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Sample GSM5061948 Query DataSets for GSM5061948
Status Public on Feb 04, 2021
Title SHR rat 2
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 SHR2
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 SAMN17771879
SRA SRX10015162

Supplementary file Size Download File type/resource
GSM5061948_SHR2.genes.results.txt.gz 578.5 Kb (ftp)(http) TXT
GSM5061948_SHR2.isoforms.results.txt.gz 1.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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