Differential Expression genes between Moniezia expansa and Moniezia benedini
Ontology highlight
ABSTRACT:
ORGANISM(S): Moniezia expansa Moniezia benedeni
PROVIDER: GSE14046 | GEO | 2009/12/01
SECONDARY ACCESSION(S): PRJNA112407
REPOSITORIES: GEO
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Project description:We used complementary DNA microarray to analyze the gene expression profiles different between Moniezia expansa and Moniezia benedini. A total of 4056 sequences including full length and partial complementary DNAs representing novel, known, and control genes were analyzed. We utilized cDNA array for detection of gene expression profiles of different proglottids of M.expansa and M.benedini. The present study provides some interesting data that only expressed in M.expansa mature proglottids, immature proglottids, gravid proglottids of M.benedini vs common reference scolex-neck proglottids tissue of M.expansa. 2 biological replicates for each experiments.
2010-05-19 | E-GEOD-14046 | biostudies-arrayexpress
Project description:This study utilized oligonucleotide microarrays to examine gene expression profiles in pheochromocytomas from 23 patients; 11 VHL tumors and 12 MEN2 tumors. RNA was extracted and linearly amplified once, then dye-labeled and co-hybridized to a microarray with over 34,000 oligos representing more than 25,000 unique human genes. In validation of our strategy, many genes known to have elevated expression in MEN2 tumors (e.g., CALM1, CHGB, CABP1and NPY) and several genes known to be specific to VHL (e.g., AQP1) were independently identified by this approach. In addition to known genes, our method has identified several hundred of previously uncharacterized genes that are enriched in the MEN2 or VHL tumors.
2008-09-15 | GSE12642 | GEO
Project description:We used complementary DNA microarray to analyze the gene expression profiles in different proglottids of Moniezia expansa. A total of 4056 sequences including full length and partial complementary DNAs representing novel, known, and control genes were analyzed. We utilized cDNA array for detection of gene expression profiles of different proglottids of M.expansa. The present study provides some interesting data to better understanding the mechanisms of procreation and may suggest some potential target molecules for a more effective treatment on verminosis. 1.Construction of microarray By clustering the 2,642 sequences from the cDNA library, 1,078 unigenes of M.expansa, including full-length and partial cDNAs representing novel or known genes, were obtained for array construction. The negative control spots of non-tapeworm origin in the chip were the rice genes (48 spots). In addition, the array included 9 known genes(54 spots) as positive control genes that were provided by our library and 24 empty spots. Unigenes and all control genes were cloned into plasmid vector. The DZH (TC) chips were constructed by United Gene Holdings Limited of China (Shanghai, China) according to the method described by Li et al. The cDNA inserts were amplified by use of the polymerase chain reaction (PCR) using universal primers to plasmid vector sequences and were then purified. All PCR products were examined by agarose gel electrophoresis to ensure the quality and the identity of the amplified clones as expected. Then the amplified PCR products were dissolved in a buffer containing 3ÃSSC solution. The solution with amplified PCR products were spotted onto glass slides (model DZH-TC) using a Cartesian PixSys 7500 motion control robot (Cartesian Technologies, Irvine, CA., USA) fitted with ChipMaker Micro-Spotting Technology (TeleChem International, Sunnyvale, CA., USA). The glass slides were then hydrated for 2 h in 70% humidity, dried for 0.5 h at room temperature, and UV crosslinked (65 mj/cm). They were further processed at room temperature by soaking in 0.2% sodium dodecyl sulfate (SDS) for 10 min, distilled H2O for 10 min, and 0.2% sodium borohydride (NaBH4) for 10 min. The slides were dried again and ready for use. 2.RNA preparation and probe labeling Total RNAs were isolated from 6 M.expansas with scolex-neck