Project description:The embryo to neonate transition is a critical period of development that has significant impact on broiler production. During this time important genetic programs governing metabolism and growth are established. The goal of this work was to study the effects of early post-hatch (PH) development and time of initiation of feeding on activation of the genetic programs regulating tissue growth and metabolism in liver, brain, duodenum and breast muscle in broiler chickens. We used chicken genome GeneChip microarrays in a replicated experiment to detail the global program of gene expression in liver, whole brain, duodenum and breast muscle during the post-hatch transition in response to the initiation of feeding. Experiment Overall Design: Tissue samples were collected at hatch and 7 days post-hatch for RNA extraction and hybridization on Affymetrix chicken genome GeneChip microarrays. We analyzed three replicate samples of total RNA on separate microarrays for each tissue at hatch and at day 7 post-hatch in order to increase the resolution of expression profiles. To that end, for each tissue we pooled samples from 4-5 individual chicks at both time points to increase representation of the replicate total RNA samples analyzed on the microarrays.
Project description:We report the presence of extensive, transcriptionally controlled oscillations in the C. elegans, developmental transcriptome. Furthermore, using ribosome profiling, we show that these oscillating transcripts are actively translated. Examination of two timecourses that were collected over C. elegans development and analyzed by RNA-seq of "RiboMinus" libraries
Project description:This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains ChIP-seq data generated on Solexa Genome Analyzer for 6 Histone modifications (H3K9me3, H3K27me3, H3K4me3, H3K4me1, H3K27Ac, H3K9Ac), PolII and CBP/p300. Each factor has been studied for 12 different time-points of Drosophila development. Keywords: Epigenetics For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf For each combination of time-point and antibody, triplicate ChIP experiments have been performed and hybridized on Agilent 244K arrays. The hybridizations have been verified by sequencing one replicate of IP and one replicate of Input following Solexa sequencing procedure.
Project description:This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. This Series contains ChIP-chip data on Agilent 244K dual-color arrays for antibody: H3K9me3 at 12 different time-points of Drosophila development. Current Dataset: [GSM382158..GSM382166]: ChIP-chip of H3K9me3 in Drosophila embryos at 12-16 hours of development [GSM384690..GSM384698]: ChIP-chip of H3K9me3 in Drosophila embryos at 0-4 hours of development [GSM384723..GSM384731]: ChIP-chip of H3K9me3 in Drosophila embryos at 4-8 hours of development [GSM384732..GSM384740]: ChIP-chip of H3K9me3 in Drosophila embryos at 16-20 hours of development [GSM384741..GSM384749]: ChIP-chip of H3K9me3 in Drosophila embryos at 20-24 hours of development [GSM384750..GSM384758]: ChIP-chip of H3K9me3 in Drosophila L1 larvae [GSM384760..GSM384768]: ChIP-chip of H3K9me3 in Drosophila L2 larvae [GSM418207..GSM418215]: ChIP-chip of H3K9me3 in Drosophila Adult male [GSM418216..GSM418224]: ChIP-chip of H3K9me3 in Drosophila embryos at 8-12 hours of development [GSM442371..GSM442379]: ChIP-chip of H3K9me3 in Drosophila Adult male - Set2 [GSM442380..GSM442388]: ChIP-chip of H3K9me3 in Drosophila Pupae [GSM442389..GSM442397]: ChIP-chip of H3K9me3 in Drosophila L3 larvae For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf For each combination of time-point and antibody, triplicate ChIP experiments have been performed and hybridized on Agilent 244K arrays. 3 arrays per genome have been used so that each time-point is a set of 9 tiling arrays.
Project description:We have infected the model legume Medicago truncatula with Meloidogyne hapla and harvested tissue over a time course. Transcriptome sequencing was performed on each sample using the Illumina RNA-Seq method. [Longitudinal Experiment] RNA was isolated from M. hapla eggs and pre-penetration juveniles (J2) and also from a time course of M. truncatula infected with M. hapla J2 at five time points: 1, 2, 4, 5, and 7 days after inoculation (DAI). Roots (local) and shoots (global) tissues from infected and uninfected plants were sampled. Each sample was loaded on five lanes for sequencing. Collectively, 22 samples were generated in total from - M. hapla egg and J2 (two samples), - infected M. truncatula root 1-2-4-5-7 DAI (five samples), - infected M. truncatula shoot 1-2-4-5-7 DAI (five samples), - uninfected M. truncatula root 1-2-4-5-7 DAI (five samples), - and uninfected M. truncatula shoot 1-2-4-5-7 DAI (five samples). Thus, 110 fastq files (= 22 samples x 5 lanes). [Diunrnal Experiment] M. truncatula roots inoculated with M. hapla was sampled at 6 time-points: 22:30, 2:00, 5:00, 6:30, 14:00, and 21:00. Lighting was turned off at 22:00 and turned on at 06:00. Four biological replicates were taken for each time point, providing 24 samples in total. Thus, 24 fastq files (= 6 time points x 4 replicates).
