Optimized single-nucleus transcriptional profiling by combinatorial indexing

Martin, Beth; Qiu, Chengxiang; Nichols, Eva; Phung, Melissa; Gladden, Rula Green; Srivatsan, Sanjay; Blecher‐Gonen, Ronnie; Beliveau, Brian J.; Trapnell, Cole; Cao, Junyue; Shendure, Jay

doi:10.1038/s41596-022-00752-0

Cited by 59 publications

(68 citation statements)

References 21 publications

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“…With the original sci-RNA-seq3 protocol [20], we generated 1,008,204 single-nucleus transcriptomes from 110 age-, sex-, and hemisphere-matched samples representing 28 brain regions of 10 year-old (mid-adult aged) macaques (N=3 animals; 2 female). Over the course of the study, we implemented improvements in nuclei isolation and preservation [21] which increased nuclear transcriptome recovery by 60% (median unique molecular indices [UMIs], before=202, after=320) and, consequently, the number of nuclei passing our UMI threshold. With the improved protocol, we generated an additional 1,702,081 singlenucleus transcriptomes from the right hemisphere of two animals, the vast majority (N=1,579,908) of which were sampled from 27 brain regions of a single 10 year-old female macaque.…”

Section: Resultsmentioning

confidence: 99%

“…For two out of the three experimental batches in our dataset, we used a protocol closely adhering to the sci-RNA-seq3 protocol described by Cao et al [19]. For the third batch, we used the improved protocol (“tiny sci”) described by Martin et al [21]. Sample order was randomized between the first two batches, and within the third batch, to minimize batch effects and other technical artifacts.…”

Section: Methodsmentioning

confidence: 99%

“…For the DSP/MeOH nuclei isolations and library construction based on Martin et al [21], we used hypotonic lysis buffer solution B (with BSA) for small vol-ume tiny sci-RNA-seq3 nuclei isolation methods. For sci-RNA-seq3 library construction, we loaded 20,000 nuclei per index 1 reverse transcriptase (RT) well in a 384 RT-well experiment with mouse and human brain added as separate quality control nuclei and nuclei from cell lines HEK293T (RRID:CVCL_0063) and NIH/3T3 (RRID:CVCL_0594) combined as barnyard controls per RT plate.…”

Section: Snrna-seq Data Generationmentioning

confidence: 99%

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A single-cell multi-omic atlas spanning the adult rhesus macaque brain

Chiou

Huang

Bohlen

et al. 2022

Preprint

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Cataloging the diverse cellular architecture of the primate brain is crucial for understanding cognition, behavior and disease in humans. Here, we generated a brain-wide single-cell multimodal molecular atlas of the rhesus macaque brain. Altogether, we profiled 2.58M transcriptomes and 1.59M epigenomes from single nuclei sampled from 30 regions across the adult brain. Cell composition differed extensively across the brain, revealing cellular signatures of region-specific functions. We also identified 1.19M candidate regulatory elements, many novel, allowing us to explore the landscape of cis-regulatory grammar and neurological disease risk in a cell-type- specific manner. Together, this multi-omic atlas provides an open resource for investigating the evolution of the human brain and identifying novel targets for disease interventions.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Snrna-seq Data Generationmentioning

confidence: 99%

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A single-cell multi-omic atlas spanning the adult rhesus macaque brain

Chiou

Huang

Bohlen

et al. 2022

Preprint

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“…We have now performed over 350 optimization experiments to overcome the above limitations (representative examples are shown in Figure S1 and S2; Methods ). Several test conditions were inspired by optimizations described in recently developed or optimized single-cell techniques (Ma et al, 2020; Martin et al, 2021). The major improvements of the resulting method, EasySci-RNA ( Figure 1A ), include: (i) one million single-cell transcriptomes prepared at a library preparation cost of around $700, less than 1/100 the cost of the commercial platforms (Ding et al, 2020) ( Figure 1B and 1C) .…”

