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Mus musculus
12 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
CD1d expression by thymocytes is required to select iNKT cells. When CD1d is expressed only on thymocytes (pLck-CD1d tg mice), iNKT cells are hyperresponsive to antigen stimulation suggesting that, in physiological conditions, these cells undergo functional education mediated by additional CD1d-expressing cells. Here, we investigated the mechanisms of this functional education. We find that peripheral iNKT cells from pLck-CD1d tg mice express significantly less SHP-1, a tyrosine phosphatase negatively regulating TCR signaling, than WT cells. iNKT cells from heterozygous SHP-1-mutated motheaten mice, displaying similar SHP-1 reduction as pLck-CD1d tg iNKT cells, are antigen-hyperresponsive. Restoring normal CD1d expression in pLck-CD1d tg mice normalizes SHP-1 expression and responsiveness of iNKT cells. In WT mice, iNKT cells upregulate SHP-1 and decrease responsiveness upon emigration from thymus to periphery. This depends on contacts with CD1d-expressing DCs. iNKT cell functional education is therefore controlled by DCs via tuning SHP-1 expression level in the periphery.
Publication Title
Functional education of invariant NKT cells by dendritic cell tuning of SHP-1.
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples- Homo sapiens
- 18 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Gene expression was studied from the blood derived RNAs of the Finnish family members as well as from 10 controls using GeneChip Human Genome U133 Plus2 (Affymetrix). Eight out of 10 family members in the expression analysis are heterozygous for the NPAT c.2437-2438delAG, three of which are NLPHL cases.
Publication Title
Exome sequencing reveals germline NPAT mutation as a candidate risk factor for Hodgkin lymphoma.
Sample Metadata Fields
Specimen part, Disease, Disease stage, Subject
View Samples- Drosophila melanogaster
- 6 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
When misexpressed in late Drosophila prepupae, the transcription factor Senseless (Sens) blocks death of the larval salivary glands that normally occurs in the early pupa. The aim of the experiment was to identify genes responding to Sens that might mediate the effect of the protein on cell death and other biological processes. The yeast transcription factor GAL4, expressed from a heat-inducible transgene (P{GAL4-Hsp70.PB}89-2-1), was used to drive expression of Sens from a UAS-sens transgene. After crossing the GAL4 and UAS lines, expression of GAL4 was induced by a 30-min heat shock treatment (37 C) of the progeny at 9 hours after puparium formation. Salivary glands were dissected at 14 hours after puparium formation and RNA isolated for microarray analysis with Affymetrix GeneChips. Control samples were obtained from animals treated the same way carrying one copy of the GAL4 transgene (progeny of a cross between flies of the P{GAL4-Hsp70.PB}89-2-1 and w1118 strains) and w1118 animals. The microarray data identified several genes associated with programmed cell death, including caspase genes, which respond to Sens. In addition, the data show that many Drosophila genes respond to the yeast transcription factor GAL4 in a UAS-independent manner. To identify target genes of Sens that are of biological relevance, gene expression patterns in the presence of Sens were compared to gene expression patterns in both the presence and the absence of GAL4. This comparison revealed that Sens seems to preferentially downregulate targets that are upregulated by GAL4, suggesting that these genes may not necessarily constitute true transcriptional targets of Sens.
Publication Title
A genomic response to the yeast transcription factor GAL4 in Drosophila.
Sample Metadata Fields
No sample metadata fields
View Samples- Drosophila melanogaster
- 5 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
When misexpressed in late Drosophila prepupae, the transcription factor Fork head (Fkh) blocks death of the larval salivary glands that normally occurs in the early pupa. The aim of the experiment was to identify genes responding to Fkh that might mediate the effect of the protein on cell death and other biological processes. Fkh was expressed in the line P[hs-Fkh111] from a heat-inducible transgene that encodes wild-type Fkh protein. Expression of Fkh was induced by incubating prepupae for 30 min in a 37 C water bath, starting at 9.5 hours after puparium formation. Salivary glands were dissected at 14 hours after puparium formation and RNA isolated for microarray analysis with Affymetrix GeneChips. Control samples were obtained from w1118 animals treated the same way. The microarray analysis identified 55 genes annotated as functioning in apoptosis whose expression was at least 1.5-fold changed by Fkh. These genes include the death genes hid and reaper, which play a central role in the control of salivary gland death. Other groups of significantly enriched genes include genes functioning in autophagy, steroid-signaling pathways, salivary gland secretion, and phospholipid metabolism. In addition, the microarray data identify genes as responsive to Fkh that are known to be controlled by the FOXA counterparts of Fkh in vertebrates, indicating that target genes and biological processes controlled by Fkh are evolutionarily conserved.
