|
| Status |
Public on Jul 04, 2022 |
| Title |
Control RV_6 |
| Sample type |
SRA |
| |
|
| Source name |
Heart Right Ventricle
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Right Ventricle
genotype/condition: Control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol (Invitrogen), according to the manufacturer’s instructions. RNA quality was checked, and RNA was quantified using a NanoDrop spectrophotometer.
RNA libraries were prepared using the TruSeq® Stranded mRNA Library
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Basecalls was performed using bcl2fastq v1.3.0
Sequenced reads were mapped to the human genome assembly (GRCh38) with STAR v2.6.1a with the following options: STAR --readFilesCommand zcat --quantMode TranscriptomeSAM --outFilterMismatchNmax 999 --sjdbGTFfile /home/dnanexus/Homo_sapiens.GRCh38.98.gtf --genomeDir ./home/dnanexus/genome --outSAMstrandField intronMotif --sjdbScore 1 --alignIntronMin 20 --outSAMattributes NH HI AS NM MD --outSAMunmapped Within --alignSJDBoverhangMin 1 --alignIntronMax 1000000 --outSAMtype BAM SortedByCoordinate --alignSJoverhangMin 8 --alignMatesGapMax 1000000 --outFileNamePrefix /home/dnanexus/outputs/ --outFilterMismatchNoverReadLmax 0.04 --outWigStrand Unstranded --runThreadN 16
The quantification of the transcriptome-mapped reads was perfomred using RSEM v1.3.1 with the following command: rsem-calculate-expression --no-bam-output --bam --paired-end --num-threads 8
The raw counts generated from rsem were normalized using the cpm function from edgeR v3.14.0
Assembly: hg38
Supplementary files format and content: csv file for normalized genes counts for all RV samples
|
| |
|
| Submission date |
Mar 14, 2022 |
| Last update date |
Jul 04, 2022 |
| Contact name |
Olivier Boucherat |
| E-mail(s) |
olivier.boucherat@criucpq.ulaval.ca
|
| Organization name |
Laval University
|
| Street address |
2325 Rue de l'Université
|
| City |
Quebec City |
| State/province |
Quebec |
| ZIP/Postal code |
G1V 0A6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE198618 |
Transcriptomic profiling of compensated and decompensated human right ventricles |
|
| Relations |
| BioSample |
SAMN26660369 |
| SRA |
SRX14464120 |
