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| Status |
Public on Oct 13, 2020 |
| Title |
Non_agg_6_rnaseq |
| Sample type |
SRA |
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| Source name |
Prefrontal cortex
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| Organism |
Bos taurus |
| Characteristics |
tissue: brain
breed: Wagyu
brain region: Prefrontal cortex
age: 3 years
genotype: non-aggressive
Sex: male
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| Extracted molecule |
total RNA |
| Extraction protocol |
PFC were removed, preserved with RNA-later and then RNA extacted with Rneasy Lipid tissue Mini kit, and RNApreserved with RNAstable, Illumina TruSeq stranded mRNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Illumina Casava1.7 software used for de-multiplex individual reads
Read quality of the sixteen RNA-seq datasets was checked and trimmed using PRINSEQ v. 0.20.4
Trimmed reads were then mapped to the bovine reference genome (Bos taurus ARS.UCD 1.2) with STAR v.2.7.3a
The SAM files generated by STAR, which contains the count of reads per base aligned to each location across the length of the genome, were converted into a binary alignment/map (BAM) format and sorted using SAMTools v.0.1.18
The aligned RNA-seq reads were assembled into transcripts and their abundance in fragments per kilobase of exon per million fragments mapped (FKPM) was determined with Cufflinks v.2.2.1
Analysis of differential gene expression across aggressive and non-aggressive groups was performed using Cuffdiff
Genome_build: Bos_taurus_ARS.UCD 1.2
Supplementary_files_format_and_content: text files include gene transcript values for each Sample
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| Submission date |
Apr 20, 2020 |
| Last update date |
Oct 24, 2020 |
| Contact name |
Paulina G. Eusebi |
| E-mail(s) |
paulig01@ucm.es
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| Organization name |
Universidad Complutense de Madrid
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| Department |
Animal Production
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| Lab |
Genetics lab
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| Street address |
Ave. Puerta del hierro
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| City |
madrid |
| State/province |
madrid |
| ZIP/Postal code |
28080 |
| Country |
Spain |
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| Platform ID |
GPL26012 |
| Series (1) |
| GSE148938 |
Gene expression profiles underlying aggressive behavior in the prefrontal cortex of cattle |
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| Relations |
| BioSample |
SAMN14644773 |
| SRA |
SRX8142664 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4486317_6.transcripts.txt.gz |
6.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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