Gene expression array of irradiated and/or lithium exposed iPSC-derived human neural progenitor cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE234353 | GEO | 2023/06/30
REPOSITORIES: GEO
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Project description:DNA isolation was performed following the DNeasy Blood and Tissue Kit (Qiagen). Cells were irradiated in an CIX2 Xstrahl X-Ray Irradiator with Aluminum filter at a focus-to-skin distance (FSD) of 40 cm and with an energy of 195kV, 10 mA, for and absorbed dose of 4 GY. To allow for assessment of irradiation damage, cells remained in the incubator for 1 hour. Pre-warmed DMEM/F-12 was mixed with the appropriate amount of LiCl powder (Sigma-Aldrich, Cat# L9650-100G), passed through a 0.22 μm filter, and supplemented with 1% Penicillin-Streptomycin, 1% N2, 0.1% B27, 0.1% EGF, and 0.1% FGF2 to produce 3mM Lithium Chloride (LiCl) hNSPC medium.
2023-06-30 | GSE236202 | GEO
Project description:The pulmonary inflammatory response to inhalation exposure to fracking sand dust (FSD) was investigated in a rat model. Adult male Sprague-Dawley rats were exposed by whole-body inhalation to air or an aerosol of FSD at concentrations of 10 or 30 mg/m3, 6 hours/day for 4 days. The control and FSD-exposed rats were euthanized at post-exposure time intervals of 1, 7 or 27days and pulmonary inflammatory, cytotoxic and oxidant responses were determined. Deposition of FSD particles was detected in the lungs of all the FSD-exposed rats. Analysis of bronchoalveolar lavage parameters of toxicity, oxidant generation, and inflammation did not reveal any significant persistent pulmonary toxicity in the FSD- exposed rats. Similarly, the lung histology of the FSD-exposed rats showed only minimal changes in influx of macrophages following the exposure. Determination of global gene expression profiles detected significant differential expressions of only six and five genes in the 10 mg/m3, 1 day post-exposure, and the 30 mg/m3, 7-day post-exposure FSD groups, respectively. Taken together, data obtained from the present study demonstrated that FSD inhalation exposure resulted in minimal/no toxicity or gene expression changes in the lungs of the rats.
2020-10-01 | GSE148255 | GEO
Project description:The pulmonary response to inhalation exposure to diesel exhaust particles (DEP) and fracking sand particles (FSD) was investigated in a rat model. Healthy adult male Sprague-Dawley rats were exposed by whole-body inhalation to air (control) or an aerosol containing DEP at a concentration of 1.0 mg/m3 combined with FSD at concentrations of 30 mg/m3, 6 hours/day for 4 days. The control and DEP/FSD exposed rats were euthanized at post-exposure time intervals of 1, 7, or 27 days and pulmonary inflammatory, cytotoxic, and oxidant responses were determined. Analysis of bronchoalveolar lavage parameters of toxicity such as lactate dehydrogenase activity, oxidant generation, and inflammation revealed only minimal changes in pulmonary toxicity in the DEP/FSD-exposed rats, compared with the time-matched controls. The lung gene expression profiles showed only minimal changes in the DEP/FSD exposed rats compared with the controls. Specifically, there were a total of 6 genes significantly differentially expressed (fold change >1.5 and FDR p<0.05) only at the one-day post-exposure group. The data obtained from the present study demonstrated that DEP/FSD inhalation exposure, under the conditions employed in the present study, resulted in only minimal changes in lung toxicity and gene expression profile in the rats.
2024-12-01 | GSE242155 | GEO
Project description:With a filter of false-discovery rate less than 0.1 and fold change greater than 1.5, 115 genes were found to be up- and 137 were down-regulated in alveolar macrophages during Pneumocystis carinii infection.
