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Mus musculus
12 Downloadable Samples
Illumina HiSeq 2000
Description
Humoral responses of mice specifically deleted for Moz (a histone acetyltransferase) or c-Myb (a transcription factor) in B cells were aberrant. RNA-sequencing analysis was performed to assess gene expression differences compared to wild-type controls in germinal center B cells or plasmablasts. Overall design: Moz f/f Aicda1-Cre, Aicda1-Cre, Myb f/f Cd23-Cre, Mybf/f (no cre) mice were immunized with NP-KLH precipitated in alum and germinal center B cells were sort-purified. Secondary plasmablasts were sort-purified from immunized mice boosted with NP-KLH in PBS (Myb experiment). Two independent experiments were conducted.
Publication Title
Regulation of germinal center responses and B-cell memory by the chromatin modifier MOZ.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 12 Downloadable Samples
Illumina MouseWG-6 v2.0 expression beadchip
Description
NP-reactive murine splenic memory B cells were sorted based on the expression of the surface markers CD80 and PD-L2
Publication Title
CD80 and PD-L2 define functionally distinct memory B cell subsets that are independent of antibody isotype.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 25 Downloadable Samples
- Illumina HiSeq 2500
Description
The overall study (Quinn et al. Cell Reports, 2018) aimed to understand why CD8 virtual memory T (TVM) cells become markedly less proliferative in response to TCR-driven signals with increasing age, whereas CD8 true naive (TN) cells maintain their proliferative capacity. Age-associated decreases in primary CD8+ T cell responses occur, in part, due to direct effects on naïve CD8++ T cells to reduce intrinsic functionality, but the precise nature of this defect remains undefined. Ageing also causes accumulation of antigen-naïve but semi-differentiated “virtual memory” (TVM) cells but their contribution to age-related functional decline is unclear. Here, we show that TVM cells are poorly proliferative in aged mice and humans, despite being highly proliferative in young individuals, while conventional naïve T cells (TN cells) retain proliferative capacity in both aged mice and humans. Adoptive transfer experiments in mice illustrated that naïve CD8 T cells can acquire a proliferative defect imposed by the aged environment but age-related proliferative dysfunction could not be rescued by a young environment. Molecular analyses demonstrate that aged TVM cells exhibit a profile consistent with senescence, marking the first description of senescence in an antigenically naïve T cell population. Overall design: In the RNA-Seq analysis uploaded here, we have sorted TN cells (CD44lo), TVM cells (CD49dlo CD44hi) and CD8 conventional memory T (TMEM) (CD49dhi CD44hi) cells from naive young mice (3 months old) or aged mice (18 months old). To sort enough cells of each type, we pooled 4 mice, so each replicate represents a pooled sample of 4 mice. Each replicate was split in half, with half the sample frozen in TRIzol immediately for our directly ex vivo or "unstim" sample and the other half of the sample stimulated with plate-bound anti-CD3 (10ug/mL), anti-CD8a (10ug/mL) and antiCD11a (5 ug/mL) and soluble recombinant human IL-2 (10U/mL) for 5 hours, before being frozen in TRIzol as our stimulated or "stim" samples. We therefore collected 2 replicates for each cell subsets (designated "1" and "2") and the "unstim" and "stim" samples are matched. Altogether, we had 24 samples (young (Y) and aged (A); replicate 1 and replicate 2, with cells pooled from 4 mice in each replicate; TN, TVM and TMEM cells; unstim and stim match across each replicate). Due to lane capacity limits for sequencing, we processed these samples for RNA and sequencing in two batches (Batch 1- Y1_Tn_Unstim, Y1_Tvm_Unstim, Y1_Tmem_Unstim, Y1_Tn_Stim, Y1_Tvm_Stim, Y1_Tmem_Stim, A1_Tn_Stim, A1_Tvm_Stim, A1_Tmem_Stim, A2_Tn_Stim, A2_Tvm_Stim, A2_Tmem_Stim. Batch 2- Y2_Tn_Unstim, Y2_Tvm_Unstim, Y2_Tmem_Unstim, Y2_Tn_Stim, Y2_Tvm_Stim, Y2_Tmem_Stim, A1_Tn_Unstim, A1_Tvm_Unstim, A1_Tmem_Unstim, A2_Tn_Unstim, A2_Tvm_Unstim, A2_Tmem_Unstim). Of note, in Batch 2 we ran a duplicate of Y1_Tn_Unstim (Y1_Tn_Unstim_norm) to test for any batch effect, but none was observed. Extracted RNA was treated with recombinant DNAse I (Roche) according to the manufacturer's instructions, purified using the RNeasy MinElute Cleanup columns (Qiagen) and analysed for RNA quality using the RNA 6000 Nano kit (Agilent) on an Agilent 2100 Bioanalyzer. Samples were prepared with the Illumina TruSeq RNA v2 sample preparation protocol (cDNA synthesis, adapter ligation, PCR amplification) (Illumina) and run using 100 bp paired end sequencing on an Illumina Hi-Seq. Adapters were trimmed with Trim Galore and trimmed reads were aligned to mm10 genome with TopHat2 version 2.1.1 (Kim et al., 2013) keeping the strand information. Only concordantly aligned read pairs were retained, duplicate fragments were removed using MarkDuplicates from Picard tools and read pairs with mapping quality less than 5 were discarded. To generate a counts matrix, retained read pairs were assigned to genes using featureCounts function (Liao et al., 2014) from Bioconductor Rsubread package taking into account strand information.
Publication Title
Metabolic characteristics of CD8<sup>+</sup> T cell subsets in young and aged individuals are not predictive of functionality.
Sample Metadata Fields
Specimen part, Subject
View Samples
GSE65840- Arabidopsis thaliana
- 6 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
A major role of NINJA is to repress root jasmonate signalling and allow normal cell elongation.
