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| Status |
Public on Apr 17, 2024 |
| Title |
Mock_CC011_D3_3 |
| Sample type |
SRA |
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| Source name |
liver
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| Organism |
Mus musculus |
| Characteristics |
tissue: liver
genotype: CC011
treatment: mock treated
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from liver samples using Trizol according to manufacturer's direction.
The RNA sequencing library was generated from 1000 ng total RNA using the KAPA Stranded RNA-Seq kit with RiboErase according to manufacturer’s directions (Roche Sequencing and Life Science). The pooled libraries were sequenced on 3 lanes Illumina NovaSeq 6000 using NovaSeq 6000 S4 XP Reagent Kit 100 Nu, paired end, with an average of 30,000,000 reads per RNA sample.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
FastQ file quality was assessed using FastQC and MultiQC.
FastQ reads were mapped and quantified using Kallisto (0.46.0) to the reference build GRCm39
Counts per million (CPM) was calculated and normalized using EdgeR, keeping only rows with at least 5 cells indicating a count-per-million (CPM) of at least 1.
Expression data was filtered and normalized using Limma's VOOM.
Differentially expressed genes (DEGs) were identified by linear modeling and Bayesian statistics using the Limma package.
Assembly: GRCm39
Supplementary files format and content: *.tar.gz files contain one of each file listed below per sample which is indicated by the "*" pattern.
Supplementary files format and content: abundance.tsv files contain abundance quantifications per sample.
Supplementary files format and content: run_info.json files contain Kallisto run information per sample.
Supplementary files format and content: abundance.h5 files are hd5f binary files containing run info, abundance estimates, bootstrap estimates, and transcript length information per sample.
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| Submission date |
Mar 20, 2024 |
| Last update date |
Apr 17, 2024 |
| Contact name |
Alexandra Schaefer |
| Organization name |
University of North Carolina at Chapel Hill
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| Street address |
3109 MHRC
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| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27551 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE262041 |
RNASeq analysis of CC011, CC074, Trimko, and Trim wt female mice on 3dpi and 6dpi after infection with Ebola virus |
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| Relations |
| BioSample |
SAMN40558926 |
| SRA |
SRX24005893 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8156434_Mock_CC011_D3_3.tar.gz |
9.2 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
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