Project description:While a first draft of the equine genome is available and predictions are made regarding resulting genes and proteins, little is known about the actual transcriptome. So far, published expressed sequence tags (ESTs) from different horse tissues were generally rather short (?600bp) and hardly annotated, reflecting the problem that good cDNA libraries are very difficult to analyse. In this approach, we aimed to establish and analyse a normalised immune cell cDNA library (using freshly isolated and activated lymphocytes, NK cells, monocytes and DC). In particular, we wanted to test next generation sequencing combined with a series of bioinformatic approaches. The resulting cDNA library contained 2x107 clones of which 1056 were used for an initial Sanger sequencing and 4x106 for the deep sequencing analysis. Through the latter we obtained >29k sequences for which more than 5000 matches where found on the equine reference sequences. Additionally we could identify more than 3500 sequences which had matches on both - non-equine RNA sequences as well as the equine genome. In these we find both extensions of existing RefSeq models and novel mRNAs alike. Less than 2% of sequences did not have any match in the mentioned databases. 1 pooled set of samples from one animal analysed
Project description:To date nothing is known about the specificity of regulatory B cells. Here we analyzed the B cell repertoire at the Ig gene level of regulatory transitional CD24(high)CD38(high) B cells of patients with multiple sclerosis (MS) in comparison with healthy donors. 5 patients with highly active MS, 4 patients with benign MS and 6 healthy donors were examined. Mononuclear cells from peripheral blood were stained against CD19, CD24 and CD38 surface markers. Subpopulation CD19(+)CD24(high)CD38(high) and total pool of CD19(+) cells were sorted individually for subsequent RNA isolation and BCR sequences comparison. Variable heavy (VH) and light (VL) chains genes of each patient were amplified from cDNA and deep sequencing of the VH and VL genes was carried out.
Project description:We characterize the TERRA transcriptome at normal and TRF2-depleted telomeres by RNA-seq and we demonstrate that TERRA upregulation is occurring at all transcribed telomeres upon depletion of TRF2. RNA-sequencing of HeLa mRNA, 4 samples: with or without TERRA enrichment by IP (respectively "IP" and "input"), with or without TFR-2 knock-down (respectively "_T" and "_EV").
Project description:Embryos and megagametophytes samples belonging to four early developmental stages during seed development in Pinus sylvestris were collected from a seed orchard in central Sweden. Dominant (DO) and subordinate (SU) zygotic embryos were collected separately. RNA was isolated from this samples and the corresponding cDNA synthesized and subjected to RNA sequencing (one biological replicate). In total nine RNA-seq libraries were constructed, five for embryo samples (E1, E2, E3DO, E3SU, E4) and four for megagametophytes (M1, M2, M3 and M4). qRT-PCR analysis have been done to validate the RNA-seq expression results.
Project description:HPLC-MS/MS analysis of proteins in serum samples using high-resolution mass spectrometry. Dataset of 50 samples from patients with schizophrenia (Series "SCH") and 50 samples from healthy volunteers (Series "CNT") and the data analysis were carried out using shotgun ultra-high resolution mass spectrometry.
Project description:Here we provide dataset from a proteomic experiment, using trypsin digestion, and reversed-phase chromatography (RPC) with tandem mass spectrometr (RPC-MS/MS), in order to relatively quantify the protein composition of skin mucus of Prussian carp Carassius gibelio. The main aim of the project is to identify the proteins specifically assotiated with fish inhabits euthophic shallow lakes lake Chany Lake (West Siberia).
Project description:Analysis of gene expression patterns in cytomegalovirus infected human fibroblasts for two cultures with differing sensitivity to the virus Total RNA obtained from 2 human fibroblast lines with differing sensitivity to CMV infection. For each line 3 types of samples are compared: pre-experimantal norm, 3 hours after infection, 3 hours without infection.
Project description:Analysis of microRNA expression patterns in cytomegalovirus infected human fibroblasts for two cultures with differing sensitivity to the virus Non-coding RNAs were cloned from total RNA extracts obtained from 2 human fibroblast lines with differing sensitivity to CMV infection. For each line 3 types of samples are compared: pre-experimantal norm, 3 hours after infection, 3 hours without infection.
Project description:Proteins were extracted using 2 mM DTT from Beauveria bassiana hyphal bodies (in vivo blastospores) were identified and quantified using Label-free quantitative mass spectrometry.