Contributors : Benjamin S Waldman ; Dominic Schwarz ; Marc H Wadsworth II ; Jeroen P Saeij ; Alex K Shalek ; Sebastian LouridoSeries Type : OtherOrganism : Toxoplasma gondiiTargeted gRNA screen against putative nucleic-acid binding proteins in a differentiation reporter strain context. By looking for gRNAs enriched in parasites no longer able to activate reporter expression, we can identify genes essential for this process
1h
Contributors : Rui Monteiro ; Rossella RispoliSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Danio rerioThe goal of this study is to analyse the open chromatin regions via ATACseq in zebrafish embryonic endothelial cells at 26-27hpf using Tg(Kdrl:GFP) transgenic zebrafish embryos. 40000-50000 cells were FAC-sorted directly into 100 µl of 1x HBSS/10 mM HEPES/0.25% BSA buffer for Tagmentation (as described by Buenrostro et al. (2013), Nat. Methods 10, 1213-1218),...
1h
Contributors : Benjamin S Waldman ; Dominic Schwarz ; Marc H Wadsworth II ; Jeroen P Saeij ; Alex K Shalek ; Sebastian LouridoSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Toxoplasma gondiiUsing an epitope-tagged BFD1-complemented strain, the genomic binding of BFD1 was assessed in alkaline-stress induced bradyzoites.
1h
Contributors : R Kawata ; T Kagawa ; S Oda ; T YokoiSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Rattus norvegicusTesticular injury is often observed in drug development. Serum hormones are usually used as non-invasive biomarkers for testicular injury; however, their sensitivity is low. Therefore, it is difficult to monitor testicular injury in pre-clinical and clinical drug developments. In recent years, molecules in body fluid exosomes are attracting attention...
1h
Contributors : Benjamin S Waldman ; Dominic Schwarz ; Marc H Wadsworth II ; Jeroen P Saeij ; Alex K Shalek ; Sebastian LouridoSeries Type : Expression profiling by high throughput sequencingOrganism : Toxoplasma gondiiUsing a differentiation reporter strain, unstressed parasites (tachyzoites) or stressed, reporter positive parasites (bradyzoites) were isolated by flow cytometry and analyzed for differential gene expression.
1h
Contributors : Satish Casie Chetty ; Andrew Koenig ; Saulius SumanasSeries Type : Expression profiling by high throughput sequencingOrganism : Danio rerioAn ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single-cell transcriptomic analysis of hematovascular development in wild-type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were...
1h
Contributors : Siyuan Feng ; Guobao TianSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Mycolicibacterium smegmatis MC2 155To understand how GreA may affect gene expression at the transcriptional level, we performed whole-transcriptome RNA-seq analyses.To examine whether GreA binds to specific chromosomal regions, we performed chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) and then...
1h
Contributors : Geoffrey M Wahl ; Kathleen E DelGiorno ; Chi-Yeh ChungSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe performed RNA-seq on pancreatic tuft cells and non-tuft epithelial cells in caerulein-induced pancreatitis
1h
Contributors : Benjamin S Waldman ; Dominic Schwarz ; Marc H Wadsworth II ; Jeroen P Saeij ; Alex K Shalek ; Sebastian LouridoSeries Type : Expression profiling by high throughput sequencingOrganism : Toxoplasma gondiiWT (ME49∆KU80), ∆BFD1, or ∆BFD1/DD-BFD1-Ty parasites were treated with the stabilizing ligand Shield-1 (all three) or vehicle alone (WT and ∆BFD1/DD-BFD1-Ty) to identify genes differentially regulated by overexpression of BFD1.
1h
Contributors : K Öllinger ; P WästerSeries Type : Expression profiling by arrayOrganism : Homo sapiensAnalysis of altered gene expression in keratinocytes exposed to extracellular vesicles. In this dataset we include the respective expression data.
1h
Series Type : Other ; Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Toxoplasma gondiiThis SuperSeries is composed of the SubSeries listed below.
1h
Contributors : Sydney Lavoie ; Sena BaeSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusBackground and aims: Gut microbial metabolites and their host signaling pathways hold therapeutic potential for colorectal cancer (CRC). One example is short-chain fatty acids (SCFA), which are microbial metabolites generated from dietary fiber. This study aims to determine the pathogenesis of CRC from the host-microbiota perspective and the contributions of Ffar2, a SCFA...
1h
Contributors : Benjamin S Waldman ; Dominic Schwarz ; Marc H Wadsworth II ; Jeroen P Saeij ; Alex K Shalek ; Sebastian LouridoSeries Type : Expression profiling by high throughput sequencingOrganism : Toxoplasma gondiiTo profile cell-cycle progression and the asynchronous process of differentiation, we performed single-cell RNA-sequencing (scRNA-Seq) of T. gondii using Seq-Well (Gierahn et al., 2017). Wild-type or ∆BFD1 parasites were grown under unstressed or stressed conditions (24, 48 or 72...
1h
Contributors : Ningning Song ; Guanghui Dang ; Ziyin Cui ; Huajun Zheng ; Siguo LiuSeries Type : Expression profiling by high throughput sequencingOrganism : Mycobacterium tuberculosis variant bovisVitamins are organic compounds and essential nutrients required by host organism. Recent studies have shown that vitamin B1(VB1) and vitamin C (Vc) could inhibit Mycobacterium tuberculosis growth. However, the precise role of VB1 and Vc in M.tuberculosis are still not well understand. Therefore, in...
