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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
Sample Metadata Fields
Sex, Specimen part, Cell line
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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
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
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 4 Downloadable Samples
- NextSeq 500
Description
Characterization of organ-targeting metastatic cancer cells
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Disease, Cell line
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
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
Sample Metadata Fields
Specimen part, Treatment
View Samples SRP111915- Homo sapiens
- 112 Downloadable Samples
- NextSeq 500
Description
The human MDA MB 231 breast cancer and MDA MB 435 melanoma cell lines were selected for isolates able to pass through narrow 3 micron pores in Transwell tissue culture inserts. In addition, MDA MB 231 breast cancer cells were selected for a population of small sized cells in parallel by flow cytometric sorting. RNA sequencing of the three populations (parental, selected, flow sorted) of MDA MB 231 breast cancer cells, and two populations (parental, selected) of MDA MB 435 melanoma cells, was performed.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Cell line, Race
View Samples SRP081135- Mus musculus
- 12 Downloadable Samples
- NextSeq 500
Description
Pancreatic cancer patient survival is the lowest of all common cancers. Given that pancreatic cancer therapies do little to improve survival, there is a significant need to identify additional potential therapeutic targets and treatment strategies. The ROCK1 locus on chromosome 18 is amplified in 15% of pancreatic patient tumors (Biankin et al. 2012), accompanied by concordant copy number/gene expression changes (Bailey et al. 2016). The ROCK1 and ROCK2 kinases promote actomyosin contractility through phosphorylation of substrates including the myosin regulatory light chain 2 (MLC2), myosin-binding subunit of the MLC phosphatase (MYPT1) and LIM kinases 1&2 (Rath and Olson 2012, Julian and Olson 2014). In addition to direct effects on the organization and dynamics of the actin cytoskeleton that impact cell morphology, ROCK-mediated cell contractility also affects gene transcription (Sanz-Moreno et al. 2011). How ROCK-mediated actomyosin contractility might contribute to pancreatic cancer by altering gene expression has not been established.In this study, mouse pancreatic ductal adenocarcinoma tumour cells were transduced with retrovirus encoding conditionally-activated estrogen-receptor hormone-binding domain (hbER) fusions with ROCK1 (ROCK1:ER) or ROCK2 (ROCK2:ER) kinase domains, or green fluorescent protein (GFP:ER). GFP:ER expressing cells were treated with ethanol vehicle or 1 micromolar 4-hydroxytamoxifen (4HT) to identify any effects of the estrogen analogue, while ROCK1:ER and ROCK2:ER cells were treated with 1 micromolar 4HT to activate the ER fusion proteins. RNA was isolated, and enriched for poly A+ transcripts prior to sequencing.Bailey, P., et al. (2016). Nature 531: 47-52.Biankin, A. V., et al. (2012). Nature 491: 399-405.Julian, L. and M. F. Olson (2014). Small GTPases 5: e29846.Rath, N. and M. F. Olson (2012). EMBO Rep 13: 900-908.Sanz-Moreno, V., et al. (2011). Cancer Cell 20: 229-245.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line
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
Sample Metadata Fields
Specimen part, Disease, Cell line
View Samples- Mus musculus
- 2 Downloadable Samples
- Illumina 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
Sample Metadata Fields
Sex, Age, Specimen part, Cell line
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