Optimization of experimental design parameters for high-throughput chromatin immunoprecipitation studies (Q36986698)

17 August 2017

Optimization of experimental design parameters for high-throughput chromatin immunoprecipitation studies (English)

1 reference

17 August 2017

Linda Z Penn

9

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Paul C. Boutros

object named as

Paul C Boutros

2

0 references

Igor Jurišica

8

object named as

Igor Jurisica

1 reference

17 August 2017

6

Fereshteh Khosravi

1 reference

17 August 2017

1

Romina Ponzielli

1 reference

17 August 2017

4

Angelina Stojanova

1 reference

17 August 2017

Sigal Katz

3

1 reference

17 August 2017

Adam P Hanley

5

1 reference

17 August 2017

Christina Bros

7

1 reference

17 August 2017

language of work or name

English

0 references

publication date

21 October 2008

1 reference

17 August 2017

Nucleic Acids Research

1 reference

17 August 2017

36

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17 August 2017

21

1 reference

17 August 2017

e144

1 reference

describes a project that uses

17 August 2017

limma

1 reference

22 June 2022

https://europepmc.org/article/PMC/2588500

inferred from PubMed Central ID database lookup

cites work

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets

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Identification of novel androgen response genes in prostate cancer cells by coupling chromatin immunoprecipitation and genomic microarray analysis

29 September 2017

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Elimination of laboratory ozone leads to a dramatic improvement in the reproducibility of microarray gene expression measurements

29 September 2017

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Comparison of sample preparation methods for ChIP-chip assays

29 September 2017

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Rat toxicogenomic study reveals analytical consistency across microarray platforms

29 September 2017

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New p63 targets in keratinocytes identified by a genome-wide approach.

29 September 2017

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Gene expression profiling in cervical cancer: an exploration of intratumor heterogeneity

29 September 2017

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Functional analysis of p53 binding under differential stresses

29 September 2017

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The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

29 September 2017

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Evaluation of external RNA controls for the assessment of microarray performance

29 September 2017

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Using RNA sample titrations to assess microarray platform performance and normalization techniques

29 September 2017

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Suz12 binds to silenced regions of the genome in a cell-type-specific manner

29 September 2017

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Linear models and empirical bayes methods for assessing differential expression in microarray experiments

29 September 2017

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Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome

29 September 2017

1 reference

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Evaluation of reference-based two-color methods for measurement of gene expression ratios using spotted cDNA microarrays.

29 September 2017

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Combinatorial analysis of transcription factor partners reveals recruitment of c-MYC to estrogen receptor-alpha responsive promoters.

29 September 2017

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Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1

29 September 2017

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CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome

29 September 2017

1 reference

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Standardizing global gene expression analysis between laboratories and across platforms.

29 September 2017

1 reference

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A robust method for the amplification of RNA in the sense orientation

29 September 2017

1 reference

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Sample size for detecting differentially expressed genes in microarray experiments.

29 September 2017

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Identification of MEF2-regulated genes during muscle differentiation

29 September 2017

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29 September 2017

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Silencing of human polycomb target genes is associated with methylation of histone H3 Lys 27.

29 September 2017

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High-throughput screening of chromatin immunoprecipitates using CpG-island microarrays

29 September 2017

1 reference

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Use of chromatin immunoprecipitation assays in genome-wide location analysis of mammalian transcription factors

29 September 2017

1 reference

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Probing chromatin immunoprecipitates with CpG-island microarrays to identify genomic sites occupied by DNA-binding proteins

29 September 2017

1 reference

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Effects of atmospheric ozone on microarray data quality

29 September 2017

1 reference

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An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets

29 September 2017

1 reference

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Statistical significance for genomewide studies

29 September 2017

1 reference

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A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells

29 September 2017

1 reference

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Microarray standard data set and figures of merit for comparing data processing methods and experiment designs

29 September 2017

1 reference

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Analysis of Myc bound loci identified by CpG island arrays shows that Max is essential for Myc-dependent repression

29 September 2017

1 reference

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Development and validation of a T7 based linear amplification for genomic DNA

29 September 2017

1 reference

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Genomic targets of the human c-Myc protein

29 September 2017

1 reference

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A large scale genetic analysis of c-Myc-regulated gene expression patterns

29 September 2017

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The UCSC Genome Browser Database

29 September 2017

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Transcriptional regulatory networks in Saccharomyces cerevisiae

29 September 2017

1 reference

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The Bioperl toolkit: Perl modules for the life sciences

29 September 2017

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Identifying genes regulated in a Myc-dependent manner

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2588500

How many replicates of arrays are required to detect gene expression changes in microarray experiments? A mixture model approach

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2588500

Gene expression changes in response to E2F1 activation.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2588500

GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp-chip analysis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2588500

Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2588500

Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2588500

DNA microarray analysis of genes involved in p53 mediated apoptosis: activation of Apaf-1.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2588500

Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2588500

Genome-wide location and function of DNA binding proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2588500

Identification of c-myc responsive genes using rat cDNA microarray.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2588500

BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2588500

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2588500

The HL60 cell line: a model system for studying human myeloid cell differentiation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2588500

Microarray analysis of the developing cortex.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2588500

Evaluation of DNA microarray results with quantitative gene expression platforms

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2588500

Characterizing dye bias in microarray experiments

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2588500

Effects of pooling mRNA in microarray class comparisons.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2588500

Statistical design of reverse dye microarrays

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2588500

Linear mRNA amplification from as little as 5 ng total RNA for global gene expression analysis

4 September 2018

1 reference

12 December 2020

Activated signal transduction kinases frequently occupy target genes

1 reference

12 December 2020

A tiling resolution DNA microarray with complete coverage of the human genome

1 reference

12 December 2020

Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKN735

1 reference

17 August 2017

1 reference

17 August 2017

1 reference