singlecell rna sequencing of batch chlamydomonas cultures

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Single-cell RNA sequencing of batch Chlamydomonas cultures ...

Single-cell RNA sequencing of batch Chlamydomonas cultures reveals heterogeneity in their diurnal cycle phase Plant Cell . 2021 May 31;33(4):1042-1057. doi: 10.1093/plcell/koab025.

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Single-cell RNA sequencing of batch Chlamydomonas cultures ...

May 31, 2021  We show that single-cell RNA-seq (scRNA-seq) can be applied to Chlamydomonas cultures to reveal the heterogeneity in bulk cultures is largely driven by diurnal ... Matteo Pellegrini, Single-cell RNA sequencing of batch Chlamydomonas cultures reveals heterogeneity in their diurnal cycle phase, The Plant Cell, Volume 33, Issue 4, April 2021 ...

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Single-Cell RNA Sequencing of Batch Chlamydomonas Cultures ...

Sep 16, 2020  One-sentence summary We show that single-cell RNA-seq (scRNA-seq) can be applied to Chlamydomonas cultures to reveal the that heterogenity in bulk cultures is largely driven by diurnal cycle phases. The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (plantcell ...

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Single-cell RNA sequencing of batch Chlamydomonas cultures ...

May 01, 2021  @article{osti_1814430, title = {Single-cell RNA sequencing of batch Chlamydomonas cultures reveals heterogeneity in their diurnal cycle phase.}, author = {Ma, Feiyang and Salomé, Patrice A and Merchant, Sabeeha S and Pellegrini, Matteo}, abstractNote = {The photosynthetic unicellular alga Chlamydomonas (Chlamydomonas reinhardtii) is a versatile reference for algal biology because of its

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RESEARCH ARTICLE - bioRxiv

Sep 15, 2020  Chlamydomonas single cell RNA sequencing RESEARCH ARTICLE Single-Cell RNA Sequencing of Batch Chlamydomonas Cultures Reveals Heterogeneity in their Diurnal Cycle Phase Feiyang Ma 1,5, Patrice A. Salomé 2,5, Sabeeha S. Merchant 2,3,4,6 and Matteo Pellegrini 1,4,6 1

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Single-Cell RNA Sequencing of Batch Chlamydomonas Cultures ...

Sep 16, 2020  Single-Cell RNA Sequencing of Batch Chlamydomonas Cultures Reveals Heterogeneity in their Diurnal Cycle Phase Feiyang Ma 1,5 , Patrice A. Salomé 2,5

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Apr 07, 2021  Single-Cell RNA Sequencing of Batch Chlamydomonas Cultures Reveals their Heterogeneity and Place Along the Diurnal Cycle: Organism: Chlamydomonas reinhardtii: Experiment type: Expression profiling by high throughput sequencing: Summary: We did single cell RNA sequencing on cultured chlamydomonas cells.

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Plantae The final (algal) frontier: Chlamydomonas enters ...

Apr 05, 2021  The final (algal) frontier: Chlamydomonas enters the age of single cell RNA-seq. April 5, 2021 / in The Plant Cell: In a Nutshell / by Plant Cell. Ma, Salomé and colleagues use single cell RNA-seq (scRNA-seq) on the unicellular green alga Chlamydomonas reinhardtii as a proof-of-concept for the application of this method to unicellular algae.

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Co-expression networks in Chlamydomonas reveal significant ...

Only a single-cell RNA-seq (scRNA-seq) analysis will allow a more detailed dissection of the diurnal contribution to the Chlamydomonas transcriptome landscape. To begin to explore this possibility, we recently performed scRNA-seq on almost 60,000 Chlamydomonas cells grown under three conditions and from two genotypes.

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The Contemporary Theory of Metaphor

Single-cell RNA sequencing of batch Chlamydomonas cultures reveals heterogeneity in their diurnal cycle phase.

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Compilation of gene lists for module score analysis and ...

