|
| Status |
Public on Aug 31, 2023 |
| Title |
27w RNA-Seq |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Equus caballus |
| Characteristics |
individual: horse 1
tissue: liver
|
| Treatment protocol |
The collected material was transferred into tubes and stored at -80°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
DNA was isolated from tissue using a PureLink RNA Mini Kit (Thermo Fisher Scientific)
The RNA-seq was performed using TruSeq RNA Library Prep Kit v2 (Illumina), according to the protocol. The libraries were ligated with different indexes, pooled in one pool and sequenced in the 150 pair-end cycles on HiSeq 4000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
27w
|
| Data processing |
Raw sequencing reads were first subjected to quality control using FastQC software (Babraham Bioinformatics, UK)
Low quality reads (phred-trimming set to 20, quality set to 20 and a minimum read length of 20 was required to pass the filter) and fragments containing adapter sequences were filtered with the use of FlexBar software (Dodt et al., 2012)
The mapping procedure was utilized using Tophat2 software (Trapnell et al., 2009), followed by counting of the reads to the gtf annotation file of Equus Caballus 3.0 assemble release v. 97 with the use of htseq-count software (Anders et al., 2015).
The differential expression analysis was performed with the use of Deseq2 software with the log transformation method (Love et al., 2014)
Genome_build: EquCab3.0
Supplementary_files_format_and_content: Files containing gene counts for every gene and every sample created with htseq-count software
|
| |
|
| Submission date |
Jan 13, 2022 |
| Last update date |
Aug 31, 2023 |
| Contact name |
Ewelina Semik-Gurgul |
| E-mail(s) |
ewelina.semik@iz.edu.pl
|
| Organization name |
National Research Institute of Animal Production
|
| Department |
Department of Animal Molecular Biology
|
| Lab |
Laboratory of Genomics
|
| Street address |
Krakowska 1
|
| City |
Balice |
| ZIP/Postal code |
32083 |
| Country |
Poland |
| |
|
| Platform ID |
GPL21401 |
| Series (1) |
| GSE193661 |
Transcriptome analysis of the three equine tissue |
|
| Relations |
| BioSample |
SAMN24964812 |
| SRA |
SRX13781296 |
