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253
datasets available to search
ShareScore release 0.9.0
Dataset results
253 results for “amplicons”
Naringenin confers protection against experimental autoimmune encephalomyelitis through the gut-brain axis by combining metabolomics, gene expression, and amplicon sequencing
GEO Series GSE238061. Mus musculus. 10 samples. Type: Expression profiling by high throughput sequencing.
16S Amplicon sequence variants (ASVs) data of NEREA Augmented Observatory
<p>Cleaned raw 16S paired-end sequences were imported into the QIIME2 pipeline v. 2022.2.0. Leftover primers and adapters’ sequences were removed through cutadapt. The amplicon sequence variants (ASV) table, which represent true biological sequences within each sample, was generated using the denoised-paired method including truncation, denoising, dereplication, and chimera filtering of the DADA2 (Divisive Amplicon Denoising Algorithm 2) plugin inside QIIME2. Default parameters were used with the exception of the forward and reverse sequence length (--p-trunc-len-f and --p-trunc-len-r), that were set to 220 and 180, respectively. For taxonomy classification, the V4-V5 region were extracted from the pre-formatted reference sequences and taxonomy file build on the SILVA 138 99% OTUS database and the vsearch v. 2.6.2 global alignment implemented in QIIME2 was used.</p>
18S Amplicon sequence variants (ASVs) data of NEREA Augmented Observatory
<p>The quality of the Illumina paired-end V9-18S raw reads (FASTQ format, 2 X 150 PE) was checked using vsearch (vsearch --fastq_stats), then pre-processed with cutadapt and vsearch to remove primer sequences, trim low quality bases and unify mixed orientation reads produced in the ligation-based library preparation. Processed reads were then used to generate amplicon sequence variants (ASVs) using the DADA2 R library; the pipeline was adapted from the one described on the program website (https://benjjneb.github.io/dada2/tutorial.html); no further quality filtering was implemented at this stage, except for discarding all reads with ambiguities (parameter maxN=0 of function filterAndTrim). Filtered F and R reads were used to train the error model and then denoised by applying the trained error model to generate ASVs. Finally, F and R reads were merged and checked for chimeras; up to 9 mismatches were allowed for read merging (parameter maxMismatch=9 of function mergePairs). ASVs were then classified with BLAST against the PR2 v5.01 reference database, integrated with 1293 sequences from Gulf of Naples protist strains and fungi environmental sequences. Highest bit score matches with the best taxonomic resolution were then selected among the returned results.</p>
Extrachromosomal circular SUZ12 amplicon dictates retinoblastoma progression through reprogramming H3K27 methylation [eccDNA-seq]
GEO Series GSE235888. Homo sapiens. 5 samples. Type: Other.
Improved split prime editors enable efficient in vivo genome editing [Amplicon_Seq_in_vitro]
GEO Series GSE270854. Homo sapiens; Mus musculus. 193 samples. Type: Other.
Extrachromosomal circular SUZ12 amplicon dictates retinoblastoma progression through reprogramming H3K27 methylation [CUT&Tag]
GEO Series GSE239785. Homo sapiens. 14 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Analyzing the process of mutation accumulation in MEK1 evolution experiment using amplicon sequencing
GEO Series GSE235328. Mesocricetus auratus. 2 samples. Type: Other.
A genetic disorder reveals a hematopoietic stem cell regulatory network co-opted in leukemia [amplicon-seq]
GEO Series GSE175518. Homo sapiens. 942 samples. Type: Other.
Analyzing the process of mutation accumulation in KRAS evolution experiment using amplicon sequencing
GEO Series GSE235327. Mesocricetus auratus. 8 samples. Type: Other.
The 8p11-p12 amplicon oncogene ASH2L regulates expression of genes involved in tumorigenic processes via promoter H3K4me3 in luminal breast cancer. (SUM-44 ASH2L knockdown H3K4me3 ChIP-seq)
GEO Series GSE99669. Homo sapiens. 12 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Robust regulatory interplay of enhancers, facilitators, and promoters in a native chromatin context [amplicon sequencing]
GEO Series GSE299355. Homo sapiens. 18 samples. Type: Other.
Example datasets from 16S rRNA amplicon Illumina paired end sequencing
<p>Six example datasets from 16S rRNA amplicon Illumina paired-end sequencing. </p>
The molecular raw data of microbial communities associated with fish gut - in vitro model system using 16S rRNA Illumina amplicon sequencing approach.
<p>This data on the microbial communities and its diversity associated with fish gut. The samples were obtained from fish gut - in vitro model system using 16S rRNA Illumina amplicon sequencing approach.</p>
ScienceDex guides
Understand access before you commit
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.