The Experts below are selected from a list of 6357 Experts worldwide ranked by ideXlab platform

Jaebum Choo - One of the best experts on this subject based on the ideXlab platform.

  • sers based multiple biomarker detection using a gold patterned Microarray Chip
    Journal of Molecular Structure, 2012
    Co-Authors: Inamurrehman Junejo, Soo-ik Chang, Jaebum Choo
    Abstract:

    We report a highly sensitive surface-enhanced Raman scattering (SERS)-based immunoassay platform for the multiplex detection of biomarkers. For this purpose, a gold-patterned Microarray Chip has been fabricated and used as a SERS detection template. Here, a typical sandwich immunocomplex protocol was adopted. Monoclonal antibodies were immobilized on gold patterned substrates, and then antigen solutions and polyclonal antibody-conjugated hollow gold nanospheres (HGNs) were sequentially added for the formation of sandwich immunocomplexes. Antigen biomarkers can be quantitatively assayed by monitoring the intensity change of a characteristic SERS peak of a reporter molecule adsorbed on the surfaces of HGNs. Under optimized assay conditions, the limits of detections (LODs) were determined to be 10 fg/mL for human IgG and 10–100 fg/mL for rabbit IgG. In addition, the SERS-based immunoassay technique can be applied in a wider dynamic concentration range with a good sensitivity compared to ELISA. The proposed method fulfills the current needs of high sensitivity and selectivity which are essential for the clinical diagnosis of a disease.

  • fabrication of a hydrophobic hydrophilic hybrid patterned Microarray Chip and its application to a cancer marker immunoassay
    Biochip Journal, 2012
    Co-Authors: Jin-goo Park, Min-yi Park, Soo-ik Chang, Jaebum Choo
    Abstract:

    In this work, we report on a simple process for fabricating a hydrophobic/hydrophilic hybrid-patterned Microarray Chip for a fast and sensitive immunoassay. Two different types of self-assembled monolayers (SAMs) were used in the fabrication of hydrophilic well patterns and hydrophobic substrates. The hydrophilic/hydrophobic hybrid SAM pattern generates a clear-cut boundary between the sample and the background. A change in the precursor molecules allows for many different types of SAMs to be employed in the fabrication process. Fluorescence image-based detection has previously been used for the quantitative immune-analysis of a specific cancer marker. Here, a titanium-coated glass substrate was utilized to suppress auto-fluorescence signals from substrate backgrounds. Angiogenin (ANG), a small polypeptide implicated in both angiogenesis and tumor growth, was used as a target cancer marker for its validation. Assay results demonstrate that the hybrid-patterned array Chip yields a narrower error deviation and a lower coefficient variation than in a conventional 96-well plate ELISA. Furthermore, the sample requirement (1 μL) for the hybrid-patterned Chip is about 50 times less than that required in an ELISA (at least 50 μL). The proposed hydrophobic/hydrophilic hybrid-patterned Microarray Chip is expected to be a highly efficient tool that can be applied to a high throughput immunoassay of a specific cancer marker.

  • Fabrication of a hydrophobic/hydrophilic hybrid-patterned Microarray Chip and its application to a cancer marker immunoassay
    BioChip Journal, 2012
    Co-Authors: Jin-goo Park, Min-yi Park, Soo-ik Chang, Jaebum Choo
    Abstract:

    In this work, we report on a simple process for fabricating a hydrophobic/hydrophilic hybrid-patterned Microarray Chip for a fast and sensitive immunoassay. Two different types of self-assembled monolayers (SAMs) were used in the fabrication of hydrophilic well patterns and hydrophobic substrates. The hydrophilic/hydrophobic hybrid SAM pattern generates a clear-cut boundary between the sample and the background. A change in the precursor molecules allows for many different types of SAMs to be employed in the fabrication process. Fluorescence image-based detection has previously been used for the quantitative immune-analysis of a specific cancer marker. Here, a titanium-coated glass substrate was utilized to suppress auto-fluorescence signals from substrate backgrounds. Angiogenin (ANG), a small polypeptide implicated in both angiogenesis and tumor growth, was used as a target cancer marker for its validation. Assay results demonstrate that the hybrid-patterned array Chip yields a narrower error deviation and a lower coefficient variation than in a conventional 96-well plate ELISA. Furthermore, the sample requirement (1 μL) for the hybrid-patterned Chip is about 50 times less than that required in an ELISA (at least 50 μL). The proposed hydrophobic/hydrophilic hybrid-patterned Microarray Chip is expected to be a highly efficient tool that can be applied to a high throughput immunoassay of a specific cancer marker.

