Transcriptomic Profiling and Microsatellite Identification in Cobia (Rachycentron canadum), Using High-Throughput RNA Sequencing

2021 ◽  
Author(s):  
David Aciole Barbosa ◽  
Bruno C. Araújo ◽  
Giovana Souza Branco ◽  
Alexandre S. Simeone ◽  
Alexandre W. S. Hilsdorf ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
High Throughput ◽  
Transcriptomic Profiling ◽  
Rachycentron Canadum

scholarly journals Cryopreservation of human cancers conserves tumour heterogeneity for single-cell multi-omics analysis

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Sunny Z. Wu ◽  
Daniel L. Roden ◽  
Ghamdan Al-Eryani ◽  
Nenad Bartonicek ◽  
Kate Harvey ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
High Throughput ◽  
Single Cells ◽  
Cellular Heterogeneity ◽  
Tumour Heterogeneity ◽  
Fresh Tissue ◽  
Human Cancers ◽  
Cryopreserved Cell ◽  
Single Cell Rna Sequencing

Abstract Background High throughput single-cell RNA sequencing (scRNA-Seq) has emerged as a powerful tool for exploring cellular heterogeneity among complex human cancers. scRNA-Seq studies using fresh human surgical tissue are logistically difficult, preclude histopathological triage of samples, and limit the ability to perform batch processing. This hindrance can often introduce technical biases when integrating patient datasets and increase experimental costs. Although tissue preservation methods have been previously explored to address such issues, it is yet to be examined on complex human tissues, such as solid cancers and on high throughput scRNA-Seq platforms. Methods Using the Chromium 10X platform, we sequenced a total of ~ 120,000 cells from fresh and cryopreserved replicates across three primary breast cancers, two primary prostate cancers and a cutaneous melanoma. We performed detailed analyses between cells from each condition to assess the effects of cryopreservation on cellular heterogeneity, cell quality, clustering and the identification of gene ontologies. In addition, we performed single-cell immunophenotyping using CITE-Seq on a single breast cancer sample cryopreserved as solid tissue fragments. Results Tumour heterogeneity identified from fresh tissues was largely conserved in cryopreserved replicates. We show that sequencing of single cells prepared from cryopreserved tissue fragments or from cryopreserved cell suspensions is comparable to sequenced cells prepared from fresh tissue, with cryopreserved cell suspensions displaying higher correlations with fresh tissue in gene expression. We showed that cryopreservation had minimal impacts on the results of downstream analyses such as biological pathway enrichment. For some tumours, cryopreservation modestly increased cell stress signatures compared to freshly analysed tissue. Further, we demonstrate the advantage of cryopreserving whole-cells for detecting cell-surface proteins using CITE-Seq, which is impossible using other preservation methods such as single nuclei-sequencing. Conclusions We show that the viable cryopreservation of human cancers provides high-quality single-cells for multi-omics analysis. Our study guides new experimental designs for tissue biobanking for future clinical single-cell RNA sequencing studies.

scholarly journals Ultra-high-throughput single-cell RNA sequencing and perturbation screening with combinatorial fluidic indexing

2021 ◽  
Author(s):  
Paul Datlinger ◽  
André F. Rendeiro ◽  
Thorina Boenke ◽  
Martin Senekowitsch ◽  
Thomas Krausgruber ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
High Throughput ◽  
Single Cell Rna Sequencing

scholarly journals Protocol to analyze circulating small non-coding RNAs by high-throughput RNA sequencing from human plasma samples

2021 ◽  
Vol 2 (3) ◽  
pp. 100606
Author(s):  
Giuseppina E. Grieco ◽  
Guido Sebastiani ◽  
Daniela Fignani ◽  
Noemi Brusco ◽  
Laura Nigi ◽  
...  
Keyword(s):  
Human Plasma ◽  
Rna Sequencing ◽  
High Throughput ◽  
Plasma Samples ◽  
Human Plasma Samples ◽  
Non Coding Rnas

scholarly journals High-throughput RNA sequencing reveals the anti-inflammatory mechanism of baicalin on Propionibacterium acnes-induced acne in rabbits

