|
| Status |
Public on Feb 04, 2021 |
| Title |
0x_D |
| Sample type |
SRA |
| |
|
| Source name |
Perkinsus marinus cells
|
| Organism |
Perkinsus marinus |
| Characteristics |
cell type: log phase Perkinsus marinus cells
strain: Perkinsus marinus monoclonal sample of ATCC 50439/D8
treatment: without lipids
|
| Treatment protocol |
For analysis of growth in defined DME media (Dungan and Hamilton, 1995), week old log phase P. marinus cell cultures were adjusted to an OD .100 and subsequently split into two groups consisting of three biological replicates: lipid replete- medium containing a 1X solution of lipid concentrate and lipid deplete -medium without lipid concentrate. Lipid replete and lipid deplete cells were exponentially grown until day 11
|
| Growth protocol |
P. marinus cells (monoclonal sample of ATCC 50439/D3 were kindly provided by Chris Dungan of the Maryland Department of Natural Resources) and cultivated as described (Dungan and Hamilton 1995) at 27°C. Growth and confluence were checked daily with a light microscope at 10X, and cell concentration was measured spectrophotometrically at an OD of 600.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
P. marinus cells were harvested from day 11 lipid replete and lipid deplete media for each biological replicate. Cells were pelleted at 3,900 RPM for 10 minutes at 4 C° using an Eppendorf 5810R Centrifuge. P. marinus total RNA was extracted per manufacturer’s protocol using the Qiagen RNeasy mini- kit; RNA quality was verified on a 1% percent agarose gel and visualized using a UV transilluminator.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Raw data were analyzed using the TopHat2.0.4 aligner with stand-specific settings and Perkinsus marinus genomic reference sequence (GCA_000006405.1 JCVI_PMG_1.0).
Differential gene expression was analyzed using the DESeq R package (Bioconductor) and the negative binomial model
Criteria for significant differences in gene expression were (1) false discovery rate (FDR) <0.05, (2) expression level >10th percentile, and (3) ≥ 2-fold change.
Genome_build: Perkinsus marinus(GCA_000006405.1 JCVI_PMG_1.0)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample
|
| |
|
| Submission date |
Feb 03, 2021 |
| Last update date |
Feb 05, 2021 |
| Contact name |
Carrie McCracken |
| E-mail(s) |
cmccracken@som.umaryland.edu
|
| Organization name |
Institute of Genome
|
| Department |
Institute for Genome Sciences
|
| Street address |
670 W. Baltimore St
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21201 |
| Country |
USA |
| |
|
| Platform ID |
GPL29693 |
| Series (1) |
| GSE166132 |
A dual omics approach to evaluate transcriptional and metabolic responses during lipid deprivation in an oyster parasite Perkinsus marinus |
|
| Relations |
| BioSample |
SAMN17773439 |
| SRA |
SRX10016439 |
