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GenomicsGenome-wide mapping of human DNA-replication origins: levels of transcription at Orc1 sites regulate origin selection and replication timing
We report the genome-wide mapping of Orc1 binding-sites in mammals and their validation as active DNA-replication origins (ORIs). Orc1 sites are universally associated with transcription start sites (TSSs) of coding or non-coding RNAs. Transcription levels at the Orc1 sites directly correlate with r...
ORGANISM(S): Homo sapiens 
2012-09-18 | E-GEOD-37583 | biostudies-arrayexpress
TranscriptomicsscGET-seq profile of patient derived organoids from colorectal cancer samples
One patient-derived organoids from liver metastasis of CRC samples were profiled by scGET-seq to analyze their genomic composition
ORGANISM(S): Homo sapiens 
2024-06-03 | E-MTAB-13126 | biostudies-arrayexpress
TranscriptomicsmiR-126 Orchestrates an Oncogenic Program in B-Cell Precursor Acute Lymphoblastic Leukemia
MicroRNA (miRNA)-126 is a known regulator of hematopoietic stem cell quiescence. We engineered murine hematopoiesis to express miRNA-126 across all differentiation stages. Thirty percent of mice developed monoclonal B cell leukemia, which was prevented or regressed when a tetracycline-repressible mi...
ORGANISM(S): Homo sapiens 
2016-06-14 | E-GEOD-78078 | biostudies-arrayexpress
TranscriptomicsA strong anti-inflammatory signature revealed by liver transcription profiling of Tmprss6-/- mice
Tmprss6 is the master inhibitor of hepcidin and its inactivation causes iron refractory iron deficiency anemia both in human and in mice. Mice with iron deficiency anemia (IDA)-low hepcidin show a pro-inflammatory response that is blunted in iron deficienct-high hepcidin Tmprss6 null mice. We invest...
ORGANISM(S): Mus musculus 
2013-10-09 | E-GEOD-46287 | biostudies-arrayexpress
TranscriptomicsEpigenetic profiles of CRC-derived samples by scGET-seq
Multiple samples of Patient Derived Xenografts (PDX) of a EGFR-resistant colorectal cancer are recovered at different times and profiled by scGET-seq.
ORGANISM(S): Homo sapiens 
2021-08-17 | E-MTAB-9659 | biostudies-arrayexpress
TranscriptomicsAnalysis of epithelial and mesenchymal populations in tumor-derived cell lines by scGET-seq
This experiment includes single cell epigenome data (by scGET-seq) for the epithelial and mesenchymal populations isolated from a pancreatic tumor induced in GEM mouse.
ORGANISM(S): Mus musculus 
2024-06-01 | E-MTAB-13052 | biostudies-arrayexpress
TranscriptomicsTranscriptome analysis of HeLa cells upon deprivation of methionine and cysteine (Met/Cys)
We have previously shown that deprivation of essential amino acids, namely methionine/cysteine or tyrosine, leads to the transcriptional reactivation of integrated silenced transgenes, and latent HIV-1 provirus. In an effort to understand the underlying mechanisms, here we investigate the overall tr...
ORGANISM(S): Homo sapiens 
2018-07-21 | E-MTAB-6452 | biostudies-arrayexpress
TranscriptomicsRNA-seq of HCT116 cells upon downregulation of PINK1
This experiment is aimed at studying the changes in transcript levels when PINK1, a key regulator of autophagy, is downregulated.
ORGANISM(S): Homo sapiens 
2023-09-01 | E-MTAB-12946 | biostudies-arrayexpress
GenomicsLoss of histone demethylase JARID1C triggers genomic instability in cancer.
Chromatin remodelers are recurrently mutated in cancer. Among these, JARID1C, (KDM5C) a histone demethylase, is frequently inactivated in clear cell renal cell carcinoma (ccRCC) patients. How the genetic inactivation of JARID1C leads to cancer remains largely unknown. Here we report that JARID1C bin...
ORGANISM(S): Homo sapiens 
2015-11-09 | E-GEOD-73267 | biostudies-arrayexpress
TranscriptomicsRNA-seq of HCT116 cells upon administration of FOLFOX or FOLFIRI at time points with or without ULK1 inhibitor
This experiment is aimed at studying the effect of two different chemotherapies (FOLFOX and FOLFIRI) and their interaction with a ULK1 inhibitor on HCT116 colorectal cancer cell line.
ORGANISM(S): Homo sapiens 
2023-09-01 | E-MTAB-12947 | biostudies-arrayexpress
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