|
| Status |
Public on Sep 29, 2020 |
| Title |
1X OS 48h replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
kidney cells (RRID:CVCL_0472)
|
| Organism |
Monodelphis domestica |
| Characteristics |
cell type: Opossum Kidney (OK) Cells
stress: orbital shear stress
time: 48h
|
| Treatment protocol |
The following day (t = 0 h), a subset of the filters were transferred to an orbital platform shaker rotating at 146 rpm (OSS) in incubation continued.
|
| Growth protocol |
OK cells (RRID:CVCL_0472) were plated on permeable supports in DMEM/F12 medium (Sigma D6421) with 10% FBS (Atlanta Biologicals) and 5 mM GlutaMAX (Gibco).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected using Accutase (BD Biosciences) and RNA was extracted using the Ambion PureLink RNA mini kit (ThermoFisher) at 12, 48, and 96 h after transferring cells to OSS and at 0, 48, and 96 h from cells maintained under static conditions. RNA from three experiments was combined to create each sample, and three independent samples were sequenced for each time point.
Library preparation was performed using the TruSEQ Stranded Total RNA Sample Preparation Kit (Illumina) according to manufacturer’s instructions.
Following removal of ribosomal RNA, the remaining RNA was fragmented for 8 min, followed by reverse transcription performed. Double stranded cDNA was subjected to 3’ adenylation and ligation of sequencing adapters. Sequencing was carried out on a NextSeq 500 (Illumina) to generate 75 bp paired-end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Raw sequence reads were cleaned for adapter sequences using cutadapt with default parameters.
The trimmed reads were mapped to the Monodelphis domestica reference genome (MonDom5) using TopHat2, allowing for a base-pair mismatch value of 6.
Prior to calculating raw count values with the Subread package featureCounts, 51reads aligned to mitochondrial genes and ribosomal RNA were removed.
Genome_build: MonDom5
Supplementary_files_format_and_content: Raw Reads, csv
|
| |
|
| Submission date |
Jul 28, 2020 |
| Last update date |
Sep 29, 2020 |
| Contact name |
Amanda Catherine Poholek |
| E-mail(s) |
poholeka@pitt.edu
|
| Organization name |
University of Pittsburgh
|
| Department |
Pediatrics
|
| Street address |
4401 Penn Ave., Rangos Research Center 8129
|
| City |
Pittsburgh |
| State/province |
Pennsylvania |
| ZIP/Postal code |
15224 |
| Country |
USA |
| |
|
| Platform ID |
GPL28940 |
| Series (1) |
| GSE155315 |
Temporal- and Orbital Shear Stress-Dependent Changes in Opossum Kidney (OK) Cell Transcription |
|
| Relations |
| BioSample |
SAMN15662395 |
| SRA |
SRX8840896 |
