C0N0
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA963080 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24356806_1.fastq.gz | Fastqsanger.gz | |||
| SRR24356806_2.fastq.gz | Fastqsanger.gz | |||
| SRR24356807_1.fastq.gz | Fastqsanger.gz | |||
| SRR24356807_2.fastq.gz | Fastqsanger.gz | |||
| SRR24356808_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 24 |
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Project description:De novo whole metagenome in 51 years old long term fertilized (LTFE) paddy soil (Under Institute project 2.1 Enhancing nutrient use efficiency in rice through advance agronomy using smart sensors, models and remediation)
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Project description:We used the mummichog (Fundulus heteroclitus) array we developed to test whether our arrays could be used to monitor the efficacy of remediation at an estuarine Superfund site. Shipyard Creek is a chromium-contaminated Superfund site in Charleston, SC undergoing remediation, therefore it provides a unique opportunity to study the efficacy of arrays as a molecular biomarker in of toxicant effects in mummichogs. Mummichogs were captured in Shipyard Creek in Charleston, SC prior to remediation (2000), after remediation began (2003), and as remediation further progressed (2005). Simultaneously, mummichogs were collected from a reference site at the Winyah-Bay National Estuarine Research Reserve (NERR). The hepatic gene expression pattern of fish captured at Shipyard Creek showed wide differences from the fish captured at NERR in 2000. As remediation progressed the gene expression pattern of fish captured at Shipyard Creek became increasingly similar to fish captured at NERR, and the number of genes differently expressed dropped from 22 to 4. The magnitude of differential gene expression of the individual genes also decreased during remediation. The recovering gene expression profile is associated with lower chromium bioavailability, demonstrated through significantly decreased body burden and sediment concentrations. For example, sediment concentrations at Shipyard Creek were 80-fold greater than NERR in 2000, 51-fold greater in 2003, and only 8-fold greater in 2005. However, hydraulic dredging in 2005 stirred up the sediments and increased body burden of chromium even though chromium sediment concentrations continued to drop. Therefore, the number of differentially expressed genes increased to 9. Overall, the data supports our hypothesis that arrays can be used to monitor site mitigation, as the number of genes differentially expressed mimics the body burden and also indicates when on-site remediation is increasing bioavailability. Keywords: Field site
2006-09-01 | GSE4212 | GEO
Project description:We used the mummichog (Fundulus heteroclitus) array we developed to test whether our arrays could be used to monitor the efficacy of remediation at an estuarine Superfund site. Shipyard Creek is a chromium-contaminated Superfund site in Charleston, SC undergoing remediation, therefore it provides a unique opportunity to study the efficacy of arrays as a molecular biomarker in of toxicant effects in mummichogs. Mummichogs were captured in Shipyard Creek in Charleston, SC prior to remediation (2000), after remediation began (2003), and as remediation further progressed (2005). Simultaneously, mummichogs were collected from a reference site at the Winyah-Bay National Estuarine Research Reserve (NERR). The hepatic gene expression pattern of fish captured at Shipyard Creek showed wide differences from the fish captured at NERR in 2000. As remediation progressed the gene expression pattern of fish captured at Shipyard Creek became increasingly similar to fish captured at NERR, and the number of genes differently expressed dropped from 22 to 4. The magnitude of differential gene expression of the individual genes also decreased during remediation. The recovering gene expression profile is associated with lower chromium bioavailability, demonstrated through significantly decreased body burden and sediment concentrations. For example, sediment concentrations at Shipyard Creek were 80-fold greater than NERR in 2000, 51-fold greater in 2003, and only 8-fold greater in 2005. However, hydraulic dredging in 2005 stirred up the sediments and increased body burden of chromium even though chromium sediment concentrations continued to drop. Therefore, the number of differentially expressed genes increased to 9. Overall, the data supports our hypothesis that arrays can be used to monitor site mitigation, as the number of genes differentially expressed mimics the body burden and also indicates when on-site remediation is increasing bioavailability. Keywords: Field site
2006-09-01 | GSE4210 | GEO
Project description:We used the mummichog (Fundulus heteroclitus) array we developed to test whether our arrays could be used to monitor the efficacy of remediation at an estuarine Superfund site. Shipyard Creek is a chromium-contaminated Superfund site in Charleston, SC undergoing remediation, therefore it provides a unique opportunity to study the efficacy of arrays as a molecular biomarker in of toxicant effects in mummichogs. Mummichogs were captured in Shipyard Creek in Charleston, SC prior to remediation (2000), after remediation began (2003), and as remediation further progressed (2005). Simultaneously, mummichogs were collected from a reference site at the Winyah-Bay National Estuarine Research Reserve (NERR). The hepatic gene expression pattern of fish captured at Shipyard Creek showed wide differences from the fish captured at NERR in 2000. As remediation progressed the gene expression pattern of fish captured at Shipyard Creek became increasingly similar to fish captured at NERR, and the number of genes differently expressed dropped from 22 to 4. The magnitude of differential gene expression of the individual genes also decreased during remediation. The recovering gene expression profile is associated with lower chromium bioavailability, demonstrated through significantly decreased body burden and sediment concentrations. For example, sediment concentrations at Shipyard Creek were 80-fold greater than NERR in 2000, 51-fold greater in 2003, and only 8-fold greater in 2005. However, hydraulic dredging in 2005 stirred up the sediments and increased body burden of chromium even though chromium sediment concentrations continued to drop. Therefore, the number of differentially expressed genes increased to 9. Overall, the data supports our hypothesis that arrays can be used to monitor site mitigation, as the number of genes differentially expressed mimics the body burden and also indicates when on-site remediation is increasing bioavailability. Keywords: Field site
2006-09-01 | GSE4211 | GEO
Project description:Adult pike Esox lucius was caught in the end of summer (August, 2020) in Teletskoye Lake (Altai region, west Siberia, Russia, 51°79’10’’ N, 87°30’43’’E). Parasite (Triaenophorus crassus) was retrieved from the intestine of pike and immediately frozen in liquid nitrogen. After that, the sample was lyophilized and sent in ice (-20 °C) to the Group of mass spectrometry of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS (Moscow, Russia) where further analysis was performed.
