Typically, the longest running validations are those of full-genome gene models, while the shortest running are array-based submissions (ChIP-chip or tiling arrays).
During our quality control procedure, we have identified duplicated content in GEO and ArrayExpress, affecting ∼14% of our data: fully or partially duplicated experiments from independent data submissions, Affymetrix chips reused in several experiments, or reused within an experiment.
We are actively retrofitting all ChIP submissions with the relevant QC metadata.
To date, we have encountered 23 different submission types, including: ChIP-seq and ChIP-chip investigations of TF or other binding sites, replication timing, histone modification and chromatin structure, gene annotation, 5′- and 3′-RACE, targeted RTPCR, and RNA tiling array and RNA-seq to identify transcription levels.
This is a side that may not pulverise teams into submission but will chip away and chip away, frustrating opponents to the extent where errors seem near inevitable.
We also describe design features for the next chip submission that are motivated by our technology evaluation.
We do not fully understand why our original results were erroneous with regard to TRIM33 occupancy in AML, but this may due to the use of a late-passage of AML cell lines for this experiment in the original submission, whereas the ChIP-seq and new ChIP-qPCR experiments was performed in early passage AML cultures.
The results achieved so far demonstrate the viability of the technology and suggest new design improvements implemented in the next prototype chips submission (APSEL2).
The first experiment contains submissions that are biological replicates of three ChIP-chip experiments to identify genome-wide localization of GCN5b over 36 900 identified protein binding sites were loaded into toxoMine as biological features.
This contribution describes the architecture and the main features of the final ALPIDE chip, planned for submission at the beginning of 2016.
The Reviewing editor and the reviewers discussed their comments before we reached this decision, and the Reviewing editor has assembled the following comments to help you prepare a revised submission. 1) Regarding the ChIP experiments, it would be useful to do some further analyses at higher resolution.
