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SRP069011
Homo sapiens
24 Downloadable Samples
NextSeq500, IlluminaHiSeq2000
Description
We used Illlumina Artseq Ribo Profile to perform ribosome footprinting on the above cell lines Overall design: We followed the manufacturer's protocol: Cells were treated with cycloheximide (0.1 mg/ml) to inhibit translation; total RNA and ribosome-protected RNA fragments were isolated and library preped for sequencing simultaneously.
Publication Title
Modulated Expression of Specific tRNAs Drives Gene Expression and Cancer Progression.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 8 Downloadable Samples
- NextSeq500
Description
We used Illlumina Artseq Ribo Profile to perform ribosome footprinting on the above cell lines Overall design: We followed the manufacturer's protocol: Cells were treated with cycloheximide (0.1 mg/ml) to inhibit translation; total RNA(tt) and ribosome-protected RNA fragments (RPF) were isolated and library preped for sequencing simultaneously.
Publication Title
Modulated Expression of Specific tRNAs Drives Gene Expression and Cancer Progression.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 8 Downloadable Samples
- NextSeq500
Description
We used Illlumina Artseq Ribo Profile to perform ribosome footprinting on the above cell lines Overall design: We followed the manufacturer's protocol: Cells were treated with cycloheximide (0.1 mg/ml) to inhibit translation; total RNA(tt) and ribosome-protected RNA fragments (RPF) were isolated and library preped for sequencing simultaneously.
Publication Title
Modulated Expression of Specific tRNAs Drives Gene Expression and Cancer Progression.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 8 Downloadable Samples
- NextSeq 500
Description
We used Illlumina Artseq Ribo Profile to perform ribosome footprinting on the above cell lines Overall design: We followed the manufacturer's protocol: Cells were treated with cycloheximide (0.1 mg/ml) to inhibit translation; total RNA(tt) and ribosome-protected RNA fragments (RPF) were isolated and library preped for sequencing simultaneously.
Publication Title
Modulated Expression of Specific tRNAs Drives Gene Expression and Cancer Progression.
Sample Metadata Fields
Cell line, Subject
View Samples- Homo sapiens
- 332 Downloadable Samples
Illumina HumanHT-12 V4.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Host Transcription Profile in Nasal Epithelium and Whole Blood of Hospitalized Children Under 2 Years of Age With Respiratory Syncytial Virus Infection.
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Disease stage
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
The Clade A PP2C Highly ABA-Induced1 (HAI1, At5g59220) is strongly up-regulated by low water potential in an ABA-dependent manner. Using knockout mutants of hai1, we found that HAI1 functions as a negative regulator of low water potential-induced proline and osmoregulatory solute accumulation. We also found a relatively weak and limited interaction of HAI1 with the RCAR/PYL family of ABA receptors. This, plus its induced expression, suggest that HAI1 remains active during stress and attenuates specific aspects of drought response.
Publication Title
Unique drought resistance functions of the highly ABA-induced clade A protein phosphatase 2Cs.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Arabidopsis thaliana
- 35 Downloadable Samples
- Illumina HiSeq 2000
Description
Transfer cells (TCs) play important roles in facilitating enhanced rates of nutrient transport at key apoplasmic/symplasmic junctions along the nutrient acquisition and transport pathways in plants. TCs achieve this capacity by developing elaborate wall ingrowth networks which serve to increase plasma membrane surface area thus increasing the cell's surface area-to-volume ratio to achieve increased flux of nutrients across the plasma membrane. Phloem parenchyma (PP) cells of Arabidopsis leaf veins trans-differentiate to become PP TCs which likely function in a two-step phloem loading mechanism by facilitating unloading of photoassimilates into the apoplasm for subsequent energy-dependent uptake into the sieve element/companion cell (SE/CC) complex. We are using PP TCs in Arabidopsis as a genetic model to identify transcription factors involved in coordinating deposition of the wall ingrowth network. Confocal imaging of pseudo-Schiff propidium iodide-stained tissue revealed different profiles of temporal development of wall ingrowth deposition across maturing cotyledons and juvenile leaves, and a basipetal gradient of deposition across mature adult leaves. RNA-Seq analysis was undertaken to identify differentially expressed genes common to these three different profiles of wall ingrowth deposition. This analysis identified 68 transcription factors up-regulated two-fold or more in at least two of the three experimental comparisons, with six of these transcription factors belonging to Clade III of the NAC-domain family. Phenotypic analysis of these NAC genes using insertional mutants revealed significant reductions in levels of wall ingrowth deposition, particularly in a double mutant of NAC056 and NAC018, as well as compromised sucrose-dependent root growth, indicating impaired capacity for phloem loading. Collectively, these results support the proposition that Clade III members of the NAC domain family in Arabidopsis play important roles in regulating wall ingrowth deposition in PP TCs. Overall design: The sampling enabled three different temporal and spatial pair-wise comparisons for RNA-Seq analysis, namely: (i) cotyledons at Day 5 vs Day 10; (ii) Leaf 1 and Leaf 2 (first juvenile leaves) at Day 10 vs Day 16; and (iii) basal vs apical third (base vs tip) of Leaf 12 at Day 31. This analysis provided temporal and spatial comparisons of tissues with absent vs abundant wall ingrowth deposition in phloem parenchyma transfer cells.
