GNPS - Mouse dietary study - iron supplementation and depletion
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive
ORGANISM(S): Mus Musculus (ncbitaxon:10090)
SUBMITTER: 
Pieter C. Dorrestein
PROVIDER: MSV000084783 | GNPS | Thu Jan 09 14:50:00 GMT 2020
REPOSITORIES: GNPS
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Project description:This study investigates how dietary iron deficiency affects the transcriptional profile of spleen-derived red pulp macrophages (RPMs) in mice. Female C57BL/6J mice were divided into two groups: Iron-deficient (ID) group: fed a low-iron diet (<5 ppm Fe) from 4 to 9 weeks of age. Iron-balanced (IB) group: maintained on a standard iron-sufficient diet (200 ppm Fe) over the same period. At 9 weeks of age, mice were sacrificed, and spleens were harvested. RPMs were FACS-sorted using F4/80 and TREML4 markers, approx. 100 000 RPMs were sorted/sample. Sorting was performed to TRIzol, and RNA was isolated using Direct-zol columns. For all samples RIN was at least 7. Sequencing was conducted on the Illumina NextSeq 500 platform at the EMBL Genomics Core Facility (Heidelberg, Germany) using 75 bp single-end reads. The dataset consists of 8 samples: 4 from iron-deficient mice (S1_DEF to S4_DEF) 4 from control mice (S5_BAL to S8_BAL) This RNA-seq dataset enables comparison of gene expression changes in red pulp macrophages under conditions of iron deficiency, contributing to our understanding of iron homeostasis and macrophage adaptation.
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Project description:Mouse Iron Distribution Dynamics
Dynamic model of iron distribution in mice. This model includes normal iron and radioactive labelled tracer iron species and was used for parameter estimation given the data from Lopes et al. 2010 for mice fed an adequate iron diet.
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Project description:Mouse Iron Distribution Dynamics
Dynamic model of iron distribution in mice. This model includes only normal iron with the parameters that fit the data from Lopes et al. 2010 for mice fed an adequate iron diet.
This model does not include the radioiron tracer species. It is appropriate to study the properties in conditions where no tracers are used (for example for steady state analysis).
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Project description:Mouse Iron Distribution Dynamics
Dynamic model of iron distribution in mice. This model includes only normal iron with the parameters that fit the data from Lopes et al. 2010 for mice fed a deficient iron diet.
This model does not include the radioiron tracer species. It is appropriate to study the properties in conditions where no tracers are used (for example for steady state analysis).
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Project description:Mouse Iron Distribution Dynamics
Dynamic model of iron distribution in mice. This model includes only normal iron with the parameters that fit the data from Lopes et al. 2010 for mice fed a rich iron diet.
This model does not include the radioiron tracer species. It is appropriate to study the properties in conditions where no tracers are used (for example for steady state analysis).
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Project description:Mouse Iron Distribution Dynamics
Dynamic model of iron distribution in mice. This model attempts to fit the radioiron tracer data from Lopes et al. 2010 for mice fed iron deficient and rich diets by adjusting the rate of iron intake (vDiet) and the hepcidin synthesis rate (vhepcidin) independently for each experiment. All other parameters are those that provide the best fit for the adequate diet.
This model includes the radioiron tracer species.
Differences in parameter values between deficient, rich, and adequate diets:
Diet
vDiet
vhepcidin
Adequate
0.00377422
1.7393e-08
Deficient
0
8.54927e-09
Rich
0.00415624
2.30942e-08
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Project description:Gene expression along the crypt-villus (C-V) axis was analyzed using cryostat sectioning to isolate fractions representing the crypts (bottom) and villus tops (top). These fractions were used for analyzing gene expression in iron replete Wistar rats (++), iron deficient Wistar rats (low iron), and in iron deficient Wistar rats fed iron for 3 and 6 days (iron-fed). Differences were observed between the crypts and villus tops in the expression of genes associated with Wnt and BNP signaling, cell proliferation and apoptosis, lipid and iron transport and metabolism. Gene expression in villus crypts and tops was also compared between Wistar and Belgrade rats (bb) and Belgrade rats fed iron (iron-fed) particularly as related to iron absorption and metabolism to define the affects of the mutation in DMT1 in the Belgrade rat on the expression of genes related to iron absorption and metabolism and the response to iron feeding. Keywords: iron stress response A colony of Wistar strain rats (++) and Belgrade (bb) rats on a Wistar background maintained in our animal quarters was used for this study. Twelve one-month old ++ rats were separated into 3 groups of four rats each. Group 1 rats (samples 1-8) were fed a normal diet and served as control animals. Group 2 (samples 9-16) and Group 3 rats (samples 17-22) were fed a low iron diet and bled 2-3 ml every three days for 4 weeks and served as iron deficient rats (low-iron). Group 3 rats, of which one rat died during anesthesia while undergoing phlebotomy, were fed iron supplementation in drinking water (50 µM Ferric ammonium citrate) for the three days before sacrifice (iron-fed). Rats were fasted overnight, killed by injection of pentobarbital sodium and a 1-cm duodenal segment 1 cm distal from the pylorus was cryostat sectioned at the right angle to the crypt-villus axis and the sections representing the top one-third of villus (top) and the bottom one-third of the villus were pooled for RNA isolation. For the study of Belgrade rats, eleven bb rats were divided into 3 groups with the 4 rats in Group 1 (samples 23-30) maintained on a normal diet, the 4 rats in Group 2 (samples 31-38) fed iron for 3 days prior to sacrifice, and the 3 rats in Group 3 (samples 39-44) fed iron for 6 days prior to sacrifice. All procedures for the bb rats were the same as described above for the ++ rats. An additional ++ rat (samples 45-46) was similarly analyzed in a separate experiment.
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