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| Status |
Public on Aug 26, 2022 |
| Title |
16149_RF |
| Sample type |
SRA |
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| Source name |
lung tissue
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| Organism |
Macaca mulatta |
| Characteristics |
tissue region: right lung
time: 4 dpi following intranasally inoculation
animal no.: 16149
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| Treatment protocol |
Rhesus monkeys (3-5 kg, 3-5years old) were used for this study. One monkey is infected by intragastric administration with 1x 10^7 PFU of SARS-CoV-2 in 1mL of PBS, and another monkey was intranasally injected with 1x10^6 of SARS-CoV-2 in 200 µl of PBS. One monkey was Intranasally and intragastrically treated with PBS as a control. We analyzed the tissues collected on the 4 dpi following Intranasal and intragastrical inoculation.
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| Extracted molecule |
total RNA |
| Extraction protocol |
For cell capture and cDNA synthesis, single cells were suspended in PBS containing 0.04% bovine serum albumin. About 8000 cells were added to each channel, and it is estimated that about 2200 target cells will be recovered. The captured cells were lysed and the released RNA was barcoded in a single GEM by reverse transcription. Reverse transcription was performed on the S1000TM Touch Thermal Cycler (Bio Rad) at 53 °C for 45 min, then at 85 °C for 5 min and held at 4 °C. The quality of cDNA was evaluated using Agilent 4200 (CapitalBio Technology, Beijing).
Single-cell suspensions were made using a gentle MACS Octo (Miltenyi Biotec). Single-cell suspensions were loaded onto the Chromium Controller (10× Genomics) for droplet formation. scRNA-seq libraries were constructed by the Single Cell 3’ Library and Gel Bead Kit V3. The libraries were sequenced by an Illumina Novaseq6000 sequencer, the sequencing depth of each cell was at least 100,000 reads, and the pairedend 150 bp (PE150) reading strategy (CapitalBio Technology, Beijing) was adopted.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
total RNA
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| Data processing |
Cellranger pipeline. The Cell Ranger software was obtained from 10× Genomics website. Alignment, filtering, barcode counting, and UMI counting were performed with cell ranger count module. Dimensionality reduction and the first ten principal components were used to generate clusters by K-means algorithm and graphbased algorithm, respectively.
Seurat pipeline. The other clustering method is Seurat 3.0(R package). Cells whose gene number was less than 200,or gene number ranked in the top 1%, or mitochondrial gene ratio was more than 25% were regarded as abnormaland filtered out. Dimensionality reduction was performed using PCA, and visualization was realized by TSNE andUMAP.
Enrichment Analysis. GO enrichment, KEGG enrichment, Reactome enrichment and Disease enrichment (humanonly) of cluster markers were performed using KOBAS software with Benjamini-Hochberg multiple testingadjustment, using top 20 markers gene of cluster. The results were visualized using R package.
Single-cell trajectories Analysis. Single-cell trajectories were built with Monocle (R package) that introducedpseudotime. Genes were filtered by the following criteria: Expressed in more than 10 cells; The average expressionvalue was greater than 0.1; Qval was less than 0.01 in different analysis.
Assembly: ftp://ftp.ensembl.org/pub/release-100/gtf/macaca_mulatta/Macaca_mulatta.Mmul_10.100.gtf.gz
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| Submission date |
Aug 21, 2022 |
| Last update date |
Aug 28, 2022 |
| Contact name |
Jiandong Shi |
| E-mail(s) |
dongdong9286@yeah.net
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| Organization name |
Institute of Medical Biology
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| Department |
Department of Vaccine Research
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| Street address |
935# Jiaoling Road
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| City |
Kunming |
| State/province |
Yunnan |
| ZIP/Postal code |
650118 |
| Country |
China |
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| Platform ID |
GPL27943 |
| Series (1) |
| GSE211741 |
SARS-CoV-2 infection activates AhR signaling |
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| Relations |
| BioSample |
SAMN30432387 |
| SRA |
SRX17165511 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6500438_16149_RF_filtered_feature_bc_matrix.tar.gz |
20.6 Mb |
(ftp)(http) |
TAR |
| GSM6500438_16149_RF_raw_feature_bc_matrix.tar.gz |
54.2 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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