GEO series

TFEB controls expression of human syncytins during cell-cell fusion [RNA-Seq]

GSE284600 Homo sapiens (human) RNA-seq (gene expression) 32 samples Submitted 2024/12/18 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 32 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: 32 samples: 7 conditions, mostly in triplicateGroups 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: TFEB controls expression of human syncytins during cell-cell fusionGenes & development · 2024

Summary (written by the submitters)

During human development, a subset of differentiating fetal cells form a temporary organ, the placenta, which invades the uterine wall to support nutrient, oxygen, and waste exchange between the mother and fetus until birth. Most of the human placenta is formed by a syncytial villous structure which arises via cell-cell fusion of underlying fetal trophoblast stem cells.

Read the full summary ↓

Genetic and functional studies have characterized the membrane protein fusogens, Syncytin-1 and Syncytin-2, that are both necessary and sufficient for human trophoblast cell-cell fusion. However, identification and characterization of upstream transcriptional regulators regulating their expression has been limited. Here, using CRISPR knockout in an in vitro cellular model of syncytiotrophoblast development (BeWo cells), we find that the transcription factor TFEB, mainly known as a regulator of autophagy and lysosomal biogenesis, is required for cell-cell fusion of syncytiotrophoblasts. TFEB translocates to the nucleus, exhibits increased chromatin interactions, and directly binds the Syncytin-1 and Syncytin-2 promoters to control their expression during differentiation. While TFEB appears to play an important role in syncytiotrophoblast differentiation, ablation of TFEB largely does not affect lysosomal gene expression or lysosomal biogenesis in differentiating BeWo cells, suggesting that TFEB plays an alternative role in placental cells.

Published in

TFEB controls expression of human syncytins during cell-cell fusion

Esbin MN, Dahal L, Fan VB et al. · Genes & development 2024 · PMID 39168638 · doi:10.1101/gad.351633.124

This dataset

Open GSE284600 in finder → Find more human RNA-seq datasets →

Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE284600_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA1199896 and SRA study SRP552272. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39168638) ↗

Study design

7 conditions, mostly in triplicate

WT BeWo 48hr FSK biol ×4 TFEB/3 DKO (#C2) BeWo 48hr FSK biol ×4 WT BeWo Untreated biol ×3 WT BeWo 2hr Torin1 biol ×3 TFEB/3 DKO (#C2) BeWo Untreated biol ×3 TFEB/3 DKO (#C2) BeWo 2hr Torin1 biol ×3 WT BeWo 48hr Torin1 biol ×3 WT BeWo DMSO biol ×1 +8 more

Supports a between-group comparison across 23 samples.

How we read this: 7 replicated groups read from 32 sample titles; they account for 23 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.