2019 ◽  
Vol 6 (3) ◽  
pp. 201-210
Author(s):  
Xingzhe Yang ◽  
Guangrui Huang ◽  
Leiming You ◽  
Honghao Sheng ◽  
Yuxiu Sun ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
High Throughput ◽  
Propionibacterium Acnes ◽  
Inflammatory Mechanism ◽  
Anti Inflammatory

Analysis of the transcriptome of green and mutant golden-yellow leaves ofAcer palmatumThunb. using high-throughput RNA sequencing

2015 ◽  
Vol 90 (4) ◽  
pp. 388-394 ◽  
Author(s):  
Shu-Shun Li ◽  
Qian-Zhong Li ◽  
Li-Ping Rong ◽  
Ling Tang ◽  
Jing-Jing Wang ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
High Throughput ◽  
Golden Yellow

Abstract 46: High-Density Lipoproteins Control Monocyte Differentiation Through microRNA Intercellular Communication

2013 ◽  
Vol 33 (suppl_1) ◽  
Author(s):  
Kasey C Vickers ◽  
Michael G Levin ◽  
Michael P Anderson ◽  
Qing Xu ◽  
Joshua Anzinger ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Sequencing ◽  
High Throughput ◽  
Small Rna ◽  
Cellular Response ◽  
Culture Media ◽  
Recipient Cell ◽  
Inflammatory Cells ◽  
High Density Lipoproteins ◽  
Small Rna Sequencing

Many HDL-microRNAs (miRNA) are well-characterized post-transcriptional regulators of inflammation, and are significantly increased on HDL with hypercholesterolemia and atherosclerosis in humans and mice. Therefore, we hypothesize that inflammatory cells uniquely control their own gene expression through cellular miRNA export to HDL and then regulate recipient cell gene expression through HDL-mediated miRNA delivery. To test this hypothesis, we used high-throughput proteomics, Open Arrays, small RNA sequencing, and gene expression microarrays. Human monocytes (plasma elutriation) were differentiated into dendritic cells and multiple macrophage phenotypes. Each cell-type was incubated with pure reconstituted HDL (rHDL), which was then purified from culture media by apolipoprotein A-I immunoprecipitation after 24 h, and both cellular and HDL-miRNAs were profiled using TaqMan Open Arrays. Macrophages were found to export high levels of miRNAs to HDL that inhibit monocyte/macrophage differentiation (miR-146a, miR-223); however, monocytes were also found to export many miRNAs associated with differentiation, including miR-92a, miR-222, miR-17, miR-20a, miR106a, and miR-21. Furthermore, many miRNAs were found to be transcribed in inflammatory cells, but completely exported to HDL and not retained in the cell. Most interestingly, HDL treatment was found to induce miR-223 transcription in monocytes, as determined by primary miR-223 transcript levels; however, intracellular levels of the mature form (miR-223) did not change. These results suggest that HDL induces the export of miRNAs it transports. PAR-CLIP with high-throughput small RNA sequencing was used to demonstrate that miRNAs are transferred from macrophages to endothelial cells and loaded onto cellular Argonaute 2-continaining RNA-induced silencing complexes. To demonstrate this in mice, human HDL, containing endogenous levels of miR-223, were injected into miR-223-null mice and inflammation-associated miRNA delivery was mapped in vivo. In summary, we found profound differences in the cellular response to HDL treatment and HDL-miRNA communication amongst inflammatory cell phenotypes that are physiologically relevant to cardiovascular disease.

scholarly journals Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection

Silence ◽  
2012 ◽  
Vol 3 (1) ◽  
pp. 9 ◽  
Author(s):  
Zhao Zhang ◽  
William E Theurkauf ◽  
Zhiping Weng ◽  
Phillip D Zamore
Keyword(s):  
Rna Sequencing ◽  
High Throughput ◽  
Rna Seq
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