LINCS L1000

• Table of Contents
• About
  • Selected Papers
• How to Access
  • Download Overview
  • File Listing
  • Issue Reporting
• How to Cite

"The LINCS L1000 project has collected gene expression profiles for thousands of perturbagens at a variety of time points, doses, and cell lines. A full list of the chemical and genetic perturbations used can be found on the CLUE website along with their descriptions."

See http://www.lincsproject.org/LINCS/tools/workflows/find-the-best-place-to-obtain-the-lincs-l1000-data for further detail.

"The NIH Common Fund’s Library of Integrated Network-based Cellular Signatures (LINCS) program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents."

"By using computational tools to integrate this diverse information into a comprehensive view of normal and disease states that can be applied for the development of new biomarkers and therapeutics. More information about the LINCS project is at http://lincsproject.org."

Excerpted from https://clue.io/lincs.

Selected Papers

• Location on Cheaha is $SHARE_PROJECT/bioitx/hosted-data/gov/nih/nlm/ncbi/ftp/geo/series.
  • GSE92742 is located at GSE92nnn/GSE92742.
  • GSE70138 is located at GSE70nnn/GSE70138.
  • GSE92743 is located at GSE92nnn/GSE92743.
• You must be a member of the bioitx Unix group to access these data.
• Data are read-only.
• SHA512 file checksums are available.
  • See GSE92nnn/GSE92742/suppl/GSE92742_SHA512SUMS.txt.gz.

Download Overview

• Download Date: Oct 9, 2017
• Total size: 1.4 TB

File Listing

"All LINCS funded L1000 data, which is used to populate the Connectivity Map (CMap) dataset, are deposited into the NCBI Gene Expression Omnibus":

• LINCS Phase I Data: GEO GSE92742.
• LINCS Phase II Data: GEO GSE70138.
• CMap-HBS-LINCS Contest Data: GEO GSE92743.

Excerpted from https://clue.io/lincs.

Issue Reporting

Relevant tracked issues on UAB GitLab (blazerid access required):

• https://gitlab.rc.uab.edu/jelaiw/infrastructure-development/issues/24
• https://gitlab.rc.uab.edu/jelaiw/infrastructure-development/issues/25

The NIH Common Fund’s Library of Integrated Network-based Cellular Signatures (LINCS) program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. All LINCS funded L1000 data, which is used to populate the Connectivity Map (CMap) dataset, are deposited into the NCBI Gene Expression Omnibus.

The data used for the analyses described in this manuscript were obtained from the NCBI GEO FTP server on 10/09/2017 and staged to dedicated shared storage at UAB in order to better facilitate researcher access to important public data. These hosted data are documented and supported in part by the Informatics Institute uab-bioitx team and infrastructure.