Genomics

Optics-free reconstruction of shapes, images and volumes with DNA barcode proximity graphs

1. Hanna Liao
2. Sanjay Kottapalli
3. Yuqi Huang
4. Matthew Chaw
5. Jase Gehring
6. Olivia Waltner
7. Melissa Phung-Rojas
8. Riza M Daza
9. Frederick A Matsen
10. Cole Trapnell
11. Jay Shendure
12. Sanjay Srivatsan

• Curated by eLife

  eLife Assessment

  This important technical study introduces SCOPE, an optics-free spatial reconstruction method based on bidirectional sender and receiver oligonucleotides on barcoded hydrogel beads. By sequencing proximity-encoded chimeric molecules, the authors computationally reconstruct 2D and 3D spatial information at an impressive scale. The technical demonstrations in synthetic bead systems are convincing and establish proof-of-principle that large spatial domains can be reconstructed without microscopy. The methodological advance is clear and the scale is impressive. This work will be of interest to those working on spatial mapping.

Reviewed by eLife

Multimodal single-cell analyses reveal distinct fusion-regulated transcriptional programs in Ewing sarcoma

1. Olivia G Waltner
2. April A Apfelbaum
3. Emma D Wrenn
4. Shruti S Bhise
5. Sami B Kanaan
6. Rula Green Gladden
7. Mark A Mendoza
8. Roger Volden
9. Zev Kronenberg
10. Anand Patel
11. Michael Dyer
12. Jay F Sarthy
13. Elizabeth R Lawlor
14. Scott N Furlan

• Curated by eLife

  eLife Assessment

  This valuable study presents an analysis of the gene regulatory networks that contribute to tumour heterogeneity and tumor plasticity in Ewing sarcoma, with key implications for other fusion-driven sarcomas. The authors employed compelling orthogonal approaches, including single-cell sequencing and xenografts, to reveal the existence and plasticity of specific gene regulatory networks (e.g., TGF-beta signaling) within Ewing sarcoma, as well as significant differences that exist between cell lines and patient tumors.

Reviewed by eLife

Breaking the cold chain: solutions for room temperature preservation of mosquitoes leading to high quality reference genomes

1. Fiona Teltscher
2. Petra Korlević
3. Edel Sheerin
4. Alex Makunin
5. Mara K N Lawniczak

Reviewed by GigaScience

Systematic identification of oscillatory gene expression in single cell types

1. Alexis Weinreb
2. Manasa Basavaraju
3. Marc Hammarlund
4. Maxwell G. Heiman

Reviewed by Review Commons