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A carrier-assisted ChIP-seq method for Estrogen Receptor-chromatin interactions from breast cancer core needle biopsy samples

ABSTRACT: A carrier-assisted ChIP-seq method for Estrogen Receptor-chromatin interactions from breast cancer core needle biopsy samples

PROVIDER: PRJEB1564 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR235698.fastq.gz	Fastqsanger.gz
	ERR235699.fastq.gz	Fastqsanger.gz
	ERR235700.fastq.gz	Fastqsanger.gz
	ERR235701.fastq.gz	Fastqsanger.gz
	ERR235702.fastq.gz	Fastqsanger.gz

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A carrier-assisted ChIP-seq method for Estrogen Receptor-chromatin interactions from breast cancer core needle biopsy samples

Project description: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 sites on the chromatin. The identification of ERa binding signatures on a genome-wide level has greatly enhanced our understanding of Estrogen Receptor biology in cell lines, but the technique has its limitations with respect its applicability in limit amounts of tumor tissue. Here, we present a refinement of the ChIP-seq procedures to enable transcription factor mapping on limited amounts of tissue culture cells and illustrate the applicability of this refined technology by mapping the ERa genome-wide chromatin binding landscape in core needle biopsy material from primary breast tumors.

2013-04-01 | E-MTAB-1534 | biostudies-arrayexpress

METSIM Subcutaneous adipose needle biopsy RNA-seq

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A carrier-assisted ChIP-seq method for estrogen receptor-chromatin interactions from breast cancer core needle biopsy samples.

Project description:BACKGROUND:The Estrogen Receptor alpha (ER?) is the key transcriptional regulator in luminal breast cancer and is therefore the main target for adjuvant treatment of this subtype. Luminal gene signatures are dictated by the transcriptional capacities of ER?, which are a direct consequence of the receptors binding preference at specific sites on the chromatin. The identification of ER? binding signatures on a genome-wide level has greatly enhanced our understanding of Estrogen Receptor biology in cell lines and tumours, but the technique has its limitations with respect to its applicability in limited amounts of tumour tissue. RESULTS:Here, we present a refinement of the ChIP-seq procedures to enable transcription factor mapping on limited amounts of tissue culture cells as well as from a limited amount of tumor tissue derived from core needle biopsies. Our approach uses a carrier that can be removed prior to DNA amplification and sequencing. CONCLUSION:We illustrate the applicability of this refined technology by mapping the ER? genome-wide chromatin binding landscape in core needle biopsy material from primary breast tumours. With this, our refined technology permits for a high-resolution transcription factor mapping even from clinical samples.

| S-EPMC3637562 | biostudies-literature

Application of a clinical assay for staging and prognosis of prostate cancer diagnosed in needle core biopsy specimens

Project description: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 core biopsies. 158 samples from diagnostic needle core biopsies (Bx) and radical prostatectomies (RP) were collected from 33 patients at three hospitals, each patient provided up to 6 tumor and benign samples. Genome-wide transcriptomic profiles were generated using Affymetrix Human Exon arrays for comparison of gene expression alterations and prognostic signatures between the Bx and RP samples. For 23 patients from UCSF and CSMC, six prostate tissue samples were obtained from each patient: tumor biopsy, tumor RP, benign adjacent biopsy, benign adjacent RP, and benign contralateral biopsy, and benign contralateral RP. For the 10 UHN patients only tumor biopsy and tumor RP samples were obtained. A total of 147 samples passed RNA, cDNA, and microarray quality control.

2016-03-09 | E-GEOD-72220 | biostudies-arrayexpress

Biop-C: A Method for Chromatin Interactome Analysis of Solid Cancer Needle Biopsy Samples

Project description:Biop-C: A Method for Chromatin Interactome Analysis of Solid Cancer Needle Biopsy Samples

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Application of a clinical assay for staging and prognosis of prostate cancer diagnosed in needle core biopsy specimens

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Expression data from paired matched breast cancer Fine needle aspiration (FNA) or Core needle biopsies (CBX)

Project description: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 coexpressed gene clusters (metagenes) corresponding to immune functions and extracellular matrix components. We compared gene expression profiles of pairs of fine-needle (stroma-poor) and core-needle (stroma-rich) biopsies from 37 cancers to identify stroma-associated genes

2011-10-31 | GSE32518 | GEO

Carrier Subclass

Project description:Carrier Subclass

| PRJNA1031099 | ENA

Expression data from paired matched breast cancer Fine needle aspiration (FNA) or Core needle biopsies (CBX)

2011-10-31 | E-GEOD-32518 | biostudies-arrayexpress