GEO series

Modulation of HDAC activity directly reprogramme embryonic stem cell to trophoblast stem cell [bulk RNA-Seq]

GSE193082 Mus musculus (mouse) RNA-seq (gene expression) 16 samples Submitted 2024/03/18 Platform GPL17021

At a glance

RNA-seq (gene expression) · mouse · 16 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: Mus musculus (mouse)
Samples: 16 samples: 6 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.

Summary (written by the submitters)

Embryonic stem cells (ESCs) can differentiate into all cell types of each of the embryonic germ layers. ESCs can also generate totipotent 2C-like cells and trophectodermal cells. However, these latter transitions occur at low frequency due to epigenetic barriers, the nature of which are not fully understood. Here, we show that mouse ESCs treated with sodium butyrate, an HDAC inhibitor, have a greatly increased 2C-like cell population and can transdifferentiate into trophoblast stem cells (TSCs).

Read the full summary ↓

Interestingly, this ESC to TSC transition is a direct reprogramming event that does not require transition through a 2C-like state. Mechanistically, butyrate inhibits Class I histone deacetylases activities in LSD1-HDAC1/2 corepressor complex, increasing acetylation levels in the regulatory regions of 2C and TSC specific genes. Importantly, butyrate treated cells acquire the capacity to generate blastocyst-like structures that can develop beyond the implantation stage in vitro and induce decidualization in vivo. These results uncover how epigenetic changes can expand the potency of ESCs.

This dataset

Open GSE193082 in finder → Find more mouse 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 GSE193082_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 PRJNA794729 and SRA study SRP353615. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

6 conditions, mostly in duplicate

MG1_TS_C1 ×5 MG1_TS_C2 ×3 MG1-GFPnegative ×2 MG1-NaB-GFPpositive ×2 OGTS ×2 DUXKO_c19_TSC ×2

Supports a between-group comparison across 16 samples.

How we read this: 6 replicated groups read from 16 sample titles; they account for 16 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

GSM5772971 MG1-GFPnegative rep1 MG1-GFPnegative
GSM5772972 MG1-GFPnegative rep2 MG1-GFPnegative
GSM5772973 MG1-NaB-GFPpositive rep1 MG1-NaB-GFPpositive
GSM5772974 MG1-NaB-GFPpositive rep2 MG1-NaB-GFPpositive
GSM7466921 OGTS.1 OGTS
GSM7466922 OGTS.2 OGTS
GSM7466923 MG1_TS_C1.1 MG1_TS_C1
GSM7466924 MG1_TS_C1.2 MG1_TS_C1
GSM7466925 MG1_TS_C1.3 MG1_TS_C1
GSM7466926 MG1_TS_C1.4 MG1_TS_C1
GSM7466927 MG1_TS_C1.5 MG1_TS_C1
GSM7466928 MG1_TS_C2.1 MG1_TS_C2
GSM7466929 MG1_TS_C2.2 MG1_TS_C2
GSM7466930 MG1_TS_C2.3 MG1_TS_C2
GSM7466931 DUXKO_c19_TSC.1 DUXKO_c19_TSC
GSM7466932 DUXKO_c19_TSC.2 DUXKO_c19_TSC

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GSE269433 Histone Deacetylase 1 (HDAC1) maintains the transcriptome of embryonic stem cells through regulating acetylation at crucial genomic sites [ChIP-seq] 18 samples shares hdac, embryonic
GSE275917 Nup153 regulates neuronal responsiveness through HDAC1-mediated epigenetic modulation [ChIP-seq] 17 samples shares hdac, modulation
GSE300192 Nup153 regulates neuronal responsiveness through HDAC1-mediated epigenetic modulation [DamID-seq] 16 samples shares hdac, modulation

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