Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

38 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chromatin immunoprecipitation of Zea mays chloroplast extracts prepared from wild type and PPR4-deficient tissue

ABSTRACT: Co-immunoprecipitation of the maize pentatricopeptide protein PPR4 and extraction of bound RNA. RNA is labelled and hybridized to a maize chloroplast genome tiling array in order to identify target RNA species of PPR4.

INSTRUMENT(S): Axon GenePix 4000B scanning hardware

ORGANISM(S): Zea mays

SUBMITTER: Athea Vichas

PROVIDER: E-MEXP-716 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Chromatin immunoprecipitation of Zea mays chloroplast extracts prepared from wild type and CRP1-deficient tissue

Project description:Identification of target transcripts for the putative chloroplast RNA binding protein CRP1 in Zea mays. CRP1 was immunoprecipitated from a chloroplast extract. Chloroplast extracts were prepared from WT and CRP1-deficient tissue. RNA from the pellet and from the supernatant for each pulldown was labelled with different fluoro-dyes and hybridized onto an array covering the complete maize chloroplast genome. Messages enriched in the immunoprecipitate from WT tissue, but not enriched in mutant tissue are likely targets for CRP1.

2005-08-01 | E-MEXP-282 | biostudies-arrayexpress

Chromatin immunoprecipitation of Zea mays chloroplast extracts using antibodies raised against OE17 and OE23 chloroplast targeted proteins

Project description:OE17 and OE23 are chloroplast targeted proteins. RNA co-immunoprecipitation was performed using antibodies raised against these proteins. RNA from the pellet and from the supernatent for each pulldown was labeled with different fluoro-dyes.

2006-09-01 | E-MEXP-784 | biostudies-arrayexpress

Chromatin immunoprecipitation of RNA binding protein CFM2 in Zea mays chloroplast extracts

Project description:Identification of target transcripts for the putative chloroplast RNA binding protein CFM2 in Zea mays. CFM2 was immunoprecipitated from a chloroplast extract. Chloroplast extracts were prepared from WT tissue. RNA from the pellet and from the supernatant for each pulldown was labelled with different fluoro-dyes and hybridized onto an array covering the complete maize chloroplast genome. Messages enriched in the immunoprecipitate from WT tissue are likely targets for CFM2.

2006-09-01 | E-MEXP-743 | biostudies-arrayexpress

Chromatin immunoprecipitation of Zea mays chloroplast extracts prepared from wild type and CAF1-deficient tissue

Project description:Immunoprecipitation of the chloroplast splicing factor CAF1 and analysis of bound RNAs with a complete Zea mays cpDNA microarray.

2005-08-01 | E-MEXP-318 | biostudies-arrayexpress

ECBiG PlasTi-microarray CSH validation

Project description:Experiment evaluating aplicability of PlasTi-microarray for cross-species hybridization studies. PlasTi-microarray is a tiling oligonucleotide microarray originally designed for cucumber plastome analysis.Chloroplast RNA from Arabidopsis, tomato and spinach leaves was extracted, labelled and hybridized to PlasTi-microarray with the cucumber samples labelled with the second dye as a control. For each species, one biological sample and one technical replicate (labelled in a dye-swap orientation) were analyzed, resulting in two microarray hybridizations per species and six microarrays (a-f) in total.

2011-05-27 | E-MEXP-3220 | biostudies-arrayexpress

RNA-seq of Staphylococcus aureus human and bovine strains cultured in TSB and 50% milk media

Project description:The aim of this experiment was to understand the different transcriptomic profiles of Staphylococcus aureus strains when cultured in 50% milk media with TSB media as a control. Bovine S. aureus strains that are capable of clotting milk where compared to both bovine and human S. aureus strains unable to clot milk. All strains are from sequence type 97.

2024-09-04 | E-MTAB-14384 | biostudies-arrayexpress

Transcription profiling time series of S. aureus grown in mixed culture with L. lactis

Project description:the transcriptomic profile of S. aureus during mixed cultures with L. lactis was established on chemically defined medium at constant pH (6.6).

2009-05-13 | E-MEXP-1837 | biostudies-arrayexpress

Meta-transcriptome analysis of a natural wheat sourdough ecosystem during a 10-day spontaneous, laboratory fermentation

Project description:Lactic acid bacteria (LAB) are of industrial importance in the production of fermented foods, among which sourdough-derived products. Despite their limited metabolic capacity LAB contribute considerably to important characteristics of fermented foods, among which extended shelf-life, microbial safety, improved texture, and enhanced organoleptic properties. Thanks to the considerable amount of LAB genomic information that became available during the last years, transcriptome, and by extension meta-transcriptome studies, are the exquisite research approaches to study whole ecosystem gene expression into more detail. In this study, microarray analyses were performed using RNA sampled during four 10-day spontaneous sourdough fermentations carried out in the laboratory, namely two wheat and two spelt fermentations with daily back-slopping. Hereto, the in-house developed functional gene LAB microarray was used, representing 406 genes that play a key role in sugar and nitrogen metabolism, functional metabolite production, stress responses and health and safety characteristics. The results reveal the activation of different key metabolic pathways, the ability to use different energy sources, and successful acid and oxidative stress responses. Also, a new algorithm was developed to compute a net expression profile for each of the represented genes, thereby exceeding the species level. The labeled aRNA of the sourdough fermentation samples was hybridized using a loop design, i.e. subsequent samples (e.g. 27 h and 51 h, 51 h and 75 h etc.) were hybridized together on the microarray and the loop was closed by hybridizing the last sample with the first.

2010-07-07 | E-GEOD-15693 | biostudies-arrayexpress

Analysis of natural wheat and spelt sourdough ecosystem during a 10-day spontaneous laboratory fermentation

Project description:This SuperSeries is composed of the following subset Series: GSE15686: Meta-transcriptome analysis of a natural wheat sourdough ecosystem during a 10-day spontaneous laboratory fermentation (I) GSE15691: Meta-transcriptome analysis of a natural spelt sourdough ecosystem during a 10-day spontaneous laboratory fermentation (I) GSE15692: Meta-transcriptome analysis of a natural spelt sourdough ecosystem during a 10-day spontaneous laboratory fermentation (II) GSE15693: Meta-transcriptome analysis of a natural wheat sourdough ecosystem during a 10-day spontaneous laboratory fermentation (II) Refer to individual Series

2010-07-07 | E-GEOD-15803 | biostudies-arrayexpress

Meta-transcriptome analysis of a natural wheat sourdough ecosystem during a 10-day spontaneous laboratory fermentation

2010-07-07 | E-GEOD-15686 | biostudies-arrayexpress