|
| Status |
Public on Sep 12, 2023 |
| Title |
AAS_06_Atopic asthmatic_convalescent_visit_L004 |
| Sample type |
SRA |
| |
|
| Source name |
AAS_06_Atopic asthmatic_convalescent_visit
|
| Organism |
Homo sapiens |
| Characteristics |
subjectid: Subject_03
visit: CV
age at visit (years): 9.09
gender: Female
hdm-specific ige: NA
total ige: NA
cat-specific ige: NA
pbmc processing day (1=sameday, 2=overnight): 1
cell type: PBMC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from viable PBMC employing TRizol (Ambion, Life Technologies) followed by RNeasy MinElute (Qiagen, Hilden, Germany). The integrity of the RNA was 9.5 ± 0.3 (mean ± SD), as assessed on the Bioanalyzer (Agilent Technologies, California, USA).
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 |
| |
|
| Description |
There are 38 samples; each sample was sequenced across two lanes.
AAS_06 sequenced on lane L004
AAS_06_C80BLANXX_GTGAAA_L004
Barcode: GTGAAA
|
| Data processing |
The Illumina bcl2fastq 1.8.4 pipeline was used to generate the sequence data.
Raw sequencing reads were aligned to the reference genome (hg19) using Rsubread and summarised at the gene-level with featureCounts. Genes were annotated using the genome wide annotation for human org.Hs.eg.db.
Genome_build: hg19
Supplementary_files_format_and_content: AAS_raw_counts.txt file includes raw-gene level counts. Sample were sequenced across two lanes and need to be collapsed prior to further downstream analysis (AAS_raw_counts_collapsed.txt). For differential expression analysis, the raw counts were used.
Supplementary_files_format_and_content: AAS_VST_transformed_counts.txt file includes DESeq2 vst transformed counts and samples need to be collapsed prior to further downstream analysis (AAS_VST_transformed_counts_collapsed.txt). For network analysis, the vst transformed data was used.
|
| |
|
| Submission date |
Mar 13, 2017 |
| Last update date |
Sep 12, 2023 |
| Contact name |
Anya Jones |
| E-mail(s) |
Anya.Jones@telethonkids.org.au
|
| Organization name |
Telethon Kids Institute, The University of Western Australia
|
| Lab |
Systems Immunology
|
| Street address |
Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue
|
| City |
Nedlands |
| State/province |
Western Australia |
| ZIP/Postal code |
6009 |
| Country |
Australia |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE96530 |
LPS binding protein and activation signatures are upregulated during asthma exacerbations in children |
|
| Relations |
| BioSample |
SAMN06563805 |
| SRA |
SRX2635319 |
