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| Status |
Public on Jun 27, 2018 |
| Title |
ApxIIANt_1 |
| Sample type |
SRA |
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| Source name |
porcine alveolar macrophage cells
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| Organism |
Sus scrofa |
| Characteristics |
strain: 3D4/31
tissue: lung
age: 27 days
agent: antigenic epitopes of actinobacillus pleuropneumoniae IIA
genotype: wildtype
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| Treatment protocol |
After 12h-cluture of PAMs at a concentration of 1×106 cells/well in 6-well cultures plates containing 2% FBS, penicillin (100U/mL), and streptomycin (100 µg/mL), cells were stimulated with the recombinant proteins of Apx toxins at 10µg/ml and DPBS as a negative control. Following centrifugation at 125×g for 5min at 20℃, the treated cells were incubated at 37℃ under 5% CO2 atmosphere for 24h.
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| Growth protocol |
Porcine alveolar macrophages (PAMs, 3D4/31, ATCC CRL-2844) was cultured in Roswell Park Memorial Institute medium (RPMI) 1640 (Gibco, USA) with 10% fetal bovine serum (FBS; Gibco), penicillin (100U/mL), and streptomycin (100 µg/mL). Cells were cultivated in a humidified incubator with 5% CO2 at 37℃.
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| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted from the cells using the RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
Apx-IIA-Nt-1_FPKM
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| Data processing |
RTA(Real Time Analysis) software used for basecalling.
To estimate expression levels and to find alternative spliced transcripts, the RNA-seq reads were mapped to the genome of sus scrofa using TopHat (Trapnell et al., 2009), which is capable of reporting split-read alignments across splice junctions and determined using Cufflinks software (Trapnell et al., 2010) in default options.
Raw data were calculated as FPKM (Fragments Per Kilobase of exon model per Millon mapped fragments) of each transcript in each sample cufflinks software. We excluded the transcripts with zeroed FPKM values more than on for total samples. We added 1 with FPKM value of the filtered transcript to facilitate log2 transformation. Filtered data was transformed by logarithm and normalized by quantile normalization method. For each transcript, we conducted independent t-test between case and control. Each transcript was determined using independent t-test.
Genome_build: Sscrofa11
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
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| Submission date |
Jun 26, 2018 |
| Last update date |
Jun 27, 2018 |
| Contact name |
Suji Kim |
| E-mail(s) |
sujiksj43@gmail.com
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| Organization name |
Seoul National University
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| Department |
Veterinary Medicine
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| Lab |
Infectious Disease
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| Street address |
1, Gwanak-ro
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| City |
Seoul |
| State/province |
Gwanak-gu |
| ZIP/Postal code |
ASI/KR/KS013 |
| Country |
South Korea |
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| Platform ID |
GPL22475 |
| Series (1) |
| GSE116263 |
Global Gene Networks in Porcine Alveolar Macrophage Cells, 3D4/31, Stimulated with Antigenic Epitopes of Actinobacillus pleuropneumoniae ApxIA, IIA and IVA |
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| Relations |
| BioSample |
SAMN09487521 |
| Supplementary data files not provided |
| Raw data are available in SRA |
| Processed data are available on Series record |
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