Transcription profiling of Hsd:ICR(CD-1) mouse intestines to study regional variations in ABC transporter expression along the mouse intestinal tract.
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: Pascale Anderle
PROVIDER: E-GEOD-849 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Regional variations in ABC transporter expression along the mouse intestinal tract.
Mutch David M DM Anderle Pascale P Fiaux Muriel M Mansourian Robert R Vidal Karine K Wahli Walter W Williamson Gary G Roberts Matthew-Alan MA
Physiological genomics 20040312 1
The ATP-binding cassette (ABC) family of proteins comprise a group of membrane transporters involved in the transport of a wide variety of compounds, such as xenobiotics, vitamins, lipids, amino acids, and carbohydrates. Determining their regional expression patterns along the intestinal tract will further characterize their transport functions in the gut. The mRNA expression levels of murine ABC transporters in the duodenum, jejunum, ileum, and colon were examined using the Affymetrix MuU74v2 G ...[more]
Similar Datasets
Project description:8 week-old male Hsd:ICR(CD-1) mice were fed ad libitum a standard chow (Harlan Teklad diet 2018S) and housed in groups of five. Animals were then divided into 3 pools (n=10) and sacrificed. The small intestine was extracted and divided into three sections, where the first 2-3 cm after the stomach comprised the duodenum, the middle third the jejunum, and the section before the ileo-ceco-colic junction comprised the ileum. Colon was not divided into proximal and distal sections and was treated as a single intestinal section. Keywords: other
2003-12-04 | GSE849 | GEO
Project description:We developed cell2location, a principled and versatile Bayesian model that is designed to resolve fine-grained cell types in spatial transcriptomic data and create comprehensive cellular maps of diverse tissues. To validate cell2location in real tissue, we applied the model to data from the mouse brain, which features diverse neural cell types organised in a well characterised spatial architecture across brain areas, thus presenting a canonical use case to test spatial genomics. We generated matched single nucleus (sn, this submission) and Visium spatial RNA-seq (10X Genomics) profiles of adjacent mouse brain sections that contain multiple regions from the telencephalon and diencephalon. To assess the biological and intra-organ technical variation in spatial mapping, we assayed two mouse brains and serial tissue sections from each brain (total of 3 and 2 matched sections from two animals, respectively, and an extra section for snRNA-seq), creating a rich multi-modal and replicated transcriptomic dataset. Tissue processing. Brains of wild-type adult C57BL/6 mice (postnatal day 56, 1 female and 1 male) were dissected, snap frozen, embedded in optimal cutting temperature compound (Tissue-Tek) and stored at -80oC. Brain hemispheres were cryosectioned at -20oC using a cryostat (Leica, CM3050S). To assess tissue quality, RNA was extracted from test tissue sections using the RNeasy Pico Kit (Qiagen) and yielded high RIN values (9.6 and 9.7) on an Agilent Bioanalyser, indicating high RNA quality. For matched single nuclei and Visium RNA-seq experiments, brain hemispheres were cryosectioned to adjacent thick (200 µm) and thin (10 µm) coronal sections, respectively, and processed the same day. In total, four consecutive sets of thick and thin tissue sections were collected from each brain. Five sets of tissue sections yielded both good quality single nuclei and Visium data (three adjacent sections from mouse 1 and two sections from mouse 2) while one additional section from mouse 2 yielded good single nuclei; these were considered for analysis in this study. Single nucleus RNA-sequencing. Thick (200 µm) mouse brain sections were cryosectioned, dissected from OCT and kept in a tube on dry ice until subsequent processing. Nuclei were extracted from each section as described previously. Briefly, nuclei were released from sections via Dounce homogenisation, Hoechst-stained, and isolated via fluorescence-activated cell sorting (FACS). Nuclei were then loaded into the 10X Chromium Single Cell 3′ Kit (v3) to obtain 3,000-7,000 nuclei per well, and library preparation was done per manufacturer’s protocol. Libraries were sequenced on an Illumina NovaSeq S4 system. Sequencing data were processed using 10X CellRanger version 3.0.2, aligned to mouse pre-mRNA genome reference version mm10 and mRNA count matrices were generated by adding intronic and exonic unique molecular identifier (UMI) counts for each gene in each cell. Initially, snRNA-seq counts were processed using standard Seurat V3 workflow without correcting batch effects between 6 individual samples.
