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Sample GSM7785103 Query DataSets for GSM7785103
Status Public on May 29, 2024
Title 21s004525
Sample type SRA
 
Source name Myocardium
Organism Homo sapiens
Characteristics tissue: Myocardium
disease: ICM
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 miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina NextSeq 500
 
Description ICM_5_miRNA
named_count_matrix_miR.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 SAMN37435023
SRA SRX21802709

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

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