|
| Status |
Public on May 15, 2022 |
| Title |
OPC Treatment, 5μM tunicamycin for 2hr, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
oligodendrocyte precursor cells
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: oligodendrocyte precursor cells
passages: 1-6
|
| Treatment protocol |
OPCs were treated with the ERSR inducer tunicamycin (0 or 5 µM) for 2- or 8h (4 samples from each experiment, 3 independent experiments were resulting in 12 samples, total).
|
| Growth protocol |
Total RNA for library construction was obtained from cultured rat oligodendrocyte precursor cells (OPCs) which are often used as a convenient model of oligodendrocytes. These cells were originally isolated from adult rat spinal cords by our collaborator Dr. Scott Whittemore. They were stored frozen. Only low passage cells were used (up to passage 6).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from OPCs was obtained using commertially avaiable Rneasy MiniKit from Qiagen cat no 74104
Libraries were prepared using the TruSeq Stranded Total RNA LT Sample Prep Kit-Set A (Cat # RS-122-2301) with Ribo-Zero Gold. Illumina NextSeq 500/550 model.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina FASTQ Generation version 1.0.0 used for basecalling
Quality control (QC) of the raw sequence data was performed using FastQC (version 0.10.1. The FastQC results indicated that all sequences were of high quality (>Q32), with the exception of the final base.
Sequences were directly aligned to the Rattus norvegicus reference genome assembly (rn6.fa). A gene annotation file for rn6, was downloaded from Ensembl. The analysis was performed using Tophat (version 2.0.4), generating alignment files in bam format.
The aligned RNA-seq reads were assembled according to the rn6 gtf annotation file using Cufflinks V2.2.1.
Differentially expressed genes (DEGS) were identified for two pairwise comparisons (Treated vs. Untreated 2hr, Treated vs. Untreated 8hr) using Cuffdiff (version 2.1.1).
Genome_build: rn6
Supplementary_files_format_and_content: Tab-delimited cuffnorm normalized FPKM values
|
| |
|
| Submission date |
May 23, 2016 |
| Last update date |
May 15, 2022 |
| Contact name |
Michal Hetman |
| E-mail(s) |
michal.hetman@louisville.edu
|
| Phone |
502-852-3619
|
| Organization name |
University of Louisville
|
| Department |
Department of Neurological Surgery
|
| Lab |
Kentucky Spinal Cord Injury Research Center
|
| Street address |
511 South Floyd Street, MDR609A
|
| City |
Louisville |
| State/province |
Kentucky |
| ZIP/Postal code |
40202 |
| Country |
USA |
| |
|
| Platform ID |
GPL20084 |
| Series (1) |
| GSE81792 |
Transcriptome response to endoplasmic reticulum stress in rat oligodendrocyte precursor cells |
|
| Relations |
| BioSample |
SAMN05164072 |
| SRA |
SRX1794096 |
