title: Control ChIP-seq from uterus (ENCSR859LXC)

status: Public on Aug 30 2019

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

type: Genome binding/occupancy profiling by high throughput sequencing

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from K562 (ENCSR861LKS)

summary:
Input control ChIP-seq on human eGFP-ZBTB40 tagged K562 cell line.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from HepG2 (ENCSR975KJI)

summary:
Control ChIP-seq on HepG2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from esophagus muscularis mucosa (ENCSR545WFH)


title: Control ChIP-seq from tibial artery (ENCSR819JOI)


status: Public on Aug 31 2019

city: Paris

first: Noémie

last: Robil

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

type: Expression profiling by high throughput sequencing

summary: Transcriptomic analysis of transferrin protective effect during retinal detachment in mice.

overall_design: 8 samples: 4 reference samples as detached retina from WT mice, 4 samples of interest as detached retina from mice expressing human transferrin (TG).

first: Emilie

last: Picard

first: Quentin

last: Le Rouzic

first: Alejandra

last: Daruich

first: Yannick

last: Marie

first: Francine

last: Behar-Cohen


title: ATAC-Seq Profiling of Open Chromatin Regions in Soybean Early-Maturation Embryos

city: Los Angeles

first: Bob

last: Goldberg

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

summary: Transcription Factors are bound to the nucleosome-depleted region or open chormatin. ATAC-Seq can help us to dissect the interactions among TFs which are important for soybean seed development.

overall_design:
Nuclei were isolated from soybean early-maturation embryos. Early maturation embryos were hand-dissected and collected from the seed with 6-7mm in length. ATAC-seq was performed on isolated nuclei from two biological replicates.

For each replicate, the library was sequenced in single-end (Run 1) and and in paired-end mode (Run 2). Only paired-end files were used in the analysis.

first: Robert

middle: B

first: John

middle: J

last: Harada

first: Nestor

last: Apuya

first: Leonardo

last: Jo

first: Min

last: Chen


title: Transcriptomic analysis of swarm motility phenotype of Salmonella enterica serovar Typhimurium mutant defective in periplasmic glucan synthesis

city: Beltsville

first: Arvind

middle: A

last: Bhagwat

state: MD

address: 10300 Baltimore Avenue

department: ARS, NEA, BARC, EMFSL

institute: United States Department of Agriculture

summary: Movement of food-borne pathogens on moist surfaces enables them to migrate towards more favorable niches and facilitate their survival for extended periods of time. Salmonella enterica serovar Typhimurium mutants defective in OPG synthesis are unable to exhibit motility on moist surfaces (swarming) however their mobility in liquid (swim motility) remains unaffected. In order to understand the role of OPG in swarm motility, transcriptomic analysis was performed using cells growing on a moist agar surface.  In the opgGH-deletion mutant, lack of OPG significantly altered transcription of 1039 genes out of total 4712 genes (22%). Introduction of a plasmid borne copy of opgGH into the opgGH-deletion mutant restored normal expression of all but 30 genes, indicating a wide-range influence of OPG on gene expression under the swarm motility condition.  Major pathways that were differentially-expressed in opgGH mutants were motility, virulence and invasion, and genes related to the secondary messenger molecule, cyclic di-GMP.  These observations provide insights and help explain the pleiotropic nature of OPG mutants such as sub-optimal virulence and competitive organ colonization in mice, biofilm formation, and sensitivity towards detergent stress.

overall_design: The study comprised nine samples, three replicates for three strains of the organism.  It compared opgGH mutant Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 with the wild type parental strain and the opgGH mutant carrying a plasmid borne wild-type copy of opgGH genes with the wild type parental strain.

first: A

first: L

last: Young


title: Akap11 is a positive regulator of osteogenesis in mouse osteoblastic cell line MC3T3-E1

city: Hong Kong

first: Vincent Ka Fai

last: Cheng

state: -- select --

address: L202 lab block 21 Sassoon road Pokfulam Hong Kong

department: Pharmacology and Pharmacy

country: Hong Kong

institute: The University of Hong Kong

summary:
Purpose: This is a post-GWAS functional study that aims to determine the effect of Akap11 knockout in mouse preosteoblastic cell line MC3T3-E1 during osteogenesis.
Methods: mRNA profile of WT (treated with CRISPR and remains unedited) and Akap11 knockout MC3T3-E1 cells were generated by RNAseq from pooled RNA (from 3 biological triplicate at equal quantity) of various timepoint during osteogenesis (Day 0, 7,16, 25).100ng total RNA was used for library construction by KAPA Stranded mRNA-Seq Kit (Roche). Pair-End 101bp sequencing was performed in the Illumin HiSq1500 sequencer using the HiSeq SBS Kit v4 (Illumina). Data was collected with SCS version 1.4.8. Base calling was performed using Illumina’s RTA (Version 1.12.4.2). 7 samples were sequenced per lane and achieved a sequencing depth of ~65 million read per sample.
Results: Expression of osteogentic markers in Akap11 knockout MC3T3-E1 cells were suppressed. Genes invovled in IGF-I signaling pathway were signficantly altered.

