GEO series

Resf1 is required for normal placental development and configuration of trophoblast cell-specific heterochromatin [RNA-seq]

GSE308515 Mus musculus (mouse) RNA-seq (gene expression) 17 samples Submitted 2026/05/21 Platform GPL21273

At a glance

RNA-seq (gene expression) · mouse · 17 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: 17 samples: 6 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.

Summary (written by the submitters)

Resf1 (Retroelement silencing factor 1) is involved in retroelement silencing cooperated with H3K9 methyltransferase SETDB1 by regulating H3K9 methylation in mouse embryonic stem cells (mESCs). However, it remains unknown whether Resf1 functions in retroelement silencing in vivo, and has a role in development. To address this question, we established Resf1-deficient mice.

Read the full summary ↓

The Resf1-deficient mice show developmental delay, partial embryonic lethality, and placental abnormalities. Remarkably, retroelements are also upregulated in the Resf1-deficient placenta, and this upregulation of retroelements correlates with elevated expression of nearby genes. Additionally, to determine whether Resf1 functions within the trophoblast lineage—given the heterogeneous cellular composition of the placenta—we established Resf1-deficient trophoblast stem cell (TSC) lines. Both undifferentiated TSCs and differentiated TSCs (D-TSCs) display increased retroelement expression along with elevated levels of genes associated with placental development. Furthermore, Resf1-deficient TSCs exhibit compromised maintenance of H3K9me3 domains, leading to instability. In summary, our findings illuminate Resf1's multifaceted roles beyond retroelement silencing, uncovering its significance in developmental processes and its intricate involvement in trophoblast lineage regulation.

This dataset

Open GSE308515 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 GSE308515_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 PRJNA1330805 and SRA study SRP621928. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

6 conditions, mostly in triplicate

RNA-seq in WT Placenta ×3 RNA-seq in Het TSC ×3 RNA-seq in KO TSC ×3 RNA-seq in Het D-TSC ×3 RNA-seq in KO D-TSC ×3 RNA-seq in KO Placenta ×2

Supports a between-group comparison across 17 samples.

How we read this: 6 replicated groups read from 17 sample titles; they account for 17 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

GSM9247269 RNA-seq in WT Placenta rep1 RNA-seq in WT Placenta
GSM9247270 RNA-seq in WT Placenta rep2 RNA-seq in WT Placenta
GSM9247271 RNA-seq in WT Placenta rep3 RNA-seq in WT Placenta
GSM9247272 RNA-seq in KO Placenta rep1 RNA-seq in KO Placenta
GSM9247273 RNA-seq in KO Placenta rep2 RNA-seq in KO Placenta
GSM9247274 RNA-seq in Het TSC rep1 RNA-seq in Het TSC
GSM9247275 RNA-seq in Het TSC rep2 RNA-seq in Het TSC
GSM9247276 RNA-seq in Het TSC rep3 RNA-seq in Het TSC
GSM9247277 RNA-seq in KO TSC rep1 RNA-seq in KO TSC
GSM9247278 RNA-seq in KO TSC rep2 RNA-seq in KO TSC
GSM9247279 RNA-seq in KO TSC rep3 RNA-seq in KO TSC
GSM9247280 RNA-seq in Het D-TSC rep1 RNA-seq in Het D-TSC
GSM9247281 RNA-seq in Het D-TSC rep2 RNA-seq in Het D-TSC
GSM9247282 RNA-seq in Het D-TSC rep3 RNA-seq in Het D-TSC
GSM9247283 RNA-seq in KO D-TSC rep1 RNA-seq in KO D-TSC
GSM9247284 RNA-seq in KO D-TSC rep2 RNA-seq in KO D-TSC
GSM9247285 RNA-seq in KO D-TSC rep3 RNA-seq in KO D-TSC

Datasets on a similar topic

GSE308516 Resf1 is required for normal placental development and configuration of trophoblast cell-specific heterochromatin [ChIP-seq] 25 samples shares resf1, heterochromatin, configuration, cell-specific, trophoblast, placental, required
GSE287379 CTCF-RNA interactions orchestrate cell-specific chromatin loop organization [RNA-seq] 26 samples shares cell-specific, rna-seq
GSE241667 Coordination between transcriptional orientation and nucleoprotein complexes generate chromatin configuration of IgH locus [Directional RNA-Seq] 20 samples shares configuration, rna-seq
GSE295845 The RNA-Seq of PCK1 intestinal epithelial cell-specific knockout mice and their littermate control mice 12 samples shares cell-specific, rna-seq
GSE288210 Comparative gene expression profiling of RNA-seq data from islets of β-cell-specific ZZEF1 knockout mice (βZKO-Mip) and their littermate controls, treated with either azoramide or DMSO. 11 samples shares cell-specific, rna-seq
GSE263441 H3K27 dimethylation dynamics reveal stepwise establishment of facultative heterochromatin in early mouse embryos [RNA-Seq] 10 samples shares heterochromatin, rna-seq
GSE287033 H3K27me3 and the PRC1-H2AK119ub pathway cooperatively maintain heterochromatin and transcriptional silencing after the loss of H3K9 methylation [RNA-seq] 8 samples shares heterochromatin, rna-seq
GSE268763 ALKBH1-mediated DNA N6-methyladenine Modification Regulates H3K9me3-dependent Heterochromatin in Neural Tube Development [RNA-Seq] 8 samples shares heterochromatin, rna-seq

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