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SRP089884
Mus musculus
12 Downloadable Samples
Illumina HiSeq 2500
Description
Granulomas are immune cell aggregates formed in response to persistent inflammatory stimuli. Granuloma macrophage subsets are diverse and carry varying copy numbers of their genomic information. The molecular programs that control the differentiation of such macrophage populations in response to a chronic stimulus, though critical for disease outcome, have not been defined. In this study, we performed scRNA-Seq experiments to gain insights into the transcriptional regulation of polyploid macrophage differentiation in response to chronically persistent inflammatory stimuli. Overall design: scRNA-Seq was performed on FACS-sorted 2c and >4c DNA content polyploid macrophages after six days of bacterial lipoprotein, FSL-1 treatment of bone marrow-derived macrophage precursors. 2c DNA content macrophages treated with M-CSF alone were used as controls. CEL-Seq2 protocol was used for single cell sequencing (Hashimshony et al. 2016).
Publication Title
DNA Damage Signaling Instructs Polyploid Macrophage Fate in Granulomas.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 99 Downloadable Samples
- Illumina HiSeq 2500
Description
Our study demonstrated that e-cigarettes, both with and without nicotine, induced sex-dependent gene expression change. This RNA-seq study examined the expression profiles of brain frontal cortex samples from mice exposed to classic tobacco flavored bluâ„¢ e-cigarettes during gestation and lactation. Overall design: Brains were extracted and sectioned from ~1-month-old male and female offspring the week following exposure, RNA was isolated and purified from frontal cotrex tissues, and gene expression profiles were analyzed by RNA Sequencing.
Publication Title
Microglia Activation and Gene Expression Alteration of Neurotrophins in the Hippocampus Following Early-Life Exposure to E-Cigarette Aerosols in a Murine Model.
Sample Metadata Fields
Sex, Specimen part, Cell line, Subject
View Samples- Danio rerio
- 7 Downloadable Samples
- Illumina HiSeq 2500
Description
We compared transcriptomes of two ependymoglial populations isolated from adult zebrafish telencephalon. Overall design: Ependymoglial cells are acutely isolated from the adult zebrafish brains form 3 months old transgenic gfap:GFP animals. GFP is experssed in all ependymoglial cells and two populations are separated using GFP intensity in FACS.
Publication Title
The Aryl Hydrocarbon Receptor Pathway Defines the Time Frame for Restorative Neurogenesis.
Sample Metadata Fields
Specimen part, Subject
View Samples- Arabidopsis thaliana
- 6 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Effect of geminivirus Cabbage leaf curl virus on Arabidopsis Col-0 at 12 days post-inoculation during short day conditions.
Publication Title
Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 218 Downloadable Samples
- Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
To understand the molecular mechanisms of human lung macrophage development, function, and role in BPD pathogenesis, we conducted a clinical study using isolated tracheal aspirate macrophages from intubated preterm infants born before 30 wk gestation. One hundred twenty-eight patients intubated for respiratory distress syndrome and surfactant administration were consented for the study.
Publication Title
Transcriptional profiling of lung macrophages identifies a predictive signature for inflammatory lung disease in preterm infants.
Sample Metadata Fields
Sex, Treatment
View Samples- Homo sapiens
- 51 Downloadable Samples
- Illumina HumanHT-12 V3.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Cellular Differentiation of Human Monocytes Is Regulated by Time-Dependent Interleukin-4 Signaling and the Transcriptional Regulator NCOR2.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 51 Downloadable Samples
- Illumina HumanHT-12 V3.0 expression beadchip
Description
Whole transcriptome profiling (Illumina Microarray) of human ex vivo lymphocytes and monocytes, as well as of human monocyte-derived cells generated in vitro by activating CD14+ monocytes with MCSF, GMCSF or the combination of GMCSF and IL4
Publication Title
Cellular Differentiation of Human Monocytes Is Regulated by Time-Dependent Interleukin-4 Signaling and the Transcriptional Regulator NCOR2.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 20 Downloadable Samples
- Illumina HiSeq 1500
Description
Whole transcriptome profiling (RNA-Seq) of a time kinetics experiment containing human monocyte-derived cells, which were activated with IL4 either directly at the start of the culture, or at different hours after an initial activation with GMCSF alone. Cells being activated solely with GMCSF were added as controls Overall design: CD14+ monocytes were FACS-sorted from blood of human healthy donors and later activated in vitro with either GMCSF alone for 72 hours to obtain Mo-GMCSF[IL4 (0h)] cells as controls, with the combination of GMCSF and IL4 for 72 hours or 144 hours to obtain Mo-GMCSF[IL4 (0-72h)] or Mo-GMCSF[IL4 (0-144h)] cells, respectively, or with first GMCSF and then with the combination of GMCSF and IL4 for different durations. For the latter, monocytes were first activated with GMCSF for either 12, 24, 48 or 72 hours, and then with GMCSF plus IL4 until a total activation time of 144 hours. This resulted in Mo-GMCSF[IL4 (12-144h)], Mo-GMCSF[IL4 (24-144h)] , Mo-GMCSF[IL4 (48-144h)] and Mo-GMCSF[IL4 (72-144h)] cells, respectively.
Publication Title
Cellular Differentiation of Human Monocytes Is Regulated by Time-Dependent Interleukin-4 Signaling and the Transcriptional Regulator NCOR2.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 6 Downloadable Samples
- Illumina HiSeq 1500
Description
Whole transcriptome profiling (RNA-Seq) was performed on human Mo-GMCSF[IL4 (0-72h)] cells with either NCOR2 being knocked down or corresponding WT cells Overall design: CD14+ monocytes were FACS-sorted from blood of human healthy donors and later activated in vitro with the combination of GMCSF and IL4 for 72h to obtain Mo-GMCSF[IL4 (0-72h)] cells. During the last 24 hours of activation, either siRNAs targeting NCOR2 or scrambled RNAs were added to obtain NCOR2 knock down cells and corresponding WT cells, respectively
Publication Title
Cellular Differentiation of Human Monocytes Is Regulated by Time-Dependent Interleukin-4 Signaling and the Transcriptional Regulator NCOR2.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 18 Downloadable Samples
- Ion Torrent Proton
Description
We report, for the first time, engineering of heteropolar cardiac tissues containing distinct atrial and ventricular ends, and demonstrate their spatially confined responses to serotonin and ranolazine. Uniquely, electrical conditioning for up to 8 months enabled modeling of polygenic left ventricular hypertrophy starting from patient cells. Overall design: hiPSC-CMs from 3 affected (Left Ventricular Hypertrophy [LVH]) and 3 non-affected donors were sequenced using ThermoFisher's whole transcriptome targeted AmpliSeq assay
Publication Title
A Platform for Generation of Chamber-Specific Cardiac Tissues and Disease Modeling.
Sample Metadata Fields
Specimen part, Disease, Subject
View Samples