overall_design: mRNA profile of Day0, 7, 16, 25 WT (treated with CRISPR and remains unedited) and Akap11 knockout MC3T3-E1 cells were generated by pooled PolyA mRNA Sequencing .

first: Gloria

middle: H

last: Li

first: Vincent

middle: K

first: C

middle: L

last: Cheung


title: Histone ChIP-seq from heart left ventricle (ENCSR799KLF)

first: ENCODE

last: DCC


title: TF ChIP-seq from upper lobe of left lung (ENCSR799TJD)


title: Control ChIP-seq from upper lobe of left lung (ENCSR750DLX)


title: Histone ChIP-seq from upper lobe of left lung (ENCSR623YMO)


title: Gene expression profiles of macrophage and multinucleated cells programmed by IL15

city: Nanjing

first: Wang

last: Hongsheng

state: Jiangsu

address: 12 Jiangwangmiao Street, Xuanwu District

country: China

institute: Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: We report gene expression profiles of macrophage and multinucleated cells programmed by IL15 including the mRNAs isolated, libraries prepared and gene expression profiles determined by RNA-seq.

overall_design: To investigate the mechanism of IL-15 induced MGC formation, adherent monocytes from three donors were treated with IL-15. Control cultures consisted of adherent monocytes in media alone and treatment with IL-4, known to induce foreign body giant cells. The percentage of MGCs was quantified at days 1, 3, 6 and 10. The cells were collected at these timepoints, the mRNAs were isolated, libraries prepared and gene expression profiles determined by RNA-seq.

last: Modlin

first: Hongsheng

last: Wang


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCSR701GIE)


title: Control ChIP-seq from K562 (ENCSR529YPZ)

summary:
Input control ChIP-seq on human eGFP-VEZF1 tagged K562 cell line.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from upper lobe of left lung (ENCSR706OFD)


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCSR845BEG)


title: Control ChIP-seq from K562 (ENCSR625UIZ)

summary:
Input control ChIP-seq on human eGFP-ZNF395 tagged K562 cell line.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from K562 (ENCSR464FDA)

summary:
Control ChIP-seq in K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Quantitative Analysis of Wild Type and Secisbp2l Conditional Knockout Spinal Cord Transcriptomes

city: Hangzhou

first: Zhong-Min

last: Dai

state: Zhejiang

address: 16 Xuelin Street, Xiasha

institute: Hangzhou Normal University

summary: The goals of this study are to analyze NGS-derived spinal cord transcriptome profiling (RNA-seq) of wild type (WT) and Olig1-Cre mediated Secisbp2l Exon3 deletion (cKO) at postnatal day 7 (P7). Spinal cord RNA profiles were generated by deep sequencing, using Illumina Hiseq 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with HISAT2 and RSeQC.

overall_design: Spinal cord RNA profiles of P7 wild type (WT) and Secisbp2l-cKO mice were generated by deep sequencing, using Illumina Hiseq 2500.

first: Wei

last: Guo


title: Control ChIP-seq from K562 (ENCSR745QMZ)

summary:
Input control ChIP-seq on human eGFP-ZNF148 tagged K562 cell line.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from K562 (ENCSR483GYO)


title: Histone ChIP-seq from upper lobe of left lung (ENCSR642DSR)


title: Histone ChIP-seq from upper lobe of left lung (ENCSR453MUW)


title: Transcriptomic analysis of differential expressed genes of human tonsillar epithelial cells UT-SCC-60B in response to EV71 infection

city: Chengde

first: Guangcheng

last: Xie

state: Hebei Province

address: Anyuan Road, Shuangqiao District

institute: Chengde Medical University

summary:
Purpose: The goals of this study are to understand the transcriptional changes of human tonsillar epithelial cells UT-SCC-60B in response to EV71 infection and determine the differential expressed genes
Methods: Transcriptional profiles of human tonsillar epithelial cells UT-SCC-60B and human tonsillar epithelial cells infected with EV71 were generated by next generation sequencing, in triplicate, using Illumina X-ten/NovaSeq. The sequence reads that passed quality filters were analyzed abundance of mRNA using StringTie, the FPKM values of genes and transcripts were calculated by Ballgown of R software, alternative splicing events were determined by rMATS
Results: Using an optimized data analysis workflow, we mapped more than 36 million sequence reads per sample. Total 11137 gene counts and 26860 transcript counts were identified in human tonsillar epithelial cells, 11347 gene counts and 27994 transcript counts were identified in EV71-infected human tonsillar epithelial cells. Total 96 genes and 499 transcripts were down-regulated, 105 genes and 550 transcripts were up-regulated according the criteria that fold changes are more than 1.5, p value less is than 0.05 and mean of FPKM value is more than 0.5 to defined as the differential expressed genes or differential expressed transcripts. Total 11563 novel genes and 14927 novel transcripts were identified and 3266 novel transcripts had the potential coding probabilities. Finally, total 5742 genes occurred alternative splicing events.
Conclusions: Our study represents the first detailed analysis of the transcriptional changes of human tonsillar epithelial cells UT-SCC-60B in response to EV71 infection, this results will provide novel insight into the interaction between human tonsillar epithelial cells and EV71

first: Dan

first: Meng

last: Su


title: Single-cell RNAseq of mouse brain tissues across 3 developmental time points

