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The Integrated Datasets is a virtual database currently indexing a variety of data sets. A list of the participating data resources is provided here.
(last updated: Jun 15, 2019)
Information| Source_ID | Project Title | Data Type | Keywords | Description | Data Creator | Release Date | ||
|---|---|---|---|---|---|---|---|---|
| ArrayExpress_E-GEOD-50660 | Cigarette Smoking Reduces DNA Methylation Levels at Multiple Genomic Loci but the Effect is Partially Reversible upon Cessation | Microarray | DNA methylation is an epigenetic event whose pattern is altered frequently in a wide variety of human diseases. Smoking affects DNA methylation possibly leading to abnormal expression of a broad spectrum of genes which in turn may result to the various side effects and diseases associated with smoking. The long term effects of smoking have been widely studied but the mechanism(s) by which those effects may be reversible by smoking cessation are not clearly understood. Here, we conducted an epigenome-wide association study in peripheral-blood DNA in 464 individuals who were current, former and never-smokers. We identified 15 distinct loci (10 of which were novel) where DNA methylation was reduced in smokers and was reversed (but did not reach non-smoking levels) upon smoking cessation within 12 weeks. Although the functional impact of this reversal of DNA methylation is still not understood, this study illustrates the potential of epigenomics to provide insights into mechanisms of environmental and lifestyle exposures, and to suggest new avenues for clinical intervention Bisulfite converted DNA from the 464 samples were hybridized to the Illumina Infinium HumanMethylation450 BeadChip | 2014-11-25 | Experiment Type: methylation profiling by array; Organism: Homo sapiens | |||
| ArrayExpress_E-GEOD-62516 | The RSC Complex localizes to coding sequences to regulate Pol II and histone occupancy (Affymetrix) | Microarray | ATP-dependent chromatin remodelers regulate chromatin structure during multiple stages of transcription. We report that RSC, an essential chromatin remodeler, is recruited to the open reading frames (ORFs) of actively transcribed genes genome-wide, suggesting a role for RSC in regulating transcription elongation. Consistent with such a role, Pol II occupancy in the ORFs of weakly transcribed genes is drastically reduced upon depletion of the RSC catalytic subunit Sth1. RSC inactivation also reduced histone H3 occupancy across transcribed regions. Remarkably, the strongest effects on Pol II and H3 occupancy were confined to the genes displaying the greatest RSC ORF enrichment. Additionally, RSC recruitment to the ORF requires the activities of the SAGA and NuA4 HAT complexes and is aided by the activities of the Pol II CTD Ser2 kinases Bur1 and Ctk1. Overall, our findings strongly implicate ORF-associated RSC in governing Pol II function and in maintaining chromatin structure over transcribed regions. In these experiments, we have analyzed Sth1 (catalytic subunit of the RSC chromatin remodeling complex) enrichment to the transcribing genes. The cells (WT and gcn4Δ) harboring STH1-MYC allele were treated by SM for 20 minutes to induce Gcn4 regulated genes. The chromatin extracts were prepared and subjected to chromatin immunoprecipitation using anti-Myc antibodies. The ChIP DNA as well the corresponding input DNA were biotinylated and hybridized to the Affymetrix tiling Arrays. Chromatin samples from two different cultures were used in this analysis. | 2014-11-24 | Experiment Type: ChIP-chip by tiling array; Organism: Saccharomyces cerevisiae | |||
| ArrayExpress_E-GEOD-45247 | Phenazine regulated genes in Pseudomonas chlororaphis 30-84 | Microarray | Pseudomonas chlororaphis strain 30-84 is an effective biological control agent against take-all disease of wheat. Phenazines, bacterial secondary metabolites produced by 30-84, are essential for 30-84 to inhibit fungal pathogens, form biofilms, and effectively colonize the rhizosphere. However, how the bacteria themselves respond to phenazines remains unknown. In this study, we conducted an RNA-seq analysis by comparing the wild type strain with a phenazine deficient mutant. RNA-seq analysis identified over 200 genes differentially regulated by phenazines. Consistent with previous findings in Pseudomonas aeruginosa PAO1, phenazines positively contribute to the expression of their own biosynthetic genes. Moreover, phenazine regulatory genes including the phzI/phzR quorum sensing system and the rpeB response regulatory were also expressed at high levels in the presence of phenazines. Besides phenazine biosynthesis and regulatory genes, genes involved in secondary metabolism, exopoysaccharide production and iron uptake as well as amino acid transport were identified as the major components under phenazine control, including many novel genes. We have also demonstrated that mutation of the primary siderophore gene pvdA resulted in up-regulation of phenazine genes when grown in iron-limiting media. These findings implicate phenazines as signaling molecules to regulate gene expression and hence alter metabolism in P. chlororaphis strain 30-84. A total of 4 samples were analyzed in AB medium + 2% casamino acids, Pseudomonas chlororaphis wild type strain (2 replicates); Pseudomonas chlororaphis ZN mutant (2 replicates). | 2014-11-25 | Experiment Type: RNA-seq of coding RNA; Organism: Pseudomonas chlororaphis subsp. aureofaciens 30-84 | |||
| ArrayExpress_E-GEOD-59739 | RNA-Seq of single cells from the mouse lumbar dorsal root ganglion | Microarray | In order to establish a consensus catalog of dorsal rott ganglion cell types, we used comprehensive transcriptome analysis of single cells for unsupervised identification and molecular classification of sensory neurons independent of any a priori knowledge of sensory subtypes. RNA-Seq was performed on 799 dissociated single cells dissected from the mouse lumbar dorsal root ganglion distributed over a total of nine 96-well plates | 2014-11-24 | Experiment Type: RNA-seq of coding RNA; Organism: Mus musculus | |||
| ArrayExpress_E-MTAB-3126 | ChIP-Chip and SACO Analysis of Pdx-1 binding in NIT-1 Insulinoma Cells | Microarray | The BCBC Promoter Chip 5B was used to identify genomic targets of Pdx-1 binding. Genomic DNA from mouse NIT-1 insulinoma cells was immunoprecipitated with a Pdx-1 Antibody, PCR amplified, and labeled to the chip. All hybridizations were versus a common reference sample which was a labeled IgG IP. Additionally a Pdx1 SACO library for NIT-1 cells was generated. | 2014-11-21 | Experiment Type: ChIP-seq, ChIP-chip by array; Organism: Mus musculus | PMID:17761679 | ||
| ArrayExpress_E-MTAB-2123 | Measurement of Isoform Specific Turnover using sequencing (MIST-Seq) after transcriptional arrest in rpb1-1 strain of budding yeast | Microarray | Transcriptional arrest is performed in the rpb1-1 strain grown at 24C in two independent biological replicates by raising the temperature instantly to 37C. Total RNA was collected at fixed time points after the arrest and sequenced using the 3' T-filling protocol as described by Wilkening et al 2013 to obtain accurate quantification of 3' isoforms. The decaying library size is corrected for the by reads mapping to the S.pombe spike-in control RNA. The decay rates are estimated on fitting a single parameter exponential decay curve after taking the technical reproducibility of low counts for every time point into account. | 2014-11-17 | Experiment Type: RNA-seq of coding RNA; Organism: Saccharomyces cerevisiae | DOI:10.1002/msb.135068 | ||
| ArrayExpress_E-GEOD-52788 | DNA copy number changes in malignant mesothelioma | Microarray | Malignant mesothelioma (MM) is an asbestos-related malignancy. Discrimination between MM and reactive mesothelial hyperplasia (RM) is often difficult. MM cells have a broad histological spectrum, and consist mainly of epithelioid, sarcomatoid, and biphasic cell types. The prognosis of MM is generally poor, but better prognosis has been reported with the epithelioid type of MM than the non-epithelioid type. We applied a genome-wide analysis to the identification of new markers that may aid in differentiating the epithelioid type of MM from other histological types and from RM cells. Array-based comparative genomic hybridization analysis was performed on malignant mesothelioma (MM) primary cell cultures, reactive mesothelial hyperplasia (RM) primary cell cultures; early passage of in vitro primary cell cultures to minimize acquisition of additional genomic changes. If available, matched peripheral blood was applied to analysis. | 2014-11-22 | Experiment Type: genotyping by array, comparative genomic hybridization by array; Organism: Homo sapiens | |||
