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Homo sapiens
145 Downloadable Samples
Description
The use of induced pluripotent stem cells (iPSC) derived from independent patients and sources holds considerable promise to improve the understanding of development and disease. However, optimized use of iPSC depends on our ability to develop methods to efficiently qualify cell lines and protocols, monitor genetic stability, and evaluate self-renewal and differentiation potential. To accomplish these goals, 57 stem cell lines from 10 laboratories were differentiated to 7 different states, resulting in 248 analyzed samples. Cell lines were differentiated and characterized at a central laboratory using standardized cell culture methodologies, protocols, and metadata descriptors. Stem cell and derived differentiated lines were characterized using RNA-seq, miRNA-seq, copy number arrays, DNA methylation arrays, flow cytometry, and molecular histology. All materials, including raw data, metadata, analysis and processing code, and methodological and provenance documentation are publicly available for re-use and interactive exploration at https://www.synapse.org/pcbc. The goal is to provide data that can improve our ability to robustly and reproducibly use human pluripotent stem cells to understand development and disease.
Publication Title
Integrated Genomic Analysis of Diverse Induced Pluripotent Stem Cells from the Progenitor Cell Biology Consortium.
Sample Metadata Fields
No sample metadata fields
View Samples- Caenorhabditis elegans
- 82 Downloadable Samples
- NextSeq 500
Description
We have used FACS to isolate fluorescent cells at multiple time points from synchronized embryos containing early and highly specific tissue/lineage markers. We then carried out RNA-seq, and observe dramatic differences in gene expression levels both between cell-types, and over time within the same population. Furthermore, we observe differential transcript usage between cell-types and over time, including differential promoter and differential exon usage that leads to additional differences between cell types.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Disease
View Samples
SRP187352- Glycine max
- 15 Downloadable Samples
- Illumina HiSeq 2000
Description
Transcriptome profiling is performed to reveal how Brassinosteroids (BRs) play a crucial role for plant vegetative growth and reproductive development.
Publication Title
No associated publication
Sample Metadata Fields
Age, Specimen part
View Samples- Mus musculus
- 12 Downloadable Samples
Affymetrix Mouse Expression 430A Array (moe430a)
Description
The aim of this experiment was to investigate the role of MIF during wound healing using BALB/C MIF null mice and in the context of reduced estrogen-associated impaired healing using ovariectomized mice (a mouse model of age-associated delayed healing). Ageing is associated with delayed cutaneous wound healing resulting from reduced estrogen levels. Macrophage migration inhibitory factor (MIF - NCBI RefSeq: NM_010798) is thought to mediate the effects of estrogen on wound healing. Gene expression was compared between wounds from ovariectomized MIF null mice and controls.
Publication Title
Macrophage migration inhibitory factor: a central regulator of wound healing.
Sample Metadata Fields
Sex, Age, Specimen part, Subject
View Samples- Glycine max
- 12 Downloadable Samples
- Illumina HiSeq 2000
Description
Soybean transcript fluctuations were observed in response to Rhizoctonia solani AG-1 IA causing Rhizoctonia foliar blight. The overall goal was to observe the general transcriptome fluctuations using RNAseq Illumina HiSeq analysis.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Disease
View Samples- Mus musculus
- 10 Downloadable Samples
- Illumina HiSeq 2500
Description
VEGF and VEGFB Play Balancing Roles in Adipose Differentiation, Gene Expression and Function
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Glycine max
- 9 Downloadable Samples
- Illumina Genome Analyzer
Description
Identification and comparative analysis of differential gene expression in soybean leaf tissue under drought and flooding stress revealed by RNA-Seq
Publication Title
No associated publication
Sample Metadata Fields
Age, Specimen part
View Samples- Rattus norvegicus
- 6 Downloadable Samples
- Affymetrix Rat Expression 230A Array (rae230a)
Description
The present study aimed to delineate the central mechanisms by which androgens delay wound repair. Blocking the conversion of testosterone to 5alpha-dihydrotestosterone (DHT) by 5alpha-reductase limits its ability to impair skin wound healing, suggesting that DHT is a more potent inhibitor of repair than is testosterone. This study aims to identify, through transcription profiling, potential mechanisms by which the 5alpha-reductase inhibitor MK-434 modulates repair. Microarray analysis of wound RNA samples from rats in which the transformation of testosterone to DHT is prevented has identified biological processes and key individual genes through which DHT may contribute to the altered healing profile in such animals. These include genes with putative roles in wound contraction and re-epithelialization.
Publication Title
5alpha-dihydrotestosterone (DHT) retards wound closure by inhibiting re-epithelialization.
Sample Metadata Fields
Sex, Age, Specimen part, Compound
View Samples- Homo sapiens
- 4 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
The aim of this experiment was measure the influence of age on cutaneous wound healing using human subjects. Increaded age has been associated with delayed wound healing in mouse models and in humans. Gene expression was compared between excisional biopsy wounds from young and old subjects.
Publication Title
Estrogen, not intrinsic aging, is the major regulator of delayed human wound healing in the elderly.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples SRP194050- Mus musculus
- 4 Downloadable Samples
- Illumina HiSeq 2500
Description
gene expression study on brain and lung under Dip2a regulation to better understand the role of Dip2a gene during mice brain and lung development.
Publication Title
Large genomic fragment deletions and insertions in mouse using CRISPR/Cas9.
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples