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Sample GSM3729005 Query DataSets for GSM3729005
Status Public on Apr 17, 2020
Title AW0: PBMC_BCG_wk0_AW
Sample type RNA
 
Source name Peripheral Blood, pre-BCG
Organism Macaca mulatta
Characteristics gender: M
infant id: A16188-AW
week post-bcg timepoint: 0
bcg status: BCG-vaccinated
Treatment protocol NA
Growth protocol NA
Extracted molecule total RNA
Extraction protocol Ficoll-paque gradient centrifugation was used to isolate 3.0EE6 macaque peripheral bllood mononuclear cells (PBMC) from EDTA-treated whole blood. Cellular RNA was extracted using the Macherey Nagel Nucleospin column purification system following the manufactureres instructions. PBMC were lysed by resuspending the 3.0EE6-cell pellat in 300µL of buffer RA1 with 1% beta-mercaptoethanol and storing long term at -80˚C. Lysed cells were thawed and RNA was purified prior to nanostring analysis.
Label NA
Label protocol NA
 
Hybridization protocol 100 nanograms of RNA was directly hybridized for 18 hours using the Non-human Primate Immunology v2.0 chipset.
Scan protocol Images were acquired from 280 fields for each sample
Data processing Raw data were processed in nSolver 4.0 using Advanced Analysis with R version 3.3.2 by running Normalization with the default settings of a threshold count value of 20 and an observation frequency of 1 with automatic selection of optimal house keeping genes.
 
Submission date Apr 17, 2019
Last update date Apr 18, 2020
Contact name Matthew Price Wood
E-mail(s) matthew.wood@seattlechildrens.org
Phone 2062568843239
Organization name Seattle Children's Research Institute
Department Global Infectious Diseases
Lab Sodora
Street address 307 Westlake Ave North
City Seattle
State/province WA
ZIP/Postal code 98106
Country USA
 
Platform ID GPL26516
Series (1)
GSE129989 BCG_CNRL_wk0vs3_infantMM

Data table header descriptions
ID_REF
VALUE Normalized fluorescent probe counts

Data table
ID_REF VALUE
PTGS1-mRNA 7.776476782
C1QBP-mRNA 9.181172337
MAFK-mRNA 3.232156266
NFE2L2-mRNA 8.379643879
SOCS1-mRNA 7.843590978
DOCK9-mRNA 7.981094502
TLR6-mRNA 7.562077152
STAT4-mRNA 7.393148143
CCL15-mRNA 5.647193765
C1QA-mRNA 6.437270696
C8B-mRNA 3.869586187
TSLP-mRNA 3.762670983
HMGB1-mRNA 12.2343462
MX1-mRNA 12.12731075
STAT2-mRNA 10.92254232
IL8-mRNA 8.695226462
ILF3-mRNA 10.55508588
DEFA1-mRNA 7.028015549
AREG-mRNA 6.957049028
IL22-mRNA 3.38415936

Total number of rows: 753

Table truncated, full table size 16 Kbytes.




Supplementary file Size Download File type/resource
GSM3729005_20181024_MW-2_AW0_03.RCC.gz 8.7 Kb (ftp)(http) RCC
Processed data included within Sample table

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