Project description:This ArrayExpress record contains meta-data and results of quantitative analysis of cell lines from the NCI-60 panel using pressure cycling technology (PCT) and SWATH-mass spectrometry. Each cell line was analyzed in duplicate. Raw data files are available at the EMBL-EBI protemics data archive (PRIDE) at accession PXD003539 (http://www.ebi.ac.uk/pride/archive/projects/PXD003539). Since the record here does not include the raw data files and hence there is no need to explicitly link individual replicate to a raw file, each sample is only listed once in the ArrayExpress samples table for clarity.
Project description:Inhibitors of glucose (IO+DHEA group) or fatty acids (ETOMOXIR group) metabolism were applied during bovine oocyte in vitro maturation (IVM). Control group was conducted in standard maturation conditions. In vitro fertilization and embryo culture were applied. Obtained blastocysts were analysed with regard to lipidome, metabolome (mass spectrometry), transcriptome (RNA Seq) and lipid droplets staining (BODIPY).
Project description:Here we studied the glycation of bovine milk proteins by lactose as dominant sugar in milk and hexoses using tandem mass spectrometry (CID and ETD mode). In a bottom-up proteomics approach after enriching glycated peptides by boronate affinity chromatography, first we could identify 260 lactosylated peptides corresponding to 124 lactosylation sites in 28 bovine milk proteins in raw milk, raw colostrum, three brands of pasteurized milk, three brands of UHT milk, and five brands of infant formula. The same regular and additionally two lactose-free milk products (pasteurized and UHT milk) where lactose is enzymatically cleaved into the more reactive hexoses were analyzed in terms of hexosylation sites that resulted in identification of 124 hexosylated tryptic peptides corresponding to 86 glycation sites in 17 bovine milk proteins. In quantitative terms glycation increased from raw milk to pasteurized milk to UHT milk and infant formula, i.e., with the harsher processing conditions. Lactose-free milk contained significantly higher hexosylation degrees than the corresponding regular milk product.
Project description:Purpose: Perform RNA-seq study on short bovine endometrial tissues to reveal important genes and biological pathways related to uterine development and physiology Methods:RNA sequencings were done using Illumina platform. Single-end reads in the FASTQ format were explored using FastQC, low-quality reads were trimmed from both 3’ and 5’ ends until a base pair of Phred quality score of 30 (99.9% accurate) or greater was found, reads having a mean quality score less than 30 and length below 30 nucleotides were filtered out. Cleaned reads were aligned against the bovine reference genome (Bos_taurus.ARS-UCD1.2) using HiSAT2. The resulting SAM files were sorted, converted to BAM files using SAMtools. Read counts mapped to bovine gene models were generated using htseq-count script from HTSeq package. Bioconductor DESeq2 was used to get the differentially expressed genes among short vs normal uterine tract groups Conclusions: Heifers with short uterine tract had significantly decreased endometrial layers, uterine glands, and altered transcriptomic profiles. The decrease in uterine glands probably resulted in lower uterine secretions necessary to support embryo growth and development. As a result, heifers with short uteri were infertile even when they were bred by fertile bulls.
Project description:This study describes the generation and analysis of the transcriptional profile of bovine inner cell mass (ICM) and trophectoderm (TE), obtained from in vivo developed embryos by using a bovine-embryo specific array (EmbryoGENE) containing 37,238 probes.
Project description:Profiles of H3K4me3, H3K27ac, H3K27me3 and H3K9me3 in bovine GV oocytes and preimplantation embryos, and the characterization of chromatin accessibility in bovine blastocyst, inner cell mass and trophectoderm.
Project description:Purpose: Perform RNA-seq study on bovine endometrial tissues during the peri-implantation period (Day16-17 of gestation) to reveal important genes and biological pathways required for conceptus growth and development Methods:RNA sequencing was done using Illumina NextSeq500. Single-end reads in the FASTQ format were explored using FastQC, low-quality reads were trimmed from both 3’ and 5’ ends until a base pair of Phred quality score of 30 (99.9% accurate) or greater was not found, reads having a mean quality score less than 30 and length below 30 nucleotides were filtered out. Cleaned reads were aligned against the bovine reference genome (Bos_taurus.ARS-UCD1.2) using HiSAT2. The resulting SAM files were sorted, converted to BAM files using SAMtools. Read counts mapped to bovine gene models were generated using htseq-count script from HTSeq package. Bioconductor DESeq2 was used to get the differentially expressed genes among pregnant vs. non-pregnant (P vs. NP), pregnant vs. cyclic (P vs. C), and non-pregnant vs. cyclic (NP vs. C) groups. Conclusions: The study demonstrated that the presence of conceptus at Day 15-17 of gestation affects the endometrial gene expression related to endometrial remodeling, immune response, nutrients and ion transporters, and relevant signaling pathways in the caruncular region of bovine endometrium during the maternal recognition of pregnancy.
Project description:The Human Induced Pluripotent Stem Cells Initiative (HipSci) is generating a large, high-quality reference panel of human IPSC lines. This is a pilot submission of mass-spectrometry analyses from 18 induced pluripotent stem cell lines generated by the HipSci project. This submission includes also data for two embryonic stem cell lines, and one reference sample comprising a mixture of 42 IPSC lines. Raw data files for this study can be accessed from the PRIDE database at EMBL-EBI under accession number PXD003903: http://www.ebi.ac.uk/pride/archive/projects/PXD003903.
Project description:Purpose: Perform RNA-seq study on infectious bovine endometrial tissues to reveal important genes and biological pathways regulating uterine physiology following uterine infections Methods:RNA sequencings were done using Illumina platform. Single-end reads in the FASTQ format were explored using FastQC, low-quality reads were trimmed from both 3’ and 5’ ends until a base pair of Phred quality score of 30 (99.9% accurate) or greater was found, reads having a mean quality score less than 30 and length below 30 nucleotides were filtered out. Cleaned reads were aligned against the bovine reference genome (Bos_taurus.ARS-UCD1.2) using HiSAT2. The resulting SAM files were sorted, converted to BAM files using SAMtools. Read counts mapped to bovine gene models were generated using htseq-count script from HTSeq package. Bioconductor DESeq2 was used to get the differentially expressed genes among infectious vs normal uterine tract groups Conclusions: The study demonstrated that uterine infections altered several genes and pathways related to inflammatory response, immune response, uterine physiology, uterine enviroment and fertility in the intercaruncular region of bovine endometrium.