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Boechera2

ABSTRACT: 16S rRNA amplicons (V4 region) of bacteria living on and in roots and leaves of Boechera stricta from field experiments in the Rocky Mountains

PROVIDER: PRJEB13148 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	ERR1336952_1.fastq.gz	Fastqsanger.gz
	ERR1336952_2.fastq.gz	Fastqsanger.gz
	ERR1336953_1.fastq.gz	Fastqsanger.gz
	ERR1336953_2.fastq.gz	Fastqsanger.gz
	ERR1336954.fastq.gz	Fastqsanger.gz

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Rocky Mountain Boechera Root and Leaf Microbiome

Project description:16S rRNA amplicons (V4 region) of bacteria living on and in roots and leaves of Boechera stricta from field experiments in the Rocky Mountains

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Expression analysis of uninfected Boechera stricta and infected Boechera stricta with Puccinia monoica forming pseudoflowers using an Arabidopsis thaliana gene expression 4x72K array design from NimbleGen.

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Project description:The expression of 30362 plant genes from uninfected flowers of Boechera stricta, uninfected steam and leaves of B. stricta and infected B. stricta with Puccinia monoica forming pseudoflowers. We hybridized cDNA from each sample to an Arabidopsis thaliana gene expression 4x72K format NimbleGen array (ATH6_60mer_expr). We used a eukaryotic gene expression array design No.5048 from NimbleGen (Cat No. A4511001-00-01). Each 5048 array measures the expression level of 30,362 target genes from Arabidopsis thaliana in a 4-plex format 4x72K with with 72,000 probes per array, a total of two probes per target gene, and 60-mer probe length. Total RNA samples recovered from infected leaves of Boechera stricta with Puccinia monoica (pseudoflowers) and uninfected stem and leaves of B. stricta. Experiments included three/two biological repllicates from each sample. We carried out total RNA extractions for all samples using RNAesy Plant Mini Kit (Qiagen, Cat No. 74904). cDNA synthesis was performed by NimbleGen.

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Project description:This experiment provides the gene expression data from seedlings of 2 different species from Boechera genus, (Boechera stricta - referred as Sex-1; Boechera gunnisoniana - referred as Apo-1 here). The main intent of the experiment is to identify expression changes in species which reproduce differently (Sexual vs apomixis) and at somatic stages (seedling) to identify mechanisms governing changes occurring in prior to reproduction stage as preparatory mechanism.

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Project description:16S and nrfA amplicons from long-term field experiments

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Project description:This data is a case study done in the context of developing methods for assessing the taxonomic composition of microbial communities using metaproteomics. For this study with analyzed phototrophic biomats from two Soda Lakes in the Canadian Rocky Mountains using metaproteomics. For protein identification we generated a metagenome from which we predicted and annotated the protein sequences used to analyze the metaproteomes. The database is available in this PRIDE submission. Lake1 refers to Goodenough Lake (GEM, 51°19'47.64"N 121°38'28.90"W) and Lake2 referes to Last Chance Lake (LCM, 51°19'39.3" N 121°37'59.3"W).

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