|
| Status |
Public on Sep 17, 2023 |
| Title |
rRNA Depleted totalRNA from heart, left ventricle from untreated BXH13 rats (rep 1, sequencing batch 3) [BXH13_1] |
| Sample type |
SRA |
| |
|
| Source name |
heart
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: heart
strain: BXH13/Cub
batch: 3
treatment: none
|
| Treatment protocol |
Tissue frozen in RNA later.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was collected from the left ventricle of the heart using the RNeasy Plus Universal Midi kits for RNA sequencing (Qiagen, Valencia, CA, USA).
Libraries were constructed using the Illumina TruSeq Stranded TotalRNA Kit (Illumina, San Diego, CA, USA).
rRNA depleted stranded totalRNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
BXH13_1_batch2
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.strainMeans.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.ensemblRR.txt
PhenoGen.HRDP.v6.totalRNA.Heart.gene.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.transcript.reconstruction.txt
PhenoGen.HRDP.v6.totalRNA.Heart.reconstruction.gtf
BXH13_1
|
| Data processing |
Cutadapt (v1.9.1) trim Illumina adapter, quality, and length, parameters: -q 20 -m 20
Remove rRNA reads by alignment with bowtie2(v2.3.4.3) to rRNA
genome Alignment Hisat2 (v2.1.0)
Stringtie (v1.3.5) reconstruction
Run Aptardi (v1.4) on each strain reconstructed GTF
Merge aptardi output reconstruction Stringtie(v1.3.5)
Run RSEM (v1.3.1) on reconstruction
Filter transcripts/genes from RSEM results if one third or more of samples have less than 1 read or if the length of the mature RNA transcript was less than 200 nucleotides
Run RSEM(v1.3.1) on filtered reconstruction
Filter transcripts/genes from RSEM results if one third or more of samples have less than 1 read or if the length of the mature RNA transcript was less than 200 nucleotides
Apply a regularized log transformation of expected read counts from RSEM (rlog function in DESeq2 package of R)
Remove technical artifacts including batch effects using Removal of Unwanted Variance (RUVg) with empirically-derived controls (RUVSeq package in R)
Assembly: rn7.2
Supplementary files format and content: TSV batch corrected/normalized expression values
Supplementary files format and content: GTF of the reconstructed transcriptome
|
| |
|
| Submission date |
Sep 12, 2023 |
| Last update date |
Sep 17, 2023 |
| Contact name |
Laura Saba |
| E-mail(s) |
Laura.Saba@cuanschutz.edu
|
| Organization name |
University of Colorado Anschutz Medical Campus
|
| Department |
Skaggs School of Pharmacy and Pharmaceutical Sciences
|
| Street address |
12850 E. Montview Blvd
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL22396 |
| Series (2) |
| GSE199987 |
RNA expression levels in the Hybrid Rat Diversity Panel for the PhenoGen website (https://phenogen.org) |
| GSE243029 |
Heart (Left Ventricle) RNA expression levels in the Hybrid Rat Diversity Panel for the PhenoGen website (https://phenogen.org) |
|
| Relations |
| BioSample |
SAMN37367640 |
| SRA |
SRX21763065 |
