Publications by Sergio Garcia-Moreno Alcantara (
TFIID summits at TATA-DBE, TATA-only and TATA-less promoters
Aim A recent structural paper on TFIID and other PIC components showed that the distance between the engaged TBP and the downstream TAFs (TAF1, 2 and 7) is different between promoters that contain TATA and downstream binding sequences (DBE) versus those that contain only TATA or downstream sequences but no TATA. THe aim of this analysis is to tes...
882 sym R (18890 sym/30 pcs) 24 img
TFIID summits at TATA-DBE, TATA-only and TATA-less promoters (DMSO)
Aim A recent structural paper on TFIID and other PIC components showed that the distance between the engaged TBP and the downstream TAFs (TAF1, 2 and 7) is different between promoters that contain TATA and downstream binding sequences (DBE) versus those that contain only TATA or downstream sequences but no TATA. THe aim of this analysis is to tes...
882 sym R (18890 sym/30 pcs) 24 img
TFIID summits at TATA-DBE, TATA-only and TATA-less promoters (Triptolide)
Aim A recent structural paper on TFIID and other PIC components showed that the distance between the engaged TBP and the downstream TAFs (TAF1, 2 and 7) is different between promoters that contain TATA and downstream binding sequences (DBE) versus those that contain only TATA or downstream sequences but no TATA. THe aim of this analysis is to tes...
821 sym R (18733 sym/28 pcs) 22 img
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Aim The aim of this analysis is to annotate TSSs in the Drosophila Melanogaster ovaries using CAGE-seq data from the modEncode project. Enviroment setup Set working directory and load required libraries and lab functions setwd("/n/projects/sga/analysis/SAGA/publication/") options(knitr.figure_dir = "plots/") #Standard packages library(GenomicAl...
420 sym R (11072 sym/6 pcs) 2 img
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Aim The aim of this analysis is to investigate whether there are differences in the occupancy of the SAGA core module at different promoter types in Drosophila kc167 cells Enviroment setup Set working directory and load required libraries and lab functions setwd("/n/projects/sga/analysis/SAGA/publication/") options(knitr.figure_dir = "plots/figu...
645 sym R (10734 sym/7 pcs) 2 img
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Aim Analysis of SAGA occupancy at active core promoters in the Drosophila ovaries Enviroment setup Set working directory and load required libraries and lab functions setwd("/n/projects/sga/analysis/SAGA/publication/") options(knitr.figure_dir = "plots/figure_4_v2") #Standard packages library(GenomicAlignments); library(GenomicRanges); library(...
738 sym R (17851 sym/12 pcs) 8 img
Correlation between replicates
#Introduction Environment Setup Set working directory and load required libraries and lab functions setwd("/n/projects/sga/analysis/tfiid/scripts/tfiid_replicates_correlations/") options(knitr.figure_dir = "plots/") #Standard packages library(rtracklayer); library(GenomicRanges); library(magrittr) ; library(Biostrings); library(reshape2); libra...
214 sym R (12496 sym/3 pcs) 1 img
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Aim Environment Setup Set working directory and load required libraries and lab functions setwd("/n/projects/sga/analysis/tfiid/scripts/flavopiridol_treatment/") options(knitr.figure_dir = "flavopiridol_treatment/") #Standard packages library(rtracklayer); library(GenomicRanges); library(magrittr) ; library(Biostrings); library(reshape2); libra...
238 sym R (11252 sym/9 pcs) 5 img
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Introduction The aim of this analysis is to analyze TBP and Pol II at tata and dpe promoters at q1 and q5 half-life datasets Computational Setup #Standard packages library(rtracklayer); library(GenomicRanges); library(magrittr) ; library(Biostrings); library(reshape2); library(BSgenome.Dmelanogaster.UCSC.dm6); library(plyr); library(dplyr); libr...
368 sym R (16413 sym/15 pcs) 4 img
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Author: Sergio Garcia-Moreno Aim Cluster TFIID at different promoter groups Environment setup 1. Loading samples and necessary data sets samples <- load_bigwig(sample_list) names(samples) <- sample_list$short_name bigwig_list_dmso <- samples[grep("dmso_", names(samples))] %>% .[!duplicated(.)] bigwig_list_tri <- samples[grep("triptolide_", nam...
286 sym R (13292 sym/12 pcs) 8 img