Back

SpaceBar enables clone tracing in spatial transcriptomic data

Kinsler, G.; Fagan, C.; Li, H.; Kaster, J.; Dunne, M.; Vander Velde, R. J.; Boe, R. H.; Shaffer, S.; Herlyn, M.; Raj, A.; Heyman, Y.

2025-02-14 genomics
10.1101/2025.02.10.637514 bioRxiv
Show abstract

We report a cellular barcoding strategy, SpaceBar, that enables simultaneous clone tracing and spatial transcriptomics profiling. Our approach uses a library of 96 synthetic barcode sequences that can be robustly detected by imaging based spatial transcriptomics (seqFISH), delivered such that each cell is labeled with a combination of barcodes. We used these barcodes to label melanoma cells in a tumor xenograft model and profiled both clone identity and spatial gene expression in situ. We developed a gene scoring metric that quantifies how strongly gene expression is driven by intrinsic cellular cues or extrinsic environmental signals. Our framework distinguishes between clonal dynamics and environmentally-driven transcriptional regulation in complex tissue contexts.

Matching journals

The top 5 journals account for 50% of the predicted probability mass.

1
Cell
○ 431 papers in training set
Top 0.1%
18.3%
Similar papers in this journal
2
Nature Communications
○ 5641 papers in training set
Top 14%
12.5%
Similar papers in this journal
3
Nature Methods
○ 385 papers in training set
Top 1%
7.8%
Similar papers in this journal
4
Nature Biotechnology
○ 172 papers in training set
Top 0.4%
6.7%
Similar papers in this journal
5
eLife
● 5828 papers in training set
Top 18%
6.7%
Similar papers in this journal
50% of probability mass above
6
Science
● 477 papers in training set
Top 2%
4.3%
7
Genome Biology
○ 637 papers in training set
Top 3%
4.0%
8
Cell Systems
○ 201 papers in training set
Top 1%
4.0%
9
Nature Genetics
○ 286 papers in training set
Top 2%
3.4%
10
Cell Reports
○ 1498 papers in training set
Top 14%
2.6%
11
Proceedings of the National Academy of Sciences
● 2444 papers in training set
Top 20%
2.6%
12
Molecular Systems Biology
○ 162 papers in training set
Top 0.9%
2.4%
13
Nature
○ 645 papers in training set
Top 6%
2.4%
14
Cell Reports Methods
○ 165 papers in training set
Top 1%
2.4%
15
Science Advances
● 1243 papers in training set
Top 20%
1.7%
16
Cell Genomics
○ 172 papers in training set
Top 3%
1.7%
17
Genome Research
● 468 papers in training set
Top 4%
1.7%
18
Nucleic Acids Research
◐ 1281 papers in training set
Top 9%
1.7%
19
Scientific Reports
○ 3612 papers in training set
Top 64%
1.1%
20
iScience
○ 1154 papers in training set
Top 30%
1.1%
21
Molecular Cell
○ 350 papers in training set
Top 5%
0.8%
22
Cancer Cell
○ 42 papers in training set
Top 1%
0.8%
23
The American Journal of Human Genetics
○ 234 papers in training set
Top 3%
0.8%
24
Current Biology
○ 665 papers in training set
Top 11%
0.6%
25
Communications Biology
○ 993 papers in training set
Top 35%
0.6%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.