A high MAPK, low WNT cell state drives metastatic dissemination in colorectal cancer
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 49 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Mus musculus (mouse)
- Samples
- 49 samples: 15 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.
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 GSE283937_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1196349 and SRA study SRP550519. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 4 samples read as cases, 4 as controls.
How we read this: 15 replicated groups read from 49 sample titles; they account for 36 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.
- GSM8674539 AKPS P1 mouse #801_rep1 AKPS P1 mouse #801
- GSM8674540 AKPS P1 mouse #802_rep2 AKPS P1 mouse #802
- GSM8674541 AKPS P1 mouse #803_rep3 AKPS P1 mouse #803
- GSM8674542 AKPS P1 mouse #804_rep4 AKPS P1 mouse #804
- GSM8674543 AKPS P5 mouse #815_rep1 AKPS P5 mouse #815
- GSM8674544 AKPS P5 mouse #816_rep2 AKPS P5 mouse #816
- GSM8674545 AKPS P5 mouse #817_rep3 AKPS P5 mouse #817
- GSM8674546 AKPS P5 3d vehicle mouse #29_rep1
- GSM8674547 AKPS P5 3d vehicle mouse #31_rep2
- GSM8674548 AKPS P5 3d vehicle mouse #37_rep3
- GSM8674549 AKPS P5 3d vehicle mouse #39_rep4
- GSM8674550 AKPS P5 3d MRTX1133 mouse #27_rep1
- GSM8674551 AKPS P5 3d MRTX1133 mouse #28_rep2
- GSM8674552 AKPS P5 3d MRTX1133 mouse #30_rep3
- GSM8674553 AKPS P5 3d MRTX1133 mouse #32_rep4
- GSM8674554 AKPS P5 16d MRTX1133 mouse #34_rep1
- GSM8674555 AKPS P5 16d MRTX1133 mouse #36_rep2
- GSM8674556 AKPS P5 16d MRTX1133 mouse #38_rep3
- GSM8674557 AKPS P5 16d MRTX1133 mouse #40_rep4
- GSM8676799 AKPS P1 mouse #801_rep1 AKPS P1 mouse #801
- GSM8676800 AKPS P1 mouse #802_rep2 AKPS P1 mouse #802
- GSM8676801 AKPS P1 mouse #803_rep3 AKPS P1 mouse #803
- GSM8676802 AKPS P1 mouse #804_rep4 AKPS P1 mouse #804
- GSM8676803 AKPS P5 mouse #815_rep1 AKPS P5 mouse #815
- GSM8676804 AKPS P5 mouse #816_rep2 AKPS P5 mouse #816
- GSM8676805 AKPS P5 mouse #817_rep3 AKPS P5 mouse #817
- GSM8676806 AKPS P5 mouse #811_814_rep4
- GSM9256280 liver metastasis rep1 liver metastasis
- GSM9256281 lung metastasis rep1 lung metastasis
- GSM9256282 liver metastasis rep2 liver metastasis
- GSM9256283 lung metastasis rep2 lung metastasis
- GSM9337767 p5_rep1 p5
- GSM9337768 p5_rep2 p5
- GSM9337769 p5_rep3 p5
- GSM9337770 A485_rep1 A485
- GSM9337771 A485_rep2 A485
- GSM9337772 A485_rep3 A485
- GSM9337773 EPZ004777_rep1 EPZ004777
- GSM9337774 EPZ004777_rep2 EPZ004777
- GSM9337775 EPZ004777_rep3 EPZ004777
+ 9 more — browse all 49 samples with per-sample file links →
- GSE237954 Oncofetal reprogramming drives phenotypic plasticity in WNT-dependent colorectal cancer 122 samples shares wnt, colorectal, drives
- GSE306627 TGFβ signaling in cancer-associated fibroblasts drives a hepatic gp130-dependent pro-metastatic inflammatory program in colorectal cancer 42 samples shares metastatic, colorectal, drives
- GSE303692 A plastic EMP1⁺ to LGR5⁺ cell state conversion as a therapeutic bypass to KRAS-G12D inhibition in metastatic colorectal cancer [RNA-Seq] 24 samples shares metastatic, colorectal, state
- GSE294822 A plastic EMP1⁺ to LGR5⁺ cell state conversion as a therapeutic bypass to KRAS-G12D inhibition in metastatic colorectal cancer [SLAM-Seq] 15 samples shares metastatic, colorectal, state
- GSE304518 A plastic EMP1⁺ to LGR5⁺ cell state conversion as a therapeutic bypass to KRAS-G12D inhibition in metastatic colorectal cancer 12 samples shares metastatic, colorectal, state
- GSE302631 Loss of tumor cell MHC Class II drives MAPK-inhibitor insensitivity of BRAF-mutant anaplastic thyroid cancers 40 samples shares mapk, drives
- GSE302629 Loss of tumor cell MHC Class II drives MAPK-inhibitor insensitivity of BRAF-mutant anaplastic thyroid cancers [RNA-seq] 24 samples shares mapk, drives
- GSE302630 Loss of tumor cell MHC Class II drives MAPK-inhibitor insensitivity of BRAF-mutant anaplastic thyroid cancers [ATAC-seq] 16 samples shares mapk, drives
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.