Glycogene CRISPR Library Viewer


Usage Instructions:

If you use this resource, please cite: Y. Zhu, T. Groth, A. Kelkar, Y. Zhou, S. Neelamegham “A GlycoGene CRISPR-Cas9 lentiviral library to study lectin binding and human glycan biosynthesis pathways”, Glycobiology, 2020 (in press) [.pdf].
All plasmids will be available from Addgene. If you need reagents urgently, please write to neel@buffalo.edu.

This app allows users to browse sgRNA and associated data collected using the Glycogene CRISPR sgRNA library. To use:

  • "Select Glycogene:" using drop-down menu
  • “Select Gene Transcript:” as many genes have more than one protein-coding transcript variant.

Information about sgRNA targeting the selected genes, location on transcript and experimental data regarding sgRNA enrichment/depletion will appear in table format.

To determine glycogene transcripts appearing in selected, common cancer cell lines:

  • Select tissue type
  • Select cell line

Data shown is rendered as heat maps using RSEM (RNA-seq by Expectation Maximization) collected from the Cancer Cell Line Encyclopedia (CCLE) (ref 3). An RSEM value of 1 corresponds to the top 20% of RSEM values in the CCLE for the selected NCI60 cell lines. Thus, RSEM values > 1 are considered to be highly expressed.

References:

  1. Y. Zhu, et al. Glycobiology, 2020 (in press) [link]
  2. Li, W. et al. Genome Biol 15, 554 (2014).
  3. [link]
  4. Barretina, J. et al. Nature 483, 603–607 (2012).
  5. [link]

sgRNA Sequence and Location Table

Gene Rank & False Discover Rate

sgRNA Log2 Fold Change Upon Lectin Enrichment

Selected CCLE Transcript RSEM Data