Introduction to HumanRNAi B37 Land Content

From Array Suite Wiki

Jump to: navigation, search


Contents

HumanRNAi_B37

RNAi-based screens have emerged as a high-throughput method of screening gene dependency on developmental processes and cellular survival. Based on customer requests, OmicSoft has generated a framework to visualize results from these screens in our 2019 Land Release 1. In this first release, data from Project Achilles and Project DRIVE using a subset of cell lines from the Cancer Cell Line Encyclopedia (CCLE) for RNAi screening is available in the Land. By browsing the gene dependency data in this Land, users have a new opportunity to pre-screen cell lines or diseases to see if a gene/drug target would be a viable option for these types of diseases, or identify novel genes/drug targets likely to affect patient cohorts.

  • Note: This Land is a Beta release - we welcome customer feedback and will work to improve the usage and update the content and framework to support more projects and views.
Land Version Genome Build Gene Model
HumanRNAi_B37 Human.B37.3 OmicsoftGene20130723

Data Source

https://portals.broadinstitute.org/achilles/datasets/all https://data.mendeley.com/datasets/y3ds55n88r/4

Achilles - The current version of HumanRNAi_B37 land consists of data from Project Achilles from early 2018:

43 cell lines screened with GeCKO CRISPR-Cas9 library (Ach 3.3.8), and 391 cell lines screened with AVANA CRISPR-Cas9 library (avana_public_18Q1)

https://portals.broadinstitute.org/achilles/about


DRIVE -

Data Types

  • RNAi Gene Dependency Scores
  • shRNA log2 fold change values


Processing Methods

A number of methodologies have been adopted to generate a combined score for Gene Dependency from multiple shRNAs that are used to target an individual gene. OmicSoft provides the original method provided by the study to summarize a gene's dependency score.

Key Meta Data Columns (OmicSoft-controlled)

  • Tissue Category: Primary Grouping Column - The body site where the cell line sample is derived from.
  • Disease State: Histological types of cancer, such as carcinoma, glioma and sarcoma.
  • Gene Dependency Algorithm: Secondary Grouping Column - The algorithm used in the sample to score a gene dependency from the fold change values of the individual sgRNAs used.
  • CellLine: The identifiers of the cell line used in the experiment.
[back to top]


Sample Distribution View

When users open HumanRNAi_B37 Land, this will be the default view showing all of the samples in the land grouped on the Y-axis by Tissue category and colored on the X axis by the Gene Dependency Algorithm used to analyze RNAi data from these samples.

RNAiSampleDistribution.png

[back to top]


Key Views

There are a number of views that help users identify whether 1) a gene is required in certain cell lines/types or 2) which cell lines likely have a dependency on the gene(s) of interest. This can viewed as a single gene search for either gene dependency or fold-change of a set of sgRNAs in a given experiment:

For example, users can identify cell lines for which a single gene is required using either a waterfall or box plot view:

File:RNAisinglegene.png

For multi-gene searches, users can also view all genes/samples in a single view, including heatmap and boxplot:

[back to top]


Related Articles

Introduction to HumanCRISPR B37 Land Content EnvelopeLarge2.png