Single-cell RNA sequencing of batch Chlamydomonas cultures reveals heterogeneity in their diurnal cycle phase Plant Cell , Feb 2, 2021; DOI: 10.1093/plcell/koab025

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Co-expression networks in Chlamydomonas reveal significant ...

May 01, 2021  @article{osti_1814429, title = {Co-expression networks in Chlamydomonas reveal significant rhythmicity in batch cultures and empower gene function discovery.}, author = {Salomé, Patrice A and Merchant, Sabeeha S}, abstractNote = {The unicellular green alga Chlamydomonas reinhardtii is a choice reference system for the study of photosynthesis and chloroplast metabolism, cilium assembly

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A test metric for assessing single-cell RNA-seq batch ...

Dec 20, 2018  Fig. 1: Batch types and the concept of kBET. Estimating the batch effect in single-cell RNA-seq data. a, Biological and technical replicates have different origins. Technical replicates are ...

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Patrice A Salomé's research works University of ...

Patrice A Salomé's 61 research works with 3,354 citations and 7,183 reads, including: Single-Cell RNA Sequencing of Batch Chlamydomonas Cultures Reveals Heterogeneity in their Diurnal Cycle Phase

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Single-cell transcriptomics reveals the heterogeneity of ...

Single-cell cDNA Library Preparation and Sequencing According to the manufacturer’s instructions and a prior report11, a single-cell 5’ Library Gel Bead Kit was used to construct single-cell RNA-seq libraries. A Illumina Novaseq 6000 sequenc-er (Illumina, San Diego, CA, USA) with a depth of at least 100,000 reads per cell was used for

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Recent Publications UCLA Chemistry and Biochemistry

Feb 2 Single-cell RNA sequencing of batch Chlamydomonas cultures reveals heterogeneity in their diurnal cycle phase - The Plant Cell. Feiyang Ma, Patrice A Salomé, Sabeeha S

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Single-cell transcriptomics - Wikipedia

The Single-cell RNA-seq technique converts a population of RNAs to a library of cDNA fragments. These fragments are sequenced by high-throughput next generation sequencing techniques and the reads are mapped back to the reference genome, providing a count of the number of reads associated with each gene.. Normalisation of RNA-seq data accounts for cell to cell variation in the efficiencies of ...

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Medscape Plant Cell - Content Listing

Feb 11, 2021  Single-cell RNA sequencing of batch Chlamydomonas cultures reveals heterogeneity in their diurnal cycle phase. February 02, 2021 [ MEDLINE Abstract] Focus on the biology of plant genomes.

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Turnover of chloroplast and cytoplasmic ribosomes during ...

Single-cell RNA sequencing of batch Chlamydomonas cultures reveals heterogeneity in their diurnal cycle phase. Ma F, Salomé PA, Merchant SS, Pellegrini M. Plant Cell, 33(4):1042-1057, 01 May 2021 Cited by: 2 articles PMID: 33585940

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Plants Free Full-Text Transcription Factor-Based ...

Moreover, recently, through the 10X Genomics chromium-based library preparation of batch-cultured Chlamydomonas cells, single-cell RNA-seq analyses illustrated the cell types of Chlamydomonas cells under various conditions, including the diurnal cycle .

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Applications of single-cell and bulk RNA sequencing in ...

May 01, 2021  The following steps of single-cell and bulk RNA-seq usually comprise reverse transcription, reads sequencing, mapping or quasi-mapping, data format transformation, count table generation and inference, such as the exploration of gene expression and/or transcript fusions ().Download : Download high-res image (772KB) Download : Download full-size image

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(PDF) RNA-Seq Analysis of Sulfur-Deprived Chlamydomonas ...

RNA-seq data have largely been analyzed in a contrasting mode, that is, by comparing the wild type to the mutant, or between untreated and treated cultures, not only in Chlamydomonas but also in ...

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Metabolic, Physiological, and Transcriptomics Analysis of ...

