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CEL-seq

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https://www.readbyqxmd.com/read/30096152/scpipe-a-flexible-r-bioconductor-preprocessing-pipeline-for-single-cell-rna-sequencing-data
#1
Luyi Tian, Shian Su, Xueyi Dong, Daniela Amann-Zalcenstein, Christine Biben, Azadeh Seidi, Douglas J Hilton, Shalin H Naik, Matthew E Ritchie
Single-cell RNA sequencing (scRNA-seq) technology allows researchers to profile the transcriptomes of thousands of cells simultaneously. Protocols that incorporate both designed and random barcodes have greatly increased the throughput of scRNA-seq, but give rise to a more complex data structure. There is a need for new tools that can handle the various barcoding strategies used by different protocols and exploit this information for quality assessment at the sample-level and provide effective visualization of these results in preparation for higher-level analyses...
August 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/30093412/spatiotemporal-gene-expression-analysis-of-the-caenorhabditis-elegans-germline-uncovers-a-syncytial-expression-switch
#2
Yonatan B Tzur, Eitan Winter, Jinmin Gao, Tamar Hashimshony, Itai Yanai, Monica P Colaiácovo
Developmental programs are executed by tightly controlled gene regulatory pathways. Here, we combined the unique sample retrieval capacity afforded by laser capture microscopy with analysis of mRNA abundance by CEL-Seq (cell expression by linear amplification and sequencing) to generate a spatiotemporal gene expression map of the Caenorhabditis elegans syncytial germline from adult hermaphrodites and males. We found that over 6000 genes exhibit spatiotemporally dynamic expression patterns throughout the hermaphrodite germline, with two dominant groups of genes exhibiting reciprocal shifts in expression at late pachytene during meiotic prophase I...
October 2018: Genetics
https://www.readbyqxmd.com/read/29179677/robust-transcriptional-signatures-for-low-input-rna-samples-based-on-relative-expression-orderings
#3
Huaping Liu, Yawei Li, Jun He, Qingzhou Guan, Rou Chen, Haidan Yan, Weicheng Zheng, Kai Song, Hao Cai, You Guo, Xianlong Wang, Zheng Guo
BACKGROUND: It is often difficult to obtain sufficient quantity of RNA molecules for gene expression profiling under many practical situations. Amplification from low-input samples may induce artificial signals. RESULTS: We compared the expression measurements of low-input mRNA samples, from 25 pg to 1000 pg mRNA, which were amplified and profiled by Smart-seq, DP-seq and CEL-seq techniques using the Illumina HiSeq 2000 platform, with those of the paired high-input (50 ng) mRNA samples...
November 28, 2017: BMC Genomics
https://www.readbyqxmd.com/read/27121950/cel-seq2-sensitive-highly-multiplexed-single-cell-rna-seq
#4
Tamar Hashimshony, Naftalie Senderovich, Gal Avital, Agnes Klochendler, Yaron de Leeuw, Leon Anavy, Dave Gennert, Shuqiang Li, Kenneth J Livak, Orit Rozenblatt-Rosen, Yuval Dor, Aviv Regev, Itai Yanai
Single-cell transcriptomics requires a method that is sensitive, accurate, and reproducible. Here, we present CEL-Seq2, a modified version of our CEL-Seq method, with threefold higher sensitivity, lower costs, and less hands-on time. We implemented CEL-Seq2 on Fluidigm's C1 system, providing its first single-cell, on-chip barcoding method, and we detected gene expression changes accompanying the progression through the cell cycle in mouse fibroblast cells. We also compare with Smart-Seq to demonstrate CEL-Seq2's increased sensitivity relative to other available methods...
April 28, 2016: Genome Biology
https://www.readbyqxmd.com/read/25975661/deep-developmental-transcriptome-sequencing-uncovers-numerous-new-genes-and-enhances-gene-annotation-in-the-sponge-amphimedon-queenslandica
#5
Selene L Fernandez-Valverde, Andrew D Calcino, Bernard M Degnan
BACKGROUND: The demosponge Amphimedon queenslandica is amongst the few early-branching metazoans with an assembled and annotated draft genome, making it an important species in the study of the origin and early evolution of animals. Current gene models in this species are largely based on in silico predictions and low coverage expressed sequence tag (EST) evidence. RESULTS: Amphimedon queenslandica protein-coding gene models are improved using deep RNA-Seq data from four developmental stages and CEL-Seq data from 82 developmental samples...
2015: BMC Genomics
https://www.readbyqxmd.com/read/24419370/technical-variations-in-low-input-rna-seq-methodologies
#6
Vipul Bhargava, Steven R Head, Phillip Ordoukhanian, Mark Mercola, Shankar Subramaniam
Recent advances in RNA-seq methodologies from limiting amounts of mRNA have facilitated the characterization of rare cell-types in various biological systems. So far, however, technical variations in these methods have not been adequately characterized, vis-à-vis sensitivity, starting with reduced levels of mRNA. Here, we generated sequencing libraries from limiting amounts of mRNA using three amplification-based methods, viz. Smart-seq, DP-seq and CEL-seq, and demonstrated significant technical variations in these libraries...
2014: Scientific Reports
https://www.readbyqxmd.com/read/22939981/cel-seq-single-cell-rna-seq-by-multiplexed-linear-amplification
#7
Tamar Hashimshony, Florian Wagner, Noa Sher, Itai Yanai
High-throughput sequencing has allowed for unprecedented detail in gene expression analyses, yet its efficient application to single cells is challenged by the small starting amounts of RNA. We have developed CEL-Seq, a method for overcoming this limitation by barcoding and pooling samples before linearly amplifying mRNA with the use of one round of in vitro transcription. We show that CEL-Seq gives more reproducible, linear, and sensitive results than a PCR-based amplification method. We demonstrate the power of this method by studying early C...
September 27, 2012: Cell Reports
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