|
| Status |
Public on Oct 23, 2023 |
| Title |
rRNA Depleted totalRNA from liver from untreated SHR rats (replicate 1b, sequencing batch 3) |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: liver
strain: SHR/OlaIpcv
batch: 3
treatment: none
|
| Treatment protocol |
Tissue frozen in RNA later.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was collected from liver 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 2000 |
| |
|
| Description |
rRNA depleted totalRNA
HRDPv6 Sample Name: SHR_1b_batch3
SHR_1b_control_3
|
| 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 filtered transcriptome 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 |
Oct 18, 2023 |
| Last update date |
Oct 23, 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 |
GPL14844 |
| Series (2) |
| GSE199986 |
Liver RNA expression levels in the Hybrid Rat Diversity Panel for the PhenoGen website (https://phenogen.org) |
| GSE199987 |
RNA expression levels in the Hybrid Rat Diversity Panel for the PhenoGen website (https://phenogen.org) |
|
| Relations |
| BioSample |
SAMN37875952 |
| SRA |
SRX22129526 |