city: Delhi

first: Debarka

last: Sengupta

state: Delhi

address: IIIT Delhi, Okhla Phase 3

department: Computational Biology and Computer Science

country: India

institute: Indraprastha Institute of Information Technology

summary:
Brains were harvested from 2-month-old adult, p12 day old mice and e18.5 day mice embryo. Brain regions of interest (Visual cortex, Thalamus and Hippocampus) were dissected from fresh brains under a light microscope.
The tissues were enzymatically dissociated by incubating in 5 ml of a papain solution containing Earle’s balanced salts (EBSS, Sigma, St. Louis,  E7510), D(+)-glucose (22.5mM), NaHCO3 (26mM), DNase (125U/ml, Worthington, Lakewood, LS002007), papain (9 U/ml, Worthington, Lakewood, NJ, LS03126), and L-cysteine (1mM, Sigma, St. Louis, C7880) at 35 °C  (incubation time varied with developmental stage: 60 minutes for adult and post-natal tissues, 30min for e18.5).  The papain solution was equilibrated with 5% CO2 and 95% O2 gas before and during papain treatment. Following papain treatment, the tissue was mildly dissociated using the gentleMACS dissociator (Miltenyi Biotec, Germany), followed by gentle trituration using a 5ml pipette. The enzymatic reaction was stopped by adding 5ml of inhibitor buffer (Ovomucoid Trypsin inhibitor, Worthington, Lakewood, LK003182) and centrifuged at 130g for 5 minutes. The cell pellet was then resuspended in 10 ml RPMI1640 medium (Sigma, St.Louis, 11875093) containing 0.02% BSA and 12.5U/ml DNase and strained through a 37um filter (STEMCELL Technologies, BC, 27215) to remove undissociated cell clumps. This cell suspension was then depleted for debris using the Dead cell removal kit (Miltenyi Biotec, Germany, 130-090-101) according to manufacturer’s instruction. Live single cells were enriched by FACS sorting cells (LIVE/DEAD cell viability assay; Molecular Probes, Life Technologies). Single cells were counted and diluted to 250-500 cells per microliter.
Cells were loaded, captured on onto C1 integrated fluidic circuits IFC (5- to 10-μm chip) for cell lysis, reverse transcription with oligo (dT) primers and amplification of cDNA on a C1 Single-cell Auto Prep System according to the mRNA-seq protocol of the manufacturer (Fluidigm, USA). After cells were captured on the chip, they were imaged using phase-contrast and fluorescence microscopy before cell lysis. Resulting cDNA was quantified with a Quant-iT PicoGreen dsDNA Assay Kit (PN P11496; Life Technologies), and quality was checked with High Sensitivity DNA Reagents (PN 5067-4626) according to the manufacturer's instructions (Agilent Technologies). Only cells with high-quality cDNA, with a concentration higher than 0.05ng/ul were processed for subsequent library preparation. Library preparation was performed using Nextera XT DNA Sample Preparation Kit (Illumina) as described in the Fluidigm manual. Following library preparation, cells were pooled and sequenced on an Illumina HiSeq 2500 platform as 1x100bp  paired-end reads.

overall_design: Profiling of 333 single-cells isolated from the mouse brain. Visual cortex, Hippocampus, and thalamus regions were profiled on Embryonic day 18.5(e18.5), 12 days old postnatal (p12) and adult mice (n=5 each).

first: Nirmala

last: Rayan


title: Histone ChIP-seq from heart left ventricle (ENCSR702OVJ)


title: Histone ChIP-seq from upper lobe of left lung (ENCSR429VWL)


title: Control ChIP-seq from heart left ventricle (ENCSR178FVP)


title: Control ChIP-seq from HepG2 (ENCSR254UDV)


title: Control ChIP-seq from HepG2 (ENCSR352VNP)


title: Control ChIP-seq from esophagus squamous epithelium (ENCSR156WTZ)


title: Control ChIP-seq from esophagus muscularis mucosa (ENCSR147KFH)


title: Histone ChIP-seq from upper lobe of left lung (ENCSR238WIK)


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCSR185JEP)


title: TF ChIP-seq from HCT116 (ENCSR101FJM)

summary:
ZNF274 HCT116 ChIP-Seq

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from uterus (ENCSR124AZR)


title: TF ChIP-seq from HEK293 (ENCSR000FCI)

summary:
ZNF274 HEK293 ChIP-Seq

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from esophagus squamous epithelium (ENCSR143XNJ)

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Astrocyte Gi signaling activation in the striatum

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary: The Khakh laboratory used astrocyte selective AAVs expressing Rpl22-HA and hM4Di, a Gi DREADD, in the striatum. Mice recieved either 1 mg/kg CNO or vehicle to compare striatal astrocyte transcriptomes with and without Gi-GPCR signaling activation.

overall_design: Whole striata were extraced from 4 adult (P63) C57BL/6J wild-type male mice 2 hours after CNO or vehicle injection in vivo. After homogenization, RNA was purified from (i) cleared lysate as the input and control, and (ii) astrocyte-specific ribosome-associated RNA precipitated via a hemagglutinin (HA) tag.