  • highly reproducible immunoassay of cancer markers on a gold patterned Microarray Chip using surface enhanced raman scattering imaging
    Biosensors and Bioelectronics, 2011
    Co-Authors: Gi Hun Seong, Soo-ik Chang, Chil Hwan Oh, Jaebum Choo
    Abstract:

    Abstract This paper reports a highly reproducible immunoassay of cancer markers using surface-enhanced Raman scattering (SERS) imaging. SERS is a highly sensitive detection method but it is limited in its ability to achieve reproducible signal enhancement because of the difficulty with precisely controlling the uniform distribution of hot junctions. Consequently, inconsistent enhancement prevents the wide exploitation of SERS detection as a bio-detection tool for quantitative analysis. To resolve this problem, we explored the use of a SERS imaging-based immunoassay. For this purpose, Raman reporter-labeled hollow gold nanospheres (HGNs), were manufactured and antibodies were immobilized onto their surfaces for targeting specific antigens. After the formation of sandwich immunocomplexes using these functional HGNs on the surfaces of gold patterned wells, the SERS mapping images were measured. For target protein markers, 12 × 9 pixels were imaged using a Raman mapping technique in the 0–10−4 g/mL concentration range, and the SERS signals for 66 pixels were averaged. Here, the SERS imaging-based assay shows much better correlations between concentration and intensity than does the conventional point-based assay. The limits of detection were determined to be 0.1 pg/mL and 1.0 pg/mL for angiogenin (ANG) and alpha-fetoprotein (AFP), respectively. This detection sensitivity is increased by three or four orders of magnitude over that of conventional ELISA method. The detectable dynamic range for SERS imaging (10−4–10−12 g/mL) is also much wider than that for ELISA (10−6–10−9 g/mL).

André Delâge - One of the best experts on this subject based on the ideXlab platform.

  • photonic wire biosensor Microarray Chip and instrumentation with application to serotyping of escherichia coli isolates
    Optics Express, 2013
    Co-Authors: Siegfried Janz, M Vachon, N Sabourin, H Mcintosh, J.h. Schmid, D.-x. Xu, Pavel Cheben, H. Ding, Shurui Wang, André Delâge
    Abstract:

    A complete photonic wire molecular biosensor Microarray Chip architecture and supporting instrumentation is described. Chip layouts with 16 and 128 independent sensors have been fabricated and tested, where each sensor can provide an independent molecular binding curve. Each sensor is 50 μm in diameter, and consists of a millimeter long silicon photonic wire waveguide folded into a spiral ring resonator. An array of 128 sensors occupies a 2 × 2 mm2 area on a 6 × 9 mm2 Chip. Microfluidic sample delivery channels are fabricated monolithically on the Chip. The size and layout of the sensor array is fully compatible with commercial spotting tools designed to independently functionalize fluorescence based bioChips. The sensor Chips are interrogated using an instrument that delivers sample fluid to the Chip and is capable of acquiring up to 128 optical sensor outputs simultaneously and in real time. Coupling light from the sensor Chip is accomplished through arrays of sub-wavelength surface grating couplers, and the signals are collected by a fixed two-dimensional detector array. The Chip and instrument are designed so that connection of the fluid delivery system and optical alignment are automated, and can be completed in a few seconds with no active user input. This Microarray system is used to demonstrate a multiplexed assay for serotyping E. coli bacteria using serospecific polyclonal antibody probe molecules.

  • Photonic wire biosensor Microarray Chip and instrumentation with application to serotyping of Escherichia coliisolates.
    Optics express, 2013
    Co-Authors: Siegfried Janz, M Vachon, N Sabourin, H Mcintosh, Shijing Wang, J.h. Schmid, D.-x. Xu, Pavel Cheben, H. Ding, André Delâge
    Abstract:

