| 1. |
- Baber, Robert, et al.
(författare)
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Development Of A Versatile And Low-Cost Droplet Microfluidic Platform For Single-Nuclei Atac-Sequencing
- 2021
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Ingår i: MicroTAS 2021 - 25th International Conference on Miniaturized Systems for Chemistry and Life Sciences. - : Chemical and Biological Microsystems Society. ; , s. 1767-1768
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Konferensbidrag (refereegranskat)abstract
- Profiling the genome-wide chromatin accessibility via Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) provides important insights into genome regulation that help understanding different biological processes. However, the heterogeneity of cell populations must be considered to gain a full understanding which is possible through droplet microfluidics enabling single-nuclei ATAC-seq (snATAC-seq). Droplet microfluidic platforms commonly used to perform snATAC-seq lack versatility and cannot be easily adapted to custom assay requirements. Here, we present a fully versatile, low-cost droplet microfluidic platform that can be readily adapted to run various droplet-based library preparation protocols for analyses at single-cell resolution such as snATAC-seq.
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| 2. |
- Banijamali, Mahsan, et al.
(författare)
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Characterizing single extracellular vesicles by droplet barcode sequencing for protein analysis
- 2022
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Ingår i: Journal of Extracellular Vesicles. - : Wiley. - 2001-3078. ; 11:11
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Tidskriftsartikel (refereegranskat)abstract
- Small extracellular vesicles (sEVs) have in recent years evolved as a source of biomarkers for disease diagnosis and therapeutic follow up. sEV samples derived from multicellular organisms exhibit a high heterogeneous repertoire of vesicles which current methods based on ensemble measurements cannot capture. In this work we present droplet barcode sequencing for protein analysis (DBS-Pro) to profile surface proteins on individual sEVs, facilitating identification of sEV-subtypes within and between samples. The method allows for analysis of multiple proteins through use of DNA barcoded affinity reagents and sequencing as readout. High throughput single vesicle profiling is enabled through compartmentalization of individual sEVs in emulsion droplets followed by droplet barcoding through PCR. In this proof-of-concept study we demonstrate that DBS-Pro allows for analysis of single sEVs, with a mixing rate below 2%. A total of over 120,000 individual sEVs obtained from a NSCLC cell line and from malignant pleural effusion (MPE) fluid of NSCLC patients have been analyzed based on their surface proteins. We also show that the method enables single vesicle surface protein profiling and by extension characterization of sEV-subtypes, which is essential to identify the cellular origin of vesicles in heterogenous samples.
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| 3. |
- Huang, Yuqing, et al.
(författare)
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Room-temperature electron spin polarization exceeding 90% in an opto-spintronic semiconductor nanostructure via remote spin filtering
- 2021
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Ingår i: Nature Photonics. - : NATURE RESEARCH. - 1749-4885 .- 1749-4893. ; 15, s. 475-482
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Tidskriftsartikel (refereegranskat)abstract
- An exclusive advantage of semiconductor spintronics is its potential for opto-spintronics, which will allow integration of spin-based information processing/storage with photon-based information transfer/communications. Unfortunately, progress has so far been severely hampered by the failure to generate nearly fully spin-polarized charge carriers in semiconductors at room temperature. Here we demonstrate successful generation of conduction electron spin polarization exceeding 90% at room temperature without a magnetic field in a non-magnetic all-semiconductor nanostructure, which remains high even up to 110 degrees C. This is accomplished by remote spin filtering of InAs quantum-dot electrons via an adjacent tunnelling-coupled GaNAs spin filter. We further show that the quantum-dot electron spin can be remotely manipulated by spin control in the adjacent spin filter, paving the way for remote spin encoding and writing of quantum memory as well as for remote spin control of spin-photon interfaces. This work demonstrates the feasibility to implement opto-spintronic functionality in common semiconductor nanostructures. An electron spin polarization of 90% is achieved in a non-magnetic nanostructure at room temperature without magnetic field. This is accomplished by remote spin filtering of InAs quantum-dot electrons via an adjacent tunnelling-coupled GaNAs spin filter.
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| 4. |
- Höjer, Pontus, et al.
(författare)
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BLR : a flexible pipeline for haplotype analysis of multiple linked-read technologies
- 2023
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 51:22
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Tidskriftsartikel (refereegranskat)abstract
- Linked-read sequencing promises a one-method approach for genome-wide insights including single nucleotide variants (SNVs), structural variants, and haplotyping. We introduce Barcode Linked Reads (BLR), an open-source haplotyping pipeline capable of handling millions of barcodes and data from multiple linked-read technologies including DBS, 10× Genomics, TELL-seq and stLFR. Running BLR on DBS linked-reads yielded megabase-scale phasing with low (<0.2%) switch error rates. Of 13616 protein-coding genes phased in the GIAB benchmark set (v4.2.1), 98.6% matched the BLR phasing. In addition, large structural variants showed concordance with HPRC-HG002 reference assembly calls. Compared to diploid assembly with PacBio HiFi reads, BLR phasing was more continuous when considering switch errors. We further show that integrating long reads at low coverage (∼10×) can improve phasing contiguity and reduce switch errors in tandem repeats. When compared to Long Ranger on 10× Genomics data, BLR showed an increase in phase block N50 with low switch-error rates. For TELL-Seq and stLFR linked reads, BLR generated longer or similar phase block lengths and low switch error rates compared to results presented in the original publications. In conclusion, BLR provides a flexible workflow for comprehensive haplotype analysis of linked reads from multiple platforms.
