title: Transcript and Metabolite Changes during the Early Phase of ABA-mediated Induction of CAM in Talinum triangulare

status: Public on Apr 11 2019

city: Düsseldorf

first: Andreas

middle: PM

last: Weber

address: Universitätsstr. 1

department: Institute for Plant Biochemistry

institute: Heinrich-Heine-University

summary: Crassulacean Acid Metabolism (CAM) has evolved as a water saving strategy and its engineering into crops offers an opportunity to improve their water-use efficiency. This requires a comprehensive understanding of the regulation of the CAM pathway. Here, we use the facultative CAM species Talinum triangulare as a model in which CAM can be induced rapidly by exogenous abscisic acid (ABA). RNA-sequencing and metabolite measurements were employed to analyse the changes underlying CAM induction and identify potential CAM regulators. Non-negative matrix factorisation followed by k¬-means clustering identified an early CAM-specific cluster and a late one, which was specific for the early light phase. Enrichment analysis revealed ABA metabolism, WRKY-regulated transcription, sugar and nutrient transport and protein degradation in these clusters. Activation of the CAM pathway was supported by up-regulation of phosphoenolpyruvate carboxylase, cytosolic and chloroplastic malic enzymes and several transport proteins as well as by increased end-of-night titratable acidity and malate accumulation. Transcription factors HSFA2, NF-YA9 and JMJ27 were identified as candidate regulators of CAM induction. With this study we promote the model species T. triangulare, in which CAM can be induced in a controlled way, enabling further deciphering of CAM regulation.

overall_design:
Talinum triangulare seeds were germinated in multiplication substrate (Floraton 3, Floragard) and four-week-old seedlings were transferred to pots with D 400 soil and Cocopor (Stender). Two weeks before the treatment, the plants were placed to controlled environment plant chamber (MobyLux GroBanks, CLF Plant Climatics) with the following growth conditions: 25 °C/23 °C, 12 h light/12 h dark. The light intensity at the leaf level was 150-200 µmoles s-1 m-2. To avoid unintended CAM induction by drought, all experimental plants were watered as needed and with the same amount of water per plant.

At the age of two months, two mature and fully illuminated leaves of each plant were treated either with (+/-) ABA (Sigma-Aldrich; 200 µM solution in 0.095 % (v/v) methanol) or mock solution (0.095 % (v/v) methanol). Both solutions contained 0.02 % (v/v) Tween-20 (PanReac AppliChem). The first treatment took place after four hours in the light, the second treatment followed four hours later. Treated leaves were harvested and shock-frozen in liquid nitrogen 40, 80, 160, 320, 640 and 1280 min after the first treatment. Two biological replicates originating from two independent plants were harvested per time point. The treated leaves from the same plant were pooled prior to all analyses.

Please note that the sample information (conditions and replicates) has been corrected on Aug 6, 2020.

first: Eva

last: Maleckova

first: Dominik

last: Brilhaus

last: Wrobel


title: Genome-wide analysis of gene expression by IFN-beta in U6A cells expressing WT or T404A STAT2

status: Public on Feb 15 2019

city: cleveland

first: Yuxin

last: Wang

state: OH

address: 9500 Euclid avenue

department: Cancer Biology

country: USA

institute: cleveland clinic foundation

summary: We used an Illumina Gene Expression Array to understand in more detail how T404 phosphorylation affects ISG induction. mRNA preparations from U6A cells expressing wild-type or T404A STAT2, treated with IFN-β for 0, 4, 8, or 24 h, were analyzed.

overall_design: Total RNA obtained from U6A cells expressing wild-type or T404A STAT2, treated with IFN-β for 0, 4, 8, or 24 h


title: Nested oscillatory dynamics in cortical organoids model early human brain network development

status: Public on Apr 25 2019

city: La Jolla

first: Jing

last: Gu

state: CA

address: 9500 Gilman Dr. MC0767

department: CMM

institute: UC San Diego

type: Expression profiling by high throughput sequencing

summary: We characterized the different cell types and their differential gene expression patterns in 1, 3, 6, and 10 month-old cortical organoids.

overall_design: Profling of single cell RNA-Seq for 1, 3, 6, and 10 month-old human cortical organoids

first: Cleber

middle: A

last: Trujillo

first: Richard

last: Gao

first: Priscilla

middle: D

last: Negraes

first: Justin

last: Buchanan

first: Sebastian

last: Preissl

first: Allen

first: Wei

last: Wu

first: Gabriel

middle: G

last: Haddad

first: Isaac

last: Chaim

first: Alain

last: Domissy

first: Matthieu

last: Vandenberghe

first: Anna

last: Devor

first: Gene

middle: W

last: Yeo

first: Bradley

last: Voytek

first: Alysson

middle: R

last: Muotri


title: Theiler’s Virus-Mediated Immunopathology in the CNS and Heart: Roles of Organ-Specific Cytokine and Lymphatic Responses [RNA-Seq]

status: Public on Apr 23 2019

city: Osakasayama

first: Seiichi

last: Omura

state: Osaka

address: 377-2 Ohnohigashi

department: Department of Microbiology

country: Japan

institute: Kindai University Faculty of Medicine

summary: Theiler’s murine encephalomyelitis virus (TMEV) induces different diseases in the central nervous system (CNS) and heart, depending on the mouse strains and time course, where cytokines play a key role for viral clearance and immune-mediated pathology (immunopathology).  In SJL/J mice, TMEV infection causes chronic TMEV-induced demyelinating disease (TMEV-IDD) in the spinal cord around 1 month post infection (p.i.).  Unlike other immunopathology models, both pro-inflammatory and anti-inflammatory cytokines can play dual roles in TMEV-IDD.  Pro-inflammatory cytokines play a beneficial role in viral clearance while they also play a detrimental role in immune-mediated demyelination.  Anti-inflammatory cytokines suppress not only protective anti-viral immune responses but also detrimental autoreactive immune responses.  On the other hand, in C3H mice, TMEV infection induces a non-CNS disease, myocarditis, with three phases: phase I, viral pathology with interferon and chemokine responses; phase II, immunopathology mediated by acquired immune responses; and phase III, cardiac fibrosis.  Although the precise mechanism how a single virus, TMEV, induces the distinct diseases in different organs is unclear, principal component analysis (PCA) of transcriptome data allows us to identify the key factors contributing to distinct immunopathology.  The PCA demonstrated that in vitro infection of a cardiomyocyte cell line could reproduce the transcriptome profile of phase I in TMEV-induced myocarditis; distinct interferon/chemokine-related responses were induced in vitro in infected cardiomyocytes, but not in infected neuronal cells.  In addition, the PCA of in vivo CNS transcriptome data showed that decreased lymphatic marker expression was associated with inflammation in TMEV infection.  Here, dysfunction of lymphatic vessels may contribute to immunopathology by delaying clearance of cytokines and immune cells from the inflammatory site, although this might confine the virus at the site, preventing virus spread via lymphatic vessels.   On the other hand, in the heart, dysfunction of lymphatics was associated with reduced lymphatic muscle contractility by pro-inflammatory cytokines.  Therefore, TMEV infection could induce different cytokine expressions as well as lymphatic vessel dysfunction by the distinct mechanism between the CNS and heart, which might contribute to organ-specific immunopathology.

overall_design: Transcriptome analysis of spinal cords from TMEV-infected mice at 4, 7, and 35 days post infection.

first: Fumitaka

last: Sato

first: Shantel

last: Vital

first: Paula

last: Polk

first: Ikuo

last: Tsunoda


title: Regulation of Translation Elongation Revealed by Ribosome Profiling [Dataset_3]

status: Public on Jan 27 2019

city: Frederick

first: Colin

state: MD

department: RNA Biology Laboratory

institute: NCI

summary: Ribosomes undergo substantial conformational changes during translation elongation to accommodate incoming aminoacyl-tRNAs and translocate along the mRNA template. We used multiple elongation inhibitors and chemical probing to define ribosome conformational states corresponding to different sized ribosome-protected mRNA fragments (RPFs) generated by ribosome profiling. We show using various genetic and environmental perturbations that the previously identified 20-22 nucleotide (nt) RPFs correspond predominantly to ribosomes in a pre-accommodation state with an open 40S ribosomal A site while the classical 27-29 nt fragments correspond to ribosomes in a pre-translocation state with an occupied 40S ribosomal A site. These distinct ribosome conformational states revealed by ribosome profiling are seen in all eukaryotes tested including fungi, worms and mammals. This high-resolution ribosome profiling approach reveals the anticipated Rck2-dependent inhibition of translocation through eEF2 phosphorylation during hyperosmotic stress. These same approaches reveal a strong translation elongation arrest during oxidative stress where the ribosomes are trapped in a pre-translocation state, but in this case the translational arrest is independent of Rck2-driven eEF2 phosphorylation. These results provide new insights and approaches for defining the molecular events that impact translation elongation throughout biology.

overall_design: 5 biological samples are included for ribosome profiling libaries prepared with CHX in the lysis buffer.

