LSD1 and CoREST2 Regulate STAT3 Activity to Promote Enteroendocrine Cell Differentiation in Mucinous Colorectal Cancer[CUT&RUN]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 13 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
- Homo sapiens (human)
- Topic
- Colorectal cancerThis series is part of our curated briefing on it.
- Samples
- 13 samples: 4 × STAT3 CUTandRUN_ISX9 vs 3 × STAT3 CUTandRUN_DMSO vs 2 × IgG CUTandRUNGroups 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.
Read the full summary ↓
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 GSE268956_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 PRJNA1119503 and SRA study SRP511402. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 9 samples.
How we read this: 3 replicated groups read from 13 sample titles; they account for 9 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.
- GSM8303234 STAT3 CUTandRUN_DMSO_R1 STAT3 CUTandRUN_DMSO
- GSM8303235 STAT3 CUTandRUN_DMSO_R2 STAT3 CUTandRUN_DMSO
- GSM8303236 STAT3 CUTandRUN_DMSO_R3 STAT3 CUTandRUN_DMSO
- GSM8303237 FLAG-CoREST2_CUTandRUN_Fixed(CoREST2 KD)
- GSM8303238 FLAG-CoREST2_CUTandRUN_Fixed
- GSM8303239 FLAG-CoREST2_CUTandRUN_native
- GSM8303240 FLAG-CoREST2_CUTandRUN_Native(CoREST2 KD)
- GSM8303241 IgG CUTandRUN_R1 IgG CUTandRUN
- GSM8303242 IgG CUTandRUN_R2 IgG CUTandRUN
- GSM8303243 STAT3 CUTandRUN_ISX9_R1 STAT3 CUTandRUN_ISX9
- GSM8303244 STAT3 CUTandRUN_ISX9_R2 STAT3 CUTandRUN_ISX9
- GSM8303245 STAT3 CUTandRUN_ISX9_R3 STAT3 CUTandRUN_ISX9
- GSM8303246 STAT3 CUTandRUN_ISX9_R4 STAT3 CUTandRUN_ISX9
- GSE12032 Inherent gene signature of stage II and III colorectal cancer leads in individual recurrence 198 samples same disease briefing · shares colorectal
- 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 · shares colorectal
- 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
- GSE303343 A unified network systems approach uncovers a core program underlying T follicular helper cell differentiation [CUT&RUN] 48 samples shares cut, run
- GSE287902 BPTF regulstes androgen receptor activity by enhancing chromatin accessibility and stabilizing the AR-FOXA1 interaction [Cut&Run] 40 samples shares cut, run
- GSE269555 Targeting the oncohistone-ASCL1 axis disrupts plasticity and suppresses pediatric gliomas [CUT&RUN] 39 samples shares cut, run
- GSE278910 Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling [CUT&RUN] 30 samples shares cut, run
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.