|
| Status |
Public on Nov 22, 2020 |
| Title |
OM_058 |
| Sample type |
SRA |
| |
|
| Source name |
Thymus
|
| Organism |
Mus musculus |
| Characteristics |
strain: BALB/c
tissue: Thymus
age: Gestation day 18.5
maternal treatment: Naïve
fetal gender: Male
|
| Treatment protocol |
Maternal OM-85 from GD9.5-17.5
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Fetal bone marrow and thymus samples were homogenised using a rotor-star homogeniser (Qiagen) and total RNA extracted via TRIzol (Ambion), followed by RNA elution using RNeasy MinElute (Qiagen). RNA integrity was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies; RIN: 10 ± 0 (mean ± SD)).
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| 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. RTA performs real-time base calling on the HiSeq instrument computer. Then the Illumina bcl2fastq 2.17.1.14 pipeline was used to generate the sequence data.
Sequencing data quality control (QC) was performed with the Bioconductor package Rqc (de Souza et al. J Statistical Software. 2018). Sequencing reads were aligned to the reference murine genome (mm10) using Subread and summarised at the gene level using featureCounts (Liao et al. Genome Biol. 2014). Sample QC was performed by analysing the distribution of the raw read counts to check for sample outliers using boxplots, relative log-transformed expression (RLE) plots and principal component analysis (PCA), before and after global-scale median normalisation.
Genome_build: mm10
Supplementary_files_format_and_content: OM_counts_mm10.csv
|
| |
|
| Submission date |
Nov 08, 2019 |
| Last update date |
Nov 22, 2020 |
| Contact name |
Kyle Mincham |
| E-mail(s) |
kyle.mincham@telethonkids.org.au
|
| Organization name |
Telethon Kids Institute
|
| Street address |
Northern Entrance, Perth Children’s Hospital, 15 Hospital Avenue, Nedlands
|
| City |
Perth |
| ZIP/Postal code |
6009 |
| Country |
Australia |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE140143 |
Transplacental Innate Immune Training via Maternal Microbial Exposure: Role of XBP1-ERN1 Axis in Dendritic Cell Precursor Programming |
|
| Relations |
| BioSample |
SAMN13243147 |
| SRA |
SRX7119239 |
