|
| Status |
Public on Apr 18, 2024 |
| Title |
Pat-33-preBL |
| Sample type |
SRA |
| |
|
| Source name |
myocardial interventricular septum biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: myocardial interventricular septum biopsy
disease state: CTEPH
individual: Pat-33
Sex: Male
treatment: pre-septal-PEA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the miRNeasy micro Kit (Qiagen) and Covaris Cryo-Prep homogenization. To avoid contamination by genomic DNA samples were treated by on-column DNase digestion (RNase-Free DNase Set, Qiagen). Total RNA and library integrity were verified on LabChip Gx Touch 24 (Perkin Elmer).
Approximately 100ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara Bio). Sequencing was performed on the NextSeq500 instrument (Illumina) using v2 chemistry with 1x75bp single end setup or NextSeq2000 using P2 flowcell with v3 chemistry with 1x72bp single-end setup.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl human genome version hg38 (Ensembl release 104) with STAR 2.7.9a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Aligned reads were filtered to remove: duplicates with Picard 2.25.5 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The Ensemble annotation was enriched with UniProt data (Activities at the Universal Protein Resource (UniProt)).
Assembly: hg38
Supplementary files format and content: The tab-delimited matrix shows raw gene counts.
|
| |
|
| Submission date |
Dec 08, 2023 |
| Last update date |
Apr 18, 2024 |
| Contact name |
Carsten Kuenne |
| E-mail(s) |
Carsten.Kuenne@mpi-bn.mpg.de
|
| Organization name |
Max Planck Institute for Heart and Lung Research
|
| Department |
Bioinformatics
|
| Street address |
Ludwigstrasse 43
|
| City |
Bad Nauheim |
| ZIP/Postal code |
61231 |
| Country |
Germany |
| |
|
| Platform ID |
GPL30173 |
| Series (2) |
| GSE249694 |
Transcriptional changes of the extracellular matrix in chronic thromboembolic pulmonary hypertension governs right ventricle remodeling and recovery [ext327_rnaseq] |
| GSE249697 |
Transcriptional changes of the extracellular matrix in chronic thromboembolic pulmonary hypertension governs right ventricle remodeling and recovery |
|
| Relations |
| BioSample |
SAMN38730620 |
| SRA |
SRX22832256 |