first: Jun

last: Nagai

first: Abha

last: Rajbhandari

first: Mohitkumar

middle: R

last: Gangwani

first: Ayaka

last: Hachisuka

first: Sotiris

middle: C

last: Masmanidis

first: Michael

middle: S

last: Fanselow

first: Baljit

last: Khakh


title: Histone ChIP-seq from heart left ventricle (ENCSR181ATL)

first: ENCODE

last: DCC


title: Transcriptional consequences of wild-type and missense mutant p53 in isogenic human acute myeloid leukemia (AML) cell lines

city: BOSTON

first: Benjamin

middle: Levine

last: Ebert

state: MASSACHUSETTS

address: 450 BROOKLINE AVENUE

department: Medical Oncology

institute: DANA-FARBER CANCER INSTITUTE

summary: TP53, encoding for the tumor suppressor p53, is the most frequently mutated gene in human cancer. The selective pressures shaping its mutational spectrum, dominated by missense mutations, have remained enigmatic, and neomorphic gain-of-function (GOF) activities have been implicated. We generated isogenic human leukemia cell lines of the most common TP53 missense mutations using CRISPR/Cas9. Functional, DNA binding, and transcriptional analyses revealed loss-of-function (LOF) without GOF effects of missense mutations. Comprehensive mutational scanning of p53 single amino acid variants demonstrated that DNA-binding domain missense variants exert dominant-negative effects (DNE). In mice, DNE of p53 missense variants confer a selective advantage on hematopoietic cells upon DNA damage in vivo. Clinical outcomes in acute myeloid leukemia patients showed no evidence of GOF for TP53 missense mutations. These findings establish dominant-negativity as the primary unit of selection for TP53 missense mutations in myeloid malignancies.

overall_design: Examination of transcriptional profiles in wild-type, null, and missense mutant (R175H, Y220C, M237I, R248Q, R273H, R282W) p53-expressing human AML cell lines (K562 and MOLM13)  under steady-state conditions (DMSO) or after induction of DNA damage (daunorubicin)

first: Steffen

last: Boettcher


title: Microarray data of REV-ERBa-deficient CCR6+ ILC3

status: Public on Aug 29 2019

city: St. Louis

first: Qianli

last: Wang

state: MO

address: 660 S. Euclid Ave.

institute: Washington University in St. Louis School of Medicine

summary: Microarray was used to determine transcriptional differences between Nr1d1+/+ CCR6+ ILC3s and Nr1d1-/- CCR6+ ILC3s isolated from small intestine lamina propria

overall_design: CCR6+ ILC3s were sorted from small intestine lamina propria of Nr1d1+/+ and Nr1d1-/- mice

first: Michelle

last: Robinette

first: Marco

last: Colonna


title: Genome-wide binding of wild-type and missense mutant p53 in isogenic human acute myeloid leukemia (AML) cell lines

overall_design: Examination of wild-type and missense mutant (R175H, Y220C, M237I, R248Q, R273H, R282W) p53 DNA-binding in two different human AML cell lines under steady-state conditions (DMSO) or after induction of DNA damage (daunorubicin)


title: Nicotinamide riboside augments the human skeletal muscle NAD+ 1 metabolome and induces transcriptomic and anti-inflammatory signatures in aged subjects: a placebo-controlled, randomized trial

city: birmingham

first: ildem

last: akerman

address: BR Tower, 3rd Floor, Room 333, Edgbaston,

department: IMSR

country: United Kingdom

institute: University of Birmingham

summary: NAD+is modulated by conditions of metabolic stress and has been reported to decline with aging, but human data are sparse. Nicotinamide riboside (NR) supplementation ameliorates metabolic dysfunction in rodents. We aimed to establish whether oral NR supplementation in aged participants can increase the skeletal muscle NAD+ metabolome, and questioned if tissue NAD+levels are depressed with aging. We supplemented 12 aged men with NR 1g per day for 21-days in a placebo-controlled, randomized, double-blind, crossover trial. Targeted metabolomics showed that NR elevated the muscle NAD+ metabolome, evident by increased nicotinic acid adenine dinucleotide and nicotinamide clearance products. Muscle RNA sequencing revealed NR-mediated downregulation of energy metabolism and mitochondria pathways. NR also depressed levels of circulating inflammatory cytokines. In an additional study, 31P magnetic resonance spectroscopy-based NAD+ measurement in muscle and brain showed no difference between young and aged individuals. Our data establish that oral NR is available to aged human muscle and identify anti-inflammatory effects of NR, while suggesting that NAD+ decline is not associated with chronological aging per se in human muscle or brain.

