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Sample GSM7794857 Query DataSets for GSM7794857
Status Public on Sep 25, 2023
Title BALF-MP-WTM-CGB090
Sample type RNA
 
Source name Bronchoalveolar lavage fluids
Organism Macaca fascicularis
Characteristics cell type: CD64+ macrophages
viral status: >221 days post infection with the wild type Wuhan strain
Growth protocol Macrophages were isolated from BALF samples using a positive selection strategy. We employed the anti-CD64 PE-conjugated monoclonal antibody (clone 10.1, BD Bioscience, USA) for this purpose.To reveal the isolated macrophages, anti-PE microbeads from Miltenyi Biotec (USA) were utilized. These macrophages were cultured for 8h.
Extracted molecule total RNA
Extraction protocol After the incubation, the cells were resuspended in 30µl of RLT buffer with beta-mercaptoethanol (Qiagen) following the Nanostring protocols recommendation for cell Lysate (MAN-10051-05).
Label n/a
Label protocol The system uses molecular “barcodes” and single molecule imaging to detect and count hundreds of unique transcripts in a single reaction.
 
Hybridization protocol Seventy microliters of hybridization buffer was added to the reporter code set to make a master mixture. 2,1µl of proteinase K were added. Eight microliters of this master mixture was then incubated in separate tubes with 5µl of the lysate's sample and 2 ul of the capture code set. This hybridization mixture was incubated at 65°C for 18 hours. The hybridization mixture bind to Cartridge with a NanoString Prepstation.
Scan protocol The cartridgenCounter™ Analysis System allows then to collect image and count barcodes.
Data processing Raw counts were normalized to geometric mean counts of the synthetic positive controls included on the codeset. nCAAM and the geNorm algorithm was used to normalize each dataset by taking the five most stable housekeeping genes across samples and using it on all datasets.
Data were analyzed by ROSALIND® (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step. Normalization, fold changes and p-values were calculated using criteria provided by Nanostring. ROSALIND® follows the nCounter® Advanced Analysis protocol of dividing counts within a lane by the geometric mean of the normalizer probes from the same lane. Housekeeping probes to be used for normalization are selected based on the geNorm algorithm as implemented in the NormqPCR R library.
 
Submission date Sep 21, 2023
Last update date Sep 25, 2023
Contact name Nicolas Huot
E-mail(s) nicolas.huot@pasteur.fr
Organization name Institut Pasteur
Street address 28, rue du Dr Roux
City Paris
ZIP/Postal code 75015
Country France
 
Platform ID GPL29936
Series (2)
GSE243731 SARS-CoV-2 viral persistence in lung alveolar macrophages is controlled by IFN-g and NK cells [BALF_Macro_SARS_NHP]
GSE243734 SARS-CoV-2 viral persistence in lung alveolar macrophages is controlled by IFN-g and NK cells

Data table header descriptions
ID_REF
VALUE Normalized signal

Data table
ID_REF VALUE
ABCB1 4.4571672666719
ABL1 8.83963690349432
ADA 7.29366853438902
AGER 4.23477484533545
AHR 10.1396603050536
AICDA 2.97174043950166
AIRE 5.4571672666719
AKT3 9.4013564037034
ALOX12 2.6498123446143
ALOX15 0.649812344614299
ALOX5 11.517091084324
ANP32B 9.95815137475371
APOE 15.0200229512809
APP 13.0716142050842
AREG 8.76875341733781
ARG1 2.6498123446143
ARG2 6.83963690349432
ARHGDIB 13.1755778234362
ATF2 8.9305831147449
ATG10 7.36405786228042

Total number of rows: 753

Table truncated, full table size 16 Kbytes.




Supplementary file Size Download File type/resource
GSM7794857_CGB090-Wu.RCC.gz 8.7 Kb (ftp)(http) RCC

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