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:
- We provide the analysis code via our GitHub account zeitlingerlab.
- We provide public Amazon Machine Images (AMI) running Linux, which contain all the raw data, processed data, analysis code and software tools necessary to reproduce the figures and tables published in a particular manuscript.
Such extended access to data is available for:
Avsec, Ž., Weilert, M., Shrikumar, A., Krueger, S. Alexandari, A., Dalal, K., Fropf, R., McAnany, C., Gagneur, J., Kundaje, A.*, Zeitlinger, J.* (2021) Base-resolution models of transcription factor binding reveal soft motif syntax. Nat Genet (epub ahead of print) * co-corresponding authors. Data | PAPER
Ramalingam, V., Natarajan, M., Johnson, J., Zeitlinger, J. (2021) TATA and paused promoters active in differentiated tissues have distinct expression characteristics. Mol Syst Biol. Feb 17; (2):e9866. Data | PAPER
Shao, W., G-M Alcantara, S., and Zeitlinger, J. (2019)
Reporter-ChIP-nexus reveals strong contribution of the Drosophila initiator sequence to RNA polymerase pausing.
eLife, April 25; 8. Data | PAPER
Shao, W., and Zeitlinger, J. (2017)
Paused RNA polymerase II inhibits new transcriptional initiation.
, July:49(7): 1045-1051. Data
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.
, 2017 Jan; 27(1):64-74. Data
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.
, 2016 Sep 27;17(1):196. Data
He, Q, Johnston, J., Zeitlinger, J. (2015)
ChIP-nexus enables improved detection of in vivo
transcription factor binding footprints.
, 2015;33:395-401. Data
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.
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.
, 2(6), 1670-1683. PAPER
| Data | Raw Sequencing Data at Geo
Original images from publications are available from the Stowers Original Data Repository (ODR)