Project description:We report HERV-K rec iCLIP-seq binding data, ribosome profiling data, and RNA-seq from ELF1 naïve hESC and RNA-seq from NCCIT cells. HERV-K Rec iCLIP-seq: 2 replicates in NCCIT. Ribosome profiling: 4 replicates each of Rec-overexpressing NCCIT vs. control NCCIT; RNAseq: 3 replicates each of HERV-K Rec siRNA vs. control siRNA in NCCIT; RNA-seq: 3 replicates each of ELF1 naïve hESC vs. primed hESC.
Project description:Provide a comprehensive picture of HERV RNA expression through both short and long read sequencing in NCCIT cells to be used in an integrated proteogenomic analysis pipeline
Project description:To investigate the role and mechanism of miR-125b on NCCIT cells without bias, we analyzed differentially expression microRNA profile among miR-125b antagomir-, miR-125b agomir-, and negative control-transfected NCCIT tumor cells by microRNA-seq.
Project description:To investigate the role and mechanism of miR-125b on NCCIT cells without bias, we analyzed differentially expression RNA profile among miR-125b antagomir-, miR-125b agomir-, and negative control-transfected NCCIT tumor cells by RNA-seq.
Project description:To investigate the cancer properties of HERV-R knockout in the colon cancer cell line DLD1, we knocked out HERV-R from Crispr-cas9 in DLD1. We performed RNA-seq to profile gene expression in DLD1, DLD1R (HERV-R KO) cells, respectively.
Project description:We used microarrays to profile gene expression of NCCIT cells to study the link between epigenetic modifications and gene transcription.
Project description:We used microarrays to profile gene expression of NCCIT cells to study the link between epigenetic modifications and gene transcription. Extract total RNA to examine gene expression of NCCIT cells in the undifferentiated and differentiated states.
Project description:The aim of the study was to characterize the role of GDF3 in NCCIT cells as a model of cancer stem cells. The NCCIT cells were stimulated for 3h with (1) 100ng/mL and (2) 300ng/mL GDF3, (3) 300ng/mL Nodal and (4) 100ng/mL GDF3 + 300ng/mL Nodal and compared to unstimulated control. Additionally a stable, lentiviral knockdown of GDF3 was performed in NCCIT cells and the transciption profile of these cells was compared to cells transduced with mock-virus.
Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of SNF5 binding in human pluripotent embryonic carcinoma NCCIT and SNF5 overexpressed NCCIT cells. We generated genome-wide cSNF5 maps of NCCIT and SNF5 overexpressed NCCIT cells from chromatin immunoprecipitated DNA. SNF5 and OCT4 seem not to share their binding in OCT4 centered binding plot in control, while SNF5 overexpression directs SNF5 to OCT4 target genes.
