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Series GSE261221 Query DataSets for GSE261221
Status Public on May 23, 2024
Title Scaffolding element rewires genome architecture during differentiation at the Zfp608 locus (ChIP-Seq)
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
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.
 
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.
 
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
 
Platforms (1)
GPL28457 DNBSEQ-G400 (Mus musculus)
Samples (189)
GSM8137864 ChIP-seq of H3K4me3 in wt ESC_R1
GSM8137865 ChIP-seq of H3K4me3 in wt ESC_R2
GSM8137866 ChIP-seq of H3K27Ac in wt ESC_R1
This SubSeries is part of SuperSeries:
GSE262551 A Scaffolding Element Rewires Local 3D Chromatin Architecture During Differentiation

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE261221_ChIP_ESC_dAB_CTCF_R0.bigWig 370.8 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_dAB_INPUT.bigWig 246.4 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_dAB_K27Ac_R0.bigWig 331.1 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_dAB_K36me3_R0.bigWig 430.0 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_dAB_K4me3_R0.bigWig 331.1 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_dAB_Pol2_R0.bigWig 270.9 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_dAB_Rad21_R0.bigWig 514.6 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_dA_CTCF_R0.bigWig 442.9 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_dA_INPUT.bigWig 468.7 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_dA_K27Ac_R0.bigWig 300.5 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_dA_K36me3_R0.bigWig 473.1 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_dA_K4me3_R0.bigWig 193.7 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_dA_Pol2_R0.bigWig 380.1 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_dA_Rad21_R0.bigWig 404.4 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_dB_CTCF_R0.bigWig 206.8 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_dB_INPUT.bigWig 367.4 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_dB_K27Ac_R0.bigWig 371.4 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_dB_K36me3_R0.bigWig 318.8 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_dB_K4me3_R0.bigWig 106.1 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_dB_Pol2_R0.bigWig 194.4 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_dB_Rad21_R0.bigWig 338.7 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_dCTCF_CTCF_R0.bigWig 368.3 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_dCTCF_INPUT.bigWig 177.2 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_dCTCF_K27Ac_R0.bigWig 327.0 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_dCTCF_Pol2_R0.bigWig 347.9 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_dCTCF_Rad21_R0.bigWig 422.6 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_dprom_CTCF_R0.bigWig 210.5 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_dprom_INPUT.bigWig 223.6 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_dprom_K27Ac_R0.bigWig 303.1 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_dprom_K36me3_R0.bigWig 326.2 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_dprom_K4me3_R0.bigWig 93.8 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_dprom_Pol2_R0.bigWig 239.3 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_dprom_Rad21_R0.bigWig 326.9 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_polyA_CTCF_R0.bigWig 234.9 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_polyA_INPUT.bigWig 234.0 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_polyA_K27Ac_R0.bigWig 273.3 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_polyA_K36me3_R0.bigWig 311.8 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_polyA_K4me3_R0.bigWig 119.3 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_polyA_Pol2_R0.bigWig 307.1 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_polyA_Rad21_R0.bigWig 357.8 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_upPAX6_INPUT.bigWig 326.9 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_upPAX6_Pax6_R0.bigWig 555.5 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_wt_CTCF_R0.bigWig 280.1 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_wt_INPUT.bigWig 235.9 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_wt_K27Ac_R0.bigWig 288.6 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_wt_K36me3_R0.bigWig 324.4 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_wt_K4me3_R0.bigWig 70.3 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_wt_Pol2_R0.bigWig 222.1 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_ESC_wt_Rad21_R0.bigWig 366.0 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dAB_CTCF_R0.bigWig 481.0 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dAB_INPUT.bigWig 162.3 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dAB_K27Ac_R0.bigWig 585.9 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dAB_K36me3_R0.bigWig 380.4 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dAB_K4me3_R0.bigWig 267.1 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dAB_Pax6_R0.bigWig 434.8 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dAB_Pol2_R0.bigWig 466.9 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dAB_Rad21_R0.bigWig 467.3 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dA_CTCF_R0.bigWig 267.4 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dA_INPUT.bigWig 470.4 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dA_K27Ac_R0.bigWig 253.6 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dA_K36me3_R0.bigWig 475.3 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dA_K4me3_R0.bigWig 189.4 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dA_Pax6_R0.bigWig 369.7 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dA_Pol2_R0.bigWig 378.3 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dA_Rad21_R0.bigWig 331.7 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dB_CTCF_R0.bigWig 231.6 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dB_INPUT.bigWig 248.0 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dB_K27Ac_R0.bigWig 325.6 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dB_K36me3_R0.bigWig 396.0 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dB_K4me3_R0.bigWig 146.9 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dB_Pax6_R0.bigWig 170.0 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dB_Pol2_R0.bigWig 134.4 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dB_Rad21_R0.bigWig 290.2 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dCTCF_CTCF_R0.bigWig 301.9 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dCTCF_INPUT.bigWig 83.4 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dCTCF_K27Ac_R0.bigWig 350.4 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dCTCF_Pol2_R0.bigWig 295.8 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dCTCF_Rad21_R0.bigWig 371.2 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dprom_CTCF_R0.bigWig 265.9 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dprom_INPUT.bigWig 227.4 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dprom_K27Ac_R0.bigWig 251.0 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dprom_K36me3_R0.bigWig 341.1 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dprom_K4me3_R0.bigWig 163.3 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dprom_Pax6_R0.bigWig 316.9 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dprom_Pol2_R0.bigWig 268.5 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_dprom_Rad21_R0.bigWig 341.7 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_polyA_CTCF_R0.bigWig 259.4 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_polyA_INPUT.bigWig 215.5 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_polyA_K27Ac_R0.bigWig 268.7 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_polyA_K36me3_R0.bigWig 313.4 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_polyA_K4me3_R0.bigWig 84.2 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_polyA_Pax6_R0.bigWig 351.0 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_polyA_Pol2_R0.bigWig 317.5 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_polyA_Rad21_R0.bigWig 283.2 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_wt_CTCF_R0.bigWig 250.9 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_wt_INPUT.bigWig 224.2 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_wt_K27Ac_R0.bigWig 284.0 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_wt_K36me3_R0.bigWig 325.4 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_wt_K4me3_R0.bigWig 140.2 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_wt_Pax6_R0.bigWig 327.8 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_wt_Pol2_R0.bigWig 237.1 Mb (ftp)(http) BIGWIG
GSE261221_ChIP_NPC_wt_Rad21_R0.bigWig 261.9 Mb (ftp)(http) BIGWIG
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Processed data are available on Series record

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