2021-11-12 | E-MTAB-11115 | biostudies-arrayexpress
Project description:We developed cell2location, a principled and versatile Bayesian model that is designed to resolve fine-grained cell types in spatial transcriptomic data and create comprehensive cellular maps of diverse tissues. To validate cell2location in real tissue, we applied the model to data from the mouse brain, which features diverse neural cell types organised in a well characterised spatial architecture across brain areas, thus presenting a canonical use case to test spatial genomics. We generated matched single nucleus (sn, this submission) and Visium spatial RNA-seq (10X Genomics) profiles of adjacent mouse brain sections that contain multiple regions from the telencephalon and diencephalon. To assess the biological and intra-organ technical variation in spatial mapping, we assayed two mouse brains and serial tissue sections from each brain (total of 3 and 2 matched sections from two animals, respectively, and an extra section for snRNA-seq), creating a rich multi-modal and replicated transcriptomic dataset. Tissue processing. Brains of wild-type adult C57BL/6 mice (postnatal day 56, 1 female and 1 male) were dissected, snap frozen, embedded in optimal cutting temperature compound (Tissue-Tek) and stored at -80oC. Brain hemispheres were cryosectioned at -20oC using a cryostat (Leica, CM3050S). To assess tissue quality, RNA was extracted from test tissue sections using the RNeasy Pico Kit (Qiagen) and yielded high RIN values (9.6 and 9.7) on an Agilent Bioanalyser, indicating high RNA quality. For matched single nuclei and Visium RNA-seq experiments, brain hemispheres were cryosectioned to adjacent thick (200 µm) and thin (10 µm) coronal sections, respectively, and processed the same day. In total, four consecutive sets of thick and thin tissue sections were collected from each brain. Five sets of tissue sections yielded both good quality single nuclei and Visium data (three adjacent sections from mouse 1 and two sections from mouse 2) while one additional section from mouse 2 yielded good single nuclei; these were considered for analysis in this study. Visium spatial transcriptomics. Thin (10 µm) mouse brain sections were cryosectioned and mounted directly onto separate capture areas on 10X Visium Spatial Gene Expression slides (beta product version). Processing was done per manufacturer’s protocols. Briefly, sections were methanol-fixed, hematoxylin and eosin (H&E)-stained, and imaged on a NanoZoomer 2.0 slide scanner (Hamamatsu). Sections were then permeabilized and further processed to obtain cDNA libraries that were quality controlled using the Agilent Bioanalyser. The cDNA libraries were sequenced on the Illumina HiSeq 4000 system, aiming at 300 million raw reads per section with read lengths 28cy R1, 8cy i7 index, 0cy i5 index, 91cy read 2. 10X Visium spatial sequencing data was aligned to mouse pre-mRNA genome reference version mm10 using 10X SpaceRanger and mRNA count matrices were generated by adding intronic and exonic reads for each gene in each location. The paired histology H&E images were processed using 10X SpaceRanger to select locations covered by tissue by aligning pre-recorded spot locations with fiducial border spots in the histology image. This allows evaluating the correspondence between cell maps produced using our method and the known brain anatomy. This also allows identifying the number of nuclei in each spot using nuclear segmentation as described in Suppl. Methods and reported in Fig S8A-D. The histology image was used to manually annotate cortical layers in the primary somatosensory cortex (SSp) region using the lasso tool in the 10X Loupe browser.
2021-11-12 | E-MTAB-11114 | biostudies-arrayexpress
Project description:Although microbiota plays a critical role for the normal development and function of host immune systems, the detail of the influence, especially on those in the large intestine (LI), remains unknown. Here, we performed transcriptome analysis using Affymetrix GeneChip on LI of germ-free (GF) and specific pathogen free (SPF) mice of IQI, an inbred strain established from ICR. Experiment Overall Design: Male germ-free (GF) and specific pathogen-free (SPF) IQI/Jic mice were bred and maintained in the laboratory of Central Institute for Experimental Animals (CIEA, Kawasaki, Kanagwa, Japan). GF mice were housed in a Trexler-type flexible film isolator in a standard germ free state and screened on a weekly basis for germ-free status by sampling feces sterilely and culturing on MRS-agar plates under aerobic and anaerobic conditions. All the GF, SPF, ex-GF mice were kept in a 12: 12-h light/dark cycle and at a temperature of 22+-2 ºC. Nine week old mice (n=3) were sacrificed by cervical dislocation and the colon was dissected (the colon was not divided into proximal and distal sections and was treated as a single intestinal section). Experiment Overall Design: The SPF mice were provided by the Central Institute for Experimental Animals of Japan. These mice were determined free of the following pathogens (by various techniques including culture, microscopic observation, serological test, and PCR): Dermatophytes, Citrobacter rodentium, Pasteurella pneumotropica, Corynebacterium kutscheri, Pseudomonas aeruginosa, Salmonella spp., Staphylococcus aureus, Mycoplasma pulmonis, Corynebacterium kutscheri, Salmonella typhimurium, Clostridium piliforme, Mycoplasma pulmonis, Mouse hepatitis virus, Sendai virus, Ectromelia virus, Lymphocytic c. virus, Hantavirus, Giardia muris, Spironucleus muris, Syphacia spp., Aspiculuris tetraptera, Ectoparasits, Intestinalprotozoa, Pinworm, Pneumocystis carinii, Helicobacter hepaticus, Helicobacter bilis, EDIM virus(Rotavirus), Pneumonia virus of mice, Minute virus of mice, Mouse adenovirus, Mouse cytomegalovirus, Mouse encephalomyelitis virus, Reovirus type3, and CAR bacillus.
2008-06-15 | E-GEOD-8006 | biostudies-arrayexpress
Project description:16S amplicon pool analyses of the four gut sections of the wood-feeding beetle, Odontotaenius disjunctus The beetle is purely wood feeding, and we aim to first characterize the community that exist within the gut sections 4 beetles, four gut sections per beetle, one PhyloChip per gut section, total = 16 chips
2012-08-13 | E-GEOD-40067 | biostudies-arrayexpress
Project description:Wood-degrading brown rot fungi are essential recyclers of plant biomass in forest ecosystems. Their efficient cellulolytic systems, which have potential biotechnological applications, apparently depend on a combination of two mechanisms: lignocellulose oxidation by reactive oxygen species (ROS) and polysaccharide hydrolysis by a limited set of glycoside hydrolases (GHs). Given that ROS are strongly oxidizing and non-selective, these two steps are likely segregated. A common hypothesis has been that brown rot fungi use a concentration gradient of chelated metal ions to confine ROS generation inside wood cell walls before enzymes can infiltrate. We examined an alternative: that lignocellulose-oxidation (LOX) components involved in ROS production are differentially expressed by brown rot fungi ahead of GH components. We used spatial mapping to resolve a temporal sequence in Postia placenta, sectioning thin wood wafers colonized directionally. Among sections, we measured gene expression by whole transcriptome sequencing (RNAseq) and assayed relevant enzyme activities. We found a marked pattern of LOX upregulation in a narrow (5-mm; 48-hr) zone at the hyphal front, which included many genes likely involved in ROS generation. Upregulation of GH5 endoglucanases and many other GHs clearly occurred later, behind the hyphal front, with notable exceptions of two likely expansins and a GH28 pectinase. Our results support a staggered mechanism for brown rot that is controlled by differential expression rather than microenvironmental gradients. This mechanism likely results in an oxidative pretreatment of lignocellulose, possibly facilitated by expansin- and pectinase-assisted cell wall swelling, before cellulases and hemicellulases are deployed for polysaccharide depolymerization. We sequenced mRNA from 9 Postia placenta samples taken from 3 wood sections of wafer design, with 3 bioreplicates for each wood section, to compare the gene expression during brown rot processes. Three wood sections of the wafer are representing early to late decay stages.
2016-07-18 | E-GEOD-84529 | biostudies-arrayexpress
Project description:Ribosome profiling on sections taken from a kidney tumor For two tumors: 2 sections of normal tissue and 4 samples of tumor tissue, for another two tumors 1 section of normal tissue and 1 section of tumor tissue
2016-02-17 | E-GEOD-59820 | biostudies-arrayexpress
Project description:Juzehtaihoto, a Japanese traditional medicine has been used for the treatment of various kinds of diseases or disorders in an enteric-flora dependent manner. Here, we performed transcriptome analysis using Affymetrix GeneChip on large intestine (LI) of germ-free (GF) and specific pathogen free (SPF) mice of IQI, an inbred strain established from ICR, and BALB/c SPF mice. Male germ-free (GF) and specific pathogen-free (SPF) mice of IQI and BALB/c strains were bred and maintained in the laboratory of Central Institute for Experimental Animals (CIEA, Kawasaki, Kanagwa, Japan). GF mice were housed in a Trexler-type flexible film isolator in a standard germ free state and screened on a weekly basis for germ-free status by sampling feces sterilely and culturing on MRS-agar plates under aerobic and anaerobic conditions. All the GF, SPF, ex-GF mice were kept in a 12: 12-h light/dark cycle and at a temperature of 22±2°C. Nine week old mice (n=3) were sacrificed by cervical dislocation and the intestines were dissected. comparison of the mice with or without enteric flora; comparison of the mice of different strains
2011-09-13 | E-GEOD-32083 | biostudies-arrayexpress
Project description:Juzehtaihoto, a Japanese traditional medicine has been used for the treatment of various kinds of disease or disorders in an enteric-flora dependent manner. Here, we performed transcriptome analysis using Affymetrix GeneChip on small intestine (SI) of germ-free (GF) and specific pathogen free (SPF) mice of IQI, an inbred strain established from ICR. Male germ-free (GF) and specific pathogen-free (SPF) IQI mice were bred and maintained in the laboratory of Central Institute for Experimental Animals (CIEA, Kawasaki, Kanagwa, Japan). GF mice were housed in a Trexler-type flexible film isolator in a standard germ free state and screened on a weekly basis for germ-free status by sampling feces sterilely and culturing on MRS-agar plates under aerobic and anaerobic conditions. All the GF, SPF, ex-GF mice were kept in a 12: 12-h light/dark cycle and at a temperature of 22±2°C. Nine week old mice (n=3) were sacrificed by cervical dislocation and the intestines were dissected. comparison of the mice with or without enteric flora
2011-09-13 | E-GEOD-32084 | biostudies-arrayexpress
Project description:Research regarding the role of astrocytes as M-NM-2-amyloid (AM-NM-2) degrading cells has broadened our view about the mechanisms how these common glia cells function in AlzheimerM-bM-^@M-^Ys disease (AD). Based on previous studies adult mouse astrocytes are able to degrade AM-NM-2 deposits from AD mouse model and human brain tissue sections ex vivo, contrary to neonatal astrocytes. In this study, we studied the possible altered gene expression profiles of adult and neonatal astrocytes cultured for 22 h on top of the AM-NM-2 burdened tg APdE9 or wild-type mouse brain sections using whole genome microarrays. Quantitative RT-PCR analysis confirmed the significant up-regulation of HtrA serine peptidase 1 (Htra1), metallopeptidase 9 (Mmp9), phosphate regulating gene with homologies to endopeptidases on the X chromosome (Phex) and scavenger receptor class A, member 5 (Scara5) in adult astrocytes, whereas neonatal astrocytes up-regulated Mmp9 and down-regulated genes related to cholesterol transport and synthesis: apolipoprotein E (Apoe), 24-dehydrocholesterol reductase (Dhcr24) and 3-hydroxy-3-methylglutaryl-CoA synthase 1 (Hmgcs1). These findings brought out novel genes which expression is altered during AM-NM-2 clearance in adult and neonatal astrocytes ex vivo. Astrocyte cultures: For the adult astrocyte cultures, hippocampi and cortices were isolated from 6-8-week-old C57Bl/6j wild-type and tg eGFP mice and the tissue was suspended in DMEM/F12 (3:1, Gibco BRL, NY, USA) containing 10 % heat-inactivated fetal bovine serum (Gibco BRL) and 100 U / ml penicillin-streptomycin (Gibco BRL). The cells were treated with Percoll (Sigma-Aldrich, St.Louis, USA) and plated onto