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Dataset results
600 results for “Contamination”
High-throughput 16S rRNA amplicon pyrosequencing of contaminated aquifer sediment
GEO Series GSE25345. aquifer metagenome. 15 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Breast cancer and liver tissue biopsies used to develop and validate an index for liver contamination in metastatic breast cancer
GEO Series GSE33116. Homo sapiens. 203 samples. Type: Expression profiling by array.
Gonadal transcriptome analysis of wild contaminated female European eels during artificial gonad maturation
GEO Series GSE64278. Anguilla rostrata; Anguilla anguilla. 15 samples. Type: Expression profiling by array.
High contaminant loads in Lake Apopka mesocosms affect the ovarian transcriptome in largemouth bass
GEO Series GSE38774. Micropterus salmoides. 20 samples. Type: Expression profiling by array.
Effects-based Monitoring of Contaminants of Emerging Concern in Great Lakes Tributaries: Calculating the Risk of Fish Developing Liver Toxicity and Cancer
GEO Series GSE146903. Homo sapiens. 71 samples. Type: Expression profiling by high throughput sequencing.
Novel Bioinformatic Analyses of Somatic Cell Contamination in Sperm Samples
GEO Series GSE246935. Homo sapiens. 16 samples. Type: Methylation profiling by array.
Application of Transcriptomics Dose-Response Modeling to Risk-Based Prioritization of Contaminants Detected in Tributaries of the North American Great Lakes [D. magna]
GEO Series GSE269991. Daphnia magna. 335 samples. Type: Expression profiling by high throughput sequencing.
Enhanced plasmid mediated bioaugmentation of RDX contaminated matrices in column studies using donor strain Gordonia sp. KTR9 [exp1]
GEO Series GSE125548. Rhodococcus jostii RHA1; Gordonia sp. KTR9. 6 samples. Type: Expression profiling by array.
Application of BiodegPhyloChip for expression profiling of functional genes from diverse contaminated habitats
GEO Series GSE38004. synthetic construct; soil metagenome. 12 samples. Type: Genome variation profiling by array; Expression profiling by array.
High contaminant loads in Lake Apopka mesocosms affect the ovarian transcriptome in largemouth bass [April]
GEO Series GSE38738. Micropterus salmoides. 8 samples. Type: Expression profiling by array.
Reproductive biomarker response to PFAS-contaminated groundwater [testis]
GEO Series GSE261668. Pimephales promelas. 22 samples. Type: Expression profiling by array.
Transcriptional profiling of the soil invertebrate (Folsomia candida) in pentachlorophenol contaminated soil
GEO Series GSE52893. Folsomia candida. 12 samples. Type: Expression profiling by array.
Impact of Hb contamination in obtaining reference profiles of exRNAs in healthy individuals
GEO Series GSE221312. Homo sapiens. 12 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Somatic Cell Contamination as an Inhibitor of Proper Sperm Methylation Analysis
GEO Series GSE237402. Homo sapiens. 48 samples. Type: Methylation profiling by array.
Source-tracking fecal contamination by genomic analysis of Escherichia coli from human and animal hosts
GEO Series GSE21115. Escherichia coli str. K-12 substr. MG1655; Escherichia coli. 24 samples. Type: Genome variation profiling by array.
Collection of AP residues from regions related to AP Waste (APW) mismanagement, potentially contaminated by MNP-Italy
<p>Part of D1.6, Chapter 2.2</p>
Taxonomic and functional diversity of the microbiome in a jet fuel contaminated site as revealed by combined application of in situ microcosms with metagenomic analysis
<p>Natural attenuation represents all processes that govern contaminant mass removal, which mainly occurs via microbial degradation in the environment. Although this process is intrinsic its rate and efficiency depend on multiple factors. This study aimed to characterize the microbial taxonomic and functional diversity in different aquifer sediments collected in the saturated zone and <em>in situ</em> microcosms (BACTRAP®s) amended with hydrocarbons (<sup>13</sup>C-labeled and non-labeled benzene, toluene and naphthalene) using 16S rRNA gene and “<em>shotgun</em>” Illumina high throughput sequencing at a jet-fuel contaminated site. The BACTRAP®s were installed to assess hydrocarbon metabolism by native bacteria. Results indicated that Proteobacteria, Actinobacteria and Firmicutes were the most dominant phyla (~98%) in the aquifer sediment samples. Meanwhile, in the benzene- and toluene-amended BACTRAP®s the phyla Firmicutes and Proteobacteria accounted for about 90% of total community. In the naphthalene-amended BACTRAP®, members of the SR-FBR-L83 family (Order Ignavibacteriales) accounted for almost 80% of bacterial community. Functional annotation of metagenomes showed that only the sediment sample located at the source zone border and with the lowest BTEX concentration, has metabolic potential to degrade hydrocarbons aerobically. On the other