|
| Status |
Public on Jan 18, 2023 |
| Title |
Pan troglodytes PBL, mock |
| Sample type |
SRA |
| |
|
| Source name |
peripheral blood
|
| Organism |
Pan troglodytes |
| Characteristics |
tissue: peripheral blood
cell type: PBMC
treatment: Mock
|
| Treatment protocol |
One million PBMCs were infected with HSV-1 or SeV at a multiplicity of infection 0.1. LPS (Sigma-Aldrich, Cat# L5024-10MG) was added at 200 ng/ml final concentration. One day post infection, infected/stimulated PBMCs were used for scRNA-seq.
|
| Growth protocol |
One million PBMCs were maintained in 500 μl RPMI 1640 (Sigma-Aldrich, Cat# R8758-500ML).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
One day post infection, infected/stimulated PBMCs were centrifuged and resuspended with PBS.
Library construction was performed following the manufacter’s instructions (Next GEM Single Cell 3' Reagent Kits v3.1, 10x Genomics). Briefly, PBMCs were washed with PBS, then resuspended in the master mix. Cells, gel-beads and oils were loaded into the Next GEM chip G to generate GEMs using Chromium controller. Reverse transcription were performed in each GEM and barcoded cDNA were produced. After cDNA amplification, enzymatic fragmentation end repair, A-tailing, adaptor ligation and index PCR were processed. QC for constructed libraries were conducted by Agilent Bioanalyzer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (10x Genomics).
Assembly: Homo sapiens: GRCh38.p13 (RefSeq accession: GCF_000001405.39); Pan troglodytes: Clint_PTRv2 (RefSeq accession: GCF_002880755.1); Macaca mulatta: Mmul_10 (RefSeq accession: GCF_003339765.1); Rousettus aegyptiacus: mRouAeg1.p (RefSeq accession: GCF_014176215.1)
Supplementary files format and content: HDF5 format including count matrices
|
| |
|
| Submission date |
Nov 17, 2022 |
| Last update date |
Jan 19, 2023 |
| Contact name |
Kei Sato |
| E-mail(s) |
su9ark@gmail.com
|
| Phone |
81364092212
|
| Organization name |
The Institute of Medical Science, The University of Tokyo
|
| Department |
Department of Microbiology and Immunology
|
| Lab |
Division of Systems Virology
|
| Street address |
4-6-1 Shiroganedai
|
| City |
Minato-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
1088639 |
| Country |
Japan |
| |
|
| Platform ID |
GPL30573 |
| Series (1) |
| GSE218199 |
Comparative analysis of innate immune responses to viral infection among animals |
|
| Relations |
| BioSample |
SAMN31772166 |
| SRA |
SRX18295177 |
