Schistosoma japonicum gender-associated differentially expressed genes
Ontology highlight
ABSTRACT:
ORGANISM(S): Schistosoma japonicum
PROVIDER: GSE3641 | GEO | 2012/03/05
SECONDARY ACCESSION(S): PRJNA93763
REPOSITORIES: GEO
Similar Datasets
Project description:Suppression subtractive hybridization(SSH) libraries of Schistosoma japanicum female and male worms were constructed by using Clontech PCR-selectTM cDNA subtraction kit. S.japonicum cDNA microarrays were fabricated using female and male cDNA clones originating from SSH libraries. female-associated and Male-associated differentially expressed gene clones were obtained, Analysis of gender-associated differentially expressed genes helps to determine which genes are important to sexual maturation of schistosome and better understand schistosome biology and host-parasite relationship, facilitate the discovery of novel gene products that could represent targets for the development of new drugs and vaccines to control chitosomiasis. Keywords: gender-associated Four Samples were analyzed about Schistosoma japonicum gender-associated differentially expressed genes
2012-03-05 | E-GEOD-3641 | biostudies-arrayexpress
Project description:We utilised a 22,575 feature custom oligonucleotide DNA microarray designed from public domain databases of schistosome expressed sequence tags to explore differential gene expression between the Philippine (SJP) and Chinese (SJC) strains of S. japonicum, and between male and female S. japonicum. We found that 593, 664 and 426 probes were differentially expressed between the two geographical strains when we compared mix sexed adults, male worms and female worms. Additionally, the study revealed that 1,163 male- and 1,016 femaleassociated probes were differentially expressed in SJP whereas 1,047 male- and 897 female-associated probes were differentially expressed in SJC. Keywords: Strain and Gender Comparison
2006-07-07 | GSE5234 | GEO
Project description:High salinity is one of the most serious threats to crop production. To 1 better understand the molecular basis of plant responses to salt stress, we combined suppression subtractive hybridization (SSH) and microarray approaches to identify the potential important or novel genes involved in salt tolerance. First, SSH libraries were constructed for two cultivated tomato (Solanum lycopersicum) genotypes: LA2711, a salt tolerant cultivar, and ZS-5, a salt sensitive cultivar, to compare salt treatment and non-treatment plants. Then a subset of clones from these SSH libraries were used to construct a tomato cDNA array and microarray analysis was carried out to verify the expression changes of this set of clones upon salt treatment at various time points compared to the corresponding non-treatment controls. A totalof 201 non-redundant genes differentially expressed upon 30 min of salt stress treatment either in LA2711 or ZS-5 were identified from microarray analysis, most of which were not previously associated with salt stress. The diversity of the putative functions of these genes indicated that salt stress resulted in a complex response in tomato plants. Keywords: gene expression, genotype, microarray, salt stress, SSH, tomato
2007-01-09 | GSE4961 | GEO
Project description:Screening cDNA clones from SSH library by hybridization with cDNA used to construct the library. Treated samples were drought-stressed cowpea plants, and control samples were cowpea plants subjected to a standard watering regime. cDNA clones from forward and reverse libraries are spotted on the same array, but data from each library were analysed separately after normalization using SSHscreen software (http://microarray.up.ac.za/SSHscreen ) to calculate Enrichment Ratio 3 (ER3) and Enrichment Ratio 2 (ER2) values for each clone. ER3 is a measure of differential expression, and was determined using a set of hybridizations with unsubtracted treated (UT) and unsubtracted control (UC) cDNA. ER2 is a measure of the relative abundance of a clone's transcript in the original tester sample, relative to other transcripts in the sample prior to the SSH process. ER2 for the forward library was determined using a set of hybridizations with subtracted treated (ST) and unsubtracted treated (UT) cDNA. ER2 for the reverse library is determined using a set of hybridizations with subtracted control (SC) and unsubtracted control (UC) cDNA.