hand, <em>in situ</em> BACTRAP®s allowed enrichment of hydrocarbon-degrading bacteria. Metagenomic data suggest that fumarate addition is the main mechanism for hydrocarbon activation of toluene. Also, indications for methylation, hydroxylation and carboxylation as activation mechanisms for benzene anaerobic conversion were found. After 120 days of exposure in the contaminated groundwater, the isotopic analysis of fatty acids extracted from BACTRAP®s demonstrated the assimilation of isotopic labeled compounds in the cells of microbes expressed by strong isotopic enrichment. We propose that the microbiota in this jet-fuel contaminated site has metabolic potential to degrade benzene and toluene by a syntrophic process, between members of the families Geobacteraceae and Peptococcaceae (genus <em>Pelotomaculum</em>), coupled to nitrate, iron and/or sulfate reduction.</p>
Single channel approach for filtering electroencephalographic signals strongly contaminated with facial electromyography
<p><strong>Data: EEG contaminated by facial EMG</strong></p> <p> </p> <p>The dataset contains the EMG and EEG signals collected for the study of contamination by facial EMG on EEG.</p> <p> </p> <p>For each volunteer (S1 to S10), there are five “.mat” files, referring to the five muscles activated to generate contamination of facial EMG on EEG.</p> <p>For each muscle there are some variables:</p> <p>1. <strong>amplifier_data</strong>:</p> <p>It is a matrix with the EMG (card A) and EEG (card B) signals collected. The</p> <p>amplifier_channels structure and the t_amplifier vector refere to <strong>amplifier_data</strong></p> <p>matrix.</p> <p>2. <strong>board_dig_in_data</strong>:</p> <p>As expected in the experimental protocol, the collection is performed with the</p> <p>eyes in two states: only open and only closed. The <strong>board_dig_in_data </strong>variable</p> <p>contains digital values (0 or 1). The first moment containing 1s marks the</p> <p>beginning of the eye-open-only state and the second moment indicates the eye-closed-only state. The board_dig_in_channels structure and the t_dig vector refere</p> <p>to <strong>board_dig_in_data </strong>variable.</p> <p>3. <strong>supply_voltage_data</strong>:</p> <p>Data collection is performed by two acquisition cards, A(EMG) and B(EEG). The</p> <p>supply voltage of each card is monitored, and the measured values are stored in</p> <p>this variable. The supply_voltage_channels structure and the t_supply_voltage</p> <p>vector refere to <strong>supply_voltage_data </strong>variable.</p> <p> </p> <p><strong>EMG and EEG data</strong></p> <p>The data of interest for the collection are in the <strong>amplifier_data </strong>variable, a matrix</p> <p>with n rows and m columns, where n is the number of channels (EMG and EEG) and m is the number of data acquired at the sampling frequency for the entire collection time interval. EMG channels are collected by “Port A”, and EEG channels are collected by “Port B”, but all EMG and EEG data are in the same <strong>amplifier_data </strong>variable. The name “Port A” or “Port B” comes from the choice of cable used to connect the acquisition cards to the RHD2000 USB interface system. Thus, based on the choice adopted in connecting the EMG and EEG cards in this research, the <strong>amplifier_data </strong>variable has the first lines belonging to “Port A” (EMG) and the other lines of the matrix being from “Port B” (EEG). The amplifier_channels structure indicates which card was used with the name “Port A” and “Port B” in the port_name field.</p> <p> </p> <p><strong>EMG data</strong></p> <p>The muscle signal data does not have a specific and fixed channel between collections. Thus, the channel number for a muscle must be verified at each data collection. The information for each channel must be consulted in the amplifier_channels structure at the custom_channel_name field.</p> <p> </p> <p><strong>EEG data</strong></p> <p>A bipolar 16-channel acquisition card acquires EEG signals. The channels of each</p> <p>EEG sensor are the same for all collections, thanks to the use of the adapted EEG cap, and the connection of the EEG signals card is always carried out on the same cable B. The EEG cap has bipolar transverse mounting configuration.</p> <p> </p> <p>EEG sensors channel list, channel x EEG sensor:</p> <p>Ch00: F3-Fz; Ch01: F4-F8; Ch02: F7-F3; Ch03: Fp1-Fp2;</p> <p>Ch04: T3-C3; Ch05: C4-T4; Ch06: T5-P3; Ch07: P4-T6;</p> <p>Ch08: Fp2-F8; Ch09: F7-Fp1; Ch10: Fz-F4; Ch11: Cz-C4;</p> <p>Ch12: O1-O2; Ch13: P3-Pz; Ch14: Pz-P4; Ch15: C3-CZ.</p>
Microbial diversity of an uncontaminated and a 2,4,6-TNT contaminated soil sample with CodeLink microarrays
GEO Series GSE3525. Pseudomonas putida; unidentified. 12 samples. Type: Other.
Bryophyte bacterial contamination 16s sequencing
<p>List of all sequenced 16s bacterial colonies from bryophyte contamination.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.