|
| Status |
Public on Apr 01, 2022 |
| Title |
rRNA Depleted total RNA from kidney from untreated HXB1 rats (replicate 2, sequencing batch 5) |
| Sample type |
SRA |
| |
|
| Source name |
kidney
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: HXB1/Ipcv
batch: 5
treatment: none
tissue: kidney
Sex: male
|
| Treatment protocol |
Tissue frozen in RNA later.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was collected from kidney 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).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
HXB1_2_batch5
|
| 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.
Merge 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).
>> updated processing pipeline for new genome version (rn7.2):
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
Repeat 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: rn6 (Rnor_6.0) -or- Rn7.2
Supplementary files format and content:
TSV batch corrected/normalized expression values
GTF of the reconstructed transcriptome
PhenoGen.HRDP.v5.totalRNA* files generated with rn6 (Rnor_6.0)
PhenoGen.HRDP.v6.totalRNA* files generated with a new genome version (rn7.2)
|
| |
|
| Submission date |
Apr 01, 2022 |
| Last update date |
Sep 14, 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) |
| GSE199976 |
Kidney 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 |
SAMN27181925 |
| SRA |
SRX14697879 |
