Filters
Technology
Platform
GSE84609
Mus musculus
6 Downloadable Samples
Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
GDF11 treatment leads to bone loss in mice and strongly stimulates RANKL-induced osteoclastogenesis of bone marrowderived macrophages (BMMs) in vitro.
Publication Title
GDF11 decreases bone mass by stimulating osteoclastogenesis and inhibiting osteoblast differentiation.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 6 Downloadable Samples
Illumina HiSeq 4000
Description
RNA-seq is a powerful tool to analyze differential expression of cellular pathways under different conditions. The goal of this study is to analyze the potential pathways involved in cellular defense against high glucose challenge with or without FGF1 intervention. Overall design: MPC cells were starved for 12 hours in serum-free RPMI-1640 medium and pretreated with FGF1 wild type or FGF1 variant (100 ng/mL) for 1 hour. Then, the cells were challenged with high glucose (25 mM) (with D-mannitol as an osmotic control) for 12 hours. After that, cells were harvested for RNA-seq analysis.
Publication Title
FGF1<sup>ΔHBS</sup> ameliorates chronic kidney disease via PI3K/AKT mediated suppression of oxidative stress and inflammation.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples- Danio rerio
- 4 Downloadable Samples
- Affymetrix Zebrafish Genome Array (zebrafish)
Description
Multiciliated cells (MCCs) possess multiple motile cilia on the cell surface and are widely distributed throughout the vertebrate body to perform important physiological functions by regulating fluid movement in the intercellular space. However, neither their function during organ development nor the molecular mechanisms underlying multiciliogenesis are yet well understood. We aim to study the function of miR-34b in multiciliogenesis.
Publication Title
miR-34b regulates multiciliogenesis during organ formation in zebrafish.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 8 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Cellular directed migration is critical to invasion-metastasis cascade of cancer cells. We used in vitro transwell model to screen two esophageal cancer cell lines (KYSE30/180) and obtained two pairs of subpopulations with distinct motility ability.
Publication Title
Guanylate-binding protein 1 (GBP1) promotes lymph node metastasis in human esophageal squamous cell carcinoma.
Sample Metadata Fields
Cell line
View Samples- Danio rerio
- 8 Downloadable Samples
- Zebrafish Gene 1.0 ST Array (zebgene10st)
Description
hematopoiesis and myelopoiesis was tightly controled by microRNAs. In the zebrafish adult kidney, specific sets of genes were dysregulated in myelomonocytes or whole kidney marrow after deletion of miR-142-3p.
Publication Title
miR-142-3p acts as an essential modulator of neutrophil development in zebrafish.
Sample Metadata Fields
Age, Specimen part
View Samples- Pseudomonas aeruginosa
- 2 Downloadable Samples
- Illumina HiSeq 2000
Description
RNAseq analysis was performed to evaluate gene expression differences between strains 1-9 and PAK-AR2.P. aeruginosa PAK-AR2 and 1-9 cells were grown to OD600 of 0.8 before harvesting. The collected cells were treated with RNAprotect Bacteria Reagent (Qiagen) and subjected to snap freezing in liquid nitrogen and delivered to BGI in dry ice for transcriptome resequencing analysis.The differentially expressed genes (DEGs) were determined between PAK-AR2 and 1-9 with the standards of false discovery rate (FDR ) = 0.001, fold change |log2Ratio|=1.A total of 4,355,305 reads matched to the referenced genome in the sample of PAK-AR2, and 3,544,484 reads in the sample of 1-9.Transcriptome data showed that expression of 361 genes were upregulated while 459 genes were down regulated by at least 2-fold when comparing the srpA mutant strain 1-9 to its parent strain PAK-AR2.These genes were classified into 21 major cellular processes based on the annotation of KEGG_B_class or further grouped into several major metabolic pathways, such as ribosomal proteins, type III secretion system (T3SS), type VI secretion system (T6SS), chemotaxis, cell motility, and cell shape control.More and more small proteins that were ignored from typical genome annotations have now been experimentally demonstrated to play important regulatory roles on various bacterial metabolic. Overall design: Gene expression of PAK-AR2 and 1-9 were generated by deep sequencing, in triplicate, using Illumina HiSeqTM 2000.
