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SRP150269
Mus musculus
78 Downloadable Samples
Illumina HiSeq 2500
Description
Purpose: We investigated the tetrachloroethylene associated changes in kidney transcriptomes among healthy mice, nonalcoholic fatty liver disease mice, and nonalcoholic steatohepatitis mice. Overall design: Male C57BL/6J mice were fed a low-fat diet (4% fat), high-fat diet (31% fat), or methionine/choline/folate deficient diet. Following an 8-week diet, mice were administered either a single dose of tetrachloroethylene (PERC, 300 mg/kg/d in 5% Alkamuls-EL620 in saline, 5 mL/kg) and euthanized at 24 hours post dose, or five consecutive daily doses of PERC or vehicle (n=8/diet/treatment) and euthanized at 4hours post dose. The harvested kidneys were subjected to mRNA sequencing using Illumina Hiseq 2500. Jac-NASH-063 was excluded from analysis because it did not have a good yield.
Publication Title
Modulation of Tetrachloroethylene-Associated Kidney Effects by Nonalcoholic Fatty Liver or Steatohepatitis in Male C57BL/6J Mice.
Sample Metadata Fields
Cell line, Treatment, Subject
View Samples- Homo sapiens
- 151 Downloadable Samples
- IlluminaGenomeAnalyzer
Description
To increase our understanding of psoriasis, we utilized RNA-seq to assay the transcriptomes of lesional psoriatic and normal skin. We sequenced polyadenylated RNA-derived cDNAs from 92 psoriatic and 82 normal punch biopsies, generating an average of ~38 million single-end 80-bp reads per sample. Comparison of 42 samples* examined by both RNA-seq and microarray [GSE13355] revealed marked differences in sensitivity, with transcripts identified only by RNA-seq having much lower expression than those also identified by microarray. RNA-seq identified many more differentially expressed transcripts enriched in immune system processes. Weighted gene co-expression network analysis (WGCNA) revealed multiple modules of coordinately expressed epidermal differentiation genes, overlapping significantly with genes regulated by the long non-coding RNA TINCR, its target gene, staufen-1 (STAU1), the p63 target gene ZNF750, and its target KLF4. Other coordinately expressed modules were enriched for lymphoid and/or myeloid signature transcripts and genes induced by IL-17 in keratinocytes. Dermally-expressed genes were significantly down-regulated in psoriatic biopsies, most likely due to expansion of the epidermal compartment. These results demonstrate the power of WGCNA to elucidate gene regulatory circuits in psoriasis, and emphasize the influence of tissue architecture in both differential expression and co-expression analysis. *The list of 42 samples examined by both RNA-seq and microarray is provided in the 'MAoverlappedsamples.txt'. Overall design: 92 psoriatic and 82 normal skin samples
Publication Title
Circadian control of interferon-sensitive gene expression in murine skin.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 45 Downloadable Samples
- IlluminaGenomeAnalyzer
Description
Together with the GSE54456 data, we used in total RNA-seq data from 99 lesional psoriatic, 27 uninvolved psoriatic, and 90 normal skin biopsies and applied computational approaches to identify and characterize expressed lncRNAs. Overall design: 7 psoriatic, 27 uninvolved, and 8 normal skin samples
Publication Title
Circadian control of interferon-sensitive gene expression in murine skin.
Sample Metadata Fields
No sample metadata fields
View Samples- Rattus norvegicus
- 27 Downloadable Samples
Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
A systems biology approach identifies a regulatory network in parotid acinar cell terminal differentiation.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 36 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Imiquimod (IMQ) is a topical therapeutic immune activator that causes psoriasiform inflammation in mice. To determine if IMQ-induced inflammation and gene expression changes depended on the time of day in which treatment is administered, we performed gene expression profiling of dorsal mouse back skin by microarray after different durations of topical 1% IMQ treatment (control = no treatment, 6 hr, 24 hr, and 5 days of IMQ treatment) at different times of day (ZT01, ZT07, ZT09 = day-time treatment; ZT13 and ZT19 = night-time treatment). We also performed a time course after IMQ treatment by collecting mouse back skin after 0 (no treatment), 1, 2, 4, 6, and 24 hours post-treatment. Lastly, we determined gene expression changes in response to IMQ in mice deleted for the core circadian clock gene, Bmal1, after 0 (no treatment) and 24 hours post-1% IMQ compared to Wt (both treated and collected during the daytime at ZT09). The results of this study are important as they show that IMQ-induced activation of interferon sensitive genes are diurnal in Wt mice after 6 hours and 24 hours but not after 5 consecutive treatments. Furthermore, we find that interferon sensitive genes are induced more robustly in the skin of Bmal1 KO mice after 24 hr IMQ compared to Wt mice. These results are important for further understanding how the circadian clock regulates immune activation in response to the theraputic agent IMQ.
