|
| Status |
Public on Jan 14, 2025 |
| Title |
AHP_T2 |
| Sample type |
SRA |
| |
|
| Source name |
whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: whole blood
time: 3 month post-intake
treatment: tick-bitten participant
batch: 1
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cellular RNA was manually extracted from whole blood collected in PAXgene blood RNA tubes using PAXgene blood miRNA kit (PreAnalytiX GmbH; Hombrechtikon, Switzerland) following manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using Illumina stranded mRNA Library Prep (Illumina; San Diego, CA, USA) following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Library name: AHP_T2
|
| Data processing |
The raw FASTQ data were transferred via RSYNC into a Linux virtual machine for pre-processing and FASTQ sequence reads with more than one file was concatenated.
Quality control was performed using FastQC v0.12.0 and MultiQC v1.13.
STAR v2.7.10b was used to align the untrimmed FASTQ sequences (inclusive of adapters and indexes) to hg38 transcripts.
The BAM files generated by STAR were indexed by Samtools 1.16.1 and SAM files.
HTseq v2.0.2 was used to perform read counts on the SAM files and generate raw RNA count files.
Assembly: Ensembl GRCh38.86
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
|
| |
|
| Submission date |
Jan 14, 2025 |
| Last update date |
Jan 14, 2025 |
| Contact name |
Wenna Lee |
| E-mail(s) |
wenna.lee@thekids.org.au
|
| Organization name |
The Kids Research Institute Australia
|
| Street address |
Perth Children's Hospital, 15 Hospital Ave, 15 Hospital Ave
|
| City |
Nedlands WA |
| State/province |
WA |
| ZIP/Postal code |
6009 |
| Country |
Australia |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE286962 |
From Local to Systemic: The Journey of Tick Bite Biomarkers in Australian patients. |
|
| Relations |
| BioSample |
SAMN45230048 |
| SRA |
SRX27266617 |