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| 5. |
- Höjer, Pontus
(författare)
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Exploring human variations by droplet barcoding
- 2024
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Biological variations are being explored at ever-increasing rates through the rapid advancement of analytical techniques. Techniques like massively parallel sequencing empower scientists to accurately differentiate individuals’ genetic compositions, cellular functionalities, and healthy tissue from diseased. The knowledge gained from these techniques brings us ever closer to grasping the complexities of life, contributing to human development. Still, to fully elucidate biological variations in different samples requires novel sensitive and high- throughput techniques, capable of placing everything in its correct context. One such technique gaining promise is droplet barcoding. Droplet barcoding leverages emulsion droplets to segregate samples into their functional components, coupled with barcodes that can group tagged molecules following sequencing. This technique constitutes a versatile tool for studying biological variations in both the phenotype and genotype. This thesis leverages droplet barcoding to explore variations relating to human biology. Droplet barcoding was used to study phenotype variations, looking at protein compositions in single extracellular vesicles (Paper I) and single cells (Paper II). Paper I studies extracellular vesicles which are naturally released from cells. They carry heterogeneous protein signatures that can inform about their cellular origin. Tens of thousands of extracellular vesicles were profiled, including approximately 25,000 from lung cancer patients. From these protein profiles, extracellular vesicles could be grouped into putative subtypes. Paper II presents a novel method for studying single cells which was used to characterize blood-derived immune cells. The method enabled the identification of most major immune cell lineages. Haplotype-resolved genetic variations were analyzed using a linked read sequencing method based on droplet barcoding. Linked-read sequencing conserves long-range information from short-read sequencing by co- barcoding subsections of long DNA fragments. Paper III presents an open-source pipeline (BLR) for whole genome haplotyping using linked reads. BLR generates accurate and continuous haplotypes, outperforming PacBio HiFi-based diploid assembly. We further show that integration with low-coverage long-read data can improve phasing accuracy in tandem repeats. With 10X Genomics linked reads, BLR generated more continuous haplotypes compared to other workflows. Paper IV applies linked read sequencing to reveal the haplotype complexities of cancer genomes. In two patients with colorectal cancer, we identified several large-scale aberrations impacting cancer-related genes. Additionally, several short somatic variants were found to impact nearly all oncogenic networks identified by TCGA. Demonstrating the importance of haplotype-resolved analysis for cancer genomics, one patient exhibited two nonsense mutations on separate haplotypes in the well-known colorectal cancer gene APC.
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| 6. |
- Höjer, Pontus, et al.
(författare)
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Identification of Major Immune Cell Lineages with DBS-Pro
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Proteins play a pivotal role in cellular function and heterogeneity. Understanding cellular diversity at the proteome level necessitates sensitive single-cell assays with high throughput. While current sequencing-based methods offer promise, they often face limitations, including reliance on expensive and inaccessible commercial platforms. Here, we have adopted the DBS-Pro method, utilizing site-specific oligonucleotide-conjugated antibodies, to analyze surface proteins in single cells. The method uses cheap degenerated barcode oligonucleotides and a simple microfluidics setup for cell encapsulation. A sample of PBMCs was examined using a panel targeting six separate immune cell markers. Using this panel we could quantify marker expression on 1,307 cells, identifying major immune cell lineages including CD4+ T-cells, CD8+ T-cells, monocytes, and B-cells. While recognizing the need for protocol improvements, our results present a promising approach for single-cell proteomics.
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| 7. |
- Puttisong, Yuttapoom, et al.
(författare)
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Effect of Crystal Symmetry on the Spin States of Fe3+ and Vibration Modes in Lead-free Double-Perovskite Cs2AgBi(Fe)Br-6
- 2020
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Ingår i: The Journal of Physical Chemistry Letters. - : AMER CHEMICAL SOC. - 1948-7185. ; 11:12, s. 4873-4878
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Tidskriftsartikel (refereegranskat)abstract
- We show by electron spin resonance (ESR) and Raman spectroscopies that the crystal phase transition of the lead-free double-perovskite Cs2AgBiBr6 has a profound symmetry-breaking effect on the high spin states of, for example, a transition-metal ion Fe3+ and the vibrational modes. It lifts their degeneracy when the crystal undergoes the cubic-tetragonal phase transition, splitting the six-fold degenerate S = 5/2 state of Fe3+ to three Kramer doublets and the enharmonic breathing mode T-g of the MBr6 octahedra (M = Ag, Bi, Fe) into E-g + A(g). The magnitudes of both spin and Raman line splitting are shown to directly correlate with the strength of the tetragonal strain field. This work, in turn, demonstrates the power of the ESR and Raman spectroscopies in probing structural phase transitions and in providing in-depth information on the interplay between the structural, spin, and vibrational properties of lead-free double perovskites, a newly emerging and promising class of materials for low-cost and high-efficiency photovoltaics and optoelectronics.
