|
| Status |
Public on Oct 12, 2023 |
| Title |
PeripheralBlood_Case13 |
| Sample type |
SRA |
| |
|
| Source name |
peripheral blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: peripheral blood
disease state: sALS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from peripheral blood using the QIASymphony automated liquid handing robot and the PAXgene Blood RNA kit (Qiagen, Hilden, Germany) as per standard protocol.
RNA-seq libraries were prepared from total RNA using the TruSeq Stranded mRNA Sample Prep kit (Illumina, CA, USA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Trimmomatic v0.38 was applied to raw FASTQ files to remove low quality reads and adaptor sequences.
Salmon v1.9.0 was used to build a transcriptome index and to quantify transcripts (default selective alignment with --seqBias and --gcBias flags).
Tximport v1.26.1 was used to convert transcript abundance estimates to gene-level counts with corresponding offset matrix.
Assembly: GRCh38
Supplementary files format and content: tab delimited text file including raw gene counts
Supplementary files format and content: tab delimited text file including tximport-generated offset matrix
|
| |
|
| Submission date |
Jun 06, 2023 |
| Last update date |
Oct 12, 2023 |
| Contact name |
Kelly Williams |
| E-mail(s) |
kelly.williams@mq.edu.au
|
| Organization name |
Macquarie University
|
| Department |
Motor Neuron Disease Centre
|
| Street address |
75 Talavera Road
|
| City |
Sydney |
| State/province |
NSW |
| ZIP/Postal code |
2109 |
| Country |
Australia |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE234297 |
RNA sequencing of peripheral blood in amyotrophic lateral sclerosis reveals distinct molecular subtypes: considerations for biomarker discovery |
|
| Relations |
| BioSample |
SAMN35652564 |
| SRA |
SRX20607844 |
