HDAC inhibition drives treatment duration-dependent changes in proliferation and effector function of tumor-infiltrating CD8 T cells.
RNA-seq (gene expression) · mouse · 16 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Mus musculus (mouse)
- Samples
- 16 samples: 4 × d10_Con_CD8 vs 4 × d10_ENT_CD8 vs 4 × d17_ENT_CD8 vs 4 × d17_Con_CD8Groups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE140285_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA589090 and SRA study SRP229625. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 16 samples.
How we read this: 4 replicated groups read from 16 sample titles; they account for 16 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM4158870 d10_Con_CD8_1 d10_Con_CD8
- GSM4158871 d10_Con_CD8_2 d10_Con_CD8
- GSM4158872 d10_Con_CD8_3 d10_Con_CD8
- GSM4158873 d10_Con_CD8_4 d10_Con_CD8
- GSM4158874 d10_ENT_CD8_1 d10_ENT_CD8
- GSM4158875 d10_ENT_CD8_2 d10_ENT_CD8
- GSM4158876 d10_ENT_CD8_3 d10_ENT_CD8
- GSM4158877 d10_ENT_CD8_4 d10_ENT_CD8
- GSM4158878 d17_ENT_CD8_1 d17_ENT_CD8
- GSM4158879 d17_ENT_CD8_2 d17_ENT_CD8
- GSM4158880 d17_ENT_CD8_3 d17_ENT_CD8
- GSM4158881 d17_ENT_CD8_4 d17_ENT_CD8
- GSM4158882 d17_Con_CD8_1 d17_Con_CD8
- GSM4158883 d17_Con_CD8_2 d17_Con_CD8
- GSM4158884 d17_Con_CD8_3 d17_Con_CD8
- GSM4158885 d17_Con_CD8_4 d17_Con_CD8
- GSE255887 HDAC1 controls the generation and maintenance of effector-like CD8+ T cells during chronic viral infection 76 samples shares hdac, cd8, effector
- GSE264650 RNA-seq of murine CD8+ tumor-infiltrating T cells following treatment with pembrolizumab and/or ABL503 20 samples shares cd8, tumor-infiltrating, treatment
- GSE296763 Mitochondrial respiration is necessary for CD8 T cell proliferation and cell fate 99 samples shares cd8, proliferation
- GSE302682 Sleeping Beauty mutagenesis identifies BACH2 and other regulators promoting CD8+ T cell persistence and effector function under tumor-associated chronic antigen stimulation - RNAseq 66 samples shares cd8, effector
- GSE306744 Pre-division TCF1 downregulation determines long-term effector and memory CD8 T cell fates [RNA-Seq] 31 samples shares cd8, effector
- GSE248272 Therapeutically targeting perivascular macrophage effector function improves CD8+ T-cell infiltration and response to chemotherapeutic drugs in cancer 30 samples shares cd8, effector
- GSE302683 Sleeping Beauty mutagenesis identifies BACH2 and other regulators promoting CD8+ T cell persistence and effector function under tumor-associated chronic antigen stimulation - esTAG 29 samples shares cd8, effector
- GSE316541 α2,6-Sialoglycan-regulated anti-tumor immunity of tumor-infiltrating CD8+ T cells in the tumor microenvironment [CD8+T] 27 samples shares cd8, tumor-infiltrating
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.