Stereo-Seq Spatial Gene Expression

Stereo-Seq Spatial

STOmics의 대표 기술인 공간 향상 해상도 오믹스 시퀀싱(Stereo-seq)은 DNA 나노볼(DNB) 기술을 기반으로 한 첨단 공간 전사체학 플랫폼입니다. 이 최첨단 시스템은 뛰어난 해상도와 처리량, 시야를 제공하여 조직, 세포, 아세포, 분자 수준 등 다양한 규모에서 포괄적인 공간 전사체 분석을 가능하게 합니다. 패턴 배열 칩과 좌표 ID(CID) 시스템을 활용해 Stereo-seq는 조직 샘플에서 직접 mRNA를 포착하고, 그 정확한 공간 좌표를 복원합니다. 혁신적인 도구로서 Stereo-seq는 연구자들이 유전자 발현, 세포 형태, 그리고 주변 미세환경 간의 복잡한 관계를 밝히는 데 큰 힘이 됩니다.

노보진 Stereo-Seq: 장점 & 특징

큰 캡쳐 에리어 & 고해상도

유전자 및 이미징 분석을 위한 최대 13cm × 13cm 포획 영역과 500nm 해상도

넓은 샘플 호환성

다양한 동물 및 식물 조직 유형의 신선 냉동 및 FFPE 시료와 호환됩니다

병리학 통합

단일 구간 염색은 병리학적 평가와 공간 전사체 분석을 동시에 가능하게 합니다

연구 및 의학 분야에서의 Stereo-Seq 활용

유전 질환, 암, 인구 연구를 위한 인간 유전학에 대한 폭넓은 통찰을 얻으세요.

종양 미세환경 연구

종양 미세환경의 분자 및 세포적 특성을 규명한다.

면역학

조직 내 면역 세포의 공간적 분포와 상호작용을 지도화합니다.

신경 과학

전례 없는 해상도로 신경 세포의 기능과 발현 패턴을 연구하세요.

바이오마커 발견

질병 진단과 치료 개발을 위한 세포 특이적 바이오마커를 규명합니다.

세부사항

샘플 준비방법

샘플 양은 참고용으로만 제시되어 있습니다. 자세한 내용은 샘플준비 가이드를 다운로드하여 확인하세요. 자세한 정보가 필요하시면 맞춤 요청을 가지고 저희에게 연락해주세요.

Sample Type	Sample Amount	Preservation	Sample QC	Shipping
FFPE block (recommended)*	1 block, FFPE block must be contained on plastic dehydrating box, otherwise could not be installed on the sectioning device	After embedding store at 4°C, protected from light	DV200% ≥ 30%	Cold pack transportation
FFPE sections	10-15 FFPE (5μm thickness) scrolls in 1.5mL tube for sample QC; 4-6 FFPE (5μm thickness) tissue sections, place each FFPE sections into a new 50 ml centrifuge tubes for library prep	Dry and sealed，storage time at 4°C< 14 days	DV200% ≥ 30%	Cold pack transportation
Fresh Frozen (OCT-embedded block)	For samples with a thickness greater than 1mm, the area should be less than 0.9cm × 0.9cm	After embedding store at -80°C , mark the cutting surface on the outside of the embedding box	RIN ≥ 4	Dry ice transportation

*FFPE blocks should be no older than 3 years.

샘플 준비방법

Sample Type	Sample Amount	Preservation	Sample QC	Shipping
FFPE block (recommended)*	1 block, FFPE block must be contained on plastic dehydrating box, otherwise could not be installed on the sectioning device	After embedding store at 4°C, protected from light	DV200% ≥ 30%	Cold pack transportation
FFPE sections	10-15 FFPE (5μm thickness) scrolls in 1.5mL tube for sample QC; 4-6 FFPE (5μm thickness) tissue sections, place each FFPE sections into a new 50 ml centrifuge tubes for library prep	Dry and sealed，storage time at 4°C< 14 days	DV200% ≥ 30%	Cold pack transportation
Fresh Frozen (OCT-embedded block)	For samples with a thickness greater than 1mm, the area should be less than 0.9cm × 0.9cm	After embedding store at -80°C , mark the cutting surface on the outside of the embedding box	RIN ≥ 4	Dry ice transportation

*FFPE blocks should be no older than 3 years.

