PROJECT ID: GSE59873

Data source GEO: GSE59873
Description Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome-wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes, they are unable to yield spatially resolved information in embryos or tissues. Microscopy-based approaches, using for example in situ hybridization, can provide spatial information about gene expression, but are limited to analyzing one or a few genes at a time. Here, we present a method where we combine traditional histological techniques with low-input RNA sequencing and mathematical image reconstruction to generate a high-resolution genome-wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially-resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly, our method enables searching for genes that are expressed in specific spatial patterns without manual image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs.
Key word in-situ hybridization; gene-expression; seq; identification; family
Publication Junker JP, Noël ES, Guryev V, Peterson KA et al. Genome-wide RNA Tomography in the zebrafish embryo. Cell 2014 Oct 23;159(3):662-75. PMID: 25417113
Abstract Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. Although genome-wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes, they are unable to yield spatially resolved information in embryos or tissues. Microscopy-based approaches, using in situ hybridization, for example, can provide spatial information about gene expression, but are limited to analyzing one or a few genes at a time. Here, we present a method where we combine traditional histological techniques with low-input RNA sequencing and mathematical image reconstruction to generate a high-resolution genome-wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. Importantly, our technique enables searching for genes that are expressed in specific spatial patterns without manual image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs.


Dataset Information

Dataset ID Tissue / Organ Technique Experiment type Sample description Source dataset ID
1. GSE59873 (shield, A to V) embryo Tomo-seq baseline shield stage, intact embryo, sectioned from animal to vegetal pole GEO: GSM1448795
2. GSE59873 (shield, V to A) embryo Tomo-seq baseline shield stage, intact embryo, sectioned from vegetal to animal pole GEO: GSM1448796
3. GSE59873 (shield, V to A, replicate) embryo Tomo-seq baseline shield stage, intact embryo, sectioned from vegetal to animal pole, replicate GEO: GSM1448797
4. GSE59873 (shield, L to R) embryo Tomo-seq baseline shield stage, intact embryo, sectioned from left to right GEO: GSM1448798
5. GSE59873 (shield, R to L) embryo Tomo-seq baseline shield stage, intact embryo, sectioned from right to left GEO: GSM1448799
6. GSE59873 (shield, V to D) embryo Tomo-seq baseline shield stage, intact embryo, sectioned from ventral to dorsal end GEO: GSM1448800
7. GSE59873 (shield, D to V) embryo Tomo-seq baseline shield stage, intact embryo, sectioned from dorsal to ventral end GEO: GSM1448801
8. GSE59873 (shield, D to V, replicate) embryo Tomo-seq baseline shield stage, intact embryo, sectioned from dorsal to ventral end, replicate GEO: GSM1448802
9. GSE59873 (10 somite, A to P) embryo Tomo-seq baseline 10 somite stage, intact embryo, sectioned from anterior to posterior end GEO: GSM1448803
10. GSE59873 (10 somite, A to P, replicate) embryo Tomo-seq baseline 10 somite stage, intact embryo, sectioned from anterior to posterior end, replicate GEO: GSM1448804
11. GSE59873 (10 somite, P to A) embryo Tomo-seq baseline 10 somite stage, intact embryo, sectioned from posterior to anterior end GEO: GSM1448805
12. GSE59873 (10 somite, V to D) embryo Tomo-seq baseline 10 somite stage, intact embryo, sectioned from ventral to dorsal end GEO: GSM1448806
13. GSE59873 (10 somite, D to V) embryo Tomo-seq baseline 10 somite stage, intact embryo, sectioned from dorsal to ventral end GEO: GSM1448807
14. GSE59873 (10 somite, L to R) embryo Tomo-seq baseline 10 somite stage, intact embryo, sectioned from left to right GEO: GSM1448808
15. GSE59873 (10 somite, R to L) embryo Tomo-seq baseline 10 somite stage, intact embryo, sectioned from right to left GEO: GSM1448809
16. GSE59873 (15 somite, A to P) embryo Tomo-seq baseline 15 somite stage, intact embryo, sectioned from anterior to posterior end GEO: GSM1448810
17. GSE59873 (15 somite, P to A) embryo Tomo-seq baseline 15 somite stage, intact embryo, sectioned from posterior to anterior end GEO: GSM1448811
18. GSE59873 (15 somite, V to D) embryo Tomo-seq baseline 15 somite stage, intact embryo, sectioned from ventral to dorsal end GEO: GSM1448812
19. GSE59873 (15 somite, D to V) embryo Tomo-seq baseline 15 somite stage, intact embryo, sectioned from dorsal to ventral end GEO: GSM1448813
20. GSE59873 (15 somite, L to R) embryo Tomo-seq baseline 15 somite stage, intact embryo, sectioned from left to right GEO: GSM1448814
21. GSE59873 (15 somite, R to L) embryo Tomo-seq baseline 15 somite stage, intact embryo, sectioned from right to left GEO: GSM1448815
22. GSE59873 (15 somite, H to T) embryo Tomo-seq baseline 15 somite stage, deyolked embryo, straightened, sectioned head to tail GEO: GSM1448816
23. GSE59873 (15 somite, T to H) embryo Tomo-seq baseline 15 somite stage, deyolked embryo, straightened, sectioned tail to head GEO: GSM1448817
24. GSE59873 (15 somite, T to H, replicate) embryo Tomo-seq baseline 15 somite stage, deyolked embryo, straightened, sectioned tail to head, replicate GEO: GSM1448819
25. GSE59873 (18 somite, T to H) embryo Tomo-seq baseline 18 somite stage, deyolked embryo, head removed, straightened, sectioned tail to head GEO: GSM1448820