|
| Status |
Public on Jul 03, 2023 |
| Title |
Donor_8 |
| Sample type |
SRA |
| |
|
| Source name |
pulmonary artery trunk
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: pulmonary artery trunk
disease: healthy heart
age: 41
Sex: M
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Snap-frozen PA specimens were subjected to TRIzol-RNA extraction. RNA quality was assessed by measuring the RNA integrity number (RIN) using a Fragment Analyzer HS Total RNA Kit (Advanced Analytical Technologies, Inc.).
Library preparation for total RNA-Seq was performed using TruSeq™ Stranded Total RNA with Ribo-Zero Gold (Illumina, Cat. Nr. RS-122-2301) starting from 1000 ng of total RNA. The size range of the final cDNA libraries was determined by applying the SS NGS Fragment 1- to 6000-bp Kit on the Fragment Analyzer (average 340 bp). Accurate quantification of cDNA libraries was performed by using the QuantiFluor™ dsDNA System (Promega).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequence images were transformed with BaseCaller Illumina software to BCL files and demultiplexed to fastq files with bcl2fastq v2.20.0.422.
Sequencing quality was determined using FastQC v. 0.11.5 software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Sequences were aligned to the reference genome Homo sapiens (hg38 version 96, https://www.ensembl.org/Homo_sapiens/Info/Index) using STAR aligner v. 2.5.2a, allowing for 2 mismatches within 50 bases.
Read counting was performed using featureCounts v. 1.5.0-p1.
Read counts were analyzed in the R/Bioconductor environment v. 3.6.1 (www.bioconductor.org) using the DESeq2 package v. 1.24.0.
Genes were annotated using the Homo sapiens GTF file hg38 version 96 (https://www.ensembl.org/Homo_sapiens/Info/Index) to quantify the reads within genes.
Supplementary files format and content: Tab-delimited gene counts
|
| |
|
| Submission date |
Jun 30, 2023 |
| Last update date |
Jul 03, 2023 |
| Contact name |
Gabriela Salinas |
| E-mail(s) |
Gabriela.Salinas-Riester@medizin.uni-goettingen.de
|
| Organization name |
Universitaetsmedizin Goettingen
|
| Department |
Department of Pathology
|
| Lab |
NGS Integrative Genomics
|
| Street address |
Kreuzbergring 57
|
| City |
Goettingen |
| State/province |
Lower-Saxony |
| ZIP/Postal code |
37075 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE236251 |
Effect of pulmonary hypertension due to left heart disease on gene expression in pulmonary arteries |
|
| Relations |
| BioSample |
SAMN36175541 |
| SRA |
SRX20851394 |
