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GSE49795
Homo sapiens
3 Downloadable Samples
Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Case story. A patient with massive infiltration of the visceral adipose tissue depot by BAT in a patient with a catecholamine secreting paraganglioma. BAT tissue was identified by protein expression of UCP1 (western blotting and immunostaining)
Publication Title
Chronic adrenergic stimulation induces brown adipose tissue differentiation in visceral adipose tissue.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 32 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
The edr1 mutant of Arabidopsis thaliana displays enhanced resistance to the powdery mildew Golovinomyces cichoracearum, resulting in cell death and an absence of visible disease symptoms. To better characterize and understand the defense response of edr1, a time course of early signaling responses was performed after inoculation with powdery mildew and compared to the responses of wild-type Col-0. These time points represent early stages in the infection process, before any signs of susceptibility or resistance are visible.
Publication Title
Negative regulation of defence signalling pathways by the EDR1 protein kinase.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 9 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
To identify factors and pathways regulated by IMP proteins and obtain leads to the mechanism behind the phenotypic changes, we compared the gene expression profiles of IMP siRNA treated cells with mock treated cells. Triplicate gene expression profiles were generated from both the IMP(1,3)A and IMP(1,3)B siRNA sets and were compared to the mock transfected cells. cRNA was hybridized to Affymetrix human U133A arrays.
Publication Title
RNA-binding IMPs promote cell adhesion and invadopodia formation.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Arabidopsis thaliana
- 17 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Global gene expression was compared between Arabidopsis lines with altered expression of ANAC102 (over-expressed and knocked-out) and wild-type. ANAC102 is a putative NAC domain transcription factor. Gene expression was compared between an ANAC102 over-expressing line and parental ecotype C24 under ambient atmosphere to determine which genes ANAC102 is capable of regulating. Gene expression was also compared between three week old plants of an ANAC102 knock-out line and parental ecotype Col-0 under 0.1% Oxygen and ambient atmosphere conditions to determine which genes may require ANAC102 for appropriate expression under these conditions. Gene expression was also compared between imbibed seeds of an ANAC102 knock-out line and parental ecotype Col-0 following a 0.1% Oxygen treatment.
Publication Title
The low-oxygen-induced NAC domain transcription factor ANAC102 affects viability of Arabidopsis seeds following low-oxygen treatment.
Sample Metadata Fields
No sample metadata fields
View Samples- Gossypium hirsutum
- 8 Downloadable Samples
- Affymetrix Cotton Genome Array (cotton)
Description
Global gene expression was compared between roots of cotton plants (variety Sicot 71) flooded for 4 hours and roots of unflooded cotton plants. Global gene expression was also compared between leaves of cotton plants (variety Sicot 71) flooded for 24 hours and leaves of unflooded cotton plants.
Publication Title
Global gene expression responses to waterlogging in roots and leaves of cotton (Gossypium hirsutum L.).
Sample Metadata Fields
Specimen part, Time
View Samples- Arabidopsis thaliana
- 4 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Global gene expression was compared between root RNA samples from three-week-old Arabidopsis Col-0 plants subjected to 0.1% oxygen (balance nitrogen) or ambient atmospheric conditions.
Publication Title
Comparisons of early transcriptome responses to low-oxygen environments in three dicotyledonous plant species.
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples- Mus musculus
- 100 Downloadable Samples
Illumina HiSeq 2000
Description
Injuries to the anterior cruciate ligament (ACL) often result in post-traumatic osteoarthritis (PTOA). PTOA accounts for ~12% of all osteoarthritis (OA) cases, yet the mechanisms contributing to OA after joint injury are not well understood. To better understand the molecular mechanisms behind PTOA development following ACL injury, we profiled ACL injury-induced gene expression changes in knee joints of three mouse strains with varying susceptibility to PTOA: STR/ort (highly susceptible), C57BL/6 (moderately susceptible) and super-healer MRL/MpJ (not susceptible) and identified genes differentially expressed between these strains at 0-day [before injury], 1-day, 1-week, and 2-weeks post-injury. This study highlights many new potential therapeutic targets and OA biomarkers. Overall design: Comparative transcriptomics to understand the molecular changes associated with early stages of PTOA development in STR/ort, C57BL/6 and MRL/MpJ mice and to identify genes that contribute to increased OA susceptibility in STR/ort and resistance to PTOA in MRL/MpJ.
Publication Title
Comparative Transcriptomics Identifies Novel Genes and Pathways Involved in Post-Traumatic Osteoarthritis Development and Progression.
Sample Metadata Fields
Age, Specimen part, Cell line, Treatment, Subject
View Samples- Homo sapiens
- 6 Downloadable Samples
- NextSeq500
Description
Technical advances have enabled the collection of genome and transcriptome data sets with single-cell resolution. However, single-cell characterization of the epigenome has remained challenging. Furthermore, because cells must be physically separated prior to biochemical processing, conventional single-cell preparatory methods scale linearly. We applied combinatorial cellular indexing to measure chromatin accessibility in thousands of single cells per assay, circumventing the need for compartmentalization of individual cells. We report chromatin accessibility profiles from over 15,000 single cells and use these data to cluster cells on the basis of chromatin accessibility landscapes. We identify modules of coordinately regulated chromatin accessibility at the level of single cells both between and within cell types, with a scalable method that may accelerate progress toward a human cell atlas. Overall design: 3 replicates from GM12878 and HL-60 cell lines collected for differential gene expression analysis.
Publication Title
Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 22 Downloadable Samples
- NextSeq 500
Description
We transduced clonally MLL-AF9 leukemia cells expressing cas9 with sgRNA targeting the jumonji and zinc finger domains of JMJD1C. GFP (MLL-AF9) and TdTomato (sgRNA) double positive cells were sorted on Day 6 after transduction. Total RNA was isolated followed by mRNA selection. cDNA libraries were generated and NextGen Sequencing was performed. Overall design: We performed RNA-seq in mouse MLL-AF9 cas9 cells harboring sgRNA against jumonji and zinc finger domains of JMJD1C or renilla.
Publication Title
Critical role of Jumonji domain of JMJD1C in MLL-rearranged leukemia.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 8 Downloadable Samples
- NextSeq 500
Description
We performed single-cell sequencing on mouse MLL-AF9-cas9 leukemia cells 7 days after transduction with sgRNA against Renilla or JMJD1C JmjC domain. We revealed heterogeneity within each population. Overall design: We performed single-cell sequencing on mouse MLL-AF9 cells harboring JMJD1C sgRNA targeting jumonji domain or renilla control sgRNA.
Publication Title
Critical role of Jumonji domain of JMJD1C in MLL-rearranged leukemia.
Sample Metadata Fields
Specimen part, Subject
View Samples