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| Status |
Public on Nov 09, 2021 |
| Title |
LM wt Nr.2 |
| Sample type |
SRA |
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| Source name |
splenocytes
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| Organism |
Mus musculus |
| Characteristics |
treatment: LM immunization on d0
strain: C57BL/6
ID: 2
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| Treatment protocol |
On day 0, recipient mice were pre-immunized with either wildtype LM (mice 2-3) or LM61 (mice 7, 8, 14, 15). On day 9 mouse 14 and 15 were used for analysis. All remaining mice (2, 3, 7, 8) received KL25HL B cells by adoptive transfer and were challenged with LCMV on day 9. On day 14, GP66-77-specific CD4 T cells (CD4+ CD44hi, B220-, CD8-, F4/80-) were purified by FACS-sorting and were subject to scRNAseq.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
GP66 specfic CD4 T cells were FACS sorted on day 9 or 14 days directly RPMI+FCS or pure FACS and processed immediately for 10x Genomics
10X: Chemistry = Single Cell 3' v3, Transcriptome = mm10-2.1.0, Pipeline Version = 3.1.0
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
d9 KL25HL B cell transfer and LCMV infection, analysis d14
UMImatrix_Lm_WT_d5.tsv.gz
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| Data processing |
Single-cell sequencing files (basecalls) were processed using the Cell Ranger Single Cell Software Suite (v3.1.0) to perform quality control, sample de-multiplexing, barcode processing, alignment to mm10 genome with STAR (version 2.6.1a_08-27), and read counting on Ensembl 93 gene model (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome).
Default parameters were used for Cell Ranger, except for the STAR parameters outSAMmultNmax set to 1 and alignIntronMax set to 10000.
UMI were counted by extracting read counts from the raw_feature_bc_matrix generated by Cell Ranger, using R and DropletUtils. The UMI matrix was filtered to keep cells with log10 library size > 3.3 and < 4.78, log number of features > 3, % mitochondrial reads >= 5, % ribosomal protein reads >= 20. Genes with average counts < .007 were removed. The UMI counts matrices are tab-separated and gzipped in the processed data files.
Genome_build: mm10
Supplementary_files_format_and_content: UMImatrix*.tsv.gz; gzipped tab-separated values text file with UMI counts. Rowname = Ensembl Stable ID. Columns named as: CellBarcode-Immunization-Timepoint-SampleNum, e.g. AAACCCAAGAAACTGT-Lm_WT-d5-Sample2
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| Submission date |
Nov 12, 2020 |
| Last update date |
Nov 09, 2021 |
| Contact name |
Daniel Pinschewer |
| Organization name |
University of Basel
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| Department |
Department of Biomedicine
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| Lab |
Experimental Virology
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| Street address |
Petersplatz 10
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| City |
Basel |
| ZIP/Postal code |
4003 |
| Country |
Switzerland |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE161356 |
Vaccine-elicited CD4 T cells prevent the deletion of antiviral B cells in chronic infection |
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| Relations |
| BioSample |
SAMN16783399 |
| SRA |
SRX9494014 |
| 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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