Tumor suppressors in Sox2-mediated lung cancers promote distinct cell-intrinsic and immunologic remodeling
RNA-seq (gene expression) · mouse · 25 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
- 25 samples: 7 conditions, mostly with about 4 replicates eachGroups 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 GSE295887_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 PRJNA1256720 and SRA study SRP577860. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 25 samples.
How we read this: 7 replicated groups read from 25 sample titles; they account for 25 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.
- GSM8907676 JH716-18 cells, rep 1 JH716-18 cells,
- GSM8907677 JH716-18 cells, rep 2 JH716-18 cells,
- GSM8907678 JH716-18 cells, rep 3 JH716-18 cells,
- GSM8907679 LN1A cells, rep 1 LN1A cells,
- GSM8907680 LN1A cells, rep 2 LN1A cells,
- GSM8907681 LN1A cells, rep 3 LN1A cells,
- GSM8907682 LN2A cells, rep 1 LN2A cells,
- GSM8907683 LN2A cells, rep 2 LN2A cells,
- GSM8907684 LN2A cells, rep 3 LN2A cells,
- GSM8958231 Tumor, LN2A, rep 1 Tumor, LN2A,
- GSM8958232 Tumor, LN2A, rep 2 Tumor, LN2A,
- GSM8958233 Tumor, LN2A, rep 3 Tumor, LN2A,
- GSM8958234 Tumor, LN2A, rep 4 Tumor, LN2A,
- GSM8958235 Tumor, p53, rep 1 Tumor, p53,
- GSM8958236 Tumor, p53, rep 2 Tumor, p53,
- GSM8958237 Tumor, p53, rep 3 Tumor, p53,
- GSM8958238 Tumor, p53, rep 4 Tumor, p53,
- GSM8958239 Tumor, PTEN, rep 1 Tumor, PTEN,
- GSM8958240 Tumor, PTEN, rep 2 Tumor, PTEN,
- GSM8958241 Tumor, PTEN, rep 3 Tumor, PTEN,
- GSM8958242 Tumor, PTEN, rep 4 Tumor, PTEN,
- GSM8958243 Tumor, SH, rep 1 Tumor, SH,
- GSM8958244 Tumor, SH, rep 2 Tumor, SH,
- GSM8958245 Tumor, SH, rep 3 Tumor, SH,
- GSM8958246 Tumor, SH, rep 4 Tumor, SH,
- GSE295824 Tumor suppressors in Sox2-mediated lung cancers promote distinct cell intrinsic and immunologic remodeling [scRNA-seq] 16 samples shares sox2-mediated, suppressors, immunologic, remodeling, distinct, promote, lung
- GSE294471 Tumor suppressors in Sox2-mediated lung cancers promote distinct cell intrinsic and immunologic remodeling [RNA-seq] 9 samples shares sox2-mediated, suppressors, immunologic, remodeling, distinct, promote, lung
- GSE299632 Elevated expression of the molecular clock suppressors Period 1 and Period 2 promote myotube atrophy in vitro with implications to the loss of limb muscle mass following androgen deprivation 20 samples shares suppressors, promote
- GSE267890 Tracing immunological interaction in trimethylamine N-oxide hydrogel-derived zwitterionic microenvironment during promoted diabetic wound regeneration 12 samples shares immunologic, promote
- GSE249969 Loss of tumor suppressors promotes a non-cell-autonomous inflammatory tumor microenvironment and enhances LAG3+T cell mediated immune suppression [RNA_seq_Cas9_PT] 8 samples shares suppressors, promote
- GSE249971 Loss of tumor suppressors promotes a non-cell-autonomous inflammatory tumor microenvironment and enhances LAG3+T cell mediated immune suppression [RNA_seq_vitro] 8 samples shares suppressors, promote
- GSE271698 B cell-intrinsic IFN-g promotes CD11c+ age-associated B cell differentiation and compromises affinity-based germinal center selection in lupus 1 samples shares cell-intrinsic, promote
- GSE249972 Loss of tumor suppressors promotes a non-cell-autonomous inflammatory tumor microenvironment and enhances LAG3+T cell mediated immune suppression 24 samples shares suppressors, promote
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.