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Sample GSM5062126 Query DataSets for GSM5062126
Status Public on Feb 04, 2021
Title 0x _A
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/D6
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
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
BioSample SAMN17773441
SRA SRX10016437

Supplementary file Size Download File type/resource
GSM5062126_Ox_A.genic.coverage.stats.rpkm.txt.gz 713.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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