Find research datasets worth reusing

opencc-by-nc-4.0Jul 2018View details →

Outgrowth of tumors in immunocompetent mice expressing libraries of PresentER minigenes

Minigene sequencing of RMA/S tumors expressing libraries of PresentER peptide antigen minigenes after 17 days of growth in immunocompetent mice. "Pool 13" are wild type peptide minigenes. "Pool 18" are mutant peptide minigenes.

opencc-by-4.0Jul 2018View details →

Finding an antibody to detect EZH1 protein expression – Part 1

Finding an antibody to determine EZH1 expression in AML patient cells.

opencc-by-4.0Aug 2018View details →

Analysis of NSD3 Isoform Expression from TCGA-LUSC Data

SGC Open Notebook Project to Characterize the HMTase NSD3 Exp028 Objective: There are two major NSD3 isoforms expressed, long (aa 1-1437) and short (aa 1-645, differing in sequence from 620-645). Importantly, the short isoform was shown to be required for the maintenance of acute myeloid leukemia (AML) [1]. This isoform lacks a SET domain and thus methyltransferase activity. It is not clear if the two isoforms are co-expressed or independently regulated. As a first attempt to study differential regulation of the two isoforms, I have used the TCGA-LUSC dataset to analyze relative expression levels in the context of squamous cell lung cancer (LUSC) [2].  References:  1. Shen C, Ipsaro JJ, Shi J, et al. NSD3-short is an adaptor protein that couples BRD4 to the CHD8 chromatin remodeler. Molecular cell. 2015;60(6):847-859. doi:10.1016/j.molcel.2015.10.033.   2. Weinstein JN, Collisson EA, Mills GB, et al. The Cancer Genome Atlas Pan-Cancer Analysis Project. Nature genetics. 2013;45(10):1113-1120. doi:10.1038/ng.2764.

Collection of graphs presenting gene expression for transgressively down-regulated genes in livers.

Transgressive gene expression was assessed for Cottus lineager of hybrid origing, compared to its parental species. Data contains graphs illustrating gene expression for genes classified af transgressively down-regulated in liver tissues.

Collection of graphs presenting gene expression for transgressively up-regulated genes in fins.

Collection of graphs presenting gene expression for transgressively up-regulated genes in livers.

Collection of graphs presenting gene expression for transgressively down-regulated genes in fins.

opencc-by-4.0Feb 2019View details →

Processed gene expression read counts from the AcLDL and IFNg+Salmonella studies

Raw and normalised read count matrices together with metadata.

opencc-by-4.0Dec 2018View details →

Quantitative data on expression of eve, gt and hb in early Drosophila embryo

This dataset is supplementary to the following manuscript: Svetlana Surkova, Alena Sokolkova, Konstantin Kozlov, Sergey V. Nuzhdin and Maria Samsonova (2019). Quantitative analysis reveals genotype- and domain- specific differences between mRNA and protein expression of segmentation genes in Drosophila. Developmental Biology,  doi: 10.1016/j.ydbio.2019.01.006. The archive contains recently obtained quantitative data on expression of eve, gt and hb in Drosophila early embryo at the level of mRNA and protein. It also includes integrated expression profiles of these genes, combined with the prior datasets (Surkova et al., 2008, Surkova et al., 2013). Embryos are classified into 8 time classes within cleavage cycle 14A. Genotype is specified as “wt” (wild type), “het” (Kr+/Kr- heterozygotes) and "mut" (Kr null mutants). Stained channels: EHG (eve mRNA, hb mRNA, gt mRNA); GGE (gt mRNA, Gt protein, eve mRNA); GE (gt mRNA, eve mRNA); ghe (gt mRNA, Hb protein, eve mRNA); HHE (Hb protein, hb mRNA, eve mRNA); GHH (gt mRNA, Hb protein, hb mRNA). The data are arranged in three folders: 1. QData_norm Includes coordinates and fluorescence intensities of segmented nuclei for each individual embryo after subtraction of non-specific background signal. Files are arranged according to time class (T1-T8) and named according to the following scheme: <stained channel><number>_norm.txt Structure of data file: A-P-coord | D-V-coord | channel 1 | channel 2 | channel 3  2. QData_registered Registered one-dimensional gene expression profiles. Files are arranged according to time class (T1-T8) and named according to the following scheme: <stained channel><number>_reg.txt Structure of data file: Number | A-P-coord | channel 3 | channel 2 | channel 1 3. Integrated_data Integrated one-dimensional profiles of eve, hb and gt expression at mRNA and protein levels for wild type embryos, Kr mutants and Kr+/Kr- heterozygotes. eve and gt profiles were normalized on stripe 1 and second anterior domain respectively (see "Materials and Methods)". Files are named according to the following scheme: <gene><genotype><gene product><time class>_100 Structure of data file: Number | A-P coord of an averaged nucleus | averaged intensity hb profiles are named according to the following scheme: <gene><genotype><gene product><time class> Structure of data file: Number | A-P coord of an averaged nucleus | averaged intensity | standard deviation References <ol> <li>Surkova S., Kosman D., Kozlov K., Myasnikova E., Samsonova A.A., Spirov A., Vanario-Alonso C.E., Samsonova M., Reinitz J. (2008). Characterization of the Drosophila segment determination morphome. Developmental biology 313(2):844-862.</li> <li>Surkova S., Golubkova E., Manu, Panok L., Mamon L., Reinitz J., Samsonova M. (2013) Quantitative dynamics and increased variability of segmentation gene expression in the Drosophila Kruppel and knirps mutants (2013). Dev Biol. 376: 99-112. doi: 10.1016/j.ydbio.2013.01.008.</li> </ol>