| ArrayExpress_E-MTAB-3063 | Transcription profiling by high throughput sequencing of samples of (local) infected and systemic, uninfected leaves of barley ?Barke? plants that were infected with Pseudomonas syringae pathovar japonica or Xanthomonas translucens pathovar cerealis or given a mock treatment | Microarray | Leaf-to-leaf, systemic immune signaling known as systemic acquired resistance (SAR) is poorly understood in monocotyledonous plants. Here, we characterize systemic immunity in barley (Hordeum vulgare) triggered after primary leaf infection with either Pseudomonas syringae pathovar japonica (Psj) or Xanthomonas translucens pathovar cerealis (Xtc). Both pathogens induced resistance in systemic, uninfected leaves against a subsequent challenge infection with Xtc. In contrast to SAR in Arabidopsis thaliana, systemic immunity in barley was not associated with NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1 or the local or systemic accumulation of salicylic acid (SA). Instead, we documented a moderate local but not systemic induction of abscisic acid (ABA) after infection of leaves with Psj. In contrast to SA or its functional analog benzothiadiazole, local applications of the jasmonic acid methyl ester or ABA triggered systemic immunity to Xtc. RNA-seq analysis of local and systemic transcript accumulation revealed unique gene expression changes in response to both Psj and Xtc and a clear separation of local from systemic responses. The systemic response appeared relatively modest and quantitative RT-PCR associated systemic immunity with the local and systemic induction of two WRKY and two ETHYLENE RESPONSIVE FACTOR-like transcription factors. Systemic immunity against Xtc was further associated with transcriptional changes after a secondary/systemic Xtc challenge infection; these changes were dependent on the primary treatment. Taken together, bacteria-induced systemic immunity in barley may be mediated in part by WRKY and ERF-like transcription factors possibly facilitating transcriptional reprogramming to potentiate immunity. | 2014-11-24 | Experiment Type: RNA-seq of coding RNA; Organism: Hordeum vulgare | DOI:10.1104/pp.114.249276 | ||
| ArrayExpress_E-MTAB-3056 | Transcriptional profiling by array of barley systemic leaf (leaf 2, leaf 3) on challenge by Xanthomonas translucens pathovar cerealis (Xtc) of plants preinfected with Pseudomonas syringae pathovar japonica (Psj), with Xanthomonas translucens pathovar cerealis (Xtc), or mock treated to study barley systemic immunity | Microarray | Leaf-to-leaf, systemic immune signaling known as systemic acquired resistance (SAR) is poorly understood in monocotyledonous plants. Here, we characterize systemic immunity in barley (Hordeum vulgare) triggered after primary leaf infection with either Pseudomonas syringae pathovar japonica (Psj) or Xanthomonas translucens pathovar cerealis (Xtc). Both pathogens induced resistance in systemic, uninfected leaves against a subsequent challenge infection with Xtc. In contrast to SAR in Arabidopsis thaliana, systemic immunity in barley was not associated with NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1 or the local or systemic accumulation of salicylic acid (SA). Instead, we documented a moderate local but not systemic induction of abscisic acid (ABA) after infection of leaves with Psj. In contrast to SA or its functional analog benzothiadiazole, local applications of the jasmonic acid methyl ester or ABA triggered systemic immunity to Xtc. RNA-seq analysis of local and systemic transcript accumulation revealed unique gene expression changes in response to both Psj and Xtc and a clear separation of local from systemic responses. The systemic response appeared relatively modest and quantitative RT-PCR associated systemic immunity with the local and systemic induction of two WRKY and two ETHYLENE RESPONSIVE FACTOR-like transcription factors. Systemic immunity against Xtc was further associated with transcriptional changes after a secondary/systemic Xtc challenge infection; these changes were dependent on the primary treatment. Taken together, bacteria-induced systemic immunity in barley may be mediated in part by WRKY and ERF-like transcription factors possibly facilitating transcriptional reprogramming to potentiate immunity. | 2014-11-24 | Experiment Type: transcription profiling by array; Organism: Hordeum vulgare | DOI:10.1104/pp.114.249276 | ||
| ArrayExpress_E-GEOD-56946 | Human endometrial cancer cell gene expression profiles of the estrogen receptor ? (ER?) hinge region mutants (H1 and H2NES) | Microarray | ERa negative Ishikawa cells were stably infected with Era: Wild type ERa, H1 ERa, H2NES ERa the design was to determine if rapid action non-genomic mediated signals would lead to gene expression changs. Four stable cell lines, vector, WT, H1 and H2NES ERa were treated for 4hr or 24 hr with 10nM Estradiol or vehicle, n=3 for each treatment group | 2014-11-24 | Experiment Type: transcription profiling by array; Organism: Homo sapiens | PMID:24947674 | ||