    A complete photonic wire molecular biosensor Microarray Chip architecture and supporting instrumentation is described. Chip layouts with 16 and 128 independent sensors have been fabricated and tested, where each sensor can provide an independent molecular binding curve. Each sensor is 50 μm in diameter, and consists of a millimeter long silicon photonic wire waveguide folded into a spiral ring resonator. An array of 128 sensors occupies a 2 2 mm2 area on a 6 9 mm2 Chip. Microfluidic sample delivery channels are fabricated monolithically on the Chip. The size and layout of the sensor array is fully compatible with commercial spotting tools designed to independently functionalize fluorescence based bioChips. The sensor Chips are interrogated using an instrument that delivers sample fluid to the Chip and is capable of acquiring up to 128 optical sensor outputs simultaneously and in real time. Coupling light from the sensor Chip is accomplished through arrays of sub-wavelength surface grating couplers, and the signals are collected by a fixed two-dimensional detector array. The Chip and instrument are designed so that connection of the fluid delivery system and optical alignment are automated, and can be completed in a few seconds with no active user input. This Microarray system is used to demonstrate a multiplexed assay for serotyping E. coli bacteria using serospecific polyclonal antibody probe molecules.

Soo-ik Chang - One of the best experts on this subject based on the ideXlab platform.

  • sers based multiple biomarker detection using a gold patterned Microarray Chip
    Journal of Molecular Structure, 2012
    Co-Authors: Inamurrehman Junejo, Soo-ik Chang, Jaebum Choo
    Abstract:

    We report a highly sensitive surface-enhanced Raman scattering (SERS)-based immunoassay platform for the multiplex detection of biomarkers. For this purpose, a gold-patterned Microarray Chip has been fabricated and used as a SERS detection template. Here, a typical sandwich immunocomplex protocol was adopted. Monoclonal antibodies were immobilized on gold patterned substrates, and then antigen solutions and polyclonal antibody-conjugated hollow gold nanospheres (HGNs) were sequentially added for the formation of sandwich immunocomplexes. Antigen biomarkers can be quantitatively assayed by monitoring the intensity change of a characteristic SERS peak of a reporter molecule adsorbed on the surfaces of HGNs. Under optimized assay conditions, the limits of detections (LODs) were determined to be 10 fg/mL for human IgG and 10–100 fg/mL for rabbit IgG. In addition, the SERS-based immunoassay technique can be applied in a wider dynamic concentration range with a good sensitivity compared to ELISA. The proposed method fulfills the current needs of high sensitivity and selectivity which are essential for the clinical diagnosis of a disease.

  • fabrication of a hydrophobic hydrophilic hybrid patterned Microarray Chip and its application to a cancer marker immunoassay
    Biochip Journal, 2012
    Co-Authors: Jin-goo Park, Min-yi Park, Soo-ik Chang, Jaebum Choo
    Abstract:

    In this work, we report on a simple process for fabricating a hydrophobic/hydrophilic hybrid-patterned Microarray Chip for a fast and sensitive immunoassay. Two different types of self-assembled monolayers (SAMs) were used in the fabrication of hydrophilic well patterns and hydrophobic substrates. The hydrophilic/hydrophobic hybrid SAM pattern generates a clear-cut boundary between the sample and the background. A change in the precursor molecules allows for many different types of SAMs to be employed in the fabrication process. Fluorescence image-based detection has previously been used for the quantitative immune-analysis of a specific cancer marker. Here, a titanium-coated glass substrate was utilized to suppress auto-fluorescence signals from substrate backgrounds. Angiogenin (ANG), a small polypeptide implicated in both angiogenesis and tumor growth, was used as a target cancer marker for its validation. Assay results demonstrate that the hybrid-patterned array Chip yields a narrower error deviation and a lower coefficient variation than in a conventional 96-well plate ELISA. Furthermore, the sample requirement (1 μL) for the hybrid-patterned Chip is about 50 times less than that required in an ELISA (at least 50 μL). The proposed hydrophobic/hydrophilic hybrid-patterned Microarray Chip is expected to be a highly efficient tool that can be applied to a high throughput immunoassay of a specific cancer marker.

