NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7147913 Query DataSets for GSM7147913
Status Public on Jul 19, 2023
Title Latent Tuberculosis 2
Sample type RNA
 
Source name Latent Tuberculosis
Organism Homo sapiens
Characteristics tissue: blood
age: 33
gender: Male
Extracted molecule total RNA
Extraction protocol Total RNA including miRNA was isolated from the sorted monocytes (Range: 1 to 2.8 million cells) in RLT buffer using Phenol-Chloroform and Qiagen miRNAeasy mini kit (Cat#217004). Samples were extracted with standard Phenol-chloroform mixture. Aqueous phase obtained after centrifugation was mixed with 700 µl of QIAzol Lysis reagent and mixed well. Lysate was incubated at room temperature for 5 minutes and 140 µl of chloroform was added for phase separation. Rest of the protocol was followed as per manufacturer’s guidelines. RNA was eluted in 20µl of nuclease free water (Ambion, Cat # AM9932). Quantitation was performed using Qubit RNA HS assay (Invitrogen, Cat # Q32855) kit and also qualitatively analysed on Agilent 2100 bioanalyzer nano chip (Agilent, Cat # 5067-1511). 100ng of total RNA was used for miRNA assay.
Label not provided
Label protocol NanoString uses combination of oligonucleotide based barcodes. Each probe hybridising the miRNAs will be unique with combination of color dye combination which are barcoded barcodes.
 
Hybridization protocol Total RNA was processed using the Nanostring nCounter v3.0a array.
Scan protocol Hybridized molecules are loaded to Nanostring sprint catridge and loaded onto nCounter SPRINT machine for scanning the barcodes. Raw counts data (.RCC) was retrieved from the machine after the scanning completes.
Data processing Raw data were normalized using nSolver 4.0 software. Normalization of the raw data was performed using the geometric mean of positive controls and top 100 highly expressed miRNAs (CV% < 50) as per the instructions in the manual (nCounter Data Analysis Guidelines for miRNA (LBL-C0046-01) and nSolverTM 4.0 Analysis Software User Manual (MAN-C0019-08)).
NSolver 4.0 software was used to compute Normalized counts.
 
Submission date Apr 05, 2023
Last update date Jul 19, 2023
Contact name Ramalingam Bethunaickan
E-mail(s) bramalingam@gmail.com
Phone 9677074680
Organization name ICMR-National Institute for Research in Tuberculosis
Department Immunology
Lab Molecular Immunology
Street address No.1. Mayor Satya murthy Road, Chetpet
City Chennai
State/province Tamil Nadu
ZIP/Postal code 600031
Country India
 
Platform ID GPL24158
Series (1)
GSE229020 Down regulation of Monocyte miRNAs: Implications for Immune Dysfunction and Disease Severity in Drug-Resistant Tuberculosis

Supplementary file Size Download File type/resource
GSM7147913_SAM1550_08.RCC.gz 7.3 Kb (ftp)(http) RCC
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.