Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1149766 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR30356204.fastq.gz | Fastqsanger.gz | |||
| SRR30356204_1.fastq.gz | Fastqsanger.gz | |||
| SRR30356204_2.fastq.gz | Fastqsanger.gz | |||
| SRR30356205.fastq.gz | Fastqsanger.gz | |||
| SRR30356205_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 120 |
Similar Datasets
Project description:We profiled Sex comb on midleg (Scm), Pc and E(z) in fly embryos and S2 based on BioTAP-XL ChIP-seq. ChIP-seq revealed that Scm is co-localized with PRC1, PRC2, and H3K27me3 in both S2 cells and embryos.
2015-07-09 | GSE66183 | GEO
Project description:The goal of this study is to proactively assess the risk of insecticide resistance development by determining susceptibility of field-collected D. suzukii and their response to insecticide treatment at the transcriptome level using next-generation sequencing technology. Methods:LC50 values were calculated for zeta-cypermethrin, spinosad, malathion treated D. suzukii field-collected and lab-reared populations. LC50 dosage survived and untreated (10 individuals per replicate) field-collected and lab reared D.suzukii transcript profiles were generated by RNA sequencing, in triplicate, using Illumina NextSeq 500. The 24 samples (paired-end reads, including replicates) were independently mapped onto the D. suzukii genome (SpottedWingFlybase v.1) by using TopHat followed by Cufflinks to estimate the expression values of the transcripts in FPKM (Fragments Per Kilobase per Million mapped reads) with the Cuffdiff 2 default geometric normalization. Differentially expressed genes (FDR < 0.05 after Benjamini-Hochberg correction for multiple-testing) were identified for insecticide-treated or untreated control for either (1) lab-reared populations or (2) field-collected populations. Results: As an approach to proactively assess the risk of insecticide resistance development, we determined the LC50 (lethal concentration, 50%) values of commonly used insecticides zeta-cypermethrin, spinosad, and malathion against laboratory-reared and field-collected D. suzukii populations. The LC50 values were significantly higher in field-collected populations when compared to lab-reared populations, indicating that field populations are less susceptible to these insecticides. Furthermore, we used RNA sequencing to analyze the response of D. suzukii at the transcriptome level upon treatment with the same three insecticide classes that are used in our bioassays. We identified differentially expressed genes (DEGs) in D. suzukii that survived LD50 doses of zeta-cypermethrin, spinosad, and malathion and gene classes that are overrepresented in DEGs. We observed that a high number of significantly DEGs are involved in detoxification and reduced cuticular penetration, especially in field population, thus providing potential molecular mechanisms for the higher LC50 values for field-collected population. Conclusion: Our study identified a high number of metabolic detoxification genes that are induced in field-collected D. suzukii upon insecticide treatment and a high degree of overlap when examining the lists of genes that are induced when D. suzukii is treated with three commonly used insecticides. Based on our results, we conclude that there is a substantial risk of insecticide resistance and cross-resistance development in D. suzukii in the field.
2016-09-23 | GSE73595 | GEO
Project description:We report a multi-omic study of sex differences and gene-by-sex interactions across a panel of 100 inbred strains of mice (the Hybrid Mouse Diversity Panel, HMDP), with a focus on metabolic and cardiovascular traits. For all traits examined, including obesity, insulin resistance, fatty liver, atherosclerosis, and gut microbiota composition, sex differences were influenced by genetic background. Loci identified by genome-wide association studies (GWAS) of the traits were frequently influenced by sex. Lyplal1, a gene implicated in human obesity, was shown to underlie a sex-specific locus for diet induced obesity. Many of the sex-dependent traits showed interdependencies as judged by correlation and shared gene expression patterns, indicating higher order regulation. Global gene expression analyses of tissues across the HMDP indicated that sex differences in mitochondrial functions in adipose contributed to many of the traits. Consistent with this, we observed that females tended to be more resistant to the adverse effects of a high fat diet, with smaller adipocytes and increased “browning” of white adipose tissue as compared to males. Sex-specific differences in mitochondrial activity were confirmed by examining respiration of isolated mitochondria. Gonadectomy experiments revealed thousands of genes influenced by sex hormones. In liver, a tissue exhibiting particularly strong differences in gene expression between tissues, sex hormones appeared to be the primary driver of the differences, whereas in adipose organizational effects of sex appeared to be more important.
2018-04-10 | GSE112947 | GEO
Project description:Mosquito microbiota cluster by host sampling location
| PRJNA477711 | ENA
Project description:We profiled Sex comb on midleg (Scm), Pc and E(z) in fly embryos and S2 based on BioTAP-XL ChIP-seq. ChIP-seq revealed that Scm is co-localized with PRC1, PRC2, and H3K27me3 in both S2 cells and embryos. Genomic binding/occupancy profiling of Scm, Pc and E(z) by high throughput sequencing
2015-07-09 | E-GEOD-66183 | biostudies-arrayexpress
Project description:To profile the cell states of interacting natural killer (NK) cells and blood cancer cells, we cultured 26 different cell lines representing diverse hematologic neoplasms either alone or with NK cells derived from three healthy human donors. After 24 h co-culture, we labeled the cells from each monoculture or co-culture condition with oligonucleotide-conjugated antibodies against ubiquitously expressed surface proteins (with different oligonucleotide for each mono- or co-culture), enabling multiplexing in the scRNA-seq using the cell hashing method. We additionally performed pooled CRISPR screens with a single-cell transcriptome readout using the CROP-seq platform in blood cancer cells cultured either alone or in the presence of NK cells to study the effects of perturbing genes that influenced sensitivity to NK cell killing in genome-scale CRISPR screens.
2023-07-24 | E-MTAB-13204 | biostudies-arrayexpress
Project description:Intratumor morphological heterogeneity of pancreatic ductal adenocarcinoma (PDAC) predicts clinical outcomes but is only partially understood at the molecular level. To elucidate the gene expression programs underpinning intratumor morphological variation in PDAC, we investigated and deconvoluted at single cell level the molecular profiles of histologically distinct clusters of PDAC cells. We identified three major morphological and functional variants that co-exist in varying proportions in all PDACs, display limited genetic diversity, and are associated with a distinct organization of the extracellular matrix: a glandular variant with classical ductal features; a transitional variant displaying abortive ductal structures and mixed endodermal and myofibroblast-like gene expression; and a poorly differentiated variant lacking ductal features and basement membrane, and showing neuronal lineage priming. Ex vivo and in vitro evidence supports the occurrence of dynamic transitions among these variants in part influenced by extracellular matrix composition and stiffness and associated with local, specifically neural, invasion.
2024-03-25 | GSE243584 | GEO
Project description:Intratumor morphological heterogeneity of pancreatic ductal adenocarcinoma (PDAC) predicts clinical outcomes but is only partially understood at the molecular level. To elucidate the gene expression programs underpinning intratumor morphological variation in PDAC, we investigated and deconvoluted at single cell level the molecular profiles of histologically distinct clusters of PDAC cells. We identified three major morphological and functional variants that co-exist in varying proportions in all PDACs, display limited genetic diversity, and are associated with a distinct organization of the extracellular matrix: a glandular variant with classical ductal features; a transitional variant displaying abortive ductal structures and mixed endodermal and myofibroblast-like gene expression; and a poorly differentiated variant lacking ductal features and basement membrane, and showing neuronal lineage priming. Ex vivo and in vitro evidence supports the occurrence of dynamic transitions among these variants in part influenced by extracellular matrix composition and stiffness and associated with local, specifically neural, invasion.
2024-03-25 | GSE243583 | GEO