opencc-by-4.0Mar 2019View details →

Cloud motion vectors used in "Formation of the Y feature at the Venusian cloud top by planetary-scale waves and the mean circulation: analysis of Venus Express VMC images"

This is dataset  of cloud motion vectors deduced used in "Formation of the Y feature at the Venusian cloud top by planetary-scale waves and the mean circulation:  analysis of Venus Express VMC images".

opencc-by-4.0Apr 2019View details →

Datasets for : High-resolution detection and differential expression analysis of transcription start sites using MAPCap

This dataset corresponds to the study: High-resolution detection and differential expression analysis of transcription start sites using MAPCap (Bhardwaj et. al. 2018) It includes:  - TSS identified using MAPCap in stage 15 embryos and larvae.  - Differentially expressed TSS using MAPCap (FDR < 0.05) in larvae.  - Common and stage-specific enhancer TSS identified in this study

FIGURE 8 in The RNA-seq approach to discriminate gene expression profiles in response to Beauveria bassiana and Micrococcus luteus microbial pathogens on Actias selene (Lepidoptera: Saturniidae)

FIGURE 8. Phylogenetic analysis was performed using the MEGA (version 5.0) program based on the four different amino acid sequences from various insects. The phylogenetic tree was constructed using the neighbor-joining algorithm method and bootstrap values (1000 repetitions) of the branches are indicated. The HSP90s from other organisms are: Antheraea pernyi (APX61061.1), Helicoverpa armigera (ATB54999.1), Spodoptera litura (ADK55517.2), Mythimna separata (ATN45250.1), Danaus plexippus plexippus (OWR53421.1), Bombyx mori (NP_001036876.1), Apis mellifera (NP_001153536.1), Plutella xylostella (NP_001296043.1), Drosophila melanogaster (NP_523899.1), Nilaparvata lugens (XP_022202749.1), Bicyclus anynana (XP_023945769.1);The PGRPs from other organisms are: Antheraea pernyi (AME17978.1), Samia ricini (BAF03522.1), Trichoplusia ni (XP_026737257.1), Helicoverpa armigera (AHK59818.1), Antheraea mylitta (ABG72709.1), Manduca sexta (AAO21509.1), Spodoptera litura (XP_022825445.1), Bombyx mori (NP_001036836.1);The Ras homolog genes from other organisms are: Spodoptera litura (XP_022819713.1), Vanessa tameamea (XP_026494920.1), Zootermopsis nevadensis (XP_021927562.1), Drosophila miranda (XP_017145574.1), Drosophila persimilis (XP_002015385.2), Nasonia vitripennis (XP_008209835.1); The MyD88s from other organisms are: Diaphorina citri (NP_001316117.1),Tribolium castaneum (XP_008190563.1), Drosophila melanogaster (NP_610479.1), Nasonia vitripennis (XP_008206894.1), Ceratitis capitata (XP_020716287.1), Bactrocera dorsalis (XP_011205590.1), Bombus terrestris (XP_003394201.1), Bombyx mori (XP_004921572.1), Antheraea pernyi (AHH80650.1).

