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accession-icon SRP133834
Transcriptome of microbiome for the nematode Caenorhabditis elegans
  • organism-icon Caenorhabditis elegans
  • sample-icon 72 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Host-microbe associations underlie many key processes of host development, immunity, and life history. Yet, none of the current research on the central model species Caenorhabditis elegans considers the worm's natural microbiome. Instead, almost all laboratories exclusively use the canonical strain N2 and derived mutants, maintained through routine bleach sterilization in monoxenic cultures with an E. coli strain as food. Here, we characterize for the first time the native microbiome of C. elegans and assess its influence on nematode life history characteristics via transcriptomics. Overall design: mRNA profiles of wild type (WT) C.elegans fed to either Ochrobactrum strain MYb65, MYb71, mixture of MYb65 and MYb71 or standard lab food E. coli OP50 at different life stages (from L2 to adults) were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.

Publication Title

The Inducible Response of the Nematode <i>Caenorhabditis elegans</i> to Members of Its Natural Microbiota Across Development and Adult Life.

Sample Metadata Fields

Cell line, Treatment, Subject, Time

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accession-icon GSE39966
Expression data from replicating and quiescent liver cells isolated from mice young liver
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

We have developed a new transgenic mouse strain, expressing a CyclinB1-GFP fusion reporter, which marks replicating cells in the S/G2/M phases of the cell cycle to isolate live replicating and quiescent cells from the liver.

Publication Title

A transgenic mouse marking live replicating cells reveals in vivo transcriptional program of proliferation.

Sample Metadata Fields

Age, Specimen part

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accession-icon SRP074850
Systems genetics reveals a transcriptional network associated with susceptibility in the maize-gray leaf spot pathosystem
  • organism-icon Zea mays
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Background: Maize plants developed typical gray leaf spot disease (GLS) symptoms initiating at the lower leaves and progressing to upper leaves through the season. Leaf material was collected at 77 days after planting, at which stage there were a large number of GLS disease necrotic lesions on lower leaves (8% surface area on average determined by digital image analysis), but very few lesions and only at chlorotic stage on leaves above the ear (average of 0.2% lesion surface area). Method:To collect material that reflected a difference between C.zeina infected B73 leaves and control B73 leaf material, samples were collected from two lower GLS infected leaves (second and third leaf internode below ear) , and two upper leaves with minimal GLS symptoms (second and third internode above ear), respectively. The two lower leaves from each plant were pooled prior to RNA extraction, and the two upper leaves from each plant were pooled prior to RNA extraction. Upper and lower leaf samples from three maize B73 plants were subjected to RNA sequencing individually. The three maize plants were selected randomly as one plant per row from three rows of ten B73 plants each. Result: A systems genetics strategy revealed regions on the maize genome underlying co-expression of genes in susceptible and resistance responses, including a set of 100 genes common to the susceptible response of sub-tropical and temperate maize. Overall design: To collect material that reflected a difference between C.zeina infected B73 leaves and control B73 leaf material, samples were collected from two lower GLS infected leaves (second and third leaf internode below ear) , and two upper leaves with minimal GLS symptoms (second and third internode above ear), respectively. The two lower leaves from each plant were pooled prior to RNA extraction, and the two upper leaves from each plant were pooled prior to RNA extraction. Upper and lower leaf samples from three maize B73 plants were subjected to RNA sequencing individually. The three maize plants were selected randomly as one plant per row from three rows of ten B73 plants each.

Publication Title

Systems genetics reveals a transcriptional network associated with susceptibility in the maize-grey leaf spot pathosystem.

Sample Metadata Fields

Subject

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accession-icon E-MEXP-2472
Transcription profiling by array of Arabidopsis after growing in dark or light conditions
  • organism-icon Arabidopsis thaliana
  • sample-icon 12 Downloadable Samples
  • Technology Badge IconUNKNOWN, Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

RNA from etiolated seedlings, light-treated seedlings, leaves and flowers was hybridized to ATH1 and AGRONOMICS1 arrays.

Publication Title

AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling.

Sample Metadata Fields

Age, Specimen part

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accession-icon SRP158520
Transcriptome analyses of somatotropes and lactotropes reveal novel regulators of cell identity in the pituitary
  • organism-icon Mus musculus
  • sample-icon 10 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 4000

Description

The differentiation of the hormone-producing cell lineages of the anterior pituitary represents an informative model of mammalian cell fate determination. The generation and maintenance of two of these lineages, the growth hormone (GH) producing somatotropes and prolactin (PRL) producing lactotropes, is dependent on the pituitary-specific POU-homeo domain transcription factor, POU1F1. While POU1F1 is expressed in both cell types, and plays a direct and essential role in the activation of both the Gh and Prl genes, GH expression is restricted to somatotropes and PRL expression is restricted to lactotropes. These observations imply the existence of additional, cell type-enriched factors, that contribute to the somatotrope and lactotrope cell identities. Here, we use a set of transgenic mouse models to facilitate sorting of somatotrope and lactotrope populations based on the expression of distinct fluorescent markers expressed under Gh and Prl gene transcriptional controls, respectively. The transcriptomic analyses reveal a concordance of gene expression profiles in the two populations. The limited number of divergent mRNAs between the two populations includes a set of transcription factors that may have roles in pituitary lineage divergence or in regulating the expression of key lineage-specific genes after lineage divergence. Four of these factors were validated for lineage enrichment at the level of protein expression, two somatotrope-enriched and two lactotrope-enriched, and three of these four factors were shown to have corresponding activities in appropriate enhancement or repression of landmark genes. These studies establish a useful database for further study of the somatotrope and lactotrope cells as well as identify novel regulators of lineage marker expression in the anterior pituitary. Overall design: 6 total samples, 3 biological replicates of the somatotrope cell type and 3 biological replicates of the lactotrope cell type

