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| Status |
Public on Aug 30, 2022 |
| Title |
Single-cell RNAseq analysis of wildtype and CaMKK2 KO immune infiltrate of CT2a preclinical murine glioma |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
CaMKK2 promotes a more pro-tumor and checkpoint blockade-resistance associated immune tumor microenvironment in glioblastoma.
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| Overall design |
Tumors were disaggregated, sorted on the basis of CD45+ and Live/Dead-, and profiled using 10x Chromium 3' v3.1 chemistry on day 14 post-implantation of CT2a.Tumor-infiltrating cells were encapsulated into droplets and libraries were prepared using a Chromium Single Cell 3’ Kit using the v3.1 chemistry with feature barcoding (10X Genomics). Cell-hashing (https://doi.org/10.1186/s13059-018-1603-1) was utilized and for each 10X channel, 4 samples were equally combined: n = 4 WT, and n = 4 CaMKK2-/-. 7,000 cells per genotype were targeted with 1,750 cells per biological replicate contributing to each genotype. The generated scRNA-seq and hashtag libraries were pooled at a 25:1 ratio and sequenced on a Novaseq S Prime Flow Cell to an average depth of 61,286 and 59,013 reads per cell for WT and CaMKK2 KO samples, respectively.
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| Contributor(s) |
Tomaszewski W |
| Citation(s) |
36309495 |
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| Submission date |
Mar 03, 2022 |
| Last update date |
Nov 17, 2022 |
| Contact name |
William Tomaszewski |
| E-mail(s) |
wht10@duke.edu
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| Organization name |
Duke University
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| Department |
Immunology
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| Lab |
Sampson
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| Street address |
303 Research Dr.
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| City |
DURHAM |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA812581 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE197879_RAW.tar |
155.8 Mb |
(http)(custom) |
TAR (of MTX, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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