Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Determining the number of individuals to pool

ABSTRACT: 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.

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Lauren McIntyre

PROVIDER: E-GEOD-5183 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Simpler mode of inheritance of transcriptional variation in male Drosophila melanogaster.

Wayne Marta L ML Telonis-Scott Marina M Bono Lisa M LM Harshman Larry L Kopp Artyom A Nuzhdin Sergey V SV McIntyre Lauren M LM

Proceedings of the National Academy of Sciences of the United States of America 20071114 47

Sexual selection drives faster evolution in males. The X chromosome is potentially an important target for sexual selection, because hemizygosity in males permits accumulation of alleles, causing tradeoffs in fitness between sexes. Hemizygosity of the X could cause fundamentally different modes of inheritance between the sexes, with more additive variation in males and more nonadditive variation in females. Indeed, we find that genetic variation for the transcriptome is primarily additive in mal ...[more]

PMID: 18003923

Similar Datasets

Determining the number of individuals to pool

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

2007-06-22 | GSE5183 | GEO

Fry et al Drosophila Ethanol Resistance Selection Experiment

Project description:Outbred D.melanogaster populations subjected to >300 generations of natural selection on either control, or 12% ethanol, or variable food (2 replicates each) and exposed, as first instar larvae, to either water control or 12% ethanol. Six experimental populations were established from an outbred base population derived from flies collected in Raleigh, NC, U.S.A. in 1995. They were selected in either control (R), ethanol (E) or variable (M) selection regimes (2 replicate populations in each) according to the following protocol. Each generation of each population was initiated by allowing 20-30 adults to lay eggs in each of 50 vials containing either standard cornmeal-molasses-agar medium (all the vials in the R populations, and half of the vials in the M populations) or medium supplemented with 12% ethanol (half of the vials in the M populations, and all of the vials in the E populations). After 14 days, progeny from the different vials are mixed before being used to set up the next generation. Gene expression experiment conducted after >300 generations of selection as described below.

2012-06-15 | E-GEOD-38036 | biostudies-arrayexpress

Adult Female Rat Hippocampal Tissue: Naïve vs. Contextual Fear Conditioned (Trained)[Experiment 1]

Project description:naïve and trained rats 24 hours after exposure to the contextual fear conditioning paradigm. Biological replicates: 3 independent pools of 3 animals each, 6 naïve and 6 trained animals, independently conditioned and tissues were independently isolated. One replicate per array.

2017-03-08 | GSE84261 | GEO

Determining the wash solution to use

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

The influence of sex and age on the lens injury response

Project description:The purpose of this study was to investigate/characterize age- and sex-dependent changes in transcriptomic profile in a mouse model of cataract surgery that mimics human cataract surgery. This surgery involves the removal of lens fiber cells (LFC) leaving behind the lens capsule and associated lens epithelial cells (LEC). The lens capsule and associated remnant LECs were harvested either following cataract surgery (0 hour) or 24 hours later. Fiber cells were collected at the time of surgery, equivalent to 0 hour, and analyzed separately from epithelial cells. For samples from LEC, each biological replicate is a pool of 5 lens capsules from 5 independent mice. For samples from LFC, each biological replicate is a pool of 2 fiber cell masses from two independent mice. Mice were either 24 months old (Aged), or 3 months old (Young).

2021-07-10 | GSE166619 | GEO

A microenvironment-inspired synthetic 3D model for pancreatic ductal adenocarcinoma organoids - PDA Matrisome

Project description:LFQ analysis of matrisome fractions enriched from 12 murine PDA or PanIN samples (samples 1 - 12) and a normal pancreas pool (samples 13) pooled from 10 pancreata of C57-Bl6 animals. Three independent enrichments have been conducted for each sample with each having had four injections.

2021-11-29 | PXD022767 | Pride

mRNA expression profile of dop-1 mutants to wild- type animals during adulthood (L4+48 hours) using RNA-seq

Project description:Developmentally synchronized animals were obtained by hypochlorite treatment of gravid adults to release embryos. Synchronized embryos were hatched on NGM plates and grown at 20°C until 48 h after the L4 stage of development. Fluorodeoxyuridine was used to prevent the development of second-generation embryos once animals reached fertile adulthood. For each RNA-seq experiment, populations for odIs77[Pcol-19::UbG76V-GFP] and dop-1(vs100); [Pcol- 19::UbG76V-GFP] were grown simultaneously under the same conditions. Total RNA was isolated from animals using trizol (Invitrogen) combined with Bead Beater lysis in 3 biological replicates, and an mRNA library (single-end, 50-bp reads) was prepared for each sample/replicate using Illumina Truseq with PolyA selection.

2016-04-30 | GSE80807 | GEO

Sex Specific Transciption in Mouse Tissues

Project description:Sex Specific Transciption in Mouse Hypothalamus, Liver, Kidney, Ovary and Testis. For each somatic tissue there are 3 biological samples from different pools comprised of 10 animals for each sex each with a technical replicate. For each of the reproductive tissues there are 3 biological samples from different pools comprised of 10 animals with a technical replicate for each. Keywords = Mouse sex-specific transcription, gonad specific gene expression Keywords: other

2004-03-28 | GSE1148 | GEO

Gene profiling of the early healing rat medial collateral ligament

Project description:The objective of the study was to better understand the mechanism behind scar formation by identifying ECM factors and other unique genes differentially expressed during rat ligament healing via microarray. Rat medial collateral ligaments (MCL) were surgically transected or left intact. MCLs were collected at day 3 or 7 post-injury and used for microarray analysis. Results were compared to the normal intact ligaments. A total of 27 rats were used in the study. Animals were randomly placed in 1 of 3 groups (day 3, day 7, intact CX) with nine animals included with each time (9 rats/group). At the time of collection, MCLs from each time were placed into 3 pools (3 MCLs/pool), resulting in 3 reps per time, and usd for microarray analysis. A total of 9 gene chips were used for the experiment (3 chips/day).

2013-06-06 | E-GEOD-47676 | biostudies-arrayexpress

Intermediolateral column, medial, and lateral motoneurons

Project description:Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5. Keywords: other

2005-12-20 | GSE2595 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data