샘플 준비방법

Sample Type	Sample Amount	Preservation	Sample QC	Shipping
FFPE block (recommended)*	1 block, FFPE block must be contained on plastic dehydrating box, otherwise could not be installed on the sectioning device	After embedding store at 4°C, protected from light	DV200% ≥ 30%	Cold pack transportation
FFPE sections	10-15 FFPE (5μm thickness) scrolls in 1.5mL tube for sample QC; 4-6 FFPE (5μm thickness) tissue sections, place each FFPE sections into a new 50 ml centrifuge tubes for library prep	Dry and sealed，storage time at 4°C< 14 days	DV200% ≥ 30%	Cold pack transportation
Fresh Frozen (OCT-embedded block)	For samples with a thickness greater than 1mm, the area should be less than 0.9cm × 0.9cm	After embedding store at -80°C , mark the cutting surface on the outside of the embedding box	RIN ≥ 4	Dry ice transportation

*FFPE blocks should be no older than 3 years.

샘플 준비방법

Sample Type	Sample Amount	Preservation	Sample QC	Shipping
FFPE block (recommended)*	1 block, FFPE block must be contained on plastic dehydrating box, otherwise could not be installed on the sectioning device	After embedding store at 4°C, protected from light	DV200% ≥ 30%	Cold pack transportation
FFPE sections	10-15 FFPE (5μm thickness) scrolls in 1.5mL tube for sample QC; 4-6 FFPE (5μm thickness) tissue sections, place each FFPE sections into a new 50 ml centrifuge tubes for library prep	Dry and sealed，storage time at 4°C< 14 days	DV200% ≥ 30%	Cold pack transportation
Fresh Frozen (OCT-embedded block)	For samples with a thickness greater than 1mm, the area should be less than 0.9cm × 0.9cm	After embedding store at -80°C , mark the cutting surface on the outside of the embedding box	RIN ≥ 4	Dry ice transportation

*FFPE blocks should be no older than 3 years.

시퀀싱 & 데이터 분석

권장 데이터 생산량과 표시되는 분석 내용은 참고용일 뿐입니다. 자세한 정보가 필요하시면 맞춤 요청을 가지고 저희에게 연락해주세요.

Tissue Type	Stereo - FFPE	Stereo - Fresh Frozen
Capture method	Random probe capture	PolyA capture
Resolution	500nm	500nm
Sequencing platform	BGI DNB-SEQ T7	BGI DNB-SEQ T7
Read length	PE 50bp+100bp	PE 50bp+100bp
Recommended Data Amount	Coverage Area 1cm1cm~ 3000 Million reads/sample Coverage Area 0.5m0.5cm~ 1000 Million reads/sample	Coverage Area 1cm1cm~ 2000 Million reads/sample Coverage Area 0.5cm0.5cm~ 1000 Million reads/sample
Analysis	Data QC Mapping and Quantification Dimensionality Reduction, Clustering, and Differential analysis: Graphclust clustering K-means clustering Seurat Analysis: PCA analysis Spatial variable gene expression analysis Clustering and dimensionality reduction analysis Differential Expression Gene Analysis (DEG) DEGs clustering heatmap Spatial distribution of DEGs Violine plot t-SNE and UMAP dimensional reduction visualization Functional Enrichment Analysis: GO enrichment KEGG enrichment Reactome enrichment

프로젝트 워크플로우

시퀀싱 & 데이터 분석

권장 데이터 생산량과 표시되는 분석 내용은 참고용일 뿐입니다. 자세한 정보가 필요하시면 맞춤 요청을 가지고 저희에게 연락해주세요.

Tissue Type	Stereo - FFPE	Stereo - Fresh Frozen
Capture method	Random probe capture	PolyA capture
Resolution	500nm	500nm
Sequencing platform	BGI DNB-SEQ T7	BGI DNB-SEQ T7
Read length	PE 50bp+100bp	PE 50bp+100bp
Recommended Data Amount	Coverage Area 1cm1cm~ 3000 Million reads/sample Coverage Area 0.5m0.5cm~ 1000 Million reads/sample	Coverage Area 1cm1cm~ 2000 Million reads/sample Coverage Area 0.5cm0.5cm~ 1000 Million reads/sample
Analysis	Data QC Mapping and Quantification Dimensionality Reduction, Clustering, and Differential analysis: Graphclust clustering K-means clustering Seurat Analysis: PCA analysis Spatial variable gene expression analysis Clustering and dimensionality reduction analysis Differential Expression Gene Analysis (DEG) DEGs clustering heatmap Spatial distribution of DEGs Violine plot t-SNE and UMAP dimensional reduction visualization Functional Enrichment Analysis: GO enrichment KEGG enrichment Reactome enrichment

프로젝트 워크플로우

시퀀싱 & 데이터 분석

권장 데이터 생산량과 표시되는 분석 내용은 참고용일 뿐입니다. 자세한 정보가 필요하시면 맞춤 요청을 가지고 저희에게 연락해주세요.