first: Rachel

last: Green


title: Systematic comparative analysis of single cell RNA-sequencing methods

status: Public on Jun 01 2019

city: Cambridge

first: Aviv

last: Regev

state: MA

address: 415 Main Street

department: Klarman Cell Observatory

institute: Broad Institute

summary: A multitude of single-cell RNA sequencing methods have been developed in recent years, with dramatic advances in scale and power, and enabling major discoveries and large scale cell mapping efforts. However, these methods have not been systematically and comprehensively benchmarked. Here, we directly compare seven methods for single cell and/or single nucleus profiling from three types of samples – cell lines, peripheral blood mononuclear cells and brain tissue – generating 36 libraries in six separate experiments in a single center. To analyze these datasets, we developed and applied scumi, a flexible computational pipeline that can be used for any scRNA-seq method. We evaluated the methods for both basic performance and for their ability to recover known biological information in the samples. Our study will help guide experiments with the methods in this study as well as serve as a benchmark for future studies and for computational algorithm development.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We systematically and directly compared seven single cell RNA-sequencing methods, including two low-throughput plate-based methods (Smart-seq2 and CEL-Seq2) and five high-throughput methods (10x Chromium (v2, v3), Drop-seq, Seq-Well, inDrops, and sci-RNA-seq), producing expression profiles from ~92,000 cells (nuclei) overall. We tested three sample types – a mixture of human and mouse cell lines, human peripheral blood mononuclear cells (PBMCs), and mouse cortex, each sample with two replicates – to generate a total of 36 different single cell RNA-sequencing libraries. For mouse cortex, we tested four single nucleus RNA-sequencing methods (Smart-seq2, 10x Chromium (v2), DroNc-seq, and sci-RNA-seq). We tested each sample type in two experiments (Mixture1 and Mixture2, PBMC1 and PBMC2, Cortex1 and Cortex2) run on different days to assess reproducibility. In each comparison experiment, we started with one sample with processing of aliquots starting at the same time for each method. The only exceptions were for Seq-Well in PBMC1, in which we thawed an identical PBMC aliquot a second time to obtain a Seq-Well dataset with sufficient cells profiled for PBMCs, and for 10x Chromium in PBMC1, in which we thawed an identical aliquot to directly compare version 2 (v2) with version 3 (v3). In each experiment, we aimed to collect data from ~350 cells for the low-throughput methods and ~3,000 cells for the high-throughput methods. In each experiment, we also used an aliquot of cells to generate a bulk RNA-sequencing library as a control. We sequenced all libraries together in an attempt to avoid batch effects due to varying sequence quality among Illumina flowcell lanes, with the following exceptions. We sequenced the inDrops libraries separately because they have an opposite read structure from those generated with the other methods. We performed additional sequencing for some libraries in an attempt to sequence similar numbers of reads per cell for each low or high throughput method. We aimed for 50,000 to 100,000 reads per cell for high-throughput methods and 750,000 to 1,000,000 reads per cell for low-throughput methods. The scRNA-seq FASTQ files are named with sample names, Illumina flowcell lanes, and library preparing methods. Different fields are separated by dots (.), for example, PBMC2.CC86JANXX.011818-DropSeq.unmapped.1.fastq.gz, where PBMC2 is the sample name (can be Mixture1, Mixture2, PBMC1, PBMC2, Cortex1, and Cortex2), CC86JANXX is the flowcell lanes, 011818 is the library preparation date, and DropSeq is the RNA-seq method (Drop-seq in this case, can be SM2, CELseq, 10X, DropSeq, DroNcSeq, SeqWell, inDrops, and SciSeq). This FASTQ file (read 1) includes cell barcodes and UMI information. The corresponding cDNA reads are in PBMC2.CC86JANXX.011818-DropSeq.unmapped.2.fastq.gz (read2). For more information about the structures of reads from different protocols, please see Supplementary Table 11 of the manuscript. FASTQ files with the same sample name and library preparation method but different flowcell lanes are from the same library but sequenced at different times, e.g., PBMC2.CCLBDANXX.68.011818-DropSeq.unmapped.1.fastq.gz. Therefore, these FASTQ files can be merged together for analyses. For 10x Chromium data, the reads from the same library are split into four files (10X_A, 10X_B, 10X_C, and 10X_D) and the reads from these files can also be merged together.

first: Jiarui

last: Ding

first: Xian

last: Adiconis

first: Sean

middle: K

last: Simmons

first: Monika

middle: S

last: Kowalczyk

first: Cynthia

middle: C

last: Hession

first: Nemanja

last: Marjanovic

first: Travis

last: Hughes

first: Marc

middle: H

last: Wadsworth

first: Tyler

last: Burks

first: Lan

middle: T

last: Nguyen

first: John

middle: Y

last: Kwon

first: Boaz

last: Barak

first: William

last: Ge

first: Amanda

middle: J

last: Kedaigle

first: Shaina

last: Carroll

first: Shuqiang

last: Li

first: Nir

last: Hacohen

first: Orit

last: Rozenblatt-Rosen

first: Alex

last: Shalek

first: Alexandra-Chloé

last: Villani

first: Joshua

middle: Z

last: Levin


title: Preeclamptic placentae release factors that damage neurons in vitro

status: Public on Feb 11 2019

city: Cardiff

first: Hannah

last: Scott

address: Hadyn Ellis Building, Maindy Road

department: UK Dementia Research Institute

country: United Kingdom

institute: Cardiff University

summary: Prenatal development is a critical period for programming of neurological disease. Preeclampsia, a pregnancy complication involving oxidative stress in the placenta, has been associated with long-term health implications for the child, including an increased risk of developing schizophrenia and autism spectrum disorders in later life. We have shown previously, in a rodent model of placental oxidative stress, that culture medium conditioned by the placenta alters neuronal characteristics when applied to primary cortical cultures in vitro and mimics many of the neurodevelopmental changes observed in the offspring brain. To further investigate if molecules released by the placenta may be important mediators in foetal programming of the brain, we analysed if placental tissue delivered from patients with preeclampsia secreted molecules that could affect cortical cells in culture. Application of culture medium conditioned by preeclamptic placentae to mixed cortical cultures caused changes in neurons and astrocytes that were related to key changes observed in brains of patients with schizophrenia and autism, including effects on dendrite lengths, astrocyte number as well as glutamate and GABA receptors. Treatment of the placental explants with an antioxidant prevented neuronal abnormalities. Furthermore, we identified that bidirectional communication between neurons and astrocytes, potentially via glutamate, is required to produce the effects of preeclamptic placenta medium on cortical cells. Analysis of possible signalling molecules in the placenta conditioned medium showed that the secretion profile of extracellular microRNA, small posttranscriptional regulators, was altered in preeclampsia and partially rescued by antioxidant treatment of the placental explants. Predicted targets of these differentially abundant microRNAs were linked to neurodevelopment and the placenta. The presented study provides further evidence that the diseased placenta may release factors that damage cortical cells in the brain and suggests the possibility of targeted antioxidant treatment of the placenta to prevent neurodevelopmental disorders.

overall_design: Total RNA was extracted from culture medium that had been conditioned by placental explants and analysed for microRNA content. Explants were derived from preeclamptic (PE) or non-diseased (ND) women and exposed to blank-NPs or MitoQ-NPs or no NPs. Samples were derived from 6 different conditions: ND+noNP, ND+blankNP, ND+MitoQNP, PE+noNP, PE+blankNP, PE+MitoQNP. Four biological replicates were measured per condition, except for PE+MitoQNP, for which 3 replicates were measured.

first: Tom

last: Phillips

first: Greer

last: Stuart

first: Mark

middle: F

last: Rogers

first: Bruno

last: Steinkraus

first: Simon

last: Grant

first: C

middle: P

last: Case


title: Non-coding and coding transcriptional profiles are significantly altered in pediatric Retinoblastoma tumors

status: Public on Apr 30 2019

first: Debashis

last: Sahoo

state: California

address: 9500 Gillman Drive

department: Pediatrics

institute: UCSD

summary: To find out the transcriptomic signature of Retinoblastoma compared to adult Retina. The methadology used was RNA sequencing using Illumina Platform.

overall_design: This is the first transcriptomic report on RB tumours from patients compared to retina. This experiment gives valuable information about gene expression fusions and Long Non-coding RNAs and RNA mutations

first: Kathleen

last: Dotts

first: Lakshmi

last: Nagaraghan

first: Swetha

last: Rajasekaran

first: Ranjith

last: Kumar

first: Pukhraj

last: Rishi

first: Vikas

last: Khetan

first: Karthikeyan

last: Sivaraman

first: Krishnakumar

last: Subramanyan

first: Moray

last: Campbell

first: Sailaja

middle: V

last: Elchuri

first: Wayne

last: Owen Miles


title: MYC dependent mRNA translation shapes gene expression and cell biology

city: Bronx

first: Kamini

last: Singh

state: NY

address: 1300 Morris Park Ave, Golding 203

department: Molecular Pharmacology

institute: Albert Einstein College of Medicine

summary: We report that MYC controls the translation of specific mRNAs in a sequence and RNA binding protein dependent manner. Specifically, using transcriptome-scale ribosome footprinting we identify 882 mRNAs whose translation depends on MYC. These mRNAs are highly significantly enriched for specific 5ÕUTR sequence motifs that bind the SRSF1/RBM42/HNRNPK complex. For example, MYC and SRFSF1/RBM42 dependent transcripts include many components of the electron transport chain and directly affect cellular respiration. Our results provide an integrated map of MYC driven gene expression programs that includes MYCÕs ability to control mRNA translation.

overall_design: Human B-cell lymphoma P493 cells were treated with Tetracycline (0.1 uM) for 24 hrs followed by cycloheximide treatment for 10 minutes in triplicates. An aliquot of cells were used for total RNA preparation and remaining cells were processed for isolation of ribosome protected fragments.

first: Jianan

last: Lin

first: Yi

last: Zhong

first: Antonija

last: Burcul

first: Prathibha

last: Mohan

first: Man

last: Jiang

first: Agnes

last: Viale

first: Justin

last: R. Cross

first: Liping

last: Sun

first: Vladimir

last: Yong

first: Ronald

last: Hendrickson

first: Gunnar

last: RŠtsch

first: Hans-Guido

last: Wendel

first: Zhengqing

last: Ouyang


title: First global gene expression profile analysis of the intestinal stem cell (ISC) niche of SAMP/YitFc (SAMP) mice

status: Public on Jan 09 2019

city: Cleveland

first: Ludovica

last: Buttó

address: 2109 ADELBERT ROAD

institute: CWRU

summary: High-throughput RNA-seq approach was used to profile transcriptional ISC niche responses in SAMP mice versus healthy controls (AKR)

overall_design: The RNA-seq transcriptional analysis was performed on ISC niche laser captured from small intestine using three independent samples (biological replicates) of each mouse group with defined total inflammatory score: ileal ISC niches from inflammation-free SAMP-5 (5-wk old) and AKR-25 (25-wk old) mice, and from highly diseased SAMP-25 mice (25-wk old) with Crohn's disease-like ileitis.

last: Buttό

first: Maneesh

last: Dave


title: Clinical and Immunologic Activity of a Single Dose of Neoadjuvant PD-1 Blockade and Predictors of Clinical Outcomes in Resectable Melanoma

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

summary: To understand some of the potential determinants of anti-PD-1 response and resistance in this cohort we used Nanostring analysis to study/compare the expression of custom set of genes

overall_design: Samples from patients with varying clinical and response characteristics were used to study their gene expression profiles using Custom Nanostring panel of genes

first: Alexander

last: Huang

last: Wherry

first: Tara

last: Mitchell


title: Differential expressed genes and microRNAs in EGF treated versus untreated control HTR-8/SVneo trophoblastic cells

status: Public on Jan 04 2019

city: New Delhi

first: Satish

middle: Kumar

last: Gupta

address: Aruna Asaf Ali Marg

country: India

institute: NAtional Institute of Immunology

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Tumor and stromal reaction under drug treatment in EUS-derived xenografts of human pancreatic adenocarcinoma

status: Public on Mar 28 2019

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary:
BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) is unique for its high stromal components play important role for tumor progression and therapeutic resistance. However, relevant preclinical models that recapitulate these tumor microenvironment are lacking and how the differences in the microenvironment affect cancer cell behavior are poorly understood. Here, we investigated the effects of tumor microenvironment on cancer cells behavior and therapeutic response.
METHODS: Previously established two behaviorally distinct patient-derived tumor xenografts (PDTX) models (moderate: PAC006 and poorly differentiated: PAC010) were re-implanted in Nude mice. Tumor volume, histology, immuno-histochemical, RNA sequencing and other molecular technique were used to characterize the models and study the effect of two classes of drugs (Gemcitabine (nucleoside analog) and Acriflavine (HIF-inhibitor)).
RESULTS: -Models- The models recapitulated the histologic, genetic and biological characteristics of the corresponding primary tumors except the replacement of human stroma with mice stroma. The growth-rate of the tumors was significantly different between both models (cell doubling time, PAC006: 5.8 days vs PAC010: 3.6 days, p=0.005). Rapid tumor growth was associated with poor tumor differentiation that may reflect the ability of our PDTX models to mimic the cellular and non-cellular features of the parental tumor. At the molecular level, the poorly differentiated model showed increased Ki-67 staining and higher phosphorylation levels of AKT, ERK and NF-kB65. In addition, RT-qPCR, NGS and protein expression showed significant up-regulation of mesenchymal markers in tumor cells (e.g. VIM, SNAI2, HIF1A and TGF-β1) and growth factors and cytokines in mice stroma. RNA sequencing analysis from tumor cells and stroma demonstrated activation of pathways related to tumor progression and aggressiveness in PAC010 compared to PAC006. Gemcitabine treatment resulted in a shrinking of the tumor and reduction of proliferation in both models. Interestingly, gemcitabine treatment also significantly enhanced the expression of mesenchymal marker (e.g. VIM, SNAI2, SPARC, ZEB1), particularly in the well-moderately differentiated tumor model. Acriflavine had little effect on tumor growth in both models.

