Determining the number of individuals to pool
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
PROVIDER: GSE5183 | GEO | 2007/06/22
SECONDARY ACCESSION(S): PRJNA96485
REPOSITORIES: GEO
Similar Datasets
Project description:We compared 10, 20 and 40 animal pools to determine the best number of intact adults to pool Keywords: Agilent microarray, pooling, Drosophila, intact adults 16 vials of flies were reared. From each vial 5 individuals were selected. For the 10 animal comparison 4 vials were used with each replicate being a pool of 5 animals over 2 independent vials. For the 20 animal comparison 8 vials were used with each replicate being a pool of 5 animals over 5 independent vials and for the 40 animal comparison each replicate was a pool of 5 animals over 8 independent vials. There are two independent replicates of each type for 6 samples which were hybridized on three chips in a loop design.
2010-06-10 | E-GEOD-5183 | biostudies-arrayexpress
Project description:We tested a new wash solution from Agilent Keywords: Agilent microarray, pooling, Drosophila, intact adults
2007-06-18 | GSE5182 | GEO
Project description:We tested a new wash solution from Agilent Keywords: Agilent microarray, pooling, Drosophila, intact adults Intact males and females for a single genotype were examined. Two independent replicates of each were compared on two slides in a dye flip.
2010-06-10 | E-GEOD-5182 | biostudies-arrayexpress
Project description:Chemoproteomics is a key platform for characterizing the mode of action (MoA) for compounds, especially for targeted protein degraders such as proteolysis targeting chimerics (PROTACs) and molecular glues. With deep proteome coverage, multiplexed tandem mass tag-mass spectrometry (TMT-MS) can tackle up to 18 samples in a single experiment. Here, we present a pooling strategy to further enhance the throughput, and apply the strategy to an FDA-approved drug library (95 best-in-class compounds). The TMT-MS-based pooling strategy was evaluated in the following steps. First, we demonstrated the capability of TMT-MS by analyzing over 15,000 unique proteins (>12,000 gene products) in HEK293 cells treated with five PROTACs (two BRD/BET degraders and three degraders for FAK, ALK, and BTK kinases). We then introduced a rationalized pooling strategy to separate structurally similar compounds in different pools, and identified the proteomic response to 14 pools from the drug library. Finally, we validated the proteomic response from one pool by re-profiling the cells under individual drug treatment with sufficient replicates. Interestingly, numerous proteins were found to change upon drug treatment, including AMD1, ODC1, PRKX, PRKY, EXO1, AEN and LRRC58 by 7-Hydroxystaurosporine; C6orf64, HMGCR and RRM2 by Sorafenib; SYS1 and ALAS1 by Venetoclax; and ATF3, CLK1 and CLK4 by Palbocilib. Thus, the pooling chemoproteomics screening provides an efficient method for dissecting the molecular targets of compound libraries.
2023-03-11 | PXD033780 | Pride
Project description:In this study 3 pooling experiments were performed. In each of the 3 cohorts, a 'case' and a 'control' blood pool was compared - the goal being to identify single nucleotide polymorphisms with significantly different estimated pooling allele frequencies between cases and controls. For cohort 1, 100 individuals with blue eye color were placed in one pool (the 'control' pool) and 100 individuals with brown eye color were placed in another pool ( the 'case' pool). In cohort 2, 131 individuals with age-related macular degeneration were placed in one pool, with 216 control individuals in another pool. In cohort 3, 100 individuals with pseudoexfoliation syndrome were placed in a case pool - in this case the cohort 2 control sample was used as 'controls'. The blue/brown pools were hybridized to Illumina HumanHap550 arrays. The cohort 2 and 3 pools were hybridized to Illumina 1M arrays. After processing, the raw data are summarized to give pooling allele frequency estimates for each pool. The abstract from the paper describing these data is as follows: Genome-wide association studies (GWAS) have now successfully identified important genetic variants associated with many human traits and diseases. The high cost of genotyping arrays in large datasets remains the major barrier to wider utilization of GWAS. We have developed a novel method in which whole blood from cases and controls respectively is pooled prior to DNA extraction for genotyping. We demonstrate proof of principle by clearly identifying the associated variants for eye color, age-related macular degeneration and pseudoexfoliation syndrome in cohorts not previously studied. Blood pooling has the potential to reduce GWAS cost by several orders of magnitude and dramatically shorten gene discovery time. This method has profound implications for translation of modern genetic approaches to a multitude of diseases and traits yet to be analysed by GWAS, and will enable developing nations to participate in GWAS.
