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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 01, 2024 |
| Title |
Mus musulus 770331 |
| 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+Ctl CpG+Iso for 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. Tumor specimens and matched muscle control were harvested and stored in RNALater (Ambion) at −80°C until all samples were collected. RNA extractions from each sample were performed using RNeasy Fibrous Tissue Mini Kit (Qiagen). Extracted total RNA quality and concentration were assessed on a NanoDrop Spectrophomoter (Thermo Fisher Scientific).
RNA-seq libraries were prepared using TruSeq Small RNA Library Preparation Kits (Illumina) following the manufacturer’s protocol. RNA sequencing was performed on an Illumina Novoseq in 151 base pair, paired-end configuration. Greater than 50,000 reads per cell were collected per the manufacturer's recommendation.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
TruSeq Small RNA Library Preparation Kits
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| Data processing |
All FASTQ files were processed using a combination of STAR v2.7.10a and Salmon v1.2.0 with the mouse build GRCh38 - mm10 as a reference). FASTQ files from the same sample, but different lanes, were merged with STAR’s fastq_channel_merged_paired function. Reads were mapped using STAR’s fastq_channel_merged_paired_star function. Picard and QC, count matrix assembly, and bam files were generated for each sample using both Picard v2.27.4, STAR v2.7.10a, and Salmon v1.2.0. TRUST4 v1.0.12 (Tcr Repertoire Utilities for Solid Tissue) were used to reconstruct TCR and BCR sequences from BAM files generated from the STAR/Salmon outputs. All parameters for TRUST4 were set to default. The final output from TRUST4 was summary matrices for each sample that included hypervariable complementarity-determining region 3 (CDR3) nucleotide and amino acid sequences, counts, frequencies, and V, D, and J chain names.
Assembly: GRCm38
Supplementary files format and content: Complete gene count matrix (expression_raw_annotated.csv), gene count matrix normalized with Deseq2 and converted to log2 scale (expression_normalized_log2.csv), output from TRUST4 algorithm (processed_trust4.zip).
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| Submission date |
Dec 28, 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 |
GPL24247 |
| Series (1) |
| GSE252213 |
Enhancing radiotherapy response via intratumoral injection of the TLR9 agonist CpG to stimulate CD8 T cells in an autochthonous mouse model of sarcoma |
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| Relations |
| SRA |
SRX23025772 |
| BioSample |
SAMN39123558 |
| 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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