RNA-seq of HTNV-infected murine bone marrow-derived macrophages (mBMDM) from 0 to 36 hours
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 3000
ORGANISM(S): Mus musculus
SUBMITTER: Hongwei Ma
PROVIDER: E-MTAB-11353 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Total RNA was extracted from WT and RBP-JCKO mBMDMs at 36 hpi (HTMV, MOI=1), using TRIzol (Invitrogen). Ribosomal RNA was removed using the Ribo-Zero™ kit (Epicentre Biotechnologies). Fragmented RNA (the average length was approximately 200 bp) was subjected to first-strand and second-strand cDNA synthesis followed by adaptor ligation and enrichment with a low cycle according to the instructions of the NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB). The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit®2.0 (Life Technologies). The libraries were paired-end sequenced (PE150, sequencing reads were 150 bp) at Guangzhou Ribo Biotechnology (Guangzhou, China) using the Illumina HiSeq 3000 platform. Transgenic mice type: RBP-JCKO (Lyz2-Cre+ RBP-Jfloxed) C57BL/6J Mice.
2022-07-22 | E-MTAB-11926 | biostudies-arrayexpress
Project description:Salmonella enterica PullorumM-oM-<M-^HS. PullorumM-oM-<M-^I is one of the most important pathogens in poultry. A better understanding of the immune response and molecular modulation resulting from infection by S. Pullorum will facilitates the control of this pathogen. In this study, we determined the relationships among identified differential expressed genes (DEGs) and pathways via deeply mining microarray data from Guangxi Huang Chicken challenged with S. Pullorum. The chicks were then sacrificed via cervical dislocation immediately after anesthesia with 150 mg/kg sodium pentobarbital. This process was repeated at 2 hours post-infection (hpi), 4 hpi, 8 hpi, 24 hpi, 3 days post-infection (dpi), 5dpi, 7dpi, 12dpi, and 21dpi.The spleens were used to carrying out the microarray experiment. After total RNA extraction and quality control for each splenic sample were performed according to the standard protocol provided by Agilent Technologies, two random mRNA samples collected from the challenged group were equally mixed to hybridize with one chicken whole genome expression chip (Agilent.SingleColor.26441M-oM-<M-^I for each time point. In the challenged group, there were three biological replications (chips) for every time point. However, in the control group at each time point only one chip was used to hybridize with equally mixed mRNA sample containing the three control samples.
2014-07-23 | E-GEOD-59663 | biostudies-arrayexpress
Project description:Cell lines derived from Chlorocebus sabaeus kidney were infected with an isolate of PRRSV-1 or PRRSV-2 and RNASeq was performed (this entry) in parallel with ribosome profiling (see related accession numbers). These RNASeq datasets provide information on the transcriptome of PRRSV-infected cells and were used to detect novel viral transcripts and perform differential gene expression analysis on host transcripts. For the PRRSV-1 experiments, MA-104 cells were infected with an isolate based on the Porcilis vaccine strain (KJ127878.1 but with several accumulated mutations, see associated publication) and harvested at 8 hpi after pre-treatment with cycloheximide (CHX). For the PRRSV-2 experiments, MARC-145 cells were infected with SD95-21 PRRSV (KC469618.1), and a mutant thereof (KO2). One group of samples was harvested at 9 hpi after pre-treatment with CHX, and another group of samples was harvested at 3, 6, 9 and 12 hpi by flash-freezing without CHX pre-treatment. For all samples, RNA was extracted, ribosomal RNA was removed using Illumina's RiboZero kit, and remaining RNA was gel purified to select fragments 25-34 nt (PRRSV-1-infected samples, CHX-pre-treated PRRSV-2- or mock-infected samples, and non-CHX-pre-treated PRRSV-2- or mock-infected 9 hpi replicate one samples) or ~50 nt long (all other samples). Fragments were cloned into adapters based on the TruSeq small RNA adapters. For all PRRSV-2-infected (or mock-infected) libraries, adapters with an additional seven random nucleotides at the 5′-end of the 3′-adapter and the 3′-end of the 5′-adapter were used. For PRRSV-1 replicate one, no random nucleotides were present on the adapters, and for PRRSV-1 replicate two, 14 random nucleotides were present at the 5′-end of the 3′-adapter. Libraries were sequenced on the Illumina NextSeq 500 platform as a single-end run. For one NextSeq run, some potyvirus amplicons, indexed using TruSeq small RNA indices 1-48, was spiked in to the pool directly before sequencing, therefore some libraries (noCHX_RNA_9hpi_KO2_1, noCHX_RNA_9hpi_KO2_2, noCHX_RNA_9hpi_mock_1, noCHX_RNA_9hpi_mock_2, noCHX_RNA_9hpi_WT_1, noCHX_RNA_9hpi_WT_2) have a small proportion of potyvirus reads, but this does not represent co-infection in the biological sample and does not affect the conclusions of the study. Note that sample nomeclature (including replicate numbers) is consistent between this and the two related accessions, and RiboSeq libraries are matched with RNASeq libraries, which were prepared from the same lysate.
