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| Status |
Public on Aug 19, 2022 |
| Title |
Horse2_inoculated_2 |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Equus caballus |
| Characteristics |
tissue: Liver
inoculation [ml]: 1
inoculation [copies]: 126760
Sex: F
breed: Trotter
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| Extracted molecule |
total RNA |
| Extraction protocol |
Snap-frozen liver biopsy specimens were used for RNA isolation and NGS. RNA was isolated from mechanically homogenized liver biopsy specimens using the Machery Nagel RNA extraction kit according to the manufacturer’s instructions
The RNA sequencing library was generated from 500 ng total RNA using Dynabeads mRNA DIRECT Micro Purification kit (Thermo Fisher Scientific, Waltham, MA) for mRNA purification, fol- lowed by NEBNext Ultra II Directional RNA Library Prep kit (New England BioLabs, Ipswich, MA), both according to the manufacturer’s protocols. The libraries were treated with Illumina Free Adapter Blocking and sequenced on Illumina NovaSeq 6000 using the NovaSeq 6000 S1 reagent kit (100 cycles, paired-end run 2 x50 bp), with an average of 5 x 10^7 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 |
Raw reads were quality- trimmed and mapped to the equine reference genome (EquCap3.0) using CLC Workbench 2020.
Supplementary files format and content: .csv
Supplementary files format and content: raw and normalized read counts
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| Submission date |
Aug 14, 2022 |
| Last update date |
Aug 19, 2022 |
| Contact name |
Daniel Todt |
| E-mail(s) |
daniel.todt@rub.de
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| Phone |
+492343222463
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| Organization name |
Ruhr University Bochum
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| Department |
Molecular & Medical Virology
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| Street address |
Universitätsstr. 150
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| City |
Bochum |
| ZIP/Postal code |
44801 |
| Country |
Germany |
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| Platform ID |
GPL26749 |
| Series (1) |
| GSE211197 |
Dose-Dependent Hepacivirus Infection Reveals Linkage between Infectious Dose and Immune Response |
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| Relations |
| BioSample |
SAMN30308116 |
| SRA |
SRX17062141 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6456016_D2_post_S26_L001.csv.gz |
1.6 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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