|
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 |