Publication Title
Circadian control of interferon-sensitive gene expression in murine skin.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Rattus norvegicus
- 4 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
Terminal differentiation in parotid acini relies on sustained changes in gene expression during the first few postnatal weeks. Little is known about what drives these changes. Expression measurements along with knowledgebased network analysis was used to develop a prospective gene regulatory network that drives differentiation.
Publication Title
A systems biology approach identifies a regulatory network in parotid acinar cell terminal differentiation.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 91 Downloadable Samples
- Illumina HiSeq 2500
Description
Defining cellular and molecular identities within the kidney is necessary to understand its organization and function in health and disease. Here we demonstrate a reproducible method with minimal artifacts for single-nucleus Droplet-based RNA sequencing (snDrop-Seq) that we use to resolve thirty distinct cell populations in human adult kidney. We define molecular transition states along more than ten nephron segments spanning two major kidney regions. We further delineate cell type-specific expression of genes associated with chronic kidney disease, diabetes and hypertension, providing insight into possible targeted therapies. This includes expression of a hypertension-associated mechano-sensory ion channel in mesangial cells, and identification of proximal tubule cell populations defined by pathogenic expression signatures. Our fully optimized, quality-controlled transcriptomic profiling pipeline constitutes a tool for the generation of healthy and diseased molecular atlases applicable to clinical samples. Overall design: Single-nucleus (sn)Drop-seq was used to generate RNA expression estimates across two kidney regions (cortex and medulla), 15 different individuals, 7 different tissue processing methods, and from tissues acquired from two different institutions (Washington University and University of Michigan through KPMP consortium). From the resulting ~18,000 sequenced nuclei passing QC filtering (>400 <5000 non-MT genes detected, >50 post-QC nuclei per library, >30 nuclei per cluster), we identified 30 different cell populations (see supplementary file UCSD-WU_Single_Nuclei_Cluster_Annotations.csv).
Publication Title
A single-nucleus RNA-sequencing pipeline to decipher the molecular anatomy and pathophysiology of human kidneys.
Sample Metadata Fields
Sex, Specimen part, Subject
View Samples- Homo sapiens
- 15 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Human T cells isolated from healthy donors were transduced with non-tonically signaling CARs or tonically signaling CARs, each with CD28z or 4-1BB costimulatory domains
Publication Title
4-1BB costimulation ameliorates T cell exhaustion induced by tonic signaling of chimeric antigen receptors.
Sample Metadata Fields
Specimen part, Subject
View Samples- Danio rerio
- 8 Downloadable Samples
- IlluminaHiSeq2500
Description
We report the gene expression comparison of zebrafish melanocytes and melanomas. These comparisons were used for integrative genomic studies that identified the BMP factor GDF6 as a new oncogene that is specifically expressed in melanomas. Overall design: Examination of gene expression in two different cell types
Publication Title
Ligand-activated BMP signaling inhibits cell differentiation and death to promote melanoma.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 123 Downloadable Samples
- IlluminaHiSeq2500
Description
Single cell RNA seq and bioinformatic analysis is used to characterize myeloid differentiation to uncover novel transcriptional networks and key drivers of hematoipoietic development Overall design: Single cell RNA seq of different hematopoietic populations integrated with Chip seq involving multiple markers
Publication Title
Single-cell analysis of mixed-lineage states leading to a binary cell fate choice.
Sample Metadata Fields
No sample metadata fields
View Samples