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Comparison of conventional target labelling to PCR and IVT amplified target populations

ABSTRACT: Our aim was to identify which stand alone amplification protocol performed best in our lab when the starting amount of total RNA was limited to 50 ng (A typical amount of total RNA we obtained by laser capture microdissection of tissues from silique samples). Since the quality of extracted RNA is very often tissue dependent and will affect the amplification efficiency, we decided to use total RNA extracted from whole siliques; better representing tissues targeted by LCM. We set out to compare two basic methods of RNA amplification, based on IVT and PCR. Keywords: Comparison of target preparation regimes from limiting amounts of RNA

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE6671 | GEO | 2007/04/02

SECONDARY ACCESSION(S): PRJNA104255

REPOSITORIES: GEO

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Project description:MicroRNAs (miRNAs) are a class of non-coding small RNAs (sRNAs) that play crucial regulatory roles in various developmental processes. Silique length indirectly influences seed yield in rapeseed (Brassica napus); however, the molecular roles of miRNAs in silique length are largely unknown. Here, backcross progenies of rapeseed with long siliques (LS) and short siliques (SS) were used to elucidate this role. Four small RNA libraries from early developing siliques were sequenced, and a total of 814 non-redundant miRNA precursors were identified, representing 65 known miRNAs, and 394 novel miRNAs. Expression analyses revealed 12 known miRNAs and 5 novel miRNAs that were differentially expressed in LS and SS lines. Furthermore, though two degradome sequencing, we annotated 522 cleavage events. An analysis of correlated expression between differentially expressed miRNAs and their targets demonstrated that some transcription factors might repress cell proliferation or auxin signal transduction to control silique length, and that a Pi/Cu deficiency might also restrict silique development. More significantly, the overexpression of miR160 in rapeseed may repress auxin response factors and result in increased silique length, illustrating that silique length could be regulated via an auxin-response pathway. These results will serve as a foundation for future research in B. napus.

2019-08-01 | GSE107056 | GEO

Homo sapiens

Project description:Effect of the amount of input total RNA on T7 amplification

| PRJNA104827 | ENA

Expression profile of Arabidopsis pistil/silique upon induction of FRUITFULL

Project description:To determine the genes that are regulated by FRUITFULL (FUL) in the pistil/silique, we identied differentially expressed genes after induction of FRUITFULL in ful-1 FUL-GR lines using the AGRONOMICS1 tiling array. The inflorescences of flowering plants were dipped in 10 uM DEX solution or in Mock Solution, and the flowers/siliques from stages 12-16 were harvested after 8 hours. RNA was extracted and DNase treated, and subsequent steps and hybridization to the AGRONOMICS Tiling array were performed by the Functional Genomics Center Zurich.

2017-11-03 | GSE79553 | GEO

seed specific genes-Establishing the network of seed gene expression and analysis of its biodiversity

Project description:gnp3_tri33-arabidoseed - seed specific genes - WP3 : Biodiversity of seed traits : state of the art - This experiment aimed to identify the genes expressed in the seeds vs siliques (easiest to harvest), and to know if the expression pattern of the whole silique could provide a valuable information. Keywords: organ comparison

2009-05-30 | GSE16244 | GEO

Total RNA analysis in extracellular vescicle of dystrophic, hypertrophic and wild type mice.

Project description:Total RNA analysis of extracellular vescicles coming from blood of dystrophic , hypertrophic and wild type mice was performed in order to detect most expressed genes in the extracellular vescicles and , if any, which differentially expressed genes would be identified between the three conditions. our analysis revealed that the amount of RNA extracted from blood-derived lurine extracellular vescicles was rather low and did not allow for az differential expression analysis even with extensive amplification of the transcripts. However, total RNA could be isolated and identified in the extracellular vescicles which allowed for a descriptive analysis of the content.

2022-10-29 | GSE216414 | GEO

Genome-wide identiﬁcation of circular RNAs in Arabidopsis thaliana

Project description:To exlore more circRNAs involved in Arabidopsis thaliana, we deeply sequenced 14 samples including whole plants from four developmental stages (rosette leaves > 1 mm in length; rosette growth complete; 50% of flowers to be produced have opened; first silique shattered), aerial part of plants from four stress treatments (control, drought, salinity and heat), five organs (roots, stems, leaves, flowers and siliques) and a mixed sample from whole plants across the lifespan (cotyledons emergence, rosette leaves﹥1 mm, rosette growth complete, first flower open, flourishing florescence, first silique shattered, senescence). The total RNA was purified by rRNA-depletion and linear RNA removal with RNAseR, and paired-end (PE) sequenced by Illumina HiSeq 2500 (read length, PE125, the mixed sample) and Illumina Hiseq X Ten (read length, PE150, 13 independent samples) platforms. We obtained 181.97 Gb raw data (151.37 Gb from 13 samples and 30.6 Gb from a mixed sample) and identified 5861 circRNAs with expression quantity. We annotated the parent genes of these circRNAs and predicted their target sites of microRNAs.

2016-09-01 | GSE77672 | GEO

Brassica napus control vs. heat stress

Project description:High temperature stress results in yield loss and alterations to seed composition during seed filling in oilseed rape (Brassica napus). However, the mechanism underlying this heat response is poorly understood. In this study, we employed a microarray analysis with silique walls and seeds from the developing siliques (20 days after flowering) of Brassica napus that had undergone heat stress.

2015-01-05 | GSE57697 | GEO

seed specific genes-Establishing the network of seed gene expression and analysis of its biodiversity

2010-05-18 | E-GEOD-16244 | biostudies-arrayexpress

Homo sapiens

Project description:Effect of Low RNA Sample Amount on Amplification Fidelity

| PRJNA108095 | ENA

Effect of the amount of input total RNA on T7 amplification

Project description:Zhao et al. Amplification Table 9 This experiment was designed to evaluate the effect of the amount of input total RNA on the fidelity, reproducibility, and yield of T7 based RNA linear amplification. BC2 total RNA was amplified using the Jeffrey lab protocol. Different amounts of T7 primer were used according to the quantity of input total RNA. Multiple amplifications were done for each quantity of input total RNA to minimize experimental variations. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

2005-11-04 | GSE3557 | GEO

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