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ProteomicsFrom stem cells to somites: revealing genetic and exogenous factors of human embryogenesis
In this project, we characterized the temporal dynamics of protein expression during the differentiation of human iPSCs to somitoids, stem cell–derived 3D models that recapitulate early embryonic somitogenesis. Using quantitative time-course proteomics, we captured how protein abundance changed as p...
ORGANISM(S): Homo sapiens (Human) 
2026-08-07 | PXD079129 | Pride
Matrigel Ipscs Human somitoids Proteomics Somitogenesis 
ProteomicsDeciphering lineage specification during early embryogenesis using multi-layered proteomics
Gastrulation is a critical stage of embryonic development during which the three germ layers are established. Deciphering the molecular mechanisms underlying this proces from a protein perspective remains a significant challenge. To address this, we employed a multilayered mass spectrometry-based pr...
ORGANISM(S): Mus musculus (Mouse) 
2024-05-21 | PXD041309 | Pride
Proteomics Dtag system Interaction proteomics Enhancers Zeb2 Transcription factors Somitoids Gastruloids Developmental biology 
ProteomicsP300 proximity labeling in human iPSCs
This dataset presents the results of proximity-dependent biotinylation targeting the transcriptional coactivator p300 in human induced pluripotent stem cells (hiPSCs). We endogenously tagged p300 with the biotin ligase miniTurboID, to enable labeling of proximal proteins and thus proteins locatd at ...
ORGANISM(S): Homo sapiens (Human) 
2026-08-07 | PXD067912 | Pride
ProteomicsP300 proximity labeling in human somitoids
This dataset presents the results of proximity-dependent biotinylation targeting the transcriptional coactivator p300 in human somitoids. We endogenously tagged p300 with the biotin ligase miniTurboID in iPSCs, to enable labeling of proximal proteins and thus proteins locatd at enhancers. hiPSCs wer...
ORGANISM(S): Homo sapiens (Human) 
2026-08-07 | PXD070251 | Pride
ProteomicsMass spectrometry-based validation of BPTF knockout in human induced pluripotent stem cells 
We generated a BPTF knockout human induced pluripotent stem cell (iPSC) line using CRISPR-Cas9 and confirmed loss of the targeted locus by genotyping. Quantitative mass spectrometry verified complete absence of BPTF protein in the knockout clone. This validated line was used for downstream functiona...
ORGANISM(S): Homo sapiens (Human) 
2026-08-07 | PXD068407 | Pride
Stem cells Bptf Knockout Ipscs 
ProteomicsFunctional analysis of somatic variants found in endometrial tumor-specific ER-alpha enhancers
Biological implications of healthy- and tumor-specific ERα cistromes in endometrial tumors have largely been understudied. Moreover, the functional impact of non-coding somatic variants has commonly been underexplored and remained elusive. This study is aimed to provide functional interpretation of ...
ORGANISM(S): Homo sapiens (Human) 
2025-04-15 | PXD029822 | Pride
Enhancers Endometrial cancer Er-alpha Somatic variants 
ProteomicsMyeloid-derived suppressor cells and tolerogenic dendritic cells are distinctively induced by PI3K and Wnt signaling pathways
Understanding the molecular mechanisms that initiate and control immunosuppression by myeloid cells is essential to overcoming the myeloid-induced disbalance of the immune system observed in patients. Myeloid cells are implicated in aggravated suppression of immunity as seen in cancer as well as in ...
ORGANISM(S): Homo sapiens (Human) 
2023-09-20 | PXD027715 | Pride
Human Mdscs Modc Fasp Hnscc Toldc Monocytes 
ProteomicsBreast cancer risk SNPs converge on estrogen receptor binding sites commonly shared between breast tumors to locally alter estrogen signalling output
Estrogen Receptor alpha (ERa) is the main driver of luminal breast cancer development and progression, and represents the main drug target in patient care. ERa chromatin binding has been extensively studied in breast cancer cell lines and a number of human tumors, often focused on differential bindi...
ORGANISM(S): Homo sapiens (Human) 
2024-05-22 | PXD045526 | Pride
Breast cancer Estrogen receptor Enhancers Snps Rs9952980 
GenomicsChIP-Seq for RIP140, using the human breast cancer cell line MCF-7 in the absence of hormone or after treatment with Estradiol
This experiment is designed to assess the role of RIP140 in estrogen receptor-dependent gene expression in MCF7 luminal breast cancer cells. Hormone deprived MCF7 cells were treated for 3 hours with E2 or DMSO control, after which samples were processed for ChIp-seq for RIp140.
ORGANISM(S): Homo sapiens 
2015-03-16 | E-MTAB-2576 | biostudies-arrayexpress
TranscriptomicssiRIP140 and gene expression effects in E2-treated MCF7 cells
This experiment is designed to assess the role of RIP140 in estrogen receptor-dependent gene expression in MCF7 luminal breast cancer cells. MCF7 cells were transfected with an siRNA to target RIP140 or siControl, and subsequently depleted from hormones for three days. Thereafter, cells were treated...
ORGANISM(S): Homo sapiens 
2015-03-17 | E-MTAB-2577 | biostudies-arrayexpress
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