FIGURE 7 in The RNA-seq approach to discriminate gene expression profiles in response to Beauveria bassiana and Micrococcus luteus microbial pathogens on Actias selene (Lepidoptera: Saturniidae)

FIGURE 7. RT-qPCR analysis of 11 immune-related DEGs in ML vs. PBS group. The y-axis shows relative expression levels (Blue colour represents the PBS control group and yellow colour represents the M. luteus treatment group, * p <0.05, **p <0.01).

FIGURE 6 in The RNA-seq approach to discriminate gene expression profiles in response to Beauveria bassiana and Micrococcus luteus microbial pathogens on Actias selene (Lepidoptera: Saturniidae)

FIGURE 6. RT-qPCR analysis of 19 immune-related DEGs in Bb vs. PBS group. The y-axis shows relative expression levels (Blue colour represents the PBS control group and red colour represents the B. bassiana treatment group, * p <0.05, **p <0.01).

FIGURE 4 in The RNA-seq approach to discriminate gene expression profiles in response to Beauveria bassiana and Micrococcus luteus microbial pathogens on Actias selene (Lepidoptera: Saturniidae)

FIGURE 4. GO classification of annotated differentially expressed genes in Bb vs. PBS group. The DEGs were categorized into 41 functional groups and were summarized in three main categories: biological process, cellular component and molecular function. The X-axis represents the number of genes noted on the GO item, and the Y-axis represents the GO functional classification.

FIGURE 5 in The RNA-seq approach to discriminate gene expression profiles in response to Beauveria bassiana and Micrococcus luteus microbial pathogens on Actias selene (Lepidoptera: Saturniidae)

FIGURE 5. GO classification of annotated differentially expressed genes in ML vs. PBS group. The DEGs were categorized into 41 functional groups and were summarized in three main categories: biological process, cellular component and molecular function. The X-axis represents the number of genes noted on the GO item, and the Y-axis represents the GO functional classification.

FIGURE 3 in The RNA-seq approach to discriminate gene expression profiles in response to Beauveria bassiana and Micrococcus luteus microbial pathogens on Actias selene (Lepidoptera: Saturniidae)

FIGURE 3. KEGG classification map of differentially expressed genes in ML vs. PBS group. The X axis was the number of genes annotated into a certain KEGG Pathway category, and the Y axis was the KEGG Pathway category. Different colors present different metabolic functions.

FIGURE 2 in The RNA-seq approach to discriminate gene expression profiles in response to Beauveria bassiana and Micrococcus luteus microbial pathogens on Actias selene (Lepidoptera: Saturniidae)

FIGURE 2. KEGG classification map of differentially expressed genes in Bb vs. PBS group. The X axis was the number of genes annotated into a certain KEGG Pathway category, and the Y axis was the KEGG Pathway category. Different colors present different metabolic functions.

openother-openJul 2019View details →

Absorption-Based Query Answering for Expressive Description Logics : Evaluation Data

Sources ( <code>Sources.zip</code> ), evaluation data ( <code>Evaluation.zip</code> ) with all ontologies and queries, as well as the evaluation results ( <code>Results.zip</code> ) of the publication "Absorption-Based Query Answering for Expressive Description Logics" from the 18th International Semantic Web Conference (ISWC), October 26-30, 2019, Auckland, New Zealand. For easily reproducing the evaluation, you can also use the Docker image koncludeeval/abqa (available at <a href="https://hub.docker.com/r/koncludeeval/abqa">https://hub.docker.com/r/koncludeeval/abqa</a>). See also readme files in archives for more details. You may only use/share/etc. the included reasoners/ontologies as restricted by their licences (see <code>Sources.zip</code>). In particular, Konclude and OWL BGP are available under the LGPLv3 (<a href="https://www.gnu.org/licenses/lgpl-3.0.en.html">https://www.gnu.org/licenses/lgpl-3.0.en.html</a>), Pellet under the AGPLv3 (<a href="https://www.gnu.org/licenses/agpl-3.0.en.html">https://www.gnu.org/licenses/agpl-3.0.en.html</a>), and PAGOdA under an Academic Licence (<a href="http://www.cs.ox.ac.uk/isg/tools/PAGOdA/PAGOdA_Academic_Licence.txt">http://www.cs.ox.ac.uk/isg/tools/PAGOdA/PAGOdA_Academic_Licence.txt</a>).