The IgY antivenom CDR sequences were determined

The IgY antivenom CDR sequences were determined from immunized B cells by amplification of VL and VH chain genes, preparation of IgY chain double-strand cDNAs, and clonal selection and sequencing of hyper-variable regions of IgY genes. The obtained sequences were submitted to Blast analysis, and the gene sequences corresponding to CDR1, CDR2 and CDR3 in IgY VL and VH anti-Bitis arietans (Ba) or C. d. terrific sequences were amplified. The encoding gene sequences and the translated amino Methods sequences served to construct an IgY 3D molecule model.
Experimental design, materials and methods
Data The data presented here includes the full list of proteins identified in the ventricles of juvenile rainbow trout hearts, and the quantitative changes to these proteins during exercise training. Mass spectra were searched against two separate databases, and the results of both searches are provided separately in alphabetical order of protein name and with corresponding accession numbers (Supplementary Table 1). The proteome was quantified in 3–4 biological replicates at each of 4 durations of exercise training: Day 0, Day 4, Day 7, and Day 14 of continuous swimming at moderate intensity. The average abundances of proteins at Day 0 can be sorted into numerical order to facilitate viewing of the most and least abundant proteins in a typical juvenile trout heart. Additionally, the relative abundance of each identified protein at Days 4, 7, and 14 were compared to control (Day 0) levels, and the complete list of differentially abundant proteins at each time point, grouped by function, is provided (Supplementary Table 2).
Experimental Design, Materials and Methods
Acknowledgments This research was funded by a National Sciences and Engineering Research Council of Canada grant to T.E.G.
Data This dataset represents a list of peptidoforms and proteoforms extracted from bovine ovarian follicular cells and identified by TD HR-MS/MS. They correspond to molecular species previously characterized by ICM-MS on whole follicular cells [1]. Depend upon the available quantity of biological materials biomolecules were analyzed by HR-MS/MS using three approaches: In total, 386 different intact proteins or fragments corresponding to 194 genes were identified (Supplementary data Table DB1-D). The distribution of molecular weight and isoelectric point of the identified masses is represented in Fig. 2A and B, respectively. Functional annotation of identified proteins was performed using Panther Functional Classification System (http://www.pantherdb.org/), GeneAnalytics and Database for Annotation, Visualization and Integrated Discovery (https://david.ncifcrf.gov/) (Fig. 3 and Supplementary data Table DB2).
Experimental design, materials and methods
Acknowledgements This work was funded by the European Regional Development Fund (ERDF), the Val-de-Loire Region general Committee, the French National Institute for Agricultural Research (INRA) and the French National Institute of Health and Medical Research (INSERM) under the SMHART (LTQ Velos Orbitrap high resolution mass spectrometer acquisition, no 3069) project and by the INRA and French National Research Agency under grant number ANR-08-GENN-03. We acknowledge the PRIDE Team for depositing our data into the ProteomeXchange Consortium.
Data HA-tagged Akt1 expressing HEK293 cells were SILAC labeled to capture changes in association of Akt1 interacting partners with Akt1 as a function of its active state. Four biological replicates were processed and analyzed. Affinity purified samples were double digested followed by acquisition and the results were obtained as 4 RAW file pairs (wiff and corresponding wiff.scan files) from AB SCIEX 5600 triple TOF instrument. Wiff files were submitted to protein pilot software version 4.0 and resulted in 16 protein pilot group files (4 group files per biological replicate). The experimental overview is as shown in Fig. 1. Data is publicly available via ProteomeXchange with identifier ProteomeXchange: PXD005976.