Tissue Type	Stereo - FFPE	Stereo - Fresh Frozen
Capture method	Random probe capture	PolyA capture
Resolution	500nm	500nm
Sequencing platform	BGI DNB-SEQ T7	BGI DNB-SEQ T7
Read length	PE 50bp+100bp	PE 50bp+100bp
Recommended Data Amount	Coverage Area 1cm1cm~ 3000 Million reads/sample Coverage Area 0.5m0.5cm~ 1000 Million reads/sample	Coverage Area 1cm1cm~ 2000 Million reads/sample Coverage Area 0.5cm0.5cm~ 1000 Million reads/sample
Analysis	Data QC Mapping and Quantification Dimensionality Reduction, Clustering, and Differential analysis: Graphclust clustering K-means clustering Seurat Analysis: PCA analysis Spatial variable gene expression analysis Clustering and dimensionality reduction analysis Differential Expression Gene Analysis (DEG) DEGs clustering heatmap Spatial distribution of DEGs Violine plot t-SNE and UMAP dimensional reduction visualization Functional Enrichment Analysis: GO enrichment KEGG enrichment Reactome enrichment

프로젝트 워크플로우

시퀀싱 & 데이터 분석

권장 데이터 생산량과 표시되는 분석 내용은 참고용일 뿐입니다. 자세한 정보가 필요하시면 맞춤 요청을 가지고 저희에게 연락해주세요.

Tissue Type	Stereo - FFPE	Stereo - Fresh Frozen
Capture method	Random probe capture	PolyA capture
Resolution	500nm	500nm
Sequencing platform	BGI DNB-SEQ T7	BGI DNB-SEQ T7
Read length	PE 50bp+100bp	PE 50bp+100bp
Recommended Data Amount	Coverage Area 1cm1cm~ 3000 Million reads/sample Coverage Area 0.5m0.5cm~ 1000 Million reads/sample	Coverage Area 1cm1cm~ 2000 Million reads/sample Coverage Area 0.5cm0.5cm~ 1000 Million reads/sample
Analysis	Data QC Mapping and Quantification Dimensionality Reduction, Clustering, and Differential analysis: Graphclust clustering K-means clustering Seurat Analysis: PCA analysis Spatial variable gene expression analysis Clustering and dimensionality reduction analysis Differential Expression Gene Analysis (DEG) DEGs clustering heatmap Spatial distribution of DEGs Violine plot t-SNE and UMAP dimensional reduction visualization Functional Enrichment Analysis: GO enrichment KEGG enrichment Reactome enrichment

프로젝트 워크플로우

세부사항

샘플 준비방법

Sample Type	Sample Amount	Preservation	Sample QC	Shipping
FFPE block (recommended)*	1 block, FFPE block must be contained on plastic dehydrating box, otherwise could not be installed on the sectioning device	After embedding store at 4°C, protected from light	DV200% ≥ 30%	Cold pack transportation
FFPE sections	10-15 FFPE (5μm thickness) scrolls in 1.5mL tube for sample QC; 4-6 FFPE (5μm thickness) tissue sections, place each FFPE sections into a new 50 ml centrifuge tubes for library prep	Dry and sealed，storage time at 4°C< 14 days	DV200% ≥ 30%	Cold pack transportation
Fresh Frozen (OCT-embedded block)	For samples with a thickness greater than 1mm, the area should be less than 0.9cm × 0.9cm	After embedding store at -80°C , mark the cutting surface on the outside of the embedding box	RIN ≥ 4	Dry ice transportation

*FFPE blocks should be no older than 3 years.

샘플 준비방법

Sample Type	Sample Amount	Preservation	Sample QC	Shipping
FFPE block (recommended)*	1 block, FFPE block must be contained on plastic dehydrating box, otherwise could not be installed on the sectioning device	After embedding store at 4°C, protected from light	DV200% ≥ 30%	Cold pack transportation
FFPE sections	10-15 FFPE (5μm thickness) scrolls in 1.5mL tube for sample QC; 4-6 FFPE (5μm thickness) tissue sections, place each FFPE sections into a new 50 ml centrifuge tubes for library prep	Dry and sealed，storage time at 4°C< 14 days	DV200% ≥ 30%	Cold pack transportation
Fresh Frozen (OCT-embedded block)	For samples with a thickness greater than 1mm, the area should be less than 0.9cm × 0.9cm	After embedding store at -80°C , mark the cutting surface on the outside of the embedding box	RIN ≥ 4	Dry ice transportation

*FFPE blocks should be no older than 3 years.

