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SRP174502
Homo sapiens
317 Downloadable Samples
Illumina HiSeq 2500
Description
We perfomed single-cell RNA-sequnecing of around 10,000 cells from normal human liver tissue to construct a human liver cell atlas. We reveal previously unknown subtypes in different cell type compartments. We also use our normal liver cell atlas to infer perturbed phenoytpes of cells from HCC samples, human cells engrafted into a mouse liver and liver organoids. Overall design: Single cells were isolated from human liver resection specimens and then sorted by FACS into 384 well plates in a unbiased way and on the basis of cell surface markers for distinct cell types. ScRNA-seq was done using the mCelSeq2 protocol cellbarcodes_cellid.csv Supplemetary file contains cellds and one of the 192 unique cellbarcode associated with the cellid.
Publication Title
A human liver cell atlas reveals heterogeneity and epithelial progenitors.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 20 Downloadable Samples
Affymetrix Human Gene 2.1 ST Array (hugene21st)
Description
Identification of filamin-A as a target for insulin and IGF1 action.
Publication Title
Genome-Wide Analyses Identify Filamin-A As a Novel Downstream Target for Insulin and IGF1 Action.
Sample Metadata Fields
Cell line, Treatment
View Samples- Mus musculus
- 13 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
We performed a microarray experiment to compare gene expression profiles of neural stem/progenitor cells (NS/PCs) with different culture conditions.
Publication Title
Identification of genes associated with the astrocyte-specific gene Gfap during astrocyte differentiation.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Homo sapiens
- 10 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Despite advance in interferon-based treatment for chronic hepatitis C, difficult-to-treat patients remain in existence yet. To identify key genes involved in difficult-to-treat characteristics, gene expression patterns of miRNA and RNA were analyzed by profiling pretreatment liver tissues from five sustained virological responders (SVR), three relapsers (R) and four non-responders (NR). Expression levels of miRNA and mRNA were compared between SVR/R and NR groups by using microarray, respectively. Quantitative real-time reverse-transcriptase polymerase chain reaction and statistical analyses validated genes with significantly differential expression levels in 50 liver tissues: proliferation-, inflammation- and anti-apoptosis-related mRNA expression levels increased significantly in NR, compared to SVR/R. Of miRNA with significantly differential expression levels on microarray, several miRNA were correlated inversely with those significant mRNA. In vitro studies by using miRNA inhibitors and mimics verified the inverse correlation between the miRNA and mRNA. These findings enhance our understanding of the difficult-to-treat molecular mechanism and identification of target molecules for novel treatments.
Publication Title
Involvement of MAP3K8 and miR-17-5p in poor virologic response to interferon-based combination therapy for chronic hepatitis C.
Sample Metadata Fields
Sex, Specimen part
View Samples- Mus musculus, Rattus norvegicus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Leptin-responsive genes in the pathway of a leptin signal from the hypothalamus to the liver has not been detected.
Publication Title
Generation of leptin-deficient Lepmkyo/Lepmkyo rats and identification of leptin-responsive genes in the liver.
Sample Metadata Fields
Sex, Age, Specimen part, Treatment
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Series of samples studying effect of knock out Emx2 in urogenital epithelium of mouse embryos at E10.5.
Publication Title
Abnormal epithelial cell polarity and ectopic epidermal growth factor receptor (EGFR) expression induced in Emx2 KO embryonic gonads.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 4 Downloadable Samples
- Illumina HiSeq 4000
Description
IL17-producing ?d T cells (?d T17) mainly develop in the prenatal phase and persist as long-living self-renewing effector cell in all kind of tissues. They express polyclonal T-cell receptors (TCR), comprising public V?4+ and V?6+ TCRs with germline-like rearrangements. In particular, V?6+ T cells have recently been found in a variety of tissues including enthesis, gingiva or skin. However, their exchange between tissues and the mechanisms of tissue-specific adaptation and residency remain poorly understood. Here, we profiled V?6+ T cells isolated from thymus, peripheral lymph nodes (pLN) and skin through single-cell RNA-seq technology and compared those to V?4+ T cells. Our data demonstrated that V?6+ T cells formed highly homogenous cell populations that could be separated by tissue-specific gene expression signatures. Overall design: Sort V?4 and V?6 ?dT cells from peripheral lymph nodes, ear skin and thymus, then do 3'-RNA single cell sequencing (10x genomics).
Publication Title
Single-Cell Transcriptomics Identifies the Adaptation of Scart1<sup>+</sup> Vγ6<sup>+</sup> T Cells to Skin Residency as Activated Effector Cells.
Sample Metadata Fields
Age, Specimen part, Cell line, Subject
View Samples- Macaca mulatta, Mus musculus, Pan troglodytes, Homo sapiens
- 11 Downloadable Samples
- Illumina HiSeq 2000, Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
An alternative pluripotent state confers interspecies chimaeric competency.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 11 Downloadable Samples
Illumina HiSeq 2000, Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
Here we show that by simple modulation of extrinsic signaling pathways, a new class of pluripotent stem cells, referred to as intrinsic state-epiblast stem cells (IS-EPIs), could be efficiently derived from different stages of the early embryo. IS-EPIs share features of primed pluripotency yet are distinct from EpiSCs in their molecular characteristics and ability to colonize post-implantation embryos. We performed Microarray analysis and compared global gene expression pattern among amplified RNA samples from ESCs, EpiSCS, IS-EPIs as well as in vivo isolated Epiblasts.
Publication Title
An alternative pluripotent state confers interspecies chimaeric competency.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 1 Downloadable Sample
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
This array set was used to identify the genes that are highly expressed in the mouse suprachiasmatic nucleus (SCN). Because pharmacological inhibition of Gai/o activity with pertussis toxin hampers intercellular synchronization and causes dampened rhythms of the entire SCN, we hypothesized that member(s) of the Regulator of G protein Signaling (RGS) family might contribute to synchronized cellular oscillations in the SCN. To test this hypothesis, we surveyed all known mouse Rgs genes for their expression by using GeneChip and selected the genes that are highly expressed in the SCN for further analysis.
Publication Title
Circadian regulation of intracellular G-protein signalling mediates intercellular synchrony and rhythmicity in the suprachiasmatic nucleus.
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Treatment, Time
View Samples