2010-03-22 | GSE20273 | GEO
Project description:In this study we have tried to utilize the unique aspects of the T. ruralis response to desiccation and rehydration to design a strategy to identify rehydrins that are of low abundance and perhaps completely novel to the desiccated or rehydration transcriptomes. We have constructed two Subtractive Suppression Hybridization (SSH) libraries (Diatchenko et al., 1996) that are designed to enrich for differentially expressed low-abundance transcripts contained within gametophytic cells either in the slow-dried state (mRNP sequestrated rehydrin transcripts) or cells that have been rapidly dried, rehydrated and sampled at 2h of hydration (rehydrin and recovery transcripts) when the translational change in gene expression is at its peak (Oliver 1991). To achieve this aim we constructed SSH libraries using PolyA RNA isolated from the polysomal (mRNP) fractions from the slow-dried and 2h rehydrated rapid dried gametophytes selected against PolyA RNA from hydrated control gametophytes as the source for driver cDNA. Collections of cDNA clones from each library were sequenced and used to generate a small T. ruralis SSH cDNA microarray for expression profiling of both total RNA extracts for transcript accumulation assessments and polysomal RNA extracts for transcript sequestration and recruitment assessments.
2009-01-31 | GSE13680 | GEO
Project description:Background: In immunodeficient mice, the growth and reproduction of schistosome were significantly retarded, and their virulence on the host was also weakened. Some studies have suggested that host factors including endocrine and immune signals can modulate the parasite’s development and maturation. However, it is still not clear for the molecular mechanisms underlying the growth and maturation regulation of schistosome. Methods: We isolated the total RNAs of female and male schistosome from immunodeficient SCID mice and immunocompetent BALB/c mice (labeled as S_F, S_M, B_F and B_M) obtained at five weeks post infection with cercariae, and constructed cDNA libraries of small RNAs using small RNA sample pre kit for small RNA deep sequencing on an Illumina (Solexa) platform. Results: Of the 122 (75 known and 47 novel) identified S. japonicum-specific miRNAs, statistical analysis revealed that 33 miRNAs (17 miRNAs were up-regulated and 16 were down-regulated, P<0.05) in female schistosome and 33 miRNAs (13 miRNAs were up-regulated and 20 were down-regulated, P<0.05) in male schistosome from SCID mice were differentially expressed when compared with those from BALB/c mice. The Venn diagram of the differentially expressed miRNAs shows 21 miRNAs were common between S_F vs B_ F and S_M vs B_M, 12 miRNAs were specific in female comparison, and other 12 were specific in male comparison. Conclusions: This study provides a comparative microRNAs expression profiles of schistosomes derived from SCID mice and immunocompetent BALB/c mice. A number of microRNAs were identified to potentially participate in regulating the development of schistosomes. These findings lay the foundation for schistosomiasis research in regulation of the development of schistosomes and provide a valuable resource for screening antischistosomal intervention targets or vaccine candidates.
2020-11-06 | GSE122318 | GEO
Project description:Systemic Lupus Erythematosus (SLE) is a systemic autoimmune disease that displays a significant gender difference in terms of incidence and severity. However, the underlying mechanisms accounting for sexual dimorphism remain unclear. To reveal the heterogeneity in the pathogenesis of SLE between male and female patients. PBMC were collected from 15 patients with SLE (7 males, 8 females) and 15 age-matched healthy controls (7 males, 8 females) for proteomic analysis. Enrichment analysis of proteomic data revealed that type I interferon signaling and neutrophil activation networks mapped to both male and female SLE, while male SLE has a higher level of neutrophil activation compared with female SLE. Our findings define gender heterogeneity in the pathogenesis of SLE and may facilitate the development of gender-specific treatments.
