August 15, 2016

Dear lincscloud.org user,

We are glad to inform you that, thanks to funding and support from the NIH, all LINCS L1000 datasets will be accessible from the NCBI Gene Expression Omnibus (GEO) in September 2016.
This mode of access is expected to have several advantages to users, including download mechanisms that are consistent with the rich set of data already accessible in GEO, standardized metadata that conforms to prevailing guidelines (e.g MIAME), and a growing set of NCBI tools for users to query and download experiments and curated gene expression profiles.
Already, the L1000 datasets deposited into GEO constitute the 2nd largest by size (See figure below).

Several technical barriers were overcome, and we thank the NIH and, in particular, the GEO curators who worked closely with the Broad Connectivity Map team to facilitate deposition of the massive LINCS L1000 dataset into GEO.
In order to focus our limited resources on the transition to GEO, our lincscloud.org site is now deprecated (though we will leave the query web app open for user-defined queries).
We appreciate your interest in our work and your patience as the data is transferred. Based on current progress we estimate the migration to be completed in September 2016.
As we transition the existing data to GEO and our project at the Broad continues to generate new profiles, this L1000 dataset will likely be the largest transcriptional compendium in the public domain. Please monitor GSE70138 for updates to the L1000 dataset.
Best,
Connectivity Map / LINCS team at the Broad Institute