2010-04-12 | GSE20149 | GEO
Project description:Background The striking association of HLA-B27 with spondyloarthritis (SpA) has been known for 50 years. However, its pathophysiological significance remains incompletely understood. In the HLA-B27/human-β2 microglobulin (hβ2m) transgenic rat (B27 rat) that spontaneously develops inflammatory phenotype characteristic of SpA, myeloid cells expressing the HLA-B27/h2m transgene are critical for disease induction and functionally impaired. Recently, we produced HLA-B27/hβ2m transgenic Drosophila to study non-canonical effects of HLA-B27. We showed that HLA-B27/h2m expressed in Drosophila wing imaginal disc deregulated BMP pathway by interacting physically with the type I bone morphogenetic protein (BMP) receptor (BMPR1) Saxophone (Sax), leading to a loss of crossveins. Methods Genetic interaction was studied between the activin/TGF pathway and HLA-B27/hβ2m in transgenic Drosophila wings. The HLA-B27-bound peptidome was characterized in wing imaginal discs from transgenic Drosophila by high-performance liquid chromatography and mass spectrometry of the peptide fraction eluted from affinity purified HLA-B27. In mesenteric lymph node (mLN) T cells from B27 rats, physical interaction between HLA-B27 and activin receptor-like kinase-2 (ALK2), ALK3 and ALK5 BMPR1s was assessed by proximity ligation assay and phosphorylation of SMADs and proteins of the non-canonical BMP/TGF pathway induced by its ligands was assessed by flow cytometry. Transcript level of several target genes of the TGF pathway was evaluated by real-time quantitative polymerase chain reaction in mLN subsets of T cells from B27 and control nontransgenic rats, with and without treatment by TGF. Results We showed that, in addition to the BMP pathway, inappropriate signaling through the activin/transforming growth factor β (TGFβ) pathway, involving Baboon (Babo) BMPR1, also contributed to the crossveinless wing phenotype. We identified a set of peptides bound to HLA-B27 with canonical binding motif in HLA-B27/hβ2m transgenic Drosophila wing imaginal disc, despite the lack of peptide loading complex. We then demonstrated specific physical interaction, between HLA-B27/h2m and both mammalian orthologues of Sax and Babo, i.e. ALK2 and ALK5 (i.e. TGF receptor I), in the mLN cells from B27 rat. The magnitude of phosphorylation of SMAD2/3 in response to TGFβ1 was increased in T cells from adult and premorbid B27 rats, showing evidence for deregulated TGF pathway. Accordingly, expression of several target genes of the pathway was increased in T cells from B27 rats, in basal conditions and/or after TGFexposure, including Foxp3, Rorc, Runx1 and Maf. Interestingly. Tgfb1 expression was reduced in naïve T cells from B27 rats, even premorbid, an observation consistent with a pro-inflammatory pattern. Conclusions This study highlights a complex interplay between HLA-B27 and the BMP/TGFβ pathways in both Drosophila and B27 rat. Given the importance of the TGF pathway in CD4+ T cells differenciation and regulation, the disturbance caused by HLA-B27 could contribute to the abnormal expansion of pro-inflammatory T helper 17 cells and the altered regulatory T cell phenotype observed in B27 rat.
2024-10-17 | PXD047119 | Pride
Project description:Erythrocytes were infected with Plasmodium chabaudi chabaudi AS strain expressing GFP. After 2 or 3 passages, a suspension of 100,000 infected erythrocytes in 1X-PBS (adjusted volume of 200µl) were injected i.p. in wild-type C57BL/6j mice and Homozygous mutant Ighm tm1Cgn mice (lacking mature B-cells). As a control, wild-type C57BL/6j mice and Homozygous mutant Ighm tm1Cgn mice were injected i.p with PBS. There were 3 mice (biological replicates) for each of the 4 experimental conditions. Parasitemia was monitored by flow cytometry and PCR weekly. 117 days post infection, mice were euthanized in CO2 chamber and femur and tibia bones were collected in 1X-HBSS/2% FBS. The cells were removed from the bones and the erythrocytes lysed by hypotonic lysis. Cells (20 million) were antibody stained and the 100K cells (Live/CD11b+/Ly6G-/F4/80+) were sorted in 1X-HBSS/20% FBS. For each sample. 50,000 viable cells were pelleted and lysed with cold ATAC-Resuspension Buffer (RSB) containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin and incubated in ice for 3 minutes. The lysaste was washed with 1 ml of cold ATAC-RSB containing 0.1% Tween-20 but NO NP40 or digitonin. Nuclei were pelleted at 500 RCF for 10 min at 4 degrees celcius. The supernatant was discarded and the pellet was resuspended in 50 uL of transposition mixture (25 ul 2x TD buffer, 2.5 ul transposase (100nM final), 16.5 ul PBS, 0.5 ul 1% digitonin, 0.5 ul 10% Tween-20, 5 ul H2O). The reaction was incubated for 30 minutes in a thermomixer with 1000 RPM mixing. Zymo DNA Clean and concentrator kit (cat# D4014) was used as a cleanup step. The DNA was amplified at 98 degrees C for 30 seconds, then 13 cycles of: 98 degrees C for 10 seconds, 63 degrees C for 30 seconds, 72 degrees C for 1 minute.The library was evaluated in an Agilent TapeStation system and the DNA concentration evaluated by Qubit. Sequencing was performed on Illumina Nextseq 500 with Buffer cartridge v2: Ref: 15057941, High output reagent cartridge v2: Ref: 15057934, NextSeq accessory Box v2: Ref: 15058251, and High output Flow Cell cartridge v2.5: Ref: 20022408