샘플 준비방법

Sample Type	Sample Amount	Preservation	Sample QC	Shipping
FFPE block (recommended)*	1 block, FFPE block must be contained on plastic dehydrating box, otherwise could not be installed on the sectioning device	After embedding store at 4°C, protected from light	DV200% ≥ 30%	Cold pack transportation
FFPE sections	10-15 FFPE (5μm thickness) scrolls in 1.5mL tube for sample QC; 4-6 FFPE (5μm thickness) tissue sections, place each FFPE sections into a new 50 ml centrifuge tubes for library prep	Dry and sealed，storage time at 4°C< 14 days	DV200% ≥ 30%	Cold pack transportation
Fresh Frozen (OCT-embedded block)	For samples with a thickness greater than 1mm, the area should be less than 0.9cm × 0.9cm	After embedding store at -80°C , mark the cutting surface on the outside of the embedding box	RIN ≥ 4	Dry ice transportation

*FFPE blocks should be no older than 3 years.

샘플 준비방법

Sample Type	Sample Amount	Preservation	Sample QC	Shipping
FFPE block (recommended)*	1 block, FFPE block must be contained on plastic dehydrating box, otherwise could not be installed on the sectioning device	After embedding store at 4°C, protected from light	DV200% ≥ 30%	Cold pack transportation
FFPE sections	10-15 FFPE (5μm thickness) scrolls in 1.5mL tube for sample QC; 4-6 FFPE (5μm thickness) tissue sections, place each FFPE sections into a new 50 ml centrifuge tubes for library prep	Dry and sealed，storage time at 4°C< 14 days	DV200% ≥ 30%	Cold pack transportation
Fresh Frozen (OCT-embedded block)	For samples with a thickness greater than 1mm, the area should be less than 0.9cm × 0.9cm	After embedding store at -80°C , mark the cutting surface on the outside of the embedding box	RIN ≥ 4	Dry ice transportation

*FFPE blocks should be no older than 3 years.

시퀀싱 & 데이터 분석

권장 데이터 생산량과 표시되는 분석 내용은 참고용일 뿐입니다. 자세한 정보가 필요하시면 맞춤 요청을 가지고 저희에게 연락해주세요.

Tissue Type	Stereo - FFPE	Stereo - Fresh Frozen
Capture method	Random probe capture	PolyA capture
Resolution	500nm	500nm
Sequencing platform	BGI DNB-SEQ T7	BGI DNB-SEQ T7
Read length	PE 50bp+100bp	PE 50bp+100bp
Recommended Data Amount	Coverage Area 1cm1cm~ 3000 Million reads/sample Coverage Area 0.5m0.5cm~ 1000 Million reads/sample	Coverage Area 1cm1cm~ 2000 Million reads/sample Coverage Area 0.5cm0.5cm~ 1000 Million reads/sample
Analysis	Data QC Mapping and Quantification Dimensionality Reduction, Clustering, and Differential analysis: Graphclust clustering K-means clustering Seurat Analysis: PCA analysis Spatial variable gene expression analysis Clustering and dimensionality reduction analysis Differential Expression Gene Analysis (DEG) DEGs clustering heatmap Spatial distribution of DEGs Violine plot t-SNE and UMAP dimensional reduction visualization Functional Enrichment Analysis: GO enrichment KEGG enrichment Reactome enrichment

프로젝트 워크플로우

시퀀싱 & 데이터 분석

권장 데이터 생산량과 표시되는 분석 내용은 참고용일 뿐입니다. 자세한 정보가 필요하시면 맞춤 요청을 가지고 저희에게 연락해주세요.

