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Sample GSM7083360 Query DataSets for GSM7083360
Status Public on Dec 15, 2023
Title c1829_STIM_canine_PHA
Sample type SRA
 
Source name Blood
Organism Canis lupus familiaris
Characteristics tissue: Blood
cell line: primary tissue
cell type: PBMC
treatment: PHA
Treatment protocol phytohemagglutinin (PHA) (Sigma-Aldrich, St. Louis, MO) was added to cultures at a concentration of 5 ug/ml
Growth protocol Following Ficoll separation, PBMC for both species were washed with PBS, counted and added to 24-well plates in triplicate cultures, at a cell density of 2 X 10^6 cells per mL in complete culture medium. Cell culture medium consisted of DMEM supplemented with amino acids (essential and non-essential), 1% penicillin-streptomycin, Glutamax (ThermoFisher Scientific, Waltham, MA) and 10% fetal bovine serum (Peak Serum, Inc, Wellington, CO). For T cell activation, phytohemagglutinin (PHA) (Sigma-Aldrich, St. Louis, MO) was added to cultures at a concentration of 5 ug/ml for 24h (RNA sequencing).
Extracted molecule total RNA
Extraction protocol RNA was extracted from cells using Qiagen RNeasy mini kit
the mRNA was purified using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was completed following end repair, A-tailing, adapter ligation, size selection, amplification, and purification.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description c1829_STIM
Partek_Canine_PBMC-_PHA_Normalized.txt
Partek_dog_vs_human_combined_normalized_ct.txt
Data processing Partek Flow software, version 10.0
Raw data were filtered by removing reads containing adapters and reads containing N > 10% and for Phred scores >30
Filtered reads were aligned with STAR 2.7.3a, using either CanFam3.1 genome assembly or GRCh38 human genome assembly
Aligned reads were annotated and counted using HT-seq with Ensembl 104 for CanFam3.1 and release 107 for GRCh38
differentially expressed genes were identified using DEseq2
Assembly: CanFam3.1 genome assembly or GRCh38 human genome assembly
Supplementary files format and content: tab-delimited text files include CPM normalized counts
 
Submission date Mar 06, 2023
Last update date Dec 15, 2023
Contact name Steven Dow
E-mail(s) sdow@colostate.edu
Organization name Colorado State University
Department Clinical Sciences
Lab ACC 254
Street address 300 W Drake Rd
City Fort Collins
State/province CO
ZIP/Postal code 80524
Country USA
 
Platform ID GPL25760
Series (1)
GSE226767 Direct Comparison of Canine and Immune Responses Using Transcriptomic and Functional Analyses
Relations
BioSample SAMN33604297
SRA SRX19578785

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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