proglottids, immature proglottids, mature proglottids and gravid proglottids. Tissue samples were ground into a fine powder in a 10 cm ceramic mortar (RNase-free) and were then homogenized in TRIzol (Biostar, Shanghai, China). After centrifugation, the supernatant was separated from the organic phase and was extracted in an equal volume of chloroform. The aqueous phase was then precipitated by an equal volume of isopropanol at 4°C, centrifuged to pellet the RNA and dissolved in Milli-Q H2O. The fluorescent cDNA probes were prepared through reverse transcription with Cy3- or Cy5-deoxy UTP (Amersham Pharmacia Biotech, Piscataway, NJ, USA) as follows: 5 μg of oligo(dT18) was added and annealed to 3μg of mRNA by heating the mixture to 70ËC for 10 min, and then chilling it on ice. The final reaction buffer mixture contained dNTPs (200 μM dATP, dCTP and dGTP; 60 μM dTTP; and 60 μM Cy3- or Cy5-dUTP), 2 μl of Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA, USA) and 1Ãreaction buffer 10μl. The reactions were carried out at 42 ºC for 2 h. RNA was hydrolyzed by adding 4 μl of 2.5 M NaOH, incubating the mixture at 65 ºC for 10 min and then neutralizing it with 4 μl of 2.5 M HCl. The RNA samples from the scolex-neck proglottids were labeled with Cy3-dUTP and those from immature proglottids, mature proglottids and gravid proglottids, respectively, were labeled with Cy5-dUTP. The two color probes were then mixed and diluted to 500 μl with TE, and concentrated using a Microcon YM-30 filter (Millipore, Bedford, MA, USA) to 10 μl. The sample was then vacuum dried. 3.Hybridization The probe was dissolved in 20 ml of hybridization solution (5ÃSSC (0.75M NaCl and 0.075M sodium citrate), 0.4% SDS, 50% formamide). Microarrays were pre-hybridized with a hybridization solution containing 0.5 mg/ml of denatured salmon sperm DNA at 42°C for 6 h. Fluorescent probe mixtures were denatured at 95°C for 5 min and then applied onto the pre-hybridized chip under a cover glass. Chips were hybridized at 42°C for 15-17 h. Next, the hybridized chips were each washed at 60°C for 10 min in solutions of 2ÃSSC and 0.2% SDS, 0.1ÃSSC and 0.2% SDS, 0.1ÃSSC and then dried at room temperature. 4.Detection and analysis The chips were scanned with a ScanArray 4000 (GSI Lumonics, Bellerica, MA, USA) at two wavelengths, 635 and 532 nm, to detect emission from both Cy5 and Cy3, respectively. The acquired images were analyzed using GenePix Pro 3.0 software. The intensities of each spot at the two wavelengths represent the quantity of Cy3-dUTP and Cy5-dUTP. Ratios of Cy5 to Cy3 were computed using the GenePix Pro 3.0 median of ratio method. Overall intensities were normalized using the corresponding GenePix default normalization factor. All spots flagged âBadâ or âNot Foundâ by GenePix software were removed from the final data. Only genes with raw intensity values for both Cy3 and Cy5 of >200 were chosen for differential analysis. Genes were identified as differentially expressed if the ratio was >2 or <0.5, or the absolute value of base 2 logarithm of the ratio was >1 or < -1. mature proglottids, immature proglottids, gravid proglottids vs common reference scolex-neck proglottids tissue. 2 biological replicates for each experiments.
2010-05-19 | E-GEOD-13892 | biostudies-arrayexpress
Project description:Chromosome conformation-capture technologies are widely used in 3D genomics; however, experimentally, such methods have high-noise limitations and, therefore, require significant bioinformatics efforts to extract reliable distal interactions. Miscellaneous undesired linear DNAs, present during proximity-ligation, represent a main noise source which needs to be minimized or eliminated. In this study, different exonuclease combinations were tested to remove linear DNA fragments from a circularized DNA preparation. This method efficiently removed linear DNAs, raised the proportion of annulation and increased valid-pairs ratio from 30-40% to 70-80% for enhanced interaction detection in standard Hi-C. This strategy is applicable for development of various 3D genomics technologies, or optimization of Hi-C sequencing efficiency.
