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Update index.md
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kendomaniac authored Sep 15, 2024
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Expand Up @@ -126,19 +126,8 @@ The above figure describes the driver genes associated to each cell line. Only a
<img border="0" src="../../images/be1.png" width="700px">
The above figure shows the sequencing statistics of the 7 cell lines.


###### BE2

The cell lines from BE1 will be used to generate surrogate tumor-tissues for spatial transcriptomics, by embedding pools of the 7 cell lines at different ratios in matrigel. For each cell ratio we will generate a slide (2 sections) using Visium for FFPE samples and six slides using [*Curio Bioscience*](https://curiobioscience.com/product/) spatial platform for OTC fresh frozen samples. In total we expect to produce three cell line ratios:

- Cell line 1 40%, cell line 2 25% cell line 3 20%, cell line 4 5%, PBMC 10%
- Cell line 1 45% cell line 2 25%, cell line 3 10%, cell line 4 10%, cell line 5 5%, PBMC 5%
- Cell line 1 25%, cell line 2 25%, cell line 3 10%, cell line 4 10%, cell line 4 10%, cell line 5 5%, cell line 6 5%, cell line 7 5%, PBMC 5%

Expected data availability: December 2024

###### BE3

PC9 and DV90 cell lines will be used to generate a combined scRNA-seq and scATAC-seq experiment using [*10X genomics technology for multi-omics*](https://www.10xgenomics.com/products/single-cell-multiome-atac-plus-gene-expression). Specifically we will generate three experiments:
- PC9 alone
- DV90 alone
Expand All @@ -149,6 +138,16 @@ All three experiments will also be analysed in triplicates for secreted microves
<img border="0" src="../../images/be3.png" width="500px">
In the above picture, the potential cross talk between PC9 and DV90 driver genes, mediated by soluble molecules, are shown. Data were generated using Ingenuity pathways analysis tool (Qiagen).

###### BE3

The cell lines from BE1 will be used to generate surrogate tumor-tissues for spatial transcriptomics, by embedding pools of the 7 cell lines at different ratios in matrigel. For each cell ratio we will generate a slide (2 sections) using Visium for FFPE samples and six slides using [*Curio Bioscience*](https://curiobioscience.com/product/) spatial platform for OTC fresh frozen samples. In total we expect to produce three cell line ratios:

- Cell line 1 40%, cell line 2 25% cell line 3 20%, cell line 4 5%, PBMC 10%
- Cell line 1 45% cell line 2 25%, cell line 3 10%, cell line 4 10%, cell line 5 5%, PBMC 5%
- Cell line 1 25%, cell line 2 25%, cell line 3 10%, cell line 4 10%, cell line 4 10%, cell line 5 5%, cell line 6 5%, cell line 7 5%, PBMC 5%

Expected data availability: December 2024

#### Spatial omics datasets

##### [SODB](https://gene.ai.tencent.com/SpatialOmics/)
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