2022-03-09 | E-MTAB-10623 | biostudies-arrayexpress
Project description:Yorkshire pigs were divergently selected for residual feed intake (RFI) for 8 generations. Pigs with low RFI have reduced feed intake. Based on the resource allocation theory, we hypothesize that these low RFI pigs might have compromised immune response to immune stimulation. To test this hypothesis, twenty eight gilts of initial body weight (BW) of 63 4 kg from pigs selected for low RFI and high RFI were randomly selected for the ISU RFI selection project and utilized in two replicates (14 pigs/replicate) for this study. All pigs were housed in individual metabolism pens, had free access to water and were fed a corn-soy-based diet twice daily, and feed restricted (1.5 kg/day) as previously described. After a 9-day adaptation period pigs were randomly assigned within line to either a control (n = 6, three pigs per line) or lipopolysaccharide (LPS) challenge (n = 8, 4 pigs per line) group. Pigs in the challenge group were then repeatedly challenged with an intramuscular injection of 30, 36, 39, and 42 g/kg BW of LPS from E. coli O5:B5 (sigma-Aldrich, St. Louis, MO) dissolved in saline solution at time points 0, 48, 96, and 144 hours post initial injection (hpi) to compensate for LPS tolerance after initial injection, respectively, while animals in the control group were injected with an equivalent volume of saline solution at the equivalent time points. Rectal temperatures of individual pigs were measured immediately before the initial injection (serving as baseline, called 0 hpi for convenience), and 2, 4, 6, and 24 hpi, and 0, 4, 24 hours after each subsequent injection for all pigs. Blood samples were collected from the jugular vein into TempusTM Blood RNA tubes (Life Technologies, Grand Island, NY) for long-term storage at -80 C, EDTA tubes (BD, Franklin Lakes, NJ) for CBC tests and serum tubes for cytokine assays at 0, 2, 6, 24 and 168 hpi. At 168 hpi, all pigs were euthanized via barbiturate overdose, exsanguinated and tissue samples including the longissimus dorsi muscle, liver, spleen, and ileum were isolated, cleaned an frozen for later use. This study only focused on samples and data collected for the first 24 hours. Total RNA was extracted from the 32 blood samples of the treatment group in Replicate 2, collected at 0, 2, 6, and 24 hpi, by using preserved blood RNA purification kit I (Norgen Biotek Corp, Thorold, Ontario) per manufacturers instruction. On-column DNA digestion was performed as described using DNase I (Qiagen, Valencia, CA). Globin transcripts (HBB and HBA) were depleted by following an RNase H-mediated method. The quantity and integrity of the RNA were monitored by using Nanodrop 2000 (Thermo Scientific, Waltham, MA) and Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) before and after globin depletion. The efficiency of globin depletion of each sample was checked by conventional RT-qPCR with -actin and GAPDH as the internal controls. Globin depletion efficiencies for all RNA samples were above 85%.
