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| Status |
Public on Jun 21, 2024 |
| Title |
Single cell RNA-seq of Oncorhynchus mykiss PBLs from infected and healthy fish |
| Organism |
Oncorhynchus mykiss |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Single cell RNA-Seq data generated on a 10x Chromium genomics platform from infected and healthy PBLs from Oncorhynchus mykiss.
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| Overall design |
Two rainbow trout were killed by benzocaine overdose. Blood was extracted with a heparinized needle from the caudal vein and diluted 10 times with Leibovitz medium. PBLs were obtained by centrifugation of diluted blood on 51% continuous Percoll density gradients. IPNV (Sp strain, ATCC VR 1318) was propagated in the RTG-2 (Rainbow Trout Gonad-2) cell line. To produce viral stocks, complete culture media was removed from 80% confluent cell cultures in 75 cm2 culture flasks and IPNV inoculated. For the in vitro infection of rainbow trout PBLs, cells resuspended in L-15 containing antibiotics and 5% FCS were disposed in 24-well plates. Cell suspensions (1,000 cells/µl ) from each sample were loaded into the chips of the Chromium™ Single Cell 5′ Gel Beads Kit (10x Genomics) and subjected to the Chromium Controller instrument to generate single cell Gel Bead-In Emulsions (GEMs). GEMs were subjected to library construction using the Chromium™ Single Cell 5′ Library Kit v1 (10x Genomics). Samples were sequenced using a NextSeq instrument (Illumina) with 150PE chemistry.
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| Contributor(s) |
Perdiguero P, Jiménez-Barrios P, Morel E, Abós B, Díaz-Rosales P, Tafalla C |
| Citation(s) |
39035000 |
| |
| Submission date |
Mar 05, 2024 |
| Last update date |
Aug 09, 2024 |
| Contact name |
Pablo Jiménez-Barrios |
| E-mail(s) |
pablo.jimenez@inia.csic.es
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| Phone |
916202300 2186
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| Organization name |
CISA-INIA (CSIC)
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| Department |
Animal Health Research Centre
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| Lab |
Fish Immunology and Pathology
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| Street address |
Carretera de Algete a El Casar, Km 8
|
| City |
Valdeolmos |
| State/province |
Madrid |
| ZIP/Postal code |
28130 |
| Country |
Spain |
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| Platforms (1) |
| GPL23004 |
Illumina NextSeq 500 (Oncorhynchus mykiss) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA1083917 |
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