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Mus musculus
12 Downloadable Samples
NextSeq 500
Description
Purpose: The goals of this study are to compare transcriptome profiling (RNA-seq) resulting from a Mesp1Cre driven ablation of Hira in the heart at E11.5 and E12.5. Methods: RNA extraction was done in triplicate from Mesp1Cre;Hira-/fl and Mesp1Cre;Hira+/fl embryonic hearts at E11.5 and E12.5 using the QIAGEN RNeasy mini kit. RNAseq was processed by the ICH genomics facility, reads were aligned and normalised using BOWTIE and DEseq R package. Strand NGS 2.5 software was used to re-analyse the aligned files (.bam). By applying the Mann Whitney unpaired test, Benjamini Hochberg False discovery rate (FDR) and filtering the genes using adjusted p-value = 0.05 and absolute fold change = 1.5, 95 % of the results were identical to the DEseq package used by the UCL Genomics facility. Results: We identified 360 coding transcripts changed in the mutant hearts (Mann Whitney unpaired test, Benjamini Hochberg FDR, p = 0.05, FC = 1.5) with no trend towards up- or down-regulation of global transcription (48.8% down vs 51.2% up) at E12.5. Conclusions: This work analyses the role of HIRA in mouse cardiac development. It was found that Tnni2 is the most upregulated gene in the absence of Hira. qRT-PCR validation of 25 targets. Little (<5%) or no variation of fold change between RNAseq and qRT-PCR data were observed. Overall design: Cardiac mRNA profiles of 11-day and 12-day embryonic days Mesp1Cre control (Ctrl) and Mesp1Cre;Hira-/fl (mut) were generated by deep sequencing, in triplicate, using Illumina GAIIx.
Publication Title
HIRA Is Required for Heart Development and Directly Regulates Tnni2 and Tnnt3.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 6 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Gene expression profiling of the inferior and superior wall of the distal midgestation arterial domain (outflow tract) of the wild type CD1 mouse embryonic heart
Publication Title
Tbx1 coordinates addition of posterior second heart field progenitor cells to the arterial and venous poles of the heart.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 18 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
The Hippo pathway is an emerging signaling cascade involved in the regulation of organ size control. It consists of evolutionally conserved protein kinases that are sequentially phosphorylated and activated. The active Hippo pathway subsequently phosphorylates a transcription coactivator, YAP, which precludes its nuclear localization and transcriptional activation. Identification of transcriptional targets of YAP in diverse cellular contexts is therefore critical to the understanding of the molecular mechanisms in which the Hippo pathway restricts tissue growth.
Publication Title
Hippo signaling regulates microprocessor and links cell-density-dependent miRNA biogenesis to cancer.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 88 Downloadable Samples
- Illumina HiSeq 2000
Description
Here we harnessed the potential of RNA sequencing in 89 human pancreatic islet donors to identify genes and exons regulated in this relevant tissue for T2D. Overall design: mRNA profiles of 89 human pancreatic islet donors having different levels of blood glucose (HbA1c) with and without T2D. The data was generated by deep sequencing using Illumina HiSeq 2000.
Publication Title
Orphan G-protein coupled receptor 183 (GPR183) potentiates insulin secretion and prevents glucotoxicity-induced β-cell dysfunction.
Sample Metadata Fields
Sex, Age, Specimen part, Subject
View Samples
GSE349- Homo sapiens
- 14 Downloadable Samples
Affymetrix Human Genome U95 Version 2 Array (hgu95av2), Affymetrix Human Genome U95A Array (hgu95a)
Description
These patients proved resistant to docetaxel treatment, exhibiting residual tumor of 25% or greater remaining volume.
Publication Title
Gene expression profiling for the prediction of therapeutic response to docetaxel in patients with breast cancer.
Sample Metadata Fields
No sample metadata fields
View Samples GSE350- Homo sapiens
- 10 Downloadable Samples
- Affymetrix Human Genome U95 Version 2 Array (hgu95av2)
Description
These patients were sensitive to docetaxel treatment, exhibiting less than 25% residual tumor.
Publication Title
Gene expression profiling for the prediction of therapeutic response to docetaxel in patients with breast cancer.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 9 Downloadable Samples
- Ion Torrent S5 XL
Description
neuroblastoma cells derived from PDOX models were treated with the kinase inhibitor. Overall design: 5 repetitions of control and IBL-302 treated cells were harvest and submitted for RNAseq analysis
Publication Title
Anti-tumor effects of PIM/PI3K/mTOR triple kinase inhibitor IBL-302 in neuroblastoma.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples- Homo sapiens
- 24 Downloadable Samples
- Affymetrix Human Genome U95 Version 2 Array (hgu95av2), Affymetrix Human Genome U95A Array (hgu95a)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Patterns of resistance and incomplete response to docetaxel by gene expression profiling in breast cancer patients.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 2 Downloadable Samples
- Illumina HiSeq 2500
Description
Single-cell RNA-seq (10X Genomics Chromium) to profile of cardiac progenitor cells, comparing the transcriptomes of diploid and tetraploid cardiac progenitor cells Overall design: Transcriptional profiling of diploid and tetraploid CPCs by scRNA-Seq approaches using 10X Genomics Chromium
Publication Title
Cardiac interstitial tetraploid cells can escape replicative senescence in rodents but not large mammals.
Sample Metadata Fields
Sex, Specimen part, Cell line, Subject
View Samples- Oryza sativa
- 12 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
Twenty one day old seedlings of the mutant and WT grown in hydroponic culture in three replications were subjected to 25% PEG stress for one hour. The leaf samples of stressed and control seedlings were collected and preserved in liquid nitrogen for RNA isolation. Total RNA from four samples i.e. mutant control (MC), mutant stress (MS), Nagina22 control (NC) and Nagina22 stress (NS) was extracted by following the manufacturer‰۪s instructions provided with SV Total RNA isolation system Kit (PROMEGA, USA). All the steps starting from cRNA preparation to hybridization were conducted following the instructions of Affymetrix (AffymetrixGeneChip Expression Analysis Technical Manual). Chips were washed and stained in the Affymetrix Fluidics Station 450, and then scanned using the Affymetrix Gene Chip Scanner 3000. The cell intensity data files (.CEL) generated by the Gene Chip Operating Software (GCOS 1.2).
Publication Title
Physiological, anatomical and transcriptional alterations in a rice mutant leading to enhanced water stress tolerance.
Sample Metadata Fields
Specimen part
View Samples