2017-03-24 | E-MTAB-5606 | biostudies-arrayexpress
Project description:A first generation Affymetrix GeneChip® Porcine genome array was used to profile the gene expression in porcine mesenteric lymph nodes over a time course of infection with S. Typhimurium, including the acute (8 hours post inoculation (hpi), 24 hpi, 48 hpi) and chronic (21 days post-inoculation (dpi)) stages of infection. Our objectives were to 1) identify and examine the stereotypical gene expression response within host MLN to S. Typhimurium infection, 2) characterize global host responses by revealing the specific features of the hostâs innate immunity pathways, and 3) explore if and how S. Typhimurium may escape the host immune response and develop into a carrier state. Our study has attempted to investigate the features of host gene expression profiling during S. Typhimurium infection at the acute and chronic infection stages and to explore the mechanism by which S. Typhimurium can escape from the host immune response and develop a carrier state in the host. In conclusion, by using the Affymetrix porcine GeneChip, 848 differentially expressed genes were identified in porcine MLN during infection and several specific features of host response were revealed by gene cluster and pathway analysis. Our data are the first report to investigate global host responses to S. Typhimurium in porcine MLN, and this new study provides data applicable for studying enteric salmonellosis of pigs, as well as humans. Experiment Overall Design: Fifteen piglets from Salmonella spp.-free sows were weaned at 10 days (d) of age, shipped to the National Animal Disease Center, Ames, IA and raised in isolation facilities. To confirm that all piglets were free of Salmonella spp. prior to challenge, bacteriological cultures were performed on rectal swabs twice. Seven week old pigs were randomly divided into 2 groups, 3 non-infected pigs and 12 infected pigs. Three non-infected control pigs were necropsied 2 days prior to experimental infection. On day 0, pigs in the infected groups were intranasally challenged with 1 billion CFU of Salmonella enterica serovar Typhimurium. Three infected pigs were necropsied at 8 hours post-inoculation (hpi), 24 hpi, 48 hpi and 21 days post-inoculation (dpi). Tissue samples from the mesenteric lymph nodes (MLN) were collected and immediately frozen in liquid nitrogen for RNA isolation.
2008-06-15 | E-GEOD-7313 | biostudies-arrayexpress
Project description:Melon RNA-Seq analysis was used to identify candidate resistance genes and to understand the early molecular processes deployed during melon versus Fusarium oxysporum f.sp. melonis Snyd. & Hans race 1.2 (FOM1.2) interaction in the resistant doubled haploid line NAD as opposed to the susceptible genotype Charentais-T at 24 and 48 hours post inoculation (hpi).
2017-09-30 | E-MTAB-4939 | biostudies-arrayexpress
Project description:Cell lines derived from Chlorocebus sabaeus kidney were infected with an isolate of PRRSV-1 or PRRSV-2 and ribosome profiling was performed (this entry) in parallel with RNASeq (see related accession number). These datasets were used to analyse the viral and host translatome, frameshifting on the viral genome, and putative frameshift-related ribosome pausing events. For the PRRSV-1 experiments, MA-104 cells were infected with an isolate based on the Porcilis vaccine strain (KJ127878.1 but with several accumulated mutations, see associated publication) and harvested at 8 hpi after pre-treatment with cycloheximide (CHX). For the PRRSV-2 experiments, MARC-145 cells were infected with SD95-21 PRRSV (KC469618.1), and a mutant thereof (KO2). One group of samples was harvested at 9 hpi after pre-treatment with CHX, and another group of samples was harvested at 3, 6, 9 and 12 hpi by flash-freezing without CHX pre-treatment. For all samples, RNase I treatment was carried out, following which ribosomes and enclosed RNA were isolated by centrifugation through a sucrose cushion. RNA was extracted, ribosomal RNA was removed using Illumina's RiboZero kit, and remaining RNA was gel purified to select fragments 25-34 nt (PRRSV-1-infected samples, CHX-pre-treated PRRSV-2- or mock-infected samples, and non-CHX-pre-treated PRRSV-2- or mock-infected 9 hpi replicate one samples) or 19-34 nt long (all other samples). Fragments were cloned into adapters based on the TruSeq small RNA adapters. For all PRRSV-2-infected (or mock-infected) libraries, adapters with an additional seven random nucleotides at the 5′-end of the 3′-adapter and the 3′-end of the 5′-adapter were used. For PRRSV-1 replicate one, no random nucleotides were present on the adapters, and for PRRSV-1 replicate two, 14 random nucleotides were present at the 5′-end of the 3′-adapter. Libraries were sequenced on the Illumina NextSeq 500 platform as a single-end run. Non-CHX-pre-treated PRRSV-2-infected 9 hpi replicate two libraries were uploaded under a separate accession number due to differences in the size selection and sequencing protocol - see associated paired-end entry. Note that sample nomeclature (including replicate numbers) is consistent between this and the two related accessions, and RiboSeq libraries are matched with RNASeq libraries, which were prepared from the same lysate. The noCHX_Ribo_9hpi_mock_3 library is deliberately absent as this was a poor quality library.
