Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10913213_1.fastq.gz | Fastqsanger.gz | |||
| SRR10913213_2.fastq.gz | Fastqsanger.gz | |||
| SRR10913214_1.fastq.gz | Fastqsanger.gz | |||
| SRR10913214_2.fastq.gz | Fastqsanger.gz | |||
| SRR10913215_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:We performed single-cell (sc)RNA-Seq on male donors FACS-sorted “primitive” (CD34+ CD133+ CD90+) and “progenitor” (CD34+ CD133+ CD90-) HSPC cells treated with IL2RG ZFN, High Specificity (HS), (Low Specificity (LS) or control RNP in a ratio 1 to 1. We also included HS RNP and the cognate repair template containing a GFP expression cassette delivered by AAV6 and sorted for targeted integration (HS/AAV6 GFP+ vs. HS/AAV6 GFP-)
2019-03-01 | GSE119594 | GEO
Project description:To acquire a better understanding of the molecular pathogenesis of HS, we performed mRNA microarray studies to compare gene expression in lesional skin to healthy skin of HS patients. A significant difference was observed in mRNA expression between lesional and clinically healthy skin of HS patients. Skin biopsy samples (n=30, LS: lesion, NL: non-lesion) were collected at baseline from patients with hidradenitis for RNA extraction and microarray analysis.
2016-01-11 | E-GEOD-72702 | biostudies-arrayexpress
Project description:Time-resolved proteomic profiling of SGs from cultured human U2OS cells over a prolonged heat-shock (HS) and a successive recovery period, sampling at the 6 time points of HS exposure (10, 20, 30, 60, 120, 180 min), as well as 2 time points of recovery (5, 10 min). From the sampled cells, we prepared SG samples using a differential centrifugation plus endogenous G3BP1 immunoprecipitation protocol. Peptides were subsequently TMT-labeled and analyzed by quantitative LC-MS/MS. In G3BP1 dataset, rep1-rep3, HS-10, 20, 30, 60, 120, 180, re5, re10, SG-ls, G3BP1-IP samples were labeled with TMT-126, 127N, 127C, 128N, 128C,129N, 129C, 130N, 130C, 131 label Reagents, respectively; G3BP1_HS0 was a dataset created to integrate a non-heat shock control (HS-0) into the G3BP1 dataset, contains HS0, HS10, and HS60, and the results was integrated into the G3BP1 dataset using the ComBat processing, HS-0_rep1, HS-0_rep2, HS-0_rep3, HS-10_rep1, HS-10_rep2, HS-10_rep3, HS-60_rep1, HS-60_rep2, HS-60_rep3 samples were labeled with TMT-126, 127N, 127C, 128N, 128C,129N, 129C, 130N, 130C label Reagents, respectively. In CAPRIN1 dataset, rep1-rep3, HS-0, 10, 20, 30, 60, 120, 180, re5, re10 samples were labeled with TMT-126, 127N, 127C, 128N, 128C,129N, 129C, 130N, 130C label Reagents, respectively.
2023-08-30 | MSV000092790 | MassIVE
Project description:The aquaculture industry has confronted severe economic losses due to infectious diseases in the last years. Piscirickettsiosis or Salmonid Rickettsial Septicaemia (SRS) is the bacterial disease caused by Piscirickettsia salmonis. This Gram-negative, non-motile, cellular pathogen has the ability to infect, survive, replicate, and propagate in salmonid monocytes/macrophages generating a systemic infection characterized by the colonization of several organs including kidney, liver, spleen, intestine, brain, ovary and gills. In this study, we attempted to determine whether global gene expression differences can be detected in different genetic groups of Atlantic salmon as a result of Piscirickettsia salmonis infection. Moreover, we sought to characterize the fish transcriptional response in order to reveal the mechanisms that might confer resistance in Atlantic salmon to an infection with Piscirickettsia salmonis. In doing so, after challenging with Piscirickettsia salmonis, we selected the families with the highest (HS) and the lowest (LS) recorded susceptibility for gene expression analysis using 32K cGRASP microarrays. Our results revealed in LS families expression changes are linked to iron depletion, as well as, low contents of iron in kidney cells and low bacterial load, indicated that the iron-withholding strategy of innate immunity is part of the mechanism of resistance against Piscirickettsia salmonis. This information contributes to elucidate the underlying mechanisms of resistance to Piscirickettsia salmonis infection in Atlantic salmon and to identify new candidate genes for selective breeding programmes. Forty full-sibling families of Atlantic salmon (Salmo salar) were infected by intraperitoneal injection with 0.2 mL Piscirickettsia salmonis (PS889, isolated from Oncorhynchus kisutch, 1M-CM-^W104 PFU/mL). After forty days, the fishes were harvested and the cumulative mortality (dead fish / total fish) for each family was calculated. For the second challenge, the six families with the highest cumulative mortality levels were considered of relatively high susceptibility (HS) and the six families with the lowest cumulative mortality levels were considered of relatively low susceptibility (LS) to the infection. Five control and five infected fish from three HS and three LS families were analyzed. For each HS and LS family, pools of RNA from control and infected fish were prepared separately and were reverse transcribed. Four slides were for each used family hybridized including two dye-swaped slides. Labeled samples were hybridized on a 32K cDNA microarray, developed at the Consortium for Genomics Research on All Salmonids Project (cGRASP), GEO accession number: GPL8904.
2013-01-04 | E-GEOD-43255 | biostudies-arrayexpress
Project description:Wood stiffness is the most important wood quality trait of forest trees for structural timber production. We investigated genes differentially transcribed in radiate pine trees with distinct wood stiffness using bulked segregant analysis (BSA) and cDNA microarrays. Transcript accumulation in earlywood (EW) and latewood (LW) of high (HS) and low stiffness (LS) trees in two progeny trials was compared.
2011-06-01 | GSE23020 | GEO
Project description:Sperm motility is one of the most important indicator for evaluating roosters’ fecundity. However, the molecular regulation underlying chicken sperm motility is not yet clear. MicroRNA (miRNA) plays epigenetic roles in reproduction. In this study, we compared the testicular miRNAs of Beijing-you roosters with high (HS) and low (LS) sperm motility using Solexa sequencing. Length distribution analysis showed that the dominant size of the small RNAs detected in the testis was 24~28 nt. In total, 518 known and 106 novel miRNAs were identified. A number of 23 miRNAs were found differentially expressed (P < 0.05, |log2fold change| ≥ 1) between the HS and LS, including 18 known and five novel miRNAs. Function enrichment of predicted target genes of the differential miRNAs indicated that the differentially expressed miRNAs were involved in the pathways of GnRH signaling, MAPK signaling, and Wnt signaling. The miRNA-gene interaction network revealed two key candidate miRNA-gene pairs that may affect chicken sperm motility viz gga-miR-155/KCNA1 and gga-miR-7480-5p/AHI1. qRCR was also used to further validate their expression. The results here provide deep insight into the expression of miRNA in the testis of chicken and suggest their roles in sperm motility regulation.
2018-01-13 | GSE109141 | GEO
Project description:Wood stiffness is the most important wood quality trait of forest trees for structural timber production. We investigated genes differentially transcribed in radiate pine trees with distinct wood stiffness using bulked segregant analysis (BSA) and cDNA microarrays. Transcript accumulation in earlywood (EW) and latewood (LW) of high (HS) and low stiffness (LS) trees in two progeny trials was compared. Radiata pine trees used for microarray experiment were selected from two progeny trials planted at Flynn and Kromelite, Australia. Based on the IML-based MOE measurement, five families with highest and lowest MOE each were selected from each trial, which represented two segregant populations with contrasting wood stiffness. Two individuals from each selected family were further sampled. Developing xylem tissues of selected trees in Flynn trial were sampled in spring (October) and autumn (April), representing earlywood (EW) and latewood (LW) of juvenile aged trees, respectively. Collection of xylem tissues from Kromelite trial was arranged in summer (late November) when latewood (LW) was formed. The xylem tissues were scraped at breast height with a sharp chisel after the bark was removed. In Flynn trial EW and LW tissues were collected from the same sampled trees on opposite sides of the trunk. Transcript accumulation was compared in trees with highest (HS) and lowest stiffness (LS) using xylem samples from Flynn collected in spring (EW) and autumn (LW), as well as Kromelite in summer (LW), respectively. Bulked segregant analysis (BSA) was used for the experiment design. Total RNA samples extracted from the five trees with HS were pooled at equal amount, and compared to the bulked five individuals with LS. This pooling strategy can partly minimize the genetic variation among different genotypes. Dye swaps were applied in each biological replicate.
