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| Status |
Public on Mar 14, 2022 |
| Title |
scRNA-seq mouse 233 |
| Sample type |
SRA |
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| Source name |
Spleen
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| Organism |
Mus musculus |
| Characteristics |
strain: B6.Sle1yaa
cell type: CD45+
chimera condition: SLE.yaa
Sex: M
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| Extracted molecule |
total RNA |
| Extraction protocol |
CD45 cells were enriched using MACS and captured in droplets according to 10X Genomics protocols.
Gene expression or VDJ libraries were prepared following reverse transcription according to 10X Genomics protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
total RNA
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| Data processing |
Cellranger (v5.0.0) was used to generate count and vdj matrices by aligning to the GRCm38 (mm10) reference genome
Gene expression matrices were read using Seurat (v4.0.0) and filtered for cells with at least 200 genes detected and genes in at least 3 cells
Cells were further filtered for 200-3000 genes detected, more than 1000 reads detected, less than 5% mitochondrial RNA content, less than 25% ribosomal R content, S phase score less than 0.15, and G2/M phase score less than 0.15
Samples were merged, normalized, and integrated by condition in Seurat (v4.0.0)
BCRs were filtered for cell barcodes with productive heavy and light chain sequences
TCRs were filtered for cell barcodes with productive alpha and beta chain sequences
Genome_build: mm10
Supplementary_files_format_and_content: Matrix with normalized gene counts for every gene (columns) for each cell barcode (rows)
Supplementary_files_format_and_content: Matrix with feature and sample-level metadata (columns) for each cell barcode (rows)
Supplementary_files_format_and_content: Matrix with BCR and sample-level metadata (columns) for each cell barcode (rows)
Supplementary_files_format_and_content: Matrix with TCR and sample-level metadata (columns) for each cell barcode (rows)
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| Submission date |
Dec 29, 2021 |
| Last update date |
Mar 14, 2022 |
| Contact name |
Elliot Akama-Garren |
| Organization name |
Harvard Medical School
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| Street address |
200 Longwood Ave
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE192762 |
Lupus susceptibility loci predispose mice to clonal lymphocytic responses and myeloid expansion |
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| Relations |
| BioSample |
SAMN24499107 |
| SRA |
SRX13553918 |
| 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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