overall_design: Tumor implantation, treatment procedure, growth and sample collection: Stored tumor tissue was implanted into a first group of 4 mice, after establishment of growth tumor tissue in these mice the tumors were used for expansion in a new generation of mice. After the tumor reach a volume of 100-200 mm3, these mice were randomly divided into three groups with eight mice in each group; A) the control group that was treated with vehicle (0.9% NaCl) and the experimental groups was treated intraperitoneally for up to 28 days with B) Gemcitabine (50 mg/kg) injected twice a week. C) Acriflavine: schedule four doses of acriflavine were injected daily with a fixed dose of 5 mg/kg Monday to Thursday and single dose of 10 mg/kg on Friday for the weekend. Prior to actual study, a toxicity study for ACF was carried out. The body weight and tumor size were measured thrice a week (Monday, Wednesday and Friday). The tumor volume was calculated using the formula: Tumor length (mm) x Tumor width (mm) x Tumor depth (mm) x (3.14/6) = Tumor volume (mm³). Tumors were harvested as soon as their volume reached 1000 – 1500  mm3. The tissue samples from each tumor were weighed, photographed and stored for histological analysis and molecular profiling.

first: Ashenafi

last: Bulle

first: Jeroen

last: Dekervel

first: Chris

last: Verslype

first: Jos

last: van Pelt


title: Long-term disulfiram supplementation activates an anti-inflammatory metabolic network to lower diet-induced obesity and related co-morbidities

status: Public on Feb 28 2019

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: According to the WHO, the obesity epidemic has become a global and grave public health concern. A small molecule to safely prevent and/or treat the negative pathophysiological consequences of obesity is urgently needed. We conducted long-term supplementation of the FDA-approved anti-inflammatory drug disulfiram (DSF, Antabuse®) in mice fed standard and high-fat diet (HFD), and measured various indicators of health in the animals. Our results uncover an abrogation of the adverse impact of HFD on insulin responsiveness and metabolic fitness through improvements in pancreatic islet morphology and b-cell function along with reduced occurrence of liver injury and cardiovascular remodeling, plausibly by its autophagy activating effect. Additionally, the treatment of obese mice with DSF robustly reversed diet-induced metabolic dysfunctions. These results show that the repurposing of DSF may represent a new strategy to combat obesity and associated metabolic disorders in human.

overall_design: The effect of disulfiram (DSF) was assessed in 14-week-old male C57BL/6J mice fed either a standard diet (SD) or high-fat diet (HFD) supplemented with a low (100 mg/kg/day) or high dose (200 mg/kg/day) of DSF for periods up to 41 weeks, and RNA isolated from  livers were used for transcriptomic analyses (N=5/group in six different treatment groups for a total of 30 animals).

first: Michel

last: Bernier

first: Sarah

first: Abhishek

last: Singh

first: Nathan

middle: L

last: Price

first: Antonio

last: Diaz

first: Devin

last: Wahl

first: Ahmed

last: Ali

first: Michael

middle: A

last: Petr

first: Huan

last: Cai

first: Alessa

last: Warren

first: Tamzin

last: Kaiser

first: Mingyi

last: Wang

first: Jing

last: Zhang

first: Li

first: Yushi

first: John

last: Mach

first: Vincent

last: Guiterrez

first: Daniel

last: Camiletti-Moiron

first: Eun-Young

last: Kim

first: Yongqing

first: Kevin

last: Becker

first: Edward

last: Lakatta

first: Josephine

middle: M

last: Egan

first: David

last: Le Couteur

first: Victoria

last: Cogger

first: Carlos

last: Fernandez-Hernando

first: Ana

last: Cuervo

first: Rafael

last: de Cabo


title: Differential expressed genes in EGF treated HTR-8/SVneo versus untreated control by next generation sequencing

first: Satish

last: Gupta

summary: The goal of this study is to compare mRNAs expressed by EGF treated HTR-8/SVneo cells to iRNAs expressed in untreated control HTR-8/SVneo cells to identify various genes which play a role during EGF-mediated HTR-8/SVneo cell invasion

overall_design: cDNA libraries were made from total RNA of untreated control and 24 h EGF treated samples by TruSeq RNA Sample prep kit. Deep sequencing of cDNA libraries were performed with the help of Illumina HiSeq.  RNA-seq reads were aligned to the hg38 genome assembly using Tophat 2.1.1. Tuxedo pipeline was used for transcripts identification and differential analysis.

first: Ankita

last: Malik


title: Differential expression of miRNAs in EGF treated HTR-8/SVneo versus untreated control by next generation sequencing

summary: The goal of this study is to compare miRNAs expressed by EGF treated HTR-8/SVneo cells to miRNAs expressed in untreated control HTR-8/SVneo cells to identify micro RNAs which play a role during EGF-mediated HTR-8/SVneo cell invasion

overall_design: cDNA libraries were made from total RNA of untreated control and 24 h EGF treated samples by TruSeq Small RNA Sample prep kit. Deep sequencing of cDNA libraries were performed with the help of Illumina Genome analyzer IIx. Raw sequence data was imported into the CLC Genomics Workbench 6.5.1. The sequence reads were trimmed for adapter sequences and low quality base. The trimmed raw sequences were subjected to miRNA-sequence analysis, by mapping them to miRBase release 21.


title: Selective translation by alternative bacterial ribosomes

city: Beijing

first: Babak

last: Javid

address: Biotechnology Building Room 4302, Tsinghua University, Haidian District

department: School of medicine

country: China

institute: Tsinghua University

summary: Mycobacteria encode several additional alternative ribosomal proteins (AltRP) and the funtion of AltRP invovling in translation is little known. In this study, we investigate the different translation landscape of AltRibo and CanRibo and found AltRibo have a relative 5' reads accumlation and preferential codon usage.

overall_design:
Using specific affinity tag to enrich different ribosome and subject to ribosome profiling to determine different translation landscape of AltRibo and CanRibo in Mycobacterium smegmatis.
Please note that processed data was generated from multiple samples/replicates as indicated in the corresponding sample description field.

first: Yuxiang

last: Chen

first: Zhiyu

last: Xu


title: Spontaneous mutation in the AgrRS two-component regulatory system of Cupriavidus metallidurans results in enhanced silver resistance via a novel mechanism involving nanoparticle formation

status: Public on Dec 31 2018

city: Mol

first: Rob

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

institute: SCK-CEN

summary:
Background: The uncontrolled and widespread use of (nano)silver compounds has led to the increased release of these compounds into the environment, raising concerns about their negative impact on ecosystems. Concomitantly, silver resistance determinants are widely spread among environmental and clinically relevant bacteria although the underlying mechanisms are not yet fully understood.

Results: In this study, we show that Cupriavidus metallidurans is able to adapt to toxic silver concentrations and explicate the genetic circuit responsible for this adaptation. None of the known silver resistant determinants present in C. metallidurans are involved in the adapted response. Instead, increased silver resistance is achieved by the concerted action of a two-component system AgrR-AgrS, previously not associated with metal resistance, and two intrinsically disordered proteins PrsQ1 and PrsQ2. Both belong to an unique group of small, uncharacterized, extracellular proteins restricted to the genera Cupriavidus and Ralstonia. This system seems to be much more efficient as it gives C. metallidurans the ability to withstand much higher silver concentrations. The latter could be facilitated by the accumulation of silver ions and the formation of silver nanoparticles.

Conclusions: Detailed knowledge and exploitation of this protein family could result in novel routes for metal nanoparticle formation and metal processing relevant for biotechnical and biomedical applications.

overall_design:
Comparison of wild-type strains with evolved strains resulting from a lab evolution experiment

Spontaneous silver resistant mutants of C. metallidurans CH34, its plasmidless derivative AE104 and C. metallidurans NA4 were generated by exposure to a toxic concentration of AgNO3. To this end, CH34S1 and CH34S2 were selected on LB agar supplemented with respectively 0.5 and 2 mM AgNO3, AE104S and NA4S were generated in MM284 supplemented with respectively 3 uM and 8 uM AgNO3.

first: Kristel

last: Mijnendonckx

first: Md

last: Ali

first: Ann

last: Provoost

first: Paul

last: Janssen

first: Max

last: Mergeay

first: Natalie

last: Leys

first: Guy

last: Vandenbussche

first: Daniël

last: Charlier

first: Pieter

last: Monsieurs


title: Collateral DNA damage and NAD+ dependence caused by reactive oxygen species signaling in inflammatory macrophages

status: Public on Mar 06 2019

first: Immunometabolism

last: Department

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

summary: Adoption of Warburg metabolism is critical for macrophage activation in response to lipopolysaccharide (LPS). Macrophages stimulated with LPS (without or with interferon-γ) increase expression of nicotinamide phosphoribosyltransferase (NAMPT), a key enzyme in NAD+ salvage, and loss of NAMPT activity alters their inflammatory potential. However, events leading to NAD+ salvage-dependence in these cells remain poorly defined. We show that NAD+ depletion and increased NAMPT expression occur rapidly after inflammatory activation and coincide with DNA damage caused by reactive oxygen species (ROS). ROS are produced by Complex III of the mitochondrial electron transport chain, and are required for macrophage activation. We show that DNA damage is associated with PARP activation, which results in NAD+ consumption and in this setting increased NAMPT expression allows the maintenance of NAD+ pools sufficient for GAPDH activity and Warburg metabolism. Our findings provide an integrated explanation for dependency on the NAD+ salvage pathway in inflammatory macrophages.

overall_design: RNA-seq was performed on bone marrow-derived macrophages (triplicate) exposed to lipopolysaccharide, interferon gamma or interleukin 4.

first: Alanna

last: Cameron

first: Angela

last: Castoldi

first: David

middle: E

last: Sanin

first: Lea

last: Flaschmann

first: Cameron

last: Field

first: Daniel

last: Puleston

first: Ryan

last: Kyle

first: Annette

last: Patterson

first: Fabias

last: Hässler

first: Joerg

last: Buescher

first: Beth

last: Kelly

first: Erika

last: Pearce

first: Edward


title: Regulation of Translation Elongation Revealed by Ribosome Profiling [Dataset_1]

first: Colin

last: Wu

overall_design: 15 samples are included for in vivo and lysate DMS-MaPseq (dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq))

first: Rachel

last: Green


title: The comparison of transcriptome profiling of mouse skin from Pp6fl/fl and K5. Pp6fl/fl mice

status: Public on Nov 28 2018

city: Shanghai

first: Fangzhou

last: Lou

address: 280 South Chongqing Road

department: Shanghai Institute of Immunology

institute: Shanghai Jiao Tong University School of Medicine

summary: RNA-seq of skin samples derived from Pp6fl/fl and K5.Pp6fl/fl mice

overall_design: Total RNA from mouse skin was isolated and subjected to NGS. The BioProject accession is PRJNA397843.