Publication Title
Multilayered Organization of Jasmonate Signalling in the Regulation of Root Growth.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The traditional view of hematopoiesis has been that all the cells of the peripheral blood are the progeny of a unitary homogeneous pool of hematopoietic stem cells (HSCs). Recent evidence suggests that the hematopoietic system is actually maintained by a consortium of HSC subtypes with distinct functional characteristics. We show here that myeloid-biased HSCs (My-HSCs) and lymphoid-biased (Ly-HSCs) can be purified according to their capacity for Hoechst dye efflux in combination with canonical HSC markers.
Publication Title
Distinct hematopoietic stem cell subtypes are differentially regulated by TGF-beta1.
Sample Metadata Fields
Sex, Specimen part
View Samples- Mus musculus
- 79 Downloadable Samples
Affymetrix Murine Genome U74A Version 2 Array (mgu74av2), Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Elevated interferon gamma signaling contributes to impaired regeneration in the aged liver.
Sample Metadata Fields
Sex, Treatment
View Samples- Mus musculus
- 46 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
The process of liver regeneration can be divided into a series of stages that include initial inductive or priming events through cellular mitosis. Following two-thirds liver resection, the liver undergoes the priming phase, in which cytokines TNF-a and IL-6 activate their respective receptors in hepatocytes. This leads to the activation of several key transcription factors: NF-kB, AP-1, Stat 3, Stat 1, and C/EBP-b and -d . These transcription factors induce the expression of immediate early genes. HGF is also expressed at this time and involved in the transition of quiescent hepatocytes into the G1 phase of the cell cycle. During the G1 phase, delayed early genes are expressed followed by induction of cell cyclerelated genes, both of which require new protein synthesis for their production. Increased expression of FoxM1B and TGF-a occurs at the G1/S transition and is correlated with increased expression of cyclinD1 and decreased expression of cdk inhibitors. During the G2/M phase of the cell cycle, FoxM1B directly elevates cyclinB1, cyclinB2, and cdc25B expression. Additionally, FoxM1B is associated with increased cyclinF and p55cdc, which are involved in completion of the cell cycle following partial hepatectomy. In mice, two-thirds partial hepatectomy promotes proliferation of liver cells and rapid growth of the remaining liver tissue, resulting in complete restoration of organ mass in approximately 7 days (Mackey S. et al. Hepatology 2003 Dec;38(6):1349-52).
Publication Title
Elevated interferon gamma signaling contributes to impaired regeneration in the aged liver.
Sample Metadata Fields
Sex, Treatment
View Samples- Mus musculus
- 33 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2), Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The process of liver regeneration can be divided into a series of stages that include initial inductive or priming events through cellular mitosis. Following two-thirds liver resection, the liver undergoes the priming phase, in which cytokines TNF-a and IL-6 activate their respective receptors in hepatocytes. This leads to the activation of several key transcription factors: NF-kB, AP-1, Stat 3, Stat 1, and C/EBP-b and -d . These transcription factors induce the expression of immediate early genes. HGF is also expressed at this time and involved in the transition of quiescent hepatocytes into the G1 phase of the cell cycle. During the G1 phase, delayed early genes are expressed followed by induction of cell cyclerelated genes, both of which require new protein synthesis for their production. Increased expression of FoxM1B and TGF-a occurs at the G1/S transition and is correlated with increased expression of cyclinD1 and decreased expression of cdk inhibitors. During the G2/M phase of the cell cycle, FoxM1B directly elevates cyclinB1, cyclinB2, and cdc25B expression. Additionally, FoxM1B is associated with increased cyclinF and p55cdc, which are involved in completion of the cell cycle following partial hepatectomy. In mice, two-thirds partial hepatectomy promotes proliferation of liver cells and rapid growth of the remaining liver tissue, resulting in complete restoration of organ mass in approximately 7 days (Mackey S. et al. Hepatology 2003 Dec;38(6):1349-52).
Publication Title
Elevated interferon gamma signaling contributes to impaired regeneration in the aged liver.
Sample Metadata Fields
Sex, Treatment
View Samples- Mus musculus
- 14 Downloadable Samples
- Affymetrix Mouse Expression 430A Array (moe430a)
Description
Age-related defects in stem cells can limit proper tissue maintenance and hence contribute to a shortened life-span. Using highly purified hematopoietic stem cells from mice aged 2 to 21 months, we demonstrate a deficit in function yet an increase in stem cell number with advancing age. Expression analysis of more than 14,000 genes identified 1500 that were age-induced and 1600 that were age-repressed. Genes associated with the stress response, inflammation, and protein aggregation dominated the upregulated expression profile, while the downregulated profile was marked by genes involved in the preservation of genomic integrity and chromatin remodeling. Many chromosomal regions showed coordinate loss of transcriptional regulation, and an overall increase in transcriptional activity with aged, and inappropriate expression genes normally regulated by epigenetic mechanisms was observed. Hematopoietic stem cells from early-aging mice expressing a mutant p53 allele reveal that aging of stem cells can be uncoupled from aging at an organismal level. These studies show that HSC are not protected from aging. Instead, loss of epigenetic regulation at the chromatin level may drive both functional attenuation of cells, as well as other manifestations of aging, including the increased propensity for neoplastic transformation.
Publication Title
Aging hematopoietic stem cells decline in function and exhibit epigenetic dysregulation.
Sample Metadata Fields
No sample metadata fields
View Samples- Drosophila melanogaster
- 5 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
dMyc is a conserved transcription factor that controls growth and proliferation by regulating its target genes.
Publication Title
MicroRNA miR-308 regulates dMyc through a negative feedback loop in Drosophila.
Sample Metadata Fields
Specimen part
View Samples