GEO series

Endometrial Cancer Susceptibility Gene CTCF is Essential for Progesterone Dependent Uterine Maturation

GSE227517 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2024/08/08 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 24 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: 24 samples: 6 × 21d-Ctcf-cKO V vs 6 × 21d-Ctcf-f/f V vs 4 × 21d-Ctcf-cKO P4 vs 4 × 21d-Ctcf-f/f P4Groups 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: Chromatin architectural factor CTCF is essential for progesterone-dependent uterine maturationFASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2023

Summary (written by the submitters)

Receptors for estrogen and progesterone frequently interact, via Cohesin/CTCF loop extrusion, at enhancers distal from regulated genes; CTCF is decreased or mutated in >20% of human endometrial tumors, indicating its importance in uterine homeostasis. To better understand how CTCF-mediated enhancer-gene interactions impact endometrial development and function, the Ctcf gene was selectively deleted in female reproductive tissues of mice.

Read the full summary ↓

Prepubertal Ctcfd/d uterine tissue exhibited normal morphology, with a significant reduction in the number of uterine glands compared to those without Ctcf deletion (Ctcff/f mice). Post-pubertal Ctcfd/d uteri were hypoplastic with significant reduction in both the size of the endometrial stroma and number of glands. Transcriptional profiling revealed increased expression of stem cell molecules Lif, EOMES and Lgr5, and enhanced inflammation pathways following Ctcf deletion. Analysis of the response of the uterus to steroid hormone stimulation showed that the response of the uterus to estrogen was not impacted, but that CTCF deletion affects a subset of progesterone responsive genes. This finding indicates 1) mediators of P signaling remain functional following Ctcf deletion and 2) certain P regulated genes are sensitive to Ctcf deletion, suggesting they depend on gene-enhancer interactions that require CTCF. The P responsive genes altered by CTCF ablation included Ihh, Fst and Errfi1, as well as other genes involved in the regulation of critical processes including hormone response, transcription, and inhibition of tumor generation. Overall, our findings reveal that uterine Ctcf plays a key role in P dependent expression of uterine genes underlying optimal post pubertal uterine development.

Published in

Chromatin architectural factor CTCF is essential for progesterone-dependent uterine maturation

Hewitt SC, Gruzdev A, Willson CJ et al. · FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2023 · PMID 37489832 · doi:10.1096/fj.202300862R

This dataset

Open GSE227517 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 GSE227517_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 PRJNA945435 and SRA study SRP427704. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 37489832) ↗

Study design

6 × 21d-Ctcf-cKO V vs 6 × 21d-Ctcf-f/f V vs 4 × 21d-Ctcf-cKO P4 vs 4 × 21d-Ctcf-f/f P4

Supports a between-group comparison across 20 samples.

How we read this: 4 replicated groups read from 24 sample titles; they account for 20 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

GSM7102045 21d-Ctcf-cKO P4-4 21d-Ctcf-cKO P4
GSM7102046 21d-Ctcf-cKO P4-5 21d-Ctcf-cKO P4
GSM7102047 21d-Ctcf-cKO P4-6 21d-Ctcf-cKO P4
GSM7102048 21d-Ctcf-cKO P4-8 21d-Ctcf-cKO P4
GSM7102049 21d-Ctcf-cKO V-9 21d-Ctcf-cKO V
GSM7102050 21d-Ctcf-cKO V-10 21d-Ctcf-cKO V
GSM7102051 21d-Ctcf-cKO V-11b
GSM7102052 21d-Ctcf-cKO V-12 21d-Ctcf-cKO V
GSM7102053 21d-Ctcf-f/f P4-1 21d-Ctcf-f/f P4
GSM7102054 21d-Ctcf-f/f P4-2 21d-Ctcf-f/f P4
GSM7102055 21d-Ctcf-f/f P4-7 21d-Ctcf-f/f P4
GSM7102056 21d-Ctcf-f/f P4-9 21d-Ctcf-f/f P4
GSM7102057 21d-Ctcf-f/f V-1b
GSM7102058 21d-Ctcf-f/f V-2 21d-Ctcf-f/f V
GSM7102059 21d-Ctcf-f/f V-3 21d-Ctcf-f/f V
GSM7102060 21d-Ctcf-f/f V-4 21d-Ctcf-f/f V
GSM7102061 21d-Ctcf-cKO V-4 21d-Ctcf-cKO V
GSM7102062 21d-Ctcf-cKO V-5 21d-Ctcf-cKO V
GSM7102063 21d-Ctcf-cKO V-11a
GSM7102064 21d-Ctcf-cKO V-13 21d-Ctcf-cKO V
GSM7102065 21d-Ctcf-f/f V-1a
GSM7102066 21d-Ctcf-f/f V-7 21d-Ctcf-f/f V
GSM7102067 21d-Ctcf-f/f V-10 21d-Ctcf-f/f V
GSM7102068 21d-Ctcf-f/f V-12 21d-Ctcf-f/f V

Datasets on a similar topic

GSE275003 CTCF tunes gene expression in a loop-dependent and -independent manner 172 samples shares ctcf, dependent
GSE260914 ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF 78 samples shares ctcf, dependent
GSE274792 CTCF tunes gene expression in a loop-dependent and -independent manner [ChIP-Seq] 30 samples shares ctcf, dependent
GSE274789 CTCF tunes gene expression in a loop-dependent and -independent manner [ATAC-Seq] 24 samples shares ctcf, dependent
GSE269216 Hoxblinc lncRNA reprograms CTCF-independent TADs to drive leukemic transcription and HSC dysregulation in NUP98 fusion transformed leukemia [ATAC-Seq] 10 samples shares ctcf, dependent
GSE269224 Hoxblinc lncRNA reprograms CTCF-independent TADs to drive leukemic transcription and HSC dysregulation in NUP98 fusion transformed leukemia [ChIRP-seq] 6 samples shares ctcf, dependent
GSE269218 Hoxblinc lncRNA reprograms CTCF-independent TADs to drive leukemic transcription and HSC dysregulation in NUP98 fusion transformed leukemia [Hi-C] 5 samples shares ctcf, dependent
GSE283303 Hoxblinc lncRNA reprograms CTCF-independent TADs to drive leukemic transcription and HSC dysregulation in NUP98 fusion transformed leukemia [CTCF-HiChIP-seq] 2 samples shares ctcf, dependent

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