NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5752017 Query DataSets for GSM5752017
Status Public on Dec 25, 2021
Title RM 3 D0
Sample type RNA
 
Source name WHOLE BLOOD
Organism Macaca mulatta
Characteristics tissue: whole blood
group based on vaccine prime regimen: Administered adjuvanted HIV Env protein
days after vaccine prime: 0
Treatment protocol The infant Rhesus macaques were immunized during the first week of life with either 15ug 1086C HIV Env protein with 10ug of 3M-052 adjuvant stable emulsiom or 15ug 1086C HIV Env protein with 10ug of 3M-052 adjuvant and MVA expressing 1086C Env
Extracted molecule total RNA
Extraction protocol The total RNA was extracted from whole blood using PAXgene blood RNA kit following the manufacturing protocol except for incubating the sample for 60min at 55℃ after the addition of BR2 and Proteinase K
Label Followed the Nanostring Protocol
Label protocol NanoString nCounter gene expression assay protocol was followed
 
Hybridization protocol NanoString nCounter gene expression assay protocol was followed
Scan protocol Samples were scanned on the nCounter prep station following ncounter protocol
Description The extracted RNA was analyzed with Nanostring Non Human Primate panel comprising 754 immune related genes
Data processing Raw data files (RCC) were uploaded to the Nanostring software nSolver v3.022 with the advanced analysis module v2.0. nSolver employed multivariate linear regression models and raw p values were adjusted to Benjamin Yekutieli method to minimize false discovery rate. The Differentially expressed genes were defined as having log 2 fold change≥ 1.5 in expression and an adjusted p value ≤0.1.. Pathway score were generated using nSolver to define potential immune pathways
 
Submission date Dec 24, 2021
Last update date Feb 07, 2022
Contact name Kristina De Paris
E-mail(s) kristina_abel@med.unc.edu
Phone 9198439560
Organization name University of North Carolina at Chapel Hill
Department Department of Microbiology and Immunology
Lab De Paris Lab
Street address Mary Ellen Jones Building , 116 manning Drive
City Chapel Hill
State/province North Carolina
ZIP/Postal code 27599
Country USA
 
Platform ID GPL29936
Series (1)
GSE192584 Nanostring ncounter NHP Immunology V2 panel

Data table header descriptions
ID_REF
VALUE Normalized log2 count

Data table
ID_REF VALUE
ABCB1 4.233
ABL1 5.376
ADA 8.134
AGER 5.263
AHR 7.961
AICDA 1.818
AIRE 2.970
AKT3 9.064
ALOX12 2.348
ALOX15 4.263
ALOX5 7.144
ANP32B 9.998
APOE 2.648
APP 7.972
AREG 2.233
ARG1 2.107
ARG2 8.239
ARHGDIB 12.995
ATF2 7.986
ATG10 6.500

Total number of rows: 753

Table truncated, full table size 8 Kbytes.




Supplementary file Size Download File type/resource
GSM5752017_RM_3_D0.RCC.gz 8.8 Kb (ftp)(http) RCC
Processed data included within Sample table

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