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Transcriptomic profiling of highly- and lowly- metastasizing pancreatic ductal carcinoma cells [mRNAseq shNPTX1]

GSE201176 Homo sapiens (human) RNA-seq (gene expression) 11 samples Submitted 2024/04/20 Platform GPL18573
At a glance

RNA-seq (gene expression) · human · 11 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
Homo sapiens (human)
Samples
11 samples: 4 × PANC1 LM3 cells shCTRL vs 4 × PANC1 LM3 cells shNPTX1_4 vs 3 × PANC1 LM3 cells shNPTX1_3Groups 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.
Paper
A Targetable Secreted Neural Protein Drives Pancreatic Cancer Metastatic Colonization and HIF1α Nuclear RetentionCancer discovery · 2024
Summary (written by the submitters)
To interrogate transcriptomic changes in highly liver metastatic pancreatic ductal carcinoma cells as relative to their isogenic lowly metastatic cells
Published in
A Targetable Secreted Neural Protein Drives Pancreatic Cancer Metastatic Colonization and HIF1α Nuclear Retention
Yamaguchi N, Wu YG, Ravetch E et al. · Cancer discovery 2024 · PMID 39028915 · doi:10.1158/2159-8290.CD-23-1323
This dataset
Open GSE201176 in finder → Find more human 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 GSE201176_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 PRJNA828602 and SRA study SRP371384. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39028915) ↗
Study design
4 × PANC1 LM3 cells shCTRL vs 4 × PANC1 LM3 cells shNPTX1_4 vs 3 × PANC1 LM3 cells shNPTX1_3

Supports a between-group comparison across 11 samples.

How we read this: 3 replicated groups read from 11 sample titles; they account for 11 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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