poly-L-lysine coated flasks in DMEM/F12 (3:1) containing 10 % heat-inactivated fetal bovine serum, 100 U / ml penicillin-streptomycin and G5 supplement (Gibco BRL). Before the experiments the glial cell cultures were shaken to remove microglia at 200 rpm for 2 h. For the neonatal astrocyte cultures, hippocampi and cortices were isolated from 2-day-old wild-type and eGFP mice according to the protocol described above, except that the culture medium was DMEM (+4500mg/l glucose, + L-glutamine, -pyruvate, Gibco BRL) without G5 supplement and the isolation method included no Percoll treatment. Standard anti-GFAP (1:500; Dako Cytomation, Glostrup, Denmark) immunocytochemistry was used to determine the purity of astrocyte cultures. The cells were incubated with biotinylated goat anti-rabbit IgG (1:200 dilution; Vector Laboratories, CA) secondary antibody and Vectastain ABC Elite kit was used (Vector Laboratories) according to manufacturerM-bM-^@M-^Ys protocol. Hydroxen peroxide (H2O2) and nickel enhanced diaminobenzidine (Ni-DAB) was added to detect the immunoreactivity. Three fields per well and at least three wells per cell type were analyzed for the percentage of Ni-DAB stained cells of all cellular profiles in the field. Adult and neonatal astrocyte cultures both contained on average 99.6 % M-BM-1 0.6 % anti-GFAP immunoreactive astrocytes. Anti-Iba (2 M-BM-5g/ml; Wako, Germany) and anti-CD11b (1:500 dilution; Serotec, UK) antibodies were used to detect possible microglial cells. The cultures contained less than 0.4 % of microglial cells in all experiments. Ex vivo treatments: tg APdE9 / wild-type mouse brain section incubated with neonatal (age 3 d) or adult (age 6-8 wks) mouse eGFP expressing astrocytes (4 x 105 cells / well), n=6. The mouse brain sections used were prepared from tg APdE9 mouse line (created by co-injection of chimeric mouse/human APPSwe and PS1-dE9 vectors, both controlled by their own mouse prion protein promoter element [APdE9 mice (Jankowsky et al. 2004) provided by Prof. Heikki Tanila] and their wild type C57Bl/6j littermates. Before the mRNA isolation process, the samples were pooled (n=3). The purity of the samples was checked with FACS (FACSCalibur, Becton Dickinson, USA) using the analyzing program CellQuestTM version 3.3 (Becton Dickinson, USA). After 22 h incubation the culture medium was removed from the wells and the brain sections with cultured eGFP astrocytes were incubated with 1 x trypsin-EDTA (500 M-BM-5l /well) for up to 15 min at 37M-BM-0 C. Partial detachment (at this point, the astrocytes should not lose the grip completely) of the astrocytes from the underlying brain section was monitored with a standard light microscope. After the incubation the brain sections with cultured astrocytes were carefully removed into small petri dishes filled with FBS-containing culture medium to inactivate the trypsin. Subsequently, the brain sections were immediately examined with fluorescence microscope (Olympus IX-71, Japan). The eGFP astrocytes were separated from the underlying brain section using a special suction hose, which was a modified version from suction hoses typically used for the microinjection techniques. In the other end of the tube there is a pipet tip as a mouthpiece, in the middle of the tube a 0.22 M-BM-5m filter and in the other end a stretched glass capillary (prepared with a Bunsen burner). The green fluorescent eGFP astrocytes were picked up gently from the underlying brain section (without breaking the brain tissue) using wavelength 468 nm of the fluorescence microscope and simultaneous light microscopy. Data normalization and analysis: The raw data was preprocessed with the robust multichip algorithm (Irizarry et al. 2003), normalized per chip to the median. 12 samples were grouped into 4 sample types: adult_wt, adult_tg, neonatal_wt, neonatal_tg. The change in the astrocyte gene expression was identified according to the sections the astrocytes were incubated (WT or TG). The differentially expressed probe sets were further processed using statistical analysis with Welch unpaired t-test assuming unequal variances (p<0.05; fold change > 2.0 or < 0.5). Benjamini-Hochberg false-discovery rate (FDR) correction for multiple testing was used to control the number of false-positives results.
2012-07-13 | E-GEOD-29317 | biostudies-arrayexpress