Tissue Type	Stereo - FFPE	Stereo - Fresh Frozen
Capture method	Random probe capture	PolyA capture
Resolution	500nm	500nm
Sequencing platform	BGI DNB-SEQ T7	BGI DNB-SEQ T7
Read length	PE 50bp+100bp	PE 50bp+100bp
Recommended Data Amount	Coverage Area 1cm1cm~ 3000 Million reads/sample Coverage Area 0.5m0.5cm~ 1000 Million reads/sample	Coverage Area 1cm1cm~ 2000 Million reads/sample Coverage Area 0.5cm0.5cm~ 1000 Million reads/sample
Analysis	Data QC Mapping and Quantification Dimensionality Reduction, Clustering, and Differential analysis: Graphclust clustering K-means clustering Seurat Analysis: PCA analysis Spatial variable gene expression analysis Clustering and dimensionality reduction analysis Differential Expression Gene Analysis (DEG) DEGs clustering heatmap Spatial distribution of DEGs Violine plot t-SNE and UMAP dimensional reduction visualization Functional Enrichment Analysis: GO enrichment KEGG enrichment Reactome enrichment

프로젝트 워크플로우

시퀀싱 & 데이터 분석

권장 데이터 생산량과 표시되는 분석 내용은 참고용일 뿐입니다. 자세한 정보가 필요하시면 맞춤 요청을 가지고 저희에게 연락해주세요.

Tissue Type	Stereo - FFPE	Stereo - Fresh Frozen
Capture method	Random probe capture	PolyA capture
Resolution	500nm	500nm
Sequencing platform	BGI DNB-SEQ T7	BGI DNB-SEQ T7
Read length	PE 50bp+100bp	PE 50bp+100bp
Recommended Data Amount	Coverage Area 1cm1cm~ 3000 Million reads/sample Coverage Area 0.5m0.5cm~ 1000 Million reads/sample	Coverage Area 1cm1cm~ 2000 Million reads/sample Coverage Area 0.5cm0.5cm~ 1000 Million reads/sample
Analysis	Data QC Mapping and Quantification Dimensionality Reduction, Clustering, and Differential analysis: Graphclust clustering K-means clustering Seurat Analysis: PCA analysis Spatial variable gene expression analysis Clustering and dimensionality reduction analysis Differential Expression Gene Analysis (DEG) DEGs clustering heatmap Spatial distribution of DEGs Violine plot t-SNE and UMAP dimensional reduction visualization Functional Enrichment Analysis: GO enrichment KEGG enrichment Reactome enrichment

프로젝트 워크플로우

시퀀싱 & 데이터 분석

권장 데이터 생산량과 표시되는 분석 내용은 참고용일 뿐입니다. 자세한 정보가 필요하시면 맞춤 요청을 가지고 저희에게 연락해주세요.

Tissue Type	Stereo - FFPE	Stereo - Fresh Frozen
Capture method	Random probe capture	PolyA capture
Resolution	500nm	500nm
Sequencing platform	BGI DNB-SEQ T7	BGI DNB-SEQ T7
Read length	PE 50bp+100bp	PE 50bp+100bp
Recommended Data Amount	Coverage Area 1cm1cm~ 3000 Million reads/sample Coverage Area 0.5m0.5cm~ 1000 Million reads/sample	Coverage Area 1cm1cm~ 2000 Million reads/sample Coverage Area 0.5cm0.5cm~ 1000 Million reads/sample
Analysis	Data QC Mapping and Quantification Dimensionality Reduction, Clustering, and Differential analysis: Graphclust clustering K-means clustering Seurat Analysis: PCA analysis Spatial variable gene expression analysis Clustering and dimensionality reduction analysis Differential Expression Gene Analysis (DEG) DEGs clustering heatmap Spatial distribution of DEGs Violine plot t-SNE and UMAP dimensional reduction visualization Functional Enrichment Analysis: GO enrichment KEGG enrichment Reactome enrichment

프로젝트 워크플로우

데이터 분석 예시

1/1

유전자 발현 공간 정량화

Space Ranger는 각 샘플의 모든 빈에서 각 유전자의 UMI를 계산하여 빈-유전자 발현 행렬을 만듭니다. 데이터 품질 관리를 수행한 후, 아래 그림은 조직의 공간 영역별로 유전자당 UMI 분포를 보여줍니다.

1/1

클러스터 분석: 공간 분포, tSNE 및 UMAP

Cluster_Spatial: 클러스터의 공간 분포 지도; Cluster_tSNE: 클러스터의 tSNE 2차원 공간 표현 지도; Cluster_UMAP: 클러스터의 2차원 공간 표현 지도

1/1

DEG의 t-SNE 및 UMAP 차원 축소 분석

각 클러스터에서 차등 발현된 상위 4개 유전자는 여러 가지 방식으로 표시됩니다. 이 그림은 차등 발현 유전자들의 t-SNE와 UMAP 차원 축소 시각화를 보여줍니다.

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