|
| Status |
Public on Dec 18, 2018 |
| Title |
Pcal |
| Sample type |
SRA |
| |
|
| Source name |
fore- and mid-brain
|
| Organism |
Peromyscus californicus |
| Characteristics |
tissue: fore- and mid-brain
Sex: male
state: reproductive
number of individuals pooled: 3
annotation genome: 3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
fore- and mid-brains were rapidly dissected and flash frozen on dry ice or preserved in RNAlater and stored at -80C until RNA was extracted using Trizol
RNA libraries were prepared for sequencing using the NEB small RNA kit (cat #E6160L or #E6160S) Illumina protocols by the University of Texas at Austin Genome Sequencing and Analysis Facility (GSAF)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
An aliquot of total RNA was then run on a Bioanalyzer Nano RNA chip (Agilent) to confirm RNA integrity score was above 7 for each sample
Trimmomatic was used to filter and trim reads using the following parameters: -phred33 ILLUMINACLIPadapters.fa:3:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
A transcriptome was assembled de novo using Trinity from the reads of each sample/species
de novo assembled contigs were annotated to reference genomes using blastx
Reads were mapped the the annotated de novo assembly using bwa mem
Raw reads were calculated as the sum of transcript counts using SAMtools and Reads Per Million of library size (RPM) were calculated as the reads mapping to de novo assembled contigs of annotated as the same gene and normalized by the size the size of the library.
Supplementary_files_format_and_content: fasta files including the de novo assembled contigs annotated using closely related reference genomes for each Sample
Supplementary_files_format_and_content: csv files including raw reads and RPMs for each sample
|
| |
|
| Submission date |
Dec 03, 2018 |
| Last update date |
Dec 20, 2018 |
| Contact name |
Rebecca L Young |
| E-mail(s) |
youngrl@utexas.edu
|
| Organization name |
University of Texas at Austin
|
| Department |
Integrative Biology
|
| Street address |
2415 Speedway
|
| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78712 |
| Country |
USA |
| |
|
| Platform ID |
GPL25884 |
| Series (1) |
| GSE123301 |
Conserved Transcriptomic Profiles Underpin Monogamy across Vertebrates |
|
| Relations |
| BioSample |
SAMN10518449 |
| SRA |
SRX5090072 |
