Dataset Information

RamDA-seq analysis of CRISPRa-mediated RELA activation for proof-of-concept validation of CATaN

ABSTRACT: This dataset was generated to validate CATaN (Canonical correlation Analysis of Transcriptome and TF-gene regulatory Networks), an unsupervised framework that integrates transcriptomic data with transcription factor (TF) gene regulatory networks. To test whether CATaN correctly recovers the transcriptional program driven by a specific TF, we activated RELA, a subunit of NF-κB, in Jurkat cells using CRISPR activation (CRISPRa; dCas9-VP64 with a single guide RNA targeting RELA) and compared it with a control guide RNA. Transcriptomes were profiled by RamDA-seq. Transductions were performed in triplicate for each condition, and cells were harvested at five, six, and seven days post-transduction. Differential expression analysis showed concordant directional changes in RELA-regulated genes; CATaN applied to these data assigned higher CC1 loadings to RELA ChIP-seq samples than to other TFs. Together, these results provide proof-of-concept support for the method.

ORGANISM(S): Homo sapiens

PROVIDER: GSE335951 | GEO | 2026/06/29

REPOSITORIES: GEO

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:Objective We have previously shown that expression of the CEACAM1 long isoform (CC1-L) in metastatic colorectal cancer (CRC) cells results in significant inhibition of liver metastasis via Chemokine (C-C motif) Ligand 2 (CCL2) and Signal Transducer and Activator of Transcription 3 (STAT3) signaling. Yet, despite recent advances in identifying molecules involved in the CC1-L inhibition of metastasis, much remains to be elucidated regarding the molecular mechanisms orchestrating this pathway. Design We performed an untargeted transcript profiling and a phosphokinase screen between CC1-L-expressing and non-expressing (CT) CRC cells. Identified targets were validated in vitro and in vivo for their involvement in signaling and invasion or metastasis. We validated our conclusions in CRC patient cohorts for time to metastasis development and long-term survival. Results Untargeted transcript profiling revealed high Decorin (Dcn) expression in CC1-L-expressing cells versus CT cells. Decorin was detected at the peri-endothelial layers of large blood vessels and in liver stellate cells. In metastatic lesions, it was expressed in pericyte-like cells covering capillary endothelium. Phosphokinase differential screening revealed reduced Ephrin type-A receptor 2 (EphA2) expression and activity in CC1-L- versus CT-expressing cells. Treatment of CT cells with recombinant Dcn led to decreased migration and invasion and decreased EphA2-mediated Erk and Akt signaling. CRC patients exhibiting high CC1 and DCN expression, in combination with low EPHA2 expression, benefit from longer 10-year survival than those with high EPHA2 expression. Conclusion CC1-L expression in poorly differentiated CRC inhibits liver metastasis through increased Decorin expression and EphA2-mediated signaling. Quadriplicate samples of each mouse colon cancer cell lines (control cells versus those expressing either short or long isoform of CEACAM1) have been used for RNA extraction

Dataset Information

RamDA-seq analysis of CRISPRa-mediated RELA activation for proof-of-concept validation of CATaN

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets