|
| Status |
Public on Jun 12, 2024 |
| Title |
Atrial Fibrillation/ Diseased [AF_39703] |
| Sample type |
SRA |
| |
|
| Source name |
Left atria
|
| Organism |
Capra hircus |
| Characteristics |
tissue: Left atria
treatment: Atrial Fibrillation/ Diseased
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from tissue was harvested using Trizol reagent. Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA)
RNA libraries were prepared for sequencing using standard NEB protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were mapped to the reference genome using HISAT2 software. The Stringtie was used to assemble the set of transcript isoforms of each bam file obtained in the mapping step. gffcompare can compare Strintie assemblies to reference annotation files and help sort out new genes from known ones. Featurecounts was used to count the read numbers mapped of each gene, including known and novel genes. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using DESeq2 R package. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR). Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed.
Supplementary files format and content: read counts for all samples
|
| |
|
| Submission date |
Mar 27, 2023 |
| Last update date |
Jun 12, 2024 |
| Contact name |
Rebecca Burton |
| Organization name |
University of Liverpool
|
| Department |
Pharmacology and Therapeutics
|
| Lab |
Burton
|
| Street address |
Nuffield Red Block, Sherrington Building
|
| City |
Liverpool |
| ZIP/Postal code |
L69 3GE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL27106 |
| Series (1) |
| GSE228289 |
Compartmentalisation proteomics revealed endolysosomal protein network changes in goat model of atrial fibrillation |
|
| Relations |
| BioSample |
SAMN33939507 |
| SRA |
SRX19785466 |
