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Series GSE140430 Query DataSets for GSE140430
Status Public on Nov 15, 2019
Title Stem and effector CD8 T-cells from human cancers
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Tumor infiltrating lymphocytes (TILs) are associated with a survival benefit in several tumor types and response to immunotherapy. However, the reason some tumors have high CD8 T cell infiltration while others do not remains an unanswered question. In this study, we investigated the requirements for maintaining a CD8 T cell response against human cancer. We find that CD8 T cells within tumors consist of distinct populations of terminally differentiated and stem-like cells. Upon proliferation, stem-like CD8 T cells give rise to more terminally differentiated, effector molecule expressing daughter cells. For many T-cells to infiltrate the tumor, it is critical that this effector differentiation process occur. In this study, we collected these different cell populations from human tumors and performed RNA sequencing and DNA methylation analysis.
Overall design Cell populations were sorted from tumors and RNA and DNA extracted using qiagen all-prep kits. RNA was sequenced using the NuGen ovation protocol for prostate and bladder, and clontech smartseq2 for bladder samples. Dna methylation libraries were prepared using the Illumina DNAmethyseq protocol. Samples were sequenced on a Hiseq 3000, or Hiseq X10.
Contributor(s) Kissick H
Citation(s) 31827286
Submission date Nov 14, 2019
Last update date Dec 20, 2019
Contact name Haydn Kissick
Phone 6172598364
Organization name Emory University
Street address 1462 Clifton Rd
City Atlanta
State/province Georgia
ZIP/Postal code 30322
Country USA
Platforms (2)
GPL20795 HiSeq X Ten (Homo sapiens)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (22)
GSM4161211 B_Ef_1
GSM4161212 B_Ef_2
GSM4161213 B_Stem_1
BioProject PRJNA589675
SRA SRP229996

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
GSE140430_bladder_counts.csv.gz 725.5 Kb (ftp)(http) CSV
GSE140430_counts.csv.gz 914.6 Kb (ftp)(http) CSV
GSE140430_methylation_counts.xlsx 27.1 Mb (ftp)(http) XLSX
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Raw data are available in SRA
Processed data are available on Series record

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