|
| Status |
Public on Feb 04, 2021 |
| Title |
SHR rat 1 |
| Sample type |
SRA |
| |
|
| Source name |
whole brain
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: brain
strain: SHR/OlaIpcvPrin
Sex: male
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted from whole brain of three naïve male rats per strains using the the miRNeasy Mini and RNeasy MinElute Cleanup Kits (Qiagen, Valencia, CA, USA).
Sequencing libraries were constructed using the Illumina TruSeq RNA Sample Preparation kit from 1 ug RNA according to manufacturer's instructions.
Library quality was assessed using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). Samples were sequenced (2x100 paired-end reads) on the Illumina HiSeq2000. Samples were multiplexed over 3 lanes of the flowcell (2 lanes with 3 samples each and 1 lane with all 6 samples).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
SHR1
|
| Data processing |
Reads were trimmed to remove adapters and low-quality base calls using cutadapt
Trimmed reads were aligned to strain-specific rn6 rat genomes (available at http://phenogen.org) using HISAT2
StringTie (v.1.3.5) was used to reconstruct the transcriptome from the RNA-Seq data. Ensembl(v.99) reference annotation from the rat was provided to guide the StringTie reconstruction. The StringTie reconstruction was further augmented for identification of active polyadenylation sites using aptardi (https://github.com/luskry/aptardi).
Individual isoforms and genes from the stringtie/aptardi transcriptome were quantitated using RSEM.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include estimated read counts, TPM, and FPKM values for each Sample (standard RSEM output)
Supplementary_files_format_and_content: estimated count matrices with genes or isoforms as rows and Samples as columns
Supplementary_files_format_and_content: GTF file for reconstructed transcriptome
|
| |
|
| Submission date |
Feb 03, 2021 |
| Last update date |
Feb 05, 2021 |
| Contact name |
Laura Maren Saba |
| E-mail(s) |
Laura.Saba@cuanschutz.edu
|
| Organization name |
University of Colorado Anschutz Medical Campus
|
| Department |
Pharmaceutical Sciences
|
| Street address |
12850 East Montview Blvd.
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL14844 |
| Series (1) |
| GSE166117 |
PolyA-selected RNA expression in whole brains of male BN-Lx/CubPrin and SHR/OlaIpcvPrin |
|
| Relations |
| BioSample |
SAMN17771864 |
| SRA |
SRX10015161 |