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| 8. |
- Sahlén, Pelin, et al.
(författare)
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Chromatin interactions in differentiating keratinocytes reveal novel atopic dermatitis– and psoriasis-associated genes
- 2020
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Ingår i: Journal of Allergy and Clinical Immunology. - : Mosby Inc.. - 0091-6749 .- 1097-6825.
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Tidskriftsartikel (refereegranskat)abstract
- Background: Hundreds of variants associated with atopic dermatitis (AD) and psoriasis, 2 common inflammatory skin disorders, have previously been discovered through genome-wide association studies (GWASs). The majority of these variants are in noncoding regions, and their target genes remain largely unclear. Objective: We sought to understand the effects of these noncoding variants on the development of AD and psoriasis by linking them to the genes that they regulate. Methods: We constructed genomic 3-dimensional maps of human keratinocytes during differentiation by using targeted chromosome conformation capture (Capture Hi-C) targeting more than 20,000 promoters and 214 GWAS variants and combined these data with transcriptome and epigenomic data sets. We validated our results with reporter assays, clustered regularly interspaced short palindromic repeats activation, and examination of patient gene expression from previous studies. Results: We identified 118 target genes of 82 AD and psoriasis GWAS variants. Differential expression of 58 of the 118 target genes (49%) occurred in either AD or psoriatic lesions, many of which were not previously linked to any skin disease. We highlighted the genes AFG1L, CLINT1, ADO, LINC00302, and RP1-140J1.1 and provided further evidence for their potential roles in AD and psoriasis. Conclusions: Our work focused on skin barrier pathology through investigation of the interaction profile of GWAS variants during keratinocyte differentiation. We have provided a catalogue of candidate genes that could modulate the risk of AD and psoriasis. Given that only 35% of the target genes are the gene nearest to the known GWAS variants, we expect that our work will contribute to the discovery of novel pathways involved in AD and psoriasis.
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| 9. |
- Shi, Yuchen, et al.
(författare)
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A comparative study of high-quality C-face and Si-face 3C-SiC(1 1 1) grown on off-oriented 4H-SiC substrates
- 2019
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Ingår i: Journal of Physics D. - : Biopress Ltd. - 0022-3727 .- 1361-6463. ; 52:34
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Tidskriftsartikel (refereegranskat)abstract
- We present a comparative study of the C-face and Si-face of 3C-SiC(111) grown on off-oriented 4H-SiC substrates by the sublimation epitaxy. By the lateral enlargement method, we demonstrate that the high-quality bulk-like C-face 3C-SiC with thickness of ~1 mm can be grown over a large single domain without double positioning boundaries (DPBs), which are known to have a strongly negative impact on the electronic properties of the material. Moreover, the C-face sample exhibits a smoother surface with one unit cell height steps while the surface of the Si-face sample exhibits steps twice as high as on the C-face due to step-bunching. High-resolution XRD and low temperature photoluminescence measurements show that C-face 3C-SiC can reach the same high crystalline quality as the Si-face 3C-SiC. Furthermore, cross-section studies of the C- and Si-face 3C-SiC demonstrate that in both cases an initial homoepitaxial 4H-SiC layer followed by a polytype transition layer are formed prior to the formation and lateral expansion of 3C-SiC layer. However, the transition layer in the C-face sample is extending along the step-flow direction less than that on the Si-face sample, giving rise to a more fairly consistent crystalline quality 3C-SiC epilayer over the whole sample compared to the Si-face 3C-SiC where more defects appeared on the surface at the edge. This facilitates the lateral enlargement of 3C-SiC growth on hexagonal SiC substrates.
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| 10. |
- Siga, Humam, et al.
(författare)
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Resolving the haplotype complexity of colorectal cancer genomes with droplet barcode sequencing
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Cancer genomes are prone to elevated rates of genomic alterations. Massive parallel sequencing technologies can answer some questions related to these aberrations; however, they remain limited when it comes to resolving the haplotype information. In this study, we applied the linked-read droplet barcode sequencing (DBS) technology to resolve the haplotype complexity of colorectal cancer genomes, using paired tumor/normal samples. The results show short somatic variants associated with almost all TCGA-identified oncogenic pathways. Several cancer-related genes had multiple variants in either one or both haplotypes. In the tumor suppressor gene APC, two nonsense variants ~2kb apart on separate haplotypes were identified in one patient. Additionally, a number haplotype-resolved somatic structural variants (SV) and copy number alterations (CNA) were detected and correlated with the small variants. The study demonstrates that DBS technology can characterize complex genetic variations in a haplotype context, revealing an extra layer of cancer genome complexity.
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