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Danio rerio
9 Downloadable Samples
Illumina 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
SRP076058- Zea mays
- 6 Downloadable Samples
- Illumina 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- Mus musculus
- 4 Downloadable Samples
- Illumina 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- Drosophila melanogaster
- 6 Downloadable Samples
- Illumina HiSeq 2500
Description
A novel transcriptional cascade involved in Fzr-mediated endoreplication
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Arabidopsis thaliana
- 4 Downloadable Samples
- Illumina HiSeq 2500
Description
There is limited knowledge on the biological function of group C MAPK. To reveal the function of MnMAPK6, a group C MAPK, in the transgenic Arabidopsis, a transcriptome analysis was performed by Illumina sequencing for the assessment of gene expression changes between WT and MnMPK6-overexpressed Arabidopsis.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 4 Downloadable Samples
- Illumina Genome Analyzer
Description
Small RNA transcriptome in murine liver during Schistosoma japonicum infection.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part, Disease, Disease stage
View Samples- Zea mays
- 4 Downloadable Samples
- Illumina 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- Bos taurus
- 4 Downloadable Samples
- Illumina HiSeq 2500
Description
Adipogenesis is a complex and precisely orchestrated process mediated by a network of adipogenic regulatory factors. The recent explosion of knowledge have demonstrated that long noncoding RNA are involved in adipogenic gene regulatory network. However, existing annotations of lncRNAs involved in adipogenic differentiation are derived from preadipocyte cell lines, researches using primary cultures of farm animals are obviously required. To comprehensively identify lncRNAs with potential functions during bovine adipogenesis, in the present study we performed Ribo-Zero-Seq to survey the transcriptome landscape of in vitro cultured bovine preadipocytes and differentiated adipocytes. A stringent set of 2882 lncRNAs were finally identified. The 2882 lncRNAs shared many of the features of their mammalian counterparts: relatively shorter in length, significantly lower expression levels and fewer in exon number than RefSeq protein coding transcripts. Comparison of the lncRNAs expression profiles identified 16 specifically regulated lncRNAs during adipogenic differentiation. Integrative computational analyses associated these lncRNAs with several signaling pathways involved in lipid metabolism, including steroid biosynthesis, PPAR signaling pathway, glycolysis/gluconeogenesis, and fatty acid metabolism. Our data provide a valuable genomic resource for the identification of lncRNAs with potential functions in adipogenic differentiation.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part
View Samples- Saccharomyces cerevisiae
- 34 Downloadable Samples
- Illumina 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
View Samples SRP165652- Homo sapiens
- 3 Downloadable Samples
- Ion Torrent S5
Description
This study presented the preliminary mechanistic studies of teniposide analogs for toxicity reduction
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Age, Specimen part
View Samples