Publication Title

Transcriptome Analyses of Female Somatotropes and Lactotropes Reveal Novel Regulators of Cell Identity in the Pituitary.

Sample Metadata Fields

Sex, Specimen part, Cell line, Subject

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accession-icon GSE21713
mRNA expression data from primary untreated neuroblastoma tumour samples
  • organism-icon Homo sapiens
  • sample-icon 20 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)

Description

The miR-17-92 microRNA cluster is often activated in cancer cells, but the identity of its targets remains largely elusive. Here we examined the effects of activation of the entire miR-17-92 cluster on global protein expression in neuroblastoma cells.

Publication Title

The miR-17-92 microRNA cluster regulates multiple components of the TGF-β pathway in neuroblastoma.

Sample Metadata Fields

Specimen part

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accession-icon GSE31355
A genome wide methylation map of neuroblastoma cell lines
  • organism-icon Homo sapiens
  • sample-icon 15 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Genome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkers.

Sample Metadata Fields

Treatment

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accession-icon GSE31229
Neuroblastoma cell lines treated with DAC (2'-deoxy-5-azacytidine), a DNA-methylation inhibitor
  • organism-icon Homo sapiens
  • sample-icon 15 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

8 neuroblastoma (NB) cell lines (CLB-GA, IMR-32, SH-SY5Y, N206, CHP-902R, LAN-2, SK-N-AS, SJNB-1) were profiled on the Affymetrix HGU-133plus2,0 platform before and after treatment with DAC (2'-deoxy-5-azacytidine) to investigate the influence on expression after inhibiting DNA-methylation

Publication Title

Genome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkers.

Sample Metadata Fields

Treatment

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accession-icon E-MTAB-1354
Transcription profiling by array of Arabidopsis root tips from arf7, arf19 double mutant and wild type plants in response to auxin
  • organism-icon Arabidopsis thaliana
  • sample-icon 156 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

A timecourse of IAA treatment on the Arabidopsis root tip

Publication Title

The circadian clock rephases during lateral root organ initiation in Arabidopsis thaliana.

Sample Metadata Fields

Specimen part, Compound, Time

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accession-icon GSE49981
Reciprocal transcriptional responses in the interaction between Arabidopsis thaliana and Tetranychus urticae.
  • organism-icon Arabidopsis thaliana
  • sample-icon 28 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

While pathogen-induced immunity is comparatively well characterized, far less is known about plant defense responses to arthropod herbivores. To date, most molecular-genetic studies of plant-arthropod interactions have focused on insects. However, plant-feeding (phytophagous) mites are also pests of diverse plants, and mites induce different patterns of damage to plant tissues than do well-studied insects (e.g., Lepidopteran larvae or aphids). The two-spotted spider mite, Tetranychus urticae, is among the most significant mite pests in agriculture. T. urticae is an extreme generalist that has been documented on a staggering number of plant hosts (more than 1,100), and is renowned for the rapid evolution of pesticide resistance. To understand reciprocal interactions between T. urticae and a plant host at the molecular level, we examined mite herbivory using Arabidopsis thaliana. Despite differences in feeding guilds, we found that transcriptional responses of A. thaliana to mite herbivory generally resembled those observed for insect herbivores. In particular, defense to mites was mediated by jasmonic acid (JA) biosynthesis and signaling. Further, indole glucosinolates dramatically increased mite mortality and development times. Variation in both basal and activated levels of these defense pathways might also explain differences in mite damage and feeding success between A. thaliana accessions. On the herbivore side, a diverse set of genes associated with detoxification of xenobiotics was induced upon exposure to increasing levels of in planta indole glucosinolates. Our findings provide molecular insights into the nature of, and response to, herbivory for a representative of a major class of arthropod herbivores.

Publication Title

Reciprocal responses in the interaction between Arabidopsis and the cell-content-feeding chelicerate herbivore spider mite.

Sample Metadata Fields

Age, Specimen part, Treatment

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Casey S. Greene, Dongbo Hu, Richard W. W. Jones, Stephanie Liu, David S. Mejia, Rob Patro, Stephen R. Piccolo, Ariel Rodriguez Romero, Hirak Sarkar, Candace L. Savonen, Jaclyn N. Taroni, William E. Vauclain, Deepashree Venkatesh Prasad, Kurt G. Wheeler. refine.bio: a resource of uniformly processed publicly available gene expression datasets.
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Note that the contributor list is in alphabetical order as we prepare a manuscript for submission.

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