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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

Alternate Accession IDs

None

Sample Metadata Fields

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

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accession-icon SRP108540
Glycine max Raw sequence reads
  • organism-icon Glycine max
  • sample-icon 35 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Transcriptome sequencing to identify differentially expressed transcripts in roots of iron deficiency chlorosis tolerant line U06-105454 and iron deficiency chlorosis sensitive line U06-625083 with low iron and alkaline treatments

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Age, Specimen part, Treatment

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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.

Alternate Accession IDs

None

Sample Metadata Fields

Age, Specimen part

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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

Alternate Accession IDs

None

Sample Metadata Fields

Specimen part

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accession-icon SRP072496
Zea mays subsp. mays Transcriptome or Gene expression
  • organism-icon Zea mays
  • sample-icon 17 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Our study revealed photoperiod influenced on not only flowering not only stress responses under long-day conditions and ZmCCT and ZmCCA1 were the key functional links between the circadian clock and adversity stress tolerance. Establishment of the molecular link reveals a new interface between the plant phtoperiod and adversity stress.

Publication Title

Dual functions of the ZmCCT-associated quantitative trait locus in flowering and stress responses under long-day conditions.

Alternate Accession IDs

None

Sample Metadata Fields

Specimen part

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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

Alternate Accession IDs

E-GEOD-56437

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon SRP077553
Transcriptome profile and gene expression in the human placenta
  • organism-icon Homo sapiens
  • sample-icon 4 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

In this study, we performed a NGS analysis to identify transcriptome landscape of the human placenta during uncomplicated single and twin pregnancy, to establish a pattern of normal placental genes expression for further comprehensive analyses. Additionall aim of these studies was to identify the differentially expressed transcripts of genes in single and twin pregnancy that may participate in human pregnancy.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Sex, Age, Specimen part, Disease

View Samples
accession-icon GSE99150
eQTL analysis - Extracting genotype information of recombinant inbred lines from transcript profiles established with high-density oligonucleotide arrays
  • organism-icon Arabidopsis thaliana
  • sample-icon 115 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

In order to identify eQTL in developing seeds of Arabidopsis thaliana 116 Arabidopsis thaliana recombinant inbred lines (C24/Col 0 and Col 0/C24, Trjk et al. 2006) were analysed.

Publication Title

No associated publication

Alternate Accession IDs

E-GEOD-99150

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE110171
Expression data of Arabidopsis grown under low or sufficient nitrogen availability
  • organism-icon Arabidopsis thaliana
  • sample-icon 72 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Nitrogen availability in the soil is a major determinant of crop yield. While the application of fertilizer can substantially increase the yield on poor soils, it also causes nitrate pollution of water resources and high costs for farmers. Increasing the nitrogen use efficiency in crop plants is a necessary step to implement low input agricultural systems. We exploited the genetic diversity present in the world-wide Arabidopsis thaliana population to study adaptive growth patterns and changes in gene expression associated with chronic low nitrate stress, with the aim to identify biomarkers associated with good plant performance under low nitrate availability.

Publication Title

No associated publication

Alternate Accession IDs

E-GEOD-110171

Sample Metadata Fields

Age, Specimen part, Treatment

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accession-icon GSE94764
Differentially expressed genes in developing seeds of Arabidopsis thaliana accessions Col-0 and C24 - Impact of polymorphic probes on the detection of differentially expressed genes
  • organism-icon Arabidopsis thaliana
  • sample-icon 36 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Tailoring high-density oligonucleotide arrays for transcript profiling of different Arabidopsis thaliana accessions using a sequence-based approach.

Alternate Accession IDs

E-GEOD-94764

Sample Metadata Fields

Specimen part

View Samples
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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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