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Development Of Pre-Clinical Murine Models For Fibrolamellar Hepatocellular Carcinoma

GSE249325 Mus musculus (mouse) RNA-seq (gene expression) 19 samples Submitted 2024/06/03 Platform GPL24247Platform GPL21103
At a glance

RNA-seq (gene expression) · mouse · 19 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
19 samples: 5 × Control treated subcutaneous FL8 allograft tumor # vs 5 × Palbociclib treated subcutaneous FL8 allograft tumor # vs 5 × embryonic liver , control-S vs 4 × embryonic liver , DNAJ1B-PKA_Overexpression-SGroups 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)
Fibrolamellar hepatocellular carcinoma(FLC) is a rare form of cancer that affects primarily adolescentsand young adults. FLC tumors are typically associated with an intrachromosomal deletion resulting in expression of a fusion protein between the chaperone DNAJ1B and the protein kinase PKA. FLC ischallenging to study because of its rarity and limited pre-clinical models.
Read the full summary ↓
Here, we developed a novel transgenic mouse model of FLC. In this model, DNAJ1B-PKA expression in the liver of mouse embryos results in perinatal lethalityassociated with liver developmental defects, while DNAJ1B-PKA expression in the liver of adult mice initiates tumors resembling FLC at low penetrance. Some of these tumors can be serially propagated in 3D cultures and in allografts, including in syngeneic hosts. One such model shows growth inhibition upon treatment with the CDK4/6 inhibitor palbociclib. New pre-clinical models of FLC will provide novel insights into the biology of this rare cancerand may help identify novel therapeutic strategies.
This dataset
Open GSE249325 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 GSE249325_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 PRJNA1048524 and SRA study SRP475742. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
5 × Control treated subcutaneous FL8 allograft tumor # vs 5 × Palbociclib treated subcutaneous FL8 allograft tumor # vs 5 × embryonic liver , control-S vs 4 × embryonic liver , DNAJ1B-PKA_Overexpression-S

Supports a case/control comparison: 9 samples read as cases, 5 as controls.

How we read this: 4 replicated groups read from 19 sample titles; they account for 19 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.