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| Status |
Public on Sep 29, 2023 |
| Title |
Decompensated RV female (Decomp-f_2) |
| Sample type |
SRA |
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| Source name |
Right ventricle
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| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Right ventricle
Sex: F
condition: Decompensated RV
batch: batch 2
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| Extracted molecule |
total RNA |
| Extraction protocol |
MCT tissues from MCT-treated rats were harvested after RHC measurements and snap-frozen. Total RNA from each batch of RV samples were isolated separately using the RNeasy Mini Kit (or miRNeasy Micro Kit, when less sample provided-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).
Following the RNA integrity measurement, approximately 2 µg of total RNA were used as starting material for library preparation using the VAHTS Stranded mRNA-seq Library preparation following manufacture’s protocol (Vazyme)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
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| Description |
processed-data-mct.xlsx
count matrix column name: Decomp-f_2
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| Data processing |
Raw reads were assessed for quality, adapter content, and duplication rates using FastQC59. Trimmomatic version 0.39 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 for each organism were normalized separately 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: BATCH 1. matrix of raw read counts for genes*samples
Supplementary files format and content: excel file containing sheet 2: BATCH 2. matrix of raw read counts for genes*samples
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| Submission date |
Aug 15, 2023 |
| Last update date |
Sep 29, 2023 |
| Contact name |
Fatemeh Khassafi |
| E-mail(s) |
s.khassafi92@gmail.com
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| Organization name |
Max Planck Institute
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| Lab |
Soni Pullamsetti
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| Street address |
Parkstrasse
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| City |
Bad Nauheim |
| ZIP/Postal code |
61231 |
| Country |
Germany |
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| Platform ID |
GPL32190 |
| Series (2) |
| GSE240923 |
Transcriptional profiling of male and female MCT-induced rats with compensated and decompensated right ventricle |
| GSE240941 |
Transcriptional profiling unveils molecular subgroups of adaptive and maladaptive right ventricular remodeling in pulmonary hypertension |
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| Relations |
| BioSample |
SAMN36996191 |
| SRA |
SRX21375603 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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