2022-08-12 | PXD033144 | Pride
Project description:In this study we have tried to utilize the unique aspects of the T. ruralis response to desiccation and rehydration to design a strategy to identify rehydrins that are of low abundance and perhaps completely novel to the desiccated or rehydration transcriptomes. We have constructed two Subtractive Suppression Hybridization (SSH) libraries (Diatchenko et al., 1996) that are designed to enrich for differentially expressed low-abundance transcripts contained within gametophytic cells either in the slow-dried state (mRNP sequestrated rehydrin transcripts) or cells that have been rapidly dried, rehydrated and sampled at 2h of hydration (rehydrin and recovery transcripts) when the translational change in gene expression is at its peak (Oliver 1991). To achieve this aim we constructed SSH libraries using PolyA RNA isolated from the polysomal (mRNP) fractions from the slow-dried and 2h rehydrated rapid dried gametophytes selected against PolyA RNA from hydrated control gametophytes as the source for driver cDNA. Collections of cDNA clones from each library were sequenced and used to generate a small T. ruralis SSH cDNA microarray for expression profiling of both total RNA extracts for transcript accumulation assessments and polysomal RNA extracts for transcript sequestration and recruitment assessments. To assess the expression characteristics of the transcripts represented by the SSH contigs we established a cDNA microarray containing the inserts (PCR derived fragment) from each of the 768 individual SSH ESTs, with the exception of thirteen that failed to generate a PCR fragment. Twelve of the missing thirteen SSH EST cDNAs were replaced with PCR fragments from previously isolated T. ruralis cDNAs four of which, representing the ribosomal proteins S14, S16, L23 and L15 (Wood et al., 2000, Zeng and Wood 2000), were previously reported to be constitutively expressed and were added to serve as normalization genes. The remaining eight clones, Tr155, Tr217, Tr403, Tr416, Tr421 (described by Scott and Oliver, 1994), and TrCDPK (U82087) were added as either positive â??up-regulatedâ?? (Tr155, Tr403, Tr421), negative â??down-regulated (Tr217, Tr416), or neutral (TrCDPK) controls based on previous northern analyses. The cDNAs were printed from two 384 well plates in 12 blocks (two columns of 6) of 24 x 8 spots such that each SSH EST and controls were represented in triplicate. Each of the triplicate cDNAs was separated within the blocks to eliminate possible spatial hybridization bias. All hybridizations were duplicated as dye swaps with two separate RNA preparations, from large populations of individual gametophytes (isolated from a minimum of three separate clumps), serving as the source for the sscDNA Cy3 and Cy5 labeled probes. The RNA preparations for the Total polyA RNA were by necessity separate samples from those used to isolate Polysomal poly A RNA.
2010-05-06 | E-GEOD-13680 | biostudies-arrayexpress
Project description:covarites phenotypes, including gender (1=Female/0=Male), age and contraceptive
| EGAD00010002147 | EGA
Project description:Screening cDNA clones from SSH library by hybridization with cDNA used to construct the library. Treated samples were drought-stressed cowpea plants, and control samples were cowpea plants subjected to a standard watering regime. cDNA clones from forward and reverse libraries are spotted on the same array, but data from each library were analysed separately after normalization using SSHscreen software (http://microarray.up.ac.za/SSHscreen ) to calculate Enrichment Ratio 3 (ER3) and Enrichment Ratio 2 (ER2) values for each clone. ER3 is a measure of differential expression, and was determined using a set of hybridizations with unsubtracted treated (UT) and unsubtracted control (UC) cDNA. ER2 is a measure of the relative abundance of a clone's transcript in the original tester sample, relative to other transcripts in the sample prior to the SSH process. ER2 for the forward library was determined using a set of hybridizations with subtracted treated (ST) and unsubtracted treated (UT) cDNA. ER2 for the reverse library is determined using a set of hybridizations with subtracted control (SC) and unsubtracted control (UC) cDNA. Direct comparison of UT and UC cDNAs to calculate ER3 values for F and R library, including dye swaps and replicate arrays. Direct comparison of ST and UT cDNAs to calculate ER2 values for F library, including dye swaps and replicate arrays. Direct comparison of SC and UC cDNAs to calculate ER2 values for R library, including dye swaps and replicate arrays.
2010-05-05 | E-GEOD-20273 | biostudies-arrayexpress