Publication Title
Regulatory protein SrpA controls phage infection and core cellular processes in Pseudomonas aeruginosa.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 12 Downloadable Samples
- Illumina HiSeq 2000
Description
Purpose: To understand the regulation of gene expression of alveolar macrophages by VD3-VDR axis Overall design: Fresh isolated WT alveolar macropahges (AM) were treated with or without 50 nM Vitamin D3 in vitro for 24hrs. Fresh AMs were isolated from WT and VDR knockout mice in 4 and 10 weeks old. RNA was isolated and purified by Qiagen Rneasy micro kit and applied to RNAseq.
Publication Title
Vitamin D<sub>3</sub>-vitamin D receptor axis suppresses pulmonary emphysema by maintaining alveolar macrophage homeostasis and function.
Sample Metadata Fields
Age, Specimen part, Subject
View Samples- Homo sapiens
- 5 Downloadable Samples
- Illumina HiSeq 2000
Description
We report the differential roles of an HDAC inhibitor-TSA during hESC nerual commitment. In the initiation of hESC differentiation, TSA could inhibit the downregulation of pluripotency genes to maintain pluripotency, whereas in the neural commitment stage, TSA could promote neural gene expression to assist hESC nerual determination. Overall design: Examination of gene expression patterns in hESCs, day 4 or day 8 differentiated cells without or with TSA treatment
Publication Title
Dual roles of histone H3 lysine 9 acetylation in human embryonic stem cell pluripotency and neural differentiation.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 50 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Pglyrp1-/-, Pglyrp2-/-, Pglyrp3-/-, and Pglyrp4-/- mice are all more sensitive than wild type (WT) mice to dextran sulfate sodium (DSS)-induced colitis. The purpose of this study was to determine which genes are differentially induced by DSS treatment in the colon of Pglyrp1-/-, Pglyrp2-/-, Pglyrp3-/-, and Pglyrp4-/- mice compared to WT mice. The results demonstrate higher induction of proinflammatory gene expression in Pglyrp1-/-, Pglyrp2-/-, Pglyrp3-/-, and Pglyrp4-/- mice than in WT mice after DSS treatment. The majority of genes whose expression is increased in Pglyrp1-/-, Pglyrp2-/-, Pglyrp3-/-, and Pglyrp4-/- mice but not in WT mice are interferon-inducible genes. Thus, Peptidoglycan Recognition Proteins Pglyrp1, Pglyrp2, Pglyrp3, and Pglyrp4 protect mice from excessive inflammatory response and damage to the colon by limiting expression of interferon-inducible genes in the colon.
Publication Title
Peptidoglycan recognition proteins protect mice from experimental colitis by promoting normal gut flora and preventing induction of interferon-gamma.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 6 Downloadable Samples
Description
The neural fate commitment of pluripotent stem cells requires repression of extrinsic inhibitory signals and activation of intrinsic positive transcription factors. However, it remains elusive how these two events are integrated to ensure appropriate neural conversion. Here, we show that Oct6 functions as an essential positive factor for neural differentiation of mouse embryonic stem cells (ESCs), specifically during the transition from epiblast stem cells (EpiSCs) to neural progenitor cells (NPCs). Chimera analysis showed that Oct6 knockdown leads to markedly decreased incorporation of ESC in neuroectoderm. By contrast, Oct6-overexpressing ESC derivatives preferentially contribute to neuroectoderm. Genome-wide ChIP-seq and RNA-seq analyses indicate that Oct6 is an upstream activator of neural lineage genes, and also a repressor of BMP and Wnt signalings. Our results establish Oct6 as a critical regulator that promotes neural commitment of pluripotent stem cells through a dual role: activating internal neural induction programs and antagonizing extrinsic neural inhibitory signals. Overall design: RNA-seq was performed to examine Oct6 function in ESC neural differentiation at Day2, Day4 and Day6 after dox induction. On Day4 EB, ChIP-seq assay was ultilized to characterize the targets of Oct6.
Publication Title
Genome-wide ChIP-seq and RNA-seq analyses of Pou3f1 during mouse pluripotent stem cell neural fate commitment.
Sample Metadata Fields
No sample metadata fields
View Samples