Project description:These data provide a basis for exploration of gene expression differences between physiologically diverse accessions of Arabidopsis thaliana. Recent studies have documented remarkable genetic variation among Arabidopsis thaliana accessions collected from diverse habitats and across its geographical range. Of particular interest are accessions with putatively locally adapted phenotypes – i.e., accessions with attributes that are likely adaptive under the climatic or habitat conditions of their sites of origin. These genotypes are especially valuable as they may provide insight into the genetic basis of adaptive evolution as well as allow the discovery of genes of ecological importance. Therefore we studied the physiology, genome content and gene expression of 18 physiologically diverse accessions. The gene expression studies were conducted under two levels of soil moisture and accompanied by physiological measurements to characterize early responses to soil moisture deficit.

2012-03-12 | GSE27550 | GEO

Transcription profiling of 4-week old Arabidopsis plants grown in soil flooded to the soil surface (root flooding) or completely submerged under 6 cm of water (submergence)

Project description:4-week old Arabidopsis plants grown in soil were flooded to the soil surface (root flooding) or completely submerged under 6 cm of water (submergence). Samples are collected at the time specified.

2013-01-30 | E-TIGR-120 | biostudies-arrayexpress

cRNA hybridizations of 10 Spring annual accessions of Arabidopsis thaliana under well-watered and mild soil drying

Project description:These data provide a basis for exploration of gene expression differences between physiologically diverse Spring annual accessions of Arabidopsis thaliana. Recent studies have documented remarkable genetic variation among Arabidopsis thaliana accessions collected from diverse habitats and across its geographical range. Of particular interest are accessions with putatively locally adapted phenotypes – i.e., accessions with attributes that are likely adaptive under the climatic or habitat conditions of their sites of origin. These genotypes are especially valuable as they may provide insight into the genetic basis of adaptive evolution as well as allow the discovery of genes of ecological importance. Therefore we studied the physiology, genome content and gene expression of 18 physiologically diverse accessions. The gene expression studies were conducted under two levels of soil moisture and accompanied by physiological measurements to characterize early responses to soil moisture deficit.

2012-03-12 | GSE27548 | GEO

Vineyard soil under cover cropping

Project description:Vineyard soil under cover cropping Raw sequence reads

| PRJNA1207036 | ENA

RNA-Seq Analysis to confirm Different Transcriptomic Profiles of Soil-Derived Functional Module Consortia.

Project description:Purpose: Deconstructing the soil microbiome into reduced-complexity functional modules represents a novel method of microbiome analysis. The goals of this study are to confirm differences in transcriptomic patterns among five functional module consortia. Methods: mRNA profiles of 3 replicates each of functional module enrichments of soil inoculum in M9 media with either 1) xylose, 2) n-acetylglucosamine, 3) glucose and gentamycin, 4) xylan, or 5) pectin were generated by sequencing using an Illumina platform (GENEWIZ performed sequencing). Sequence reads that passed quality filters were aligned to a soil metagenome using Burrows Wheeler Aligner. Resulting SAM files were converted to raw reads using HTSeq, and annotated using Uniref90 or EGGNOG databases. Results: To reduce the size of the RNA-Seq counts table and increase its computational tractability, transcripts containing a minimum of 75 total counts, but no more than 3 zero counts, across the 15 samples were removed. The subsequent dataset was normalized using DESeq2, resulting in a dataset consisting of 6947 unique transcripts across the 15 samples, and 185,920,068 reads. We identified gene categories that were enriched in a sample type relative to the overall dataset using Fisher’s exact test. Conclusions: our dataset confirms that the functional module consortia generated from targeted enrichments of a starting soil inoculum had distinct functional trends by enrichment type.

2020-01-14 | GSE143587 | GEO

Single-cell transcriptomes of paired peripheral blood mononuclear cells collected before and 7 days after irreversible electroporation in patients with localized prostate cancer

Project description:This submission describes paired single-cell RNA-sequencing profiles of peripheral blood mononuclear cells (PBMCs) from five patients with clinically localized prostate cancer undergoing irreversible electroporation (IRE). For each participant, one PBMC sample was collected immediately before IRE and one PBMC sample was collected 7 days after IRE, generating ten independent single-cell libraries. Raw sequencing reads were previously submitted to SRA under BioProject PRJNA1497318 and are linked here through the corresponding SRA accessions. The GEO submission provides the processed filtered gene-barcode matrices used for downstream quality control, integration, clustering, and annotation.

2026-08-01 | GSE341191 | GEO

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