scholarly journals RNA-Seq analysis of laser-capture microdissected cells of the developing central starchy endosperm of maize

Genomics Data ◽  
2014 ◽  
Vol 2 ◽  
pp. 242-245 ◽  
Author(s):  
Dhiraj Thakare ◽  
Ruolin Yang ◽  
Joshua G. Steffen ◽  
Junpeng Zhan ◽  
Dongfang Wang ◽  
...  
Keyword(s):  
Rna Seq ◽  
Starchy Endosperm ◽  
Laser Capture ◽  
Laser Capture Microdissected

scholarly journals Transcriptional landscapes of floral meristems in barley

2021 ◽  
Vol 7 (18) ◽  
pp. eabf0832
Author(s):  
J. Thiel ◽  
R. Koppolu ◽  
C. Trautewig ◽  
C. Hertig ◽  
S. M. Kale ◽  
...  
Keyword(s):  
High Resolution ◽  
Hordeum Vulgare ◽  
Reproductive Success ◽  
Regulatory Networks ◽  
Cereal Crops ◽  
Organ Development ◽  
Rna Seq ◽  
Floral Meristems ◽  
Laser Capture ◽  
Laser Capture Microdissected

Organ development in plants predominantly occurs postembryonically through combinatorial activity of meristems; therefore, meristem and organ fate are intimately connected. Inflorescence morphogenesis in grasses (Poaceae) is complex and relies on a specialized floral meristem, called spikelet meristem, that gives rise to all other floral organs and ultimately the grain. The fate of the spikelet determines reproductive success and contributes toward yield-related traits in cereal crops. Here, we examined the transcriptional landscapes of floral meristems in the temperate crop barley (Hordeum vulgare L.) using RNA-seq of laser capture microdissected tissues from immature, developing floral structures. Our unbiased, high-resolution approach revealed fundamental regulatory networks, previously unknown pathways, and key regulators of barley floral fate and will equally be indispensable for comparative transcriptional studies of grass meristems.

scholarly journals Cell Walls of Developing Wheat Starchy Endosperm: Comparison of Composition and RNA-Seq Transcriptome

2011 ◽  
Vol 158 (2) ◽  
pp. 612-627 ◽  
Author(s):  
Till K. Pellny ◽  
Alison Lovegrove ◽  
Jackie Freeman ◽  
Paola Tosi ◽  
Christopher G. Love ◽  
...  
Keyword(s):  
Cell Walls ◽  
Rna Seq ◽  
Starchy Endosperm

scholarly journals Extensive phylogenies of human development reveal variable embryonic patterns

2020 ◽  
Author(s):  
Tim H. H. Coorens ◽  
Luiza Moore ◽  
Philip S. Robinson ◽  
Rashesh Sanghvi ◽  
Joseph Christopher ◽  
...  
Keyword(s):  
Progenitor Cell ◽  
Spatial Effect ◽  
Lineage Tracing ◽  
Substantial Variation ◽  
Normal Tissues ◽  
Multiple Organs ◽  
Naturally Occurring ◽  
Adult Body ◽  
Laser Capture ◽  
Laser Capture Microdissected

ABSTRACTStarting from the zygote, all cells in the developing and adult human body continuously acquire mutations. A mutation shared between two different cells implies a shared progenitor cell and can thus be used as a naturally occurring marker for lineage tracing. Here, we reconstruct extensive phylogenies of normal tissues from three adult individuals using whole-genome sequencing of 511 laser capture microdissected samples from multiple organs. Early embryonic progenitor cells inferred from the phylogenies often contribute in different proportions to the adult body and the extent of this asymmetry is variable between individuals, with ratios between the first two reconstructed cells ranging from 56:44 to 92:8. Asymmetries also pervade subsequent cell generations and can differ between tissues in the same individual. The phylogenies also resolve the spatial embryonic origins and patterning of tissues, revealing a spatial effect in the development of the human brain. Supplemented by data on eleven men, we timed the split between soma and germline, with the earliest observed segregation occurring at the first cell divisions. This research demonstrates that, despite reaching the same ultimate tissue patterns, early bottlenecks and lineage commitments lead to substantial variation in embryonic patterns both within and between individuals.

scholarly journals Differential stromal reprogramming in benign and malignant naturally occurring canine mammary tumours identifies disease-promoting stromal components

