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Sample GSM5815766 Query DataSets for GSM5815766
Status Public on Aug 31, 2023
Title 34w RNA-Seq
Sample type SRA
 
Source name liver
Organism Equus caballus
Characteristics individual: horse 4
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 34w
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 SAMN24964803
SRA SRX13781305

Supplementary file Size Download File type/resource
GSM5815766_34wcount.txt.gz 108.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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