| ArrayExpress_E-GEOD-37490 | StromeWA30834809_H3K4ME2_N2_EEMB | Microarray | modENCODE_submission_3198 This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Early Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population; NUMBER OF REPLICATES: 2; EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; temp (temperature) 20 degree celsius; Antibody WA308-34809 H3K4me2 (target is H3K4me2); Strain N2 | 2012-04-22 | Experiment Type: ChIP-chip by tiling array; Organism: Caenorhabditis elegans | |||
| ArrayExpress_E-GEOD-62519 | The RSC Complex localizes to coding sequences to regulate Pol II and histone occupancy (Agilent) | Microarray | ATP-dependent chromatin remodelers regulate chromatin structure during multiple stages of transcription. We report that RSC, an essential chromatin remodeler, is recruited to the open reading frames (ORFs) of actively transcribed genes genome-wide, suggesting a role for RSC in regulating transcription elongation. Consistent with such a role, Pol II occupancy in the ORFs of weakly transcribed genes is drastically reduced upon depletion of the RSC catalytic subunit Sth1. RSC inactivation also reduced histone H3 occupancy across transcribed regions. Remarkably, the strongest effects on Pol II and H3 occupancy were confined to the genes displaying the greatest RSC ORF enrichment. Additionally, RSC recruitment to the ORF requires the activities of the SAGA and NuA4 HAT complexes and is aided by the activities of the Pol II CTD Ser2 kinases Bur1 and Ctk1. Overall, our findings strongly implicate ORF-associated RSC in governing Pol II function and in maintaining chromatin structure over transcribed regions. ChIP-chip experiments to measure Sth1, Rpb3 and H3 occupancy in WT and various mutants (histone acetyltransferase and Pol II CTD kinase mutants). The histone H3 and Rpb3 occupancy were also measured in cells upon Sth1 depletion. The WT and mutant strains were grown in Synthetic complete or YPD media to an O.D. 600 of 0.6-0.8. For inducing Gcn4, the cells grown in SC were treated with Sulfometuron methyl for 20-25 minutes and process for chromatin immunoprecipitation using antibodies again Myc, Rpb3 or histone H3. | 2014-11-24 | Experiment Type: ChIP-chip by tiling array; Organism: Saccharomyces cerevisiae | |||
| ArrayExpress_E-GEOD-62189 | A computational algorithm to predict shRNA potency | Microarray | This SuperSeries is composed of the SubSeries listed below. Refer to individual Series | 2014-11-24 | Experiment Type: other, RNA-seq of coding RNA, RNA-seq of non coding RNA; Organism: Gallus gallus, Homo sapiens, Mus musculus, synthetic construct | |||
| ArrayExpress_E-GEOD-53862 | Chromatin occupancy and target genes of TCF7L2 in hepatocytes | Microarray | TCF7L2 regulates multiple metabolic pathways in hepatocytes through a transcriptional network involving HNF4α For the identification of Tcf7l2 target genes using a RNA-seq timecourse, and for identifying the binding sites of Tcf7l2 and Hnf4a, Tcf7l2 was silenced in rat H4IIE hepatocytes using siRNA for Tcf7l2 with a scrambled siRNA as control. Treatment times for RNA-seq samples were 3, 6, 9, 12, 15, 18, 48, and 96 hours, and for ChIP-seq samples 15 h. RNA-seq timecourse was performed in duplicate or triplicate, and the ChIP-seq in duplicate for Tcf7l2 and in singlicate for Hnf4a. The H4IIE-specific transcriptome was defined from an independent set of pooled 24 h siRNA treated samples (N=3 for siRNA for Tcf7l2 and N=3 for scrambled siRNA). | 2014-11-24 | Experiment Type: ChIP-seq, RNA-seq of coding RNA; Organism: Rattus norvegicus | DOI:10.1093/nar/gku1225 | ||