Samples in this study

GSM8688962 WT BeWo Untreated biol rep 1 WT BeWo Untreated biol
GSM8688963 WT BeWo 2hr Torin1 biol rep 1 WT BeWo 2hr Torin1 biol
GSM8688964 WT BeWo 48hr FSK biol rep 1 WT BeWo 48hr FSK biol
GSM8688965 TFEB/3 DKO (#C2) BeWo Untreated biol rep 1 TFEB/3 DKO (#C2) BeWo U…
GSM8688966 TFEB/3 DKO (#C2) BeWo 2hr Torin1 biol rep 1 TFEB/3 DKO (#C2) BeWo 2…
GSM8688967 TFEB/3 DKO (#C2) BeWo 48hr FSK biol rep 1 TFEB/3 DKO (#C2) BeWo 4…
GSM8688968 WT BeWo Untreated biol rep 2 WT BeWo Untreated biol
GSM8688969 WT BeWo 2hr Torin1 biol rep 2 WT BeWo 2hr Torin1 biol
GSM8688970 WT BeWo 48hr FSK biol rep 2 WT BeWo 48hr FSK biol
GSM8688971 TFEB/3 DKO (#C2) BeWo Untreated biol rep 2 TFEB/3 DKO (#C2) BeWo U…
GSM8688972 TFEB/3 DKO (#C2) BeWo 2hr Torin1 biol rep 2 TFEB/3 DKO (#C2) BeWo 2…
GSM8688973 TFEB/3 DKO (#C2) BeWo 48hr FSK biol rep 2 TFEB/3 DKO (#C2) BeWo 4…
GSM8688974 WT BeWo Untreated biol rep 3 WT BeWo Untreated biol
GSM8688975 WT BeWo 2hr Torin1 biol rep 3 WT BeWo 2hr Torin1 biol
GSM8688976 WT BeWo 48hr FSK biol rep 3 WT BeWo 48hr FSK biol
GSM8688977 TFEB/3 DKO (#C2) BeWo Untreated biol rep 3 TFEB/3 DKO (#C2) BeWo U…
GSM8688978 TFEB/3 DKO (#C2) BeWo 2hr Torin1 biol rep 3 TFEB/3 DKO (#C2) BeWo 2…
GSM8688979 TFEB/3 DKO (#C2) BeWo 48hr FSK biol rep 3 TFEB/3 DKO (#C2) BeWo 4…
GSM8688980 WT BeWo DMSO biol rep 1
GSM8688981 WT BeWo 48hr FSK biol rep 4 WT BeWo 48hr FSK biol
GSM8688982 WT BeWo 48hr Torin1 biol rep 1 WT BeWo 48hr Torin1 biol
GSM8688983 WT BeWo 48hr Torin1 biol rep 2 WT BeWo 48hr Torin1 biol
GSM8688984 WT BeWo 48hr Torin1 biol rep 3 WT BeWo 48hr Torin1 biol
GSM8688985 TFEB/3 DKO (#C2) BeWo DMSO biol rep 1
GSM8688986 TFEB/3 DKO (#C2) BeWo 48hr FSK biol rep 4 TFEB/3 DKO (#C2) BeWo 4…
GSM8688987 TFEB/3 DKO (#C2) BeWo 48hr Torin1 biol rep 1
GSM8688988 TFEB KO (clone #c13) DMSO biol rep 1
GSM8688989 TFEB KO (clone #c13) 48hr FSK biol rep 1
GSM8688990 TFEB KO (clone #c13) 48hr Torin1 biol rep 1
GSM8688991 TFEB KO (clone #c20) DMSO biol rep 1
GSM8688992 TFEB KO (clone #c20) 48hr FSK biol rep 1
GSM8688993 TFEB KO (clone #c20) 48hr Torin1 biol rep 1

Datasets on a similar topic

GSE211032 Expression Analysis (RNA-Seq) of adult Myelodysplastic Syndromes (MDS)/Acute Myeloid Leukemia (AML) with isolated monosomy 7 compared to controls 45 samples shares controls, rna-seq
GSE301166 PURPL bidirectionally controls senescence: depletion rejuvenates fibroblasts while overexpression accelerates aging [RNA-Seq2] 18 samples shares controls, rna-seq
GSE327386 RNA-Seq of paired diagnosis and relapse AML specimens with healthy controls 130 samples shares controls, rna-seq
GSE250160 IRF2BP2-mediated MHC-I expression controls cytotoxic T cell responses in acute myeloid leukemia [RNA-Seq] 12 samples shares controls, rna-seq
GSE328351 Bulk RNA-seq of dorsolateral prefrontal cortex tissue collected during deep brain stimulation neurosurgery in obsessive-compulsive disorder and neurological controls 10 samples shares controls, rna-seq
GSE247367 Pathogenic TSC2 variants alter developmental trajectories of human cortical organoids and perturb cell-cell communication networks [bulk RNA-seq] 80 samples shares cell-cell, rna-seq
GSE215924 Small bowel RNA-seq data from patients with Crohn's disease and patients with colon cancer (non-CD controls) 79 samples shares controls, rna-seq
GSE301283 KLF5 controls subtype-independent highly interactive enhancers in pancreatic cancer to regulate cell survival [RNA-Seq] 36 samples shares controls, rna-seq

Search all human RNA-seq datasets in GEO →

Share this dataset

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.