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TranscriptomicsApplication of a clinical assay for staging and prognosis of prostate cancer diagnosed in needle core biopsy specimens
Molecular and genomic analysis of microscopic quantities of tumor from formalin-fixed and paraffin-embedded (FFPE) biopsies has many unique challenges. Here we evaluated the feasibility of obtaining transcriptome-wide RNA expression to measure prognostic classifiers from diagnostic prostate needle c...
ORGANISM(S): Homo sapiens 
2016-03-09 | E-GEOD-72220 | biostudies-arrayexpress
TranscriptomicsExpression data from paired matched breast cancer Fine needle aspiration (FNA) or Core needle biopsies (CBX)
Paired FNA and CBX specimens were prospectively collected from 37 breast cancers before any systemic therapy during a biomarker discovery study at The University of Texas M. D. Anderson Cancer Center. We identified 293 probe sets overexpressed in core biopsies; these included five highly coexpresse...
ORGANISM(S): Homo sapiens 
2011-10-31 | E-GEOD-32518 | biostudies-arrayexpress
TranscriptomicsThe effects of timing of fine needle aspiration biopsies on gene expression profiles in breast cancers
Paired fine needle aspiration biopsies (FNABs) of breast cancers were taken before (PRE) and after (POST) surgeries from 16 patients and compared the cDNA microarray data to determine the genes that were differentially expressed between the FNABs taken at the two time points. The timing of fine need...
ORGANISM(S): Homo sapiens 
2008-09-09 | E-GEOD-12072 | biostudies-arrayexpress
GenomicsA carrier-assisted ChIP-seq method for Estrogen Receptor-chromatin interactions from breast cancer core needle biopsy samples
The Estrogen Receptor alpha (ERa) is the key transcriptional regulator in luminal breast cancer and the main target for adjuvant treatment. Luminal gene signatures are dictated by the transcriptional capacities of ERa, which are a direct consequence of the receptors binding preference at specific si...
ORGANISM(S): Homo sapiens 
2013-04-01 | E-MTAB-1534 | biostudies-arrayexpress
ProteomicsA non-hazardous deparaffinization protocol enables quantita-tive proteomics of core needle biopsy-sized formalin-fixed and paraffin embedded (FFPE) tissue specimens.
Most human tumor tissues that are obtained for pathology and diagnostic purposes are forma-lin-fixed and paraffin embedded (FFPE). To perform quantitative proteomics of FFPE samples, paraffin has to be removed and formalin-induced crosslinks have to be reversed prior to prote-olytic digestion. A c...
ORGANISM(S): Homo sapiens (Human) 
2022-05-19 | PXD031946 | Pride
Clinical proteomics  tumor tissues  ffpe  quantitative proteomics  core needle biopsy  cancer research  molecular pathology  breast ductal carcinoma  in-situ cancer 
TranscriptomicsNormal vs. Tumor Prostate miRNA
Comparison of miRNA expression profiles in a small set of prostate needle core biopsies or fine needle aspirates. Keywords: Expression profiling of prostate needle core biopsies MicroRNA expression was compared between a pooled normal sample consisting of 10 separate normal adjacent to tumor prost...
ORGANISM(S): Homo sapiens 
2010-06-11 | E-GEOD-4574 | biostudies-arrayexpress
UnknownA retrospective comparative study on the diagnostic efficacy and the complications: between CassiII rotational core biopsy and core needle biopsy.
Not available
S-EPMC10562690 | biostudies-literature
ProteomicsInvestigative needle core biopsies support multimodal deep-data generation in glioblastoma
Glioblastoma (GBM) is a primary brain cancer with an abysmal prognosis with few effective therapies. The ability to investigate the tumor microenvironment before and during treatment would greatly enhance both our understanding of disease response and progression, as well as the delivery and impact ...
ORGANISM(S): Homo sapiens (Human) 
2025-05-06 | PXD046857 | Pride
Stereotactic biopsy Multi-omics Single cell sequencing Metabolomics Sampling variance Glioblastoma Immunopeptidomics Spatial 
GenomicsA carrier-assisted ChIP-seq method for Estrogen Receptor-chromatin interactions from breast cancer core needle biopsy samples
A carrier-assisted ChIP-seq method for Estrogen Receptor-chromatin interactions from breast cancer core needle biopsy samples
PRJEB1564 | ENA
ProteomicsPhosphoproteomics scaled-down to tumor biopsy level. Part 2: biopsies
Mass spectrometry-based phosphoproteomics of tumor tissue or cell line lysates provides insight in aberrantly activated signaling pathways and potential drug targets. For improved understanding of the individual patient’s tumor biology, analysis of the phosphoproteome should be feasible and reproduc...
ORGANISM(S): Homo sapiens (Human) 
2019-10-28 | PXD003814 | Pride
Human Biopsy Single-shot Ptyr Crc Label-free Phosphoproteomics Colorectal cancer 
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