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Sample GSM7712180 Query DataSets for GSM7712180
Status Public on Sep 29, 2023
Title late decompensated (DECOMP-MCT69-RV14)
Sample type SRA
 
Source name Right ventricle
Organism Rattus norvegicus
Characteristics tissue: Right ventricle
Sex: M
condition: late decompensated
batch: batch 1
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)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 2000
 
Description processed-data-mct.xlsx
count matrix column name: DECOMP-MCT69-RV14
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
 
Submission date Aug 15, 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)
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
Relations
BioSample SAMN36996213
SRA SRX21375581

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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