We are fully committed to transparency and reproducibility of genomics research.
We advocate literate programming, a technology that integrates the writing of prose and the execution of programming code within the same document. Literate programming promotes transparency and reproducibility in scientific research by improving documentation, collaborative interactions and code sharing upon publication.
For maximum transparency and reproducibility, we not only publish our raw data in GEO but also provide full access to our analyses in most of our recent publications:
Such extended access to data is available for:
Pascual, J., Jacobs, J., Sansores-Garcia, L., Natarajan, M., Zeitlinger, J., Aerts, S., Halder, G., and Hamaratoglu, F. (2017)
Hippo Reprograms the Transciptional Response to Ras Signaling.
Developmental Cell, 2017 September 25; 42(6): 667-680.e4. Data | PAPER
Shao, W., and Zeitlinger, J. (2017)
Paused RNA polymerase II inhibits new transcriptional initiation.
Nature Genetics, July:49(7): 1045-1051. Data | PAPER
Koenecke, N., Johnston, J., He, Q., Meier, S., and Zeitlinger, J. (2017)
Drosophila poised enhancers are generated during tissue patterning with the help of repression.
Genome Research, 2017 Jan; 27(1):64-74. Data | PAPER
Koenecke, N., Johnston, J., Gaertner, B., Natarajan, M. and Zeitlinger J. (2016)
Genome-wide identification of Drosophila dorso-ventral enhancers by differential histone acetylation analysis.
Genome Biology, 2016 Sep 27;17(1):196. Data | PAPER
He, Q, Johnston, J., Zeitlinger, J. (2015)
ChIP-nexus enables improved detection of in vivo transcription factor binding footprints.
Nature Biotechnology, 2015;33:395-401. Data | PAPER
Chen, K., Johnston, J., Shao, W., Meier, S., Staber, C., Zeitlinger, J. (2013)
A global change in RNA Polymerase II pausing during the Drosophila mid bastula transition.
eLife 2013;2:e00861 Data | PAPER
Gaertner, B.*, Johnston, J.*, Chen, K., Wallaschek, N., Paulson, A., Garruss, A.S., Gaudenz, K., De Kumar, B., Krumlauf, R., Zeitlinger, J. (2012)
Poised RNA Polymerase II changes over developmental time and prepares genes for future expression.
Cell Reports, 2(6), 1670-1683. PAPER | Data | Raw Sequencing Data at Geo
Original images from publications are available from the Stowers Original Data Repository (ODR)