1h
Contributors : Chaomin Sun ; Ning MaSeries Type : Expression profiling by high throughput sequencingOrganism : Brevibacterium linensA urease positive marine actinobacterium Brevibacterium lines was demonstrated to form and dissolve calcite precipitation in conditions with different concentration of Ca2+. Next-generation sequencing (NGS) was used to analyze the transcriptome of B. lines under 0, 50 and 150 mM Ca2+ after 24 h incubation to discover the differentially expressed genes involved. Results...
1h
Contributors : Courtney Sakolish ; Alan Chramiec ; Yizhong Liu ; Zunwei Chen ; John House ; Susan P Halligan ; Gordana Vunjak-Novakovic ; Ivan RusynSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe investigated changes in bone and Ewing’s Sarcoma transcriptomes among control and treated cells grown in 2D plates, or within engineered bone scaffolds.
9h
Contributors : Yeqiao Zhou ; Jelena Petrovic ; Gregory W Schwartz ; Robert B FaryabiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPurpose: To characterize heterogeneity of GSI-responsive and -resistant T-ALL cellsMethod: We generated GSI-resistant T-ALL DND41 cells and profiled their transcriptome using single-cell RNA sequencing.Result: We report here the presence of resistant-like subpopulation in drug naïve DND41 T-ALL cells.Conclusion: While other popular...
10h
Contributors : Joel Uchuya-Castillo ; Michelina PlaterotiSeries Type : Expression profiling by arrayOrganism : Mus musculusThe aim of the study was to analyse the impact of the TRa1 nuclear receptor on Apc+/1638N-dependent intestinal tumorigenesis
10h
Contributors : Sanne Arjaans ; Brandie D Wagner ; Peter M Mourani ; Erica W Mandell ; Brenda B Poindexter ; Rolf M Berger ; Steven H AbmanSeries Type : Protein profiling by protein arrayOrganism : Homo sapiensIntroduction: Early pulmonary vascular disease in preterm infants is associated with the subsequent development of bronchopulmonary dysplasia (BPD) and pulmonary hypertension (PH), however, mechanisms that contribute to or identify infants with increased susceptibility for BPD and/or PH are...
11h
Contributors : Kishor K Sivaraj ; Hyun-Woo Jeong ; Katsuhiro Kato ; Ralf H AdamsSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusIn long bone, the metaphyseal region is less hypoxic than the bone marrow (bone shaft). To study the regional differences of vasculatures, we isolated endothelial cells (ECs) expressing membrane-anchored mTomato protein and nuclear H2B-GFP from Cdh5-mT/nG transgenic reporter femoral metaphysis and diaphyseal bone marrow cavity by...
11h
Contributors : Stephanie L Tsai ; Douglas A MeltonSeries Type : Expression profiling by high throughput sequencingOrganism : Ambystoma mexicanumThe wound epidermis is required for limb regeneration. To elucidate the roles of the wound epidermis during early regeneration, we examined how the transcriptional programs of early dividing cells (enriched for blastemal progenitors) and non-dividing cells in regenerating stump tissues as well as epithelial cells change when we prevented wound epidermis formation.
13h
Contributors : Stephanie L Tsai ; Douglas A MeltonSeries Type : Expression profiling by high throughput sequencingOrganism : Ambystoma mexicanumTreatment with midkine inhibitor iMDK inhibits limb regeneration. To elucidate the transcriptional mechanisms of iMDK treatment, we sequenced regenerating limbs treated with either DMSO or iMDK (bulk) in biological triplicate at 11 days post-amputation (dpa).
13h
Contributor : Alejandro Toledo-AranaSeries Type : Expression profiling by high throughput sequencingOrganism : Staphylococcus capitis ; Staphylococcus epidermidis ; Staphylococcus simiaeThe goal of our study was to perform RNA sequencing of whole transcripts to determine and compare the real length of 3’UTRs among closely-related staphylococcal species. We found that most of the mRNAs encoding orthologous genes in staphylococcal species have 3’UTRs with different lengths in addition to sequence...
14h
Contributors : Helena G Asenjo ; Amador Gallardo ; Jordi Martorell-Marugan ; Pedro Carmona-Saez ; David LandeiraSeries Type : Genome binding/occupancy profiling by high throughput sequencing ; OtherOrganism : Mus musculusWe report ChIP-seq of Polycomb proteins and 4sU-seq data using cell-cycle fractions in mouse embryonic stem cells
15h
Contributors : Maximiliano Escalante ; Ana Vigliocco ; Sebastián Moschen ; Paula Fernández ; Ruth Heinz ; Francisco Garcia-Garcia ; Julio A Di Rienzo ; Andrea Andrade ; Sergio AlemanoSeries Type : Expression profiling by arrayOrganism : Helianthus annuusThis study characterizes and compares the gene expression profiles between aerial part and roots of two sunflower inbred lines with contrasting response to water stress: B59 (sensitive) and B71 (tolerant) under non-stress and water stress...
15h
Contributor : Angelo VeroneseSeries Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensColorectal cancer stem cells (CR-CSCs) are implicated in tumor development, metastasis, and therapy resistance, however little is known about their epigenetic features. Here we describe the DNA methylation profiles of eight CR-CSC lines and their distinctive patterns, which are maintained following in vivo passages in immune-compromised mice.
15h
Contributors : Xi Qiao ; Jukka WestermarckSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPurpose: The goal of this study is to compare the transcriptome changes between Negative control, UBR5 depleted and MYC depleted HeLa cellsMethods: Gene expression profiles of Negative control, UBR5 depleted and MYC depleted HeLa cells were generated by deep sequencing, in triplicate.Results:The data were analyzed, and we sucessfully detected global differences in the...
19h
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