Vitamin D opposes multilineage cell differentiation induced by Notch inhibition and BMP pathway activation in human colon organoids
RNA-seq (gene expression) · human · 18 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
- 18 samples: 18 samples, each with a distinct title — no replicated groupsGroups 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
- Vitamin D opposes multilineage cell differentiation induced by Notch inhibition and BMP4 pathway activation in human colon organoidsCell death & disease · 2024
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 GSE248274_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 PRJNA1043146 and SRA study SRP473085. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 18 sample titles: 18 distinct titles with little repetition. 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.
- GSM7910769 Patient #92, human colon organoids, proliferation (PROL) medium - control
- GSM7910770 Patient #92, human colon organoids, differentiation (B+D) medium - control
- GSM7910771 Patient #92, human colon organoids, differentiation (B+D) medium - calcitriol
- GSM7910772 Patient #158, human colon organoids, proliferation (PROL) medium - control
- GSM7910773 Patient #158, human colon organoids, differentiation (B+D) medium - control
- GSM7910774 Patient #158, human colon organoids, differentiation (B+D) medium - calcitriol
- GSM7910775 Patient #159, human colon organoids, proliferation (PROL) medium - control
- GSM7910776 Patient #159, human colon organoids, differentiation (B+D) medium - control
- GSM7910777 Patient #159, human colon organoids, differentiation (B+D) medium - calcitriol
- GSM7910778 Patient #161, human colon organoids, proliferation (PROL) medium - control
- GSM7910779 Patient #161, human colon organoids, differentiation (B+D) medium - control
- GSM7910780 Patient #161, human colon organoids, differentiation (B+D) medium - calcitriol
- GSM7910781 Patient #166, human colon organoids, proliferation (PROL) medium - control
- GSM7910782 Patient #166, human colon organoids, differentiation (B+D) medium - control
- GSM7910783 Patient #166, human colon organoids, differentiation (B+D) medium - calcitriol
- GSM7910784 Patient #172, human colon organoids, proliferation (PROL) medium - control
- GSM7910785 Patient #172, human colon organoids, differentiation (B+D) medium - control
- GSM7910786 Patient #172, human colon organoids, differentiation (B+D) medium - calcitriol
- GSE341139 A conserved HAND2-BMP5-SMAD1/5/9 axis drives hepatic stellate cell activation and extracellular matrix overproduction in multiple fibrotic etiologies 10 samples shares bmp, activation
- GSE254732 Inhibition of PCSK9 with evolocumab modulates lipoproteins and monocyte activation in high-risk ASCVD subjects 215 samples shares inhibition, activation
- GSE306950 Dysregulated NK Cell Activation and Myeloid-Lymphoid Imbalance Underpin COPD Progression: Insights from High-Dimensional Immune Profiling and Smoking-Induced Immune Remodeling 35 samples shares activation, induced
- GSE297994 Native long-read RNA sequencing of human monocytes reveals activation-induced alternative splicing toward functional isoforms 22 samples shares activation, induced
- GSE309979 GeoMx GeoMx-DSP Toxic Lipid-induced Epigenetic Activation of ICAM1 in Liver Sinusoidal Endothelium Regulates Myeloid-Driven Fibro-inflammatory Response in MASH 217 samples shares activation, induced
- GSE279781 CD137 agonism enhances anti-PD1 induced activation of clonally expanded CD8+ T cells in a neoadjuvant pancreatic cancer clinical trial 30 samples shares activation, induced
- GSE306620 TCR signaling via NFATc1 constrains IL-15-induced NK-like activation of human memory CD8+ T cells 26 samples shares activation, induced
- GSE274680 Inflammation and lymphocyte activation during longitudinal progression to rheumatoid arthritis in at-risk individuals 243 samples shares activation
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.