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915
datasets available to search
ShareScore release 0.7.1
Dataset results
915 results for “metagenomics”
Metagenomic analysis of phytoplasma infected apple trees
GEO Series GSE306190. Malus domestica. 6 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Human Pegivirus detected in a patient with severe encephalititis using a metagenomic pan-virus array
GEO Series GSE67021. Homo sapiens; synthetic construct. 2 samples. Type: Other.
Metagenomic sequencing and 16S rRNA sequence of gut microbiota associated with autism spectrum disorders patients
GEO Series GSE113701. feces metagenome. 346 samples. Type: Other.
Transepithelial barrier dysfunction drives microbiota dysbiosis to initiate epithelial clock-driven inflammation [metagenome]
GEO Series GSE212393. Mus musculus. 10 samples. Type: Other.
Test data for metagenome-atlas
<p>Two simulated metagenome samples which could generate some MAGs</p>
Data for "Uncovering natural sources of LAB bacteriocins through the use of metagenomics"
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Reads of the iMESS simulated metagenomic datasets
<p>Reads of the iMESS simulated metagenomic datasets</p>
Triglyceride Reduction in Mice Receiving Gut Microbiota Transplants from Patients with Chronic Hepatitis B: A Whole Metagenomic Shotgun Sequencing Study
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BACTERIAL_GENOME_METAGENOMICS_FINAL_EXAM
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Integrating Plasma Metagenomics and Host Response for Accurate Diagnosis of Infected Pancreatic Necrosis in a Prospective Multicenter Cohort of Acute Necrotizing Pancreatitis
ClinicalTrials.gov study NCT07308600. IPD Sharing: Not stated. Countries: 0. Publications: 0.
Discovery of Microbiome-based Biomarkers for Patients With Cancer Using Metagenomic Approach
ClinicalTrials.gov study NCT04567446. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Metagenomic and Immune-inflammatory Analysis of Individuals With Generalized Aggressive Periodontitis and Their Descendants.
ClinicalTrials.gov study NCT03933514. IPD Sharing: UNDECIDED. Countries: 0. Publications: 0.
The Value of Full-targeted Pathogen Capture Metagenomics Next Generation Sequencing in Etiological Diagnosis of Sepsis
ClinicalTrials.gov study NCT05540808. IPD Sharing: NO. Countries: 0. Publications: 0.
Bioinformatics approaches for viral metagenomics in plants using short RNAs : model case of study and application to a Cicer arietinum population
GEO Series GSE63378. Cicer arietinum. 1 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Integrated host-microbe metagenomics of cell-free nucleic acid for sepsis diagnosis in critically ill adults
GEO Series GSE189403. Homo sapiens. 359 samples. Type: Expression profiling by high throughput sequencing.
Metagenome profiling of feces from mice flown on the RRRM-1 mission
In Rodent Research Reference Mission-1 (RRRM-1), forty female BALB/cAnNTac mice were flown on the International Space Station. To assess differences in outcomes due to age, twenty 10-12 week-old and twenty 32 week-old mice were flown, respectively. To directly assess spaceflight effects, half of the young and old mice (10 old, 10 young) were sacrificed on-orbit after 22-23 days (ISS Terminal, ISS-T), while the other half (10 old, 10 young) were returned live to Earth after 40 days and allowed to recover for 2 days (Live Animal Return, LAR) before sacrifice. Both the ISS-T and LAR animals had independent ground controls (10 mice housed in flight hardware in matched environmental conditions), basal controls (10 mice sacrificed 1 day after launch), and vivarium controls (10 mice housed within standard vivarium habitats). Thus RRRM-1 included a total of 160 mice. Feces were removed from 145 animals and preserved by flash freezing in liquid nitrogen and stored at -80 ˚C until DNA was extracted, and libraries generated and sequenced (target 10 M clusters per sample, PE 251 bp). This dataset features whole-genome shotgun metagenomics sequencing data from 8-10 feces samples per group.
