title: Hela cell line microRNA profiles following CFIm25 knockdown

status: Public on Feb 20 2018

city: Houston

first: Hyun Jung

last: Park

state: TX

address: One Baylor Plaza

department: Dan L. Duncan Cancer Center

institute: Baylor College of Medicine

summary: Purpose: When CFIm25 knockdown induces global APA events, we aim to investigate ceRNA landscape change based on microRNA expression change. Methods: microRNA from HeLa cells treated with control siRNA and CFIm25 siRNA were subject to RNA-Seq. Results: Consistent with our observations in TCGA breast cancer, we found a surprisingly high enrichment of 3ʹUTR shortening genes' ceRNA partners to tumor suppressors and their down-regulation. Conclusion: Our work indicated that the shortened 3ʹ-UTRs might direct the released miRNAs to repress their ceRNA partners in trans, which are enriched in ceRNET hubs and tumor suppressors, thereby effectively disrupting normal ceRNET and contributing to tumorigenesis.

overall_design: Hela cell line microRNA profiles of control treated and CFIm25 knockdown were generated by RNA-Seq using Illumina GAIIx.

first: C

middle: P

last: Masamha

first: H

first: W

first: E

last: Wagner


title: Integrative analysis of methylomic and transcriptomic data in fetal sheep muscle tissues in response to maternal diet during pregnancy

status: Public on Jan 24 2018

city: Piacenza

first: Marcello

last: Del Corvo

address: Via Emilia Parmense, 84

department: Institute of Zootechnics, Faculty of Agricultural, Food and Environmental Sciences

country: Italy

institute: Università Cattolica del S. Cuore

type: Methylation profiling by high throughput sequencing

summary: Numerous studies have established a link between maternal diet and the physiological and metabolic phenotypes of the offspring. In previous studies in sheep, we demonstrated that different maternal diets had altered the transcriptome of fetal tissues. However, the mechanisms underlying those transcriptomic changes are poorly understood. DNA methylation is an epigenetic mark regulating transcription and is largely influenced by dietary components of the one-carbon cycle, a generator of the methyl group donor. Therefore, in the present study, we hypothesized that different maternal diets during pregnancy will alter the DNA methylation and gene expression patterns in fetal tissues. Pregnant ewes were randomly divided into two groups each of which received a hay or corn diet from mid-gestation (day 67±5) until necropsy (day 131 ± 1). The diets were formulated to meet the nutritional needs of ewes during pregnancy. On the day of necropsy, longissimus dorsi (LD) muscle tissues were collected from the fetuses and then used for DNA methylation analysis and gene expression profiling.

overall_design: Genomic DNA was extracted from a total of 16 fetal LD samples, eight per dietary treatment, following a salt-chloroform extraction protocol. Methyl-binding domain (MBD) enrichment was performed, subsequently construction of the sequencing library was implemented and libraries were quality checked and quantified. The 16 samples were then used for cluster generation and following sequencing in two lanes of an Illumina Hi-Seq 2000 and 100-base paired-end reads were generated.

first: Hadjer

last: Namous

first: Francisco

last: Peñagaricano

first: Hasan

last: Khatib


title: Differential miRNA and mRNA Expression in Immortalized Human Keratinocytes (HaCaT) after Low Arsenic Exposure

status: Public on Jan 23 2018

city: Louisville

first: J.

middle: Christopher

last: States

state: KY

address: 505 S. Hancock St., Rm 304

department: Department of Pharmacology & Toxicology

country: USA

institute: University of Louisville

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: This SuperSeries is composed of the SubSeries listed below.

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Developmental Maturation and Alpha-1 Adrenergic Receptors-Mediated Gene Expression Changes in Ovine Middle Cerebral Arteries

status: Public on Jan 18 2018

city: TUCSON

first: Ravi

last: Goyal

state: Arizona

address: 1501 N. Campbell Ave

institute: University of Arizona

summary: The Alpha Adrenergic Signaling Pathway is one of the chief regulators of cerebrovascular tone and cerebral blood flow (CBF), mediating its effects in the arteries through alpha1-adrenergic receptors (Alpha1AR). In the ovine middle cerebral artery (MCA), with development from a fetus to an adult, others and we have shown that Alpha1AR play a key role in contractile responses, vascular development, remodeling, and angiogenesis. Importantly, Alpha1AR play a significant role in CBF autoregulation, which is incompletely developed in a premature fetus as compared to a near-term fetus. However, the mechanistic pathways are not completely known. Thus, we tested the hypothesis that as a function of maturation and in response to Alpha1AR stimulation there is a differential gene expression in the ovine MCA. We conducted microarray analysis on transcripts from MCAs of premature fetuses (96-day), near-term fetuses (145-day), newborn lambs, and non-pregnant adult sheep (2-year) following stimulation of Alpha1AR with phenylephrine (a specific agonist). We observed several genes which belonged to pro-inflammatory and vascular development/angiogenesis pathway significantly altered in all of the four age groups. We also observed age-specific changes in gene expression–mediated by Alpha1AR stimulation in the different developmental age groups. These findings imply complex regulatory mechanisms of cerebrovascular development.

overall_design: For these studies, we used cerebral arteries from premature fetuses (gestational age - 96-days old), near-term fetuses (gestational age 140 days), newborn lambs (5 days old) and non-pregnant adult sheep (18-24 months) obtained from Nebeker Ranch (Lancaster, CA).  For each experiment, four animals were used; in case of fetus twins only one of the twins was included in the study. In our previous studies, we have described the isolation of MCA from sheep 38,52,53. Briefly, pregnant and non-pregnant ewes were anesthetized with thiopental sodium (10mg/kg, Intravenous) and anesthesia was maintained with inhalation of 1% of isoflurane in oxygen throughout surgery. Following the delivery of the fetus by hysterotomy, fetuses and ewes were euthanized with an overdose of proprietary euthanasia solution, Euthasol (pentobarbital sodium 100mg/kg and phenytoin sodium 10mg/kg; Virbac, Ft. Worth, TX). Studies were performed in isolated MCAs cleaned of adipose and connective tissue. From each animal, cleaned MCA were cut into segments ∼4 mm length, and placed in tissue baths containing Krebs buffer (containing in mM: 120 NaCl; 4.8 KCl; 1.2 K2HPO4; 25 NaHCO3; 1.2 MgCl2; 2.5 CaCl2 and 10 glucose) bubbled with 95% O2/5% CO2 for 30 minutes. We exposed the arteries to PHE (10µM) at 38°C, the contraction of the arteries was monitored and following exposure for 30 minutes arterial segments were snap frozen in the organ bath and stored in -80 degrees for RNA isolation.


title: BMS_IM101042_Baseline_WB_study

status: Public on Feb 07 2018

city: Atlanta

first: Hanjoong

last: Jo

state: GA

address: 1760 Haygood Drive, Health Sciences Research Bldg E170

department: Coulter Department of Biomedical Engineering

institute: Georgia Tech and Emory Univ

summary: The goal of this study is to define the molecular signatures of SLE patients at baseline in BMS IM101042 trial. IM101042 (NCT00119678) is a phase IIb, multi-center, randomized, double-blind, placebo-controlled study to evaluate the efficacy and safety of abatacept vs placebo on a background of oral glucocorticosteroids in the treatment of subjects with systemic lupus erythematosus and the prevention of subsequent lupus flares, sponsored by Bristol-Myers Squibb.

overall_design: Total RNA from patients with SLE were collected, and profiled together with samples from normal healthy controls.

first: Yanhua

last: Hu

first: Julie

last: Carman


title: Transcriptome determinants of lung seeding by mammary tumor cells

status: Public on Jan 01 2018

city: Brno

first: Lucia

last: Knopfova

address: Kamenice 5

department: Department of Experimental Biology

country: Czech Republic

institute: Faculty of Science, Masaryk University

type: Expression profiling by high throughput sequencing

summary: Metastasis accounts for most of cancer-related deaths. Paracrine signaling between tumor cells and the stroma induces changes in the tumor microenvironment required for metastasis. Transcription factor c-Myb was associated with breast cancer (BC) progression but its role in metastasis remains unclear. Here we show that increased c-Myb expression in BC cells inhibits spontaneous lung metastasis through impaired tumor cell extravasation. On contrary, BC cells with increased lung metastatic capacity exhibited low c-Myb levels. We identified a specific inflammatory signature, including Ccl2 chemokine; that was expressed in lung metastatic cells but was suppressed in tumor cells with higher c-Myb levels. Tumor cell-derived Ccl2 expression facilitated lung metastasis and rescued trans-endothelial migration of c-Myb overexpressing cells. Clinical data show that the identified inflammatory signature, together with a MYB expression, predicts lung metastasis relapse in BC patients. These results demonstrate that the c-Myb-regulated transcriptional program in BCs results in a blunted inflammatory response and consequently suppresses lung metastasis.

overall_design: The study objective was to compare the transcriptomes of two independent variants of 4T1 cells with altered capacity to colonize lungs: (1) genetically modified 4T1 with Myb oncogene overexpression (MYBup), (2) 4T1 cells selected in vivo for high efficiency in lung seeding (lung3). Myb overexpression reduces the capacity of 4T1 cells to seed in lungs in experimental setting and to produce overt pulmonary metastases in orthotopic setting, whereas in vivo passaging rendered cells with enhanced metastatic ability. We tested the hypothesis that c-Myb drives transcriptional program preventing lung colonization by breast cancer cells, which is blunted in highly metastatic cells. To identify components of the program, we performed RNAseq and searched for genes that are either down-regulated in MYBup (compared to mock-transfected) and up-regulated in lung3 (compared to wt) or vice versa. All samples (mock, MYBup, wt, and lung3) were analysed in triplicates.

first: Petr

last: Benes

first: Lubor

last: Borsig


title: DNA-binding of IRF3, IRF5 and IRF7 transcription factors

status: Public on Jan 12 2018

city: Boston

first: Trevor

last: Siggers

state: MA

address: 24 Cummington Mall

department: Department of Biology

institute: Boston University

summary: The Interferon Regulatory Factors (IRFs) are essential regulators of the innate immune response to viruses. IRFs 3, 5, and 7 drive type-1-interferon and cytokine production in a cell-type and stimulus-specific manner, suggesting regulatory complexity. IRFs 3, 5 and 7 bind DNA as phosphorylation-activated dimers and are classically described as binding a doublet of the canonical IRF binding site: 5'-AANNGAAA-3’. IRF3/5/7 have both common and distinct gene targets and the simple canonical motif does not capture the regulatory complexity of IRF-dependent gene expression. Previous studies, both low and high throughput, have refined our understanding of IRF regulation, yet a systematic comparison of DNA binding preferences for active, dimeric IRF complexes has not been performed. To address this, we designed an IRF-specific, custom protein-binding microarray (PBM) that includes synthetic IRF binding sites as well as type-1-interferon and cytokine promoters. Using constitutively active, phosphomimetic IRF3, 5 and 7 dimers, we find key DNA binding differences for these factors with implications for IRF-dependent gene regulation.