| ArrayExpress_E-GEOD-62187 | An optimized microRNA scaffold increases shRNA processing and target knockdown | Microarray | Two shRNAs were placed into expression vectors harboring mir30 microRNA scaffold and an optimized scaffold where the artificial restriction sights in mir30 have been removed. After infection and selection shRNA processing was assessed by small-RNA cloning. For both shRNAs, placement into the optimized scaffold resulted in a ~two-fold increase in processing (based on smallRNA levels). Purpose: Others have reported that the EcoRI site that was introduced to the mir30 scaffold results in decreased smallRNA processing and hence reduced target knockdown. We've developed an alternative scaffold (termed ultramir) where this site is removed. smallRNA cloning was used to determine if the movement of this sight resulted in an increase in shRNA processing. Method: Two shRNAs (one targeting Renilla Luciferase and one targeting Human RPA3) were cloned into the original mir30 cassette the ultramir cassette. Each of the 4 constructs were infected in duplicate at single copy into cells and the cells seltected unitil infection percentages reached >90% (the shRenilla hairpin was infected into HEK293T cells and the shRPA3 construts into the Gallus gallus cell line ERC. After selection smallRNA cloning was perfromed and the amount of smallRNAs corrresponding to the two shRNAs compared to the endogenous microRNA populatlon. Results: smallRNA levels of the two shRNAs doubled relative to the microRNA population when they were placed into the ultramir scaffold. | 2014-11-24 | Experiment Type: RNA-seq of non coding RNA; Organism: Gallus gallus, Homo sapiens | |||
| ArrayExpress_E-GEOD-62186 | shRNA Sensor Analysis of 5' U converted shRNAs reveals 3' target bias exists in addition to 5' guide bias | Microarray | shRNAs selected with the shERWOOD algorithm were converted to have a U at the 5' end of their guide. When endogenous 1U shRNAs were compared to artificial shRNA via the sensor algorithm, the endogenous shRNAs were found to be more efficacious. Purpose: Structural studies have hinted that the 5' end of shRNA guides is engulfed in the RISC complex. It has also been reported that shRNAs with a 5' U are more efficacious than those with other 5' caps. We wished to determine whether replacement of shRNA guide 5' nucleotides with a U, regardless of the corresponding target base, would increase their efficacy. Method: For each gene in the "druggable genome" 10 shRNAs were selected with the shERWOOD algorithm. In each case the score was assessed as if the guide had a 5' U. Sensor constructs were designed pairing 1U-guide shRNAs with their endogenous target. shRNAs were assessed for efficacy via the shRNA sensor assay (Fellmann et al. Mol Cell 2011). Results: shRNAs with artificial 5' Us were found to be less efficacious than those with an endogenous 5' U, | 2014-11-24 | Experiment Type: other; Organism: synthetic construct | |||
| ArrayExpress_E-GEOD-39380 | Genome-wide analysis of primary plasma cell leukemia identifies recurrent imbalances associated with transcriptional Profile alterations (Copy number) | Microarray | Primary plasma cell leukaemia (pPCL) is a rare, yet aggressive form of de novo plasma cell tumor, distinguished from secondary PCL (sPCL) which represents a leukemic transformation of pre-existing multiple myeloma (MM). Here, we performed a comprehensive molecular analysis of a prospective series of pPCLs by means of FISH, single nucleotide polymorphism (SNP) array and gene expression profiling (GEP). IGH@ translocations were identified in 87% of pPCL cases, with prevalence of t(11;14) (40%) and t(14;16) (30.5%), whereas the most frequently altered regions were located at 1p (38%), 1q (48%), 6q (29%), 8p (42%), 13q (74%), 14q (71%), 16q (53%) and 17p (35%). A relevant finding of our study was the identification of a minimal biallelical deletion (1.5 Mb) in 8p21.2 encompassing the putative tumor suppressor gene PPP2R2A that was significantly down-regulated in deleted cases. Mutations of TP53 were identified in 4 cases all but one associated with a monoallelic deletion of the gene, whereas activating mutations of BRAF occurred in one case and were absent for N- and K-RAS. To evaluate the influence of allelic imbalances in transcriptional expression we performed an integrated genomic analysis with GEP data, showing a significant dosage effect of genes involved in transcription, translation, methyltransferases activity, apoptosis as well as Wnt and NF-kB signaling pathways. Overall, we provide a compendium of genomic alterations in a prospective series of pPCLs which may contribute to our understanding of this particular form of plasma cell dyscrasia and to better elucidate the mechanisms of tumor progression in MM. This series of microarray experiments contains the genome-wide profiles of 17 primary Plasma Cell Leukemia. 