2022-03-09 | E-MTAB-10621 | biostudies-arrayexpress
Project description:Transcriptional profiling of ZF-4 cells comparing mock infection cells with cells infected with NNV. This assay is used for determination of gene expression profiling at 6 hpi under NNV infection. Two-condition experiment, Mock infection vs. NNV infection (5 MOI).
2015-05-12 | E-GEOD-57600 | biostudies-arrayexpress
Project description:The parasite Plasmodium falciparum is responsible for severe malaria, which is still one of the major causes of death in developing countries. To provide a new RNA-seq reference dataset for its blood-stage transcriptome according to current guidelines and best practices, we performed a time course experiment with three independent biological replicates of synchronized P. falciparum 3D7 cells, that were cultivated at a haematocrit of 5% in human O+ erythrocytes. RNA-seq samples were taken at 8 developmental stages including young ring stage (8 hpi), late ring stage/early trophozoite (16 hpi), mid-age trophozoite (24 hpi), late trophozoite (32 hpi), early schizont (40 hpi), schizont (44 hpi), late schizont (48 hpi) and purified merozoites (0 hpi). Red blood cell pellets were lysed with Trizol and total RNA was purified using column-based purification (PureLink RNA Kit) including DNase treatment on the column and controlling for absence of genomic DNA contamination using qPCR. Whole blood total RNA samples were depleted of human globin mRNA using magnetic bead isolation technology (GLOBINclear kit). After RNA sample quality control and optimized cDNA libraries preparation for AT-biased genomes for Illumina sequencing, RNA-seq was performed at BGI Genomics (Shenzhen, China) on HiSeq 4000 to generate 100 bp paired-end sequencing reads.
2019-07-02 | E-MTAB-7731 | biostudies-arrayexpress
Project description:A network model has been generated that describes the immediate gene expression cascade surrounding three similar but distinct NAC transcription factors that have roles to play in leaf senescence and in many stress responses in Arabidopsis. ANAC019, ANAC055 and ANAC072 belong to the same clade of NAC domain genes and have overlapping expression patterns. A combination of promoter DNA/protein interactions identified using yeast 1 hybrid analysis and modeling using gene expression time course data has been used to predict the regulatory network upstream of these genes. Similarities and divergence in regulation during a variety of stress responses are predicted by different combinations of upstream transcription factors binding and also by the modeling. Mutant analysis with potential upstream genes was used to test and confirm some of the predicted interactions.. Gene expression measurements in mutants of ANAC019 and ANAC055 at different times during leaf senescence have shown a distinctly different role for each of these genes. To assess mutant response to Botrytis cinerea infection, Col-0, myb2 and myb108 leaves were inoculated with 4-6 (depending on leaf size) evenly spaced 10μl droplets of B. cinerea spores. Infected leaves were harvested to provide 4 biological replicates. Samples for the comparison between myb108 and Col-0 were harvested at 26 and 30 hpi. Samples for the comparison between myb2 knockout line and Col-0 or myb2 knockout line and Col-0 were harvested at 26 and 30 hpi or 24 and 30 hpi respectively. Analysis of expression differences between Col-0 and myb2 and Col-0 and myb108 under each condition, using dye swaps, was performed using the R Bioconductor package limmaGUI (Wettenhall and Smyth, 2004).
2013-04-23 | E-GEOD-45594 | biostudies-arrayexpress