Publication Title
Transcript Profiling Identifies NAC-Domain Genes Involved in Regulating Wall Ingrowth Deposition in Phloem Parenchyma Transfer Cells of <i>Arabidopsis thaliana</i>.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
To address the functional role of KDM6A in the regulation of Rhox genes, male and female mouse ES cells were transfected with a mixture of three small interfering RNA duplexes, each of which targets a different region of Kdm6a mRNA. We found that Kdm6a knockdown in mouse ES cells caused a decrease in expression of a subset of Rhox genes, Rhox6 and 9. Furthermore, Rhox6 and 9 expression was decreased in female ES cells but not male ES cells indicating that KDM6A regulates Rhox gene expression in a sexually dimorphic manner.
Publication Title
Female bias in Rhox6 and 9 regulation by the histone demethylase KDM6A.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Arabidopsis thaliana
- 6 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Two Clade E Growth Regulating PP2Cs EGR1 and EGR2 (EGR1, At3g05640; EGR2, At5g27930) are strongly up regulated by low water but much less affected by ABA. EGR mutants maintained higher seedling root elongation and dry weight at low water potential and higher levels of stress protective metabolite proline.
Publication Title
Protein Phosphatase 2Cs and <i>Microtubule-Associated Stress Protein 1</i> Control Microtubule Stability, Plant Growth, and Drought Response.
Sample Metadata Fields
Age, Specimen part
View Samples- Pseudomonas aeruginosa
- 5 Downloadable Samples
- Affymetrix Pseudomonas aeruginosa Array (paeg1a)
Description
b-Oxidative enzymes for fatty acid degradation (Fad) of long-chain fatty acid (LCFA), a component of lung surfactant phosphatidylcholine, are induced in vivo during lung infection in cystic fibrosis patients, which could contribute to nutrient acquisition and pathogenesis of Pseudomonas aeruginosa. In addition, fatty acid biosynthesis (Fab) is essential for the syntheses of two virulence controlling acylated-homoserine-lactone molecules in this organism. We mapped the promoter regions of the fadBA5-operon (PA3014 and PA3013) and a fadE homologue (PA2815) involved in Fad and the fabAB-operon involved in Fab. Focusing on the transposon mutagenesis of strain PAO1 carrying the PfadBA5-lacZ fusion, we identified a regulator for the fadBA5-operon to be PsrA (PA3006). Transcriptome analysis of the DpsrA mutant indicates its importance in regulating b-oxidative enzymes, which confirms a previous proteomic study. We further showed that induction of the fadBA-operon responds to LCFA signals, and this induction requires the presence of PsrA, suggesting that PsrA binds to LCFA to derepress fadBA5. Electrophoresis mobility shift assay indicate specific binding of PsrA to the fadBA5-promoter region. This binding is disrupted by specific LCFA (C18:1D9, C16:0, and to a lesser extent C14:0), but not by the first intermediate of b-oxidation, acyl-CoA. We proposed that PsrA is a Fad-regulator that binds and responds to LCFA signals in Pseudomonas aeruginosa.
Publication Title
The Pseudomonas aeruginosa PsrA responds to long-chain fatty acid signals to regulate the fadBA5 beta-oxidation operon.
Sample Metadata Fields
No sample metadata fields
View Samples