  • Fabrication of a hydrophobic/hydrophilic hybrid-patterned Microarray Chip and its application to a cancer marker immunoassay
    BioChip Journal, 2012
    Co-Authors: Jin-goo Park, Min-yi Park, Soo-ik Chang, Jaebum Choo
    Abstract:

    In this work, we report on a simple process for fabricating a hydrophobic/hydrophilic hybrid-patterned Microarray Chip for a fast and sensitive immunoassay. Two different types of self-assembled monolayers (SAMs) were used in the fabrication of hydrophilic well patterns and hydrophobic substrates. The hydrophilic/hydrophobic hybrid SAM pattern generates a clear-cut boundary between the sample and the background. A change in the precursor molecules allows for many different types of SAMs to be employed in the fabrication process. Fluorescence image-based detection has previously been used for the quantitative immune-analysis of a specific cancer marker. Here, a titanium-coated glass substrate was utilized to suppress auto-fluorescence signals from substrate backgrounds. Angiogenin (ANG), a small polypeptide implicated in both angiogenesis and tumor growth, was used as a target cancer marker for its validation. Assay results demonstrate that the hybrid-patterned array Chip yields a narrower error deviation and a lower coefficient variation than in a conventional 96-well plate ELISA. Furthermore, the sample requirement (1 μL) for the hybrid-patterned Chip is about 50 times less than that required in an ELISA (at least 50 μL). The proposed hydrophobic/hydrophilic hybrid-patterned Microarray Chip is expected to be a highly efficient tool that can be applied to a high throughput immunoassay of a specific cancer marker.

  • highly reproducible immunoassay of cancer markers on a gold patterned Microarray Chip using surface enhanced raman scattering imaging
    Biosensors and Bioelectronics, 2011
    Co-Authors: Gi Hun Seong, Soo-ik Chang, Chil Hwan Oh, Jaebum Choo
    Abstract:

    Abstract This paper reports a highly reproducible immunoassay of cancer markers using surface-enhanced Raman scattering (SERS) imaging. SERS is a highly sensitive detection method but it is limited in its ability to achieve reproducible signal enhancement because of the difficulty with precisely controlling the uniform distribution of hot junctions. Consequently, inconsistent enhancement prevents the wide exploitation of SERS detection as a bio-detection tool for quantitative analysis. To resolve this problem, we explored the use of a SERS imaging-based immunoassay. For this purpose, Raman reporter-labeled hollow gold nanospheres (HGNs), were manufactured and antibodies were immobilized onto their surfaces for targeting specific antigens. After the formation of sandwich immunocomplexes using these functional HGNs on the surfaces of gold patterned wells, the SERS mapping images were measured. For target protein markers, 12 × 9 pixels were imaged using a Raman mapping technique in the 0–10−4 g/mL concentration range, and the SERS signals for 66 pixels were averaged. Here, the SERS imaging-based assay shows much better correlations between concentration and intensity than does the conventional point-based assay. The limits of detection were determined to be 0.1 pg/mL and 1.0 pg/mL for angiogenin (ANG) and alpha-fetoprotein (AFP), respectively. This detection sensitivity is increased by three or four orders of magnitude over that of conventional ELISA method. The detectable dynamic range for SERS imaging (10−4–10−12 g/mL) is also much wider than that for ELISA (10−6–10−9 g/mL).

  • high throughput screening of novel peptide inhibitors of an integrin receptor from the hexapeptide library by using a protein Microarray Chip
    Journal of Biomolecular Screening, 2004
    Co-Authors: Dongku Kang, Soo-ik Chang, Incheol Kang
    Abstract:

    3Protein Microarray is an emerging technology that makes high-throughput analysis possible for protein-protein interactions and analysis of proteome and biomarkers in parallel. The authors investigated the application of a novel protein Microarray Chip, ProteoChip, in new drug discovery. Integrin αvβ3 Microarray immobilized on the ProteoChip was employed to screen new active peptides against the integrin from multiple hexapeptide sublibraries of a positional scanning synthetic peptide combinatorial library (PS-SPCL). The integrin αvβ3-vitronectin interaction was successfully demonstrated on the integrin Microarray in a dose-dependent manner and was inhibited not only by the synthetic RGD peptide but also by various integrin antagonists on the integrin Microarray Chip. Novel peptide ligands with high affinity to the integrin were also identified from the peptide libraries with this Chip-based screening system by a competitive inhibition assay in a simultaneous and highthroughput fashion. The authors have confirmed antiangiogenic functions of the novel peptides thus screened through an in vitro and in vivo angiogenesis assay. These results provide evidence that the ProteoChip is a promising tool for highthroughput screening of lead molecules in new drug development. (Journal of Biomolecular Screening 2004:687-694)

Shouki Yatsushiro - One of the best experts on this subject based on the ideXlab platform.

