 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 09, 2023 |
| Title |
Capture Hi-C in (EV and ZFP661-3HA OE) mESCs and E16.5 mouse forebrains |
| Organism |
Mus musculus |
| Experiment type |
Other
|
| Summary |
This assay aimed to investigate the regulatory role of ZFP661 in modulating the permeability of CTCF barriers. To achieve this, we generated Capture Hi-C maps on several regions bound by ZFP661 using E16.5 forebrains from wild-type (WT) and Zfp661 knockout (KO) mice, as well as empty vector (EV) control and ZFP661-3HA overexpressing (OE) mESCs. Our findings reveal that ZFP661 modulates the permeability of CTCF barriers, thereby balancing between the interactions that are trapped at the barriers and those passing over them.
|
| |
|
| Overall design |
We compared the interactions being trapped at the barriers and those passing over them in WT and Zfp661 KO E16.5 forebrains, as well as EV control and ZFP661-3HA OE mESCs. For the E16.5 forebrain samples, three pairs of littermates were used, while two biological replicates were used for each genotype in mESCs.
|
| |
|
| Contributor(s) |
Jin J, Macfarlan T |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
May 07, 2023 |
| Last update date |
Feb 22, 2024 |
| Contact name |
Jinpu Jin |
| Organization name |
NICHD
|
| Lab |
Section on Mammalian Development and Evolution
|
| Street address |
Building 6B, Room 2B-211, 6 Center Drive
|
| City |
Bethesda |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
|
| Samples (14)
|
| GSM7305315 |
Capture_HiC, EV control replicate 1, library 1 |
| GSM7305316 |
Capture_HiC, EV control replicate 1, library 2 |
| GSM7305317 |
Capture_HiC, EV control replicate 2, library 1 |
| GSM7305318 |
Capture_HiC, EV control replicate 2, library 2 |
| GSM7305319 |
Capture_HiC, ZFP661OE replicate 1, library 1 |
| GSM7305320 |
Capture_HiC, ZFP661OE replicate 1, library 2 |
| GSM7305321 |
Capture_HiC, ZFP661OE replicate 2, library 1 |
| GSM7305322 |
Capture_HiC, ZFP661OE replicate 2, library 2 |
| GSM7305323 |
E16.5 forebrain, Capture HiC, WT replicate 1 |
| GSM7305324 |
E16.5 forebrain, Capture HiC, WT replicate 2 |
| GSM7305325 |
E16.5 forebrain, Capture HiC, WT replicate 3 |
| GSM7305326 |
E16.5 forebrain, Capture HiC, Zfp661 KO replicate 1 |
| GSM7305327 |
E16.5 forebrain, Capture HiC, Zfp661 KO replicate 2 |
| GSM7305328 |
E16.5 forebrain, Capture HiC, Zfp661 KO replicate 3 |
|
| This SubSeries is part of SuperSeries: |
| GSE231869 |
Modulation of CTCF barrier permeability by ZFP661 enhances protocadherin diversity for proper cortical dendritic projection in mammals |
|
| Relations |
| BioProject |
PRJNA968173 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE231864_E16.5_forebrain_Capture_HiC_WT_pooled.allValidPairs.txt.gz |
387.8 Mb |
(ftp)(http) |
TXT |
| GSE231864_E16.5_forebrain_Capture_HiC_Zfp661_KO_pooled.allValidPairs.txt.gz |
436.8 Mb |
(ftp)(http) |
TXT |
| GSE231864_RAW.tar |
1.6 Gb |
(http)(custom) |
TAR (of TXT) |
| GSE231864_mESCs_Capture_HiC_EV_control_pooled.allValidPairs.txt.gz |
436.2 Mb |
(ftp)(http) |
TXT |
| GSE231864_mESCs_Capture_HiC_ZFP661_OE_pooled.allValidPairs.txt.gz |
424.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...