 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 29, 2023 |
| Title |
Control RV [CTRL_4] |
| Sample type |
SRA |
| |
|
| Source name |
Control RV
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Right ventricle
Sex: male
tissue type: Control RV
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RV tissues from PAB-treated rats were harvested after RHC measurements and snap-frozen. Total RNA was isolated from RV samples using miRNeasy Micro Kit (Qiagen) and snap-frozen. Purification of total RNA was performed as described in the RNeasy handbook, using DNase I digestion (RNase-Free DNase Set, Qiagen).
RNA and library preparation integrity were verified with LabChip Gx Touch 24 (Perkin Elmer), and 2 µg of total RNA was used as input forVAHTS Stranded mRNA-seq Librarypreparation following manufacture’s protocol (Vazyme).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
processed-data-pab.xlsx
|
| Data processing |
Raw reads were assessed for quality, adapter content, and duplication rates using FastQC. Trimmomatic was employed to trim reads following a quality drop (below a mean of Q15) in a window of five nucleotides
STAR mapping: mode: single-end, keep duplicates: no, keep multi-mapping: no, keep ribosomal: no, keep mitochondria: no --outFilterMismatchNoverLmax 0.1 --outFilterMatchNmin 20 --alignEndsProtrude 10 ConcordantPair --alignMatesGapMax 2000 --limitOutSAMoneReadBytes 10000000 --outMultimapperOrder Random --sjdbOverhang 100 --alignIntronMax 200000 --outFilterMultimapNmax 999 --outSAMmultNmax -1 --genomeDir /rattus_norvegicus/104/index_star
FEATURE COUNT: The number of reads that aligned to genes was counted using featureCounts version 1.6.5 from the Subread package. Only reads mapping at least partially inside exons were aggregated and counted per gene. Reads aligning to multiple regions or genes were excluded. -t exon -g gene_id -s 2; multi-mapping: no; duplicates: no
Raw count values were normalized using DESeq2 version 1.30.0, then transformed into regularized logarithm values for further analysis. The normalized data were the basis of downstream analysis.
Assembly: Rn06/104/
Supplementary files format and content: excel file containing sheet 1: sample labels and mapping parameters
Supplementary files format and content: excel file containing sheet 2: matrix of raw read counts for genes*samples
|
| |
|
| Submission date |
Aug 31, 2023 |
| Last update date |
Sep 29, 2023 |
| Contact name |
Fatemeh Khassafi |
| E-mail(s) |
s.khassafi92@gmail.com
|
| Organization name |
Max Planck Institute
|
| Lab |
Soni Pullamsetti
|
| Street address |
Parkstrasse
|
| City |
Bad Nauheim |
| ZIP/Postal code |
61231 |
| Country |
Germany |
| |
|
| Platform ID |
GPL32190 |
| Series (2) |
| GSE240941 |
Transcriptional profiling unveils molecular subgroups of adaptive and maladaptive right ventricular remodeling in pulmonary hypertension |
| GSE242014 |
Transcriptional profiling of male PAB rats with compensated and decompensated right ventricule |
|
| Relations |
| BioSample |
SAMN37209925 |
| SRA |
SRX21545416 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