Analysis of Batch Cultures of the Green Microalga Chlamydomonas Grown on Di erent ... To understand the responses to higher acetate concentrations, Chlamydomonas cells were cultivated in batch mode in the light at 17, 31, 44, and 57 mM acetate. ... The RNA-seq

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Histones of Chlamydomonas reinhardtii. Synthesis ...

Histones of the green alga Chlamydomonas reinhardtii were prepared by a new method and fractionated by reversed-phase high-performance liquid chromatography. Acid-urea-Triton gel analysis and tritiated acetate labeling demonstrated high levels of steady-state acetylation for the single histone H3 pr

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Single-cell RNA sequencing of cultured human endometrial ...

May 29, 2021  Overview of the single-cell RNA sequencing. As summarized in Fig. 1, endometrial aspirates from the menstrual phase of three women and full-thickness endometrium from the secretory phase of three women were used in this study (Table S1).After enzyme dispersion of the tissues, the CD140b + CD146 + endometrial perivascular cells (ePCs) were obtained from in vitro expanded

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Frontiers in Biostatistics: Single-Cell RNA-Seq Data ...

May 11, 2021  This new technology provides unprecedented opportunities to study disease heterogeneity at the cellular level. However, unique characteristics of scRNA-seq data, including large dimensionality, high dropout rates, and possibly batch effects, bring great difficulty into the analysis of such data.

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Microbial single-cell RNA sequencing by split-pool ...

Feb 19, 2021  Single-cell genomics in bacteria has lagged relative to in eukaryotes because of their tough bacterial cell walls, low messenger RNA content, and lack of many posttranscriptional modifications. To tackle this challenge, Kuchina et al. developed microbial split-pool ligation transcriptomics, or microSPLiT, a single-cell sequencing method for both Gram-negative and Gram

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单细胞文章快讯202105期 - 知乎

May 07, 2021  Single-cell RNA sequencing of batch Chlamydomonas cultures reveals heterogeneity in their diurnal cycle phase: Cancer Res: 9.727: Single-Cell RNA Sequencing Reveals the Cellular Origin and Evolution of Breast Cancer in BRCA1 Mutation Carriers: Proc Natl Acad Sci U S A: 9.412

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Compartmentalization of mRNAs in the giant, unicellular ...

The highest yield of total RNA was obtained using the “Total RNA purification kit” with an elution volume of 40 μl (used for batch 26, 27, 45 and 46), which gave approximately four times more total RNA compared to the “Single Cell RNA purification kit” with an elution volume of 10 μl (used for batch

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Frontiers Single-Cell Technologies to Understand the ...

Dec 18, 2020  There is a growing interest in continuous manufacturing within the bioprocessing community. In this context, the chemostat process is an important unit operation. The current application of chemostat processes in industry is limited although many high yielding processes are reported in literature. In order to reach the full potential of the chemostat in continuous manufacture, the output ...

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Medscape Plant Cell - Content Listing

Feb 11, 2021  Single-cell RNA sequencing of batch Chlamydomonas cultures reveals heterogeneity in their diurnal cycle phase. February 02, 2021 [ MEDLINE Abstract] Focus on the biology of plant genomes.

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Single-cell genomic analysis of human cerebral organoids

In this protocol, we describe how to generate single-cell RNA-seq and ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) data from the same suspension of organoid cells and focus on reducing batch effects by multiplexing multiple individuals in one experiment.

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A Simple Method for Removal of the Chlamydomonas ...

Dec 19, 2018  Single-cell RNA sequencing of batch Chlamydomonas cultures reveals heterogeneity in their diurnal cycle phase. Ma F, Salomé PA, Merchant SS, Pellegrini M. Plant Cell, 33(4):1042-1057, 01 May 2021 Cited by: 2 articles PMID: 33585940

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Recent Publications UCLA Chemistry and Biochemistry

Feb 2 Single-cell RNA sequencing of batch Chlamydomonas cultures reveals heterogeneity in their diurnal cycle phase - The Plant Cell. Feiyang Ma, Patrice A Salomé, Sabeeha S

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