Amanda Raine

Exploring a pico-well based scRNA-seq method (HIVE) for simplified processing of equine bronchoalveolar lavage cells

Fegraeus, Kim; Riihimäki, Miia; Nordlund, Jessica; Akula, Srinivas et al.

Ingår i PLOS ONE, 2025

• DOI för Exploring a pico-well based scRNA-seq method (HIVE) for simplified processing of equine bronchoalveolar lavage cells
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Multi-modal single cell sequencing of B cells in primary Sjögren's Syndrome.

Arvidsson, Gustav; Czarnewski, Paulo; Johansson, Alina; Raine, Amanda et al.

Ingår i Arthritis & Rheumatology, s. 255-267, 2024

• DOI för Multi-modal single cell sequencing of B cells in primary Sjögren's Syndrome.
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A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing

Lysenkova, Mariya; Arvidsson, Gustav; Bunikis, Ignas; Lundmark, Anders et al.

Ingår i Life Science Alliance, 2024

• DOI för A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing
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An endothelial regulatory module links blood pressure regulation with elite athletic performance

Fegraeus, Kim; Rosengren, Maria K.; Naboulsi, Rakan; Orlando, Ludovic et al.

Ingår i PLOS Genetics, 2024

• DOI för An endothelial regulatory module links blood pressure regulation with elite athletic performance
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Comparison of high-throughput single-cell RNA-seq methods for ex vivo drug screening

Gezelius, Henrik; Enblad, Anna Pia; Lundmark, Anders; Åberg, Martin et al.

Ingår i NAR Genomics and Bioinformatics, 2024

• DOI för Comparison of high-throughput single-cell RNA-seq methods for ex vivo drug screening
• Ladda ner fulltext (pdf) av Comparison of high-throughput single-cell RNA-seq methods for ex vivo drug screening

Exploring a pico-well based scRNA-seq method (HIVE) for simplified processing of equine bronchoalveolar lavage cells

Fegraeus, Kim; Riihimäki, Miia; Nordlund, Jessica; Akula, Srinivas et al.

Ingår i PLOS ONE, 2025

• DOI för Exploring a pico-well based scRNA-seq method (HIVE) for simplified processing of equine bronchoalveolar lavage cells
• Ladda ner fulltext (pdf) av Exploring a pico-well based scRNA-seq method (HIVE) for simplified processing of equine bronchoalveolar lavage cells

Multi-modal single cell sequencing of B cells in primary Sjögren's Syndrome.

Arvidsson, Gustav; Czarnewski, Paulo; Johansson, Alina; Raine, Amanda et al.

Ingår i Arthritis & Rheumatology, s. 255-267, 2024

• DOI för Multi-modal single cell sequencing of B cells in primary Sjögren's Syndrome.
• Ladda ner fulltext (pdf) av Multi-modal single cell sequencing of B cells in primary Sjögren's Syndrome.

A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing

Lysenkova, Mariya; Arvidsson, Gustav; Bunikis, Ignas; Lundmark, Anders et al.

Ingår i Life Science Alliance, 2024

• DOI för A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing
• Ladda ner fulltext (pdf) av A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing

An endothelial regulatory module links blood pressure regulation with elite athletic performance

Fegraeus, Kim; Rosengren, Maria K.; Naboulsi, Rakan; Orlando, Ludovic et al.

Ingår i PLOS Genetics, 2024

• DOI för An endothelial regulatory module links blood pressure regulation with elite athletic performance
• Ladda ner fulltext (pdf) av An endothelial regulatory module links blood pressure regulation with elite athletic performance

Comparison of high-throughput single-cell RNA-seq methods for ex vivo drug screening

Gezelius, Henrik; Enblad, Anna Pia; Lundmark, Anders; Åberg, Martin et al.

Ingår i NAR Genomics and Bioinformatics, 2024

• DOI för Comparison of high-throughput single-cell RNA-seq methods for ex vivo drug screening
• Ladda ner fulltext (pdf) av Comparison of high-throughput single-cell RNA-seq methods for ex vivo drug screening

Genomic, transcriptomic and epigenomic sequencing data of the B-cell leukemia cell line REH

Lysenkova Wiklander, Mariya; Övernäs, Elin; Lagensjö, Johanna; Raine, Amanda et al.

