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Series GSE113602 Query DataSets for GSE113602
Status Public on Apr 24, 2021
Title Single-cell RNA-seq of sorted CD8+ T cells from B16 melanoma tumors
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary The response of naive CD8 T cells to acute infections results in the generation of defined yet heterogeneous pools of effector and memory cells. In contrast, the complexity of tumor infiltrating CD8 T cell states is still not fully elucidated. To delineate the landscape of tumor infiltrating CD8 T cells in an unbiased manner, we performed single-cell (full-length) RNA-Seq of CD8 T cells infiltrating mouse B16 melanomas. Our analysis of cell heterogeneity revealed the presence of multiple distinct CD8 T cell subtypes including exhausted, terminal effector, naive and memory-like CD8 T cells, as well as novel intermediate states. TCR reconstruction and pseudotime ordering enabled us to follow differentiation of single clones and suggested distinct trajectories towards T-cell exhaustion.
 
Overall design single-cell (full-length) RNA-Seq of CD8 T cells infiltrating mouse B16 melanomas
Please note that [1] there are 192 samples included in the study, and the processed data was generated from the 135 quality filtered samples (filetering parameters are provided in the data processing steps) [2] The cell subtype information for each sample is described and provided in the associated publication.
 
Contributor(s) Singer M
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Submission date Apr 24, 2018
Last update date Apr 24, 2021
Contact name Aviv Regev
E-mail(s) nmdespot@gmail.com
Organization name Broad Institute
Lab Regev Lab
Street address 415 MAIN ST
City CAMBRIDGE
State/province MASSACHUSETTS
ZIP/Postal code 02142-1027
Country USA
 
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (192)
GSM3109438 S10
GSM3109439 S298
GSM3109440 S11
Relations
BioProject PRJNA453200
SRA SRP142490

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE113602_index_CD8_all.csv.gz 642 b (ftp)(http) CSV
GSE113602_matrix_TPM_CD8TCELL_filtered_log2.csv.gz 1.2 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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