MORC2 regulates RBM39-mediated CDK5RAP2 alternative splicing to promote EMT and metastasis in colon cancer
RNA-seq (gene expression) · human · 14 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)
- Topic
- Colorectal cancerThis series is part of our curated briefing on it.
- Samples
- 14 samples: 3 × SW480 cells, shCtrl (control for shMORC2), vs 3 × SW480 cells, shMORC2, vs 3 × SW480 cells, shCtrl (control for shRBM39), vs 3 × SW480 cells, shRBM39,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.
- Paper
- MORC2 regulates RBM39-mediated CDK5RAP2 alternative splicing to promote EMT and metastasis in colon cancerCell death & disease · 2024
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE246916_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1035090 and SRA study SRP469954. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 14 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.
- GSM7874128 SW480 cells, RBM39_Input
- GSM7874129 SW480 cells, RBM39_IP, Abcam
- GSM7880614 SW480 cells, shCtrl (control for shMORC2), rep1 SW480 cells, shCtrl (co…
- GSM7880615 SW480 cells, shCtrl (control for shMORC2), rep2 SW480 cells, shCtrl (co…
- GSM7880616 SW480 cells, shCtrl (control for shMORC2), rep3 SW480 cells, shCtrl (co…
- GSM7880617 SW480 cells, shMORC2, rep1 SW480 cells, shMORC2,
- GSM7880618 SW480 cells, shMORC2, rep2 SW480 cells, shMORC2,
- GSM7880619 SW480 cells, shMORC2, rep3 SW480 cells, shMORC2,
- GSM7880783 SW480 cells, shCtrl (control for shRBM39), rep1 SW480 cells, shCtrl (co…
- GSM7880784 SW480 cells, shCtrl (control for shRBM39), rep2 SW480 cells, shCtrl (co…
- GSM7880785 SW480 cells, shCtrl (control for shRBM39), rep3 SW480 cells, shCtrl (co…
- GSM7880786 SW480 cells, shRBM39, rep1 SW480 cells, shRBM39,
- GSM7880787 SW480 cells, shRBM39, rep2 SW480 cells, shRBM39,
- GSM7880788 SW480 cells, shRBM39, rep3 SW480 cells, shRBM39,
- GSE12032 Inherent gene signature of stage II and III colorectal cancer leads in individual recurrence 198 samples same disease briefing
- GSE109308 Single-cell transcriptomic survey of adenomatous polyposis patients with germline APC mutations 97 samples same disease briefing
- GSE110009 Single cell transcriptome landscape of primary and metastatic tumor in colon cancer 76 samples same disease briefing
- GSE250000 Bulk RNA-sequencing of transduced colorectal cancer cell line HCT-116 and breast cancer cell line MCF-7 overexpressing full-lenght p53β or p53β-stop-lost. 4 samples same disease briefing
- GSE246915 MORC2 regulates RBM39-mediated CDK5RAP2 alternative splicing to promote EMT and metastasis in colon cancer [shRBM39 mRNA-seq] 6 samples shares cdk5rap2, morc2, emt, rbm39-mediated, alternative, metastasis, splicing, promote
- GSE246909 MORC2 regulates RBM39-mediated CDK5RAP2 alternative splicing to promote EMT and metastasis in colon cancer [shMORC2 mRNA-seq] 6 samples shares cdk5rap2, morc2, emt, rbm39-mediated, alternative, metastasis, splicing, promote
- GSE216843 Hypoxia-induced CTCF mediates alternative splicing via coupling chromatin looping and RNA Pol II pause to promote EMT in breast cancer 18 samples shares emt, alternative, splicing, promote
- GSE279474 PRMT5 regulates alternative splicing of TCF3 under hypoxia to promote EMT and invasion in breast cancer 4 samples shares emt, alternative, splicing, promote
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.