|
| Status |
Public on Jul 20, 2023 |
| Title |
hSCG_diseased2 |
| Sample type |
SRA |
| |
|
| Source name |
sympathetic ganglion
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: sympathetic ganglion
Sex: male
disease state: heart disease
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated using RNeasy midi-prep kit (Qiagen). The integrity and quantity of RNA was determined using Agilent TapeStation 4200.
Libraries were prepared from 1 µg RNA using Illumina TruSeq Stranded mRNA kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Illumina TruSeq Stranded mRNA
|
| Data processing |
bcl2fastq for basecalling, fastq conversion and demultiplexing
RNA STAR (in Galaxy) with default parameters for alignment
StringTie (in Galaxy) was used for transcript assembly and quantification
Assembly: DESeq2 (in Galaxy) for differential expression analysis and normalizing the counts
Supplementary files format and content: GRCh38, Gencode annotation v34
Supplementary files format and content: Excel files include gene abundance values for each sample
|
| |
|
| Submission date |
May 05, 2023 |
| Last update date |
Jul 20, 2023 |
| Contact name |
Karin A. Ziegler |
| E-mail(s) |
[email protected]
|
| Organization name |
Technical University of Munich
|
| Street address |
Biedersteiner Str. 29
|
| City |
Munich |
| ZIP/Postal code |
80802 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE231763 |
RNA-seq of heart healthy and heart diseased SCGs |
| GSE231767 |
heart healthy and heart diseased SCGs |
|
| Relations |
| BioSample |
SAMN34622687 |
| SRA |
SRX20235495 |
