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| Status |
Public on May 23, 2024 |
| Title |
Scaffolding element rewires genome architecture during differentiation at the Zfp608 locus (cHi-C) |
| Organism |
Mus musculus |
| Experiment type |
Other
|
| Summary |
Upon differentiation chromatin rewires in order to reflect its new cellular identity and function. Zfp608 locus is rewired following the differentiation from the ESCs to the NPCs. During this process the local chromatin content is remodelled with activating marks littering the region, local 3D chromatin conformation compacts the region through local chromatin contacts and the Zfp608 expression amplifies. This study investigates the cis genetic elements as well as trans elements that drive this process in order to better understand how differentiation rewiring occurs.
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| Overall design |
cHi-C experiments of mouse ESC or NPC wt cells. cHi-C experiments of partial Zfp608 deletion, polyA insertion at the Zfp608 TSS, deletion of element A, deletion of element B, dual deletion of element A and B, deletion of CTCF motif at the element A - all in ESC and NPC cells. cHi-C of mouse ESCs that overexpress Pax6.
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| Contributor(s) |
Jerković I, Di Stefano M, Reboul H, Szalay MF, Normanno D, Papadopoulos GL, Bantignies F, Cavalli G |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| BioProject |
PRJNA1083571 |
| |
| Submission date |
Mar 08, 2024 |
| Last update date |
May 23, 2024 |
| Contact name |
Ivana Jerkovic |
| E-mail(s) |
ivana866@gmail.com
|
| Phone |
+33434359997
|
| Organization name |
IGH, CNRS
|
| Street address |
141 rue de la Cardonille
|
| City |
Montpellier |
| State/province |
Occitanie |
| ZIP/Postal code |
34000 |
| Country |
France |
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| Platforms (1) |
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| Samples (30)
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| GSM8137834 |
cHiC of wt mouse ESC at the Zfp608 locus_R1 |
| GSM8137835 |
cHiC of wt mouse ESC at the Zfp608 locus_R2 |
| GSM8137836 |
cHiC of Zfp608 promoter deletion in mouse ESC at the Zfp608 locus_R1 |
| GSM8137837 |
cHiC of Zfp608 promoter deletion in mouse ESC at the Zfp608 locus_R2 |
| GSM8137838 |
cHiC of polyA insertion at Zfp608 in mouse ESC at the Zfp608 locus_R1 |
| GSM8137839 |
cHiC of polyA insertion at Zfp608 in mouse ESC at the Zfp608 locus_R2 |
| GSM8137840 |
cHiC of element A deletion in mouse ESC at the Zfp608 locus_R1 |
| GSM8137841 |
cHiC of element A deletion in mouse ESC at the Zfp608 locus_R2 |
| GSM8137842 |
cHiC of element B deletion in mouse ESC at the Zfp608 locus_R1 |
| GSM8137843 |
cHiC of element B deletion in mouse ESC at the Zfp608 locus_R2 |
| GSM8137844 |
cHiC of element A and B deletion in mouse ESC at the Zfp608 locus_R1 |
| GSM8137845 |
cHiC of element A and B deletion in mouse ESC at the Zfp608 locus_R2 |
| GSM8137846 |
cHiC of CTCF motif deletion at element A in mouse ESC at the Zfp608 locus_R1 |
| GSM8137847 |
cHiC of CTCF motif deletion at element A in mouse ESC at the Zfp608 locus_R2 |
| GSM8137848 |
cHiC of Pax6 upregulation in mouse ESC at the Zfp608 locus_R1 |
| GSM8137849 |
cHiC of Pax6 upregulation in mouse ESC at the Zfp608 locus_R2 |
| GSM8137850 |
cHiC of wt mouse NPC at the Zfp608 locus_R1 |
| GSM8137851 |
cHiC of wt mouse NPC at the Zfp608 locus_R2 |
| GSM8137852 |
cHiC of Zfp608 promoter deletion in mouse NPC at the Zfp608 locus_R1 |