2021-10-28 | PXD028112 | Pride
Project description:This study examines how aging influences the proteomic landscape of human spermatozoa. Proteomic analysis was done on sperm samples from three groups of normal, fertile men: young adults (21–30 years), late adults (31–40 years), and advanced age (41–51 years). The analysis revealed dynamic age-related alterations in human sperm proteins potentially impacting key sperm physiological functions such as motility, metabolism, and fertilization.
2025-07-21 | PXD062650 | Pride
Project description:Wireless, closed-loop, smart bandage with integrated sensors and stimulators for advanced wound care and accelerated healing
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Project description:Murine tumour infiltrating lymphocytes (CD8+ T cells) were index-sorted based on expression of CD8a and CD3e. Subsequently cDNA was generated from these samples using the Smart-seq2 protocol. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2016-06-01 | E-ERAD-467 | biostudies-arrayexpress
Project description:The objective was to determine age-associated changes in the transcriptome of granulosa cells recovered from the dominant follicle at the time of selection. Granulosa cells were collected from the dominant follicle of aged and young cows after ovariectomy (15 ±1.5 years, n=3 and 6 ± 1.1 years, n=3), or ultrasound-guided follicle aspiration (16±2.1 years, n=4 and 7±1.2 years, 6 ± 1.1 years, n=4) 3-days after ovulation (Day 0). Messenger-RNA was extracted, amplified, labeled with florescent dyes, and hybridized with bovine-specific microarrays (GEO accession # GPL13226). Target intensities were analyzed to determine differential gene expression in granulosa cells from aged vs. young cows. A total 169 genes were differentially expressed (≥ 2 fold-change; P≤0.05) between age groups. In conclusion, granulosa cells collected at the time of selection of the dominant follicle exhibited age-related changes in the transcriptome that may explain follicle-associated loss of oocyte competence in aged cows.
2016-03-31 | GSE52480 | GEO
Project description:The study of genomic imprinting in mammals started with analysis of parthenogenetic embryos. At the phenotypic level, embryos with two maternal genomes and no paternal genome proceed through early development unimpaired, and only begin to fail after implantation. The most recognizable early defect is reduced or non-existent trophoblast, the tissue that gives rise to the placenta. We applied the procedure for establishing Trophoblast Stem cells (TS cells) developed in the Rossant lab to parthenogenetic embryos, and were successful in making four different TS cell lines, three from MI oocyte derived blastocysts and one from MII derived blastocysts. Initial molecular characterization, including microarray analysis, indicates that these cells are indistinguishable from fertilized TS cells, with the single exception of null expression of the paternally expressed gene Snrpn. The only significant difference between parthenogenetic and fertilized TS cells was the frequency with which they could be derived. In our hands, fertilized blastocyst outgrowths produced TS cells at robust rates (10-12 colonies per blastocyst), while parthenogenetic blastocyst outgrowths produced only 4 colonies in 50 outgrowths, 100 times less frequently than fertilized embryos. This led us to hypothesize that those few TS cells that arose in parthenogenetic outgrowths were probably a result of very low frequency stochastic variation in the imprint status of a gene or genes required for either establishment or maintenance of stem cells, or both. The corollary to this hypothesis posits that the early failure of parthenogenetic embryos, and in particular parthenogenetic trophoblast, is a function of impaired stem cell function. This raises the intriguing possibility that microarray comparisons of parthenogenetic, fertilized and androgenetic blastocysts may reveal the identities of genes important for stem cell biology. To this end, my colleague Keith Latham, at the Fels Institute, Temple University, Philadelphia, made amplified cDNAs from pools of ten each of androgenetic, gynogenetic, or fertilized blastocysts. Three separate pools for each type of embryo were prepared for microarray analysis. The embryos were all produced by nuclear transfers between zygotes, a difficult technique that is Keith's special expertise. He used the Brady/Iscove protocol to generate quantitative 3' end biased cDNAs. We would like to compare the transcriptomes of these embryos using the MOE430 2.0 arrays. We expect that important insights into the biology of uniparental embryos in general, and stem cells in particular may be revealed. Keywords: other
2007-12-01 | GSE8163 | GEO