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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 21, 2022 |
| Title |
Sex-determining 3D regulatory hubs revealed by genome spatial auto-correlation analysis [RNA-seq] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Mammalian sex is determined by a network of antagonistic genes that are well characterized. However, its non-coding regulation is still largely unknown. Here we explore the 3D chromatin landscape of sex determination in vivo. We integrate Hi-C with ChIP-seq experiments using METALoci, a novel genome spatial auto-correlation analysis approach that identifies 3D regulatory hubs across the genome. We uncover a prominent rewiring of chromatin interactions during sex determination. By combining predictive approaches and validations in transgenic mice we identify a novel Fgf9 regulatory hub, which deletion results in male-to-female sex reversal.
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| Overall design |
RNA-seq experiments in E13.5 XY WT and E13.5 XY Fgf9 Δ306 mouse gonads.
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| Contributor(s) |
Mota-Gomez I, Rodriguez JA, Dupont S, Lao O, Jedamzick J, Kühn R, Lacadie S, Garcia-Moreno SA, Hurtado A, Acemel RD, Capel B, Marti-Renom MA, Lupianez DG |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Nov 09, 2022 |
| Last update date |
Sep 19, 2024 |
| Contact name |
Irene Mota-Gomez |
| E-mail(s) |
irene211092@gmail.com
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| Organization name |
Max Delbruck Center
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| Lab |
Dario Lupianez
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| Street address |
Hannoversche strasse 28
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| City |
Berlin |
| ZIP/Postal code |
10115 |
| Country |
Germany |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (26)
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| GSM6722715 |
RNA-seq in XY E13.5 Fgf9 Δ306 gonads rep1 |
| GSM6722716 |
RNA-seq in XY E13.5 Fgf9 Δ306 gonads rep2 |
| GSM6722717 |
RNA-seq in XY E13.5 Fgf9 Δ306 gonads rep3 |
| GSM6722718 |
RNA-seq in XY E13.5 WT gonads rep1 |
| GSM6722719 |
RNA-seq in XY E13.5 WT gonads rep2 |
| GSM6722720 |
RNA-seq in XY E13.5 WT gonads rep3 |
| GSM8521762 |
RNA-seq in XY E13.5 Meis1 KO gonads, biol rep 1 |
| GSM8521763 |
RNA-seq in XY E13.5 Meis1 KO gonads, biol rep 2 |
| GSM8521764 |
RNA-seq in XY E13.5 Meis1 KO gonads, biol rep 3 |
| GSM8521765 |
RNA-seq in XY E13.5 Meis1 KO gonads, biol rep 4 |
| GSM8521766 |
RNA-seq in XY E13.5 Fgf9 Δ104 gonads, biol rep1 |
| GSM8521767 |
RNA-seq in XY E13.5 Fgf9 Δ104 gonads, biol rep2 |
| GSM8521768 |
RNA-seq in XY E13.5 Fgf9 Δ104 gonads, biol rep3 |
| GSM8521769 |
RNA-seq in XY E13.5 Fgf9 Δ104 gonads, biol rep4 |
| GSM8521770 |
RNA-seq in XY E13.5 Fgf9 Δ225 gonads, biol rep 1 |
| GSM8521771 |
RNA-seq in XY E13.5 Fgf9 Δ225 gonads, biol rep 2 |
| GSM8521772 |
RNA-seq in XY E13.5 Fgf9 Δ225 gonads, biol rep 3 |
| GSM8521773 |
RNA-seq in XY E13.5 Fgf9 Δ225 gonads, biol rep 4 |
| GSM8521774 |
RNA-seq in XY E13.5 Fgf9 Δ225 gonads, biol rep 5 |
| GSM8521775 |
RNA-seq in XY E13.5 Fgf9 Δ225 gonads, biol rep 6 |
| GSM8521776 |
RNA-seq in XY E13.5 Fgf9 Δ93 gonads, biol rep 1 |
| GSM8521777 |
RNA-seq in XY E13.5 Fgf9 Δ93 gonads, biol rep 2 |
| GSM8521778 |
RNA-seq in XY E13.5 Fgf9 Δ93 gonads, biol rep 3 |
| GSM8521779 |
RNA-seq in XY E13.5 Fgf9 Δ93 gonads, biol rep 4 |
| GSM8521780 |
RNA-seq in XY E13.5 Fgf9 Δ93 gonads, biol rep 5 |
| GSM8521781 |
RNA-seq in XY E13.5 Fgf9 Δ93 gonads, biol rep 6 |
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| This SubSeries is part of SuperSeries: |
| GSE217618 |
Sex-determining 3D regulatory hubs revealed by genome spatial auto-correlation analysis |
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| Relations |
| BioProject |
PRJNA899837 |
| SRA |
SRP407014 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE217617_Counts.csv.gz |
354.7 Kb |
(ftp)(http) |
CSV |
| GSE217617_Counts_Fgf9-full.tsv.gz |
1.1 Mb |
(ftp)(http) |
TSV |
| GSE217617_Counts_Meis1.csv.gz |
400.0 Kb |
(ftp)(http) |
CSV |
| GSE217617_DESeq2_Fgf9-full.tsv.gz |
22.2 Mb |
(ftp)(http) |
TSV |
| GSE217617_DEseq2.csv.gz |
1.1 Mb |
(ftp)(http) |
CSV |
| GSE217617_Deseq2_Meis1.csv.gz |
1.4 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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