|
| Status |
Public on Jan 31, 2024 |
| Title |
Healthy control-1 |
| Sample type |
SRA |
| |
|
| Source name |
PBMCs
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: PBMCs
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from the peripheral blood mononuclear cells (PBMCs) of the patient and healthy controls using Blood RNA purification kit (Macherey-Nagel).
RNA libraries were prepared using an Illumina Stranded mRNA Prep kit according to the manufacturer's protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Adapters were trimmed using cutadapt version 4.1 and the following parameters: -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT --minimum-length=18 --error-rate 0.2 --overlap=5
Reads were aligned to the hg38 reference genome using STAR version 2.7.7a, producing gene counts for each sample
Assembly: GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz using RefSeq annotations
Supplementary files format and content: <library_name>.hg38.ReadsPerGene.out.tab: tab-separated gene counts file for each sample
Supplementary files format and content: gene_counts.tsv: tab-separated file containing strand-specific gene counts for all samples
|
| |
|
| Submission date |
Sep 14, 2023 |
| Last update date |
Feb 24, 2024 |
| Contact name |
Nick Warnock |
| E-mail(s) |
nick.warnock@unisa.edu.au
|
| Organization name |
SA Pathology
|
| Department |
Centre for Cancer Biology
|
| Lab |
ACRF Cancer Genomics Facility
|
| Street address |
UniSA Bradley Building, North Terrace
|
| City |
Adelaide |
| State/province |
South Australia |
| ZIP/Postal code |
5000 |
| Country |
Australia |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE243237 |
Effect of R22W mutation in TFRC gene on gene expression in PBMCs |
|
| Relations |
| Reanalyzed by |
GSM8105761 |
| BioSample |
SAMN37397222 |
| SRA |
SRX21778811 |
