NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5589843 Query DataSets for GSM5589843
Status Public on Sep 20, 2024
Title post-treatment, unstimulated control, OM85 NT021
Sample type SRA
 
Source name PBMC
Organism Homo sapiens
Characteristics subject_id: Subject_43
gender: NA
age at pre-treatment (days): 117
Treatment protocol PBMC cultured in vitro with LPS, PolyI:C or unstimulted controls for 24 hours.
Growth protocol PBMC isolation and storage as per standard protocols
Extracted molecule total RNA
Extraction protocol RNA was extracted using RNeasy mini kit (Qiagen) per the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description post-treatment, unstimulated control, OM85
post-treatment, unstimulated control, OM85
Data processing Image analysis was performed in real time by the HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3, running on the instrument computer.
the Illumina bcl2fastq 2.17.1.14 pipeline was used to generate the sequence data.
Read libraries were mapped to the GRCh37 (hg19) Human genome using HISAT2 (v2.0.4)
Gene-level quantitation (counts) of HISAT2 alignments was performed using SummarizeOverlaps
Genome_build: hg19
Supplementary_files_format_and_content: genecounts.csv file contains a matrix of raw gene counts (filtered and normalised data)
 
Submission date Sep 20, 2021
Last update date Sep 20, 2024
Contact name Niamh Troy
E-mail(s) Niamh.troy@telethonkids.org.au
Organization name Telethon Kids Institute
Street address Perth Children's Hospital, 15 Hospital Avenue Nedlands
City Perth
ZIP/Postal code 6009
Country Australia
 
Platform ID GPL11154
Series (1)
GSE184487 RNA-sequencing of PBMC cultured with PolyI:C or LPS, from a pediatric cohort who received OM85 or placebo.
Relations
BioSample SAMN21527313
SRA SRX12275856

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
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.