Metagenomic analysis of feces from mice flown on the RR-6 mission
The objective of the Rodent Research-6 (RR-6) study was to evaluate muscle atrophy in mice during spaceflight and to test the efficacy of a novel therapeutic to mitigate muscle wasting. The experiment involved an implantable subcutaneous nanochannel delivery system (nDS; between scapula), which delivered the drug formoterol (FMT; a selective β2 adrenoceptor agonist), over the course of time. To this end, a cohort of forty 32-weeks-old female C57BL/6NTac mice were either sham operated or implanted with vehicle or treatment-filled nDS, launched in two Transporters (20 mice per Transporter) on SpaceX-13 on December 15, 2017. They were transferred to Rodent Habitats onboard the International Space Station (ISS), and maintained in microgravity for 29 days (N=20, Live Animal Return Spaceflight [LAR FLT]), or >50 days (N=20, ISS Terminal Spaceflight [ISS-T FLT]). After 29 days, the 20 LAR FLT animals were returned live to back to Earth on January 13, 2018. After splashdown, the animals were ambulatory on-ground for ~4 days, until all subjects were processed during one day of dissections. There were two Basal (BSL) groups of animals sacrificed (LAR BSL & ISS-T BSL; N=20; 40 animals; ~36 weeks old) at Kennedy Space Center (KSC; 12/9/17). LAR BSL animals were dissected, and samples were collected upon euthanasia. A Ground Control (GC) group, LAR GC, mimicked the LAR FLT group, which was housed at KSC, then shipped alive, to Novartis’s Facilities, where both the LAR FLT and LAR GC groups were processed (~41 weeks old; 1/16/18). All were anesthetized with isoflurane, blood samples were obtained by closed-chest cardiac puncture, and the animals were euthanized by exsanguination and thoracotomy. The 20 ISS-T FLT mice were anesthetized via intraperitoneal injection of ketamine/xylazine/acepromazine over the course of a four days of dissections (2/6/18 until 2/9/18; 53-56 days after launch; 44 weeks old at time of on-orbit dissections). Blood samples and euthanasia were conducted the same as LAR groups. Following blood draw and hind limb dissection, the ISS-T FLT animal carcasses were wrapped in aluminum foil, placed in a ziploc bag and placed in storage at -80˚C or colder until return. The ISS-T Ground Control (ISS-T GC) (at KSC) followed the same euthanasia timeline, methods, and preservation. The final processing of frozen ISS-T FLT, frozen ISS-T GC and frozen 0-day ISS-T BSL animals were completed at Houston Methodist Research Institute, in Houston, TX (5/21/18 until 5/24/18). GeneLab received feces from only sham treated animals (no drug treated animals) from the following groups. FLT: LAR (n=9), ISS-T (n=7); GC: LAR (N=7), ISS-T (N=9); BSL: LAR (n=7), ISS-T (n=9). DNA was extracted and analyzed by sequencing using a variety of different targeted and un-targeted metagenome profiling assays.
Metagenome profiling of feces from mice flown on the RR-23 mission
The objective of the RR-23 mission was to better understand the effects of spaceflight on the eyes, specifically on the structure and function of the arteries, veins, and lymphatic vessels that are needed to maintain vision. To this end, twenty male, C57BL/6J, 16-17 weeks-old mice were delivered to the ISS on SpaceX-21 in a single transporter, transferred to two rodent habitats, and maintained in microgravity for 38 days. Flight mice were then returned to Earth alive (Jan 13th, 2021). After splashdown in the Atlantic Ocean, mice were transported to Kennedy Space Center via helicopter. The 20 Flight, 20 Habitat Ground Control (HGC), and 20 Vivarium Ground Control (VGC) mice were removed from Rodent Transporters (Flight and HGC) or vivarium cages (VGC), placed into shipping containers, and flown to Texas A and M University. There, mice underwent post-flight procedures, before euthanasia and tissue collection. Flight, HGC and VGC animals were euthanized and dissected on Jan 14th, 17th or 20th of 2021, respectively. Feces were removed from the animals and preserved by flash freezing in liquid nitrogen and stored at -80 ˚C until DNA was extracted, and libraries generated and sequenced (target 10 M clusters per sample, PE 250 bp). This dataset features 9 samples from the Flight group, 9 samples from the HGC group, and 9 samples from the VGC group.
SpaceX Inspiration4 Oral, Nasal, and Skin Metagenomic and Metatranscriptomic Microbial Swabs
The SpaceX Inspiration4 mission was a 3-day mission with four private astronauts to low Earth orbit that occurred in September 2021. The crew collected biospecimen samples before, during, and after flight. One of these biospecimen collections included oral, nasal, and skin microbial swabs collected from ten locations (oral, nasal cavity, post-auricular, axillary vault, volar forearm, occiput, umbilicus, gluteal crease, glabella, and toe web space). Skin swabs were first dipped in nuclease-free water before swabbing each region for 30 seconds. Oral and nasal swabs did not include this swab-wetting step. Nuclease-free water samples were sequenced as controls. Swabs were collected at three pre-flight timespoints (L-92, L-44, L-3), two in-flight timepoints (flight day 2 (FD2), and flight day 3 (FD3)), and three post-flight timepoints (R+1, R+45, R+82). Swabs were stored in 400uL of Zymo Research DNA/RNA Shield at 4C until nucleic acid extraction. DNA and RNA were extracted from the same swab to generate metagenomic and metatranscriptomic profiles.
Sphingomonas Metagenomic assembly
Metagenome Assembled Genome (MAG) of Sphingomonas sanguinis from the International Space Station metagenome
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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.