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TranscriptomicsDNA copy number detection from exome sequencing - Exploiting the off-targets (Nimblegen)
Current methods for detection of copy number aberrations (CNA) from whole-exome sequencing (WES) data are based on the read counts of the captured exons only. However, accurate CNA determination is complicated by the non-uniform read depth and uneven distribution of exons. Therefore, we developed EN...
ORGANISM(S): Mus musculus 
2014-08-12 | E-GEOD-60254 | biostudies-arrayexpress
TranscriptomicsDNA copy number detection from exome sequencing - Exploiting the off-targets (SNP)
Current methods for detection of copy number aberrations (CNA) from whole-exome sequencing (WES) data are based on the read counts of the captured exons only. However, accurate CNA determination is complicated by the non-uniform read depth and uneven distribution of exons. Therefore, we developed EN...
ORGANISM(S): Homo sapiens 
2014-08-12 | E-GEOD-60168 | biostudies-arrayexpress
TranscriptomicsImmortalization capacity of HPV types is inversely related to chromosomal instability in immortal descendants.
Human papillomavirus (HPV) induced immortalization of human foreskin keratinocytes (HFK) is a two-step process, including 1) the bypass of replicative senescence and acquisition of an extended lifespan, and 2) the outgrowth of immortal cells. Our previous study showed that the immortalization capaci...
ORGANISM(S): Homo sapiens 
2016-08-01 | E-GEOD-72063 | biostudies-arrayexpress
TranscriptomicsGenetic Aberrations Relate Early and Advanced Stage Ovarian Cancer and are Associated with Survival
BACKGROUND: Because of the distinct clinical presentation of early and advanced stage ovarian cancer, we aim to clarify whether these disease entities are solely separated by time of diagnosis or whether they arise from distinct molecular events. METHODS: Sixteen early and sixteen advanced stage ova...
ORGANISM(S): Homo sapiens 
2012-08-22 | E-GEOD-24418 | biostudies-arrayexpress
TranscriptomicsPARALLEL IN VIVO AND IN VITRO MELANOMA RNAi DROPOUT SCREENS
To identify factors preferentially necessary to drive tumor expansion we performed parallel in vitro and in vivo negative selection shRNA screens. Melanoma cells harboring shRNAs targeting several DNA Damage Response (DDR) kinases had a greater selective disadvantage in vivo than in vitro, indicatin...
ORGANISM(S): Homo sapiens 
2014-09-30 | E-GEOD-61826 | biostudies-arrayexpress
TranscriptomicsLow MITF/AXL ratio predicts early resistance to multiple targeted drugs in melanoma
Increased MITF expression contributes to melanoma progression and resistance to BRAF pathway inhibition. We show that, unexpectedly, lack of MITF is associated with more severe resistance to a range of inhibitors. Indeed, the presence of endogenous MITF was essential for robust drug responses. Both ...
ORGANISM(S): Homo sapiens 
2014-09-19 | E-GEOD-61544 | biostudies-arrayexpress
Genomicsena-DATASET-SC-15-06-2016-10:23:08:608-358 - samples
Description not provided
EGAD00001002191 | EGA
GenomicsEGAS00001000415-sc-2019-08-21T10:34:41Z - samples
We have collected material from a patient who had BrafV600E mutant melanoma that was treated with PLX4032. We have germline DNA from the patient and DNA and RNA from distinct lesions before and after treatment with PLX4032. We would like to exome sequence these samples to gain a snap shot of the mec...
EGAD00001005278 | EGA
GenomicsAnalysis of resistance to PLX4032
We have collected material from a patient who had BrafV600E mutant melanoma that was treated with PLX4032. We have germline DNA from the patient and DNA and RNA from distinct lesions before and after treatment with PLX4032. We would like to exome sequence these samples to gain a snap shot of the mec...
EGAS00001000415 | EGA
TranscriptomicsUnderstanding Vitamin D resistance using expression microarrays
Vitamin D is the strongest known natural anti-proliferative. A large number of studies in a wide spectrum of cancers, including epidemiological, in vitro and animal models, demonstrate that the active form of Vitamin D has anti-cancer benefits, affecting both progression and metastasis. Alike the ro...
ORGANISM(S): Homo sapiens 
2008-05-31 | E-GEOD-9867 | biostudies-arrayexpress
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