Decoder-seq enhances mRNA capture efficiency in spatial RNA sequencing
© 2024. The Author(s), under exclusive licence to Springer Nature America, Inc..
Spatial transcriptomics technologies with high resolution often lack high sensitivity in mRNA detection. Here we report a dendrimeric DNA coordinate barcoding design for spatial RNA sequencing (Decoder-seq), which offers both high sensitivity and high resolution. Decoder-seq combines dendrimeric nanosubstrates with microfluidic coordinate barcoding to generate spatial arrays with a DNA density approximately ten times higher than previously reported methods while maintaining flexibility in resolution. We show that the high RNA capture efficiency of Decoder-seq improved the detection of lowly expressed olfactory receptor (Olfr) genes in mouse olfactory bulbs and contributed to the discovery of a unique layer enrichment pattern for two Olfr genes. The near-cellular resolution provided by Decoder-seq has enabled the construction of a spatial single-cell atlas of the mouse hippocampus, revealing dendrite-enriched mRNAs in neurons. When applying Decoder-seq to human renal cell carcinomas, we dissected the heterogeneous tumor microenvironment across different cancer subtypes and identified spatial gradient-expressed genes related to epithelial-mesenchymal transition with the potential to predict tumor prognosis and progression.
| Medienart: |
E-Artikel |
|---|
| Erscheinungsjahr: |
2024 |
|---|---|
| Erschienen: |
2024 |
| Enthalten in: |
Zur Gesamtaufnahme - year:2024 |
|---|---|
| Enthalten in: |
Nature biotechnology - (2024) vom: 16. Jan. |
| Sprache: |
Englisch |
|---|
| Beteiligte Personen: |
Cao, Jiao [VerfasserIn] |
|---|
| Links: |
|---|
| Themen: |
|---|
| Anmerkungen: |
Date Revised 16.01.2024 published: Print-Electronic Citation Status Publisher |
|---|
| doi: |
10.1038/s41587-023-02086-y |
|---|
| funding: |
|
|---|---|
| Förderinstitution / Projekttitel: |
|
| PPN (Katalog-ID): |
NLM367193302 |
|---|
| LEADER | 01000naa a22002652 4500 | ||
|---|---|---|---|
| 001 | NLM367193302 | ||
| 003 | DE-627 | ||
| 005 | 20240117232246.0 | ||
| 007 | cr uuu---uuuuu | ||
| 008 | 240117s2024 xx |||||o 00| ||eng c | ||
| 024 | 7 | |a 10.1038/s41587-023-02086-y |2 doi | |
| 028 | 5 | 2 | |a pubmed24n1262.xml |
| 035 | |a (DE-627)NLM367193302 | ||
| 035 | |a (NLM)38228777 | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rakwb | ||
| 041 | |a eng | ||
| 100 | 1 | |a Cao, Jiao |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Decoder-seq enhances mRNA capture efficiency in spatial RNA sequencing |
| 264 | 1 | |c 2024 | |
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a ƒaComputermedien |b c |2 rdamedia | ||
| 338 | |a ƒa Online-Ressource |b cr |2 rdacarrier | ||
| 500 | |a Date Revised 16.01.2024 | ||
| 500 | |a published: Print-Electronic | ||
| 500 | |a Citation Status Publisher | ||
| 520 | |a © 2024. The Author(s), under exclusive licence to Springer Nature America, Inc. | ||
| 520 | |a Spatial transcriptomics technologies with high resolution often lack high sensitivity in mRNA detection. Here we report a dendrimeric DNA coordinate barcoding design for spatial RNA sequencing (Decoder-seq), which offers both high sensitivity and high resolution. Decoder-seq combines dendrimeric nanosubstrates with microfluidic coordinate barcoding to generate spatial arrays with a DNA density approximately ten times higher than previously reported methods while maintaining flexibility in resolution. We show that the high RNA capture efficiency of Decoder-seq improved the detection of lowly expressed olfactory receptor (Olfr) genes in mouse olfactory bulbs and contributed to the discovery of a unique layer enrichment pattern for two Olfr genes. The near-cellular resolution provided by Decoder-seq has enabled the construction of a spatial single-cell atlas of the mouse hippocampus, revealing dendrite-enriched mRNAs in neurons. When applying Decoder-seq to human renal cell carcinomas, we dissected the heterogeneous tumor microenvironment across different cancer subtypes and identified spatial gradient-expressed genes related to epithelial-mesenchymal transition with the potential to predict tumor prognosis and progression | ||
| 650 | 4 | |a Journal Article | |
| 700 | 1 | |a Zheng, Zhong |e verfasserin |4 aut | |
| 700 | 1 | |a Sun, Di |e verfasserin |4 aut | |
| 700 | 1 | |a Chen, Xin |e verfasserin |4 aut | |
| 700 | 1 | |a Cheng, Rui |e verfasserin |4 aut | |
| 700 | 1 | |a Lv, Tianpeng |e verfasserin |4 aut | |
| 700 | 1 | |a An, Yu |e verfasserin |4 aut | |
| 700 | 1 | |a Zheng, Junhua |e verfasserin |4 aut | |
| 700 | 1 | |a Song, Jia |e verfasserin |4 aut | |
| 700 | 1 | |a Wu, Lingling |e verfasserin |4 aut | |
| 700 | 1 | |a Yang, Chaoyong |e verfasserin |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t Nature biotechnology |d 1996 |g (2024) vom: 16. Jan. |w (DE-627)NLM08998398X |x 1546-1696 |7 nnns |
| 773 | 1 | 8 | |g year:2024 |g day:16 |g month:01 |
| 856 | 4 | 0 | |u http://dx.doi.org/10.1038/s41587-023-02086-y |3 Volltext |
| 912 | |a GBV_USEFLAG_A | ||
| 912 | |a GBV_NLM | ||
| 951 | |a AR | ||
| 952 | |j 2024 |b 16 |c 01 | ||