Project description:Raw data from E-MTAB-1585 was normalized by using reads per million. https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585/ Strand specific RNA-Seq data E-MTAB-1585 was normalized and subtracted control from knockdown to generate tracks that more clearly displayed the unusual pattern of RNA expression caused by knockdown of 7SK. The following wig files were generated from multiple samples (i.e.raw data files), as indicated in the 'readme.txt' file. 7sk_3p_KD_norm.wig: 7SK 3P Knockdown normalized 7sk_3p_KDF_norm.wig: 7SK 3P Knockdown normalized (Forward) 7sk_3p_KDR_norm.wig: 7SK 3P Knockdown normalized (Reverse) 7sk_5p_KD_norm.wig: 7SK 5P Knockdown normalized 7sk_5p_KDF_norm.wig: 7SK 5P Knockdown normalized (Forward) 7sk_5p_KDR_norm.wig: 7SK 5P Knockdown normalized (Reverse) 7sk_Control_norm.wig: 7SK Control normalized 7sk_ControlF_norm.wig: 7SK Control normalized (Forward) 7sk_ControlR_norm.wig: 7SK Control normalized (Reverse) 7sk_3p_KDF-ControlF.wig: 7SK 3P Knockdown-Control (Forward) 7sk_3p_KDR-ControlR.wig: 7SK 3P Knockdown-Control (Reverse) 7sk_5p_KDF-ControlF.wig: 7SK 5P Knockdown-Control (Forward) 7sk_5p_KDR-ControlR.wig: 7SK 5P Knockdown-Control (Reverse)
Project description:Molecular profiling of small-molecules offers invaluable insights on compound functionality and allows for hypothesis generation of targets. However, current profiling methods are either limited in the number of measurable parameters or throughput. Here, we developed a multiplexed, unbiased framework that by linking genetic to drug-induced changes in nearly a thousand metabolites allows for high-throughput functional annotation of compound libraries in Escherichia Coli. First, we generated a reference map of metabolic changes from (CRISPR) interference with 352 genes in all major essential biological processes. Next, based on the comparison of essential gene knockdown metabolic profiles with 1342 drug-induced metabolic changes we demonstrated the ability to make de novo predictions of compound functionality and revealed drugs interfering with unconventional antibacterial targets. The same framework that combines dynamic gene silencing with metabolomics we implemented in E. coli can be adapted and applied as a general strategy for comprehensive high-throughput analysis of compound functionality, from bacteria to human cells.
Project description:DNA-binding proteins are promising therapeutic targets but notoriously difficult to drug. Here, we evaluate a chemoproteomic DNA interaction platform as a complementary strategy for parallelized compound profiling. To enable this approach, we determined the proteomic binding landscape of 92 immobilized DNA sequences. Perturbation-induced activity changes of captured transcription factors in disease-relevant settings demonstrated functional relevance of the enriched sub-proteome. Chemoproteomic profiling of >300 cysteine-directed compounds against a coverage optimized bead mixture, which specifically captures >150 DNA binders, revealed competition of several DNA-binding proteins, including the transcription factors ELF1 and ELF2. We also discovered the first compound which displaces the DNA-repair complex MSH2-MSH3 from DNA. Compound binding to cysteine 252 on MSH3 was confirmed using chemoproteomic reactive cysteine profiling. Overall, these results suggested that chemoproteomic DNA bead pull-downs enable the specific read-out of transcription factor activity and can identify functional “hot-spots” on DNA binders towards expanding the druggable proteome.
Project description:Transcription profiling of chicken development The experiment were perfomed as a part of our Vertebrate Evo-Devo project. The aim of the project is to compare transcription profiles of normal (unmanipulated, wild-type, whole embryo) vertebrate embryos. Total RNA was collected from wild type G.gallus whole embryos at 15 different stages (Stages:HH1,2,4,6,8,9,11,14,16,19,24,27,32,34,38), and hybridized to the Affymetrix Chicken Genome Array. All the stages contains data from two biological replications. Each staged-samples consists of pooled total RNA from several whole embryos.
Project description:Transcription profiling of chicken development The experiment were perfomed as a part of our Vertebrate Evo-Devo project. The aim of the project is to compare transcription profiles of normal (unmanipulated, wild-type, whole embryo) vertebrate embryos.
Project description:Transcription profiling of mouse development The experiment were perfomed as a part of our Vertebrate Evo-Devo project. The aim of the project is to compare transcription profiles of normal (unmanipulated, wild-type, whole embryo) vertebrate embryos.
Project description:Transcription profiling of X.laevis development. The experiment were perfomed as a part of our Vertebrate Evo-Devo project. The aim of the project is to compare transcription profiles of normal (unmanipulated, wild-type, whole embryo) vertebrate embryos.
Project description:Illumina bodyMap2 transcriptome Transcription profiling by high throughput sequencing of individual and mixture of 16 human tissues RNA. Additional supplementary files available at foot of this record. Additional information available as supplementary files at the foot of this record. ArrayExpress Release Date: 2011-03-17 Person Roles: submitter Person Last Name: Khrebtukova Person First Name: Irina Person Mid Initials: Person Email: ikhrebtukova@illumina.com Person Phone: 1-510-723-9219 Person Address: 25861 Industrial Blvd, Hayward CA 94545, USA Person Affiliation: Illumina