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Tumour PSGL-1 suppresses macrophage phagocytosis via impeding LFA-1 activation

GSE243998 Mus musculus (mouse) RNA-seq (gene expression) 13 samples Submitted 2024/12/31 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 13 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
13 samples: 7 × immune cells, EL4 subcutaneous tumour, Control, vs 6 × immune cells, EL4 subcutaneous tumour, psgl1 ko,Groups 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.
Summary (written by the submitters)
To investigate the immune suppression of PSGL-1 on hematological tumour cells, we established PSGL-1 KO EL4 cell line with CRISPR-Cas9 technique, which is used to construct subcutaneous model of hematoma on mice. After inoculation, CD45 positive immune cells were sorted from resected tomour tissue and prepared for RNA-seq in two groups: vector EL4 tissue and PSGL-1 KO EL4 tissue. We then analyzed gene expression profiling using sequencing data to look for differences occurred inside TME.
This dataset
Open GSE243998 in finder → Find more mouse RNA-seq datasets →
Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE243998_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA1020859 and SRA study SRP463091. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
7 × immune cells, EL4 subcutaneous tumour, Control, vs 6 × immune cells, EL4 subcutaneous tumour, psgl1 ko,

Supports a between-group comparison across 13 samples.

How we read this: 2 replicated groups read from 13 sample titles; they account for 13 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.

Samples in this study
Datasets on a similar topic

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