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ZFP36L2 orchestrates stress-adaptive plasticity in intestinal regeneration and colorectal cancer metastasis (bulk RNAseq)

GSE336319 Homo sapiens (human) Single-cell RNA-seq 12 samples Submitted 2026/07/20 Platform GPL34284
At a glance

Single-cell RNA-seq · human · 12 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Homo sapiens (human)
Topic
Colorectal cancerThis series is part of our curated briefing on it.
Samples
12 samples: 6 conditions, mostly in duplicateGroups 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)
Bulk RNA sequencing was performed on MSK107Li patient-derived colorectal cancer (CRC) liver metastasis organoids to characterize transcriptional changes resulting from CRISPR-Cas9-mediated ZFP36L2 knockout during dedifferentiation. ZFP36L2 was disrupted using two independent sgRNAs; two validated knockout clones per sgRNA were pooled for sequencing, with control organoids serving as comparators.
Read the full summary ↓
To assess dedifferentiation capacity, organoids were cultured in intestinal growth factor-free (IGFF) medium for 13 days to induce differentiation, then dissociated into single cells and passaged into HISC medium; samples were harvested on day 7 of dedifferentiation. Total RNA was extracted using the RNeasy Mini Kit (Qiagen) and submitted to Plasmidsaurus for 3′ end RNA-seq library preparation and sequencing. Libraries were generated using a 3′ end counting approach with unique molecular identifiers (UMIs) incorporated during cDNA synthesis. ZFP36L2 knockout organoids exhibited decreased ISC-associated gene signatures and increased expression of canonical and non-canonical differentiation programs, including osteoblast, squamous, and neuroendocrine lineages, relative to controls.
This dataset
Open GSE336319 in finder → Find more human RNA-seq datasets → Colorectal cancer landscape →
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 GSE336319_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1481252 and SRA study SRP711985. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
6 conditions, mostly in duplicate
PDO MSK107Li, Control, culture 1, ×2 PDO MSK107Li, Control, culture 2, ×2 PDO MSK107Li, ZFP36L2 gRNA1 generated clone 1, ×2 PDO MSK107Li, ZFP36L2 gRNA1 generated clone 2, ×2 PDO MSK107Li, ZFP36L2 gRNA2 generated clone 1, ×2 PDO MSK107Li, ZFP36L2 gRNA2 generated clone 2, ×2

Supports a between-group comparison across 12 samples.

How we read this: 6 replicated groups read from 12 sample titles; they account for 12 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
More Colorectal cancer datasets

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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.