250 nanograms of genomic DNA was processed and, in accordance with the manufacturer's protocols, 90 micrograms of fragmented biotin-labeled DNA were hybridized on GeneChip Human Mapping 250K NspI Arrays (Affymetrix Inc.). The arrays were scanned using the GeneChip Scanner 3000 7G. The images were acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. The raw data for individual SNPs were extracted from CEL files and converted into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares using the Hidden Markov Model algorithm with a genomic smoothing window set to 0. After the pre-processing, piecewise constant estimates of the underlying local DNA copy number (CN) variation was calculated using the DNAcopy Bioconductor package, which looks for optimal breakpoints using circular binary segmentation (CBS). genotyping analysis of 17 primary Plasma Cell Leukemia | 2012-10-12 | Experiment Type: genotyping by array, comparative genomic hybridization by array; Organism: Homo sapiens | |||
| ArrayExpress_E-GEOD-62185 | Sub-genomewide shRNAs constructed using an optimized selection algorithm and microRNA backbone provide stronger evidence for follow-up studies | Microarray | Sub-genomewide shRNA libraries were constructed using the current RNAi consortium constructs as well as using the DSIR (siRNA algoirthm) and a novel shRNA specific algorithm (shERWOOD). All libraries were placed into mir30 expression vectors. The shERWOOD libraries were also placed in a vector harboring an optimized mir cassette (ultramir). Each library was screened using the pancreatic cell line A385. A concensus set of essential genes identified as the set for which two shRNAs depleted in each of the libries. For these genes, a great percentage of shERWOOD seletected shRNA depleted. In addition the placement of shERWOOD selected constructs into ultramir scaffoled increased the rate of shRNA depletion for essential genes further. Purpose: shRNA screens were carried out using various library construction strategies to identify the strategy that provides the best shRNA screening results. Method: Libraries were constructed using the TRC shRNA set as well as shRNAs identified using the DSIR and shERWOOD algorithms. shRNA libraries were cloned into mir30 expression vectors. shERWOOD shRNAs were also cloned into an expression vector harboring an optimized microRNA scaffold termed ultramir. Each resultant library was screened using the pancreatic cell line A385. Each library was analyzed separately to identify a set of genes where at least two shRNAs depleted. These gene sets were intersected to develop a set of essential genes. Results: The shERWOOD shRNA libraries provided the highest number depleting shRNAs for each essential gene. Further these shRNAs depleted to a greater extent than did the shRNAs from the other libraries. When shERWOOD libraries were placed into the ultramir cassette a greater number of shRNAs per essential gene depleted. | 2014-11-24 | Experiment Type: other; Organism: synthetic construct | |||
| ArrayExpress_E-GEOD-62184 | shRNA off target analysis via RNAseq | Microarray | shRNAs were assessed for off-target effects by comparing the gene expression profiles of cells that they had been infected into. shRNAs designed with the shERWOOD algorithm and house in the ultramir microRNA scafold were found to have very little off targeting. Purpose: A major detriment to RNAi is off-targeting. We wished to assess the level of off targeting of microRNA (ultramiR) housed shERWOOD shRNAs as compared to similar shRNAs in the TRC collection. Methods: 5 shRNAs targeting each of two genes were infected into the 4T1 cell line. For each gene one shRNA was selected from the TRC collection and one based on the shERWOOD algorithm. For each gene, the exrpession profiles of the corresponding shRNA infected cells were compared using RNAseq. Conclusions: Highly similar profiles were observed between shERWOOD selected shRNAs. TRC shRNAs produced profiles indicative of off-targeting. | 2014-11-24 | Experiment Type: RNA-seq of coding RNA; Organism: Mus musculus | |||
| ArrayExpress_E-GEOD-62183 | shRNA Sensor Analysis of DSIR Selected shRNAs | Microarray | Purpose: Generate a large, high quality database of paired shRNA efficacy/sequence datapoints. Methods:Twelve shRNAs for each Refseq annotated human gene were selected based on the DSIR algorithm. Twelve batches of ~22K shRNAs (corresponding to 12 agilent chips) were then assessed for efficacy via the sensor method outlined in Fellmann et al, Mol Cell, 2011. Conclusions: Neighboring nucleotide combinations are best at predicting shRNA efficacy. | 2014-11-24 | Experiment Type: other; Organism: synthetic construct |
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