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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 16, 2020 |
| Title |
Mouse RAW macrophages, 10^7 cells, poly(I:C) for 6 h |
| Sample type |
SRA |
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| Source name |
RAW macrophages
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| Organism |
Mus musculus |
| Characteristics |
cell line: macrophage cell line RAW24.7
genotype: control
treatment: poly(I:C)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from RAW macrophages by using Qiagen kit
Libraries were prepared with the Illumina mRNA Library Preparation kit. mRNA is enriched using oligo(dT) beads. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Li0014
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| Data processing |
The qualified libraries are fed into Illumina sequencers after pooling according to its effective concentration and expected data volume
Paired-end reads were directionally mapped to the genomic loci of mouse genome (GRCm38.p6) by TopHat2.
Cufflinks/Cuffdiff analysis was run to identify the dysregulated RNAs
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Gene expression file generated by cuffdiff analysis
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| Submission date |
Mar 15, 2020 |
| Last update date |
Mar 17, 2020 |
| Contact name |
CHAOQUN HUANG |
| E-mail(s) |
chaoqh@okstate.edu
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| Phone |
405-744-3410
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| Organization name |
Oklahoma State University
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| Department |
Physiological Sciences
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| Lab |
Lundberg-Kienlen Lung Biology and Toxicology Laboratory
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| Street address |
264 McElroy Hall
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| City |
Stillwater |
| State/province |
OK |
| ZIP/Postal code |
74078 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE147001 |
Cytosolic dsRNA-induced gene expression in mouse RAW24.7 macrophages and FIP200 knockout RAW cells |
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| Relations |
| BioSample |
SAMN14380579 |
| SRA |
SRX7913856 |
| 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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