Epigenetic changes regulating the epithelial-mesenchymal transition in human trophoblast differentiation
RNA-seq (gene expression) · human · 22 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
- 22 samples: 22 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
- Epigenetic changes regulating the epithelial-mesenchymal transition in human trophoblast differentiationbioRxiv : the preprint server for biology · 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 GSE256412_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 PRJNA1079368 and SRA study SRP491130. 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 22 sample titles: 22 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.
- GSM8098148 A116_EVT
- GSM8098149 A117_EVT
- GSM8098150 A122_EVT
- GSM8098151 A139_EVT
- GSM8098152 A147_EVT
- GSM8098153 A151_EVT
- GSM8098154 A152_EVT
- GSM8098155 A154_EVT
- GSM8098156 A158_EVT
- GSM8098157 A116_CTB
- GSM8098158 A117_CTB
- GSM8098159 A122_CTB
- GSM8098160 A139_CTB
- GSM8098161 A147_CTB
- GSM8098162 A151_CTB
- GSM8098163 A152_CTB
- GSM8098164 A154_CTB
- GSM8098165 A158_CTB
- GSM8098166 A139_vCTB
- GSM8098167 A147_vCTB
- GSM8098168 A154_vCTB
- GSM8098169 A158_vCTB
- GSE298139 Therapy-resistance in AT/RT is driven by epithelial-mesenchymal transition, extracellular matrix changes, and enrichment of CD1A+ CD207+ dendritic cells [snRNA-seq] 16 samples shares epithelial-mesenchymal, transition, changes
- GSE262636 Histone Variant H2A.J is a Key Epigenetic Regulator in Human Trophoblast Development 58 samples shares trophoblast, epigenetic
- GSE294916 IFNγ-induced memory in human macrophages is not sustained by epigenetic changes but the durability of the cytokine itself [CUT&Tag] 28 samples shares epigenetic, changes
- GSE263716 Epigenetic Analysis of SLE Disease Activity in Resting Naive (rN) and Transitional (T1T2) B cells 62 samples shares epigenetic, transition
- GSE336960 Phenotypic CRISPR screening identifies ZBTB10 as a novel regulator of human trophoblast differentiation 22 samples shares trophoblast
- GSE314342 Genome-scale perturb-seq in primary human CD4+ T cells reveals genes regulating T cell programs and human immune traits. 577 samples shares regulating
- GSE232076 In vitro reconstitution of epigenetic reprogramming in the human germ line [RNA-Seq] 89 samples shares epigenetic
- GSE306915 Integrated epigenetic and genetic programming of primary human T cells [RNA-seq] 77 samples shares epigenetic
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.