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| Status |
Public on Aug 10, 2022 |
| Title |
B16_CD8--CD8_rep2 |
| Sample type |
SRA |
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| Source name |
cell
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| Organism |
Mus musculus |
| Characteristics |
tissue: cell
cell type: OT1 CD8_cytotoxic
treatment: co-culture with B16f10-mcherry-ova
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| Extracted molecule |
total RNA |
| Extraction protocol |
1×104 naive TRPV1Cre::QuASR2fl/wt DRG neurons were co-cultured with 1 × 105 B16F10-mCherry-OVA overnight in T-cell media (supplemented with 0.05 ng/μL NGF (Life Technologies, #13257-019), 0.002 ng/μL GDNF (PeproTech, #450-51-10). One day after, 4 ×105 stimulated OVA-specific CD8+ T-cells under Tc1 condition were added to the co-culture. After 48h, the cells were detached and TRPV1 neurons (CD45- eGFP+ mCherry-), B16F10-mCherry-OVA (CD45- eGFP- mCherry+), and OVA-specific CD8+ T-cells (eGFP- mCherry- CD45+ CD3+ CD8+) were FACS-purified using a FACSAria IIu cell sorter (Becton Dickinson).
RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
peformed by FULGENT (temple, CA)
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| Data processing |
Illumina sequencing was performed at the Fulgent Genetics (Temple City, CA). Reads were aligned to the Mouse mm10 reference genome using STAR v2.732.
Aligned reads were assigned to genic regions using featureCounts function from subread v1.6.4 33. Gene expression levels were represented by TPM (Transcripts Per Kilobase Million).
Hierarchical clustering was computed using heatmap.2 function (ward.D2 method) from gplots R package. Differential gene expression analysis was carried out by DeSeq2 v1.28.134.
Supplementary files format and content: Gene expression levels were represented by TPM (Transcripts Per Kilobase Million).
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| Submission date |
Jun 10, 2022 |
| Last update date |
Aug 10, 2022 |
| Contact name |
sebastien Talbot |
| E-mail(s) |
sebastien.Talbot@umontreal.ca
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| Organization name |
university of Montreal
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| Department |
pharmacology
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| Street address |
2900 Boulevard Edouard-Montpetit,
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| City |
montreal |
| State/province |
quebec |
| ZIP/Postal code |
H3T 1J4 |
| Country |
Canada |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE205864 |
Nociceptor neurons affect cancer immunosurveillance [RNA-seq 2] |
| GSE205866 |
Nociceptor neurons affect cancer immunosurveillance |
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| Relations |
| BioSample |
SAMN28968133 |
| SRA |
SRX15670508 |
| 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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