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accession-icon SRP076058
Zea mays Raw sequence reads
  • organism-icon Zea mays
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

This study presented the differentially expressed genes post maize infected by Rhizoctonia solani.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Specimen part

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accession-icon SRP170079
Effect of post-silking drought stress on the expression profiles of genes involved in carbon and nitrogen metabolism during leaf senescence in maize (Zea mays L.)
  • organism-icon Zea mays
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

transcriptional regulation of specific carbon and nitrogen metabolism genes in maize plants exposed to post-silking (PD) drought stress.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Specimen part, Treatment

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accession-icon SRP142026
Saccharomyces cerevisiae Raw sequence reads
  • organism-icon Saccharomyces cerevisiae
  • sample-icon 34 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

As an ancient winning strategy of microorganisms, glucose repression mechanism has become specialized to perfection in Saccharomyces cerevisiae. The galactose (GAL) metabolism network is stringently regulated by glucose repression in yeast and has been a classic system for studying gene regulation. We show here that the population of S. cerevisiae living in fermented milks has autonomously reinstated an ancient version of the structural GAL genes through introgression. The introgressed GAL network has completely abolished the glucose repression and conversed from a strictly inducible to a constitutive system through coordinative polygenic changes in the regulatory components of the network, including transitions in the upstream repressing sequence site of GAL4 that impair Mig1p-mediated repression and loss of function of the inducer Gal3p and the repressor Gal80p. In addition, the introgressed GAL2 gene has been duplicated while the native HXT6 and HXT7 genes have been inactivated, resulting in galactose-over-glucose preference and elevated galactose utilization rate. Relying on the reverse evolution of the GAL network, the non-lactose fermenting yeast has become a dominant species co-existing with other lactose fermenting microorganisms in fermented milks. Our results also provide new clues for developing yeast strains devoid of barriers to co-utilization of different sugars.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Specimen part, Disease, Cell line

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accession-icon SRP151834
RNA-seq results of WT and CKIP-1 KO mouse macrophages
  • organism-icon Mus musculus
  • sample-icon 2 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

The differential expression of gene in bone marrow derived macrophages from Ckip-1 KO mice and WT mice.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Sex, Age, Specimen part, Cell line

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accession-icon SRP094817
Zea mays(B73) RNA-Seq
  • organism-icon Zea mays
  • sample-icon 2 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 3000

Description

Transposons in maize may be involved in the formation of circRNAs and further modulate phenotypic variation. To test our hypothesis, we performed circRNA-Seq(RNase R treated) on B73 seedlings(third leaves of V3 stage), and uncovered 1,572 high-confidence maize circRNAs, which show distinct genomic features compared to linear transcripts. Comprehensive analyses showed that LINE1-like elements (LLE) and their reverse complementary pairs (RCPLLEs) are significantly enriched in the flanking regions of circRNAs.

Publication Title

Circular RNAs mediated by transposons are associated with transcriptomic and phenotypic variation in maize.

Alternate Accession IDs

None

Sample Metadata Fields

Specimen part, Disease

View Samples
accession-icon SRP167225
Characterization of Transcriptomic Profile in Early Zebrafish PGCs by Single Cell Sequencing
  • organism-icon Danio rerio
  • sample-icon 9 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Single cell RNA-seq was applied for studying the transcriptomic profile in early zebrafish PGCs(primordial germ cells) by choosing three time points during zebrafish embryonic development. The three time points were 6hpf(hours post fertilization, also called shield stage), 11hpf(also called 3-somite stage) and 24hpf(also called prim-5 stage).

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Sex, Specimen part, Cell line

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accession-icon SRP128611
Pex3 deficiency effect on mouse testis
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Pex3 plays an essential role in peroxisomal membrane proteins (PMPs) import. Loss of Pex3 leads to a spermatogenic arrest.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Sex, Specimen part, Cell line

View Samples
accession-icon SRP092222
Homo sapiens Raw sequence reads
  • organism-icon Homo sapiens
  • sample-icon 5 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

we compared the gene expression of CD106+MSCs and CD106-MSCs

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Sex, Age, Specimen part

View Samples
accession-icon SRP044629
Mus musculus strain:a C57BL/6;129/SvEv mixed background Transcriptome or Gene expression
  • organism-icon Mus musculus
  • sample-icon 4 Downloadable Samples
  • Technology Badge IconIllumina Genome Analyzer II

Description

To investigate the molecular mechanism which caused the defect of aberrant somatic cell differentiation in Wt1-deficient gonads, the differentially expressed genes between control and Wt1-deficient gonads at E11.5 was analyzed by RNA Seq analysis.After tamoxifen injection at E9.5, total RNA was prepared from control and Wt1-deficient gonads at E11.5 using RNeasy Minikit (Ambion, Austin, TX). Gonads of the same genotype (about 12 pairs each) were pooled together. For RNA-Seq, the main reagents and instruments used for RNA library construction and deep sequencing were the Illumina Gene Expression Sample Prep Kit, Solexa Sequencing Chip (flowcell), Illumina Cluster Station and Illumina HiSeq 2000 System. Sequence tags were prepared using the Illumina Digital Gene Expression Tag Profiling Kit, according to the manufacturer's protocol. Raw data was filtered to remove adaptor tags, low quality tags, and tags with a single copy number. Paired-end reads were mapped to the mouse genome (mm9) with TopHat and further analyzed by Cufflinks-Cuffdiff (Trapnell et al., 2009; Trapnell et al., 2010) pipelines to identify differentially expressed transcripts (DETs) between control and Wt1-deficient gonads.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon SRP149205
the sequencing of PDK1 deleted LSK cells
  • organism-icon Mus musculus
  • sample-icon 2 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

RNA sequencing analysis showed PDK1 deleted LSKs enriched in development, PI3K-AKT, apoptosis and cell cycle-related pathways in contrast to controls

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Sex, Specimen part, Cell line

View Samples
...

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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Developed by the Childhood Cancer Data Lab

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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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