|
| Status |
Public on May 29, 2024 |
| Title |
21s004505 |
| Sample type |
SRA |
| |
|
| Source name |
Myocardium
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Myocardium
disease: DCM
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using miRNeasy Tissue/Cells Advanced Micro Kit (Qiagen). 1.5 ug of total RNA was used for the construction of sequencing libraries
Standard-specific mRNA sequencing (mRNA-seq) libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA). Standard miRNA libraries were generated using the NEXTFLEX small RNA-seq kit v3 (Perkin Elmer, Waltham, MA, USA)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
DCM_18_mRNA
named_count_matrix.xlsx
|
| Data processing |
European version of the Galaxy platform (https://usegalaxy.eu/)
Reads were trimmed with the Trim Galore software (Galaxy Version 0.6.7+galaxy0)
Trimmed sequences reads were aligned to the built-in human reference genome Dec. 2013 (GRCh38/hg38) with the RNA STAR Gapped-read mapper (Galaxy Version 2.7.10b+galaxy3)
For gene expression analyses, bam files were downloaded from the Galaxy server and further analyzed with the different RStudio packages downloaded from the Bioconductor website (http://bioconductor. org).
Reads were assigned to genes by means of the “featureCounts” function of the “Rsubread” package, version 2.10.5. and annotation files human release 43 (GRCh38.p13) (https://www.gencodegenes.org/human/release_43.html) and Chromosomal coordinates of Homo sapiens microRNAs (https://www.mirbase.org/ftp/CURRENT/genomes/hsa.gff3) for mRNA and miRNA analysis respectively.
Assembly: hg38
Supplementary files format and content: execel file includes raw mRNA count for each sample
Supplementary files format and content: execel file includes raw miRNA count for each sample
|
| |
|
| Submission date |
Sep 18, 2023 |
| Last update date |
May 29, 2024 |
| Contact name |
Francisco Hernandez-Torres |
| E-mail(s) |
fhtorres@ugr.es
|
| Phone |
+34 637833588
|
| Organization name |
Universidad de Granada
|
| Department |
Dept. of Biochemistry, Molecular Biology III and Immunology
|
| Street address |
Avda. de la Investigación, 11
|
| City |
Granada |
| State/province |
Granada |
| ZIP/Postal code |
18016 |
| Country |
Spain |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE243406 |
Unravelling the etiology of dilated cardiomyopathy through differential miRNA-mRNA interactome |
|
| Relations |
| BioSample |
SAMN37435025 |
| SRA |
SRX21802707 |
