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accession-icon SRP095378
Arabidopsis thaliana Raw sequence reads
  • organism-icon Arabidopsis thaliana
  • sample-icon 2 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Transcriptomic analysis of BnLATE-regulated pathways to investigate the genome-wide effects of BnLATE overexpression on transcription

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Specimen part

View Samples
accession-icon SRP002572
Drosophila transcriptome
  • organism-icon Drosophila melanogaster
  • sample-icon 2 Downloadable Samples
  • Technology Badge IconIllumina Genome Analyzer

Description

Illumina/Solexa sequencing of CG3985 mutant and wildtype testes transcriptome (0-1 day males)

Publication Title

A young Drosophila duplicate gene plays essential roles in spermatogenesis by regulating several Y-linked male fertility genes.

Alternate Accession IDs

None

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon SRP068329
pig transcriptome
  • organism-icon Sus scrofa
  • sample-icon 1 Downloadable Sample
  • Technology Badge IconIllumina HiSeq 2500

Description

The placenta has shown morphological and functional adaption in Meishan and Yorkshire pig breeds during late gestation. While the vast difference of uterine capacity and conceptus genotype between Western and Chinese pig breeds affects the pattern of placental development. Whether the placenta within Chinese pig breed also has similar adaptive changes is still unknown. So, we measured the weight and area of 80 Chinese indigenous Diannan small-ear pig placentas and further selected 6 placentas from extremely high and low litter size groups (HL and LL) for deep RNA-sequencing to detect the molecular basis relate to the observed placental phenotype difference.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Sex, Specimen part

View Samples
accession-icon SRP132132
Arabidopsis thaliana strain:Col-0 Raw sequence reads
  • organism-icon Arabidopsis thaliana
  • sample-icon 4 Downloadable Samples
  • Technology Badge IconNextSeq 500

Description

This study is aimed to compare the gene expression between wild type and 35S:6MYC-HARP1 in response to wounding treatment.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Age, Specimen part, Treatment

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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 DRP002851
Long non-coding RNA UPAT promotes colon tumorigenesis by inhibiting degradation of UHRF1
  • organism-icon Homo sapiens
  • sample-icon 8 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000, Illumina Genome Analyzer IIx

Description

1. To identify lncRNA regulating colorectal tumorigenesis, we performed RNA-seq analysis of cells with high and low tumorigenicity 2. To study the role of UPAT in colorectal cancer cells, we investigated the gene expression profiles of HCT116 cells in which UPAT expression had been suppressed by siRNA.

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Cell line

View Samples
accession-icon SRP065059
Zea mays cultivar:Shandan 609 Raw sequence reads
  • organism-icon Zea mays
  • sample-icon 4 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

This study provide a dynamic atlas of endosperm development from Shaanxi within China

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Specimen part

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

View Samples
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

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
...

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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