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accession-icon E-MEXP-1138
Transcription profiling of mature pollen grains from wild type and AtMIKC* MADS-box gene knock-out Arabidopsis plants
  • organism-icon Arabidopsis thaliana
  • sample-icon 28 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Effects of loss-of-function of AtMIKC* MADS-box genes on the mature Arabidopsis pollen transcriptome.

Publication Title

MADS-complexes regulate transcriptome dynamics during pollen maturation.

Sample Metadata Fields

Age, Specimen part

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accession-icon SRP139292
miR-218
  • organism-icon Mus musculus
  • sample-icon 8 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Small RNA seq following over expression of miR-218 in HepG2 cells; mRNA expression following perturbation of miR-218 in primary mouse motor neurons

Publication Title

No associated publication

Sample Metadata Fields

Sex, Specimen part

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accession-icon SRP114906
Transcriptomic analysis of progranulin-deficienct mouse brains
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Progranulin mutations found in frontotemporal lobar degeneration (FTLD) cases typically result in heterozygous loss-of-function. To assess the impact of PGRN deficiency on gene expression, particularly of genes associated with lipid metabolism, in the brain, we sequenced the total RNA extracted from whole brains from 7-month-old female Grn+/+, Grn+/–, and Grn–/– mice and determined the differential expression of transcripts in PRGN-deficient (Grn+/- and Grn-/-) and wild type (Grn+/+) brains.

Publication Title

No associated publication

Sample Metadata Fields

Sex, Age, Specimen part, Cell line

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accession-icon SRP096846
Histone Acetyltransferase GCN5 Contributes to Stem Cuticular Wax Biosynthesis by Acetylating ECERIFERUM 3 (CER3) in Arabidopsis thaliana
  • organism-icon Arabidopsis thaliana
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Cuticular wax is a major composition of plant surface cuticle, which exerts crucial functions in optimizing plant growth. Histone acetylation regulates gene expression of diverse biological processes, but little is known about its role in cuticular wax synthesis. Here we observed that mutation of Arabidopsis histone acetyltransferase GCN5 gene impaired stem cuticular wax accumulation. Furthermore, three target genes of GCN5 (CER3, CER26 and CER1-L1) were identified by RNA-Seq and ChIP assays. Consistently, H3K9/14 acetylation levels in promoter regions of CER3, CER26 and CER1-L1 were significantly decreased in gcn5 as compared to wild type. Notably, overexpression of CER3 in the gcn5 mutant restored the stem cuticular wax accumulation. Collectively, these data demonstrate that Arabidopsis GCN5 is involved in stem cuticular wax accumulation by modulating CER3 expression via H3K9/14 acetylation, which present evidence that histone acetylation plays an important role in cuticular wax biosynthesis

Publication Title

No associated publication

Sample Metadata Fields

Specimen part

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accession-icon E-MEXP-739
Transcription profiling of by array of Arabidopsis plants infected with powdery mildew and treated with Syringolin A
  • organism-icon Arabidopsis thaliana
  • sample-icon 24 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Powdery mildew, caused by the fungus Blumeria graminis (DC) Speer, is one of the most important foliar diseases of cereals worldwide. It is an obligate biotrophic parasite, colonising leaf epidermal cells to obtain nutrients from the plant cells without killing them. Syringolin A (sylA), a circular peptide secreted by the phytopathogenic bacterium Pseudomonas syringae pv. syringae, triggers a hypersensitive cell death reaction (HR) at infection sites when sprayed onto powdery mildew infected wheat which essentially eradicates the fungus. The rational was to identify genes whose expression was specifically regulated during HR, i.e. genes that might be involved in the switch of compatibility to incompatibility.<br></br>Powdery mildew-infected or uninfected plants were treated with syringolin two days after infection and plant material for RNA extraction was collected at 0.5, 1, 2, 4, 8, 12 hours after treatment (hat), resulting in an early (2 and 4 hat) and late pool (8 and 12 hat). Plant material that was uninfected prior to syringolin treatment was collected 8 and 12 hat (late pool of uninfected plant material), and 1 hat, respectively.

Publication Title

Transcriptional changes in powdery mildew infected wheat and Arabidopsis leaves undergoing syringolin-triggered hypersensitive cell death at infection sites.

Sample Metadata Fields

Compound, Time

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accession-icon SRP075626
Mycobacterial infection of adult zebrafish
  • organism-icon Danio rerio
  • sample-icon 12 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq2500

Description

RNA-seq-based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.

Publication Title

No associated publication

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE56437
Transcriptome characterization of genotype-dependent effects of CaCl2 treatment on drought adaptation in barley (Hordeum vulgare L.).
  • organism-icon Hordeum vulgare
  • sample-icon 72 Downloadable Samples
  • Technology Badge Icon Affymetrix Barley Genome Array (barley1)

Description

The hypothesis whether CaCl2 seed treatment prior to sowing (osmopriming) can enhance drought stress tolerance, and/or alleviate the effect on plant growth was tested.

Publication Title

No associated publication

Sample Metadata Fields

No sample metadata fields

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accession-icon SRP132125
ZmGRP1 CRISPR/Cas9 RNA sequencing
  • organism-icon Zea mays
  • sample-icon 7 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

To study the splicing factor role of ZmGRP1

Publication Title

No associated publication

Sample Metadata Fields

Sex, Specimen part, Disease, Disease stage, Cell line, Treatment

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accession-icon SRP020868
Glycine max Transcriptome or Gene expression
  • organism-icon Glycine max
  • sample-icon 9 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

To provide novel insights into the molecular basis of floral initiation, RNASeq was used to characterize the soybean transcriptome of leaf and micro-dissected shoot apical meristem at different time points after short-day treatment.

Publication Title

No associated publication

Sample Metadata Fields

No sample metadata fields

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accession-icon SRP113626
Saccharomyces cerevisiae RNAseq Raw sequence reads
  • organism-icon Saccharomyces cerevisiae
  • sample-icon 338 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

WT cells and mutants during growth on low phosphate levels and recovery

Publication Title

No associated publication

Sample Metadata Fields

Specimen part, Disease, Cell line

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refine.bio is a repository of uniformly processed and normalized, ready-to-use transcriptome data from publicly available sources. refine.bio is a project of the Childhood Cancer Data Lab (CCDL)

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Cite refine.bio

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.
URL: https://www.refine.bio

Note that the contributor list is in alphabetical order as we prepare a manuscript for submission.

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