Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13279858_1.fastq.gz | Fastqsanger.gz | |||
| SRR13279858_2.fastq.gz | Fastqsanger.gz | |||
| SRR13279859_1.fastq.gz | Fastqsanger.gz | |||
| SRR13279859_2.fastq.gz | Fastqsanger.gz | |||
| SRR13279860_1.fastq.gz | Fastqsanger.gz |
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Project description:Recurrent otitis (ROM) is a pathological conditions in which a children have at least three episodes of acute otitis media over a course of 6 months. In this study we focused in proteins dysregulated between ROM and adenotonsillar hypertrophy (ATH). Tissue sample of seven ROM and seven ATH were obtained and submitted to two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS) for protein identification and western-blotting for data validation. We identified 23 significantly (p<0.05) protein spots. The expression of two proteins were validated by western-blotting. The 2-DE coupled with MS approach identified several proteins involved in cellular and metabolic processes. Further study are needed to better understanding the role of this proteins in ROM.
2020-12-10 | PXD022477 | Pride
Project description:Background: Loss of motion and arthrofibrosis after anterior cruciate ligament reconstruction (ACLR) can be a devastating complication for athletes. The cellular and molecular pathogenesis of arthrofibrosis is poorly understood, limiting prevention and treatment options. Synovial inflammation may contribute to post-ACLR arthrofibrosis. Hypothesis/Purpose: We hypothesized that higher synovial immune cell infiltration and inflammatory/catabolic gene expression patterns at the time of ACLR would correlate with poorer motion-related outcomes. Study Design: Case Series Methods: Patients aged 10-18 undergoing primary ACLR were enrolled in a prospective pilot study, and synovial tissue biopsies were obtained during ACLR. Flow cytometry and single cell RNA-sequencing explored synovial cell types/frequencies and gene expression. Principle component analysis followed by clustering grouped patients into distinct immunophenotypes based on their synovial cell composition. Clinical follow-up with knee range of motion (ROM), need for lysis of adhesions, and patient reported outcome measures were collected and compared between immunophenotypes. Results: Enrolled patients (n = 17) underwent ACLR at a median of 37 days post-injury. Analysis revealed three distinct immunophenotypes. Type 1 comprised patients with the longest time between injury and surgery and the lowest hematopoietic and T cell infiltration. Types 2 and 3 had similar times between injury and surgery, and Type 2 had intermediate while Type 3 had the highest hematopoietic and T cell percentages. Type 3 was associated with worse ROM at 2- and 6-weeks post-op; T cell prevalence and ROM were inversely correlated at those time points. The only patient requiring lysis of adhesions for arthrofibrosis was in Type 3. Conclusion: Synovial immune infiltration after ACL injury shows variability between patients that clusters into three immunophenotypes correlating with early ROM and the risk of arthrofibrosis. T cell recruitment and infiltration was the strongest factor correlated with ROM outcomes and presents an exciting venue for future research on post-ACLR arthrofibrosis.
2024-11-10 | GSE280537 | GEO
Project description:Illumina HiSeq Sequencing on Breast cancer PDX samples
| PRJNA454798 | ENA
Project description:Hybridizations were performed in triplicate, using total of 7 RNA samples extracted from 3 independent batches of proliferating cardiomyocyte cell line derived from p38alpha knockout mouse. In two hybridizations (Ambrosino 1, Ambrosino 2), the RNAs from p38alpha-/- and wt cells were labeled with Cy-5 and Cy-3-dUTP, respectively, whereas in the third hybridization (Ambrosino 3), the dyes were swapped. The multiple spike-in control RNA templates were added to the sample upon direct labeling, and the successful labeling and hybridization was confirmed in each hybridizations. Twelve housekeeping genes in the array (GAPDH, HPRT and S16, S9, and S8 ribosomal proteins) gave average value of Ratio of Medians (ROM), 1.30 ± 0.26, which was confirmed to be acceptable. GenePix Pro program calculates the Normalization Factor, based on the premise that the arithmetic mean of the ratios from every feature on the given array should be equal to 1. Normalization was therefore performed by multiplying the Factor to ROM in each gene. The program also identifies features that did not give good alignment to the expected spotted area as “flagged” spots, indicative of the impaired-quality hybridization of the specific genes. All flagged genes were removed from the list before further analysis. The genes that passed all these criteria were sorted by ROM and those that showed more than ±1.5 fold changes were selected in the data table from each hybridization. Finally, the data tables from the 3 independent hybridizations were compared and only those genes that appeared in all 3 experiments were selected in the final list (manuscript submitted). Keywords = NIA mouse 15K Keywords = cardiomyocytes Keywords = p38alpha MAPK Keywords: repeat sample
2004-12-01 | GSE1568 | GEO
Project description:We examined the effect of acetaminophen (APAP) on the transcriptional response induced by interferon-β (IFN-β). Transcript levels from total RNA isolated rom murine livers were determined using G4121B whole genome arrays. Keywords: Pharmakinetics, drug treatment
2010-10-18 | GSE18949 | GEO
Project description:We generated a Tcf7l2 F/F mouse and harvested preadipocytes rom these mice, immortalized them, and then transduced them with a retroviral vector containing CreERT2 and , differentiated them, performed ChIP-seq, and RNA-seq. We also generated and adipsoe specific knockout mouse where we crossed our Tcf7 F/Fmouse with an Adiponectin-Cre mice and performed RNA-seq on the inguimal white adipose tissue after 16 weeks of high fat diet, 65%
2019-08-01 | GSE129403 | GEO
Project description:Stefania coxi isolate:ROM 39478 Targeted Locus (Loci)
| PRJNA338581 | ENA
Project description:We performed the miRNA-seq analysis of 3 plasma exosomes from Legg-Cavé-Perthes patients and 3 plasma exosomes from healthy volunteers based on the Illumina Hiseq 2500 platform and obtained data of 6 samples.
2022-04-05 | GSE171044 | GEO
Project description:The goal of this study is to identify genomic signatures predicitve of cell-of-origin in acute myeloid leukemia Cryopreserved leukemic bone marrow samples were thawed, and 50,000 bulk leukemia (GFP+) cells were sorted by FACSAria (BD). Samples were placed at 37oC and 5% CO2 in IMDM plus 10% fetal calf serum for 30 minutes, then harvested, washed with 1X PBS, and ATAC-seq libraries were prepared. Quantitative PCR using the Library Quantitation kit (Kapa Biosystems) was used to estimate library concentrations. Libraries were sequenced on the Illumina HiSeq 2000 platform generating 2x150bp paired end reads at a sequencing depth of ~30-50 million reads per sample. Libraries were sequenced on the Illumina HiSeq 2000 platform.
2016-07-12 | GSE74688 | GEO
Project description:Placental abnormalities occur frequently in cloned animals. To investigate DNA methylation profile of trophoblast cell lineage of somatic cell nuclear transferred (NT) embryos, we established TS cells from blastocysts produced by NT at the blastocyst stage. Three independent TS cell lines derived from NT embryos rom BDF1 background were used in this study. Two control lines, derived from native blastocysts of BDF1 background, were also used.
2010-05-16 | E-GEOD-17104 | biostudies-arrayexpress