first: Honglin

last: Wang


title: Persistent DNA-break potential near telomeres increases initiation of meiotic recombination on short chromosomes

status: Public on Jan 10 2019

city: New York

first: Andreas

last: Hochwagen

address: 1009 Silver Center 100 Washington Square East

institute: New York University

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Faithful meiotic chromosome inheritance and fertility relies on the stimulation of meiotic crossover recombination by potentially genotoxic DNA double-strand breaks (DSBs). To avoid excessive damage, feedback mechanisms down-regulate DSBs on chromosomes that have successfully initiated crossover repair. In Saccharomyces cerevisiae, this regulation requires the removal of the conserved DSB-promoting protein Hop1/HORMAD during chromosome synapsis. Here, we identify privileged end-adjacent regions (EARs) spanning roughly 100 Kb near all telomeres that escape DSB downregulation. These regions retain Hop1 and continue to break in pachynema despite normal synaptonemal complex deposition. Differential retention of Hop1 requires the disassemblase Pch2/TRIP13, which preferentially removes Hop1 from telomere-distant sequences, and is modulated by the histone deacetylase Sir2 and the nucleoporin Nup2. Importantly, the uniform size of EARs among chromosomes contributes to disproportionately high DSB and repair signals on short chromosomes in pachynema, suggesting that EARs partially underlie the curiously high recombination rate of short chromosomes.

Grant ID: Research grant #6-FY16-208
Grant title: Meiotic segregation of small chromosomes
Funding Source: March of Dimes Foundation
Affiliation: NEW YORK UNIVERSITY
Name: Andreas Hochwagen

overall_design:
ChIP-seq analysis of Hop1, Red1, Zip1, pH2A, Mek1 and Rad51 in S. cerevisiae in meiosis. Each bedgraph file is the combined results from two biological replicates (each with a paired Input and ChIP sample).

Please note that as processed data was generated from multiple samples, the corresponding processed data file is indicated in each sample description field.

first: Vijayalakshmi

last: Subramanian


title: mRNA-seq comparison of C. elegans L1 larvae with parents experiencing dietary restriction or ad libitum conditions

status: Public on Nov 01 2018

city: Eugene

first: Amy

middle: K

last: Webster

state: Oregon

address: Institute of Ecology and Evolution

institute: University of Oregon

summary: Well-fed N2 worms were bleached as adults and embryos were placed in liquid culture under ad libitum (AL) or dietary restriction (DR) conditions. After 96 hr, AL and DR adults were bleached. AL and DR progeny were collected for mRNA-seq as starved L1 larvae

overall_design: 3-4 biological replicates were sequenced for each of two conditions: AL progeny and DR progeny

first: J

last: Jordan

middle: D

last: Hibshman

first: A

first: C

last: Maxwell

first: B

last: Bowman

first: L

middle: R

last: Baugh


title: RNA-seq of FSHD and control immortalised myoblasts II

status: Public on Dec 07 2018

city: London

first: Christopher

middle: Raja Socrates

last: Banerji

address: New Hunts House

department: Randall Division of Cell and Molecular Biophysics

institute: King's College London

summary: FSHD myoblasts show a suppression of ESRRA and PPARGC1A during myogenesis

overall_design: FSHD Myoblasts 54-2, 54-12, 54-A5, 16A and 12A and matched controls 54-6, 54-A10, 16U and 12U were plated at 312,000 cells per 12 well plate in proliferation media and cultured for 48 hours or until 100% confluent, then induced to differentiate for 3.5 days, samples were taken at 8 time points during differentation for 54-6 and 54-12 and at confluency and terminal differentiation in the remaining lines. RNA-sequencing was performed on high quality (RIN > 8.0) DNA free RNA.

middle: S

first: Peter

last: Zammit


title: Regulation of Translation Elongation Revealed by Ribosome Profiling [Dataset_2]

institute: NCI

summary: Ribosomes undergo substantial conformational changes during translation elongation to accommodate incoming aminoacyl-tRNAs and translocate along the mRNA template. We used multiple elongation inhibitors and chemical probing to define ribosome conformational states corresponding to different sized ribosome-protected mRNA fragments (RPFs) generated by ribosome profiling. We show using various genetic and environmental perturbations that the previously identified 20-22 nucleotide (nt) RPFs correspond predominantly to ribosomes in a pre-accommodation state with an open 40S ribosomal A site while the classical 27-29 nt fragments correspond to ribosomes in a pre-translocation state with an occupied 40S ribosomal A site. These distinct ribosome conformational states revealed by ribosome profiling are seen in all eukaryotes tested including fungi, worms and mammals. This high-resolution ribosome profiling approach reveals the anticipated Rck2-dependent inhibition of translocation through eEF2 phosphorylation during hyperosmotic stress. These same approaches reveal a strong translation elongation arrest during oxidative stress where the ribosomes are trapped in a pre-translocation state, but in this case the translational arrest is independent of Rck2-driven eEF2 phosphorylation. These results provide new insights and approaches for defining the molecular events that impact translation elongation throughout biology.

overall_design: 6 samples are included for TIG lysate DMS-MaPseq.


title: human pulmonary artery (endothelial and smoorh muscle) cells : control vs ARSB-siRNA transfected

status: Public on Oct 01 2018

city: Gliwice

first: Magdalena

last: Olbryt

address: Wybrzerze AK 15

department: Center for Translational Research and Molecular Biology of Cancer

country: Poland

institute: Cancer Center and Institute of Oncology

summary: Transcriptional profiling of human pulmonary artery endothelial (HAPEC) and smooth muscle (PASM) cells comparing control untreated cells with cells transfected with ARSB-siRNA. Goal was to determine the effects of silenced of arylsufatase B on global gene expression in HAPEC and PASM cells.

overall_design:
Two-condition experiment, non-transfected vs. ARSB-siRNA transfected cells. Biological replicates: 2 cell lines, 4 control replicates, 4 transfected replicates.

Please note that the experiments were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but the results were processed as they are single channel (Cy3 and Cy5 signals are calculated; total 8 raw data files for  16 sample records). Raw data file (associated with each sample) is indicated in the sample description field and  is linked to the corresponding control sample records.

first: Anna

last: Lalik

first: Adam

last: Golda

first: Sebastian

last: Student


title: Deep sequencing of circulating exosomal microRNA allows non-invasive glioblastoma diagnosis

status: Public on Nov 14 2018

city: Sydney

first: Fatemeh

last: Vafaee

state: UNSW

address: Gate 11 Botany Street, UNSW Sydney, School of BABS

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

summary:
Background: Safe and sensitive methods for glioblastoma diagnosis and disease monitoring are urgently needed. Exosomes are nano-sized extracellular vesicles that contain molecules characteristic of their cell-of-origin, including microRNA. Exosomes released by glioblastoma tumors cross the blood-brain-barrier ino the peripheral circulation.
Methods: Serum exosomal-microRNA isolated from IDH-wildtype glioblastoma (n=12) and IDH-mutant glioma grades II-III (n=10) were analyzed using small-RNA next generation sequencing and compared to age- and gender-matched healthy controls. Differentially expressed miRNAs (|fold change|³2 and p-value ≤ 0.05 in three statistical tests, Fischer-exact, t-test, and Wilcoxon) were identified and the predictive power of individual and subsets of miRNAs were tested using univariate (logistic regression) and multivariate (Random Forest) analyses. Additional glioblastoma sera (n=4) and independent sets of healthy (n=9) and non-glioma (n=10) controls were used to further test the predictive power of our glioblastoma miRNA signature.
Results: Twenty-six miRNAs were differentially expressed in glioblastoma relative to healthy controls. Seven miRNAs (miR-182-5p, miR-328-3p, miR-339-5p, miR-340-5p, miR-485-3p, miR-486-5p and miR-543) were the most stable for classifying glioblastoma, achieving a predictive power of 91.7%. Strikingly, the combined expressions of miR-182-5p, miR-328-3p miR-485-3p miR-486-5p distinguished glioblastoma patients from controls with perfect accuracy. This miRNA panel was able to correctly classify all specimens in validation cohorts (n=23). An analogous approach was used to identify 23 dysregulated miRNAs in IDH-mutant gliomas, including a distinct subset of stable miRNAs for classifying patients with lower-grade IDH-mutant gliomas.
Conclusions: Our serum exosomal-miRNA signature can accurately diagnose glioblastoma preoperatively. These findings have significant scope to revolutionize glioblastoma tumor diagnosis and disease monitoring.
IMPORTANCE OF STUDY: There is a real need for accurate biomarkers that can measure glioblastoma disease activity and treatment response in a safe and timely manner. This study demonstrates that exosome-associated microRNAs have exceptional utility as blood-based biomarkers in glioma patients. This work also shows the potential for exosomal microRNA profiles to be used for glioma subtyping, grading and determining mutational states. The development of specific, sensitive and non-invasive screening tests would have significant clinical benefit by reducing costs of treatment monitoring, improving accessibility and quality-of-life measures. Moreover, such tests have the potential to provide objectively measured surrogate endpoints to allow clinical trial protocols to be more dynamic and adaptive.

overall_design: Serum exosomal miRNA profiles ofIDH-wildtype glioblastoma, IDH-mutant glioma grades II-III, their matched healthy controls, and additional GBM patients, non_GBM patients and healthy controls were generated by deep sequencing, single end, using Illumina HiSeq. 2000 System at the Ramaciotti Centre for Genomics.

first: Saeideh

last: Ebrahimkhani

first: Susannah

last: Hallal

first: Heng

last: Wei

first: Paul

last: Young

first: Maggie

middle: Y

last: Lee

first: Laveniya

last: Seelan

first: Heidi

last: Beadnall

first: Michael

middle: H

last: Barnett

first: Brindha

last: Shivalingam

first: Catherine

last: Suter

last: Buckland

first: Kimberley

last: Kaufman


title: Expression data of genes and noncoding genes from the ADSCs and adipogenic-induced ADSCs

status: Public on Sep 12 2018

city: Chengdu

first: Yuanwei

last: Chen

address: No.14 South Renmin road

institute: Sichuan University

summary:
Adipogenesis participates in many physiological and pathological processes such as obesity and diabetes, and is regulated by a series of precise molecular events. However, the molecules involved in this regulation have not been fully characterized.
We used microarrays to detail the full transcriptome expression profiles of undifferentiated and adipogenic-induced ADSCs.

overall_design: The ADSCs was designed as control groups and the adipogenic-induced ADSCs was designed as experimental groups. All groups were managed in  same condition.

