Project description:In order to comprehensively identify genes directly regulated by AP4, a genome-wide chromatin-immunoprecipitation analysis (ChIP) followed by next generation sequencing (ChIP-seq) was performed after activation of a conditional AP4 allele in DLD-1 cells. One DLD-1 Sample was sequenced.

2013-05-31 | E-GEOD-46935 | biostudies-arrayexpress

Transcriptome of DLD-1 co-cultured with or without extracellular vesicels derived from Fusobacterium nucleatum

Project description:To explore the impact of FnEV on transcriptome of colorectal cancer cell line DLD-1

2024-05-01 | GSE241656 | GEO

Analysis of gene expression with the Hmga2 allelic series.

Project description:In this study, we introduced a series of expression constructs into a mouse lung cancer cell line (482N1): (1) a control short hairpin RNA (shluc) plus the empty expression vector (empty); (2) an shRNA targeting Hmga2 (shHmga2) plus empty; (3) shHmga2 plus an expression vector for the full-length Hmga2 cDNA with the shRNA site mutated (shHmga2 wt); (4) shHmga2 plus the full-length shRNA-mutated Hmga2 with let-7 sites in the 3' UTR mutated (shHmga2 m7); (5) shHmga2 plus the full-length shRNA-mutated Hmga2 with the start codon mutated (shHmga2 ATG wt); and (6) shHmga2 plus the full-length shRNA-mutated Hmga2 with the start codon and let-7 sites mutated (shHmga2 ATG m7).

2013-09-18 | GSE50932 | GEO

RNA-seq profiling of ADAM10 inhibition in DLD-1 and SW620 colorectal cancer cell lines

Project description:This study examines the transcriptomic effects of ADAM10 inhibition in two human colorectal cancer cell lines, DLD-1 and SW620. Cells were treated with vehicle control or the conformation-specific ADAM10 monoclonal antibody 1H5 for 48 hours, followed by extraction of total RNA and paired-end RNA sequencing. The dataset enables comparative analysis of ADAM10-regulated pathways across different CRC genetic backgrounds, including alterations in Notch and EGFR signaling, metabolic gene programs, and other pathways associated with tumor progression.

2026-01-19 | GSE311253 | GEO

HMGA2 overexpression

Project description:Overexpression of high mobility group AT-hook 2 (HMGA2) associated with truncations of its 3’ untranslated region (UTR) with let-7 micro RNA-complementary sequences have been identified in patients with paroxysmal nocturnal hemoglobinuria (PNH). Here, we generated transgenic mice (∆Hmga2 mice) with a 3’UTR-trncated Hmga2 cDNA that overexpress Hmga2 mRNA and protein in hematopoietic organs. ∆Hmga2 mice showed proliferative hematopoiesis that mimicked a myeloproliferative neoplasm (MPN)-like phenotype with increased numbers of all lineages of peripheral blood cells, hypercellular bone marrow (BM), splenomegaly with extramedullary erythropoiesis, and erythropoietin-independent erythroid colony formation compared to wild-type mice. ∆Hmga2 BM-derived cells took over most of hematopoiesis in competitive repopulations during serial BM transplants. When we bred mice with circulating PNH cells (Piga- mice) with ∆Hmga2 mice, the lack of GPI-linked proteins did not add an additional clonal advantage to the ∆Hmga2+ cells. In summary, our results showed that the overexpression of a 3’UTR-truncated Hmga2 leads to a proliferative hematopoiesis with clonal advantage, which may explain clonal expansion in PNH or MPN at the level of HSC.

2011-02-06 | GSE24071 | GEO

Ectopic expression of AP4 in human colorectal cancer cells DLD-1 for different times

Project description:To characterize the transcriptome of the transcription factor AP4 DLD-1 cells were infected with AP4 coding viruses for different periods of time. Adenovirus amplification and purification was performed as previously described (He et al., 1998). The minimal amount of virus needed to reach more than 90% infection efficiency was determined by monitoring GFP signals with fluorescence microscopy. DLD-1 cells were infected in serum-free medium with adenovirus for 3 hours. After removal an equal amount of medium containing 20% FBS was added.

2013-05-31 | GSE46578 | GEO

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