Ingår i BMC Research Notes, 2023

• DOI för Genomic, transcriptomic and epigenomic sequencing data of the B-cell leukemia cell line REH
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Single-cell transcriptomics delineates the immune cell landscape in equine lower airways and reveals upregulation of FKBP5 in horses with asthma.

Riihimäki, Miia; Fegraeus, K. Jaderkvist; Nordlund, Jessica; Waern, Ida et al.

Ingår i Scientific Reports, s. 16261, 2023

• DOI för Single-cell transcriptomics delineates the immune cell landscape in equine lower airways and reveals upregulation of FKBP5 in horses with asthma.
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Comparison of EM-seq and PBAT methylome library methods for low-input DNA

Han, Yanan; Zheleznyakova, Galina Yurevna; Marincevic-Zuniga, Yanara; Kakhki, Majid Pahlevan et al.

Ingår i Epigenetics, s. 1195-1204, 2022

• DOI för Comparison of EM-seq and PBAT methylome library methods for low-input DNA
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Environmentally induced DNA methylation is inherited across generations in an aquatic keystone species

Feiner, Nathalie; Radersma, Reinder; Vasquez, Louella; Ringner, Markus et al.

Ingår i iScience, 2022

• DOI för Environmentally induced DNA methylation is inherited across generations in an aquatic keystone species
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scSPLAT, a scalable plate-based protocol for single cell WGBS library preparation

Raine, Amanda; Lundmark, Anders; Annett, Alva; Wiman, Ann-Christin et al.

Ingår i Scientific Reports, 2022

• DOI för scSPLAT, a scalable plate-based protocol for single cell WGBS library preparation
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Quantitative Transcriptome Analysis of Purified Equine Mast Cells Identifies a Dominant Mucosal Mast Cell Population with Possible Inflammatory Functions in Airways of Asthmatic Horses

Akula, Srinivas; Riihimaki, Miia; Waern, Ida; Abrink, Magnus et al.

Ingår i International Journal of Molecular Sciences, 2022

• DOI för Quantitative Transcriptome Analysis of Purified Equine Mast Cells Identifies a Dominant Mucosal Mast Cell Population with Possible Inflammatory Functions in Airways of Asthmatic Horses
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Leukocytes with chromosome Y loss have reduced abundance of the cell surface immunoprotein CD99

Mattisson, Jonas; Danielsson, Marcus; Hammond, Maria; Davies, Hanna et al.

Ingår i Scientific Reports, 2021

• DOI för Leukocytes with chromosome Y loss have reduced abundance of the cell surface immunoprotein CD99
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The SEQC2 epigenomics quality control (EpiQC) study

Foox, Jonathan; Nordlund, Jessica; Lalancette, Claudia; Gong, Ting et al.

Ingår i Genome Biology, 2021

• DOI för The SEQC2 epigenomics quality control (EpiQC) study
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Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole-genome sequencing

Nordlund, Jessica; Marincevic-Zuniga, Yanara; Cavelier, Lucia; Raine, Amanda et al.

Ingår i Scientific Reports, 2020

• DOI för Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole-genome sequencing
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Data quality of whole genome bisulfite sequencing on Illumina platforms

Raine, Amanda; Liljedahl, Ulrika; Nordlund, Jessica

Ingår i PLOS ONE, 2018

• DOI för Data quality of whole genome bisulfite sequencing on Illumina platforms
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Transcriptome sequencing in pediatric acute lymphoblastic leukemia identifies fusion genes associated with distinct DNA methylation profiles

Marincevic-Zuniga, Yanara; Dahlberg, Johan; Nilsson, Sara; Raine, Amanda et al.

