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| Status |
Public on Jan 01, 2024 |
| Title |
770279 treatment Grp 4-NO RT+Iso for OX40+Ctrl CpG+Iso PD-1 |
| Sample type |
SRA |
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| Source name |
p53/MCA sarcoma
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| Organism |
Mus musculus |
| Characteristics |
tissue: p53/MCA sarcoma
genotype: 129/SVJ WT
treatment: Grp 4-NO RT+Iso for OX40+Ctrl CpG+Iso PD-1
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tumors were dissected from mice, minced, and digested using the Miltenyi Biotec tumor dissociation kit. Dissociated cells were prepared for fluorescence-activated cell sorting of CD45+ cells for single-cell RNA sequencing. Single-cell suspensions from sorted live CD45+ cells were loaded on a Chromium Controller (10x Genomics) to generate single-cell beads in emulsion, and scRNA-seq libraries were prepared using the Chromium Single Cell 3′ Reagent Kits (v3.1 Single Index Kit), Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3.1, Chromium Next GEM Chip G Single Cell Kit, and Single Index Kit T Set A (10x Genomics) following the manufacturer’s protocol
Single-cell barcoded cDNA libraries were qualified and quantified using Agilent Bioanalyzer. cDNA libraries were sequenced on an Illumina NextSeq 500 (Illumina). Read lengths were 26 bp for read 1, 8 bp for i7 index, and 98 bp for read 2. Ten thousand cells from each sample were sequenced with greater than 50,000 reads per cell as recommended by the manufacturer.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
10x Genomics
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| Data processing |
CellRanger output generated data for sample.
Assembly: GRCm38
Supplementary files format and content: Count matrix and cell metadata from the 10X output after de-multiplexing.
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| Submission date |
Dec 27, 2023 |
| Last update date |
Jan 01, 2024 |
| Contact name |
Vincent Michael Perez |
| E-mail(s) |
vincentmichaelperez@gmail.com
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| Phone |
4172883742
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| Organization name |
Tempus AI
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| Department |
Translational reasearch
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| Street address |
25 Alexandria Wy
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| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27703 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE252143 |
Enhancing radiotherapy response via intratumoral injection of the TLR9 agonist CpG to stimulate CD8 T cells in an autochthonous mouse model of sarcoma (single-cell RNA-seq analysis) |
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| Relations |
| SRA |
SRX23024481 |
| BioSample |
SAMN39122330 |
| 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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