2019 ◽  
Author(s):  
Parisa Amini ◽  
Sina Nassiri ◽  
Alexandra Malbon ◽  
Enni Markkanen
Keyword(s):  
Screening Method ◽  
Malignant Tumours ◽  
Differential Abundance ◽  
Naturally Occurring ◽  
Mammary Tumours ◽  
Ffpe Specimen ◽  
Summary Statement ◽  
Benign Tumours ◽  
Laser Capture ◽  
Laser Capture Microdissected

AbstractThe importance of cancer-associated stroma (CAS) for initiation and progression of cancer is well accepted. However, as stromal changes in benign forms of naturally occurring tumours are poorly understood, it remains unclear how CAS from benign and malignant tumours compare. Spontaneous canine mammary tumours are viewed as excellent models of human mammary carcinomas (mCA). We have recently reported highly conserved stromal reprogramming between canine and human mCA based on transcriptome analysis of laser-capture-microdissected FFPE specimen. To identify stromal changes between benign and malignant mammary tumours, we have analysed CAS and matched normal stroma from 13 canine mammary adenomas and compared them to 15 canine mCA. Our analyses revealed distinct stromal reprogramming even in small benign tumours. While similarities in stromal reprogramming exist, the CAS signature clearly distinguished adenomas from mCA, suggesting that it may reliably discriminate between benign and malignant tumours. We identified strongly discriminatory genes and found strong differential enrichment in several hallmark signalling pathways between benign and malignant CAS. The distinction between CAS from adenoma and mCA was further substantiated by differential abundance in cellular composition. Finally, to determine key players in CAS reprograming between adenomas and mCA, a network-based gene screening method identified modules of co-expressing genes with distinct expression profile in benign and malignant CAS, and revealed several hub genes as potential molecular drivers in CAS. Given the relevance of canine CAS as a model for the human disease, our approach identifies potential stromal drivers of tumour malignancy with implications for human mCA.Summary statementRNAsequencing-based analysis of stromal reprogramming between benign and malignant naturally occurring canine mammary tumours identifies potential molecular drivers in cancer-associated stroma that support tumour growth and malignancy.

scholarly journals Comparison of Ethanol Versus Formalin Fixation on Preservation of Histology and RNA in Laser Capture Microdissected Brain Tissues

2004 ◽  
Vol 14 (2) ◽  
pp. 175-182 ◽  
Author(s):  
Jack Meng Fen Su ◽  
Laszlo Perlaky ◽  
Xiao-Nan Li ◽  
Hon-Chiu Eastwood Leung ◽  
Barbara Antalffy ◽  
...  
Keyword(s):  
Formalin Fixation ◽  
Laser Capture ◽  
Laser Capture Microdissected ◽  
Brain Tissues

scholarly journals Proteomics Pipeline for Biomarker Discovery of Laser Capture Microdissected Breast Cancer Tissue

2012 ◽  
Vol 17 (2) ◽  
pp. 155-164 ◽  
Author(s):  
Ning Qing Liu ◽  
René B. H. Braakman ◽  
Christoph Stingl ◽  
Theo M. Luider ◽  
John W. M. Martens ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Biomarker Discovery ◽  
Breast Cancer Tissue ◽  
Cancer Tissue ◽  
Laser Capture ◽  
Laser Capture Microdissected

scholarly journals Spatially Resolved Proteome Mapping of Laser Capture Microdissected Tissue with Automated Sample Transfer to Nanodroplets

2018 ◽  
Vol 17 (9) ◽  
pp. 1864-1874 ◽  
Author(s):  
Ying Zhu ◽  
Maowei Dou ◽  
Paul D. Piehowski ◽  
Yiran Liang ◽  
Fangjun Wang ◽  
...  
Keyword(s):  
Spatially Resolved ◽  
Laser Capture ◽  
Sample Transfer ◽  
Laser Capture Microdissected

Collection and Analysis of Expressed Sequence Tags Derived from Laser Capture Microdissected Switchgrass (Panicum virgatum L. Alamo) Vascular Tissues

2010 ◽  
Vol 3 (3) ◽  
pp. 278-294 ◽  
Author(s):  
Avinash C. Srivastava ◽  
Karuppaiah Palanichelvam ◽  
Junying Ma ◽  
Jarrod Steele ◽  
Elison B. Blancaflor ◽  
...  
Keyword(s):  
Expressed Sequence Tags ◽  
Panicum Virgatum ◽  
Vascular Tissues ◽  
Panicum Virgatum L ◽  
Laser Capture ◽  
Expressed Sequence ◽  
Laser Capture Microdissected
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