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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 07, 2020 |
| Title |
BRBS283 |
| Sample type |
SRA |
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| Source name |
splenic plasmacytoid dendritic cells
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| Organism |
Mus musculus |
| Characteristics |
mouse genotype: Ifnb1Eyfp
cell type: pDC
tissue: spleen
infection time: 36H
eyfp status: MCMV YFPneg
plate: P2
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single cells were FACS sorted into 96-well PCR plates (Eppendorf), each well containing 10 µl of TCL buffer (Qiagen) supplemented with 1% β-mercaptoethanol. Plates were spun down at 800g for 1 min, flash frozen on dry ice and stored at -80°C until further processing (Villani and Shekhar, 2017).
Single cell RNA-sequencing libraries were generated using an adaptation of Smart-Seq2 (Villani and Shekhar, 2017).
Full-length RNA-sequencing was performed.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
MCMV_96
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| Data processing |
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequenced reads were mapped to mouse genome GRCm38 using STAR version 2.2.1 with default parameters except --sjdbOverhang 49 --outSAMstrandField intronMotif --outFilterMultimapNmax 1 (The max number of multiple alignments allowed for a read is 1. if exceeded, the read is considered unmapped).
Read counting was performed using HTSeq-Count (version 0.9.1) with parameters --stranded=no -m union, and using the annotations of mouse genome GRCm38 release 94 downloaded from the ENSembl website. In short, our RNA-Seq data has not been made with a strand-specific protocol. When a read was mapped to more than one gene, it was considered as ambiguous and assigned to none of them.
Genome_build: GRCm38 with an additional artificial chromosome for the YFP sequence
Supplementary_files_format_and_content: Text files with tab delimiters including raw gene counts and metadata (including index sorting information) for each sample
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| Submission date |
May 27, 2020 |
| Last update date |
Jul 07, 2020 |
| Contact name |
Thien-Phong Vu Manh |
| Organization name |
CIML
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| Street address |
163 avenue de Luminy
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| City |
marseille |
| ZIP/Postal code |
13288 |
| Country |
France |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE151246 |
Single-cell analysis of mouse plasmacytoid dendritic cells (pDCs) unravels their activation trajectory and their molecular regulation in vivo during a viral infection [Ss2_pDC1] |
| GSE151248 |
Single-cell analysis of mouse plasmacytoid dendritic cells (pDCs) unravels their activation trajectory and their molecular regulation in vivo during a viral infection |
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| Relations |
| BioSample |
SAMN15030858 |
| SRA |
SRX8403923 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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