2022-01-12 | E-MTAB-10086 | biostudies-arrayexpress
Project description:Patients received standardized coartem therapy. Briefly, each pill contains 20 mg of artemether and 120 mg of lumefantrine. The dose and total coarse of tablets is based on the patients body weight. Blood was drawn from patients prior to anti-malarial treatment (day 0) and after treatment (day42 for children and day 28 for adults). Peripheral Blood Mononuclear Cells were isolated from all patients. Briefly, for PBMC isolation, whole blood from was diluted 1:2 in sterile PBS and overlaid on Ficoll Paque-PLUS in 50 mL conical tubes and centrifuged 800xg for 15 minutes at 25°C with no brake. Resulting buffy coats were collected and washed twice in RPMI 1640 medium, and then cells were treated with Red Blood Cell Lysis Buffer for 3 minutes at room temperature. Cells were washed in RPMI and counted on a hemacytometer. Monocytes were purified from PBMC using a miltenyi Pan Monocyte Isolation negative selection kit according to the manufacturer's instructions. For each sample. 50,000 viable cells were pelleted and lysed with cold ATAC-Resuspension Buffer (RSB) containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin and incubated in ice for 3 minutes. The lysaste was washed with 1 ml of cold ATAC-RSB containing 0.1% Tween-20 but NO NP40 or digitonin. Nuclei were pelleted at 500 RCF for 10 min at 4 degrees celcius. The supernatant was discarded and the pellet was resuspended in 50 uL of transposition mixture (25 ul 2x TD buffer, 2.5 ul transposase (100nM final), 16.5 ul PBS,0.5 ul 1% digitonin, 0.5 ul 10% Tween-20, 5 ul H2O). The reaction was incubated for 30 minutes in a thermomixer with 1000 RPM mixing. Zymo DNA Clean and concentrator kit (cat# D4014) was used as a cleanup step. The DNA was amplified at 98 degrees C for 30 seconds, then 13 cycles of: 98 degrees C for 10 seconds, 63 degrees C for 30 seconds, 72 degrees C for 1 minute.The library was evaluated in an Agilent TapeStation system and the DNA concentration evaluated by Qubit. Sequencing was performed on Illumina Nextseq 500 with Buffer cartridge v2: Ref: 15057941, High output reagent cartridge v2: Ref: 15057934, NextSeq accessory Box v2: Ref: 15058251, and High output Flow Cell cartridge v2.5: Ref: 20022408
2022-04-24 | E-MTAB-11643 | biostudies-arrayexpress
Project description:HLA-B27 is a class I major histocompatibility (MHC-I) allele that confers susceptibility to the rheumatic disease ankylosing spondylitis (AS) by an unknown mechanism. ERAP1 is an aminopeptidase that trims peptides in the endoplasmic reticulum for binding to MHC-I molecules. ERAP1 shows genetic epistasis with HLA-B27 in conferring susceptibility to AS. Male HLA-B27 transgenic rats develop arthritis and serve as an animal model of AS, whereas female B27 transgenic rats remain healthy. We used large-scale quantitative mass-spectrometry to identify over 15,000 unique HLA-B27 peptide ligands, isolated after immunoaffinity purification of the B27 molecules from the spleens of HLA-B27 transgenic rats. Heterozygous deletion of ERAP1, which reduced ERAP1 level to less than half, had no qualitative or quantitative effects on the B27 peptidome. Homozygous deletion of ERAP1 affected approximately one third of the B27 peptidome, but left most of the B27 peptidome unchanged, suggesting the possibility that some of the HLA-B27 immunopeptidome is not processed in the presence of ERAP1. Deletion on ERAP1 was permissive for the AS-like phenotype. Deletion of ERAP1 increased mean peptide length, and increased the frequency of C-terminal hydrophobic residues and of N-terminal Ala, Ser or Lys. The presence of ERAP1 increased the frequency of C-terminal Lys and Arg, of Glu and Asp at intermediate residues, and of N-terminal Gly. Several peptides of potential interest in AS pathogenesis, previously identified in human cell lines, were isolated. However, rats susceptible to arthritis had B27 peptidomes similar to those of non-susceptible rats, and no peptides were found to be uniquely associated with arthritis. Whether specific B27-bound peptides are required for AS pathogenesis remains to be determined.
2017-02-13 | PXD005502 | Pride