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Mus musculus
18 Downloadable Samples
Affymetrix Mouse Gene 1.0 ST Array (mogene10st), Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Mast cells mediate malignant pleural effusion formation.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st), Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
Nave mast cells were cultured from murine bone marrow using incubation with IL-3 alone (samples 1-4) or IL-3 and KITL (samples 5-8).
Publication Title
Mast cells mediate malignant pleural effusion formation.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 25 Downloadable Samples
Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Profiling peripheral nerve macrophages reveals two macrophage subsets with distinct localization, transcriptome and response to injury.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 25 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
We performed ontogenic, transcriptomic and spatial characterization of sciatic nerve Macs (snMacs). Using multiple fate-mapping systems, we show that snMacs do not derive from the early embryonic precursors colonizing the CNS, but originate primarily from late embryonic precursors and get replaced by bone marrow-derived Macs over time. Using single-cell profiling, we identified a tissue-specific core signature of snMacs and found two spatially-separated snMacs: Relmα + Mgl1 + snMacs in the epineurium and Relmα Mgl1 snMacs in the endoneurium. Globally, snMacs lack most core signature genes of microglia, with only the endoneurial subset expressing a restricted number of these genes. Single-cell transcriptomics revealed that in response to injury both snMacs respond differently and that the PNS, in contrast to the CNS, is permissive to prolonged engraftment of monocyte-derived Macs recruited upon injury.
Publication Title
Profiling peripheral nerve macrophages reveals two macrophage subsets with distinct localization, transcriptome and response to injury.
Sample Metadata Fields
No sample metadata fields
View Samples
SRP075376- Homo sapiens
- 12 Downloadable Samples
Illumina HiSeq 2000
Description
Paired-end sequencing of Vector and H-Ras expressing cell lines: p53-del and WT-p53 We found that activated forms of H-Ras and PIK3CA oncogene lead to repression of p63, a p53 family member. They also lead to induction of EMT, a cancer-related process. Our results suggest that, through Ras regulation of p63, this oncogene can drive mammary epithelial cells towards greater invasive ability. Overall design: 4 samples analyzed with 3 replicates each, control samples for each H-Ras line are the Vector cell line created at the same time
Publication Title
Repression of p63 and induction of EMT by mutant Ras in mammary epithelial cells.
Sample Metadata Fields
Cell line, Subject
View Samples- Oryza sativa
- 78 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
Rice (Oryza sativa, ssp. Japonica, cv. Nipponbare 1) plants were grown in a Conviron PGR 15 growth chamber using precise control of temperature, light, and humidity.<br></br>Diurnal (driven) conditions included 12L:12D light cycles and 31C/20C thermocycles in three different combinations. These were: photocycles (LDHH), 12 hrs. light (L)/12 hrs. dark (D) at a constant temperature (31C; HH); photo/thermocycles (LDHC): 12 hrs. light (L) /12 hrs. dark (D) with a high day temperature (31C) and a low night temperature (20C); and thermocycles (LLHC): continuous light (LL) with 12 hrs. high/12 hrs. low temperature (31C, day; 20C, night). Light intensity and relative humidity were 1000 micromol m-2s-2 and 60%, respectively.<br></br>Three-month-old rice plants were entrained for at least one week under the respective condition prior to initiation of each experiment. Leaves and stems from individual rice plants were collected every four hours for 48 hrs in driven (diurnal) conditions followed by a two day freerun spacer under continuous light/temperature followed by two additional days of sampling under the same continuous free run condition.<br></br>
Publication Title
Global profiling of rice and poplar transcriptomes highlights key conserved circadian-controlled pathways and cis-regulatory modules.
Sample Metadata Fields
Age, Specimen part, Time
View Samples- Oryza sativa
- 37 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
Rice (Oryza sativa, spp. Indica, cv. 93-11) plants were grown in a Conviron PGR 15 growth chamber using precise control of temperature, light, and humidity.<br></br>Diurnal (driven) conditions included 12L:12D light cycles and 31C/20C thermocycles in three different combinations. These were: photocycles (LDHH), 12 hrs. light (L)/12 hrs. dark (D) at a constant temperature (31C; HH); photo/thermocycles (LDHC): 12 hrs. light (L) /12 hrs. dark (D) with a high day temperature (31C) and a low night temperature (20C); and thermocycles (LLHC): continuous light (LL) with 12 hrs. high/12 hrs. low temperature (31C, day; 20C, night). Light intensity and relative humidity were 1000 micromol m-2s-2 and 60%, respectively.<br></br>Three-month-old rice plants were entrained for at least one week under the respective condition prior to initiation of each experiment. Leaves and stems from individual rice plants were collected every four hours for 48 hrs in driven (diurnal) conditions followed by a two day freerun spacer under continuous light/temperature followed by two additional days of sampling under the same continuous free run condition.
Publication Title
Global profiling of rice and poplar transcriptomes highlights key conserved circadian-controlled pathways and cis-regulatory modules.
Sample Metadata Fields
Age, Specimen part, Time
View Samples- Mus musculus
- 36 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Tissue-resident macrophages can derive from yolk sac macrophages, fetal liver monocytes or adult bone marrow monocytes. Whether these precursors can give rise to transcriptionally identical alveolar macrophages is unknown. Here, we transferred traceable yolk sac macrophages, fetal liver monocytes, adult bone marrow monocytes or adult alveolar macrophages as a control, into the empty alveolar macrophage niche of neonatal Csf2rb-/- mice. All precursors efficiently colonized the alveolar niche and generated alveolar macrophages that were transcriptionally almost identical, with only 22 genes that could be linked to their origin. Underlining the physiological relevance of our findings, all transfer-derived alveolar macrophages self-maintained within the lungs for up to 1 year and durably prevented alveolar proteinosis. Thus, precursor origin does not affect the development of functional self-maintaining tissue-resident macrophages.
Publication Title
Yolk Sac Macrophages, Fetal Liver, and Adult Monocytes Can Colonize an Empty Niche and Develop into Functional Tissue-Resident Macrophages.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 19 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Self-renewing tissue-resident macrophages are thought to be exclusively derived from embryonic progenitors. However, whether circulating monocytes can also give rise to such macrophages has not been formally investigated. Here we use a new model of diphtheria toxin-mediated depletion of liver-resident Kupffer cells to generate niche availability and show that circulating monocytes engrafted in the liver, gradually adopt the transcriptional profile of their depleted counterparts and become long-lived self-renewing cells. Underlining the physiological relevance of our findings, circulating monocytes also contribute to the expanding pool of macrophages in the liver shortly after birth, when macrophage niches become available during normal organ growth. Thus, like embryonic precursors, monocytes can and do give rise to self-renewing tissue-resident macrophages if the niche is available to them.
Publication Title
Bone marrow-derived monocytes give rise to self-renewing and fully differentiated Kupffer cells.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 7 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
The Transcription Factor ZEB2 Is Required to Maintain the Tissue-Specific Identities of Macrophages.
Sample Metadata Fields
Specimen part
View Samples