Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

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

PROVIDER: PRJNA701288 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13681168_1.fastq.gz	Fastqsanger.gz
	SRR13681168_2.fastq.gz	Fastqsanger.gz
	SRR13681169_1.fastq.gz	Fastqsanger.gz
	SRR13681169_2.fastq.gz	Fastqsanger.gz
	SRR15654687_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 16

Similar Datasets

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

Project description:Our results demonstrate the utility of our Biop-C method in investigating the 3D genome organization in solid cancers, and the importance of 3D genome organization in regulating oncogenes in nasopharyngeal cancer.

2021-09-03 | GSE166570 | GEO

METSIM Subcutaneous adipose needle biopsy RNA-seq

Project description:METSIM Subcutaneous adipose needle biopsy RNA-seq

| PRJNA1004679 | ENA

METSIM Subcutaneous adipose needle biopsy ATAC-seq

Project description:METSIM Subcutaneous adipose needle biopsy ATAC-seq

| PRJNA1004680 | ENA

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

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

| PRJEB1564 | ENA

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

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

Proteomic and Clinical Analysis of a Fine-needle Aspirate Biopsy from a Single Cold Thyroid Nodule: A Case Study

Project description:Purpose: To clinically and proteomically profile a fine-needle aspirate biopsy (FNAB) from a single in situ cold thyroid nodule (CTN). Experimental Design: The FNAB lysate was digested with trypsin, and analysed by LC-MSMS on an LTQ Orbitrap Velos. Remaining peptides were separated by reversed-phase chromatography and fractions analysed as technical duplicates. Identified proteins were analysed by Gene Ontology and protein abundance were calculated using the Top3 label-free method. The proteomic data was complemented with ultrasonography and scintigraphy of the thyroid gland; and cytology of the CTN FNAB. Results: Sixty seven and 2,595 non-redundant protein groups (2 unique peptides) were identified from unfractionated and fractionated CTN FNAB, respectively. Label-free protein abundance ranged over 6 orders of magnitude from the most abundant proteins, haemoglobin and thyroglobulin; to the low-abundance protein SON. Many previously-reported markers of thyroid cancer were in the top 23% of the identified proteins. GO analysis revealed high-enrichment for extracellular vesicular exosome and vesicle (cellular component); regulation of biological quality (biological processes); and structural molecule activity (molecular function). Conclusions and Clinical Significance: The CTN was clinically-classified as benign. Proteomic data from FNAB can provide additional diagnostic candidates indicative of benign or cancerous CTN without the need for invasive surgical intervention.

2017-10-26 | PXD001978 | Pride

TRANSCRIPTOMIC ANALYSIS ON ENDOSCOPIC ULTRASOUND FINE NEEDLE ASPIRATION MATERIALS FROM PRIMARY PANCREATIC ADENOCARCINOMA

Project description:The study aimed to compare the molecular profiles of metastatic, locally advanced, and resected primary pancreatic adenocarcinoma at the genomic and transcriptomic levels. DNA and mRNA were extracted from endoscopic ultrasound-guided fine needle aspiration-biopsy material of primary tumors from 397 patients, and they were subsequently analyzed by targeted deep sequencing and RNAseq.

2024-01-18 | GSE253260 | GEO

The effects of timing of fine needle aspiration biopsies on gene expression profiles in breast cancers

Project description: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 needle aspiration biopsies can be a confounding factor in microarray data analyses in breast cancer. FOS-related genes, which have been implicated in early hypoxia as well as the development of breast cancers, were differentially expressed before and after surgery. Therefore, it is important that future studies take timing of tissue acquisition into account. Keywords: Breast cancer, fine needle, biopsy timing, microarray standardization, early hypoxic genes

2008-09-09 | GSE12072 | GEO

Phosphoproteomics scaled-down to tumor biopsy level. Part 2: biopsies

Project description: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 reproducible using tumor needle biopsies. We hereto scaled down a pTyr-phosphopeptide enrichment protocol to biopsy-level protein input and show its performance using colorectal cancer (CRC) cell line and needle biopsies from patients. In this study, the feasibility of label-free pTyr-phosphoproteomics at the biopsy level is demonstrated. Unsupervised cluster analysis shows that this approach can identify patient-specific profiles, which will improve our understanding of individual tumor biology and may enable future pTyr-phosphoproteomics-based TKI treatment selection.

2019-10-28 | PXD003814 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data