RNA-Seq Data and Expression Matrices for Brain and Liver from Mice Mutation Accumulation and Control Lines
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina NovaSeq X
ORGANISM(S): Mus musculus
SUBMITTER: Eugenio López Cortegano
PROVIDER: E-MTAB-14914 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:This study examined NAc gene expression in a pair short-term selected lines bred for high or low response to methamphetamine (MA). We sought to identify candidate genes preferentially expressed among individuals showing either large or small acute responses to MA. Additionally, we sought to identify genes and networks differentially expressed by MA exposure within these divergent lines. Keywords: Short-term selected lines (STSLs), saline (SAL), methamphetamine (MA), nucleus acumbens (NAc)
2008-08-09 | GSE12387 | GEO
Project description:Since the first human conceived through in vitro fertilisation in 1978, over 8 million babies have been born by assisted reproductive technologies (ART). Although most ART babies and children seem healthy, in recent years, several human and animal model studies have evidenced a potential impact of ART on long-term development. However, the long-term follow-up data in this field is still limited. Till now, studies are mainly focused on techniques such as in vitro fertilisation or in vitro culture, being the information from gametes/embryos cryopreservation field practically missing. Herein, we have developed an animal model to determine whether vitrified-thawed embryo transfer procedure has long-term consequences over the offspring. The birth weight, growth performance and adult body weight of the rabbits derived from vitrified-thawed embryos was compared with that of the naturally-conceived animals. In adulthood, the liver, heart, kidneys, spleen, lungs, gonads and adrenal glands of the males were weighed and compared. Moreover, some haematological and biochemical parameters were assessed on peripheral blood. Besides, some liver samples were obtained to perform a comparative proteomic study. The embryo vitrification-transfer process modified the birth weight and the growth pattern of the offspring, reducing the growth performance in a sex-specific manner. In adulthood, animals derived from vitrified embryos showed a significantly lower body, liver and heart weight. Molecular analyses revealed that vitrified-thawed embryo transfer procedure triggers concordant reprogramming of the liver proteome. The most relevant metabolic alteration denoted by the protein profile was that related to the oxidative phosphorylation, suggesting an impaired oxidative metabolism in the mitochondria. Furthermore, hints of dysregulation in the zinc and lipid metabolism were identified. These results evidence long-term consequences in the offspring derived from cryopreserved-transferred embryos and represented an evident example of the phenotypic plasticity exhibited by the mammalian embryo.
2021-09-08 | PXD016677 | Pride
Project description:8 neuroblastoma (NB) cell lines (CLB-GA, IMR-32, SH-SY5Y, N206, CHP-902R, LAN-2, SK-N-AS, SJNB-1) their methylome is determined by sequencing after MBD2-capture using MethylCollector (ActiveMotif) 8 NB cell lines were included (CLB-GA, IMR-32, SH-SY5Y, N206, CHP-902R, LAN-2, SK-N-AS, SJNB-1) in this study. After shearing (fragments of about 200 bp), DNA was captured using MBD2-capture (MethylCollector - ActiveMotif) followed by library preparation and multiplexing. Captured sequence tags were sequenced paired-end (2 x 45 bp) on Illumina GAIIx.
2012-09-13 | E-GEOD-31353 | biostudies-arrayexpress
Project description:The paired-end next-generation sequencing of all small RNAs of less than 200 nucleotides in length from four different human cell lines (SKOV3ip1, MCF-7, BJ-Tielf, INOF) allowed us to determine the exact sequence(s) and variations of human box C/D snoRNAs (small nucleolar RNAs), revealing processing patterns of this class of molecules. Two distinct groups of box C/D snoRNAs were identified based on the position of their ends with respect to their characteristic boxes and the terminal base pairing potential. Short box C/D snoRNAs start sharply 4 or 5 nucleotides upstream of their box C and end 2 or 3 nucleotides downstream of their box D. In contrast, long box C/D snoRNAs start 5 or 6 nucleotides upstream of their box C and end 4 or 5 nucleotides downstream of their box D, increasing the likelihood of formation of a k-turn between their boxes C and D. Sequencing of SKOV3ip1 cells following the depletions of NOP58, a core box C/D snoRNA-binding protein and of RBFOX2, a splicing factor, shows that the short box C/D snoRNA forms are significantly more affected by the depletion of RBFOX2 while the long snoRNA forms, which display more canonical box C/D snoRNA features, are significantly more affected by the depletion of NOP58. Together the data suggest that box C/D snoRNAs are divided into at least two groups of RNA with distinct maturation and functional preferences. Small RNAs (<200 nucleotides) were isolated from different human cell lines that were either untreated or depleted of NOP58 or RBFOX2 using specific siRNAs. The resulting libraries were multiplexed and paired-end sequenced using Illumina HiSeq.
2014-07-01 | E-GEOD-55946 | biostudies-arrayexpress
Project description:DNase I footprinting is an established assay for identifying transcription factor (TF)-DNA interactions with single base pair resolution. High throughput DNase-seq assays have recently been used to detect in vivo DNase footprints across the genome. A number of computational approaches have been developed to accurately identify DNase-seq footprints and these methods have been used as a predictor of TF-DNA interactions by itself or in combination with other epigenetic features. However, recent studies have pointed to a substantial cleavage bias of DNase and its impact on footprinting, casting doubts on its predictive performance. To assess the potential for using DNaseI to identify individual binding sites, we performed DNase-seq experiments on deproteinized naked genomic DNA isolated from two different cell types and determined sequence cleavage bias associated with the DNase-seq protocol. This allowed us to build cleavage bias corrected footprint models specific to individual transcription factors. The predictive performance of these DNase-seq-based binding site models demonstrated that predicted footprints corresponded to high confidence TF-DNA interactions. To quantify the DNase I sequence-dependent cleavage bias, we performed DNase-seq experiments using deproteinized DNA from K562 and MCF7 cell lines.