first: Lei

last: Liu


title: In situ transcriptome characteristics are lost following culture adaptation of adult cardiac stem cells

city: San Diego

first: Taeyong

last: Kim

address: 5500 Campanile Drive

department: Biology

institute: San Diego State University

overall_design: Refer to individual Series


title: In situ transcriptome characteristics are lost following culture adaptation of adult cardiac stem cells (10X Genomics scRNA-seq)

summary: Single-cell RNA-seq (10X Genomics Chromium) to profile of cardiac progenitor cells, comparing the transcriptomes of freshly isolated and cultured cardiac progenitor cells

overall_design: Transcriptional profiling of freshly isolated CPCs and their cognate in vitro expanded derivatives was performed by scRNA-Seq approaches using 10X Genomics Chromium

first: Mark

last: Sussman


title: Global RNA half lives in cyanobacteria

status: Public on Jan 01 2019

city: Madison

first: Gina

last: Gordon

state: WI

address: 1415 Engineering Dr

department: Chemical and Biological Engineering

institute: University of Wisconsin Madison

summary: We calculated global RNA half lives for all genes in the cyanobacteria Synechococcus sp. strain PCC 7002. Samples from three replicates of the WT strain were taken before and following the addition of the antibiotic rifampicin to stop nascent transcription. RNA spike-ins were added for normalization and using the number of RNA-sequencing reads we were able to calculate half lives for genes, transcripts, and for each position on the genome.

overall_design: Samples were taken from three replicates of WT PCC 7002 (labeled 2,3,and 4). Samples taken before the addition of rifampicin were called '0 minutes' and labeled with 'A'. Subsequent timepoints (0.5 minutes, 1 minute, 2.5 minutes, 5 minutes, 7.5 minutes, and 10 minutes) were labeled respectively B, C, D, E, F, and G. Three replicates were taken with 7 timepoints each leading to 21 samples total.

middle: C

first: Jeffrey

last: Cameron

first: Brian

last: Pfleger


title: In situ transcriptome characteristics are lost following culture adaptation of adult cardiac stem cells (Smart-Seq2 scRNA-seq)

summary: Single-cell RNA-seq (Smart-Seq2) to profile of cardiac progenitor cells

overall_design: Transcriptional profiling of cultured CPCs was performed by scRNA-Seq approaches using Smart-Seq2 technology


title: Oncogenic Serine-Threonine Kinase Receptor Associated Protein Supports Hepatocellular Carcinoma Cell Growth by Enhancing Wnt/β-catenin Signaling

status: Public on Sep 03 2018

city: Rotterdam

first: Wenhui

last: Wang

address: Wytemaweg 80

country: Netherlands

institute: Erasmus MC

summary: Serine-threonine kinase receptor-associated protein (STRAP) is upregulated in breast, colorectal and lung cancers, promoting their growth. We identify the upregulation of STRAP in hepatocellular carcinomas. Elevated STRAP endows tumor cells with growth advantage by reprograming a variety of metabolic processes and signaling pathways critical for hepatocellular carcinoma progression. Especially, enhanced Wnt/β-catenin signaling is likely to be a major effector of its tumor-promoting role.

overall_design: mRNA profiles of STRAP knock-out (KO) and control (CON) hepatocellular carcinoma cells were generated by deep sequencing, in triplicate.

first: H

middle: G

last: van de Werken

first: Ron

last: Smits


title: Multi-omics analysis of mutant and wild-type β-catenin networks

status: Public on Jul 17 2018

city: Southampton

first: Rob

last: Ewing

address: Building 85, Life Sciences, Highfield Campus

institute: University of Southampton

summary: This study describes the systematic transcriptomic and expression and interaction proteomic analysis of isogenic HCT116 colorectal cancer cells with either mutant CTNNB1/Beta-catenin allele disrupted or wild-type CTNNB1/Beta-catenin allele disrupted.

overall_design: RNA-Seq analysis of mutant or wild-type Beta-catenin HCT116 cells using Illumina High-Scan paired end sequencing. Three replicates of each cell-line, total = 6 samples.


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and α7nAChR-/- Peritoneal macrophage Transcriptomes with Nicotine and/or LPS treatment

status: Public on Sep 01 2018

city: 4-6-1, Komaba, Meguroku

first: Takahide

last: Kohro

state: Tokyo

institute: LSBM, RCAST

summary:
Purpose: The cholinergic anti-inflammatory pathway (CAP) links the nervous and immune systems and modulates innate and adaptive immunity. The goals of this study are to identify the new downstream signaling of α7nAChR in macrophages.
Methods: Peritoneal macrophages isolated from α7nAChR+/+ and α7nAChR-/- mice were treated with nicotine (10 μM) and/or LPS (100 ng/ml), then RNA-seq was performed.
Results: Genes were selected that had more than 4-fold relative gene expression in nicotine-treated cells compared to the control group (vehicle-treated). The same calculation was applied to nicotine+LPS-treated cells and LPS-treated cells and 264 genes were identified as genes commonly induced by nicotine based on these two comparisons. Then relative gene expression was compared between α7nAChR+/+- and α7nAChR-/- -derived cells. 18 genes were finally selected whose expressions are suppressed (<1/2) in α7nAChR-/- -derived peritoneal macrophages.
Conclusions: Our study represents the first detailed analysis focused on the new downstream signaling of α7nAChR in macrophages, generated by RNA-seq technology. We newly revealed the important anti-inflammatory role of Hes1 in the CAP using some functional experiments.

overall_design: Peritoneal macrophage's mRNA profiles of wild type (WT) and α7nAChR-/- mice treated with Nicotine and/or LPS were generated by deep sequencing.

first: Tsuyoshi

last: Inoue

first: Youichiro

last: Wada

last: Okusa


title: ChIP-seq analysis of SOX9 in hES-RPE cells

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

summary: SOX9 binding sites were profiled in RPE cells generated from human embryonic stem cells (hES-RPE)

overall_design: SOX9 binding profile was generated in hES-RPE cells in triplicates

first: Yamit

last: Cohen-Tayar

first: Rani

first: Ruth

last: Ashery-Padan


title: Transcriptome analysis of influenza infected GFP+ AEC compared to bystander GFP- AEC

status: Public on Aug 29 2018

first: Peter

last: Katsikis

institute: Erasmus MC University Medical

summary: A GFP-expressing recombinant A/Puerto Rico/8/1934 influenza virus was used to infect C57BL/6 wild type mice and on day 3 post infection, lung alveolar epithelial cells (AEC) were isolated and sorted based on GFP expression. GFP+ AEC represent the infected AEC and GFP- AEC represent the bystander AEC. AEC were also sorted from uninfected mice to serve as controls.

overall_design: AEC from infected mice were pooled to make three (3) infected GFP+ AEC replicates for sequencing. Five (5) bystander GFP- replicates and five (5) uninfected AEC replicates were also isolated for sequencing


title: human dermal papilla cells were grown in spheres and treated with vehicle control, ruxolitinib and tofacitinib for 2 days

status: Public on May 26 2018

first: Jane

middle: E.

last: Cerise

address: 1150 St. Nicholas Avenue

institute: Columbia University

summary: Dermal papilla cells derived from 3 individual donors were propagated and cultured using the hanging drop method (Higgins et al., PNAS 2013). Cells were cultured in drugs for two days

overall_design: total RNA was extracted from DP spheres cultured in DMSO, ruxolitinib or tofacitinib for two days. Drugs were used at  400nM.Cells were derived from three individual donors

first: Sivan

last: Harel

first: Angela

last: Christiano


title: Ribosome profiling of G2019S LRRK2 human dopamine neurons

status: Public on Jul 01 2018

city: Berkeley

first: Jungwoo Wren

last: Kim

address: Barker Hall, Room 416

department: Molecular and Cell Biology

institute: UC Berkeley

summary: G2019S mutaion of LRRK2 is known to increase mRNA translation. We perform ribosome profiling to study defective translation using human dopamine neuron models. Patient-derived human dopamine neurons with G2019S LRRK2 mutation were generated and used. Also a mutation-corrected isogenic pair line was used.

overall_design: hDA neurons: 60 days old samples were used.

first: Ted

last: Dawson

first: Valina


title: Transcriptomic analysis of senescent cells upon knockdown of 38 candidate SASP-specific regulators.

status: Public on Jun 25 2018

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

institute: MRC London Institute of Medical Sciences

summary: IMR90 ER:RAS cells were transfected with scramble siRNA or 2 deconvoluted siRNAs targeting each of 38 candidate genes or positive control siRNAs targeting the senescence regulators p16 and p53 and the SASP regulators NF-kappaB, p38alpha and CEBPbeta. The next day the cells were treated with 4OHT to induce senescence. 6 days later the cells were collected for total mRNA analysis. Our previous experiments had shown that these 38 genes regulate the secretome of senescent cells without affecting other senescence phenotypes such as the growth arrest. By performing RNA-seq we confirmed that knockdown of these genes affected the expression of multiple pro-inflammatory factors in senescence. More importantly, the secreted factors were differentially regulated across the different knockdown conditions indicating potential for specific manipulation of immune response genes.

overall_design: 92 conditions were examined: proliferating cells (Noninduced), senescent cells (Water, Allstars), senescent cells transfected with 2 siRNAs targeting 38 different genes (Hs_GeneID_n), senescent cells transfected with positive control siRNAs (p16, p53, CEBPB, p38, p65) and additional conditions included proliferating and senescent IMR90 ER:RAS cells mock-transfected or transfected with various non-targeting siRNAs (Extras1-8) to monitor changes in gene epression independent of gene knockdown.

first: Athena

last: Georgilis

first: Jesús

last: Gil

first: Thomas

last: Carroll


title: Neonatal Tbr1 Dosage Controls Cortical Layer 6 Connectivity.

status: Public on Sep 02 2018

city: San Francisco

first: Siavash

last: Fazel Darbandi

address: 1550 4th Street

department: Psychiatry

institute: University of California San Francisco

summary:
An understanding of how heterozygous loss-of-function mutations in ASD risk genes, such as TBR1, contribute to ASD remains elusive.
Conditional Tbr1 deletion during late mouse gestation in cortical layer 6 neurons (Tbr1layer6 mutants) provides novel insights into its function, including dendritic patterning, synaptogenesis, and cell intrinsic physiology.
These phenotypes occur in heterozygotes, providing insights into mechanisms that may underlie ASD pathophysiology. Restoring expression of Wnt7b, largely rescues the synaptic deficit in Tbr1layer6 mutant neurons.
Furthermore, Tbr1layer6 heterozygotes have increased anxiety-like behavior, a phenotype seen ASD. Integrating TBR1 ChIP-Seq and RNA-Seq data from layer 6 neurons, and activity of TBR1 bound candidate enhancers, provides evidence for how TBR1 regulates layer 6 properties.
Moreover, several putative TBR1 targets are ASD risk genes, placing TBR1 in a central position both for ASD risk and for regulating transcriptional circuits that control multiple steps in layer 6 development essential for the assembly of neural circuits.

overall_design: Examination of TBR1 genomic binding in P2 wildtype mouse cortex and transcriptional profiling of P5 wildtype and TBR1 constitutive null mouse cortex.

middle: F

last: Darbandi

first: Matthew

last: State

first: John

last: Rubenstein


title: Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease

status: Public on Nov 04 2018

city: Jerusalem

first: Joshua

last: Moss

address: Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem

department: Developmental Biology and Cancer Research

institute: Hebrew University of Jerusalem

summary: Genome wide DNA methylation profiling of 59 cfDNA samples, 27 isolated cell populations used in deconvolution of cfDNA samples, and 15 samples used as technical controls.

