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GSE94886
Bos taurus
6 Downloadable Samples
Affymetrix Bovine Genome Array (bovine)
Description
Vitamin A (VA) restriction for beef cattle improves meat marbling. However, its molecular mechanisms are not completely elucidated.
Publication Title
Microarray analysis of Longissimus thoracis muscle gene expressions in vitamin A-restricted Japanese Black steers in middle fattening stage.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Homo sapiens
- 24 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
Comparison of the gene expression profiles of a recombinant protein producing Hek 293 cell line (referred to as producer) and its non-producing parental cell line Hek293F (referred to as non-producer). The parental cell line was obtained from Invitrogen, Carlsbad, CA. The producer was transfected with a heavy chain variable region fused to the Fc region of a human IgG (dAb-Fc). The aim of this study was to gain a better understanding of the process of recombinant protein production in Hek293 cells and to identify targets for the engineering of an improved host cell line.
Publication Title
A multi-omics analysis of recombinant protein production in Hek293 cells.
Sample Metadata Fields
Cell line, Time
View Samples- Mus musculus
- 6 Downloadable Samples
Illumina HiSeq 2000
Description
The goal of this study was to identify genes which are differentiatlly expresesd upon induced inactivation of Rfx6 in beta cell in adult mice Overall design: Rfx6fl/fl; Ins1-CreERT2 (mut) and Rfx6fl/fl (ctrl) 8 weeks old mice were injected subcutaneously with tamoxifen daily during 3 days. Pancreatic islets were isolated 5 days after the first injection and RNA purified.
Publication Title
Rfx6 maintains the functional identity of adult pancreatic β cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 12 Downloadable Samples
- Illumina HiSeq 2000
Description
Purpose: to identify the effects on the transcriptome of deleting ZFP36L1 in MZ B cells Overall design: Method (MZ B cells): RNAseq libraries were prepared from 5ng RNA isolated from sorted ex-vivo MZ B cells. Total RNA samples were sent to Aros Applied Biotechnology A/S and were prepared using the Clontech SMARTer kit. Libraries were sequenced (100bp paired end) on the Illumina Hiseq. Method (FO B cells): RNAseq libraries were prepared from RNA isolated from sorted ex-vivo FO B cells. Total RNA samples were sent to Aros Applied Biotechnology A/S and were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina). Libraries were sequenced (100bp single end) on the Illumina Hiseq.
Publication Title
Maintenance of the marginal-zone B cell compartment specifically requires the RNA-binding protein ZFP36L1.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Danio rerio
- 3 Downloadable Samples
- IlluminaHiSeq2500
Description
Individual organisms age at different rates, however, it remains unclear how aging alters the properties of individual cells. Here we show that zebrafish pancreatic beta-cells exhibit heterogeneity in both gene expression and proliferation with age. Individual beta-cells show marked variability in transcripts involved in endoplasmic reticulum stress, inhibition of growth factor signaling and inflammation, including NF-kB signaling. Using a reporter line, we show that NF-kB signaling is indeed activated heterogeneously with age. Notably, beta-cells with higher NF-kB activity proliferate less compared to neighbors with lower activity. Furthermore, NF-kB-signalinghigh beta-cells from younger islets upregulate socs2, a gene naturally expressed in beta-cells from older islets. In turn, socs2 can inhibit proliferation cell-autonomously. NF-kB activation correlates with the recruitment of tnfa-expressing immune cells, pointing towards a role for the islet microenvironment in this activity. We propose that aging is heterogeneous across individual beta-cells and identify NF-kB signaling as a marker of heterogeneity. Overall design: We used fluorescence-activated cell sorting (FACS) coupled with next generation RNA-Sequencing to profile beta-cells from 3 month post fertilization and 1 year post fertilization animals. total RNA was extracted from FACS sorted beta-cells using Quick-RNA MicroPrep kit (R1050 Zymo Research). Sequencing was performed on llumina HiSeq2500 in 2x75bp paired-end mode. Reads were splice-aligned to the zebrafish genome, GRCz10, using HISAT2. htseq-count was used to assign reads to exons thus eventually getting counts per gene.
