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Transcriptomic profiling of LLC LeptoM vector control, Nr1h2/3 DKO and RXRa/b/g TKO upon stimulation with 1μM 9 cis-retinoic acid (RA) in vitro

GSE277622 Mus musculus (mouse) RNA-seq (gene expression) 17 samples Submitted 2024/10/13 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 17 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
17 samples: 6 conditions, mostly in triplicateGroups 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 understand transcriptional regulation of nuclear receptors, LXRs and RXRs, in leptomeningeal metastatic cancer cells, we use CRISPR-Cas9 to knockout Nr1h2/3 genes (encoding LXRβ/α) or RXRa/b/g genes (encoding RXRα/β/γ) in LLC LeptoM cell lines, with small guide RNA targeting lacZ as vector control. We then subjected these cell lines for bulk RNA sequencing with or without stimulation of 1μM 9 cis-RA.
Read the full summary ↓
Pathway analysis of the differentially expressed genes between LLC LeptoM vector control with RA stimulation to DMSO treatment revealed upregulation of developmental related pathways and lipid metabolism pathways. Meanwhile, loss of function in LXR or RXR both resulted in dysregulation of multiple lipid metabolism pathways, in which RXR made a broader impact.
This dataset
Open GSE277622 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 GSE277622_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 PRJNA1162927 and SRA study SRP533679. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
6 conditions, mostly in triplicate
ctrl_DMSO ×3 LXRDKO_DMSO ×3 LXRDKO_RA ×3 RXRTKO_DMSO ×3 RXRTKO_RA ×3 ctrl_RA ×2

Supports a between-group comparison across 17 samples.

How we read this: 6 replicated groups read from 17 sample titles; they account for 17 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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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.