2014-09-04 | E-GEOD-61105 | biostudies-arrayexpress
Project description:We used massively parallel DNA sequencing of paired-end ditags (DNA-PET) to identify structural genetic factors associated with disease progression and drug-resistance in representative samples from four CML patients and one CML cell line. The functional consequences of our genetic findings were evaluated in primary CML cells and cell lines, and validated in a larger CML cohort. We discovered a novel intronic deletion that correlated with imatinib-resistance, and was subsequently confirmed to be a polymorphism in normal East-Asian, but not African or Caucasian, populations. We found that the polymorphism favored expression of transcripts lacking a pro-apoptotic domain, which is critical for imatinib-induced cell death. A CML cell line containing the polymorphism also exhibited BCR-ABL-independent imatinib-resistance. Structural variations of 5 human CML samples were identified by long span paired-end sequencing
2012-02-27 | E-GEOD-28303 | biostudies-arrayexpress
Project description:The DNA, its epigenetic information and signals from the direct environment, all work together to orchestrate the development of the single fertilized oocyte into a new individual. The concept of developmental programming, attributed to the embryonic plasticity, suggests that the early life environment influences offspring characteristics in later life, but also further generations. There is increasing awareness about the use of Assisted Reproductive Technologies (ART), because, due to its high inefficiency mimicking in vivo optimal conditions, implies an extraordinary change in the environment where the beginning of a new organism takes place. Here we assessed the transgenerational effects of the cryopreserved embryo replacement on a maternal tract using the rabbit as a model. Then, one progeny derived from vitrified-transferred embryos (VT group) was compared to a cohort of animals naturally-conceived (NC group). A multi-omic approach (metabolome, proteome and epigenome) were addressed on the liver tissue in order to complete or previous phenotypic and transcriptomic characterization of F3 animals. LC-ESI-MS and LC-APCI-MS analysis were performed to interrogate the semi-polar and non-polar metabolomes, respectively. For the proteomic study, the analysis was carried on by LC-SWATH-MS. Finally, genome-wide DNA methylation profiling was studied by MBD-Seq. The healthy state was evaluated by a haematological and biochemical analysis of the peripheral blood. Targeted and untargeted metabolome analysis revealed a global metabolome alteration in the VT livers, particularly for those pathways related with the lipid metabolism. Here was detected some disturbances in the metabolism of long-chain polyunsaturated fatty acids (LC-PUFA), which was corroborated by the proteomic data. Functional analysis of the subset of proteins that differs between VT and NC livers revealed significant changes in the metabolism of the linoleic (LIN) and arachidonic (ARA) acids, whose downstream consequences directly was related with dysregulations in the growth and immune system responses. Overall results denoted that these metabolic disturbances participated in a complex network of physiological pathways that together promotes the phenotypic deviations currently observed after an embryo cryopreservation-transfer procedure (CTP). The underlying hypothesis supported by our results, is that these developmental deviations respond to changes in the epigenome, as consequence of direct perturbation of the reprogramming process by ART, which are dragged until adult life and inherited by further generations. Changes in the epigenetic suggested possible interactions between lipid and apoptotic pathways that jointly reprograms the physiology of the liver. However, based on peripheral blood parameters, the healthy status of VT animals was comparable to that of the NC group. Our data provides valuable information about the transgenerational long-term molecular effects of the embryo CTP using high-throughput sciences, which should highlight the need to study ART not only to increase pregnancy rates, but also to use ART in the safest way possible.
2022-02-15 | PXD017972 | Pride
Project description:Label-free absolute quantitative proteomics is commonly used for absolute quantification of the proteome or specific proteins of interest in various biological samples. Current label-free absolute protein quantification (APQ) methods determine MS1 intensities, MS2 spectral counts or intensities to absolutely quantify protein concentrations from data obtained from data-dependent acquisition (DDA). In recent years, label-free data-independent acquisition (DIA) has seen increasing use as a powerful tool for relative protein quantification. Here we present a novel label-free DIA-based absolute protein quantification (DIA-APQ) method for the absolute quantification of protein expressions from DIA data. To validate this method, both DDA and DIA experiments were performed on 36 individual human liver microsome and S9 samples. The DIA-APQ assay was able to quantify approximately twice as many proteins as the DDA MS1-based APQ method whereas protein concentrations determined by the two methods were comparable. To evaluate the accuracy of the DIA-APQ method, we absolutely quantified carboxylesterase 1 concentrations in human liver samples using an established SILAC internal standard-based proteomic assay; the SILAC results were consistent with those obtained from DIA-APQ analysis. Finally, we employed a unique algorithm in DIA-APQ to distribute the MS signals from shared peptides to different protein isoforms and successfully applied the DIA-APQ method to the absolute quantification of several drug-metabolizing enzyme isoforms in human liver microsomes. This novel DIA-based APQ method not only provides a powerful approach for absolutely quantifying entire proteomes and specific candidate proteins, but also has with the capacity differentiating protein isoforms.
2019-03-20 | PXD010912 | Pride