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Multi-omics analyses reveal DjTcf4 critical for proper timing of differentiation in planarian regeneration [scRNA-DjTcf4]

ABSTRACT: Multi-omics analyses reveal DjTcf4 critical for proper timing of differentiation in planarian regeneration [scRNA-DjTcf4]

PROVIDER: PRJNA1307515 | ENA |

REPOSITORIES: ENA

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Multi-omics analyses reveal DjTcf4 critical for proper timing of differentiation in planarian regeneration [scRNA-DjTcf4]

Project description:The blastema is key to forming complete tissues in regenerating Dugesia japonica (D. japonica). However, the dynamic changes in cellular compositions and transcription landscapes in blastema during regeneration are understudied. Here, through genome reannotation, 3D spatial transcriptome construction, scRNA-seq and scATAC-seq analyses of changes in gene expression and chromatin structures, we delineated key transcription factors regulating the developmental trajectories of major cell clusters in the regenerating head. Importantly, we found that the T-cell factor 4 positive (DjTcf4+) cells highly accumulated at wound areas, and its gene network is critical for proper timing of development during regeneration in multiple progenitor cells. Depletion of DjTcf4 and its target genes led to singular eye and/or dull tail phenotypes and delayed regeneration. Taken together, we built multi-omics atlases in D. japonica and revealed noncanonical function of the DjTcf4 network in developmental pattern formation, laying a foundation for studies of regeneration in D. japonica.

2025-09-01 | GSE305722 | GEO

Multi-omics analyses reveal DjTcf4 critical for proper timing of differentiation in planarian regeneration

Project description:Multi-omics analyses reveal DjTcf4 critical for proper timing of differentiation in planarian regeneration

| PRJNA1303604 | ENA

Multi-omics analyses reveal DjTcf4 critical for proper timing of differentiation in planarian regeneration

2025-10-13 | GSE304962 | GEO

Multi-omics analyses reveal DjTcf4 critical for proper timing of differentiation in planarian regeneration [scATAC_head]

Project description:Multi-omics analyses reveal DjTcf4 critical for proper timing of differentiation in planarian regeneration [scATAC_head]

| PRJNA1307516 | ENA

Multi-omics analyses reveal DjTcf4 critical for proper timing of differentiation in planarian regeneration [mRNA_DjTcf4]

Project description:Multi-omics analyses reveal DjTcf4 critical for proper timing of differentiation in planarian regeneration [mRNA_DjTcf4]

| PRJNA1307512 | ENA

Multi-omics analyses reveal DjTcf4 critical for proper timing of differentiation in planarian regeneration [scRNA_head]

Project description:Multi-omics analyses reveal DjTcf4 critical for proper timing of differentiation in planarian regeneration [scRNA_head]

| PRJNA1307514 | ENA

Multi-omics analyses reveal DjTcf4 critical for proper timing of differentiation in planarian regeneration [scRNA_head]

2025-09-01 | GSE305724 | GEO

Multi-omics analyses reveal DjTcf4 critical for proper timing of differentiation in planarian regeneration [scATAC_head]

2025-09-01 | GSE305723 | GEO

Multi-omics analyses reveal DjTcf4 critical for proper timing of differentiation in planarian regeneration [mRNA_DjTcf4]

2025-09-01 | GSE305721 | GEO

Replication timing of siRNA control and siRNA PolQRKO cells

Project description:The human A-family DNA polymerase M-NM-8 (Pol q) is a large, multidomain enzyme whose physiological function is still unclear despite its in vitro translesion synthesis capacity in front of DNA damage and its involvement in some features of DNA repair after external stress. Here we present evidence that Pol q holds a novel role in the absence of external stress as a critical determinant of the replication timing program in human cells. Pol q binds to chromatin at early G1 and is required for proper formation of pre-replicative complexe and replication origin activation. Pol q-depleted cells show modified spatial organization of chromatin-loop structures at replication factories. Genome-wide analysis of replication timing shows delayed replication of a part of early replicating domains and advanced replication of a part of late replicating domains following Pol q depletion. Our results identify Pol q as one of the first critical human factors discovered in the replication timing programme. Two-condition experiment, siRNA control vs. siRNA polQ cells. Biological replicates: 2 control replicates, 2 transfected replicates.

2014-06-19 | E-GEOD-49693 | biostudies-arrayexpress

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