overall_design: Double blind, randomized, cross over controlled study. Muscle biopsies collected in a fasted state 14 hours after the last NR dose. A total of 36 RNA-seq samples from human muscle  were collected from a total of 12 patients.  12 samples were were untreated, 12 were placebo treated and 12 were collected after NAD treatment

first: Yasir

last: Elhassan

first: Ildem

last: Akerman

first: Gareth

last: Lavery


title: Gene expression changes associated with resistance to tagraxofusp (SL-401)

city: Boston

first: Andrew

last: Lane

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary: The goal of this experiment was to determine the gene expression changes that occur in the setting of human leukemia cells with acquired resistance to tagraxofusp (SL-401), a recombinant interleukin 3 - diphtheria toxin fusion targeted cytotoxin

overall_design: Human leukemia cell lines CAL1, derived from a patient with BPDCN, and SHI1, derived from a patient with AML, were cultured in repeated dosing with tagraxofusp to generate resistance. Three replicates of each were treated with vehicle and three were treated in tagraxofusp to generate biological triplicates of parental and resistant cultures of each cell line. N=12 lines in total. 3 CAL1 parental, 3 CAL1 resistant, 3 SHI1 parental, 3 SHI1 resistant


title: Gene expression profiling of human neuroblastoma cell line LA1-55n expressing shGFP or shRNA to glycine decarboxylase (GLDC)

city: Birmingham

first: Han-Fei

last: Ding

state: Alabama

address: WTI 602D, 1824 6th Avenue South

department: Pathology

institute: University of Alabama at Birmingham

summary: Microarray gene expression profiling reveals that silencing GLDC expression downregulates genes required for DNA replication and cell cyle progression

overall_design: Affymetrix Human Gene 2.0 ST Array was performed according to the manufacturer's directions on total RNA isolated from three independent samples of LA1-55n_teton-shGFP or -shGLDC99 cells cultured in the presence of 0.5µg/ml doxycycline for 7 days

first: Ahmet

last: Alptekin


title: 17-beta estradiol protects esophageal epithelium from IL-13-induced barrier dysfunction and remodeling

city: New York

first: Jazib

last: Uddin

state: New York

address: 413 E 69th Street, BB-709

department: Medicine

institute: Weill Cornell Medicine

summary: We performed demographic and incidence analysis of EoE in males and females from a single center cohort. Estrogen responsive gene expression analysis were performed.

overall_design: Examination of sex hormone response gene in esophogeal biopsy samples from RNA sequencing data from a previous data series (GSE58640). Samples analysed include GSM1415906, GSM1415907, GSM1415908, GSM1415909, GSM1415910, GSM1415911, GSM1415912, GSM1415913, GSM1415914, GSM1415915, GSM1415916, GSM1415917, GSM1415918, GSM1415919, GSM1415920, GSM1415921.

first: Justin

last: Wheeler

first: Simon

last: Hogan


title: Loss of DNMT3A/B in human ES cells triggers increased cell-cell variability and transcriptional repression

city: Cambridge

first: Alex

last: Shalek

address: 45 Carleton Street

department: Chemistry

institute: MIT

summary: Maintenance of human pluripotent stem cells is dependent on extrinsic signals and cross talk between transcriptional and epigenetic regulators. Methylation of cytosines through the de novo methyltransferases DNMT3A and 3B plays an important role for exiting pluripotency and facilitating proper differentiation. Here, we generated and analyzed single cell expression data from wild-type and DNMT3A/B knockout human embryonic stem cells to better understand the precise effects on pluripotency and differentiation. Although DNA methylation is generally associated with gene silencing, we find unexpected and widespread transcriptional repression upon loss of DNMT3A or DNMT3A/3B. Furthermore, the transcriptional misregulation in DNMT3A knockout cells is largely propagated during differentiation towards mesoderm. Additionally, we observe increased cellular and transcriptional heterogeneity in undifferentiated cells upon deactivation of DNMTs as well as a notable change in cell cycle gene expression. Taken together, our single-cell RNA sequencing data provides several new insights into the role of DNA methylation in human pluripotent stem cells.

overall_design: Single-cell RNA-Sequencing of in vitro embryonic stem cells at different stages of differentiation and conditions

first: Marc

last: Wadsworth II

last: Tsankov

last: Meissner


title: Molecular fingerprint of bovine embryos produced by superovulation with high competence to establish pregnancy

city: Utrecht

first: Maria

middle: Belen

last: Rabaglino

address: Yalelaan 7

department: Population Health Science

country: Netherlands

institute: Utrecht University

summary: The objective of the current experiment was to identify the transcriptome profile of in vivo-derived embryos with high competence to establish and maintain gestation. Using P < 0.01 and a fold change > 2-fold or < 0.5 fold as cut-off, there were 837 DEG (789 upregulated and 48 downregulated) between embryos that survived to day 60 versus those that did not. Using a more stringent criteria, a FDR < 0.05 and a fold-change of > 2-fold or < 0.5, there were 558 DEG (505 upregulated and 33 downregulated) between embryos that survived to day 60 versus those that did not.

overall_design: Blastocysts produced from superovulated Holstein heifers were flushed from the uterus 8 days after anticipated ovulation and bisected. One demi-embryo from a single blastocyst was transferred into a synchronized recipient and the other half was used for RNA-seq analysis by Illumina NextSeq. Recipients were diagnosed for pregnancy at day 30 and 60 of gestation. All cows diagnosed as pregnant at day 30 maintained pregnancy until day 60.

