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accession-icon SRP099206
Coupling RNA-seq and virus induced gene silencing to identify gene networks regulated by GmMEKK1 in Glycine max
  • organism-icon Glycine max
  • sample-icon 8 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

GmMEKK1 silencing was performed in Glycine max (Williams 82) using virus-induced gene silencing (VIGS) mediated by Bean pod mottle virus (BPMV). Rna-Seq was performed to compare the transcriptional profile of GmMEKK1-silenced plants to vector control plants.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Age, Specimen part, Disease, Treatment

View Samples
accession-icon SRP151943
Rpp1 encodes a ULP-NBS-LRR protein that controls immunity to Phakopsora pachyrhizi in soybean
  • organism-icon Glycine max
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Virus induced gene silencing coupled with RNA-seq was used to identify genes in the Rpp1 signaling network

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Age, Specimen part, Disease, Treatment

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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

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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

View Samples
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

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accession-icon GSE94763
Differentially expressed genes in developing seeds of Arabidopsis thaliana accessions Col-0 and C24 - Impact of the exclusion of polymorphic probes via a sequence-based approach
  • organism-icon Arabidopsis thaliana
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

In order to identify differentially expressed genes in developing seeds of Arabidopsis thaliana three different stages of seed development were analysed (9-10, 10-11 and 12-13 days after flower opening) for two Arabidopsis thaliana accessions, Col-0 and C24. For each stage and accession three biological replicates were analysed.

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-94763

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE94762
Differentially expressed genes in developing seeds of Arabidopsis thaliana accessions Col-0 and C24
  • organism-icon Arabidopsis thaliana
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

In order to identify differentially expressed genes in developing seeds of Arabidopsis thaliana three different stages of seed development were analysed (9-10, 10-11 and 12-13 days after flower opening) for two Arabidopsis thaliana accessions, Col-0 and C24. For each stage and accession three biological replicates were analysed.

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-94762

Sample Metadata Fields

Specimen part

View Samples
accession-icon SRP189768
Porcine Jejunum Transcriptome Sequencing
  • organism-icon Sus scrofa
  • sample-icon 25 Downloadable Samples
  • Technology Badge IconNextSeq 500

Description

RNA-Seq of jejunum for 30 pigs with divergent feed efficiency phenotypes

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Sex, Specimen part

View Samples
accession-icon SRP189144
Porcine Hypothalamus Transcriptome Sequencing
  • organism-icon Sus scrofa
  • sample-icon 28 Downloadable Samples
  • Technology Badge IconNextSeq 500

Description

RNASeq of hypothalamus for 30 pigs with divergent feed efficiency phenotypes

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Sex, Specimen part

View Samples
accession-icon GSE107497
Genomic analysis for hematopoietic stem and progenitors cells (HSPC) generated in vitro according to ex vivo expansion protocols and their comparison with HSPC obtained fresh
  • organism-icon Homo sapiens
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Transcriptome Array 2.0 (hta20)

Description

Expansion for hematopoietic cells from umbilical cord blood is a strategy for use this cell source in clinic transplants, however, it is important to know about the genomic changes that can occur in expanded cells. In order to detect global expression profiles changes in hematopoietic stem and progenitors cells generated in vitro, we analyzed hematopoietics populations obtained by FACS in fresh from umbilical cord blood. HSC (fHSC) was defined as CD34+ CD38- CD71- CD45RA- Lin- and were cocultured with stromal cell line OP-9 plus FL, SCF, IL3, IL6, TPO, GMCSF and G-CSF by 7 days, after time we repurified HSC population by FACS using same immunophenotype (ivHSC). In other hand, fresh erythroid progenitors cells (fEPC) were identified as CD34+CD38+CD71+CD45RA- Lin- and fresh myeloid progenitors cells (fMPC) were identified as CD34+CD38+CD71-CD45RA+Lin-. In vitro progenitors cells (ivEPC and ivMPC) were obtained by culturing fHSC in Stemspan serum-free media plus SCF, TPO, IL6, FL and IL3 by 10 days, after time cells were repurified by FACS using same immunophenotype for fresh progenitors. In vitro generated cells were compared with their corresponding fresh population cells.

Publication Title

Functional Integrity and Gene Expression Profiles of Human Cord Blood-Derived Hematopoietic Stem and Progenitor Cells Generated In Vitro.

Alternate Accession IDs

E-GEOD-107497

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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