2020-04-08 | GSE125656 | GEO
Project description:We used complementary DNA microarray to analyze the gene expression profiles in different proglottids of Moniezia expansa. A total of 4056 sequences including full length and partial complementary DNAs representing novel, known, and control genes were analyzed. We utilized cDNA array for detection of gene expression profiles of different proglottids of M.expansa. The present study provides some interesting data to better understanding the mechanisms of procreation and may suggest some potential target molecules for a more effective treatment on verminosis. 1.Construction of microarray By clustering the 2,642 sequences from the cDNA library, 1,078 unigenes of M.expansa, including full-length and partial cDNAs representing novel or known genes, were obtained for array construction. The negative control spots of non-tapeworm origin in the chip were the rice genes (48 spots). In addition, the array included 9 known genes(54 spots) as positive control genes that were provided by our library and 24 empty spots. Unigenes and all control genes were cloned into plasmid vector. The DZH (TC) chips were constructed by United Gene Holdings Limited of China (Shanghai, China) according to the method described by Li et al. The cDNA inserts were amplified by use of the polymerase chain reaction (PCR) using universal primers to plasmid vector sequences and were then purified. All PCR products were examined by agarose gel electrophoresis to ensure the quality and the identity of the amplified clones as expected. Then the amplified PCR products were dissolved in a buffer containing 3×SSC solution. The solution with amplified PCR products were spotted onto glass slides (model DZH-TC) using a Cartesian PixSys 7500 motion control robot (Cartesian Technologies, Irvine, CA., USA) fitted with ChipMaker Micro-Spotting Technology (TeleChem International, Sunnyvale, CA., USA). The glass slides were then hydrated for 2 h in 70% humidity, dried for 0.5 h at room temperature, and UV crosslinked (65 mj/cm). They were further processed at room temperature by soaking in 0.2% sodium dodecyl sulfate (SDS) for 10 min, distilled H2O for 10 min, and 0.2% sodium borohydride (NaBH4) for 10 min. The slides were dried again and ready for use. 2.RNA preparation and probe labeling Total RNAs were isolated from 6 M.expansas with scolex-neck proglottids, immature proglottids, mature proglottids and gravid proglottids. Tissue samples were ground into a fine powder in a 10 cm ceramic mortar (RNase-free) and were then homogenized in TRIzol (Biostar, Shanghai, China). After centrifugation, the supernatant was separated from the organic phase and was extracted in an equal volume of chloroform. The aqueous phase was then precipitated by an equal volume of isopropanol at 4°C, centrifuged to pellet the RNA and dissolved in Milli-Q H2O. The fluorescent cDNA probes were prepared through reverse transcription with Cy3- or Cy5-deoxy UTP (Amersham Pharmacia Biotech, Piscataway, NJ, USA) as follows: 5 μg of oligo(dT18) was added and annealed to 3μg of mRNA by heating the mixture to 70˚C for 10 min, and then chilling it on ice. The final reaction buffer mixture contained dNTPs (200 μM dATP, dCTP and dGTP; 60 μM dTTP; and 60 μM Cy3- or Cy5-dUTP), 2 μl of Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA, USA) and 1×reaction buffer 10μl. The reactions were carried out at 42 ºC for 2 h. RNA was hydrolyzed by adding 4 μl of 2.5 M NaOH, incubating the mixture at 65 ºC for 10 min and then neutralizing it with 4 μl of 2.5 M HCl. The RNA samples from the scolex-neck proglottids were labeled with Cy3-dUTP and those from immature proglottids, mature proglottids and gravid proglottids, respectively, were labeled with Cy5-dUTP. The two color probes were then mixed and diluted to 500 μl with TE, and concentrated using a Microcon YM-30 filter (Millipore, Bedford, MA, USA) to 10 μl. The sample was then vacuum dried. 3.Hybridization The probe was dissolved in 20 ml of hybridization solution (5×SSC (0.75M NaCl and 0.075M sodium citrate), 0.4% SDS, 50% formamide). Microarrays were pre-hybridized with a hybridization solution containing 0.5 mg/ml of denatured salmon sperm DNA at 42°C for 6 h. Fluorescent probe mixtures were denatured at 95°C for 5 min and then applied onto the pre-hybridized chip under a cover glass. Chips were hybridized at 42°C for 15-17 h. Next, the hybridized chips were each washed at 60°C for 10 min in solutions of 2×SSC and 0.2% SDS, 0.1×SSC and 0.2% SDS, 0.1×SSC and then dried at room temperature. 4.Detection and analysis The chips were scanned with a ScanArray 4000 (GSI Lumonics, Bellerica, MA, USA) at two wavelengths, 635 and 532 nm, to detect emission from both Cy5 and Cy3, respectively. The acquired images were analyzed using GenePix Pro 3.0 software. The intensities of each spot at the two wavelengths represent the quantity of Cy3-dUTP and Cy5-dUTP. Ratios of Cy5 to Cy3 were computed using the GenePix Pro 3.0 median of ratio method. Overall intensities were normalized using the corresponding GenePix default normalization factor. All spots flagged “Bad” or “Not Found” by GenePix software were removed from the final data. Only genes with raw intensity values for both Cy3 and Cy5 of >200 were chosen for differential analysis. Genes were identified as differentially expressed if the ratio was >2 or <0.5, or the absolute value of base 2 logarithm of the ratio was >1 or < -1.