overall_design: Five protein binding microarray (PBM) experiments of human Interferon Regulatory Factor (IRF) transcription factors were performed. These PBM experiments involved binding GST-tagged, constitutively active IRF3, IRF5, IRF7 as well as the DNA binding domain mutants IRF5-K96S and IRF7-S101K to double-stranded 180K Agilent microarrays. DNA sequences tested on the array include: 1) predicted IRF binding sites from human and mouse type-I-interferon proximal promoters; 2) synthetic IRF binding sites with every possible single base pair substitution. All genomic and synthetic binding sites are centered within the same constant flanking sequence. Each DNA sequence is present between 4 and 6 times as replicate array spots: synthetic IRF binding sites have 6 replicate spots, genomic IRF binding sites have 5 replicate spots, and background control sequences have 4 replicate spots. Here we report the normalized signal intensity for each DNA spot.

first: Kellen

middle: K

last: Andrilenas

first: Vijendra

last: Ramlall


title: BMS_Prednisolone_WB_InVitro_study

status: Public on Feb 06 2018

summary: The goal of this study is to validate genes that are regulated by glucocorticoids or partial GR agonists in whole blood in vitro.

overall_design: Human whole blood was cultured for 5 hours with either dimethyl sulfoxide (DMSO) vehicle,  5 μM prednisolone, 5 μM BMS-791826, or 10 μM BMS-776532.


title: BMS_Prednisolone_hPBMC_InVitro_study_1

status: Public on Feb 03 2018

summary: The goal of these studies is to identify genes that are regulated by glucocorticoids in human peripheral blood mononuclear cells in vitro.

overall_design: hPBMCs were cultured for 6 hours with either dimethyl sulfoxide (DMSO) vehicle or 1 μM prednisolone.


title: A Forward Genetic Screen Targeting the Endothelium Reveals a Regulatory Role for the Lipid Kinase Pi4ka in Myelo- and Erythropoiesis

status: Public on Jan 30 2018

city: Los Angeles

first: Safiyyah

last: Ziyad

state: CA

address: 621 Charles E. Young Drive, South

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles


title: A Forward Genetic Screen Targeting the Endothelium Reveals a Regulatory Role for the Lipid Kinase Pi4ka in Myelo- and Erythropoiesis [mutant]

summary: Definitive hematopoietic cells arise from hemogenic endothelium during mid-gestation, indicating a direct link between blood and the endothelial-lined vessels. We sought to determine whether mutations initiated in the hemogenic endothelium would yield hematopoietic abnormalities or malignancies. Here we demonstrate that transposon mutagenesis targeting endothelial cells in mice promotes the development of hematopoietic pathologies that are both myeloid and lymphoid in nature. Sequencing of the disrupted genes identified several previously recognized candidate cancer drivers and furthermore revealed that mutations in the lipid kinase Pi4ka can result in myeloid and erythroid dysfunction. Subsequent validation experiments showed that targeted inactivation of the Pi4ka catalytic domain or reduction in mRNA expression inhibited myeloid and erythroid cell differentiation in vitro and promoted anemia in vivo through a mechanism that includes, but it is not limited to deregulation of Akt signaling. Finally, we provide evidence linking PI4KAP2, previously considered a “pseudogene”, with human myeloid and erythroid leukemia.

overall_design: mRNA transcriptional profiling of three SBxVEC-Cre+ animals and three control animals to assess cellular composition.

first: Trent

last: Su

first: Marco

last: Morselli

first: M

middle: L

last: Iruela-Arispe


title: A Forward Genetic Screen Targeting the Endothelium Reveals a Regulatory Role for the Lipid Kinase Pi4ka in Myelo- and Erythropoiesis [clonality]

overall_design: mRNA transcriptional comparison between two pieces of spleen from three SBxVEC-Cre+ animals and three control animals to assess clonality of each spleen as a whole.


title: Differential miRNA and mRNA Expression in Immortalized Human Keratinocytes (HaCaT) after Low Arsenic Exposure [miRNA]

summary: Determining the miRNA and mRNA expression profiles in HaCaT cells at early and late stages of arsenite exposure to reveal early and late changes in the HaCaT cells transformation process.

overall_design: 4 biological rereplicates of HaCaT cells exposed to 100 nM sodium arsenite and unexposed HaCaT cells (Control)

first: Laila

last: Al-Eryani

first: Sabine

last: Waigel

first: Samantha

last: Jenkins

first: Vennila

last: Arumugam

first: J

middle: C


title: Drosophila melanogaster embryonic development RAMPAGE time series (Biological replicate #2)

status: Public on Dec 19 2017

city: Woodbury

first: Philippe

last: Batut

state: NY

address: 500 Sunnyside Blvd.

institute: CSHL

summary: Multicellular development is largely determined by transcriptional regulatory programs that orchestrate the expression of thousands of protein-coding and noncoding genes. To decipher the genomic regulatory code that specifies these programs, and to investigate globally the developmental relevance of noncoding transcription, we profiled genome-wide promoter activity throughout embryonic development in 5 Drosophila species. We show that core promoters, generally not thought to play a significant regulatory role, in fact impart broad restrictions on the developmental timing of gene expression on a genome-wide scale. We propose a hierarchical model of transcriptional regulation during development in which core promoters define broad windows of opportunity for expression, by defining a limited range of transcription factors from which they are able to receive regulatory inputs. This two-tiered mechanism globally orchestrates developmental gene expression, including noncoding transcription on a scale that defies our current understanding of ontogenesis. Indeed, noncoding transcripts are far more prevalent than ever reported before, with ~4,000 long noncoding RNAs expressed during embryogenesis. Over 1,500 are functionally conserved throughout the melanogaster subgroup, and hundreds are under strong purifying selection. Overall, this work introduces a hierarchical model for the developmental regulation of transcription, and reveals the central role of noncoding transcription in animal development.

overall_design: 23 Samples of Drosophila melanogaster

middle: J

first: Thomas

middle: R

last: Gingeras


title: Dlx5 signaling cascade controls cranial neural crest and myoblast interaction during oropharyngeal patterning and development

status: Public on Oct 15 2017

first: Hideki

last: Sugii

address: 2250 Alcazar Street CSA103

department: craniofacial molecular biology

institute: University of Southern California

summary: Craniofacial development depends on cell-cell interactions, coordinated cellular movement and differentiation under the control of regulatory gene networks, which include the distal-less (Dlx) gene family. However, the functional significance of Dlx5 in patterning the oropharyngeal region has remained unknown. Here we show that loss of Dlx5 leads to a shortened soft palate and an absence of the levator veli palatini, palatopharyngeus, and palatoglossus muscles that are derived from the 4th pharyngeal arch (PA), but the tensor veli palatini, derived from the 1st PA, is unaffected. Dlx5-positive cranial neural crest (CNC) cells are in direct contact with myoblasts derived from the pharyngeal mesoderm, and Dlx5 disruption leads to altered proliferation and apoptosis of CNC and muscle progenitor cells. Moreover, the FGF10 pathway is downregulated in Dlx5-/- mice, and activation of FGF10 signaling rescues CNC cell proliferation and myogenic differentiation in these mutant mice. Collectively, our results indicate that Dlx5 plays critical roles in patterning of the oropharyngeal region and development of muscles derived from the 4th PA mesoderm in the soft palate, likely via interactions between CNC-derived and myogenic progenitor cells.

overall_design: Control; 3 samples, Dlx5 knockout mice; 3 samples

first: Yuxing

last: Guo

first: Jingyuan

last: Li

first: Yuan

last: Yuan


title: Differential miRNA and mRNA Expression in Immortalized Human Keratinocytes (HaCaT) after Low Arsenic Exposure [mRNA]

first: J.

last: States


title: RNA-Sequencing of Drosophila melanogaster Head Tissue on High Sugar and High Fat Diets

status: Public on Sep 28 2017

city: Monroe

first: Wayne

last: Hemphill

state: Louisiana

address: 700 University Ave

institute: University of Louisiana at Monroe

summary: Obesity has been shown to increase risk for cardiovascular disease and type-2 diabetes. In addition, it has been implicated in aggravation of neurological conditions such as Alzheimer’s. In the model organism Drosophila melanogaster, a physiological state mimicking diet-induced obesity can be induced by subjecting fruit flies to a solid medium disproportionately higher in sugar than protein (HSD) or that has been supplemented with a rich source of saturated fat (HFD). These flies can exhibit increased circulating glucose levels, increased triglyceride content, insulin-like peptide resistance, and behavior indicative of neurological decline, such as decreased climbing ability. We subjected Oregon-R-C flies to variants of the HSD, HFD, or normal (control) diet (ND), followed by a total RNA extraction from fly heads of each diet group for the purpose of Poly-A selected RNA-Sequencing. We targeted at least 50 million paired-end, stranded reads of 75 basepairs in size, and analyzed 4 biological replicates per dietary condition. Our objective was to identify the effects of obesogenic diets on transcriptome patterns, how they differed between obesogenic diets, and identify genes that may relate to pathogenesis accompanying an obesity-like state.  Functional annotation and enrichment analysis among genes whose expression was significantly affected by the obesogenic diets indicated an overrepresentation of genes associated with immunity, metabolism, and hemocyanin in the HFD group, and CHK, cell cycle activity, and DNA binding and transcription in the HSD group. Heat map representation of genes affected by both diets illustrated a large fraction of differentially expressed genes between the two diet groups.  Diets high in sugar and diets high in fat both have notableeffects on the Drosophila transcriptome in head tissue. The impacted genes, and how they may relate to pathogenesis in the Drosophila obesity-like state, warrant further experimental investigation.  Our results also indicate differences in the effects of the HFD and HSD on expression profiles in head tissue of Oregon-R-C flies, despite the reportedly similar phenotypic impacts of the diets.

overall_design: Flies were reared on one of three diets (high fat, high sugar, or normal).  6 replicates, with twenty flies each, from each diet treatment were collected for a total of 18 samples.  The heads of the flies were then obtained, and RNA extracted from each of those samples.  4 of the RNA samples from each diet group (12 samples total) were sequenced.

middle: O

first: Osvaldo

middle: G

last: Rivera

first: Matthew

middle: E

last: Talbert


title: Comparative transcriptomic analysis provides insights into high-altitude adaptation

status: Public on Sep 06 2017

city: Chengdu

first: Mingzhou

state: Sichuan

address: No.211 Huimin Road, Wenjiang District

country: China

institute: Sichuan Agricultural University

summary:
Purpose: High-altitude adaptive evolution of transcription, and the convergence and divergence of transcriptional alteration across species in response to high-altitude environments, is an important topic of broad interest to the general biology community. Our study aims to answer this important biological question.
Methods: We generated deep transcriptome data of high- and low- altitude populations across four species: chicken, pig, goat and sheep, as well as high-altitude yak and low-altitude cattle, from six tissues (heart, kidney, liver, lung, skeletal muscle and spleen).
Results: Here we provide a comprehensive comparative transcriptome landscape of expression and alternative splicing variation between low- and high-altitude populations across multiple species for distinct tissues.
Conclusions: Our data serves a valuable resource for further study on adaptive transcription evolution and identification of candidate adaptive genes.

sample_organism:
Gallus gallus
Sus scrofa
Bos taurus
Capra hircus
Ovis aries
Bos grunniens

overall_design: RNA-seq data from 138 samples derived from six tissues (heart, kidney, liver, lung, skeletal muscle and spleen) of three unrelated adult females for each of five animals (chicken, pig, cattle/yak, sheep and goat) from high- and low-altitude regions.

first: Qianzi

last: Tang


title: Transcriptomic analysis provides insights into the high-altitude adaptation in domestic goats

summary:
Purpose: Domestic goats distributed in a wide range of habitats and have evolved genetic adaptations to their local environmental conditions. The goal of this study s to investigate the dramatic gene expression changes of goats that are shaped by high altitude adaptation.
Methods: We performed RNA-seq on 27 samples from the three hypoxia-sensitive tissues (heart, lung and skeletal muscle) in three indigenous populations residing in distinct altitudes (600 m, 2,000 m and 3,000 m).
Results: We identified numerous differentially expressed genes which exhibited distinct expression patterns, and nonsynonymous SNVs-containing genes which highly differentiated between the high- and low-altitude populations.
Conclusions: These identified genes have known or potential roles in hypoxia response, and enriched in functional gene categories potentially responsible for high altitude adaptation, are appealing candidates for further investigation of the adaptive evolution in harsh high-altitude environment.

overall_design: RNA-seq on 27 samples from the three tissues (heart, lung and skeletal muscle) in three indigenous populations residing in distinct altitudes (600 m, 2,000 m and 3,000 m)


title: Drosophila species embryonic development RAMPAGE time series

sample_organism:
Drosophila ananassae
Drosophila erecta
Drosophila melanogaster
Drosophila pseudoobscura
Drosophila simulans


title: Drosophila erecta embryonic development RAMPAGE time series

overall_design: 23 Samples of Drosophila erecta


title: Drosophila simulans embryonic development RAMPAGE time series

overall_design: 22 Samples of Drosophila simulans


title: SETBP1-WT and SETBP1-G870S transcriptional profiles [RNA-Seq]

status: Public on Sep 01 2017

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

institute: Ospedale San Raffaele

summary: RNA-Seq experiments on SETBP1-G870S and Empty cells was performed in order to assess if the presence of mutated SETBP1 may induce differential RNA expression.

overall_design: n=6: 2 conditions, namely SETBP1-WT and SETBP1-G870S, in triplicate

first: Rocco

last: Piazza

first: Vera

last: Magistroni

first: Sara

last: Redaelli

first: Mario

last: Mauri

first: Marco

last: Peronaci

first: Caterina

last: Mezzatesta

first: Alessandra

last: Pirola

first: Carlo

last: Gambacorti-Passerini


title: SETBP1-WT and SETBP1-G870S DNA binding propensity [ChIP-Seq TF]

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ChIP-seq against V5 has been performed in order to investigate the role of SETBP1 as a DNA binding protein

overall_design: n=3: 3 ChIP-seq against V5 have been performed in HEK 293FLP cells expressing SETBP1-WT, SETBP1-G870S or Empty vector


title: Drosophila pseudoobscura embryonic development RAMPAGE time series

first: Philippe

last: Batut

overall_design: 29 Samples of Drosophila pseudoobscura

first: Thomas

last: Gingeras


title: Drosophila ananassae embryonic development RAMPAGE time series

overall_design: 22 Samples of Drosphila ananassae


title: SETBP1-WT and SETBP1-G870S epigenetic landscapes [ChIP-Seq]

summary: ChIP-Seq experiments targeting H3K4me2, H3K4me3, H3K9ac, H3K27ac, H3K36me3 histone modifications have been performed in order to assess if SETBP1 binding to gDNA was associated with chromatin remodeling and to further characterize the mechanisms responsible for SETBP1-mediated transcriptional regulation

overall_design: n=10: 5 histone marks in 2 conditions: Empty vector and SETBP1-G870S


title: Gene expression analysis in fly ovaries carrying Sco homozgyous clones

status: Public on Nov 22 2017

city: Taipei

first: Hweijan

last: Hsu

address: no 128, Sec 2,  Academia Rd. Nankang

department: Institute of Cellular Biology

country: Taiwan

institute: Academia Research

summary:
Purpose: The goal of this study is to analyze genes affected by Sco mutation using RNA-seq.
Ovarian mRNA prolife of 7-day-old control flies and flies carring Sco mutant follicle cell clones were generated by deep sequence, in duplicate. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.

first: Cheng-Yuan

last: Tseng


title: Sugarcane transcriptome: Lxx inoculated (LxxI) vs. mocked inoculated (MI) plants

status: Public on Nov 13 2017

city: Piracicaba

first: Luis

middle: Eduardo

last: Aranha Camargo

state: São Paulo

address: Av. Pádua Dias

department: Phytopathology

country: Brazil

institute: University of São Paulo

summary: Transcriptional profile of sugarcane plants variety SP80-3280 inoculated with the pathogen Leifsonia xyli subsp. xyli (Lxx) compared with mocked inoculated ones 30 and 60 days after inoculation (DAI). Goal was to determine the effects of the increase in Lxx title on global sugarcane gene expression.

overall_design: Lxx inoculated vs. Mocked inoculated plants. Time point analysis: 30 and 60 days after inoculation. Biological replicates: 2 control replicates, 2 Lxx inoculated replicates, in each time.

first: Mariana

last: Cia

last: Camargo


title: Amyotrophic Lateral Sclerosis associated FUS mutation shortens mitochondria and induces neurotoxicity

status: Public on Nov 01 2017

city: Baltimore

first: Manolis

last: Maragkakis

state: MD

address: 251 Bayview Blvd

institute: National Institute on Aging

summary: We employ CLIP-Seq, RNA-Seq and Ribo-Seq in cultured neurons expressing R495X or wild-type FUS to identify effects of the mutation on the FUS targetome and on the neuronal transcriptome at the expression and translation level

overall_design: We set up an inducible expression system based on lentiviral transduction of FLAG-tagged human R495X or wild-type FUS in neurons differentiated from mouse Embryonic Stem cells. we performed CLIP-Seq , RNA-Seq and Ribo-Seq in neurons expressing WT or R495X.

first: Tadashi

last: Nakaya


title: The use of targeted next-generation sequencing to determine the regulatory function of TGF‐β1 in kidney fibrosis [MeDIP-seq]

status: Public on Oct 24 2018

city: shenzhen

first: Guanyu

last: Ji

state: GuangDong

address: 14th of middle jinxiu road

department: R&D

institute: GENEDOHEALTH

summary: Transforming growth factor‐beta (TGF‐β1) plays an important regulatory role in the progression of chronic kidney failure. Further, damage to kidney glomerular mesangial cells is central to the progression of diabetic nephropathy. The aim of this study was to explore the genetic associations between mRNA, microRNA, and epigenetics in mesangial cells in response to TGF‐β1. The regulatory effects of TGF‐β1 on mesangial cells were investigated at different molecular levels by treating mesangial cells with TGF‐β1 for 3 days followed by genome‐wide miRNA, RNA, MeDIP-seq, and H3K27Me3 expression profiling using next-generation sequencing (NGS). Each sample was designed with 3 repeat samples.

overall_design: Whole genome MeDIP-seq, miRNA, H3K27me3 and RNA-seq of mouse. This dataset includes the MeDIP-seq data.

first: Bo

last: Wang

first: David

last: Powell

first: Wenjun

first: Haroon

last: Naeem

first: Phillip

last: Kantharidis

first: Sharon

last: Ricardo


title: Transcriptomic insights into human decidual and peripheral blood CD8 T cells

status: Public on Oct 18 2017

city: Shanghai

first: Wei

last: Guisheng

address: Chifeng road 65

institute: shanghaitech

summary: We performed the analysis of transcriptional and alternative splicing landscapes for paired decidual and peripheral blood CD8 T cells at the first trimester of human healthy pregnancy by high-throughput mRNA sequencing.

overall_design: Healthy women at the first trimester of pregnancy were recruited, and FACS was performed to isolate and purify the CD8+ T cells from the decidua and maternal peripheral blood. We sequenced the mRNA samples on an Illumina Hiseq 2500 platform.

first: Weihong

last: Zeng

first: Yi

last: Lin


title: Characterization of three Epithelial Ovarian Cancer cell lines resistant to cisplatin.

status: Public on Jul 24 2017

city: Aviano

first: Riccardo

last: Bomben

address: Via Franco Gallini 2

department: D-RT

institute: CRO Aviano

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Characterization of three Epithelial Ovarian Cancer cell lines resistant to cisplatin (mRNA).

summary: Epithelial ovarian cancer (EOC) represents the gynecologic cancer with the highest mortality rate. Despite a high initial response to chemotherapy, the majority of patients with advanced EOC relapses and subsequently develops chemoresistance that results in treatment failure and death of the patient. AIM: we have generated an isogenic model of PT-resistance in a panel of 3 EOC cell lines. Gene Expression Profile (GEP) was used to identify new molecular pathawy that regulate chemoresistance.

overall_design: GEP experiments were performed in 3 Epithelian Ovarian Cancer cell lines Platinum-resistant vs their parental, with Agilent platform. Bioinformatics analyses were performed by Gene Springs

first: Maura

last: Sonego

first: Ilenia

last: Pellizzari

first: Gustavo

last: Baldassarre


title: Expression data from 10-day-old Arabidopsis Col-0 and rns2-2 seedlings

status: Public on Sep 15 2017

city: Ames

first: Stephanie

last: Morriss

state: Iowa

department: Biochemistry, Biophysics and Molecular Biology

institute: Iowa State University

summary:
Housekeeping degradation of normal ribosomal RNA in eukaryotes is completed by the RNase T2 family of ribonucleases. This family of ribonucleases is found through eukaryotes, and the Arabidopsis RNase T2 which degrades ribosomal RNA is RNS2. A null mutant in RNS2, rns2-2, has higher levels of RNA, vacuolar accumulation of rRNA and constitutive autophagy.
We used microarray to detail the global changes in gene expression in response to mutation of RNS2 (rns2-2) and identified key biological processes differentially regulated in response to this mutation.

overall_design: RNA was extracted from 10-day-old Arabidopsis seedlings of two genotypes, Col-0 (the control) and rns2-2, the experimental. RNA was hybridized on Affymetrix ATH1 microarrays. Twenty seedlings were grown on MS-agar for ten days. Three independent biological samples were taken, forming three biological replicates.

last: MacIntosh

first: Diane

last: Bassham

first: Xiaoyi

last: Liu


title: ChIP-Seq data of the Streptomyces venezualae protein Sven2756 (MtrA) over a time course of 10h, 12h, 14h, 16h, 18h and 20h.

status: Public on Jul 12 2017

city: Norwich

first: John

middle: Tyson

last: Munnoch

address: Norwich Research Park

department: Schol of Biological Sciences

country: United Kingdom

institute: University of East Anglia

summary: We report the results of ChIP-Seq experiment investigating the MtrA TCS response regulator.  The experiment utilised an in trans copy of mtrA with an N-terminal 3xFlag tag encoded on the plasmid pMS82 (containing a phiBT1 integration site).  The experiment utilised beads associated with anti-flag antibodies, specific for the Flag tagged protein.  We report important targets involved in cell division and salt stress with key findings supporting the hypothesis that MtrA is essential. Samples were taken over a time course of 10h, 12h, 14h, 16h, 18h and 20h.

overall_design: An mtrA::apr mutant with an in trans 3xFlag tagged copy of mtrA.  Due to the use of strain independent antibodies there is no clean negative control (as would be found with WT using mono/polyclonal antibodies specific to the WT protein.

first: Nicolle

last: Som

middle: T


title: De novo assembly and analysis of Artemisia argyi transcriptome and identification of genes involved in terpenoid biosynthesis

status: Public on Dec 21 2017

city: Hefei

first: Meiqi

last: Zhou

address: Meishan Road 103

institute: Anhui University of Chinese Medicine

summary: Artemisia argyi Lev. et Vant., a common ancient compositae species, is widely utilized in traditional Chinese medicine. The underlying mechanism of terpenoid biosynthesis in leaf has been suggested to play an important role in this medicine. However, the transcriptome of A. argyi has not been established. Here, we performed RNA sequencing in leaf, root and stem tissues to identify all possibly transcribed genes. We assembled a total of 99,807 unigenes by analyzing the expression profiling that were generated from the three tissues. Of them, 67,446 unigenes (67.58%) were annotated from public databases including GO, KEGG, COG. We further performed differential gene expression analysis between leaf with stem and root tissue. Our findings revealed that a total of 7,725 unigenes were specified transcribed in leaf. In particular, we determined multiple genes, which encode significant enzymes including HMGR, MVD, DXS, DXR, HDS and HDR, and transcription factors related to terpenoid synthesis. This study established a valuable resource of transcriptome and identified many transcribed genes related to terpenoid biosynthesis, providing the genomic basis for further studies on the molecular mechanism of the medicine for this species.

first: Jiawen

last: Wu


title: Genetic-to-epigenetic Therapy for Pancreatic Cancer

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

summary: We utilized RNA-Seq to define molecular markers for the effect of chaetocin and MLN8237 combination. PDAC cells were treated with individual drugs or their combination and compared to vehicle. Treatment was limited to 24 hours to extract RNA before significant mitotic catastrophe occurred to capture the transcriptional effect.

overall_design: PANC-1 mRNA profiles following 24 hrs of treatment with vehicle (DMSO), chaetocin (30nM), MLN8237 (90nM) or a combination of chaetocin(30nM)+MLN3237(90nM). Each condition was performed in triplicate.

first: Angela

last: Mathison


title: Multi-tissue RNA-seq data across three species

first: Mingzhou

last: Li

summary: We performed mRNA-seq on 27 samples from the three tissues (heart, liver and kidney) across three species (cattle, sheep, goat)

sample_organism:
Bos taurus
Capra hircus
Ovis aries

platform_organism:
Bos taurus
Capra hircus
Ovis aries

first: Qianzi

last: Tang


title: Expression data from T cells in vivo

status: Public on Jun 30 2017

city: Bethesda

first: Li

last: Jia

address: 10 Clinic center

institute: NCI/NIH

summary: Induced pluripotent stem cells (iPSC) might provide an unlimited source of T cells for a variety of clinical applications, including restoration of T cell immunity following stem cell transplantation and generation of minimally differentiated antigen-specific T cells for adoptive immunotherapy.  However, current methods of differentiating T cells from iPSC using OP9/DLL1, an extrinsic source of Notch signaling, result in the accumulation of unconventional T cells either lacking CD8 co-receptors or expressing CD8αα homodimers.  We sought to explore the conditions that cause iPSC to give rise to unconventional T cells, and to test whether alternative culture conditions that convey physiologic signals for selection at various stages of in vitro differentiation could allow for the generation of conventional T cells.  Here, we demonstrate that inappropriate signals for selection are a major driver of the unconventional T cell fate, and that a non-substrate bound thymic culture system can provide the requisite signals required for selection and survival of conventional T cells expressing the CD8αβ heterodimer.  This culture system is capable of generating large numbers of both polyclonal and antigen-specific T cells that recapitulate the phenotypic, functional, and gene expression profiles of bona fide naïve CD8αβ+ T cells.  These data represent an important proof-of-concept that therapeutically useful mature T cells can be generated from iPSC entirely in vitro, a finding with major implications for the use of reprogramming technology for cellular therapy.

overall_design: Samples were injected into 6 week old littermate Rag1-/- female recipients with 2e7 recombinant vaccinia with hgp100.  Mice were sacrificed 25 days later and spleens were recovered.  Live, congenically marked cells were recovered by FACS.

first: Nicholas

middle: D

last: Klemen

last: Restifo


title: Gene expression signatures in SPIN1 siRNA- and negative control-transfected breast cancer cell line MCF-7/ADM

status: Public on Aug 01 2017

city: Jinan

first: Peng

last: Gao

address: Wen Hua Xi Road 44

institute: Shandong University

summary: To screen potential target genes of SPIN1 in breast cancer, human gene expression microarray was performed to identify differentially expressed mRNAs in SPIN1 siRNA or negative control transfected MCF-7/ADM cells. After transfection with SPIN1 siRNA, 4409 genes were differentially expressed by >2-fold in MCF-7/ADM cells compared with negative control-transfected cells, of which 2413 were significantly downregulated and the other 1996 were upregulated. Differentially expressed genes were submitted to GO and KEGG pathway analysis.

overall_design: A two chip study using total RNA recovered from MCF-7/ADM breast cancer cells transfected with  SPIN1 siRNA or negative control. Each chip measures the expression 45033 genes were collected from the authoritative data source including NCBI.

first: Xu

last: Chen


title: Tissue specific expression data from maturing wheat seeds (20-50 DAA) of two genotypes

city: Winnipeg

first: Belay

middle: T.

last: Ayele

state: MB

address: 222 Agriculture Building

department: Plant Science

country: Canada

institute: University of Manitoba

summary:
Transcriptomic analysis of the embryo and endosperm tissue of maturing wheat seeds of two geneotypes, namely AC Domain and RL4452, was performed
We used Affymetrix GeneChip Wheat Genome Array to detail transcriptional programs and regulatory networks underlying seed maturation/desiccation in wheat

overall_design: Maturing seeds (20 to 50 DAA) of two wheat genotypes, AC Domain and RL4452, characterized by contrasting final seed size/weight and degree of tolerance to preharvest sprouting were used for RNA extraction and hybridization on Affymetrix GeneChip.

first: Mark

last: Jordan

first: Yuji

last: Yamasaki


title: Characterization of three Epithelial Ovarian Cancer cell lines resistant to cisplatin (microRNA).

first: Riccardo

last: Bomben

summary: Epithelial ovarian cancer (EOC) represents the gynecologic cancer with the highest mortality rate. Despite a high initial response to chemotherapy, the majority of patients with advanced EOC relapses and subsequently develops chemoresistance that results in treatment failure and death of the patient. AIM: we have generated an isogenic model of PT-resistance in a panel of 3 EOC cell lines. microRNA profiling was used to identify new molecular pathway that regulate chemoresistance.

overall_design: microRNA experiments were performed in 3 Epithelian Ovarian Cancer cell lines Platinum-resistant vs their parental, with Agilent platform according to Agilent protocol for microRNA profile. Bioinformatics analyses were performed by Gene Springs

first: Maura

last: Sonego

first: Ilenia

last: Pellizzari

first: Gustavo

last: Baldassarre


title: Context-Specific Transcription Factor Functions Regulate Epigenomic and Transcriptional Dynamics During Cardiac Reprogramming [ATAC-seq]

status: Public on Jul 03 2019

city: San Francisco

first: Nicole

last: Stone

address: 1650 Owens St.

institute: Gladstone Institutes - UCSF

summary: To determine the molecular mechanisms by which expression of Gata4, Mef2c, and Tbx5 (GMT) induces direct reprogramming from a cardiac fibroblast toward an induced cardiomyocyte, we performed a comprehensive transcriptomic and epigenomic interrogation of the reprogramming process. Single cell RNA sequencing indicated that a reprogramming trajectory was acquired within 48 hours of GMT introduction, did not require cell division, and was limited mainly by successful expression of GMT. Evaluation of chromatin accessibility by ATAC-seq supported the expression dynamics and revealed widespread chromatin remodeling at early stages of the reprogramming process. Chromatin immunoprecipitation followed by sequencing of each factor alone or in combinations revealed that GMT bind DNA individually and in combination, and that ectopic expression of either Mef2c or Tbx5 is sufficient in some contexts to increase accessibility. We also find evidence for cooperative facilitation and refinement of each factor’s binding in a combinatorial setting. A random-forest classifier that integrated the observed gene expression dynamics with regions of dynamic chromatin accessibility suggested Tbx5 binding is a primary driver of gene expression changes and revealed additional transcription factor motifs co-segregating with reprogramming factor motifs, suggesting new factors that may be involved in the reprogramming process.

overall_design: Examination of genome-wide accessibility of induced cardiomyocytes. ATAC-seq analyses were performed with three biological replicates.

first: Casey

middle: A

last: Gifford

first: Deepak

last: Srivastava


title: Effect of dimethyl fumarate (DMF) and transforming growth factor (TGFb) on gene expression in dermal fibroblasts

status: Public on Jun 22 2017

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: Primary adult dermal fibroblasts isolated from forearm skin biopsy of 3 healthy donors were treated with DMF and TGFb.

overall_design: 3 cell lines of dermal fibroblasts were derived from skin biopses from healthy donors. All cell lines were subjected to 4 treatments: control (DMSO), dimethyl fumarate (DMF), TGFb, and TGFb+DMF. The goal of the study was to identify sets of genes regulated by different treatments.

first: Agnieszka

last: Grzegorzewska

first: Paul

last: Haines

first: Maria

last: Trojanowska


title: The rectal mucosal transcriptome of men who have sex with men (MSM) engaging in condomless receptive anal intercourse (CRAI) compared with men who have never engaged in anal intercourse (controls)

status: Public on Jun 19 2017

city: Atlanta

first: Gregory

last: Tharp

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: We report differences in mRNA gene expression in rectal biopsies from MSM compared to controls and for MSM timed with episodes of CRAI.

overall_design: Rectal biopsies were obtained from MSM at two study timepoints: 1. after who abstaining from CRAI for >72 hours and 2.after engaing in CRAI within the last 24 hours.  Rectal biopsies were also obtained from men who never engaged in AI.

first: Colleen

middle: F

last: Kelley

first: Steven

last: Bosinger

first: Rama

last: Amara

middle: S

last: Kraft

first: Tom

last: DeMan

first: Chandini

last: Duphare

first: Hyun-Woo

last: Lee

first: Jing

last: Yang

first: Kirk

last: Easley

middle: M

last: Mulligan

first: Patrick

last: Sullivan

first: Nirav

last: Patel


title: RNA-sequencing analysis of non silencing or ILF2 shRNA-transduced H929 cells

status: Public on May 23 2017

first: Mehmet

middle: Kemal

last: Samur

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

summary: To understand whether ILF2 is required to ensure the alternative splicing and processing of specific pre-mRNAs in Multiple Myeloma (MM) in physiological conditions, we performed RNA sequencing (RNA-Seq) analysis of ILF2-  and  non-silencing shRNA  transduced  H929 cells.

overall_design:
Total RNA from H929 cells transduced with a non-silencing or ILF2 shRNA (two independent replicates per condition) were isolated with the RNeasy Mini kit (Qiagen). Libraries were constructed using the TruSeq® Stranded Total RNA LT - (with Ribo-Zero TM Gold) - Set A (Illumina) according to the manufacturer’s instructions.
Transcriptomic RNA-Seq was performed on the Illumina 2000 HiSeq platform using the standard paired-end protocol. In total, 60-160 million 76-bp reads were generated per sample. An initial sequence-level quality assessment was performed using FastQC (version 0.10.1, Simon Andrews). The RNA-Seq reads were then mapped to the reference human genome (GRCh37) using Tophat2, allowing a maximum of two mismatches per 76-bp sequencing end. Differential splicing was assessed by multivariate analysis of transcript splicing (MATS) using an FDR<0.05. Pathway enrichment analysis was performed with Pathway Studio.

first: Anil

first: Simona

last: Colla

first: Matteo

last: Marchesini


title: SETBP1-WT and SETBP1-G870S epigenetic landscapes

city: Milano

first: Luca

last: Massimino

address: Via Olgettina, 58

institute: Ospedale San Raffaele


title: The transcriptional consequences of inhibiting CDK8 in the context of innate immune activation

status: Public on Aug 14 2017

city: Cambridge

first: Mukund

last: Varma

address: 415 Main Street

institute: Broad Institute

summary: TF-seq analysis conducted on the same set of lysates identified 3 primary pathways modulated by CDK8 inhibition: suppression of NF-kB and STAT1 and de-repression of AP-1.  The results with STAT1 are consistent with literature identifying a role for CDK8 in IFN-driven STAT1 transcriptional activation.  In addition, there is patent literature indicating that CDK8 inhibition can suppress NF-kB activation.  We expect to see changes in the global RNA-seq expression profiles consistent with the TF-seq data – namely, reduced expression of NF-kB and STAT1 target genes.

overall_design: BMDMs were pre-treated with the CDK8 inhibitors dCA (100 nM), or BRD-6989 (1 uM) for 24 hours, then stimulated with a cohort of 11 different TLR ligands for 8 time points from 0-4 hours.

last: Sundberg

first: Daniel

last: O'Connell

first: Liv

last: Johannessen

first: Raivo

last: Kolde

first: Xavier

last: RJ


title: RNA immunoprecipitation and sequencing of ILF2-bound transcripts in Multiple Myeloma

summary: To understand the mechanistic basis of ILF2’s regulation of mRNA splicing in response to DNA damage in Multiple Myeloma, we performed RNA immunoprecipitation (RIP) and sequencing of ILF2-bound transcripts under both physiological and DNA damage (melphalan treatment) conditions. Cells were treated with melphalan for 10 hours. RNA immunopreciptation (RIP) and sequencing of ILF2-bound RNAs was performed in the JJN3 and H929 cell lines (two biological replicates/condition). Cells were treated with melphalan for 10 hours.

overall_design: RNA immunoprecipitation (RIP) analyses were performed on untreated or melphalan treated JJN3 and H929 cells using anti-ILF2 (Abcam, ab113205) or anti-YB-1 (Abcam, ab12148) antibodies. In brief, cells were cross-linked in 0.1% formaldehyde for 10 min prior to harvest and lysis. RIP was performed using the Magna RIP RNA-binding protein immunoprecipitation kit (Millipore) according to the manufacturer’s instructions. RNA in each eluted sample was sequenced. Libraries were constructed using the Ovation RNA-Seq System V2 (Nugen) according to the manufacturer’s instructions. Reads were mapped to the human genome (GRCh38) using STAR . Isoform abundances were quantified using Cufflinks (version 2.2.1) . Low-abundance isoforms in the immunoprecipated samples (Fragments Per Kilobase of transcript per Million mapped reads [FPKM]<3) were excluded. Isoforms with significantly increased ILF-2 or YB-1 binding were identified using a q value <0.05 and a fold change >1.5 as cutoffs between the input and immunoprecipitate of each sample.

middle: K


title: RNA immunoprecipitation and sequencing of YB-1-bound transcripts in Multiple Myeloma

summary: To understand the mechanistic basis of YB-1’s regulation of mRNA splicing in response to DNA damage in Multiple Myeloma, we performed RNA immunoprecipitation (RIP) and sequencing of ILF2-bound transcripts under both physiological and DNA damage (melphalan treatment) conditions. Cells were treated with melphalan for 10 hours. (RIP) and sequencing of YB-1-bound RNAs was performed in the JJN3 line (two biological replicates/condition).


title: Transcriptome analysis of photoperiodic flowering in soybean.

status: Public on Jul 21 2017

city: Urbana

first: Yoshie

last: Hanzawa

state: IL

address: 1201 West Gregory Drive

department: Cropsciences

institute: University of illinois at Urbana Chammpaign, USA

summary: In order to identify candidate genes that are involved in soybean flowering transition in response to photoperiods, we performed RNA sequencing analysis under different photoperiod treatments. We identified genes exhibiting daily oscillation patterns under different photoperiod treatments, genes under control of maturity loci (E1, E2, E3 and E5), and genes that constitute the soybean flowering gene network.

sample_organism:
Glycine max
Glycine soja

platform_organism:
Glycine max
Glycine soja

overall_design: RNA sequencing analysis was performed using Williams 82, Clark and four NILs in Clark that are polymorphic for E loci (E1, E2, E3 and E5), as well as the wild soybean Glycine soja, under different photoperiod treatments.

first: Waseem

last: Haider


title: Systems-guided forward genetic screen reveals critical role of the replication stress response protein ETAA1 in T cell clonal expansion

status: Public on Jun 12 2017

city: Melbourne

first: Ian

last: Parish

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

summary: We have examined the role of the  replication stress protein Etaa1 in mouse effector T cell expansion. While immune development and other steady state phenotypes are relatively normal in Etaa1 deficient mice, these mice have a selective defect in T cell expansion after vaccination or viral infection. To better determine the cause of this defect, we conducted RNA-seq analysis on Etaa1 wild-type or splice mutant LCMV-specific P14 CD8+ T cells at day 5 p.i. with LCMV-Armstrong. We find that mutant cells exhibit a strong enrichment of a p53 DNA damage signature within their transcriptome, and we independently validated this change by demonstrating  increased staining for the DNA damage response factor gamma-H2AX within mutant T cells. Collectively these data suggest that Etaa1 plays a surprisingly specific role in preventing DNA damage accumulation within proliferating effector T cells.

overall_design: 5x10^4 CD45.1+ Etaa1+/+ or Etaa1 DEx2/DEx2 were injected i.v. into wild-type C57BL/6N mice that were subsequently infected with 2x10^5 pfu LCMV-Armstrong strain i.p.  At day 5 p.i., spleens were isolated and pooled according to P14 genotype (typically 3-8 spleens per P14 genotype), and then a splenocyte suspension was sorted by FACS to isolate CD45.1+ CD8+ T cells.

first: Christopher

middle: C

last: Goodnow


title: ILF2 Regulates RNA splicing of DNA Damage Response Genes to confer poor prognosis in 1q21-Amplified Multiple Myeloma

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Testis transcriptional profiling of males deriving from two high fertility mouse lines (FL1, FL2) which have been long-term selected for the characteristics large and heavy litters in comparison to randomly selected control line (Ctrl)

city: Dummerstorf

first: Alexander

last: Sobczak

state: Mecklenburg Western-Pomerania

address: Wilhelm-Stahl-Allee 2

department: Institute for Reproductive Biology

country: Germany

institute: Leibniz Institute for Farm Animal Biology Dummerstorf (FBN)

summary:
As generally known, reproduction is referred to as a couple’s challenge. Many genes generally coding for reproduction performance are shared by both sexes.  For investigating the impact of ‘high fertility’ breeding on murine males testis transcriptomic profile was examined of two worldwidely unique outbred long-term mouse lines which have been selected for large and heavy litters -  Fertility Lines 1 and 2 (FL1, FL2); also known as DUK and DUC. After >170 generations of generally female focused breeding both high fertile mouse lines dramatically increased the number of offspring as well as the total litter weight up to 180%, which is additionally accompanied by raised ovulation rate as could be shown by previous data.
Concomitantly with the improved fertility phenotype, for the FL males several line-specific phenotypic characteristics could already be revealed like physiological parameters (e.g. higher bodyweight, accelerated puberty and life expectancy), behavioural parameters (e.g. explorative behaviour in an open field and decreased endurance fitness on a treadmill) or testicular cell type composition (e.g. altered haploid and diploid cell content shown by flow cytometric analysis). By this combination of phenotypic characterization and profound transcriptomic profiling we hope to ensure for future perspective that these genetically heterogeneous mouse models will provide new insights into molecular and cellular mechanisms of enhancing male fertility.

overall_design: Two separated microarray experiments (sets) were performed. Initially, for array set I each testis transcriptome of 8 mouse bucks per line was hybridized to 8 single microarray chips (n=8).  These males are deriving from the 4th of entirely 5 replicates of a recently accomplished comprehensive two-factorial breeding experiment with the aim to scrutinize the impact of males and females on fertility parameters (recently submitted (08.16)). Beside the accompanying effect of being able to correlate breeding experiment observations with gene expression results, along the first array set we had the objective to develop a first profound hint about differential gene expression between these three lines. The resulting lists were experimentally verified with a second microarray set which was based on testis samples from 8 biologically independent bucks per line also involved in the two-factorial breeding experiment, 2nd replicate (n=8). Contrary to the first array set, a testis-RNA pool of the separated line specimens had been generated before these line pools were hybridized to one microarray regarded as pool-chip. By means of this approach we ensured a profound verification of the entirety of gained gene expression results. This handily served for exclusion of ‘false positive’ transcripts which were initially indicated as differentially expressed but then could not keep validity in biologically independent reevaluation.

first: Marten

last: Michaelis

first: Joachim

last: Weitzel


title: Expression analysis of Lysobacter enzymogenes OH11 delta-clp mutant

status: Public on Jun 26 2017

city: Nanjing

first: Wang

last: Yansheng

address: No.1 Weigang

department: Department of Plant Pathology

institute: Nanjing Agricultural University

summary: Investigation of whole genome gene expression level changes in a Lysobacter enzymogenes OH11 delta-clp mutant, compared to the wild-type strain.

overall_design: A four chip study using total RNA recovered from two separate wild-type cultures of Lysobacter enzymogenes OH11 and two separate cultures of mutant delta-clp. Delta-clp represented the mutant with clp deletion in Lysobacter enzymogenes OH11. Each chip measures the expression level of 5,180 genes from Lysobacter enzymogenes OH11.

first: Fengquan

last: Liu

first: Yansheng

last: Wang


title: Myoz3 overexpression and knockdown CEFs

city: Chendu

first: Maosen

last: Ye

address: Huiming road

institute: Sichuan Agriculture University

summary: To identify novel pathways and genes that are respond to chMyoz3’s expression level change, we knock-down and over-expressed Myoz3 in chicken embryonic fibroblasts (CEF, stem cell that is wildly used to study chicken gene functions), respectively. RNA-seq and following analyses were then performed to identify genes and pathways involved in the process of Myoz3’s expression level change. We found multiple pathways and genes that were regulated by Myoz3, providing evidence for furhter study.

overall_design: CEFs RNA sequencing under Overexpression, siRNA knockdown and their respectively control.

first: Fei


title: Quantitative analysis of the DNA methylation sensitivity of transcription factor complexes

status: Public on Jun 13 2017

city: New York City

first: Harmen

middle: J

last: Bussemaker

state: New York

address: 1212 Amsterdam Avenue, MC 2441

department: Biological Sciences

institute: Columbia University

summary: EpiSELEX-seq method was used to characterize the binding preference of human TF complexes to methylated DNA, including BZIP proteins ATF4 and CEBPb, homeodomain TF heterodimers of HM(Meis1)-Pbx1 together with either HoxA1, HoxA5 or HoxA9 and tumor suppressor protein p53.

overall_design: One round of EpiSELEX-seq was performed for all TFs tested as described in Kribelbauer et al. Purified TFs were incubated with a mix of methylated and unmethylated randomized 16bp (26bp for p53) DNA libraries of sequence GGTAGTGGAGG-TGGG-CCTGG-16xN/26xN-CCAGG-GAGGTGGAGTAGG for unmethylated and GGTAGTGGAGG-GCAC-CCTGG-16xN/26xN-CCAGG-GAGGTGGAGTAGG for methylated library. Bound fractions were amplified and sequenced.

first: Richard

last: Mann

first: Judith

last: Kribelbauer


title: Genome-wide maps of five major transcription factors in epiblast stem cells

status: Public on May 01 2017

city: Takatsuki

first: Hisato

last: Kondoh

state: Osaka

address: Murasakicho 1-1

country: Japan

institute: Biohistory Research Hall

summary: ChIP-seq data of ZIC2, OTX2, SOX2, POU5F1 and POU3F1 in EpiSCs

overall_design: ChIP-seq using biotinylated transcription factors

first: Kazunari

last: Matsuda

first: Tomoyuki

last: Mikami

first: Shuji

last: Shigenobu


title: Molecular Mediators of Cardiac Pathology in Cardiorenal Syndrome Type 4 [anti-miR-21]

status: Public on May 04 2017

city: Milwaukee

first: Alison

middle: J.

last: Kriegel

state: WI

address: 8701 Watertown Plank Rd.

department: Physiology

institute: Medical College of Wisconsin

summary: We report the changes in left ventricle mRNA abundance in response to miR-21-5p suppression in 5/6 nephrectomized rats.

overall_design: Ten week old male Sprague Dawley rats were subjected to the excision model of 5/6 nephrectomy (5/6Nx) surgery.  LNA-anti-scrambled or LNA-anti-miR-21-5p was delivered intravenously in 3 daily doses of 1 mg/kg at 1 and 4 weels post-surgery.  Left ventricle tissue was collected for mRNA sequencing 7 weeks after surgery.

first: Sandra

last: Chuppa

first: Mingyu

last: Liang

first: Pengyuan

first: Yong

first: Marc

last: Casati

first: Allen

middle: W

last: Cowley

first: Leah

last: Patullo


title: Molecular Mediators of Cardiac Pathology in Cardiorenal Syndrome Type 4 [miRNA]

type: Non-coding RNA profiling by high throughput sequencing

summary: We report the changes in left ventricle miRNA abundance in response to 5/6 nephrectomy surgery

overall_design: Ten week old male Sprague Dawley rats were subjected to the excision model of 5/6 nephrectomy (5/6Nx) or sham surgery. Left ventricle tissue was collected 2, 4, 5 or 7 weeks later for miRNA sequencing.


title: Immunologic Control of Zika Virus in Rhesus Monkeys

status: Public on May 05 2017

first: MALIKA

last: AID

state: MA

address: 3 blackfan street

institute: BIDMC

summary:
Zika virus (ZIKV) is responsible for a major current outbreak in the Americas and has been causally associated with fetal microcephaly as well as Guillain-Barre syndrome in adults.  However, the immune responses associated with controlling ZIKV replication remain poorly characterized.  Here we report a detailed analysis of innate and adaptive immune responses following ZIKV infection in 16 rhesus monkeys.  A robust proinflammatory innate immune response was observed within the first few days of infection, including upregulation of type 1 interferon, which correlated directly with viral loads.  Immunomodulatory pathways, including IL-10 and TGF-β, were also upregulated.  ZIKV-specific neutralizing antibodies emerged rapidly by day 7 and correlated inversely with viral loads, which were undetectable in peripheral blood by day 6-10.  In contrast, virus replication persisted in cerebrospinal fluid (CSF) for at least 21-42 days in 75% (3 of 4) of the monkeys that received the lowest dose of ZIKV tested, and ZIKV-specific antibodies were essentially undetectable in CSF.  These data suggest that antibodies play a critical role in the rapid control of acute viremia in the periphery but were largely excluded from the central nervous system, allowing viral persistence at this immuonoprivileged site.
16 outbred, Indian-origin, adult male and female rhesus monkeys (Macaca mulatta) were included in this study.  All monkeys were housed at Bioqual, Rockville, MD.  Animals were infected with 103-106 pfu (106-109 vp) of our ZIKV-BR or ZIKV-PR challenge stocks by the s.q. route (N=2/group).  All animal studies were approved by the appropriate Institutional Animal Care and Use Committee (IACUC).

overall_design: 16 outbred, Indian-origin, adult male and female rhesus monkeys (Macaca mulatta) were included in this study.  All monkeys were housed at Bioqual, Rockville, MD.  Animals were infected with 103-106 pfu (106-109 vp) of our ZIKV-BR or ZIKV-PR challenge stocks by the s.c. route (N=2/group).  All animal studies were approved by the appropriate Institutional Animal Care and Use Committee (IACUC).Microarrays were performed on day 0 pre-infection and on day  2 , 4, 6 and 14 post-infection.

first: Dan

middle: H

last: Barouch

first: Aid

last: Malika

first: Peter

last: Abbink

first: Rafael

last: Larocca

last: De La Barrera

first: Alan

last: Perelson

first: Mark

middle: G

last: Lewis


title: Molecular Mediators of Cardiac Pathology in Cardiorenal Syndrome Type 4 [mRNA]

summary: We report the changes in left ventricle mRNA abundance in response to 5/6 nephrectomy surgery

overall_design: Ten week old male Sprague Dawley rats were subjected to the excision model of 5/6 nephrectomy (5/6Nx) or sham surgery. Left ventricle tissue was collected 2, 4, 5 or 7 weeks later for mRNAsequencing.

last: Liu


title: MeDIP assay using human myometrium of women with preterm labor of different phenotypes vs. normal term labor

city: San Antonio

first: Kohzoh

last: Mitsuya

state: Texas

address: 7703 Floyd Curl Drive

department: Center for Pregnancy and Newborn Research

institute: University of Texas Health Science Center San Antonio

type: Methylation profiling by genome tiling array

summary:
Preterm birth is multifactorial in origin with several distinct clinical phenotypes of differing etiologies, including idiopathic preterm birth. Preterm birth involves the interaction of genetic, societal and environmental factors such as nutrition, lifestyle and stress that may modulate the length of gestation via the epigenome. DNA methylation is a well-studied epigenetic modification whereby promoter methylation commonly represses gene expression and vice versa.
Myometrial tissue was obtained at cesarean section at term with or without labor, preterm without labor, idiopathic preterm labor, and twin gestations with labor. Differences in the myometrial epigenomes were identified at gene promoters, CpG islands, CpG island shores and shelves, gene bodies across the genome between the groups of women with preterm labor of different phenotypes vs. normal term labor. Functional clustering analysis indicated the significantly enriched pathways of hypomethylated genes (permissive) were related to acute inflammatory and acute-phase responses. By contrast, genes that are hypermethylated (repressive) revealed enrichment for contractile fibers and cell. This study provides the first high-resolution DNA methylome of human myometrium with evidence for differences in the methylome that may relate to idiopathic preterm birth via regulation of gene expression. The findings extend previous observations that idiopathic preterm labor is associated with subclinical intrauterine infection and inflammatory pathways and point to targets for further molecular characterization of preterm delivery.

overall_design: Comparison of the human myometrial epigenomes in pregnancies with preterm labor of different phenotypes vs. normal term labor

first: Leslie

last: Myatt


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type (WT) and dek37 mutant Transcriptomes

status: Public on Mar 15 2017

city: Gainesville

first: Dawei

last: Dai

state: Florida

address: 2550 Hull Rd

department: Horticultural Sciences

institute: University of Florida

summary: Analysis of  gene expression level. The hypothesis tested in the present study was that dek37 mutant affects cis-splicing of maize mitochondrial nad2 intron 1 . Results provide important information of the gene expression level regulation of mitochondrial  pathway associated genes.

overall_design: Endosperm mRNA profiles of 18DAP WT and dek37 mutant were generated by deep sequencing using Illumina Hiseq 2500 (Zea mays).

first: Weiwei

last: Qi


title: MeDIP and hMeDIP assays using human placentas of obese and lean (healthy weight) pregnancies

summary: Maternal obesity has both a direct effect on the outcome of pregnancy but also programs the fetus for obesity and metabolic syndrome in later life. Due to its roles at the interface between mother and fetus, the placenta transduces and mediates the effects of the obese intrauterine environment on the fetus. Here we have generated genome-scale high-resolution maps of 5mC and 5hmC in human placentas of obese and healthy weight pregnancies. Widespread alterations to the placental epigenome identified across the genome in the setting of maternal adiposity are primarily characterized by increase in 5mC and reciprocal decrease in 5hmC. This is also evident at the two pregnancy-associated gene clusters on chromosomes 17 and 19. In addition, maternal adiposity is associated with downregulation of ten-eleven translocation (TET) and isocitrate dehydrogenase (IDH) family genes and is accompanied by decreased levels of α-ketoglutarate (αKG) in the placenta. Of note, αKG levels exhibit a close positive correlation with both ascorbate and aconitate levels and less substantial but significant association with global 5hmC levels and placenta-specific gene expression. These observations suggest a mechanistic linkage between obesogenic environment and conversion efficiency of 5mC to 5hmC and highlight the idea that TET-mediated active DNA demethylation pathway can sense and respond to metabolic derangements and plays a role in subsequent cellular adaptation. Collectively, this study demonstrates that altered DNA demethylation process is likely one of the mechanisms underlying metabolic modulation of the placental epigenome with maternal adiposity.

overall_design: Comparison of lean vs obese epigenomes in human pregnancies


title: Stromal fibroblasts exhibit a similar transcriptome to mesenchymal stem cells in the perimenopausal endometrium

status: Public on Mar 29 2017

first: Linda

middle: C.

last: Giudice

state: CA

address: 499 Illinois St., Sixth Floor

department: Center for Reproductive Health at Mission Bay

institute: UC San Francisco

summary: Mesenchymal stem cells (eMSC) from perimenopausal (PeriM) endometrium do not exhibit significantly different transcriptomes from their premenopausal (PreM) counterparts, but PeriM endometrial stromal fibroblasts (eSF) demonstrate altered pathway activation.We compared transcriptomes of PeriM and PreM eSF, investigated if eMSC persist in PeriM endometrium, and whether eMSC and eSF undergo changes as a result of the perimenopausal endocrine milieu.Endometrium was obtained from 9 PeriM and 9 PreM women. Microarray analysis was performed on FACS-isolated eSF and eMSC and data were validated by quantitative RT-PCR. eMSC were immuofluorescently localized to the perivascular region of PeriM endometrium.Principal component analysis showed that cells clustered into three distinct groups in 3-dimensional space:  PeriM eMSC and PreM eMSC clustered together, while PeriM eSF and PreM eSF formed two discrete clusters separate from eMSC. Hierarchical clustering revealed a branching pattern consistent with the PCA results, indicating that eMSC from PreM and PeriM women exhibited a similar transcriptomic signature. Pathway analysis revealed dysregulation of cytoskeleton, proliferation, and survival pathways in PeriM vs. PreM eSF. A number of small nucleolar RNAs were also differentially regulated in PeriM eSF.Cell populations have altered gene expression in PeriM vs. PreM endometrium. While eMSC populations exhibited similar transcriptomes, PeriM eSF had altered pathway activation when compared to PreM eSF. This study provides insight into aging endometrium with relevance to function, including pregnancy establishment in reproductively older women.

overall_design: A total of 33 samples were used. Samples were analyzed by cell type and menopause status. Comparisons are as follows: PeriM eSF vs. PeriM eMSC; PeriM eMSC vs. PreM eMSC; PeriM eSF vs. PreM eSF; PreM eSF vs. PreM eMSC

first: David

last: Erikson

first: Fatima

last: Barragan

first: Terhi

last: Piltonen

first: Joseph

last: Chen

first: Shaina

last: Balayan

first: Juan

last: Irwin


title: Cytosine modifications modulate the chromatin architecture of transcriptional enhancers

status: Public on Mar 03 2017

city: Rennes

first: Gilles

last: Salbert

address: 263 Av. Gal. Leclerc

department: IGDR UMR6290

country: France

institute: University Rennes 1

summary: The dynamics of cytosine modifications such as 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) have been correlated with activation of transcriptional enhancers. However, their functional relationship with the regulation of enhancer activity by pioneer transcription factors remains elusive. To gain insights into their function, we interrogated chromatin characteristics of enhancers bound by the pioneer factors FOXA1, MEIS1 and PBX1at different ime points during differentiation of mouse embryonal carcinoma cells into neural progenitors.

overall_design: Genomic DNA or chromatin from P19 mouse embryonal carcinoma (EC) cells treated with retinoic acid (RA) and collected at 0 (vehicle, veh), 6, 12, 18, 24 or 48 hrs, were extracted and submitted to immunoprecipitation with 5mC (MeDIP) or 5hmC (hMeDIP) antibodies for genomic DNA or with H3K4me1, H3K27ac, FoxA1, Meis1, Pbx1 and Tet2 antibodies for chromatin. In addition, Formaldehyde Assisted Isolation of Regulatory Elements (FAIRE) was run with chromatin in order to map open chromatin regions. Reads were mapped to the mouse mm8 genome.

first: Elise

last: Mahé

first: Stéphane

last: Avner


title: Transcriptome analysis revealed that SMD regulates neuronal differentiation.

status: Public on Feb 27 2017

city: Seoul

first: younseo

last: Oh

address: 222, Wangsimni-ro, Seongdong-gu, Seoul, Republic of Korea

country: South Korea

institute: Hanyang University

summary: Transcriptome analysis from Staufen-mediated mRNA (SMD) targets during differentiation confirmed that STAU1 was a key factor in neuronal differentiation.

overall_design: Because the levels of STAU1 and UPF1 were reduced during differentiation, the levels of SMD target transcripts had to increase. These speculations drove us to further determine which transcripts were upregulated by both UPF1 and STAU1 depletion and differentiation.

first: Younseo


title: Central nervous system muscarinic receptor type-1 primes HSC mobilization from bone marrow via glucocorticoid-mediated relay

status: Public on Feb 15 2017

city: Bronx

first: Halley

last: Pierce

state: NY

address: 1301 Morris Park Ave.

department: Ruth L. and David S. Gottesman Stem Cell Institutue

institute: Albert Einstein College of Medicine

summary: Here we show that muscarinic type-1 (Chrm1) signaling in the central nervous system (CNS) promotes G-CSF-elicited HSC migration from the BM. Blockade of Chrm1 in the CNS, but not the periphery, reduced HSC mobilization. In Chrm1−⁄− mice, reduced mobilization was rescued by wild-type parabionts, suggesting the contribution of a soluble factor. We found that corticosterone levels were dramatically reduced in the BM, and its exogenous administration normalized the mobilization deficit of Chrm1−⁄− animals. Chrm1−⁄− HSCs have reduced nuclear glucocorticoid receptors (Nr3c1) and alterations in the expression of actin-organizing molecules.  Polymerized actin formation and HSC mobilization are also impaired in mice harboring Nr3c1-deficient hematopoietic cells.

overall_design: RNA for microarray analysis was isolated by sorting HSC (Lineage-Sca1+cKit+Flt3- directly into RLT buffer from the RNeasy Plus Micro kit (Qiagen) according to the manufacturer’s instructions.  Amplification and subsequent microarray was performed by the Genomics Core Facility at Albert Einstein College of Medicine using the One-Direct RNA amplification system (NuGEN) and GeneChip mouse gene 2.0 ST array (Affymetrix).  Analysis was performed by first processing the chip through Transcriptome analysis center (TAC) software (Affymetrix) to determine fold changes and p-values which were then analyzed by gene set enrichment analysis (GSEA).

first: Claire

last: Magnon

first: Daniel

last: Lucas

first: Matthew

last: Huggins

first: Gary

last: Schwartz

first: Paul

last: Frenette


title: Expression of long non-coding RNAs in autoimmunity and linkage to enhancer function and autoimmune disease risk genetic variants

status: Public on Apr 11 2017

city: Nashville

first: Charles

last: Spurlock III

state: Tennessee

address: 1161 21st Avenue South

department: Medicine

institute: Vanderbilt University School of Medicine

summary: Genome-wide association studies have identified numerous genetic variants conferring autoimmune disease risk.  Most of these genetic variants lie outside protein-coding genes hampering mechanistic explorations. Numerous mRNAs are also differentially expressed in autoimmune disease but their regulation is also unclear.  The majority of the human genome is transcribed yet its biologic significance is incompletely understood.  We performed whole genome RNA-sequencing [RNA-seq] to categorize expression of mRNAs, known and novel long non-coding RNAs [lncRNAs] in leukocytes from subjects with autoimmune disease and identified annotated and novel lncRNAs differentially expressed across multiple disorders. We found that loci transcribing novel lncRNAs were not randomly distributed across the genome but co-localized with leukocyte transcriptional enhancers, especially super-enhancers, and near genetic variants associated with autoimmune disease risk.  We propose that alterations in enhancer function, including lncRNA expression, produced by genetics and environment, change cellular phenotypes contributing to disease risk and pathogenesis and represent attractive therapeutic targets.

overall_design: We extracted RNA from peripheral whole blood across healthy control and disease subjects.

last: Spurlock

first: Thomas

last: Aune


title: Molecular Mediators of Cardiac Pathology in Cardiorenal Syndrome Type 4

first: Alison

last: Kriegel

summary:
We report the changes in left ventricle mRNA and miRNA abundance in response to 5/6 nephrectomy surgery

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series

first: Sandra

last: Chuppa

first: Mingyu

last: Liang

first: Pengyuan

last: Liu

first: Yong

first: Marc

last: Casati

first: Allen

last: Cowley

first: Leah

last: Patullo


title: Identification of miRNA transcription start sites from nascent transcriptome

status: Public on Apr 20 2017

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

summary: miRNAs are key post-transcriptional regulators of gene expression. However, it is still poorly understood how miRNAs themselves are regulated, mainly due to the sparse annotation of miRNA transcription start sites (TSSs). Here, we developed a novel method  for identifying active miRNA TSSs from nascent transcriptomes generated by nuclear run-on sequencing. With the least data requirement, our method demonstrated better performance than existing methods. Moreover, it provided ways not only to recognize miRNA TSSs but also to quantify primary miRNA expression in one experiment, which is very useful for revealing miRNAs directly regulated by the regulator(s) of interest.

overall_design: PRO-seq was performed for five human cell lines including Kasumi-1, Daudi, Ly-1, MV4-11 and U936. Biological replicates were included for each cell line.

first: Scott

last: Hiebert

first: Qi


title: RNA-Seq analysis facilitates quantitative analysis to identify DEGs in lung cancer cell lines regulated by S100A7A introduction in comparison with Cl1-0 control and S100A7A knockdown in comparison with CL1-5 control.

status: Public on Jan 31 2017

city: Kaohsiung

first: Kuang-Den

last: Chen

address: 123, Ta-Pei Rd., Niao-Sung Dist.

department: Translational Research Center in Biomedical Sicences

institute: Kaohsiung Chang Gung Memorial Hospital

summary:
Methods: The cDNA libraries from 3 pooled samples of cultured cells for each group were sequenced to generate RNA profiles using Illumina Miseq platform
Results: The sequencing runs yielded a total of 95.01 M reads with an average length of 73-74 bp. The high-throughput sequencing performed for liver samples with different treatments showed similar numbers of yielded reads ranged from 5.57 to 5.74 M and the same average length. The Strand NGS software (version 2.1) was used using default parameters for pre-alignment and post-alignment quality control analysis and 100% of the raw reads remained in the dataset. Of these, 19.02 M reads (84%) were mapped into contigs of the rat genome (rn5) and identified 31457 transcripts in liver samples.

overall_design: The mRNA profiles of CL1-0 lung adenocarcinoma cells with S100A7A overexpression and CL1-5 cells with S100A7A knockdown were generated with the respective controls by sequencing, using Illumina Miseq platform

first: Yung-Che


title: Transcriptome analyses of cerebral ischemia reveal functional lncRNAs in ischemia stroke

status: Public on Feb 23 2017

city: Shanghai

first: Kunshan

last: Zhang

address: 389 Xincun Road

department: Stem cell Translational Research center

institute: Tongji Hospital, Tongji University

summary:
Background and Purpose: Long noncoding RNAs (lncRNAs) are an emerging class of genomic regulatory molecules reported in neurodevelopment and many diseases. Despite extensive studies have identified lncRNAs and discovered their functions in CNS diseases, the function of lncRNAs in ischemia stroke remains poorly understood.

Method: Ischemia was induced by transient middle cerebral artery occlusion. Expression profiles of lncRNAs, miRNAs and mRNAs after ischemia stroke were obtained using high throughput sequencing technology. A correlation network was constructed to predict lncRNA functions. LncRNA-miRNA-mRNA network was constructed to discover ceRNAs.

Results: 1924 novel lncRNAs were identified, indicating that the ischemia stroke has a complex effect on lncRNAs. The top 10 regulated lncRNAs was validated by qRT-PCR. We have also predicted function of lncRNAs, and subjected them to gene co-expression network analysis, revealing the involvement of lncRNAs in many important biological process including injury and repair that are implicated in the regulation of ischemia stroke. Furthermore, lncRNAs mediated SMD (Staufen1-mediated mRNA decay) was analyzed and ceRNA (competitive endogenous RNAs) network was constructed in ischemia stroke.

Conclusions: This study reports the genome-wide lncRNA profiles in ischemia stroke using high throughput sequencing and constructs a systematic lncRNA-miRNA-mRNA network which reveals a complex functional noncoding RNA regulatory network in ischemia stroke.

overall_design: Rat brain mRNA, miRNA, lncRNA profiles after 24 hours of middle cerebral artery occlusion (MCAO) were generated by deep sequencing, 5 biological replicates, using Illumina HiSeq 2500.

first: Juan

first: Zhifeng

last: Deng


title: Gene expression data from aminoglycoside-treated vaginal tissues.

status: Public on Feb 16 2017

city: New Haven

first: Smita

last: Gopinath

state: CT

address: 300 Cedar St., TAC S640

department: Immunobiology

institute: Yale University

summary:
C57 Bl/6 mice were treated subcutaneously with Depo-provera. Five days after Depo treatment mice were treated intravaginally with 1mg neomcyin or equivalent volume of saline every day for six days. On the seventh day, mice were scarificed, vaginal tissue harvested and RNA extracted.
Matrix normalized data is provided as neomycin expression data normalized against pbs expression data.

overall_design: Total RNA obtained from vaginal tissues of neomycin or pbs control mice.

last: Kong

first: Akiko

last: Iwasaki


title: A novel metastasis–associated lncRNA destabilizes p21 through cooperative interactions with the NF90/NF45 complex

status: Public on Mar 01 2017

city: Philadelphia

first: Xiaowei

state: PA

address: 333 Cottman Avenue

institute: Fox Chase Cancer Center

summary: Long non-coding RNAs (lncRNA) have emerged as important regulators of gene expression at both the transcriptional and post-transcriptional levels.  While altered expressions of lncRNAs have been observed in breast cancer (BCa) development, their roles in BCa progression and metastasis are still poorly understood.  To identify novel BCa-associated lncRNA candidates, we have employed a high-density SNP array based approach to uncover lncRNA genes at intergenic region that are aberrantly expressed in BCa.  Here we report the role of a novel lncRNA, LincIN, in breast cancer progression and metastasis.  High levels of LincIN expression are frequently observed in tumors compared to adjacent normal tissues, and are strongly associated with aggressive breast cancers.  Importantly, analysis of The Cancer Genome Atlas (TCGA) data further suggested that high LincIN expression was associated with poor overall survival in patients with breast cancer (P<0.05).  Our gain-and-loss experiments demonstrate that LincIN play a role in tumor cell migration and invasion and knockdown of LincIN diminishes tumor cell invasion in vitro and lung metastasis in a mouse xenograft model.  We also identified a LincIN-binding protein complex, NF90/NF45, through which LincIN destabilizes tumor suppressor p21 mRNA post-transcriptionally and thereby represses its protein expression.  In summary, our findings delineated an oncogenic role of LincIN in breast tumor progression-metastasis, and mechanistically uncovered its cooperative actions with NF90/NF45 in regulating tumor suppressor gene expression at the post-transcriptional level.

overall_design: Stable lines expressing empty GFP vector or LincIN shRNAs (1 or 2) were generated using MDA-MB-231-Luc-D3H1 cells.  And total RNAs were collected from vector control and shRNA cells in two independent experiments. After examining the RNA qualities by Bioanalyzer, we performed unbiased transcriptome analysis using GeneChip® Human Gene 2.0 ST Arrays. The bioinformatics tool provided by the Affymatrix will be used in our computations.

first: Zhengyu

last: Jiang

first: Carolyn

last: Slater

first: Yan

last: Zhou

first: Karthik

last: Devarajan

first: Yueran

last: Li

first: Kathy

middle: Q

last: Cai

first: Mary

last: Daly


title: De novo transcription analysis of Haloxylon ammodendron in response to osmotic stress

status: Public on Jan 18 2017

city: Lanzhou

first: Jinlin

address: Tianshui South Road No.222

institute: Lanzhou Univeisity

summary:
Purpose: To elucidate the potential molecular mechanisms that are involved in drought tolerance of Haloxylon ammodendron.
Method: Pathways and candidate genes drought-resistant genes were identified in shoots and roost of Haloxylon ammodendron under sorbitol treatment for 6 and 24h using RNA-seq and Digital Gene Expression.
Results: 3,353 differently expressed genes in shoots and 4,564 in roots were successfully indentified.
Conclusion: A detailed investigation of the pathways and candidate genes identified in this study promote the research on the molecular mechanisms of drought resistance in the xerophytic species, and lay a solid foundation for developing stress-tolerant forage and crop species by using excellent genes relevant to drought tolerance in Haloxylon. ammodendron.

overall_design: RNA from shoots and roots of Haloxylon. ammodendron seedling treated with 0.4% sorbitol for 6 and 24h were sequenced.

first: Huijuan

last: Gao

first: Xinpei

last: Lv

first: Ling


title: PLATE-Seq for Genome-Wide Regulatory Network Analysis of High-Throughput Screens

status: Public on Apr 07 2017

city: New York

first: Peter

last: Sims

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

summary: Pharmacological and functional genomic screens play an essential role in the discovery and characterization of therapeutic targets and associated pharmacological inhibitors. Although these screens affect thousands of gene products, the typical readout is based on low-complexity rather than genome-wide assays. To address this limitation, we introduce Pooled Library Amplification for Transcriptome Expression (PLATE-Seq), a low-cost, genome-wide mRNA profiling methodology specifically designed to complement high-throughput screening (HTS) assays. Introduction of sample-specific barcodes during reverse transcription supports pooled library construction and low-depth sequencing that is 10 to 20-fold less expensive than conventional RNA-Seq. The use of network-based algorithms to infer protein activity from PLATE-Seq data results in comparable reproducibility to 30M read sequencing. Indeed, PLATE-Seq reproducibility compares favorably to other large-scale perturbational profiling studies such as the Connectivity Map (CMap) and Library of Integrated Network-based Cellular Signatures (LINCS).

overall_design: We use automated liquid-handling to introduce lysis buffer, capture polyadenylated mRNA with an oligo(dT)-grafted plate, and deliver well-specific, barcoded oligo(dT) primers to every sample in a multi-well plate (Figure 1A). After reverse transcription, the cDNA in each well contains a specific barcode sequence on its 5’-end and a common adapter, such that all samples can be combined into a single pool for purification and concentration. We then use Klenow Large Fragment for pooled second-strand synthesis from adapter-linked random primers. Because this polymerase lacks strand-displacement and 5’-to-3’ exonuclease activities, each cDNA molecule produces at most, one second-strand synthesis product containing the sample barcode (Figure 1B). Finally, the pooled library is enriched in a single PCR prior to sequencing. The resulting libraries represent the 3’-ends of mRNAs and are sequenced to a depth of 0.5-2 million raw reads per sample.

first: P


title: MicroRNA microarray of mouse in response to atmospheric PM2.5 inhalation

status: Public on Jan 24 2017

city: Taiyuan City

first: Tingting

last: Ku

state: Shanxi province

address: 92 Wucheng Road

institute: Shanxi University

summary: To determine the epigenetic mechanism by which PM2.5 deteriorated synaptic transmission and spatial learning and memory, we determined miRNA expression in hippocampi of mice in absent or present of PM2.5 exposure using GenoExplorer microRNA microarray analysis.

overall_design: MiRNA expression in hippocampi of mice was determined after mice received oropharyngeal aspiration of saline and PM2.5 at 1 and 5 mg/kg every other day for 4 weeks. Three independent experiments were performed with three repliactes in each groups.

first: Ben

first: Rui

first: Yingying

first: Wei

last: Yan

first: Xiaotong

last: Ji

first: Guangke

last: Sang


title: To analyze the effect of deletion of RTA3 on the transcriptome in Candida albicans

status: Public on Jan 05 2017

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: Similar to S. cerevisiae Rta1 (role in 7-aminocholesterol resistance) and Rsb1 (flippase); putative drug-responsive regulatory site; induced by fluphenazine, estradiol, ketoconazole, caspofungin; rat catheter biofilm induced

overall_design:
Agilent Custom  Whole Genome Candida albicans 8x15k Gene Expression  (AMADID: 026377) designed by Genotypic Technology private Limited, Bangalore  , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)
rta3 mutant samples vs. wt samples; samples were not treated

first: Sneh

middle: L

last: Panwwar


title: ChIPseq analysis of patient-derived luminal breast cancer xenografts with progestins

status: Public on Jan 04 2017

city: Aurora

first: Jessica

last: Finlay-Schultz

state: CO

department: Pathology

institute: University of Colorado Denver Anschutz Medical Campus

summary: Primary breast cancer xenografts

overall_design: Primary xenograft treated with estrogen or estrogen plus progesterone in triplicate. ChIP for estrogen receptor, progesterone receptor. Includes input and IgG negative control.

first: Austin

middle: E

last: Gillen

last: Kabos

first: Carol

last: Sartorius


title: Comparison of healthy, plaque psoriasis and pustular psoriasis FFPE skin biopsies

status: Public on Jan 27 2017

city: Ann Arbor

first: Andrew

last: Johnston

state: Michigan

address: 1301 East Catherine Street

department: Dermatology

institute: University of Michigan

summary: Generalized pustular psoriasis (GPP) is a rare, debilitating, and often life-threatening inflammatory disease characterized by episodic infiltration of neutrophils into the skin, pustule development, and systemic inflammation, which can manifest in the presence or absence of chronic plaque psoriasis (PV). Current treatments are unsatisfactory thus a better understanding the pathogenesis of GPP is warranted. To assess the pathophysiological differences between GPP and PV we performed a gene expression study on formalin-fixed paraffin-embedded biopsies of GPP (n=30) and PV (n=12) lesions and healthy control (n=20) skin. Compared with healthy skin, GPP lesions yielded 365 and PV 898 differentially expressed genes respectively, with 190 upregulated in both diseases. We detected higher expression of IL-1 and IL-36 cytokines in GPP lesions compared with PV, and this occurred proximal to neutrophils. We show both activated neutrophils and isolated neutrophil proteases can activate IL-36. Diverging from the Th1/Th17 pathophysiology of PV, significantly fewer IL23A, IL17A, IFNG, CXCL9, CXCL10 and MX1 transcripts were detected in GPP lesions. Our data indicate a level of sustained activation of IL-1 and IL-36 in GPP, inducing neutrophil chemokine expression, infiltration and pustule formation, suggesting that the IL-1 and IL-36 inflammatory axes are the main drivers of disease pathology in GPP.

overall_design: 20 normal healthy skin biopsies, 12 chronic plaque psoriasis, 32 generalized pustular psoriasis

first: Johann

last: Gudjonsson


title: RNAseq analysis of patient-derived luminal breast cancer xenografts treated with progestins

summary: Primary breast cancer xenografts

overall_design: Two primary xenografts with different treatments in triplicate


title: Sub-chronic pulmonary transcriptional response to coal tar, a PAH-containing complex mixture, in adult male MutaTMMouse.

status: Public on Jan 01 2017

city: Ottawa

first: Sarah

last: Labib

state: Ontario

address: 204b-50 Colombine

institute: Health Canada

summary: Polycyclic aromatic hydrocarbons (PAHs) are a class of hundreds of structurally similar chemicals ubiquitously present in our environment. They are created during the incomplete combustion of organic materials, such as oil, wood, tobacco, and charbroiled meat. As such, human exposure to mixtures of PAHs can occur through consumption of PAH-containing foods and water, inhalation of polluted air, or dermal contact. Several PAHs have been classified as carcinogenic to humans or probably carcinogenic to humans by the International Agency for Research on Cancer. The mice in this study were exposed to a complex mixture of PAHs - coal tar. In the present study, we sought to determine the dose-dependent changes in gene expression upon oral exposure to this PAH mixture in the lung tissue. Adult male MutaTMMouse were exposed to three doses of the coal tar or vehicle control (olive oil) for 28 days and sacrificed three days after the final exposure.

overall_design: This experiment examined the pulmonary transcriptional response of male mice exposed to coal tar extract for 28 days at three different doses, including D1 (1.3 mg BaP equivalents/kg-bw/day), D2 (2.5 mg BaP equivalents/kg-bw/day), and D3 (5.1 mg BaP equivalents/kg-bw/day) and vehicle control (D0).  Each dose group was examined 72 hours following the final exposure.  Each dose group had 5 biological replicates. There were a total of 20 samples (arrays) from the lung included in the final analysis using a two-colour reference design.

last: Williams

first: Sabina

last: Halappanavar


title: Sub-chronic pulmonary transcriptional response to mixtures of polycyclic aromatic hydrocarbons (PAHs)

summary: This SuperSeries is composed of the SubSeries listed below.