GEO series
Scaffolding element rewires genome architecture during differentiation at the Zfp608 locus (ChIP-Seq)
GSE261221
Mus musculus
Genome binding/occupancy profiling by high throughput sequencing
189 samples
Submitted 2024/05/23
Platform GPL28457
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.
This dataset
Download
Direct links to NCBI, no account and no request form: the whole study as GSE261221_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 189 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1083571 and SRA study SRP493257. Searching any of these in the dataset finder brings you back here.
Study design
19 conditions, mostly in duplicate
ChIP-seq of H3K4me3 in wt ESC ×2
ChIP-seq of H3K27Ac in wt ESC ×2
ChIP-seq of H3K36me3 in wt ESC ×2
ChIP-seq of CTCF in wt ESC ×2
ChIP-seq of Rad21 in wt ESC ×2
ChIP-seq of Pol2 in wt ESC ×2
ChIP-seq of H3K4me3 in wt NPC ×2
ChIP-seq of H3K27Ac in wt NPC ×2
+13 more
Supports a between-group comparison across 38 samples.
19 replicated groups read from the first 40 of 189 sample titles; they account for 38 of them. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- 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
- GSM8137867 ChIP-seq of H3K27Ac in wt ESC_R2
- GSM8137868 ChIP-seq of H3K36me3 in wt ESC_R1
- GSM8137869 ChIP-seq of H3K36me3 in wt ESC_R2
- GSM8137870 ChIP-seq of CTCF in wt ESC_R1
- GSM8137871 ChIP-seq of CTCF in wt ESC_R2
- GSM8137872 ChIP-seq of Rad21 in wt ESC_R1
- GSM8137873 ChIP-seq of Rad21 in wt ESC_R2
- GSM8137874 ChIP-seq of Pol2 in wt ESC_R1
- GSM8137875 ChIP-seq of Pol2 in wt ESC_R2
- GSM8137876 ChIP-seq INPUT in wt ESC
- GSM8137877 ChIP-seq of H3K4me3 in wt NPC_R2
- GSM8137878 ChIP-seq of H3K4me3 in wt NPC_R1
- GSM8137879 ChIP-seq of H3K27Ac in wt NPC_R2
- GSM8137880 ChIP-seq of H3K27Ac in wt NPC_R1
- GSM8137881 ChIP-seq of H3K36me3 in wt NPC_R2
- GSM8137882 ChIP-seq of H3K36me3 in wt NPC_R1
- GSM8137883 ChIP-seq of CTCF in wt NPC_R2
- GSM8137884 ChIP-seq of CTCF in wt NPC_R1
- GSM8137885 ChIP-seq of Rad21 in wt NPC_R2
- GSM8137886 ChIP-seq of Rad21 in wt NPC_R1
- GSM8137887 ChIP-seq of Pol2 in wt NPC_R2
- GSM8137888 ChIP-seq of Pol2 in wt NPC_R1
- GSM8137889 ChIP-seq of Pax6 in wt NPC_R2
- GSM8137890 ChIP-seq of Pax6 in wt NPC_R1
- GSM8137891 ChIP-seq INPUT in wt NPC
- GSM8137892 ChIP-seq of H3K4me3 in Zfp608 promoter deletion ESC_R1
- GSM8137893 ChIP-seq of H3K4me3 in Zfp608 promoter deletion ESC_R2
- GSM8137894 ChIP-seq of H3K27Ac in Zfp608 promoter deletion ESC_R1
- GSM8137895 ChIP-seq of H3K27Ac in Zfp608 promoter deletion ESC_R2
- GSM8137896 ChIP-seq of H3K36me3 in Zfp608 promoter deletion ESC_R1
- GSM8137897 ChIP-seq of H3K36me3 in Zfp608 promoter deletion ESC_R2
- GSM8137898 ChIP-seq of CTCF in Zfp608 promoter deletion ESC_R1
- GSM8137899 ChIP-seq of CTCF in Zfp608 promoter deletion ESC_R2
- GSM8137900 ChIP-seq of Rad21 in Zfp608 promoter deletion ESC_R1
- GSM8137901 ChIP-seq of Rad21 in Zfp608 promoter deletion ESC_R2
- GSM8137902 ChIP-seq of Pol2 in Zfp608 promoter deletion ESC_R1
- GSM8137903 ChIP-seq of Pol2 in Zfp608 promoter deletion ESC_R2
+ 149 more — browse all 189 samples with per-sample file links →
Similar datasets
- GSE272524 Chromatin-dependent motif syntax defines differentiation trajectories [ChIP-seq] 76 samples
- GSE297574 H3K9 di-methylation dynamics underlies mouse minor zygotic genome activation [spike-in ChIP-seq of mESC] 64 samples
- GSE295340 Polycomb Chromatin Topology Enables Long-Range Enhancer Recruitment during Craniofacial Development [ChIP-seq] 42 samples
- GSE267882 Foxp3 and BATF cooperatively direct cis-regulatory programs and gene expression for effector Treg cell differentiation [ChIP-Seq] 34 samples
- GSE163008 Loop extrusion by cohesin plays a role in enhancer-activated gene expression early in differentiation (ChIP-seq) 26 samples
- GSE306869 The RNA binding protein LIN28A mediates chromatin dynamics during neuronal differentiation 24 samples
- GSE294851 Utx (Kdm6a) promotes differentiation non-catalytically in somatic self-renewing epithelia [ChIP-seq] 17 samples
- GSE304211 H4K16ac contributes to chromatin compartment reorganization during mitotic and meiotic transitions [CUTnTAG] 128 samples
Share this dataset
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.