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| Status |
Public on Mar 29, 2020 |
| Title |
PakiT03 - pIC - IRF1 - 6h |
| Sample type |
SRA |
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| Source name |
PakiT03-IRF1-g4-1D
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| Organism |
Pteropus alecto |
| Characteristics |
crispr ko: IRF1
parental cell: PakiT03
treatment: polyIC
time: 6h
Sex: F
agent: dsRNA - polyIC 1mg/ml (transfected - Fugene)
treatment: polyIC transfected for 6h
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| Treatment protocol |
IFNα Treatment (~500U/ml) at 0h, 3h, 6h, 9h, polyIC treatment (1mg,ml, transfected) at 0h, 6h, 9h, or infection with Melaka Virus (PRV3M, MOI 1) for 0h, 9h, 24h timepoints
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| Growth protocol |
PakiT03 cells were grown in DMEM supplemented with 10% FBS.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed into TRK lysis buffer supplemented with β-ME, freeze-thawed, homogenised and extracted as per manufacturers protocol (OMEGA EZNA total RNA Kit I).
Total RNA was checked using the RNA 6000 LabChip Kit on the Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA). RNAseq libraries were prepared using Illumina Tru-Seq Stranded Total RNA with Ribo-Zero Gold kit following the manufacturer’s instructions (Illumina, San Diego, California, USA). Libraries were validated with an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA), diluted and applied to an Illumina flow cell using the Illumina cBOT system. Sequencing was performed on an Illumina HiSeq 3000 sequencer at the Duke-NUS Genome Biology Facility with the paired-end 150-bp read option.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Data processing |
After trimming and cleaning for quality assurance (including distribution of reads)
reads were mapped to the P.alecto reference genome (NCBI genome database:ASM32557v1 scaffold3, v1.01 ) with Bowtie and RSEM abundance estimation was performed
FPKM was calculated using TopHat/Cufflinks v2.2.1 using :ASM32557v1 as a guide for reference mapping and genome size .
HTseq and edgeR were used for subsequent counting and DEG analysis
Genome_build: ASM32557v1 , 101
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
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| Submission date |
Apr 05, 2019 |
| Last update date |
Mar 30, 2020 |
| Contact name |
Linfa Wang |
| Organization name |
Duke-NUS Medical School
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| Department |
Programme in Emerging Infectious Diseases
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| Lab |
Laboratory of Emerging Zoonotic Viruses
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| Street address |
8 college road
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| City |
Singapore |
| ZIP/Postal code |
169857 |
| Country |
Singapore |
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| Platform ID |
GPL26396 |
| Series (1) |
| GSE129390 |
Transcriptomic profiling of bat PakiT03 cells with immune stimulation |
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| Relations |
| BioSample |
SAMN11350537 |
| SRA |
SRX5647032 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3712288_pic-IRF1-6h.fpkm.txt.gz |
626.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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