first: Adriana

middle: M

last: Zolini

first: Jeremy

last: Block

first: Gonzalo

last: Rincon

first: Michael

last: Hoelker

first: John

last: Bromfield

first: Peter

last: Hansen


title: Proteasome dysfunction in alveolar type 2 epithelial cells is associated with acute respiratory distress syndrome

city: Cincinnati

first: Sneha

last: Sitaraman

state: Ohio

address: 3333 Burnet Avenue

department: Pulmonary Biology

institute: Cincinnati Children's Hospital Medical Center

summary:
Proteasomes are a critical component of quality control that regulates turnover of short-lived, unfolded, and misfolded proteins. Proteasome activity has been therapeutically targeted and considered as a treatment option for several chronic lung disorders including pulmonary fibrosis. Though pharmacologic inhibition of proteasome activity effectively prevents the transformation of fibroblasts to myofibroblasts, the effect on alveolar type 2 (AT2) epithelial cells is not clear.
To address this knowledge gap, we generated a genetic model in which a proteasome subunit, RPT3, which promotes assembly of active 26S proteasome, was conditionally deleted in AT2 cells of mice. Targeted deletion of RPT3 in AT2 cells resulted in 26S proteasome dysfunction, leading to augmented cell stress and death. Acute loss of AT2 cells resulted in depletion of alveolar surfactant, disruption of the alveolar epithelial barrier and, ultimately, lethal acute respiratory distress syndrome.
This study underscores the need for further investigation into the differential effect of proteasome inhibition in lung cell types.

overall_design: RPT3AT2Δ/Δ and SftpcWT/CreER mice (n=3 mice /genotype) were fed tamoxifen chow for 7 days followed by extraction of RNA from freshly isolated alveolar type 2 epithelial cells. RNA sequencing was performed on Illumina platform.

first: Cheng-Lun

first: Li

last: Yang

first: Alyssa

last: Filuta

first: James

middle: P

last: Bridges

first: Timothy

middle: E

last: Weaver


title: KSDM1b Role in Ewing Sarcoma

city: Columbus

first: Cenny

last: Taslim

address: 700 Children's Drive

institute: Nationwide Children's Hospital

summary: This study looks at the  transcriptional profile of LSD2 knockdown in A673 Ewing sarcoma cells.

overall_design: RNA-seq data for A673 cells infected with retroviral vector expressing shRNA for Luciferase or KDM1b. 2 biological replicates were performed.

first: Priyal

last: Patel

first: Stephen

last: Lessnick


title: Mitochondrial damage activates the STING pathway to promote chronic kidney disease

city: Philadelphia

first: Xin

last: Sheng

institute: University of Pennsylvania

summary: Fibrosis of the kidney is the final common pathway leading to end stage renal failure. By analyzing kidneys of patients and animal models with fibrosis we observed a significant mitochondrial defect, including the loss of the mitochondrial transcription factor A (TFAM) in kidney tubule cells. Here, we generated mice with tubule-specific deletion of TFAM (Ksp-Cre/Tfam flox/flox). While these mice developed severe mitochondrial loss and energetic deficit (ATP level decline) by 6 weeks of age, kidney fibrosis, immune cell infiltration and progressive azotemia causing death was only observed around 12 weeks of age. Mechanistic studies demonstrated that in the TFAM KO mice aberrant packaging of the mitochondrial DNA (mtDNA) resulted in escape of the mtDNA into the cytosol of the renal cells, activation of the cytosolic cGAS-STING (Stimulator of interferon genes) DNA sensing pathway, and thus cytokine expression and immune cell recruitment. Genetic deletion or pharmacological inhibition of STING ameliorated kidney fibrosis in mouse models of chronic kidney disease, demonstrating that in addition to its essential role in metabolism TFAM sequesters mtDNA to prevent the activation of innate immune pathways and fibrosis.

overall_design: RNA-seq of kidneys of 12 weeks old control mice (Tfam flox/flox without Ksp cre) and Kspcre Tfam flox/flox  mice

first: Chung

last: Ki Wung

first: Dhillon

last: Poonam

first: Sheng

last: Xin

first: Susztak

last: Katalin


title: BCL6 reinforces brown adipocyte cellular identity to preserve thermogenic fitness

city: San Francisco

first: Vassily

middle: Igor

last: Kutyavin

address: 555 Mission Bay Boulevard South

department: Physiology

institute: University of California - San Francisco

summary: Brown adipose tissue (BAT) generates heat via uncoupled respiration, providing mammals with an evolutionary defense against environmental cold. Although the molecular pathways by which cold activates brown adipocytes are well understood, little is known about how BAT maintains its thermogenic capacity during adaptation to environmental warmth. Here, we identify the transcriptional repressor BCL6 as the switch for maintaining brown adipocyte cellular identity under warm conditions. Mice lacking BCL6 in their brown adipocytes display normal thermogenic responses when housed in a cool environment, but fail to maintain thermogenic fitness when housed under warm conditions. In a temperature-dependent manner, BCL6 suppresses apoptosis, fatty acid storage, and coupled respiration to maintain thermogenic competence in brown adipocytes. Enhancer analysis revealed that BCL6 reinforces brown-specific while opposing white-specific enhancers to maintain cellular identity. Thus, unlike other regulators, BCL6 is dispensable for differentiation and activation of brown adipocytes, but specifically required for their maintenance in warmth.

