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GEO help: Mouse over screen elements for information. |
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Status |
Public on Jan 01, 2024 |
Title |
770226 treatment Grp 2-RT+Iso 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 2-RT+Iso 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 |
SRX23024468 |
BioSample |
SAMN39122317 |
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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