Publication Title
Genes and biological processes controlled by the Drosophila FOXA orthologue Fork head.
Sample Metadata Fields
No sample metadata fields
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E-MEXP-1020- Saccharomyces cerevisiae
- 1 Downloadable Sample
- Affymetrix Yeast Genome S98 Array (ygs98)
Description
Gene regulations that are affected by TBP1(E186D) at 28°C
Publication Title
TFIIB/SUA7(E202G) is an allele-specific suppressor of TBP1(E186D).
Sample Metadata Fields
Sex
View Samples- Drosophila melanogaster
- 6 Downloadable Samples
Illumina HiSeq 2000
Description
We performed RNAseq on l(3)mbt mutant somatic ovaries to gain a genome-wide view of tissue-specific gene expression changes in L(3)mbt-depleted somatic ovaries. Overall design: Examination of gene expression changes in mutant and control somatic ovaries.
Publication Title
L(3)mbt and the LINT complex safeguard cellular identity in the <i>Drosophila</i> ovary.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 24 Downloadable Samples
- Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)
Description
Compare the gene expression profiles from the 6 and 24 month old WT with RXRa specific hepatic deficiency mice in both genders
Publication Title
Hepatocyte RXRalpha deficiency in matured and aged mice: impact on the expression of cancer-related hepatic genes in a gender-specific manner.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Behavioral analysis confirmed that the 14-day social defeat sessions resulted in induction of depressive-like states measured in social interaction and light/dark tests. The combined data show that stress-induced depressive states are associated with molecular and structural changes that demyelinate the prefrontal cortex.
Publication Title
Chronic social defeat reduces myelination in the mouse medial prefrontal cortex.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 10 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
We have generated tumorigenic (S2N) and non-tumorigenic (S2), normal-like to basal-like breast cancer cell lines from primary tumors. At high in vivo inoculation cell numbers of 10^6 cells/mouse both S2N and S2 monolayer as well as sphere culture cells grew at similar rates. However, at low inoculation cell numbers down to 10^3 cells only S2N sphere cells generated xenograft tumors. mRNA profiling revealed a unique cluster pattern of the tumorigenic S2N sphere cells, but a detailed analysis of TIC relevant transcription factors like Oct3, Sox and Nanog family members, Myc, Slug or Twist1 revealed no consistently increased expression in the highly tumorigenic cell lines. Our data indicate that the intrinsic genetic and functional markers investigated are not solely indicative of the in vivo tumorigenicity of putative breast tumor-initiating cells.
Publication Title
Established breast cancer stem cell markers do not correlate with in vivo tumorigenicity of tumor-initiating cells.
Sample Metadata Fields
Disease, Cell line
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
We investigated the effects of diabetes, physical training, and their combination on the gene expression of cardiac muscle. Mice were divided to control (C), training (T), streptozotocin-induced diabetic (D), and diabetic training (DT) groups. Training groups performed 1, 3, or 5 weeks of endurance training on a motor-driven treadmill. Muscle samples from T and DT groups together with respective controls were collected 24 hours after the last training session. Gene expression of cardiac muscles were analyzed using Affymetrix Gene chip MG U74Av2 (Affymetrix , Inc., Santa Clara, CA).
Publication Title
Effects of streptozotocin-induced diabetes and physical training on gene expression of titin-based stretch-sensing complexes in mouse striated muscle.
Sample Metadata Fields
No sample metadata fields
View Samples