2009-08-08 | GSE17557 | GEO
Project description:The experiment was based on 3 arrays (3 Illumina HumanHap300 and 3 Affymetrix Genechip HindIII arrays) of each type being hybridized to a single pool which contained equal amounts of DNA from each of 384 individuals. The goal is to estimate a pooling allele frequency, the average frequency of allele 1, say, in the set of 384 individuals. After processing, the raw data are summarized to give pooling allele frequency estimates for each array. Abstract from paper comparing two arrays (one affy, one illumina) is as follows; Genome wide association (GWA) studies to map genes for complex traits are powerful yet costly. DNA pooling strategies have the potential to dramatically reduce the cost of GWA studies. Pooling using Affymetrix arrays has been proposed and used but the efficiency of these arrays has not been quantified. We compared and contrasted Affymetrix Genechip HindIII and Illumina HumanHap300 arrays on the same DNA pools and show that the HumanHap300 arrays are substantially more efficient. In terms of effective sample size, HumanHap300 based pooling extracts >80% of the information available with individual genotyping (IG). In contrast, Genechip HindIII based pooling only extracts ~30% of the available information. With HumanHap300 arrays concordance with IG data is excellent. Guidance is given on best study design and it is shown that even after taking into account pooling error, one stage scans can be performed for >100 fold reduced cost compared with IG. With appropriately designed two stage studies, IG can provide confirmation of pooling results whilst still providing ~20 fold reduction in total cost compared with IG based alternatives. The large cost savings with Illumina HumanHap300 based pooling imply that future studies need only be limited by the availability of samples and not cost. Keywords: DNA pooling experiment
2007-11-06 | GSE9307 | GEO
Project description:Wild type versus reference pool. Reference pools from either the CuSO4 or BCS timecourse were compared with wildtype cells taken from mid-log cultures.
2006-04-03 | E-UMCU-17 | biostudies-arrayexpress
Project description:In this study 3 pooling experiments were performed. In each of the 3 cohorts, a 'case' and a 'control' blood pool was compared - the goal being to identify single nucleotide polymorphisms with significantly different estimated pooling allele frequencies between cases and controls. For cohort 1, 100 individuals with blue eye color were placed in one pool (the 'control' pool) and 100 individuals with brown eye color were placed in another pool ( the 'case' pool). In cohort 2, 131 individuals with age-related macular degeneration were placed in one pool, with 216 control individuals in another pool. In cohort 3, 100 individuals with pseudoexfoliation syndrome were placed in a case pool - in this case the cohort 2 control sample was used as 'controls'. The blue/brown pools were hybridized to Illumina HumanHap550 arrays. The cohort 2 and 3 pools were hybridized to Illumina 1M arrays. After processing, the raw data are summarized to give pooling allele frequency estimates for each pool. The abstract from the paper describing these data is as follows: Genome-wide association studies (GWAS) have now successfully identified important genetic variants associated with many human traits and diseases. The high cost of genotyping arrays in large datasets remains the major barrier to wider utilization of GWAS. We have developed a novel method in which whole blood from cases and controls respectively is pooled prior to DNA extraction for genotyping. We demonstrate proof of principle by clearly identifying the associated variants for eye color, age-related macular degeneration and pseudoexfoliation syndrome in cohorts not previously studied. Blood pooling has the potential to reduce GWAS cost by several orders of magnitude and dramatically shorten gene discovery time. This method has profound implications for translation of modern genetic approaches to a multitude of diseases and traits yet to be analysed by GWAS, and will enable developing nations to participate in GWAS. Pools were typed with Illumina arrays. Estimates of pooling allele frequency were obtained.
2009-08-08 | E-GEOD-17557 | biostudies-arrayexpress
Project description:Transcriptional profiling of human lung minimally invasive adenocarcinoma cells comparing control lepidic growth (LG) cell pool with micro-invasion (MI) cell pool. Two-condition experiment, LG vs. MI cell pools. Biological replicates: 1 control LG cancer cell, 1 MI cancer cell in an individual MIA tumor. One replicate per array.
2012-01-02 | E-GEOD-30663 | biostudies-arrayexpress
Project description:The fidelity of motor control requires the precise positional arrangement of motor pools and the establishment of synaptic connections between these pools. In the developing spinal cord, motor nerves project to specific target muscles and receive proprioceptive input from the muscles via the sensorimotor circuit. LIM-homeodomain transcription factors are known to successively restrict specific motor neuronal fates during neural development; however, it remains unclear to what extent they contribute to limb-based motor pools and locomotor circuits. Here, we showed in mice that deletion of Isl2 resulted in scattered motor pools, primarily in the median motor column and lateral LMC (LMCl) populations, and lacked Pea3 expression in the hindlimb motor pools, accompanied by reduced terminal axon branching and disorganized neuromuscular junctions. Transcriptomic analysis of Isl2-deficient spinal cords revealed that a variety of genes involved in motor neuron differentiation, axon development, and synapse organization were downregulated in hindlimb motor pools. Moreover, the loss of Isl2 impaired sensorimotor connectivity and hindlimb locomotion. Together, our studies indicate that Isl2 plays a critical role in organizing motor pool position and sensorimotor circuits in hindlimb motor pools.
2023-11-01 | GSE217297 | GEO