overall_design: The temperature-dependent regulation of the mouse brown adipocyte transcriptome and epigenome by BCL6 was studied via RNA-Seq and H3K27ac ChIP-Seq in brown adipose tissue isolated from Ucp1-Cre BCL6-floxed mice housed at different temperatures. The BCL6 cistrome in mouse brown adipocytes was studied via BCL6 ChIP-Seq in brown adipose tissue isolated from Ucp1-Cre BCL6-floxed mice housed at 30 deg. C.

first: V

first: A

last: Chawla


title: Expression profile analysis of the oxygen deficit response in Carrizo citrange rootstock

city: Verona

first: Andrea

last: Minio

address: Via dell'Artigliere 8

department: Applied Biotechnologies

country: Italy

institute: Università di Verona

summary: The deficit of oxygen in plants is a frequent phenomenon in nature. The main causes may be due to flooding or excessive irrigation or to an excess of aerobic microflora in the soil. The Intergovernmental Panel on Climate Change (IPCC) reported that the anthropogenically induced change of world climate increases the frequency of heavy precipitation and tropical cyclone activity. This is likely to engender more frequent flooding events in river flood plains and arable farmland, particularly affecting the world’s poorest farmers.   The stress caused by lack of oxygen in plants mainly produces a reduction of the respiration, and then a low energy production and accumulation of toxic compounds of anaerobic metabolism. To alleviate this problem plants have developed morphological and metabolic adaptations, the main of which include the induction of anaerobic and fermentative pathways.   In the present study we used a Combimatrix platform, made up of around 8,000 ESTs of roots isolated in citrus and its rootstocks. The chip was hybridized with RNA wild type Carrizo citrange roots and a transgenic line highly expressing a transcription factor involved in the response to the deficiency of oxygen in Oryza sativa. The aim of the work consists in the study of the up and down expressed genes in wild type and transgenic lines subjected and not to anaerobiosis, in order to understand the mechanisms that are activated under anoxia. In general, the hybridization of the chip has led to the activation of 492 genes, of which 28.95% is involved in redox processes, 28.41% in the response to stress, 18.28% in response to chemical stimuli. The up and down-regulation of differentially expressed transcripts in response to oxygen deficiency were confirmed through real-time RT-PCR   The results obtained showed the activation of main genes involved in the glycolytic and fermentative pathways, such as pyruvate decarboxylase, alcohol dehydrogenase and sucrose synthase. In transgenic plants of Carrizo the response to oxygen deficit appears to be more pronounced, therefore genes of glycolytic, fermentation and pentose phosphate pathway are activated.

overall_design: Comparison of wild type Carrizo citrange and a transgenic line subjected and not to anaerobiosis in triplicate samples

first: Paola

last: Caruso

first: Franca

last: Locatelli

last: Tononi

first: Massimo

last: Delledonne

first: Concetta

last: Licciardello


title: Transcriptonal and epigenetic changes of adult liver cells in vivo and in vitro

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

type: Methylation profiling by high throughput sequencing

summary: RNA profile, TET1 and H3K4me3 occupancy in adult ductal cells grown as organoids in vitro; RNA profile, 5mC and 5hmC sites at single base resolution in adult ductal cells in vivo upon damage

first: Luigi

last: Aloia

first: Gregoire

last: Vernaz

first: Meritxell

last: Huch


title: Distinct effects of genetic and pharmacological inhibition of galectin-3 on cardiac fibrosis and function in a mouse model of dilated cardiomyopathy

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

summary: Background: Galectin-3 is upregulated in heart disease, and its inhibition has been reported to confer benefits on cardiac remodeling and dysfunction. It remains unknown whether galectin-3 plays a biological role in a setting of dilated cardiomyopathy (DCM). We determined galectin-3 expression in transgenic (TG) mice with cardiac-restricted overexpression of mammalian sterile 20-like kinase 1 (Mst1-TG), and studied the effects of pharmacological and genetic inhibition of galectin-3 on the DCM phenotype. Methods and results: The DCM phenotype of male Mst1-TG mice was assessed at 2, 3 and 6 months of age. Galectin-3 deletion in Mst1-TG mice was achieved by cross-breeding Mst1-TG with galectin-3 knockout (KO) mice to produce genotypes of non-TG (nTG), KO, Mst1-TG, and Mst1-TG mice with partial or complete deletion of the galectin-3 gene. Pharmacological inhibition of galectin-3 was tested by treating Mst1-TG mice with modified citrus pectin for 4 months. Changes in the DCM phenotype were assessed by serial echocardiography, ECG recording and biochemical assays. Mst1-TG mice exhibited upregulated levels of cardiac galectin-3 expression by 40~50-fold, atrial dilatation, reduced left ventricular (LV) ejection fraction, increased LV volume at systole and diastole, atrial conduction delay, severe cardiac fibrosis, and upregulated fibrosis-related genes. Galectin-3 gene deletion in Mst1-TG mice attenuates increased LV volume at systole and diastole, atrial conduction delay and cardiac fibrogenesis. Treatment with modified citrus pectin in Mst1-TG mice did not confer benefit on the DCM phenotype, possibly due to the very high expression of galectin-3. Conclusion: Galectin-3 expression is markedly increased in Mst1-TG hearts exhibiting DCM. Galectin-3 gene deletion effectively suppressed cardiac fibrotic signaling and LV dilatation, and was associated with better function. Thus, suppression of galectin-3 expression may represent a potential therapeutic approach in DCM. The development of new galectin-3 inhibitors are warranted.