2011-06-01 | E-GEOD-23020 | biostudies-arrayexpress
Project description:Most patients affected by glycogen storage disease type 1a (GSD-1a), an inherited metabolic disorder caused by mutations in the enzyme glucose-6-phosphatase-alpha (G6Pase- α), develop renal and liver complications, including development of hepatocellular adenoma/carcinoma. The purpose of this study was to identify potential biomarkers of the pathophysiology of the GSD1a affected liver. To this end, we utilized the plasma exosomes of a murine model of GSD-1a, LS-G6pc-/- mice, to uncover microRNA expression modulation associated with the disease. Differentially expressed microRNA between LS-G6pc-/- and wild type mice, LS-G6pc-/- mice with hepatocellular adenoma and LS-G6pc-/- mice without adenoma, and LS-G6pc-/- mice with amyloidosis and LS-G6pc-/- mice without amyloidosis were identified. Pathway analysis demonstrated that the target genes of the differentially expressed miRNAs were significantly enriched for insulin signaling pathway, glucose and lipid metabolism, Wnt-beta catenin, telomere maintenance and hepatocellular carcinoma, and chemokine and immune regulation signaling pathways. While some microRNA were common to the different pathologic conditions, others were unique to cancerous or inflammatory status of the animals. Therefore, the altered expression of several microRNA correlates with various pathologic liver statuses and may help discriminate during the progression of the disease and the development of late GSD1-associated complications.
2020-09-09 | GSE157656 | GEO
Project description:Fast-growing Eucalyptus grandis trees are one of the most efficient producers of wood in South Africa. It is essential to maximize the effectiveness of these plantations by increasing their productivity, the quality and value of their products. We used microarray-based DNA-amplified fragment length polymorphism (AFLP) analysis in combination with expression profiling to develop fingerprints and profile gene expression of wood-forming tissue of seven individual E. grandis trees. A 1532-probe cDNA microarray was constructed by arraying 768 cDNA-AFLP fragments and 810 cDNA library clones from seven individual E. grandis trees onto silanised slides. The results revealed that 32% of the spotted fragments showed distinct expression patterns (with a fold change of at least 1.4 or -1.4 and a p value of 0.01) and could be grouped into clusters representing co-expressed genes. Evaluation of the binary distribution of cDNA-AFLP fragments on the array showed that the individual genotypes could be discriminated. A simple, yet general method was developed for genotyping and expression profiling of wood-forming tissue of E. grandis trees differing in their splitting characteristics and in their lignin contents. Evaluation of gene expression profiles and the binary distribution of cDNA-AFLP fragments on the chip suggest that the prototype chip developed could be useful for transcript profiling and for the identification of Eucalyptus trees with preferred wood quality traits in commercial breeding programmes. Transcriptional profiling and genotyping of seven E. grandis trees , namely (741-H (high lignin), 108-L (low lignin), 243-L (low lignin), 1/23/4-HS (high splitting), 1/71/6-HS (high splitting), 1/91/7-LS (low splitting) and 1/92/7-LS (low splitting), were performed with an in-house spotted cDNA microarray. All trees were characterized for their splitting qualities and lignin content and only the trees best corresponding to the selected traits were used for further analysis (Verryn and Turner 2000). RNA was isolated and cDNA synthesis was performed. A reference design microarray experiment was conducted and tree 1/23/4-HS served as a reference. Samples were fluorescently labelled with Cy5 or Cy3 dye and co-hybridized overnight. Two biological and one technical replicate (using independent labelling reactions) was performed, each replication consisting of a reverse labelling experiment.
2009-10-01 | E-GEOD-14707 | biostudies-arrayexpress