iMAP is a user-friendly platform for browsing, searching and analyzing iMAP perturbation data.
Datasets
iMAP currently hosts two major perturbation datasets: iMAP-100 and iMAP-91. The iMAP-100 dataset covers 39 tissues and cell types, while iMAP-91 expands to 46 tissues and cell types with enhanced coverage of neural tissues and immune cell populations. Together, these datasets provide comprehensive perturbation atlas data across diverse biological systems, enabling researchers to explore gene functions in various contexts. More datasets with expanded tissue coverage are currently in development and will be available soon.
| Name | Description | Tissues | Link |
|---|---|---|---|
| iMAP-100 | 90 genes, including 87 "embryonic essential genes" whose functions in adults KO are poorly define. | 39 mouse tissues | Liu et al. |
| iMAP-91 | 71 (51%) of RNA modification factors (writers, readers, erasers) | 46 mouse tissues | Wei et al. |
Perturbation Atlases
- Tissue atlas: bulk PCR-NGS is used to read out the effects of perturbations on cell numbers at the population level, which reflects the functions of the target genes in cell proliferation, survival and/or differentiation.
- Single-cell atlas: scRNA-seq is used to read out the the perturbation effects on the transcriptome of individual cells, which is more informative than the tissue atlas.
Currently, only tissue atlases are available.
Tissue Atlas Analysis
- Heatmap View: displays interactive Guide x Tissue atlases , with functionally related genes and tissues clustered together.
- Gene Search: enables query for the abundance of guides of interest across tissues.
- Network View: presents an interactive network of the guides surrounding a guide of interest, with relevant information indicated, such as fold-changes of the guides, the number of tissues impacted by a guide, the distances among the guides and the total number of guides connected with a particular guide.
- Compare tissues: identifies the guides differentially represented between a pair of selected tissues.
iMAP Versions
- V1: the original version, where the recombination is biased toward the proximal guides due to the presence of a recombination hotspot, leading to underpresentation of the distal guides. This necessitates the use of more cells to cover the underrepresented guides, thus reducing the sensitivity of th technology and hampering the analysis of rare cells in the body. V1 is used in iMAP-100.
- V2: An inert sequence lacking LoxP sites (“stuffer”) is used to replace the recombination hotspot in V1, thus mitigating the recombination bias, making the guide representation as uniform as that in conventional lentiviral sgRNA libraries. V2 is used in iMAP-91.
- 91 sgRNAs in total.
- 78 sgRNAs targeting 71 RNA modification enzyme-related genes
- Includes positive control (gPolr2a) and markers (gCd19, gCd45)
- 9 non-targeting negative controls for background assessment
- Optimized library structure with stuffer sequence for uniform recombination
iMAP Introduction
iMAP (inducible Mosaic Animal for Perturbation), a transgenic platform enabling in situ CRISPR targeting of at least 100 genes in parallel throughout the mouse body. iMAP combines Cre-loxP and CRISPR-Cas9 technologies and utilizes a germline-transmitted transgene carrying a large array of individually floxed, tandemly linked gRNA-coding units. Cre-mediated recombination triggers expression of all the gRNAs in the array but only one of them per cell, converting the mice to mosaic organisms suitable for phenotypic characterization and also for high-throughput derivation of conventional single-gene perturbation lines via breeding. Using gRNA representation as a readout, we can characterize the effects of gene knockout (KO) on cells in different tissue types, which yields rich insights into context-dependent gene functions.