Project description:The amount of energy that can be extracted from a diet varies between individuals. Apparent Metabolizable Energy (AME) is a measure of energy utilization efficiency and represents the difference between the energy consumed and the energy lost via the excreta. There are significant differences in the energy utilization capability of individual birds that have a similar genetic background and are raised under identical conditions. We analyzed duodenal gene expression and microbiota differences between birds with different efficiencies in food to energy conversion using microarrays and sequencing of 16s rRNA genes. Differences were found in duodenal gene expression between high and low AME birds, they were however mostly related to genes of unknown function. The flock of 96 chickens was used to study ability of the bird to utilise the energy from feed. We measured energy content in feed and in excreta of individually housed birds. The microarrays were used to compare expression between the best and worst energy utilisers.
Project description:This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains ChIP-chip data on Agilent 244K dual-color arrays for 6 Histone modifications (H3K9me3, H3K27me3, H3K4me3, H3K4me1, H3K27Ac, H3K9Ac), PolII and CBP/p300. Each factor has been studied for 12 different time-points of Drosophila development. This SuperSeries is composed of the following subset Series: GSE15422: ChIP-chip of H3K9me3 in Drosophila at different time points of development GSE15423: ChIP-chip of H3K27me3 in Drosophila at different time points of development GSE15424: ChIP-chip of H3K4me3 in Drosophila at different time points of development GSE15425: ChIP-chip of H3K4me1 in Drosophila at different time points of development GSE15426: ChIP-chip of H3K9Ac in Drosophila at different time points of development GSE15427: ChIP-chip of CBP/p300 in Drosophila at different time points of development GSE15430: ChIP-chip of H3K27Ac in Drosophila at different time points of development GSE16013: Genome-wide maps of chromatin state in staged Drosophila embryos, ChIP-seq GSE16702: ChIP-chip of PolII in Drosophila at different time points of development GSE18068: Genome-wide maps of chromatin state in staged Drosophila embryos, RNA-seq For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf ChIP-chip: For each combination of time-point and antibody, triplicate ChIP experiments have been performed and hybridized on Agilent 244K arrays. 3 arrays per genome have been used so that each time-point is a set of 9 tiling arrays. ChIP-seq: For each combination of time-point and antibody, triplicate ChIP experiments have been performed and hybridized on Agilent 244K arrays. The hybridizations have been verified by sequencing one replicate of IP and one replicate of Input following Solexa sequencing procedure. RNA-seq: For each time-point (E-0-4h, E-4-8h, E-8-12h, E-12-16h, E-16-20h, E20-24h, L1, L2, L3, Pupae, Adult Males and Adult Females) a total RNA extraction has been performed. After conversion into double stranded DNA, the samples have been sequenced in duplicate on Solexa Genome Analyzer following Solexa sequencing procedure.
Project description:This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains ChIP-chip data on Agilent 244K dual-color arrays for H3K4me3 at 12 different time-points of Drosophila development. Current Dataset: [GSM385397..GSM385405]: ChIP-chip of H3K4me3 in Drosophila embryos at 12-16 hours of development [GSM386032..GSM386040]: ChIP-chip of H3K4me3 in Drosophila embryos at 0-4 hours of development [GSM386088..GSM386096]: ChIP-chip of H3K4me3 in Drosophila embryos at 4-8 hours of development [GSM386097..GSM386105]: ChIP-chip of H3K4me3 in Drosophila embryos at 16-20 hours of development [GSM386106..GSM386114]: ChIP-chip of H3K4me3 in Drosophila embryos at 20-24 hours of development [GSM386115..GSM386123]: ChIP-chip of H3K4me3 in Drosophila L1 larvae [GSM386125..GSM386133]: ChIP-chip of H3K4me3 in Drosophila L2 larvae [GSM386996..GSM387004]: ChIP-chip of H3K4me3 in Adult Male [GSM418254..GSM418262]: ChIP-chip of H3K4me3 in Drosophila embryos at 8-12 hours of development [GSM442287..GSM442292]: ChIP-chip of H3K4me3 in Pupae [GSM442293..GSM442301]: ChIP-chip of H3K4me3 in Adult Female [GSM442302..GSM442310]: ChIP-chip of H3K4me3 in Drosophila L3 larvae For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf For each combination of time-point and antibody, triplicate ChIP experiments have been performed and hybridized on Agilent 244K arrays. 3 arrays per genome have been used so that each time-point is a set of 9 tiling arrays.