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Status |
Public on Jul 31, 2023 |
Title |
Sick mouse 1 |
Sample type |
SRA |
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Source name |
Joint_Sick_mouse
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Organism |
Mus musculus |
Characteristics |
strain: 129/Sve age: 8 weeks old Sex: female disease: Sick tissue: Joint
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Treatment protocol |
After pre-sensitization to mBSA, antigen induced arthritis (AIA) was triggered in 8 weeks old, female mice. The healthy control mice were injected with phosphate-buffered saline. One week after triggering, the mice were sacrificed. Successful AIA was ensured among the sick mice by immunohistochemistry, and whole joints were prepared for scRNA-seq using the Seq-Well method. To increase read coverage, each sample was sequenced multiple times.
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Extracted molecule |
polyA RNA |
Extraction protocol |
The bam files were extracted following all the steps of James Nemesh, McCarrol’s lab Drop-seq Core Computational Protocol (version 1.0.1) (http://mccarrolllab.com), using bcl2fastq conversion and Picard software. The fastq files from the same sample (multiple sequencing rounds) were merged after bcl2fastq extraction. Libraries were prepared from GRCh38 (April 2017, Ensembl) using STAR software.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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Data processing |
Processed of scRNA-seq data into digital gene expression matrices following James Nemesh, McCarrol’s lab Drop-seq Core Computational Protocol (version 1.0.1) (http://mccarrolllab.com) using bcl2fastq conversion and Picard software. The indexed reference for alignment of the reads was generated from GRCm38 (June 2017, Ensembl) using STAR software. NCBI Gene Symbols were used for annotation. Quality control, where cells with less than 10,000 reads, 400 transcripts, or 200 genes, or more than 20% mitochondrial genes were sorted out. Genes expressed in less than three cells were excluded. Genome_build: mm9 Supplementary_files_format_and_content: Matrix table with transcript counts of each gene (rows) within each cell (columns).
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Submission date |
Jan 12, 2022 |
Last update date |
Jul 31, 2023 |
Contact name |
Sandra Lilja |
Organization name |
Linköping University
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Department |
BKV
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Street address |
Sandbäcksgatan 7
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City |
Linköping |
ZIP/Postal code |
582 25 |
Country |
Sweden |
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Platform ID |
GPL19057 |
Series (1) |
GSE193536 |
Network analyses of single cell-based digital twins for individualized treatment of antigen induced arthritis in mice. |
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Relations |
BioSample |
SAMN24898261 |
SRA |
SRX13753855 |
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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