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| Status |
Public on Mar 21, 2022 |
| Title |
PRRSV NSP1a-1 |
| Sample type |
SRA |
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| Source name |
3D4/31_PRRSV NSP1a
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| Organism |
Sus scrofa |
| Characteristics |
cell line: 3D4/31
cell type: macrophage cell line
tissue source: lung
genotype/variation: PRRSV NSP1 alpha-pBabepuro (PRRSV NSP1a)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from 3D4/31 cells using TRIzol reagent according to the manufacturer's instructions.
In order to construct cDNA libraries with the TruSeq mRNA LT library kit (Illumina, USA), 1 ug of total RNA was used. The protocol consisted of polyA-selected RNA extraction, RNA fragmentation, random hexamer primed reverse transcription and 100nt paired-end sequencing by Illumina NovaSeq 6000
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
processed data file: data3_PRRSV_Nsp1a_vs_mock_fc2 & raw.p
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| Data processing |
The raw reads from the sequencer to remove low quality and adapter sequence before analysis and aligned the processed reads to the Sus scrofa (GCF_000003025.6_Sscrofa11.1) using HISAT v2.1.0
HISAT utilizes two types of indexes for alignment (a global, whole-genome index and tens of thousands of small local indexes). These two types’ indexes are constructed using the same BWT (Burrows–Wheeler transform)/ a graph FM index (GFM) as Bowtie2
Transcript assembly and abundance estimation using StringTie version 1.3.4d. After alignment, StringTie v1.3.4d was used to assemble aligned reads into transcripts and to estimate their abundance.
It provides the relative abundance estimates as FPKM values (Fragments Per Kilobase of exon per Million fragments mapped) of transcript and gene expressed in each sample.
Genes with one more than zeroed FPKM values in the samples were excluded. To facilitate log2 transformation, 1 was added to each FPKM value of filtered genes
Genome_build: GCF_000003025.6_Sscrofa11.1
Supplementary_files_format_and_content: Excel spreadsheet format which includes contents; 1) Gene_symbol, 2) NCBI Protein accession ID, 3) Product, 4) Fold change, 5) Volume, 6) KEGG stat, 7) KEGG genes, 8) DAVID chart
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| Submission date |
Mar 27, 2019 |
| Last update date |
Mar 21, 2022 |
| Contact name |
In byung Park |
| Organization name |
Korea University
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| Street address |
145, Anam-ro, Seongbuk-gu, Seoul
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| City |
Seoul |
| ZIP/Postal code |
02841 |
| Country |
South Korea |
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| Platform ID |
GPL26351 |
| Series (1) |
| GSE128929 |
Transcriptome analysis of PRRSV Nsp1 overexpressed 3D4/31 cells |
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| Relations |
| BioSample |
SAMN11265683 |
| SRA |
SRX5581737 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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