Data · dataset · 2022
Single-nucleus transcriptomic profiling of multiple organs in a rhesus macaque model of SARS-CoV-2 infection
Listed in ScienceDB
We performed single-nucleus RNA sequencing (a substitute method of famous single-cell RNA sequencing) with multiple organs (lung, liver, kidney, cerebral cortex) obtained from SARS-CoV-2-infected macaques and uninfected control to analyze cellular and molecular changes of host after SARS-CoV-2 infection.
Description
Firstly, we obtained organ tissues from animals and isolated cell nuclei from tissue blocks; Secondly, we performed single-nucleus RNA-seq for each sample with popular 10X Genomics platform; Thirdly, we constructed cDNA libraries for each sample according to manufacture's instructions; Finally, we got the sequencing data files (fastq format) with Illumina Novaseq platform.
We and other readers who want to reuse these data can align fastq files to human reference genome using 'Cellranger' software, and then read the output matrix to single-cell data analysis toolkit including famous 'Seurat' and 'Scanpy'. We also provided the integrated dataset file (h5ad format) containing gene expression informations of all samples in this project, it was generated with 'Scanpy'.
Links
Where it is published
- DOI doi.org/10.57760/sciencedb.06252 ↗
DOI / persistent id · from scidb cn
Catalogue records · 1
- OAI-PMH record scidb.cn/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=10.57760%2… ↗
metadata API · from scidb cn
Topics
- From keywords
- Earth & Environmental Science · Engineering · Humanities · Life Sciences · Social Science
- Inferred from text
- RNA sequencing 75% · Sequencing 75% · Single-cell RNA sequencing 75%
Provenance · 1 source records, 13 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| ScienceDB | 10.57760/sciencedb.06252 | 12 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:earth-environmental | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:engineering | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:humanities | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:social-science | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[modality].local:modality:rna-seq | enrichment · scidb cn | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[modality].local:modality:sequencing | enrichment · scidb cn | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[modality].local:modality:single-cell-rna-seq | enrichment · scidb cn | keyword-concept-rules@1.0.0 | title+description (75%) |
| description | source · scidb cn | connector:scidb_cn@1.0.0 | /metadata/dc/description |
| license | source · scidb cn | connector:scidb_cn@1.0.0 | /metadata/dc/rights |
| publication_date | source · scidb cn | connector:scidb_cn@1.0.0 | |
| title | source · scidb cn | connector:scidb_cn@1.0.0 | /metadata/dc/title |