overall_design: Bisulphite converted DNA from the 48 samples were hybridised either to the Illumina 450K array or the Illumina EPIC array.

first: Tommy

last: Kaplan

first: Yuval

last: Dor


title: Gene expression of Natural Killer cell-primed monocytes and their subsequent derived dendritic cells

status: Public on Jul 03 2018

city: Sao Paulo

first: Maria

middle: A.

last: Clavijo-Salomon

state: SP

address: Av. Prof. Lineu Prestes 1730 Room 254

department: Department of Immunology

country: Brazil

institute: University of Sao Paulo

summary:
Transcriptome analysis of monocytes directly exposed to cell-to-cell contact with Natural Killer (NK) cells or separated by a transwell membrane and their subsequent monocyte-derived dendritic cells.
The role of Natural Killer (NK) cells in the early differentiation of monocytes into dendritic cells (DCs) is poorly understood. Their interaction is thought to be restricted to a bilateral cross talk of soluble cytokines. However, many authors have shown that NK cells effect over myeloid cells is dependent on direct cell-to-cell contact. In order to understand what determines a major effect of NK cells over monocytes and their derived DCs, total RNA samples from purified monocytes and monocyte-derived DCs, exposed to direct contact with NK cells or separated by a transwell membrane were amplified and hybridized to the Affymetrix Human GeneChip 2.0 ST array. Analyses were performed using BRB-ArrayTools version 4.5.0, developed by Dr. Richard Simon and the BRB-ArrayTools Development Team. We found that compared to untouched monocytes, cell-to-cell contact with NK cells modified the expression of 283 genes whereas contact through a transwell membrane modified the expression of 35 genes. After differentiation and compared to DCs derived from untouched monocytes, DCs derived from monocytes allowed to direct cell-to-cell contact with NK cells had the expression of 128 genes modified whereas DCs derived from monocytes primed through a transwell membrane had only 2 genes modified. Our results suggested that cell-to-cell interactions with NK cells are important to imprint a stable transcriptional program in monocytes lasting even after their further differentiation into DCs.

overall_design: We analyzed RNA samples extracted from purified monocytes and their subsequent derived DCs obtained from blood of 5 unrelated healthy male donors from the NIH Clinical Center Department of Transfusion Medicine, protocol No. 99-CC-0168), previously exposed to autologous NK cells. Samples were analyzed using the Affymetrix Human GeneChip 2.0 ST array and data was processed by BRB-ArrayTools developed by Dr. Richard Simon and the BRB-ArrayTools Development Team and Partek (Partek Inc.). No technical replicates were performed.

first: Rosalba

last: Salcedo

first: Soumen

last: Roy

first: Helioswilton

last: Sales-Campos

first: Rodrigo

middle: X

last: das Neves

first: Karen

last: Steponavicius-Cruz

first: Jonathan

last: Badger

first: Amiran

last: Dzutsev

first: Jose

last: Barbuto

first: Giorgio

last: Trinchieri


title: Analyses of long non-coding RNAs in human retinal endothelial cells following glucose treatment

status: Public on Nov 06 2018

first: Saumik

last: Biswas

state: Ontario

address: 1151 Richmond Street

department: Pathology and Laboratory Medicine

country: Canada

institute: University of Western Ontario

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

summary: The differential expression of lncRNAs in human retinal endothelial cells (HRECs) was investigated with a commericially available microarray (ArrayStar Human LncRNA Microarray V3.0; ArrayStar Inc., Rockville, Maryland USA). Approximately 28,035 lncRNAs and 21,407 coding transcripts were detected using this microarray. In addition to the array findings, lncRNAs were further constructured using transcriptome databases (including RefSeq, Gencode, UCSC). Sequences were selected using proprietary strategies and each transcript is represented by a specific exon or splice junction probe, which can accurately identify an individual transcript. Nevertheless, both postive and negative probes for housekeeping genes were additionally used as controls.

overall_design: In the present study, two control groups (normal glucose conditions, 5 mM/L; and high glucose, 25 mM/L) and two treatment groups (high glucose conditions, 25 mM/L) were established using HRECs.

first: Subrata

last: Chakrabarti

first: Shali

last: Chen


title: Modulation of SF3B1 causes global intron retention and downregulation of the B-cell receptor pathway in chronic lymphocytic leukemia

status: Public on May 17 2018

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

institute: Augusta University

summary: Splicing factor SF3B1 is frequently mutated in chronic lymphocytic leukemia (CLL) patients and has been suggested as a potential therapeutic target. In this study, we performed RNA-seq analysis to evaluate the global impact of SF3B1 modulator sudemycin D6 (SD6) on alternative splicing. Our analysis revealed significant increases in global intron-retention in SD6-treated CLL cells. Pathway analysis of the genes associated with increased intron-retention suggested that B-cell receptor (BCR), protein ubiquitination, and PI3K signaling pathways were among the top canonical pathways being affected by SD6. The increases in intron-retention were inversely correlated with deceases in mRNA and protein levels of the affected BCR/PI3K pathway molecules such as BLNK, BTK, AKT1, PLCγ2 and PI3Kδ. SD6 also induced a time-dependent exon-skipping event in mRNA of MCL1 and resulted in significant down-regulation of another anti-apoptotic gene TRAF1, which may contribute to the SD6-induced apoptosis. Finally, SD6 can overcome the pro-survival and pro-growth signals and synergize with ibrutinib, idelalisib and venetoclax to induce apoptosis in primary CLL cells co-cultured with bone marrow stromal cells and in the presence of T-cell-derived cytokines. Cumulatively, these results provide a strong rationale for future clinical development of spliceosome modulators and combinatory therapies based on spliceosome modulators in CLL.

overall_design: To determine the global impacts of SD6 treaments on transcriptome in CLL cells, we performed RNA-seq analysis in MEC1 and GM12878 cell lines treated with 125nM for three different time points (2, 6, and 24 hours), respectively.


title: Best practices for eCLIP experiments and analysis [poor quality]

status: Public on Jun 08 2018

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: Enhanced cross-linking immunoprecipitation (eCLIP) featuring a size-matched input control has been recently applied to profile the binding sites of more than one hundred RNA binding proteins (RBPs). However computational pipelines and quality control metrics needed to process CLIP data at scale have yet to be well defined. Here, we describe our ENCODE eCLIP processing pipeline (https://github.com/YeoLab/eclip), enabling users to go from raw reads to processed peaks that are enriched above paired input, reproducible across biological replicates, and can be directly compared against the public ENCODE eCLIP resource. In particular, we discuss processing steps designed to address common artifacts, including properly quantifying unique RNA fragments bound by both unique genomic- and repetitive element-mapped reads. Using manual quality annotation of 350 ENCODE eCLIP experiments, we develop metrics for quality assessment of eCLIP experiments prior to and after sequencing, including library yield, number of unique fragments in the library, total binding relative information, and biological reproducibility. In particular, we quantify the commonly believed linkage between depth of sequencing and peak discovery, and derive methods for estimating required sequencing depth based on pre-sequencing metrics. Finally we provide recommendations for the common question of integrating RBP binding information with RNA-seq to generate splicing maps representing the positional effect of binding on alternative splicing. These pipelines and QC metrics enable large-scale processing and analysis of eCLIP data, and will help to standardize rigorous analysis of RBP binding data.

overall_design: eCLIP-seq in HepG2 and K562 Cells.  Datasets in this subseries failed technical and manual quality assessment and are submitted to GEO only as negative controls.  These datasets should never be used to draw biological conclusions.

first: Gabriel

last: Pratt

first: Eric

middle: L

last: Van Nostrand

first: Brian

last: Yee

first: Alain

last: Domissy

first: Steven

last: Blue

first: Chelsea

last: Gelboin-Burkhart

first: Thai

middle: B

last: Nguyen

first: Ines

last: Rabano

first: Keri

last: Elkins

first: Ruth

last: Wang

first: Balaji

last: Sundararaman

last: Garcia

first: Rebecca

last: Stanton

middle: W


title: Dissecting the molecular rewiring facilited by Pp6 deletion in keratinocytes

status: Public on Nov 20 2018

city: Shanghai

first: Fangzhou

last: Lou

address: 280 South Chongqing Road

institute: Shanghai Jiao Tong University School of Medicine

summary: RNA-seq of keratinocytes derived from Pp6fl/fl and K5.Pp6fl/fl mice

overall_design: Total RNA from primary keratinocytes was isolated and subjected to NGS.

first: Honglin


title: Best practices for eCLIP experiments and analysis

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

overall_design: Refer to individual Series


title: Deep sequencing and miRNA profiles in alcohol-induced neuroinflammation and the TLR4 response in mice cerebral cortex

status: Public on Sep 25 2018

city: Valencia

first: Francisco

middle: García

last: García

address: Eduardo Primo Yúfera, 3

department: Bionformatics & Biostatistics Unit

country: Spain

institute: CIPF

summary: Alcohol abuse can induce brain injury and neurodegeneration, and recent evidence shows  the participation of immune receptors  toll-like in the neuroinflammation and brain damage. We evaluated the role of miRNAs as potential modulators of the neuroinflammation associated with alcohol abuse and the influence of the TLR4 response. Using mice cerebral cortex and next-generation sequencing (NGS), we identified miRNAs that were differentially expressed in the chronic alcohol-treated versus untreated WT or TLR4-KO mice. We observed a differentially expression of miR-183 Cluster (C) (miR-96/-182/-183), miR-200a and miR-200b, which were down-regulated, while mirR-125b was up-regulated in alcohol-treated WT versus (vs.) untreated mice. These miRNAs modulate targets genes related to the voltage-gated sodium channel, neuron hyperexcitability (Nav1.3, Trpv1, Smad3 and PP1-γ), as well as genes associated with innate immune TLR4 signaling response (Il1r1, Mapk14, Sirt1, Lrp6 and Bdnf). Functional enrichment of the miR-183C and miR-200a/b family target genes, revealed neuroinflammatory pathways networks involved in TLR4 signaling and alcohol abuse. The changes in the neuroinflammatory targets genes associated with alcohol abuse were mostly abolished in the TLR4-KO mice. Our results show the relationship between alcohol intake and miRNAs expression and open up new therapeutically targets to prevent deleterious effects of alcohol on the brain.

overall_design: Comparison of 4 experimental groups from  microRNA-Seq data

first: Juan

last: Ureña-Peralta

first: Silvia

last: Alfonso-Loeches

first: Carlos

middle: M

last: Cuesta-Diaz

last: Garcia-Garcia

first: Consuelo

last: Guerri


title: Carbendazim induced genomic instability in yeast

status: Public on Mar 21 2018

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

institute: College of Life Sciences, Zhejiang University

type:
Genome variation profiling by array
Genome variation profiling by SNP array

summary: Carbendazim (Methyl benzimidazol-2-ylcarbamate; MBC) is an antimitotic drug used for broad-spectrum fungicide, antineoplastic and mutagen in microbial breeding. Using a customized SNP microarray technology, this work revealed the effect of MBC on genomic instability (loss of heterozygosity, chromosomal rearrangements and aneuploidy) in the diploid yeast Saccharomyces cerevisiae JSC25.

overall_design: By SNP microarrays specific for chromosome 4, we analyzed 40 JSC25-derived mutants  treated with MBC to uncover the details of MBC-induced genomic instability.

first: Lei

last: Qi

first: Dao-Qiong


title: Transcriptomic analysis of circumvallate papillae (CVP) from lean and DIO mice

status: Public on Mar 13 2018

city: DIJON

first: Arnaud

last: BERNARD

address: Agrosup Dijon, 1 esplanade Erasme

country: France

institute: INSERM U1231

summary: Diet-induced obesity (DIO) is associated with a decreased oral fat detection in rodents. This blunted gustatory detection has been explained by an impairment of the lipid-mediated signaling in taste bud cells (TBC). However, factors responsible for this defect remain elusive. To better understand the mechanisms involved, circumvallate papillae from Lean, DIO and former DIO mice were analyzed with a transcriptomic approach. [using Agilent Sureprint G3 Mouse microarrays (8x60K, design 028005)]

overall_design: After a one-week acclimatization period, the mice (C57Bl6/j) were fed ad libitum either a standard laboratory chow (4RF21, Mucedola, Italy; containing 3% fat, w/w) or an obesogenic diet high fat diet, rich in saturated fatty acids described in (Chevrot et al, 2013). Some DIO mice were calorie restricted (= 60% energy of ad libitum energy intake).CVP from control and DIO mice were isolated according to the procedure described in (Laugerette et al, 2005). Briefly, lingual epithelium was separated from connective tissue by enzymatic dissociation (elastase and dispase mixture, 2 mg/ml each in Tyrode buffer: 140 mM NaCl, 5 mM KCl, 10 mM HEPES, 1 mM CaCl2, 10 mM glucose, 1 mM MgCl2, 10 mM Na pyruvate, pH 7.4) and the papilla was dissected under a binocular microscope. CVP were snap-frozen in liquid nitrogen then stored at -80°C. Plasma was obtained after centrifugation of blood (5000 g for 10 min, 4°C).

last: Bernard

first: Philippe

last: Besnard

first: Claire

last: Naylies

first: Yannick

last: Lippi


title: Genome-wide analysis identifies NR4A1 as a key mediator of T cell dysfunction

status: Public on Mar 24 2018

city: Beijing

first: Huiping

last: Lu

address: Tsinghua university

institute: Tsinghua university

summary: The molecular mechanism underlying T cell tolerance remains unclear. Here we utilize an in vitro T cell tolerance induction system to characterize genome-wide epigenetic and gene expression features intolerant T cells, which reveals they are distinct from effector and regulatory T cells. Importantly, transcription factor Nr4a1 is stably expressed at high levels in tolerant T cell.Nr4a1 overexpression inhibits effector T cell differentiation, whereas deletion of Nr4a1 overcomes T cell tolerance, exaggerates effector function, and enhances immunity against tumor and virus. Mechanistically, Nr4a1 is preferentially recruited to AP-1 sites and inhibits the recruitment of c-Jun and BATF as a mechanism for effector gene repression. On the other hand, for activation of tolerance-related genes, Nr4a1 binding promotes acetylation of histone H3 at K27.This study thus identifies Nr4a1 as a key regulator in T cell tolerance, which may be targeted in tumor immunotherapy.

overall_design: Genome-wide examination of H3K4me3 and H3K27me3 histone modifications across in vitro-generated CD4+ T cell subsets including naive, Th1, Th2, Th17, nTreg, and tolerant T cell. Genome-wide examination of Nr4a1, C-Jun, and Batf bindings, as well as H3k27ac  peaks across chromain in Nr4a1-overexpressed T cell, Naive T cell, TCR/co-stimulation-activated T cell, as well as Nr4a1-deficient T cells.

first: Xindong

last: Liu

first: Xiaowei

last: Yan


title: Best practices for eCLIP experiments and analysis [uncertain quality]

first: Gene

last: Yeo

overall_design: eCLIP-seq in HepG2 and K562 Cells.  Datasets in this subseries failed manual quality assessment for various reasons, but may still have useful, although unusual binding information.

first: Gabriel

middle: A

last: Pratt

first: Eric

last: Van Nostrand

first: Brian

last: Yee

first: Alain

last: Domissy

first: Steven

last: Blue

first: Chelsea

last: Gelboin-Burkhart

first: Thai

last: Nguyen

first: Ines

last: Rabano

first: Keri

last: Elkins

first: Ruth

last: Wang

first: Balaji

last: Sundararaman

last: Garcia

first: Rebecca

last: Stanton


title: Gene expression profile of SoNar-high and SoNar-low fetal liver blood cells

status: Public on Feb 06 2018

first: Hao

last: Gu

address: 280 South Chongqing Road, Shanghai

summary: To dissect the metabolic state of fetal liver HSCs, we have developed a genetically encoded fluorescent sensor (SoNar) for tracking cytosolic NADH and NAD+ redox states and constructed the transgenic mouse. Based on the NADH/NAD+ ratio, we have sorted SoNar-high and SoNar-low fetal liver blood cells to employ whole genome microarray expression profiling as a discovery platform to identify genes with the potential to regulate fetal liver HSC metabolism.

overall_design: SoNar-high and SoNar-low two population blood cells from E13.5 fetal liver were sorted to measure gene expression.

first: Junke

last: Zheng


title: RG/RGG boxes are common binding motifs in RNA-G-quadruplex-interacting proteins

status: Public on Apr 30 2018

city: Cambridge

first: Giovanni

last: Marsico

address: Robinson Way

institute: CRUK Cambridge Institute

summary: G-quadruplexes (rG4s) are recognized as key structures involved in RNA biology and are linked to neurodegenerative disease and cancer. However, detailed knowledge of rG4s and their binding partners is lacking. Here, a systematic, unbiased affinity proteomics approach identified 80 potential high-confidence interactors of the rG4 structure in the 5’UTR of the NRAS oncogene. Using epitope-tagged protein expression, we validated a subset of interactions including DDX3X, DDX5, DDX17, DHX9, DHX36, FXR1, FXR2, GRSF1 and NSUN5. More than half of the identified rG4 interactors were enriched in glycine-arginine (GAR) domains, and for DDX3X and DDX17, we show that the GAR domain is required for rG4 interaction. Transcriptome-wide binding analysis using DDX3X iCLIP revealed a striking association with rG4s in 5’UTRs that was lacking in the GAR-domain mutant. Overall, our work highlights a hitherto unrecognized complexity in rG4 structure-protein interactions that should be considered for the understanding of rG4 function.

overall_design: 6 libraries for Flp-In T-Rex 293 cell line iCLIP experiment: 3 for mutant-DDX3X and 3 for WT-DDX3X; 11 libraries for Flp-In T-Rex 293 cell line RNA-seq experiment: 4 for WT-DDX3X, 4 for mutant-DDX3X and 3 for no expression (negative).

first: Clemens

last: Meyer

first: Barbara

last: Herdy

first: Dhaval

last: Varshney

first: Chris

last: Taylor

first: Clive

last: D'Santos

first: David

last: Tannahill

first: Shankar

last: Balasubramanian


title: RNA-Seq of CD8+ T cell subsets during LCMV infection

status: Public on Dec 15 2017

first: John

middle: Justin

last: Milner

address: 9500 Gilman Dr. MC0377

summary: Tissue-resident memory CD8+ T cells (Trm) are positioned at common sites of pathogen exposure where they elicit rapid and robust protective immune responses1,2. However, the molecular signals controlling Trm differentiation and homeostasis are not fully understood. Here we show that mouse Trm precursor cells represent a unique CD8+ T cell subset that is distinct from the precursors of circulating memory populations at the levels of gene expression and chromatin accessibility. Exploiting computational and functional RNAi in vivo screens, we identified the transcription factor (TF) Runx3 as a key regulator of Trm differentiation and homeostasis. Runx3 was required to establish Trm populations in diverse tissue environments and supported expression of critical tissue-residency genes while suppressing genes associated with tissue egress and recirculation. Analysis of the accessibility of Runx3 target genes in Trm-precursor cells revealed a distinct regulatory role for Runx3 in controlling Trm differentiation despite relatively widespread and uniform expression among all CD8+ T cell subsets. Further, we show that human and murine tumor-infiltrating lymphocytes (TIL) share a core tissue-residency gene-expression signature with Trm. In a mouse model of adoptive T cell therapy for melanoma, Runx3-deficient CD8+ TIL failed to accumulate in tumors, resulting in greater rates of tumor growth and mortality. Conversely, overexpression of Runx3 enhanced TIL abundance, delayed tumor growth, and prolonged survival. In addition to establishing Runx3 as a central regulator of Trm differentiation, these results provide novel insight into the signals that promote T cell residency in tissues, which could be leveraged to enhance vaccine efficacy or adoptive cell therapy treatments that target cancer.

overall_design: 8 samples, 2 replicates each, naïve P14 cells or Day 7 LCMV infection CD8+ T cell subsets

first: J

middle: J

first: A

last: Goldrath


title: Transcriptomic changes in broiler chicken hypothalamus and pitutary during ontogenesis

status: Public on Oct 27 2017

city: Balice

first: Kacper

last: Zukowski

address: Krakowska 1 Street

summary: We sequenced mRNA from 16 hypothalamus (3-week-old= 8 and 6-week old=8) and 16 pitutary (3-week-old= 8 and 6-week old=8) of Ross308 fast growing-chicken line. In which groups were chickens characterized with high growth rate (n=4) and low growt rate (n=4). The cockerels were reared in a deep-litter facility in experimental farm of the National Research Institute of Animal Production located in Aleksandrowice till 22 or 42 days of age, under the same, optimal, electronically controlled environmental conditions (temperature, lighting regime, air humidity) and were fed ad libitum with the same complete starter (1-21 days of age), grower (22-35 days of age) and finisher (36-42 days of age) diets containing 22, 20.5 and 20.5% crude protein and 2990, 3130 and 3130 kcal/kg metabolic energy.

overall_design: Examination of mRNA levels between chicken groups differing in age and growth rate. The study was supported by statutory activity of National Research Institute of Animal Production (no. 01-013.1) and National Multidisciplinary Laboratory of Functional Nanomaterials NanoFun nr POIG.02.02.00-00-025/09 (Innovative Economy Operational Programme, Priority Axis 2: R&D Infrastructure, Action 2.2: Support of Formation of Common Research Infrastructure of Scientific Units

first: K

last: Piórkowska

last: Żukowski

last: Połtowicz

last: Nowak

last: Ropka-Molik

first: D

last: Wojtysiak

first: N

last: Derebecka

last: Wesoły


title: Runx3 programs CD8+ T cell residency in non-lymphoid tissues and tumours


title: γδ T cells producing IL-17A regulate adipose Treg homeostasis and thermogenesis

status: Public on May 10 2018

city: Be'er Sheva

first: Tal

last: Shay

address: Ben Gurion

department: Life scuences

institute: Ben-Gurion University

summary: RNA sequencing of PLZF+ and PLZF- γδ T cell subsets from adipose tissue for gene expression analysis

overall_design: PLZF+ and PLZF- γδ T cells were sorted from adipose tissue of PLZF-GFP mice for subsequent RNA sequencing and gene-expression analysis. Two replicates for each subset pooled from 10 mice each were used for the study.

first: Ayano

last: Kohlgruber

first: Lydia

last: Lynch

first: Michael

last: Brenner

first: Shani

last: Gal-Oz


title: RNA-seq of FSHD and control immortalised myoblasts I

status: Public on Aug 19 2017

city: London

first: Christopher

middle: Raja Socrates

last: Banerji

address: New Hunts House

institute: King's College London

summary: FSHD and control immortalised myoblasts show repression of Pax7 target genes

overall_design: FSHD Myoblasts 54-2, 54-12, 54-A5, 16A and 12A and matched controls 54-6, 54-A10, 16U and 12U were plated at 312,000 cells per 12 well plate in proliferation media and cultured for 48 hours or until 100% confluent. RNA-sequencing was performed on high quality (RIN > 8.0) DNA free RNA.

middle: R

first: Peter

middle: S

last: Zammit


title: Differential expression data of BMDMs of mice infected with avian influenza influenza A (H7N9) viruses

status: Public on Apr 13 2018

city: Hang Zhou

first: Juan

last: Liu

institute: Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University

summary: To clarify the underlying mechanism that regulates the response of iron metabolism to influenza A virus infection, we analyzed gene expression profiles in mouse, bone marrow-derived macrophages (BMDMs) infected with H7N9 virus. In addition, We also analysed the chemokine, inflammation, innate-immunity, lipid-metabolism, transcription mRNA level by micrroarray. So, we gain the global transcriptional response in the BMDMs of mice infected with H7N9 virus.

overall_design: BMDMs were seperated from 4-6 week-old BALB/C mice (wild type, WT and Hfe KO) and inoculated with H7N9 virus for 6h and 12h, and the uninfected BMDMs were as a control.The cells were collected to RNA extraction and hybridization on Agilent microarrays. Samples were named as follows: Control (WT-1), treatment(WT-12h-2, WT-6h-34, KO-5, KO-6h-67, KO-12h-8).

first: Xiao

middle: P

last: Wu


title: Reduced dosage of the chromosome axis factor Red1 selectively disrupts the meiotic recombination checkpoint in Saccharomyces cerevisiae

status: Public on Jul 18 2017

city: New York

first: Andreas

last: Hochwagen

address: 1009 Silver Center 100 Washington Square East

institute: New York University

summary: Meiotic chromosomes assemble characteristic “axial element” structures that are essential for fertility and provide the chromosomal context for meiotic recombination, synapsis and checkpoint signaling. Whether these meiotic processes are equally dependent on axial element integrity has remained unclear. Here, we investigated this question in S. cerevisiae using the putative condensin allele ycs4S. We show that the severe axial element assembly defects of this allele are explained by a linked mutation in the promoter of the major axial element gene RED1 that reduces Red1 protein levels to 20-25% of wild type. Intriguingly, the Red1 levels of ycs4S mutants support meiotic processes linked to axis integrity, including DNA double-strand break formation and deposition of the synapsis protein Zip1, at levels that permit 70% gamete survival. By contrast, the ability to elicit a meiotic checkpoint arrest is completely eliminated. This selective loss of checkpoint function is supported by a RED1 dosage series and is associated with the loss of most of the cytologically detectable Red1 from the axial element. Our results indicate separable roles for Red1 in building the structural axis of meiotic chromosomes and mounting a sustained recombination checkpoint response.

overall_design: ChIP-seq analysis of Red1 and Hop1 in S. cerevisiae at 3h meiotic time point. Each wiggle file is the combined results from two biological replicates (each with a paired Input and ChIP sample).

first: Tovah

middle: E

last: Markowitz


title: Gene expression profiling in Abatacept treated Rheumatoid Arthritis patients according to response

status: Public on May 17 2017

city: Rouen cedex

first: Celine

last: Derambure

address: 22 Bvd Gambetta

institute: INSERM U905

summary: The objective of this study was to identify specific gene expression profiles able to predict the response  of rheumatoid arthritis patients treated with methotrexate /abatacept (Aba). Thirty six RA patients were received Abatacept. The drug efficacy was evaluated with the DAS28 score after 6 months of treatment according to the EULAR response criteria. Among 36 Aba RA patients, 17 were responders and 19 were classified as no-responders.  A blood sample was carried out in patients just before the first injection of treatment in PaxGene tubes.

overall_design: Two color experiments : patient(Cy5)/Control pool (Cy3).


title: Total RNA sequencing of ovary tissues at 49 days post coitus in Large White and Meishan pigs.

status: Public on Jun 12 2017

first: Zhonglin

last: Tang

address: No. 2 Yuanmingyuan West Road, Beijing, 100193, P.R.China,

department: Institute of Animal Science

institute: Chinese Academy of Agricultural Sciences

summary: We collected the ovary samples at 49 days post coitus in Large White and Meishan adult female pigs, identified the differentially expressed protein coding genes and long non-coding RNAs between these two breeds. three individuals of each breed were harvested as biological replicates.

overall_design: Identification of differentially expressed protein-coding genes and long non-coding RNAs in ovary at 49 days post coitus between Large White and Meishan pigs.

first: Kui

last: Li


title: Genome wide analysis of androgen-receptor binding sites and associated factors in prostate cancer cells

status: Public on Apr 23 2018

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

institute: Tokyo Metropolitan Institute of Gerontology

summary: Prostate cancer is the most common cancer in men and AR downstream signalings promote prostate cancer cell proliferation. To investigate the AR signaling, we performed ChIP sequence analysis in AR positive prostate cancer cell line, LNCaP and VCaP. In addition, we used hormone-refractory prostate cancer model cells, long term androgen deprivation (LTAD) to explore the differences of androgen signaling in prostate cancer progression.

overall_design: ChIP sequence analysis of AR binding sites, assocaited factors and epigenetic condition in two prostate cancer cells


title: HCoV-229E infection in A549 cells: gene regulation in cells adjacent and distant to infected cells

status: Public on Mar 15 2017

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

summary: In A549 cells,  infection with human Coronavirus 229E spreads lateraly through the cell layer. This offers the opportunity to compare the gene expression patterns of infected cells with those of nearby unifected cells and to analyze paracrine effects occuring during infection. The aim of the experiment is to identify and compare changes in host gene expression of infected cells, cells immediately adjacent to infected cells and more distant cells with uninfected cells.  To separate the different cell population, a Leica LMD6000 system was used. Individual cells were stained for the expression of the viral N protein or for DNA polymerase II by a shortened immunfluorescence protocol. After drying, the cell populations were visualized by fluorescence microscopy and separated by microdissection, collected in tubes and RNA was isolated on a small scale by column purification.

overall_design: Single-color hybridization of RNA from laser-microdissected cells. Duplicates.

last: Kracht

last: Poppe


title: Gene expression profile of SoNar-high and SoNar-low fetal liver blood cells and B-cell acute lymphoblastic leukemia (B-ALL) cells

first: Hao

last: Gu

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

overall_design: Refer to individual Series


title: Early response of three Pycnoporus species to various carbon sources [Pycnoporus cinnabarinus]

status: Public on Feb 21 2017

city: Marseille

first: Marie-Noëlle

last: Rosso

address: 163 avenue de Luminy

department: Biodiversity and Biotechnology of Fungi - BBF

institute: INRAE - Aix Marseille University

summary: White-rot basidiomycete fungi are potent degraders of plant biomass with the ability to mineralize all lignocellulose components. Recent comparative genomics studies showed that these fungi use a wide diversity of enzymes for wood degradation. Deeper functional analyses are however necessary to understand the enzymatic mechanisms leading to lignocellulose breakdown. In the present study we analyzed the early response of the Polyporales fungi Pycnoporus coccineus CIRM-BRFM310, Pycnoporus cinnabarinus CIRM-BRFM137 and Pycnoporus sanguineus CIRM-BRFM 1264  to various carbon sources including lignocellulosic biomass.

overall_design: Examination of mRNA levels in fungal mycelium after 3 days growth in liquid cultures on maltose, Avicel, xylans-galactomannans, wheat straw, pine or aspen.

first: François

last: Piumi

first: Marie-Pierre

last: Franquin-Gomez

first: Igor

middle: V

last: Grigoriev

first: Anna

last: Lipzen


title: Early response of three Pycnoporus species to various carbon sources [Pycnoporus sanguineus]


title: Expression pattern of mRNA of liver and mammary in dairy cows fed two different level of forage/concentrate ration

status: Public on Feb 14 2017

first: Dengpan

last: Bu

address: No.2 Yuanmingyuan West Rd,Haidian District

institute: Institute of Animal Science,Chinese Academy of Agricultural Sciences

summary: Liver and mammary gland are among the most prominent organs during lactation in dairy cows. With the purpose to understand 1) the adaptation of liver and mammary to different levels of forage/concentrate ration (60:40 vs. 40:60) and 2) the crosstalk between the two organs during lactation, a transcriptome analysis was performed on liver and mammary tissues of 10 primiparous dairy cows in mid-lactation. The analysis was performed using a 4x44K Bovine Agilent microarray chip. The mammary and liver samples were obtained from a subset of animals from a larger experiment where cows were fed two different levels of forage/concentrare ration (Archives of Animal Nutrition, 68:1, 63-71).

overall_design: Liver and mammary tissues were collected through biopsy from 10 dairy cows in mid-lactation fed with  40% forage and 60% concentrate (CS; n=5) or 60% forage and 40% concentrate (MF; n=5)

first: Massimo

last: Bionaz

first: Mengzhi

last: Wang

first: Xuemei

first: Lu

last: Ma

first: Jiaqi


title: Transcriptomic Profiling of Trophoblast Subpopulations in Severe Preeclampsia Reveals Novel Aspects of RNA Dysregulation

status: Public on Jan 24 2017

city: SAN FRANCISCO

first: Susan

last: Fisher

state: CA

address: 513 PARNASSUS AVE

department: Obstretrics, Gynecology and Reproductive Sciences

institute: UCSF

summary: The maternal signs of preeclampsia, principally the new onset of high blood pressure, are thought to occur secondary to faulty placentation. Previous studies profiled the gene expression patterns of chorionic villi, the maternal-fetal interface or isolated cytotrophoblasts in this pregnancy complication. We theorized that transcriptomic analyses of trophoblast subpopulations in situ would give us new insights into the role of these cells in preeclampsia pathogenesis.

overall_design: This was a cross-sectional analysis of placentas collected at birth from women who were diagnosed with severe preeclampsia (n=4). Gestational age-matched controls were placentas from women who had a preterm birth with no signs of infection (n=4). Laser microdissection enabled the isolation of samples that were enriched for syncytiotrophoblasts, invasive cytotrophoblasts or endovascular cytotrophoblasts. A microarray approach was used for global transcriptional profiling.

first: M

last: Gormley

first: K

last: Ona

last: Kapidzic

first: T

last: Garrido-Gomez

last: Zdravkovic

first: S