complex. The reporter probes are molecular barcodes provided by NanoString. The samples were placed in a pre-heated 65°C thermal cycler and incubated for 20h to allow the hybridization.
Scan protocol Scanning was conducted using the nCounter Digital Analyser acording to the manufacture's instructions. In general, it collects data by taking images of the immobilized fluorescent reportes in the sample cartridge with a CCD camera trough a microscope objective lens. The images are processed and each lane generates one RRC (Reporter Code Count) file that contains the number of reporters counted.
Data processing All analysis were done in R version 3.6.0. Raw RCC files were loaded into R and quality analysis was done with NanoStringQCPro1.16.0. For principal component analysis (PCA) and visualization of gene counts the data was normalized with a variance stabilizing transform using NanoStringNorm. PCA was done with the built in R function, prcomp. Differential expression was done with NanoStringDiff 1.14.0, which uses a negative binomial model and includes an empirical Bayes shrinkage procedure to estimate dispersion (Wang et al., 2016). A 2 x 2 factorial model was used and the effect of infection was tested (p < 0.05) on samples.
 
Submission date Feb 27, 2020
Last update date Mar 02, 2020
Contact name Nathan Peters
E-mail(s) ncpeters@ucalgary.ca
Organization name University of Calgary
Department Microbiology, Immunology and Infectious Diseases
Street address 3330 Hospital Dr NW
City Calgary
State/province AB
ZIP/Postal code T2N4N1
Country Canada
 
Platform ID GPL20885
Series (1)
GSE146022 Th1/Th2 cross-regulation controls early Leishmania infection in the skin by modulating the size of the permissive monocytic host cell reservoir

Data table header descriptions
ID_REF
VALUE Normalized Log2 expression

Data table
ID_REF VALUE
Ager 0.3426
Alox12 0.3426
Alox15 0.3426
Alox5 0.3426
Areg 0.3426
Arg1 3.541
Atf2 2.356
Bcl2l1 0.3426
Bcl6 2.699
Birc2 1.492
C1qa 3.293
C1qb 3.396
C1ra 0.3426
C1s 2.008
C2 1.492
C3 3.175
C3ar1 3.202
C4a 2.224
C6 1.492
C7 0.3426

Total number of rows: 248

Table truncated, full table size 2 Kbytes.




Supplementary file Size Download File type/resource
GSM4355786_Monocyte_RFP+_3.RCC.gz 2.9 Kb (ftp)(http) RCC
Processed data included within Sample table

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