Section: Introductionmentioning

confidence: 99%

“…(C) Bar plot comparing different single-cell RNA-seq methods in terms of their cost of the library preparation for 1 million single-nucleus transcriptomes. The cost of sci-RNA-seq3 and SPLiT-seq were calculated using data from (Martin et al, 2021; Rosenberg et al, 2018). The cost of other techniques was calculated using data from (Ding et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

A global view of aging and Alzheimer’s pathogenesis-associated cell population dynamics and molecular signatures in the human and mouse brains

Sziraki

Lee

et al. 2022

Preprint

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Although several studies have applied single-cell approaches to explore gene expression changes in aged brains, they were limited by the relatively shallow sampling of brain cell populations, and thus may have failed to capture aspects of the molecular signatures and dynamics of rare cell types associated with aging and diseases. Here, we set out to investigate the age-dependent dynamics of transcription and chromatin accessibility across diverse brain cell types. With EasySci, an extensively improved single-cell combinatorial indexing strategy, we profiled ~1.5 million single-cell transcriptomes and ~400,000 single-cell chromatin accessibility profiles across mouse brains spanning different ages, genotypes, and both sexes. With a novel computational framework designed for characterizing cellular subtypes based on the expression of both genes and exons, we identified > 300 cell subtypes and deciphered the underlying molecular programs and spatial locations of rare cell types (e.g., pinealocytes, tanycytes) and subtypes. Leveraging these data, we generate a global readout of age-dependent cell population dynamics with high cellular subtype resolution, providing insights into cell types that expand (e.g., rare astrocytes and vascular leptomeningeal cells in the olfactory bulb, reactive microglia and oligodendrocytes) or are depleted (e.g., neuronal progenitors, neuroblasts, committed oligodendrocyte precursors) as age progresses. Furthermore, we explored cell-type-specific responses to genetic perturbations associated with Alzheimer's disease (AD) and identify rare cell types depleted (e.g., mt-Cytb+, mt-Rnr2+ choroid plexus epithelial cells) or enriched (e.g., Col25a1+, Ndrg1+ interbrain and midbrain neurons) in both AD models. Key findings are consistent between males and females, validated across the transcriptome, chromatin accessibility, and spatial analyses. Finally, we profiled a total of 118,240 single-nuclei transcriptomes from twenty-four human brain samples derived from control and AD patients, revealing highly cell-type-specific and region-specific gene expression changes associated with AD pathogenesis. Critical AD-associated gene signatures were validated in both human and mice. In summary, these data comprise a rich resource for exploring cell-type-specific dynamics and the underlying molecular mechanisms in both normal and pathological mammalian aging.

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Recent Progress in MOF‐Aerogel Fabrication and Applications

Guo,

Mashhadimoslem,

Choopani

et al. 2024

Small

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Recent advancements in metal–organic frameworks (MOFs) underscore their significant potential in chemical and materials research, owing to their remarkable properties and diverse structures. Despite challenges like intrinsic brittleness, powdered crystalline nature, and limited stability impeding direct applications, MOF‐based aerogels have shown superior performance in various areas, particularly in water treatment and contaminant removal. This review highlights the latest progress in MOF‐based aerogels, with a focus on hybrid systems incorporating materials like graphene, carbon nanotube, silica, and cellulose in MOF aerogels, which enhance their functional properties. The manifold advantages of MOF‐based aerogels in energy storage, adsorption, and catalysis are discussed, with an emphasizing on their improved stability, processability, and ease of handling. This review aims to unlock the potential of MOF‐based aerogels and their real‐world applications. Aerogels are expected to reshape the technological landscape of MOFs through enhanced stability, adaptability, and efficiency.

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Optimized single-nucleus transcriptional profiling by combinatorial indexing

Cited by 59 publications

References 21 publications

A single-cell multi-omic atlas spanning the adult rhesus macaque brain

A single-cell multi-omic atlas spanning the adult rhesus macaque brain

A global view of aging and Alzheimer’s pathogenesis-associated cell population dynamics and molecular signatures in the human and mouse brains

Recent Progress in MOF‐Aerogel Fabrication and Applications

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