1、粉状干冰:用研钵和杵准备干冰粉。 2、冷冻 OCT:将 OCT 放在冰上≥30 分钟( 注:OCT 请使用指定品牌)。 3、预冷镊子:将镊子放在干冰中≥30 分钟。 4、包埋盒上需标记组织样本的方向( 注:在添加 OCT 和组织之前,需先在包埋盒上标记,因为一旦冻结,OCT 将迅速变成白色,这使得以后很难确定组织方向)。 5、用冷却的 OCT 铺平包埋盒底部,避免产生气泡。 6、从不锈钢烧杯中取出冰冻的组织,加入到 OCT 的包埋盒中心位置,继续倒入 OCT 完全覆盖样本。需避免气泡产生,尤其在组织附近。 7、立即将含有组织和 OCT 的包埋盒放在干冰粉上,直至完全冻结(约 20min 以上)。 8、将包埋盒放置到密封袋中,干冰运输。
A、本研究包括三种人类心脏组织的发育阶段。B、本研究所采用的分子生物学方法:(1)利用空间转录组技术(ST),鉴定出了解剖学区域特异的 marker;(2)用 scRNA-seq 技术分析心脏中间时间点的细胞类型异质性;(3)用 ISS 技术定位亚细胞分辨率的关键基因;(4)构建器官水平的 3D 基因表达图谱。
案例三 单细胞 RNA 测序 & 空间转录组测序“强强联手”揭示肠道发育 Spatiotemporal analysis of human intestinal development at single-cell resolution
▲图 植物的空间解析转录组分析 参考文献 伯豪生物提供冰冻样本空间转录组测序、空间基因表达专业技术服务解决方案[1]. Ståhl PL, Salmén F, Vickovic S, et al. Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science 2016, 353(6294):78-82. [2]. Peng G, Suo S, Chen J, et al. Spatial Transcriptome for the Molecular Annotation of Lineage Fates and Cell Identity in Mid-gastrula Mouse Embryo. Dev Cell 2016, 36(6):681-697. [3]. https://www.spatialomics.org/SpatialDB/ [4]. Michaela Asp, Stefania Giacomello, et al. A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart[J]. Cell, 2019, 179, 1647–1660. [5]. Maniatis S, Äijö T, Vickovic S, et al. Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis[J]. Science, 2019, 364(6435): 89-93. [6]. Carlberg K, Korotkova M, Larsson L, Catrina AI, Stahl PL, Malmstrom V. Exploring inflammatory signatures in arthritic joint biopsies with Spatial Transcriptomics[J]. Scientific reports. 2019,9(1):18975. [7]. José, Fernández, Navarro, et al. ST viewer: a tool for analysis and visualization of spatial transcriptomics datasets.[J]. Bioinformatics (Oxford, England), 2019. [8]. Berglund E , Maaskola J , Schultz N , et al. Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity[J]. Nature Communications, 2018, 9(1). [9]. ST Spot Detector: a web-based application for automatic spot and tissue detection for spatial Transcriptomics image datasets[J]. Bioinformatics, 2018. [10]. Anna L , Natalija G , Tove B , et al. Gene expression profiling of periodontitis-affected gingival tissue by spatial transcriptomics[J]. Scientific Reports, 2018, 8(1):9370. [11]. Kim T , Hanna E , Jonas M , et al. Spatially resolved transcriptomics enables dissection of genetic heterogeneity in stage III cutaneous malignant melanoma[J]. Cancer Research, 2018:canres.0747.2018. [12]. Salmen F, Stahl PL, Mollbrink A, Navarro JF, Vickovic S, Frisen J, et al. Barcoded solid-phase RNA capture for Spatial Transcriptomics profiling in mammalian tissue sections[J]. Nature protocols. 2018,13(11):2501-34. [13]. Giacomello S , Fredrik Salmén, Terebieniec B K , et al. Spatially resolved transcriptome profiling in model plant species[J]. Nature Plants, 2017, 3(6):17061. [14]. Asp M , Salmén, Fredrik, St?Hl P L , et al. Spatial detection of fetal marker genes expressed at low level in adult human heart tissue[J]. Scientific Reports, 2017, 7(1):12941. [15]. Stahl P L , Salmen F , Vickovic S , et al. Visualization and analysis of gene expression in tissue sections by spatial transcriptomics[J]. Science, 2016, 353(6294):78-82. [16]. Vickovic S , St?Hl P L , Salmén, Fredrik, et al. Massive and parallel expression profiling using microarrayed single-cell sequencing[J]. Nature Communications, 2016, 7:13182. [17]. Anders, Jemt, Fredrik, et al. An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries.[J]. Scientific reports, 2016. [18] Berglund E , Maaskola J , Schultz N , et al. Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity[J]. Nature Communications, 2018, 9(1). [19] Chen W T , Lu A , Craessaerts K , et al. Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer's Disease[J]. Cell, 2020. [20] Giacomell S , Fredrik Salmén, Terebieniec B K , et al. Spatially resolved transcriptome profiling in model plant species[J]. Nature Plants, 2017. [21] David Fawkner-Corbett, et al. Spatiotemporal analysis of human intestinal development at single-cell resolution[J]. Cell. 2021 Feb 4;184(3):810-826.e23. doi: 10.1016/j.cell.2020.12.016. Epub 2021 Jan 5. 更多详情请咨询 伯豪生物在线客服 伯豪生物提供 空间转录组测序专业技术服务解决方案咨询热线:021-58955370 (打电话) 企业官网:https://www.shbio.com (在线留言) 企业邮箱:market@shbio.com (写邮件)
伯豪生物项目发文: 1、Clinical challenges of tissue preparation for spatial transcriptome 2、Single-cell and spatial analysis reveal interaction of FAP+ fibroblasts and SPP1+ macrophages in colorectal cancer