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GSE138351
Homo sapiens
41 Downloadable Samples
Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Effects of Electronic Cigarette Constituents on the Human Lung: A Pilot Clinical Trial.
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 41 Downloadable Samples
- Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
E-cig use is continuing to increase, particularly among youth never-smokers, and is used by some smokers to quit. The acute and chronic toxicity of e-cig use is unclear generally in the context of increasing reports of inflammatory-type pneumonia in some e-cig users. To assess lung effects of e-cigs without nicotine or flavors, we conducted a pilot study with serial bronchoscopies over 4 weeks in 30 never-smokers, randomized either to a four-week intervention with the use of e-cigs containing only 50% propylene glycol (PG) and 50% vegetable glycerine (VG) or to a no-use control group. Compliance to the e-cig intervention was assessed by participants sending daily puff counts and by urinary propylene glycol (PG). Inflammatory cell counts and cytokines were determined in bronchoalveolar lavage (BAL) fluids. Genome-wide expression, microRNA, and mRNA were determined from bronchial epithelial cells. There were no significant differences in changes of BAL inflammatory cell counts or cytokines between baseline and follow-up, comparing the control and e-cig groups. However, in the intervention but not the control group, change in urinary PG as a marker of e-cig use and inhalation, was significantly correlated with change in cell counts (cell concentrations, macrophages, and lymphocytes) and cytokines (IL-8, IL-13, and TNF-α), although the absolute magnitude of changes was small. There were no significant changes in mRNA or microRNA gene expression. Although limited by study size and duration, this is the first experimental demonstration of an impact of e-cig use on inflammation in the human lung among never-smokers.
Publication Title
Effects of Electronic Cigarette Constituents on the Human Lung: A Pilot Clinical Trial.
Sample Metadata Fields
Age, Specimen part
View Samples- Mus musculus
- 4 Downloadable Samples
- Illumina MouseWG-6 v2.0 R2 expression beadchip
Description
Examination of gene expression patterns in lineage negative FLT3-ITD and pMIG-transduced BM cells via microarray study.
Publication Title
RIPK3 Restricts Myeloid Leukemogenesis by Promoting Cell Death and Differentiation of Leukemia Initiating Cells.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 135 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Expression data were generated on 136 subjects from the COPDGene study using Affymetrix microarrays. Multiple linear regression with adjustment for covariates (gender, age, body mass index, family history, smoking status, pack years) was used to identify candidate genes and Ingenuity Pathway Analysis was used to identify candidate pathways.
Publication Title
Peripheral blood mononuclear cell gene expression in chronic obstructive pulmonary disease.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
The objective of this experiment was to test the effect, at a transcrptomic level, of lymphotoxin-beta receptor activation in HBV-infected differentiated HepaRG cells
Publication Title
Specific and nonhepatotoxic degradation of nuclear hepatitis B virus cccDNA.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 9 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
A375P melanoma cells were treated with 1uM of the MEK inhibitor PD184352 or 0.4uM of the V600EBRAF inhibitor PLX4720 for 2hr, 6hr and 24hrs.
Publication Title
Identification of direct transcriptional targets of (V600E)BRAF/MEK signalling in melanoma.
Sample Metadata Fields
Cell line, Treatment, Time
View Samples- Homo sapiens
- 124 Downloadable Samples
- Affymetrix Human Genome U133B Array (hgu133b)
Description
GBM samples were clusered using gene expression of AKT pathway genes to reveal at least 5 GBM AKT subtypes, having distinct DNA copy number alterations, enrichment in oncogenes and tumor suppressor genes and patterns of expression for PI3K/AKT/mTOR signaling components.
Publication Title
AKT pathway genes define 5 prognostic subgroups in glioblastoma.
Sample Metadata Fields
Sex, Age
View Samples- Mus musculus
- 4 Downloadable Samples
Illumina HiSeq 2000
Description
Lamins, the major components of the nuclear lamina, have diverse functions in many cellular processes. Despite broad expression, lamins have been implicated in cell type-specific roles in development, aging and disease by regulating gene expression. Yet, due to the lack of in depth lineage-specific functional studies, it remains unclear whether or how lamins regulate cell type-specific functions. Using targeted knockout of lamin B1 in the olfactory sensory neuron lineage, we show that lamin B1 is not required for early stages of olfactory sensory neuron differentiation but is needed for formation of mature neurons that properly respond to odor stimulation. Lamin B1 mutant cells exhibited decreased expression of genes involved in mature neuron function, increased expression of genes atypical of the olfactory lineage and clustered nuclear pore distribution. These results demonstrate that the universally expressed lamin B1 regulates cell type-specific gene expression and terminal differentiation. Overall design: Transcriptome profiles were generated from sorted regenerated olfactory epithelium cells lacking Lamin B1 (Lmnb1) and control (heterozygous cells). Each sample is collected from one mouse. Data are from two experimental groups (G1,G2), each containing a control and a mutant sample. Different groups differ in treatment, parents, age and sex. Within a group, treatment, sample preparation, sequencing, animal sex, age, and parents are the same.
Publication Title
Lamin B1 is required for mature neuron-specific gene expression during olfactory sensory neuron differentiation.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
Alveolar macrophages from never smokers and active smokers were isolated by bronchoalveolar lavage and gene expression was measured. Chronic cigarette smoke exposure, as occurs in smoker's lungs, leads to significant changes in gene expression. Of note, RNA was isolated immediately following bronchoscopy. Alveolar macrophage levels were >95%.
Publication Title
Cigarette smoking decreases global microRNA expression in human alveolar macrophages.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 69 Downloadable Samples
- Illumina HiSeq 2000
Description
The development of high-throughput genomic technologies has revealed that a large fraction of the genomes of eukaryotes is associated with the expression of noncoding RNAs. One class of noncoding RNA, the cis-natural antisense transcripts (cis-NATs), are particularly interesting as they are at least partially complementary to the protein-coding mRNAs. Although most studies described cis-NATs involved in the regulation of transcription, a few reports have shown recently that cis-NATs can also regulate translation of the cognate sense coding genes in plants and mammals. In order to identify novel examples of translation regulator cis-NATs in Arabidopsis thaliana, we designed a high-throughput experiment based on polysome profiling and RNA-sequencing. Expression of cis-NATs and translation efficiency of the cognate coding mRNAs were measured in roots and shoots in response to various conditions, including phosphate deficiency and treatment with phytohormones. We identified several promising candidates, and validated a few of them experimentally, in Arabidopsis thaliana transgenic lines over-expressing in trans the translation regulator candidate cis-NATs. Overall design: total RNA and polysomal RNA was sequenced from Arabidopsis thaliana whole seedlings grown in high or low pohsphate content, or from roots or shoots from seedlings treated or not with different phytohormones (Ctrl, IAA, ABA,MeJA and ACC). 3 biological replicates were analyzed for each of the 12 experimental conditions.
Publication Title
Prediction of regulatory long intergenic non-coding RNAs acting in trans through base-pairing interactions.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples