Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1259063 | ENA |
REPOSITORIES: ENA
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Project description:The discovery of the small regulatory RNA populations has changed our vision of cellular regulations. Indeed, loaded on Argonaute proteins they formed ribonucleoprotein complexes that target complementary sequences and achieved widespread silencing mechanisms conserved in most eukaryotes. The recent development of deep sequencing approaches highly contributed to their detection. Small RNA isolation form cells and/or tissues remains a crucial stage to generate robust and relevant sequencing data. In 2006, a novel strategy based on anion-exchange chromatography has been purposed as an alternative to the standard size-isolation purification procedure. However, the eventual biases of such a method have been poorly investigated. Moreover, this strategy not only relies on advanced technical skills and expensive material but is time consuming and requires an elevated starting biological material amount. Using bioinformatic comparative analysis of six independent small RNA-sequencing libraries of Drosophila ovaries, we here demonstrate that anion-exchange chromatography purification prior to small RNA extraction unbiasedly enriches datasets in bona fide reads (small regulatory RNA reads) and depletes endogenous contaminants (ribosomal RNAs and degradation products). The resulting increase of sequencing depth provides a major benefit to study rare populations. We then developed a fast and basic manual procedure to purify loaded small non coding RNAs using anion-exchange chromatography at the bench. We validated the efficiency of this new method and used this strategy to purify small RNAs from various tissues and organisms. We moreover determined that our manual purification increases the output of the previously described anion-exchange chromatography procedure. Comparison of small regulatory RNA populations obtained after three different small RNA purification procedures
2013-06-13 | E-GEOD-40748 | biostudies-arrayexpress
Project description:The discovery of the small regulatory RNA populations has changed our vision of cellular regulations. Indeed, loaded on Argonaute proteins they formed ribonucleoprotein complexes that target complementary sequences and achieved widespread silencing mechanisms conserved in most eukaryotes. The recent development of deep sequencing approaches highly contributed to their detection. Small RNA isolation form cells and/or tissues remains a crucial stage to generate robust and relevant sequencing data. In 2006, a novel strategy based on anion-exchange chromatography has been purposed as an alternative to the standard size-isolation purification procedure. However, the eventual biases of such a method have been poorly investigated. Moreover, this strategy not only relies on advanced technical skills and expensive material but is time consuming and requires an elevated starting biological material amount. Using bioinformatic comparative analysis of six independent small RNA-sequencing libraries of Drosophila ovaries, we here demonstrate that anion-exchange chromatography purification prior to small RNA extraction unbiasedly enriches datasets in bona fide reads (small regulatory RNA reads) and depletes endogenous contaminants (ribosomal RNAs and degradation products). The resulting increase of sequencing depth provides a major benefit to study rare populations. We then developed a fast and basic manual procedure to purify loaded small non coding RNAs using anion-exchange chromatography at the bench. We validated the efficiency of this new method and used this strategy to purify small RNAs from various tissues and organisms. We moreover determined that our manual purification increases the output of the previously described anion-exchange chromatography procedure.
2013-06-13 | GSE40748 | GEO
Project description:The associated files are mass spec data from individual fractions of ion exchange or size exclusion fractionations of native nuclear extract made from broccoli florets (Brassica oleracea var. italica). Ion exchange chromatography was on a concatenated WAX-WAX-CAT column series.
2019-10-28 | PXD013322 | Pride
Project description:Transcription profiling of Brassica rapa, Brassica oleracea and Brassica napus I and II The nuclear genomes of the resynthesised B. napus lines should be identical but, as one (B. napus I) involved a cross of B. oleracea onto B. rapa, and the other (B. napus II) involved a cross of B rapa onto B. oleracea, they differ in cytoplasm, and hence contain different chloroplast and mitochondrial genomes.
2009-05-03 | GSE15915 | GEO
Project description:The associated files are mass spec data from individual fractions of mixed-bed ion exchange fractionations of native extract made from broccoli plant leaves (Brassica oleracea var. italica).
2019-10-28 | PXD013282 | Pride
Project description:Deep sequencing of mRNA from seven different tissues of Brassica oleracea Analysis of ploy(A)+ RNA of multiple different tissues of Brassica oleracea containing Bud, Callus, Root, Stem, Leaf, Flower and Silique.
2014-05-27 | E-GEOD-42891 | biostudies-arrayexpress
Project description:Gene expression changes during the initial stages of black spot disease caused by Alternaria brassicicola on Brassica oleracea (Brassica oleracea var. capitata f. alba, white cabbage) leaves were investigated with Arabidopsis thaliana oligonucleotide microarrays. Transcriptional profiling of infected B. oleracea leaves revealed that photosynthesis was the most negatively regulated biological process. The negative regulation of 6 photosynthesis-related genes, mainly the genes involved in the photosynthesis light reaction and Calvin cycle, was observed as early as 12 hours post infection (hpi). It progressed through 48-hpi stage, when 44 down-regulated photosynthesis-related genes were detected. The analyses of infected leaves at microscopic, ultrastructural and physiological levels supported the microarray-based observations and indicated that the photosynthetic processes are suppressed in B. oleracea as a result of the fungal infection.
2020-07-25 | GSE155051 | GEO
Project description:Transcription profiling of Brassica rapa, Brassica oleracea and Brassica napus I and II The nuclear genomes of the resynthesised B. napus lines should be identical but, as one (B. napus I) involved a cross of B. oleracea onto B. rapa, and the other (B. napus II) involved a cross of B rapa onto B. oleracea, they differ in cytoplasm, and hence contain different chloroplast and mitochondrial genomes. Four-condition experiment, comparison of transcription profiles of the genomes. Four biological replicates were used, independently grown and harvested. One replicate per array.
2010-05-19 | E-GEOD-15915 | biostudies-arrayexpress
Project description:A purification platform that integrates ultrafiltration (UF) with anion exchange chromatography in a fast protein liquid chromatography (FPLC) system, which provides superior resolution, reproducibility, and automation, making it an ideal choice for scaling up exosome isolation.
2025-08-25 | PXD063392 | Pride
Project description:Deep sequencing of mRNA from seven different tissues of Brassica oleracea
2014-05-27 | GSE42891 | GEO