| GSM8137853 |
cHiC of Zfp608 promoter deletion in mouse NPC at the Zfp608 locus_R2 |
| GSM8137854 |
cHiC of polyA insertion at Zfp608 in mouse NPC at the Zfp608 locus_R1 |
| GSM8137855 |
cHiC of polyA insertion at Zfp608 in mouse NPC at the Zfp608 locus_R2 |
| GSM8137856 |
cHiC of element A deletion in mouse NPC at the Zfp608 locus_R1 |
| GSM8137857 |
cHiC of element A deletion in mouse NPC at the Zfp608 locus_R2 |
| GSM8137858 |
cHiC of element B deletion in mouse NPC at the Zfp608 locus_R1 |
| GSM8137859 |
cHiC of element B deletion in mouse NPC at the Zfp608 locus_R2 |
| GSM8137860 |
cHiC of element A and B deletion in mouse NPC at the Zfp608 locus_R1 |
| GSM8137861 |
cHiC of element A and B deletion in mouse NPC at the Zfp608 locus_R2 |
| GSM8137862 |
cHiC of CTCF motif deletion at element A in mouse NPC at the Zfp608 locus_R1 |
| GSM8137863 |
cHiC of CTCF motif deletion at element A in mouse NPC at the Zfp608 locus_R2 |
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| This SubSeries is part of SuperSeries: |
| GSE262551 |
A Scaffolding Element Rewires Local 3D Chromatin Architecture During Differentiation |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSE261220_cHiC_ESC_dAB_merge.mcool |
37.3 Mb |
(ftp)(http) |
MCOOL |
| GSE261220_cHiC_ESC_dAB_scores_merge.tar.gz |
361.4 Mb |
(ftp)(http) |
TAR |
| GSE261220_cHiC_ESC_dA_merge.mcool |
27.7 Mb |
(ftp)(http) |
MCOOL |
| GSE261220_cHiC_ESC_dA_scores_merge.tar.gz |
203.0 Mb |
(ftp)(http) |
TAR |
| GSE261220_cHiC_ESC_dB_merge.mcool |
23.2 Mb |
(ftp)(http) |
MCOOL |
| GSE261220_cHiC_ESC_dB_scores_merge.tar.gz |
111.8 Mb |
(ftp)(http) |
TAR |
| GSE261220_cHiC_ESC_dCTCF_merge.mcool |
29.6 Mb |
(ftp)(http) |
MCOOL |
| GSE261220_cHiC_ESC_dCTCF_scores_merge.tar.gz |
240.1 Mb |
(ftp)(http) |
TAR |
| GSE261220_cHiC_ESC_dprom_merge.mcool |
29.5 Mb |
(ftp)(http) |
MCOOL |
| GSE261220_cHiC_ESC_dprom_scores_merge.tar.gz |
231.2 Mb |
(ftp)(http) |
TAR |
| GSE261220_cHiC_ESC_polyA_merge.mcool |
38.6 Mb |
(ftp)(http) |
MCOOL |
| GSE261220_cHiC_ESC_polyA_scores_merge.tar.gz |
356.4 Mb |
(ftp)(http) |
TAR |
| GSE261220_cHiC_ESC_upPAX6_merge.mcool |
34.8 Mb |
(ftp)(http) |
MCOOL |
| GSE261220_cHiC_ESC_upPAX6_scores_merge.tar.gz |
277.1 Mb |
(ftp)(http) |
TAR |
| GSE261220_cHiC_ESC_wt_merge.mcool |
18.8 Mb |
(ftp)(http) |
MCOOL |
| GSE261220_cHiC_ESC_wt_scores_merge.tar.gz |
60.0 Mb |
(ftp)(http) |
TAR |
| GSE261220_cHiC_NPC_dAB_merge.mcool |
48.5 Mb |
(ftp)(http) |
MCOOL |
| GSE261220_cHiC_NPC_dAB_scores_merge.tar.gz |
481.9 Mb |
(ftp)(http) |
TAR |
| GSE261220_cHiC_NPC_dA_merge.mcool |
23.5 Mb |
(ftp)(http) |
MCOOL |
| GSE261220_cHiC_NPC_dA_scores_merge.tar.gz |
108.8 Mb |
(ftp)(http) |
TAR |
| GSE261220_cHiC_NPC_dB_merge.mcool |
23.6 Mb |
(ftp)(http) |
MCOOL |
| GSE261220_cHiC_NPC_dB_scores_merge.tar.gz |
105.7 Mb |
(ftp)(http) |
TAR |
| GSE261220_cHiC_NPC_dCTCF_merge.mcool |
23.2 Mb |
(ftp)(http) |
MCOOL |
| GSE261220_cHiC_NPC_dCTCF_scores_merge.tar.gz |
125.5 Mb |
(ftp)(http) |
TAR |
| GSE261220_cHiC_NPC_dprom_merge.mcool |
30.8 Mb |
(ftp)(http) |
MCOOL |
| GSE261220_cHiC_NPC_dprom_scores_merge.tar.gz |
237.2 Mb |
(ftp)(http) |
TAR |
| GSE261220_cHiC_NPC_polyA_merge.mcool |
42.3 Mb |
(ftp)(http) |
MCOOL |
| GSE261220_cHiC_NPC_polyA_scores_merge.tar.gz |
400.8 Mb |
(ftp)(http) |
TAR |
| GSE261220_cHiC_NPC_wt_merge.mcool |
21.2 Mb |
(ftp)(http) |
MCOOL |
| GSE261220_cHiC_NPC_wt_scores_merge.tar.gz |
92.8 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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