2009-12-01 | GSE13892 | GEO
Project description:To identify changes in gene expression with apoptosis, we investigated differential gene expression in a colon carcinoma model established in human cell line CaCO2. We arrayed 384 oligos (representing 384 genes including positive and negative controls) related with Apoptosis for detection of differences at gene expression levels in some of the very important apoptotic biomarkers
2016-01-01 | GSE53701 | GEO
Project description:This study utilized oligonucleotide microarrays to examine gene expression profiles in pheochromocytomas from 23 patients; 11 VHL tumors and 12 MEN2 tumors. RNA was extracted and linearly amplified once, then dye-labeled and co-hybridized to a microarray with over 34,000 oligos representing more than 25,000 unique human genes. In validation of our strategy, many genes known to have elevated expression in MEN2 tumors (e.g., CALM1, CHGB, CABP1and NPY) and several genes known to be specific to VHL (e.g., AQP1) were independently identified by this approach. In addition to known genes, our method has identified several hundred of previously uncharacterized genes that are enriched in the MEN2 or VHL tumors. A 34k expression arrays were generated by printing Oligo nucleotides from the Qiagen HV3 set onto epoxy coated slides (Corning, Inc). Total RNA from pheochrmocytoma tumors or normal adrenals was amplified using an Ambion kit (Cat#1753), labeled with Cy5 and cy3 dyes respectively and hybridized overnight to the oligo chip in a MAUI chamber.
2008-09-15 | E-GEOD-12642 | biostudies-arrayexpress
Project description:Angiotensin II type 1 receptors (AT1Rs) are one of the most widely studied G protein-coupled receptors. To fully appreciate the diversity in cellular signaling profiles activated by AT1R transducer-biased ligands, we utilized peroxidase-catalyzed proximity labeling to capture proteins in close proximity to AT1Rs in response to six different ligands: Angiotensin II (full agonist), S1I8 (partial agonist), TRV055 and TRV056 (G protein-biased agonists), TRV026 and TRV027 (β-arrestin biased agonists) at 90s, 10min, and 60min after stimulation. We systematically analyzed the kinetics of AT1R trafficking and determined that distinct ligands lead AT1R to different cellular compartments for downstream signaling activation and receptor degradation/recycling. Distinct proximity labelling of proteins from a number of functional classes, including GTPases, adaptor proteins, and kinases were activated by different ligands suggesting unique signaling and physiological roles of the AT1R. Ligands within the same class, i.e. either G protein-biased or -arrestin-biased, shared high similarity in their labelling profiles. Comparison between ligand classes revealed distinct signaling activation such as greater labeling by G protein biased ligands on ESCRT-0 complex proteins that act as sorting machinery for ubiquitinated proteins. Our study provides a comprehensive analysis of AT1R receptor trafficking kinetics and signaling activation profiles induced by distinct classes of ligands.
2021-03-25 | PXD023814 | Pride
Project description:To study the fibroblast to myofibroblast differentiation in a normal or pathological situation, NHDF (Normal human dermal fibroblast) obtained from two different healthy donors (donors A and B) were either left untreated (T-E-) either treated with TGF-beta alone (T+E-), or with exudate from chronic wounds (T-E+) or both (T+E+). For each different treatment we performed mRNA deep sequencing 3 times : twice with cells from donor A and once with cells from donor B.We focused our study on gene expression profile as a representation of cell fate. We performed mRNA deep sequencing analysis of the 4 different conditions. For each condition, mRNA deep sequencing was performed 3 times : twice with cells from donor A and once with cells from donor B.Comparing the mRNA abundance between the different treatments, we identified 3 lists of genes characterizing the different gene expression states: 171 genes in List I representing the genes differentially expressed during normal fibroblast to myofibroblast differentiation, 409 genes in List II representing the genes differentially expressed upon exudate-only treatment and 1006 genes in List III representing the genes differentially expressed upon the combination of exudate and TGF-beta treatments.
2015-12-16 | GSE49159 | GEO