|
| Status |
Public on May 18, 2019 |
| Title |
RNA_BW35772-T |
| Sample type |
SRA |
| |
|
| Source name |
Ear punch
|
| Organism |
Peromyscus maniculatus |
| Characteristics |
stock: BW
cell type: fibroblasts
developmental stage: 4-weeks old postnatal
treatment: tunicamycin
|
| Treatment protocol |
Cells were split into 6-well plates, 300,000 cells/well, and cultivated for 24 hours. Then cells were treated with tunicamycin (5 mg/mL) for 5 hours, immediately followed by RNA extraction.
|
| Growth protocol |
Fresh ear punches were collected from deer mice. Ear punches were washed for 2 minutes in 70% EtOH and moved to RPMI-1640 medium (HyClone) supplemented with 10% FBS (Gibco), 500 u/mL Penicillin and 500 uL/mL L-Glutamine (complete RPMI). Ear punches were minced into small pieces and then digested by collagenase I (5 mg/ml in RPMI-1640) for 1 hour. Tissue debris from digested ear punches was removed once cells were visible. Cells were cultivated in complete RPMI at 37°C in a humidified incubator containing 5% CO2, and passaged when cells were at 90% confluency or above.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were extracted with Qiagen RNeasy Plus Mini kit (Qiagen, Valencia, CA, USA). RNA integrity was assessed using the Agilent Bioanalyzer and samples had a quality score >8.0.
RNA libraries were prepared using established protocol with NEBNExt Ultra II Directional Library Prep Kit for Illumina, (NEB, Lynn, MA). Each library was made with one of the TruSeq barcode index sequences and samples were sequenced across three lanes. The pools were clustered at 6.5 pM on a pair end read flow cell and sequenced for 300 cycles on an Illumina Hiseq 4000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
S4
|
| Data processing |
Sequences were aligned to the Pman_1.0 genome using STAR version 2.6.1 and output as sam files
The sam files were then converted to bam files with Samtools version 1.6 with parameters -bh -F 3840 -q 255
Reads were counted using the featureCounts function of the Subreads package (Liao et al., 2013) in R using Gencode M6 GTF and summarized at exon, transcript, or gene level
Genome_build: Pman_1.0
Supplementary_files_format_and_content: comma-separated values file with counts for each sample
|
| |
|
| Submission date |
May 17, 2019 |
| Last update date |
May 20, 2019 |
| Contact name |
Youwen Zhang |
| E-mail(s) |
youwen@email.sc.edu
|
| Organization name |
University of South Carolina (Columbia)
|
| Department |
Drug Discovery and Biomedical Sciences
|
| Lab |
Dr. Hippokratis Kiaris
|
| Street address |
715 Sumter Street CLS109
|
| City |
Columbia |
| State/province |
South Carolina |
| ZIP/Postal code |
29208 |
| Country |
USA |
| |
|
| Platform ID |
GPL26686 |
| Series (1) |
| GSE131429 |
Whole Transcriptome RNA-seq in Peromyscus maniculatus fibroblasts |
|
| Relations |
| BioSample |
SAMN11672445 |
| SRA |
SRX5858969 |
