This SuperSeries is composed of the SubSeries listed below.

Serially transplantable mammary epithelial cells express the Thy-1 antigen.

Thy-1 Expression Enriches for Self-Renewing Murine MRUs

Enriched cell populations from murine mammary epithelium were isolated by FACS and subjected to Affymetrix Mouse 430 2.0 microarray analysis.

Thy-1 Expression Enriches for Self-Renewing Murine MRUs [BL6]

TAMs play an important role in MM drug resistance and progression. To determine the mechanisms about how tumor microenvironment regulate the generation of TAMs from normal MΦs in vitro and in vivo. We generated TAMs in vitro by tumor cells-MΦs coculture from CD36 WT and KO mice bone marrow cells. Total RNAs of 2 x 106 MΦs and TAMs were extracted by RNeasy Mini Kit (Qiagen). 5-10 µg RNA samples were sent to Gene Expression and Genotyping Facility at Case Western Reserve University (Cleveland, OH) for RNA-seq followed by data analysis.

Enhanced Lipid Accumulation and Metabolism Are Required for the Differentiation and Activation of Tumor-Associated Macrophages.

Expression data from mice normal MΦs and multiple myeloma tumor-associated macrophages (TAMs)

Thy-1 Expression Enriches for Self-Renewing Murine MRUs [FVB]

Using microarray, the anther transcript profiles of the three indica rice CMS lines revealed 622 differentially expression genes (DEGs) in each of the three CMS lines. GO and Mapman analysis indicated that these DEGs were mainly involved in lipid metabolic and cell wall organization. Comprised with the gene expression of sporophytic and gametophytic CMS lines, 303 DEGs were differentially expressed and 56 of them were down-regulated in all the CMS lines. Co-expression network analysis suggested that many genes were significantly differentially expressed in the CMS lines. These down-regulated DEGs in the CMS lines were found to be involved in tapetum or cell wall formation and their suppressed expression might be related to male sterility. The present study will give some information for the nuclear gene regulation by different cytoplasmic genotypes and provide some candidate genes for pollen development in rice.

Comparative transcript profiling of alloplasmic male-sterile lines revealed altered gene expression related to pollen development in rice (Oryza sativa L.).

Comparative transcript profiling of alloplasmic male-sterile lines revealed altered gene expression related to pollen development in rice (Oryza sativa L.)

RNAseq transcriptional profiling of Drosophila brains from wildtype, and period loss-of-function animals with time points taken over two days. Overall design: 2 days of brain collection, time points at ZT0, ZT6, ZT12, and ZT18; wildtype and per0 flies.  10-12 brains per time point.

Deep sequencing the circadian and diurnal transcriptome of Drosophila brain.

Deep sequencing the circadian transcriptome of Drosophila brain

We found that IL-7 pretreatment enhanced Th9 differentiation. To clarify the underlying mechanisms, we examine the gene expression profiles of CD4+ T cell and Th9 cells with or without IL-7 pretreatment. In Th9 cells, we found that Th9 related genes were greatly increased in IL-7 Th9 group, which demonstrated an enhanced Th9 differentiation.  In CD4+ T cells, we found that IL-7 treatment resulted in a global gene expression change especially on chromatin remodeling related genes, which facilitated the entry of transcriptional factor to the Il9 promoter region and promoted Il9 transcription.

Foxo1 and Foxp1 play opposing roles in regulating the differentiation and antitumor activity of T&lt;sub&gt;H&lt;/sub&gt;9 cells programmed by IL-7.

Effect of IL-7 on CD4+ T cell and Th9 cells

Hep3B and Huh7 are two types of human hepatoma cell lines (HCC). In our laboratory, we cultured their stem-like cancer cells (HCSCs), Hep3B-C and Huh7-C. And we have demonstrated that these cells had enhanced stem cell properties, drug resistance, properties of EMT, and stronger tumor-initiating capabilities. To explore functionally crucial mRNAs in HCSCs, 2 samples of HCSCs and 2 samples of HCCs were sequenced by the Illumina Genome Analyzer II. Through differential expression analysis, we finally identified 115 up- and 402 down-regulated miRNAs which were consistently up- and down-regulated in two stem cells compared to the cancer cells. Overall design: Expression analysis using total RNAs extracted from 2 HCSC cell lines (Hep3B-C and Huh7-C), and 2 HCC cell lines (Hep3B and Huh7).

Integrated analysis of miRNA, gene, and pathway regulatory networks in hepatic cancer stem cells.

Identification of differentially expressed mRNAs in HCSC cell lines compared with HCC cell lines

we have investigated molecular and functional properties in  early B-lineage  cells from Pax-5 deficient animals crossed to a B-lineage restricted reporter mouse. Gene expression analysis of ex  vivo isolated progenitor cells revealed that Pax-5 deficiency has a minor impact on Bcell specification.By  comparison  of  gene  expression  patterns  in  ex  vivo isolated Pax-5 and Ebf-1 deficient progenitors, it was possible to identify a set of B-cell restricted genes dependent of Ebf-1 but not Pax-5, supporting the idea that B-cell  specification  and  commitment  is  controlled  by  distinct  regulatory networks.

Single-cell analysis of early B-lymphocyte development suggests independent regulation of lineage specification and commitment in vivo.

Expression data from early B cell progenitors including CLP,ProB and PreB of Pax5 knockout and wild type C57Bl6 mice

Tumor formation constitutes a major obstacle to the clinical application of embryonic stem cells (ESCs). As P-RPCs could successfully integrate into host eyes without development of teratomas or NOG, we sought to identify differentially expressed genes between P-RPCs and ESC-RPCs through genome-wide transcript profiling. Inhibition of Wnt signaling by DKK1 promotes the commitment of ESC-RPCs to more mature retinal cells and reduces the occurrence of NOG to 3%. DKK1-treated ESC-RPCs efficiently integrate to the host retina, form synaptic connections and restore visual function.