  • Pseudo-Infected Red Blood Cell Beads as Positive Control for Cell Microarray Chip–Based Detection of Plasmodium-Infected RBCs
    Journal of Parasitology, 2018
    Co-Authors: Muneaki Hashimoto, Shouki Yatsushiro, Masahiko Numata, Masato Tanaka, Kazuaki Kajimoto, Masatoshi Kataoka
    Abstract:

    Abstract The cell Microarray Chip is a polystyrene plate with 20,944 microchambers, and it is used to detect red blood cells (RBCs) infected with the causative agent of malaria, Plasmodium. Plasmodium-infected red blood cells (iRBCs) stained with a nuclear staining dye (SYTO 21) form a monolayer on the bottom of the microchambers, and about 130 RBCs are accommodated in each such microchamber of the Chip. The iRBCs in the RBC monolayer (containing 2.7 million RBCs) can be identified using a fluorescence detector, and the infection rate can be calculated by counting the number of fluorescent-positive RBCs. This diagnostic device is highly sensitive and hence advantageous for early diagnosis of malaria infections in endemic areas. However, a standard positive control for Plasmodium-infected RBCs is required to ensure that the reagents and detectors of these cell Microarray Chips are working efficiently in remote endemic areas. Here, we introduce “pseudo-iRBC beads,” which consist of a mixture of DEA beads mi...

  • prognostic impact of circulating tumor cell detected using a novel fluidic cell Microarray Chip system in patients with breast cancer
    EBioMedicine, 2016
    Co-Authors: Takeshi Sawada, Shohei Yamamura, Shouki Yatsushiro, Jungo Araki, Toshinari Yamashita, Manami Masubuchi, Tsuneko Chiyoda, Mayu Yunokawa, Kumiko Hoshi, Masatoshi Kataoka
    Abstract:

    Various types of circulating tumor cell (CTC) detection systems have recently been developed that show a high CTC detection rate. However, it is a big challenge to find a system that can provide better prognostic value than CellSearch in head-to-head comparison. We have developed a novel semi-automated CTC enumeration system (fluidic cell Microarray Chip system, FCMC) that captures CTC independently of tumor-specific markers or physical properties. Here, we compared the CTC detection sensitivity and the prognostic value of FCMC with CellSearch in breast cancer patients. FCMC was validated in preclinical studies using spike-in samples and in blood samples from 20 healthy donors and 22 breast cancer patients in this study. Using spike-in samples, a statistically higher detection rate (p = 0.010) of MDA-MB-231 cells and an equivalent detection rate (p = 0.497) of MCF-7 cells were obtained with FCMC in comparison with CellSearch. The number of CTC detected in samples from patients that was above a threshold value as determined from healthy donors was evaluated. The CTC number detected using FCMC was significantly higher than that using CellSearch (p = 0.00037). CTC numbers obtained using either FCMC or CellSearch had prognostic value, as assessed by progression free survival. The hazard ratio between CTC + and CTC − was 4.229 in CellSearch (95% CI, 1.31 to 13.66; p = 0.01591); in contrast, it was 11.31 in FCMC (95% CI, 2.245 to 57.0; p = 0.000244). CTC detected using FCMC, like the CTC detected using CellSearch, have the potential to be a strong prognostic factor for cancer patients.

  • application of a cell Microarray Chip system for accurate highly sensitive and rapid diagnosis for malaria in uganda
    Scientific Reports, 2016
    Co-Authors: Shouki Yatsushiro, Shohei Yamamura, Takeki Yamamoto, Eriko Obana, Takahiro Nogami, Takuya Hayashi, Takashi Sesei, Joseph Okelloonen, Emmanuel I Odongoaginya, Mary Auma Alai
    Abstract:

    Application of a cell Microarray Chip system for accurate, highly sensitive, and rapid diagnosis for malaria in Uganda

  • abstract 500 prognostic impact of ctc detected using a novel fluidic cell Microarray Chip ctc detection system in patients with breast cancer
    Cancer Research, 2016
    Co-Authors: Takeshi Sawada, Shohei Yamamura, Shouki Yatsushiro, Jungo Araki, Toshinari Yamashita, Manami Masubuchi, Tsuneko Chiyoda, Mayu Yunokawa, Kumiko Hoshi, Masatoshi Kataoka
    Abstract:

    No current circulating tumor cell (CTC) enumeration system provides better prognostic value than CellSearch. We have developed a novel semi-automated CTC enumeration system (fluidic cell Microarray Chip system, FCMC) that captures CTC independently of tumor-specific markers or physical properties. This system was validated in preclinical studies and in blood samples from 20 healthy donors and 22 breast cancer patients in this study. Using spike-in samples, a statistically higher detection rate (p = 0.010) of MDA-MB-231 cells and an equivalent detection rate (p = 0.497) of MCF-7 cells were obtained with FCMC in comparison with CellSearch. The number of CTC detected in samples from patients that was above a threshold value as determined from healthy donors was evaluated. The CTC number detected using FCMC was significantly higher than that using CellSearch (p = 0.00037). CTC numbers obtained using either FCMC or CellSearch had prognostic value, as assessed by time-to-treatment-failure. The hazard ratio between CTC+ and CTC- was 4.043 in CellSearch (95% CI, 1.248 to 13.10; p = 0.01985); in contrast, it was 10.97 in FCMC (95% CI, 2.18 to 55.21; p = 0.003662). CTC detected using FCMC have the potential to be a better prognostic factor than CTC detected using CellSearch. Citation Format: Takeshi Sawada, Jungo Araki, Toshinari Yamashita, Manami Masubuchi, Tsuneko Chiyoda, Mayu Yunokawa, Kumiko Hoshi, Shoichi Tao, Shohei Yamamura, Shouki Yatsushiro, Kaori Abe, Masatoshi Kataoka, Tatsu Shimoyama, Yoshiharu Maeda, Katsumasa Kuroi, Kenji Tamura, Tsuneo Sawazumi, Hironobu Minami, Yoshihiko Suda, Fumiaki Koizumi. Prognostic impact of CTC detected using a novel fluidic cell Microarray Chip CTC detection system in patients with breast cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 500.

  • Development of a cell Microarray Chip for detection of circulating tumor cells
    Journal of Physics: Conference Series, 2012
    Co-Authors: Shouhei Yamamura, Shouki Yatsushiro, Yoshinobu Baba, Masatoshi Kataoka
    Abstract:

    Detection of circulating tumor cells (CTCs) in the peripheral blood of metastatic cancer patients has clinical significance in earlier diagnosis of metastases. In this study, a novel cell Microarray Chip for accurate and rapid detection of tumor cells from human leukocytes was developed. The Chip with 20,944 microchambers (105 μm diameter and 50 μm depth) was made from polystyrene, and the surface was rendered to hydrophilic by means of reactive-ion etching, which led to the formation of mono-layers of leukocytes on the microchambers. As the model of CTCs detection, we spiked human bronchioalveolar carcinoma (H1650) cells into human T lymphoblastoid leukemia (CEM) cells suspension and detected H1650 cells using the Chip. A CEM suspension contained with H1650 cells was dispersed on the Chip surface, followed by 10 min standing to allow the cells to settle down into the microchambers. About 30 CEM cells were accommodated in each microchamber, over 600,000 CEM cells in total being on a Chip. We could detect 1 H1650 cell per 106 CEM cells on the Microarray by staining with fluorescence-conjugated antibody (Anti-Cytokeratin) and cell membrane marker (DiD). Thus, this cell Microarray Chip has highly potential to be a novel tool of accurate and rapid detection of CTCs.

Peter J. Park - One of the best experts on this subject based on the ideXlab platform.

  • design and analysis of Chip seq experiments for dna binding proteins
    Nature Biotechnology, 2008
    Co-Authors: Peter J. Park, Peter V Kharchenko, Michael Y Tolstorukov
    Abstract:

    Recent progress in massively parallel sequencing platforms has enabled genome-wide characterization of DNA-associated proteins using the combination of chromatin immunoprecipitation and sequencing (Chip-seq). Although a variety of methods exist for analysis of the established alternative Chip Microarray (Chip-Chip), few approaches have been described for processing Chip-seq data. To fill this gap, we propose an analysis pipeline specifically designed to detect protein-binding positions with high accuracy. Using previously reported data sets for three transcription factors, we illustrate methods for improving tag alignment and correcting for background signals. We compare the sensitivity and spatial precision of three peak detection algorithms with published methods, demonstrating gains in spatial precision when an asymmetric distribution of tags on positive and negative strands is considered. We also analyze the relationship between the depth of sequencing and characteristics of the detected binding positions, and provide a method for estimating the sequencing depth necessary for a desired coverage of protein binding sites.