Raw files of samples of gills from Hippocampus reidi
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ABSTRACT: In this project are deposited the raw files of gills samples extracted individually from three adult male specimens of seahorse Hippocampus reidi
Project description:Hippocampus transcriptome analysis of Ms5Yah carrying a 7.7Mb deletion on chromosome 16 and wild-type littermates. We analyzed hippocampi from 8 wild-type and 9 Ms5Yah male mice using the Affymetrix Mouse Exon 1.0 ST platform. Array data was processed by Affymetrix Exon Array Computational Tool.
Project description:A novel one-dimensional on-line pH gradient-eluted strong cation exchange (SCX)-nano-ESI-MS/MS method was developed for protein identification and tested with mixture of six standard proteins, total lysate of HuH7 and N2a cells, as well as membrane fraction of N2a cells. This method utilized an on-line nano-flow SCX column in a nano-LC system coupled with a nano-electrospray high-resolution mass spectrometer. Protein digests were separated on a nano-flow SCX column with a pH gradient and directly introduced into a mass spectrometer through nano-electrospray ionization. SCXLC-MS/MS showed identification capability for higher proportion of basic peptides compared to RPLC-MS/MS method, especially for histidine-containing peptides. Our SCXLC-MS/MS method is an excellent alternative method to the RPLC-MS/MS method for analysis of standard proteins, total cell and membrane proteomes.
Project description:We report RNA-seq of single nuclei isolated from the adult C57BL/6 male mouse Hippocampus region. Majority of the nuclei were isolated from 12 weeks old mice (4 different animal), with an additional set of nuclei from 3 months and 2 years old animals. In addition a set of GFP labeled nuclei driven by a VGAT promoter .
Project description:Serial analysis of gene expression (SAGE) was used to get a global view of the gene profile in human hippocampus. A library were generated from control hippocampus, obtained by rapid autopsy. Keywords: hippocampus human inventory genes Control hippocampus (used to construct the SAGE control library) was obtained from a 48 years old man without history of seizures or other neurological diseases and no brain abnormalities at autopsy and histologically normal hippocampus. Autopsy was performed within 4 hours after death. Tissue was snap-frozen and stored at –80 0C until use. Total RNA was isolated from control hippocampus and hippocampal surgical specimens, using the Trizol method according to the manufacturer’s instructions (Invitrogen - Life Technologies, The Netherlands). Part of the anterior hippocampus of control (including sectors CA1- CA4 and dentate gyrus, DG) was used. Poly(A)+ RNA isolation, cDNA synthesis and all subsequent steps of the SAGE procedure were essentially performed as described (Velculescu et al., 1995) with minor modifications given previously (Michiels et al., 1999).
Project description:A variety of neurological disorders, including Alzheimer’s disease, Parkinson’s disease, major depressive disorder, dyslexia and autism, are differentially prevalent between females and males. To better understand the possible molecular basis for the sex-biased nature of neurological disorders, we measured both mRNA and protein in the hippocampus of female and male mice at 1, 2, and 4 months of age with RNA-sequencing and mass-spectrometry respectively. Differential expression analyses identify 2699 genes that are differentially expressed between animals of different ages. 198 transcripts are differentially expressed between females and males at one or more ages. The number of transcripts that are differentially expressed between females and males is greater in adult animals than in younger animals. Additionally, we identify 69 transcripts that show complex and sex-specific patterns of temporal regulation across all ages, 8 of which are heat-shock proteins. We also find a modest correlation between levels of mRNA and protein in the mouse hippocampus (Rho = 0.53). This study adds to the substantial body of evidence for transcriptomic regulation in the hippocampus during postnatal development. Additionally, this analysis reveals sex differences in the transcriptome of the developing mouse hippocampus, and further clarifies the need to include both female and male mice in longitudinal studies involving molecular changes in the hippocampus.
Project description:We report RNA-seq of single nuclei isolated from the adult C57BL/6 male mouse Hippocampus region. Majority of the nuclei were isolated from 12 weeks old mice (4 different animal), with an additional set of nuclei from 3 months and 2 years old animals. In addition a set of GFP labeled nuclei driven by a VGAT promoter . Microdissections of dentate gyrus, CA1 and CA2/3 regions of the Hippocampus were placed into ice-cold RNA-later for fixation and stored at 4âc overnight, then stored in -80âc. Nuclei were isolated by sucrose gradient centrifugation and kept on ice until sorting using Fluorescence Activated Cell Sorting (FACS) into 96 well plates containing RNA lysis buffer. Single nucleus RNA was first purified then derived cDNA libraries were generated following a modified Smart-seq2 protocol. For VGAT nuclei: high titer AAV1/2 of pAAV-EF1a-DIO-EYFP-KASH-WPRE-hGH-polyA was injected into dorsal and/or ventral Hippocampus, animals were sacrificed two weeks after injections, and GFP labeled nuclei were sorted into plates and processed as described above.