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393 results for “MEF”
Super-resolved Reflectance Confocal Microscopy data on Diatom shells and live MEF cells
<p>This dataset is linked to a paper submission in Open Research Europe. It contains the RAW data of confocal reflectance super-resolved point spread function, diatom shell zstack and time lapse imaging of a living Mouse Embryonic Fibroblast cell. </p>
Super-resolved Reflectance Confocal Microscopy time-lapse imaging of a living MEF cell lamellipod
<p>This movies presents a time-lapse of a label-free living Mouse embryonic fibroblast cell observed with super-resolved rescanned reflectance confocal microscopy.. </p>
Transcriptome analysis of WT versus H2A.J-KO MEFs for the paper entitled: The H2A.J histone variant contributes to Interferon-Stimulated Gene expression in senescence by its weak interaction with H1 and the derepression of repeated DNA sequences
<p>Abstract for overall study:</p> <p>The histone variant H2A.J was previously shown to accumulate in senescent human fibroblasts with persistent DNA damage to promote inflammatory gene expression, but its mechanism of action was unknown. We show that H2A.J accumulation contributes to weakening the association of histone H1 to chromatin and increasing its turnover. Decreased H1 in senescence is correlated with increased expression of some repeated DNA sequences, increased expression of STAT/IRF transcription factors, and transcriptional activation of Interferon-Stimulated Genes (ISGs). The H2A.J-specific Val-11 moderates the transcriptional activity of H2A.J, and H2A.J-specific Ser-123 can be phosphorylated in response to DNA damage with potentiation of its transcriptional activity by the phospho-mimetic S123E mutation. Our work demonstrates the functional importance of H2A.J-specific residues and potential mechanisms for its function in promoting inflammatory gene expression in senescence.</p> <p>Specific description for this dataset:</p> <p>We further tested a role for H2A.J in Interferon-Stimulated Gene expression by analyzing the transcriptome of WT and H2A.J MEFs induced into senescence by etoposide. TruSeq stranded DNA libraries were prepared from polyA-selected RNA and sequenced as 43 bp paired-end reads. The fastq sequences were mapped to Gencode.vM24.transcripts.fa.gz (GRCm38 transcriptome) with salmon. Read counts were then aggregated to the gene level with tximeta, and differential gene expression was analysed with DESeq2, edgeR, and limma-voom. Gene set enrichment analysis was performed with camera.</p> <p>The transciptomes of senescent WT and H2AFJ-KO showed strong separation from proliferating MEFs, and a weaker separation distinguished WT and H2A.J-KO MEFs. Strikingly, gene set enrichment analysis indicated highly significant defects in Interferon Response Gene Expression in the H2A.J-KO MEFs in senescence with significant down-regulation in senescent H2A.J-KO cells of a series of oligoadenylate synthase genes (Oas1g, Oas1a, Oasl1, Oas2, Oasl2) and several ISGs. Thus, H2A.J also contributes to ISG expression in the heterologous context of senescent MEFs.</p>
Development of a multi-excitation fluorescence (MEF) imaging method to improve the information content of benthic coral reef surveys
<p>Benthic surveys are a key component of monitoring and conservation efforts for coral reefs worldwide. While traditional image-based surveys rely on manual annotation of photographs to characterise benthic composition, automatic image annotation based on computer vision is becoming increasingly common. However, accurate classification of some benthic groups from reflectance images presents a challenge to local ecologists and computers alike. Most coral reef organisms produce one or a combination of fluorescent pigments, such as Green Fluorescent Protein (GFP)-like proteins found in corals, chlorophyll-a found in all photosynthetic organisms, and phycobiliproteins found in red macroalgae, crustose coralline algae (CCA) and cyanobacteria. Building on the potential of these pigments as a target for automatic image annotation, we developed a novel imaging method based on off-the-shelf components to improve classification of coral and other biotic substrates using a multi-excitation fluorescence (MEF) imaging system. We used RGB cameras to image the fluorescence emission of coral and algal pigments stimulated by narrow-waveband blue and green light, and then combined the information into 3-channel pseudocolour images. Using a set of <i>a priori</i> rules defined by the relative pixel intensity produced in different channels, the method achieved successful classification of organisms into three categories based on the dominant fluorescent pigment expressed, facilitating discrimination of traditionally problematic groups. This work provides a conceptual foundation for future technological developments that will improve the cost, accuracy and speed of coral reef surveys.</p>
Development of a multi-excitation fluorescence (MEF) imaging method to improve the information content of benthic coral reef surveys
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Next-generation sequencing analysis of chemically induced neurons from wild type (WT), Actb+/- (HET) and Actb-/- (KO) mouse embryonic fibroblasts (MEFs)
GEO Series GSE113733. Mus musculus. 9 samples. Type: Expression profiling by high throughput sequencing.
ATAC-seq data in MEF and mESC sequenced by BGI DNBSEQ-G400 platform and Illumina HiseqX10 instruments
GEO Series GSE201577. Mus musculus. 12 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Chip-chip from MEF cells with H3ac, H4ac, H4K20me1, H3K27me3, H3K9me3, H4K20me3, H3K4me2, H3K4me3 and H3K9ac
GEO Series GSE11335. Mus musculus. 34 samples. Type: Genome binding/occupancy profiling by genome tiling array.
Identification of E2F targets in MEFs
GEO Series GSE71376. Mus musculus. 5 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Bcl11b and Atoh8 binding on chromatin in MEFs
GEO Series GSE181196. Mus musculus. 9 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
MEF-CM and UM_GTA re-stimulation experiment with human ES cells
GEO Series GSE9059. Homo sapiens. 3 samples. Type: Expression profiling by array.
RNA Seq analysis of Mefs Isolated from STC1+/+ and STC1-/- mice
GEO Series GSE47395. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Next Generation Sequencing Facilitates Quantitative Analysis of interferon stimulated MEFs Transcriptomes [RNA-Seq]
GEO Series GSE89349. Mus musculus. 10 samples. Type: Expression profiling by high throughput sequencing.
Identification of genes upregulated and downregulated in mouse embryonic fibroblasts (MEFs) upon Atoh8 depletion
GEO Series GSE143592. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
Gene expression profiling of late reprogramming stages during in vitro reprogramming of mouse embryonic fibroblasts (MEFs) to induced pluripotent stem cells (iPSCs)
GEO Series GSE119830. Mus musculus. 42 samples. Type: Expression profiling by high throughput sequencing.
Synertistic effects of Arid1a inactivation and oncogenic Kras mutation on chromatin accessbility in mouse embryonic cells (MEFs)
GEO Series GSE207888. Mus musculus. 12 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
ChIP-seq of E4F1 in primary mouse embryonic fibroblasts (MEFs) and in p53-/-, Ha-RasV12-transformed MEFs
GEO Series GSE57228. Mus musculus. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Identification of genes regulated by Rb in wild-type and SREBP1 KO MEFs
GEO Series GSE90571. Mus musculus. 16 samples. Type: Expression profiling by array.
Genome-wide mapping of 8-oxodG and gH2AX in growing MCF10A cells and MEFs
GEO Series GSE100234. Homo sapiens; Mus musculus. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Analysis of gene expression in control, Hic1 KO and p53 KO mouse embrynoic fibroblast (MEF) cell lines II
GEO Series GSE104393. Mus musculus. 9 samples. Type: Expression profiling by array.
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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)
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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.