Ingår i Journal of Hematology & Oncology, 2017

• DOI för Transcriptome sequencing in pediatric acute lymphoblastic leukemia identifies fusion genes associated with distinct DNA methylation profiles
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SPlinted Ligation Adapter Tagging (SPLAT), a novel library preparation method for whole genome bisulphite sequencing

Raine, Amanda; Manlig, Erika; Wahlberg, Per; Syvänen, Ann-Christine et al.

Ingår i Nucleic Acids Research, 2017

• DOI för SPlinted Ligation Adapter Tagging (SPLAT), a novel library preparation method for whole genome bisulphite sequencing
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DNA methylome analysis of acute lymphoblastic leukemia cells reveals stochastic de novo DNA methylation in CpG islands

Wahlberg, Per; Lundmark, Anders; Nordlund, Jessica; Busche, Stephan et al.

Ingår i Epigenomics, s. 1367-1387, 2016

• DOI för DNA methylome analysis of acute lymphoblastic leukemia cells reveals stochastic de novo DNA methylation in CpG islands
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Deep targeted sequencing in pediatric acute lymphoblastic leukemia unveils distinct mutational patterns between genetic subtypes and novel relapse-associated genes

Lindqvist, C. Mårten; Lundmark, Anders; Nordlund, Jessica; Freyhult, Eva et al.

Ingår i Oncotarget, s. 64071-64088, 2016

• DOI för Deep targeted sequencing in pediatric acute lymphoblastic leukemia unveils distinct mutational patterns between genetic subtypes and novel relapse-associated genes

Histological characterization of orphan transporter MCT14 (SLC16A14) shows abundant expression in mouse CNS and kidney

Roshanbin, Sahar; Lindberg, Frida; Lekholm, Emilia; Perland, Emelie et al.

Ingår i BMC Neuroscience, 2016

• DOI för Histological characterization of orphan transporter MCT14 (SLC16A14) shows abundant expression in mouse CNS and kidney
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The Mutational Landscape in Pediatric Acute Lymphoblastic Leukemia Deciphered by Whole Genome Sequencing

Lindqvist, C Mårten; Nordlund, Jessica; Ekman, Diana; Johansson, Anna et al.

Ingår i Human Mutation, s. 118-128, 2015

• DOI för The Mutational Landscape in Pediatric Acute Lymphoblastic Leukemia Deciphered by Whole Genome Sequencing

PAT4 is abundantly expressed in excitatory and inhibitory neurons as well as epithelial cells

Roshanbin, Sahar; Hellsten, Sofie V; Tafreshiha, Atieh; Zhu, Yinan et al.

Ingår i Brain Research, s. 12-25, 2014

• DOI för PAT4 is abundantly expressed in excitatory and inhibitory neurons as well as epithelial cells
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Simultaneous binding of trigger factor and signal recognition particle to the E. coli ribosome.

Raine, Amanda; Ivanova, Natalia; Wikberg, Jarl E S; Ehrenberg, Måns

Ingår i Biochimie, s. 495-500, 2004

Targeting and insertion of heterologous membrane proteins in E. coli

Raine, A; Ullers, R; Pavlov, M; Luirink, J et al.

Ingår i Biochimie, s. 659-668, 2003

Interplay of signal recognition particle and trigger factor at L23 near the nascent chain exit site on the Escherichia coli ribosome

Ullers, R S; Houben, E N G; Raine, A; ten Hagen-Jongman, C M et al.

Ingår i J. Cell Biology, s. 679-684, 2003

Computational and Statistical Analysis of Array-Based DNA Methylation Data

Nordlund, Jessica; Backlin, Carin; Raine, Amanda

Ingår i Cancer Bioinformatics, s. 173-191, Springer, 2019

• DOI för Computational and Statistical Analysis of Array-Based DNA Methylation Data

Identification of somatic single nucleotide variants inleukemia by targeted sequencing of non-indexed overlapping pools

Lindqvist, Carl Mårten; Dahlberg, Johan; Raine, Amanda; Övernäs, Elin et al.

Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia with linked-read whole genome sequencing

Nordlund, Jessica; Marincevic-Zuniga, Yanara; Cavelier, Lucia; Raine, Amanda et al.