Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Synthetic regulatory genomics uncovers enhancer context dependence at the Sox2 locus

ABSTRACT: Synthetic regulatory genomics uncovers enhancer context dependence at the Sox2 locus

PROVIDER: PRJNA852558 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Synthetic regulatory genomics uncovers enhancer context dependence at the Sox2 locus.

Project description:Sox2 expression in mouse embryonic stem cells (mESCs) depends on a distal cluster of DNase I hypersensitive sites (DHSs), but their individual contributions and degree of interdependence remain a mystery. We analyzed the endogenous Sox2 locus using Big-IN to scarlessly integrate large DNA payloads incorporating deletions, rearrangements, and inversions affecting single or multiple DHSs, as well as surgical alterations to transcription factor (TF) recognition sequences. Multiple mESC clones were derived for each payload, sequence-verified, and analyzed for Sox2 expression. We found that two DHSs comprising a handful of key TF recognition sequences were each sufficient for long-range activation of Sox2 expression. By contrast, three nearby DHSs were entirely context dependent, showing no activity alone but dramatically augmenting the activity of the autonomous DHSs. Our results highlight the role of context in modulating genomic regulatory element function, and our synthetic regulatory genomics approach provides a roadmap for the dissection of other genomic loci.

| S-EPMC10081970 | biostudies-literature

Synthetic regulatory genomics uncovers enhancer context dependence at the Sox2 locus

Project description:Sequencing and coverage data produced as part of the Big-IN genome engineering sequence verification pipeline.

2023-01-17 | GSE206863 | GEO

Identification the Expression of Sox2 in Colorectal Cancer Tissues

Project description:Sox2 has been studied in several types of human solid tumors. The investigators found that Sox2 had higher expression level in colorectal cancer and metastatic tissues than normal tissues. So the investigators assumed that whether Sox2 plays an important role in the progression and migration of colon cancer.

| 2124687 | ecrin-mdr-crc

4C on Sox2 Locus with tetO/cuO Modifications

Project description:We have profiled the chromosomal contacts of the Sox2 promoter in wild-type ESCs as well as cell lines with a genetically altered Sox2 locus.

2019-05-16 | GSE127901 | GEO

ysblcc sox2

Project description:ysblcc sox2

| PRJEB2061 | ENA

CUT&RUN of Sox2 binding in the mouse P0 visual thalamus (dLGN)

Project description:CUT&RUN was performed for Sox2 on ex-vivo dissected visual thalamic nuclei from P0 mice, revealing context specific activity of Sox2 binding in differentiated neurons.

2023-06-03 | E-MTAB-13004 | biostudies-arrayexpress

Survival and PN Dependence in SBS Patients

Project description:Short bowel syndrome (SBS) is a rare condition resulting from the loss of portions of the small intestine, and can cause a spectrum of metabolic and physiologic disturbances.The objective of this study was to determine the longterm survival and parenteral nutrition dependence of adult patients with SBS.

| 114861 | ecrin-mdr-crc

Pluripotency reprogramming by competent and incompetent POU factors uncovers temporal dependency for Oct4 and Sox2

Project description:Pluripotency reprogramming by competent and incompetent POU factors uncovers temporal dependency for Oct4 and Sox2

| PRJNA407838 | ENA

Antisocial Drug Dependence

Project description:Antisocial Drug Dependence

| PRJNA547656 | ENA

CIDR Alcohol Dependence

Project description:CIDR Alcohol Dependence

| PRJNA75517 | ENA