Publication Title
Age-related islet inflammation marks the proliferative decline of pancreatic beta-cells in zebrafish.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 5 Downloadable Samples
- Illumina Genome Analyzer IIx
Description
Purpose: Conditional knockout of Zfp36l1 Zfp36l2 in pro-B cells perturbs B cell development leading to reduced V(D)J recombination and diminished numbers of cells in successive stages of development. This RNA seq experiment aimed to determine the molecular pathways affected by loss of Zfp36l1 and Zfp36l2, and to deduce direct targets of these RNA binding proteins. Methods: RNAseq libraries were prepared from 0.1 µg of RNA from sorted control and DCKO late pre-B cells using TruSeq RNA sample preparation kit v2 modified to be strand specific using the dUTP method. Libraries were sequenced by an Illumina genome analyzer II measuring 54bp single-end reads. Over 30 million reads were measured from each sample. The reads were trimmed to remove adapter sequences using Trim Galore then mapped using Tophat (version 1.1.4) to the NCBIm37 mouse assembly (April 2007, strain C57BL/6J); reads with an identical sequence to more than one genomic locus were not mapped. Quality control analysis was carried out with FastQC. Results: Read counts for each gene were generated in SeqMonk: transcripts from the same gene were collapsed into a single transcript containing all exons, so total reads were counted without considering alternative splice forms. Since the libraries were strand-specific only reads on the opposing strand were counted. Differences in the abundance of transcripts between DCKO and control late pre-B cells were calculated in the R/Bioconductor program DESeq (version 1.12.1). Adjusted P values for differential expression were calculated in DESeq using a Benjamini-Hochberg correction: genes with an adjusted p-value of less than 5% were considered significant. Differentially expressed mouse transcripts identified using DESeq were analyzed for gene set enrichment using Toppfun. Conclusions: We identified an enrichment of mRNAs involved in cell cycle progression within Zfp36l1 Zfp36l2 double conditional knockouts. Overall design: RNAseq of late pre-B cells from control and Zfp36l1, Zfp36l2 double conditional knockout mice.
Publication Title
RNA-binding proteins ZFP36L1 and ZFP36L2 promote cell quiescence.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Exogenous 17-estradiol (E2) accelerates the progression of ovarian cancer in the transgenic tgCAG-LS-TAg mouse model of the disease. We hypothesized that E2 has direct effects on ovarian cancer cells and this study was designed to determine the molecular mechanisms by which E2 accelerates ovarian tumour progression. Mouse ovarian cancer ascites (MASE2) cell lines were derived from tgCAG-LS-TAg mice. Following intraperitoneal engraftment of MASE2 into SCID mice, exogenous E2 significantly decreased the survival time and increased the tumour burden.
Publication Title
17β-estradiol upregulates GREB1 and accelerates ovarian tumor progression in vivo.
Sample Metadata Fields
No sample metadata fields
View Samples- Saccharomyces cerevisiae
- 6 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
Examined gene expression changes in a histone H2A R78A mutant in Saccharomyces cerevisiae relative to wild-type cells. THe overall goal of this study was to determine the functions of histone 'sprocket' arginine residues, which insert into the DNA minor groove in the nucleosome. We examined the roles of sprocket arginine mutants in gene expression, histone incorporation, and DNA repair.
Publication Title
Histone Sprocket Arginine Residues Are Important for Gene Expression, DNA Repair, and Cell Viability in Saccharomyces cerevisiae.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 17 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
HD R6/1 transgenic mouse line brain hemispheres dissected. RNA targets were created for transgenics and wildtypes at time points 18, 22 and 27 weeks. Profiles and data analysis performed using the Bioconductor software and linear model contrasts using LIMMA on RMA probeset summarys.
Publication Title
Brain gene expression correlates with changes in behavior in the R6/1 mouse model of Huntington's disease.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Recent advances in multiple whole genome technologies provide unprecedented opportunities to profile epigenomic signatures in cancer cells. Previously we used a human gene promoter tiling microarray platform to identify genome-wide DNA methylation changes in a cell line model of breast cancer metastasis. Interestingly, the clustered nature of epigenetic targets that we identified, along with our concurrent karyotype analyses, have now led us to hypothesize that complex genomic alterations in cancer cells (deletions, translocations and ploidy) may be superimposed over promoter-specific methylation events that are responsible for gene-specific expression changes.
Publication Title
Multi-platform whole-genome microarray analyses refine the epigenetic signature of breast cancer metastasis with gene expression and copy number.
Sample Metadata Fields
Cell line
View Samples