Published Dataset Availability

From MGED Wiki

[edit] Facilitating Data Deposition

The MGED Society mission includes facilitating deposition of functional genomics datasets (e.g. microarray studies) in public archives. In addition to addressing what and how data gets deposited, we are very much concerned with seeing that authors adhere to journal requirements for data deposition. Unfortunately, the requirement for data deposition is not being sufficiently met and important datasets are not accessible (see for example Ochsner et al Nature Methods 2008).

Therefore, we ask that investigators seeking microarray and UHTS functional genomics datasets from studies published in journals requiring deposition contact us if they are unable to get them. We will then contact the authors on your behalf and inform the journal where the study was published. We will document the results on the MGED web site to assist others seeking the same dataset and to aid reviewers of related publications and grants.

We hope that you will help us in our mission.

[edit] Missing Data

Citation	Authors	When the request was submitted	Any responses from the journal or authors
Use of Gene Expression Profiles of Peripheral Blood Lymphocytes to Distinguish BRCA1 Mutation Carriers in High Risk Breast Cancer Families. Cancer Inform 2009, 7:41-56.	Vuillaume ML, Uhrhammer N, Vidal V, Vidal VS, Chabaud V, Jesson B, Kwiatkowski F, Bignon YJ	13th Oct 2009	Corresponding author was emailed Oct. 16, 2009 - no response. Publisher and Editorial Board members were contacted Oct. 29, 2009 - discussion started Nov. 19, 2009 about policy. Policy requiring microarray deposition posted Jan. 22, 2010.
Gene expression analysis in a canine model of X-linked Alport syndrome. Mamm Genome. 2006 Sep;17(9):976-90. (Pubmed ID 16964446)	Greer KA, Higgins MA, Cox ML, Ryan TP, Berridge BR, Kashtan CE, Lees GE, Murphy KE.	15th Jan 2010	Corresponding author was emailed Jan. 20, 2010 - no response. Journal was contacted March 1, 2010. Managing editor responded March 9, 2010 requesting wording for policy.
Single-Cell Expression Profiling of Dopaminergic Neurons Combined with Association Analysis Identifies Pyridoxal Kinase as Parkinson’s Disease Gene. Ann Neurol. 2009 Dec;66(6):792-8.	Elstner M, Morris CM, Heim K, Lichtner P, Bender A, Mehta D, Schulte C, Sharma M, Hudson G, Goldwurm S, Giovanetti A, Zeviani M, Burn DJ, McKeith IG, Perry RH, Jaros E, Krüger R, Wichmann HE, Schreiber S, Campbell H, Wilson JF, Wright AF, Dunlop M, Pistis G, Toniolo D, Chinnery PF, Gasser T, Klopstock T, Meitinger T, Prokisch H, Turnbull DM	15th Jan 2010	Corresponding author was emailed Jan. 20, 2010 - Responded Jan 22 that data was still being analyzed for a future publication. Journal was contacted Feb 13. Managing editor responded and requested wording for policy and also contacted authors. Policy requiring microarray deposition adopted Feb. 26, 2010.