Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

In situ synthesis of peptide microarrays - shadow mask design [3]

ABSTRACT: In this paper several computer programs were used to simulate in situ synthesis of peptides using shadow masks and BOC synthesis. The peptides were designed to be random, or pseudo-random, but fulfill requirements of immunosignaturing. This file contains data from actual 330,000 peptide arrays that used the first iteration of the peptide generation algorithm. Monoclonal antibodies were bound to the microarrays and the total number of peptides that distinguished each monoclonal was measured. This provides a baseline against which to compare purely random sequences. One replicate of each peptide was printed on 1 330k peptide microarray. One microarray were tested for each sample. Image was qualified using in-house metrics for quality assurance.

ORGANISM(S): Mus musculus

SUBMITTER: Phillip Stafford

PROVIDER: E-GEOD-50571 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

In situ synthesis of peptide microarrays - shadow mask design [1]

Project description:A computer program was used to create random amino acid sequences based on and restricted by physical shadow masks which will be used for lithography-based synthesis of peptides. The output from this algorithm was used to create peptides that were synthesized by Sigma Aldrich, and printed onto glass slides. The arrays contained 384 peptides printed in duplicate for each of 4 different mask designs. 52 different monoclonal antibodies were incubated on these microarrays and analyzed for their propensity to bind the peptides created from each mask set. The diversity of binding served as a proxy for the 'randomness' of these peptides, and provided information about how many masks are needed to truly generate random sequence peptides. two replicates of each peptide was printed on 1 Mask peptide microarray. A minimum of Two microarrays were tested for each sample. Image was qualified using in-house metrics for quality assurance.

2014-01-16 | E-GEOD-49217 | biostudies-arrayexpress

In situ synthesis of peptide microarrays - shadow mask design [2]

Project description:An experiment was designed to use a computer program to create lithography masks using a pseudo-random pattern generator. The data in this file are results from immunosignaturing 8 different monoclonals using a 10,000 peptide random-sequence microarray. Peptides were synthesized by Sigma Aldrich, and printed onto glass slides and used to test several different parameters. One replicate of each peptide was printed on 1 CIM_10K_v2 peptide microarray. One microarray were tested for each sample. Image was qualified using in-house metrics for quality assurance.

2014-01-16 | E-GEOD-50044 | biostudies-arrayexpress

An Immunosignature system for diagnosis of cancer [Cancer immunosignaturing - test 2]

Project description:This dataset contains peptide array information from 1516 patients from 12 different cancer types, 2 infectious diseases, and healthy controls using leave one out cross validation. This array is library 2 (GPL14921). A 1:500 dilution of human serum is added to a peptide array (GPL14921). This array is a one-up design, with 10286 peptides printed in duplicate on a standard glass microscope slide. 1516 patients samples from 14 different diseases and 1 control cohort were analyzed

2013-12-15 | E-GEOD-52581 | biostudies-arrayexpress

An Immunosignature system for diagnosis of cancer [Cancer immunosignaturing - test 1]

Project description:This dataset contains peptide array information from 120 patients from 5 different cancer types using classic blinded test/train method. This array is library 1 (GPL17600). A 1:500 dilution of human serum is added to a peptide array (GPL17600). This array is a two-up design, with 10420 peptides printed on the top and bottom of a standard glass microscope slide. Samples were run in duplicate. The average of the duplicates are listed here. 20 train and 20 blinded test samples were run.

2013-12-15 | E-GEOD-52580 | biostudies-arrayexpress

Immunosignatures can predict vaccine efficacy

Project description:Mice were immunized with either formalin fixed Influenza A/PR/8/34 (Killed PR8), the 2006-2007 seasonal influenza vaccine, the 2007-2008 seasonal influenza vaccine, a sublethal infection (live PR8) or mock immunized (PBS). Array data was used to distinguish the immunogens from each other and predict which of the three inactivated vaccines would be protective against A/PR/8/34 challenge. two replicates of each peptide was printed on 1 CIM_10kv3 peptide microarray. One microarray were tested for each sample. Image was qualified using in-house metrics for quality assurance.

2013-11-04 | E-GEOD-51623 | biostudies-arrayexpress

In situ synthesis of peptide microarrays - shadow mask design

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-01-16 | E-GEOD-50045 | biostudies-arrayexpress

In situ synthesis of peptide microarrays - shadow mask design [3]

Project description:In this paper several computer programs were used to simulate in situ synthesis of peptides using shadow masks and BOC synthesis. The peptides were designed to be random, or pseudo-random, but fulfill requirements of immunosignaturing. This file contains data from actual 330,000 peptide arrays that used the first iteration of the peptide generation algorithm. Monoclonal antibodies were bound to the microarrays and the total number of peptides that distinguished each monoclonal was measured. This provides a baseline against which to compare purely random sequences.

2014-01-16 | GSE50571 | GEO

An Immunosignature system for diagnosis of cancer

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-12-15 | E-GEOD-52582 | biostudies-arrayexpress

In situ synthesis of peptide microarrays - shadow mask design [1]

2014-01-16 | GSE49217 | GEO

In situ synthesis of peptide microarrays - shadow mask design [2]

2014-01-16 | GSE50044 | GEO