overall_design: We performed RNA-seq on left ventricle samples from control and Gal-3 knock-out mice in two genetic backgrounds: wild type C57BL6 and the Mst-1 overexpressing mouse that is frequently used as a model for dilated cardiomyopathy. Between 5 and 8 replicates from each group were processed.

first: Haloom

last: Rafehi

first: Assam

last: El-Osta

first: My-Nhan

last: Nguyen

first: Helen

last: Kiriazis

first: Zara

last: Thomas

first: Yidan

last: Su

first: Daniel

last: Donner

first: Junichi

last: Sadoshima

first: Anthony

last: Dart

first: Julie

last: McMullen

first: Xiao-Jun

last: Du


title: Differential gene expression between wild type and Pax9-null pharyngeal arch tissue

status: Public on Aug 28 2019

city: Newcastle upon Tyne

first: Simon

middle: D.

last: Bamforth

address: Central Parkway

department: Institute of Genetic Medicine

institute: Newcastle University

summary: The aim of this study was to identify differentially expressed genes within the pharyngeal arches of Pax9-null embryos at E9.5. Mice null for Pax9 die in the neonatal period with complex cardiovascular defects, caused by abnormal morphogenesis of the pharyngeal arch arteries.

overall_design: Total RNA was isolated from dissected pharyngeal arch region of E9.5 mouse embryos. Pax9-null pharyngeal arches were compared to stage-matched wild type controls. Three biological replicates for each group (wild type vs. mutant) were collected. Samples represent a mix of female and male animals. Isolated RNA was subjected to high throughput sequencing analyses to identify differentially expressed transcripts.

first: Anastasia

middle: I

last: Kousa


title: Histone ChIP-seq from heart left ventricle (ENCSR803MVC)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone crotonylation links metabolism with gene expression

first: Graeme

last: Gowans

address: Gilbert Building, 371 Serra Mall

department: Biology

institute: Stanford University

summary: We performed RNA-seq across the yeast metabolic cycle (YMC) in wild-type and a strain containing a point mutant in TAF14 (W81A) that abolishes binding to acylated histones. We also performed ChIPseq using antibodies directed against histone H3K9acetyl, histone H3K9crotonyl, histone H3 across the wild-type YMC.

overall_design: RNA-seq/ChIP-seq in wild-type and TAF14[W81A] yeast.

middle: J

first: Joseph

middle: B

last: Bridgers

first: Raghuvar

last: Dronamraju

first: Ashby

last: Morrison

first: Brian

last: Strahl


title: Profiling microarray expression of mesenchymal stem cell genes differentially expressed by colorectal cancer cells

city: seoul

first: In-Rok

last: Oh

address: 145, Anam-ro, Seongbuk-gu, Seoul, Republic of Korea

country: South Korea

institute: korea university

summary: To comprehensively screen for the changed genes in the MSCs that make up the microenvironment of cancer cells, the characteristics of the risk genes considered in this analysis were compared using microarray analysis.

overall_design: Understanding the Microenvironment in Colorectal Cancer Cells


title: Real-time quantitative PCR analysis of human neonatal and adult monocytes

city: São Paulo

first: Anna Cláudia

middle: Calvielli

last: Castelo Branco

state: São Paulo

address: Avenida Doutor Enéas de Carvalho Aguiar, 470. IMT prédio II, 3o andar

country: Brazil

institute: University of São Paulo

summary: To evaluate the effect of histamine on LPS induced proinflammatory state of purified monocytes from healthy adults and newborns, we performed a qPCR for 84 genes related to toll-like receptor (TLR) signalling

overall_design: qPCR gene expression profiling.  Purified monocytes from healthy adults and newborns in an unstimulated condition, stimulated with LPS,  or LPS and histamine for 4 h. A total of 84 genes related to TLR signaling were assessed by qPCR.

first: Anna

first: Maria

last: Notomi Sato


title: AtERF#111/ABR1 is involved in the wounding response

city: Bayreuth

first: Angelika

last: Mustroph

address: Universitaetsstr. 30, NWI

department: Plant Physiology

country: Germany

institute: University Bayreuth

summary: AtERF#111/ABR1 belongs to the group X of the ERF/AP2 transcription factor family (GXERFs) and is shoot specifically induced under submergence and hypoxia. It was described to be an ABA-response repressor, but our data hint at a completely different function. Here we present evidence that AtERF#111 is involved in the wounding response. Expression profiling of ERF#111-overexpressing (OE) plants demonstrates that AtERF#111 is a transcriptional activator of wounding response genes. Furthermore, direct target genes of AtERF#111 were identified by microarray analyses. However, knockout mutants of AtERF#111 only show a slightly reduced wounding response, suggesting the involvement of other GXERFs in wound signaling and repair mechanisms.

overall_design: Three experimental sets with two replicates each were performed. Experiment 1: Comparison of 7-day-old seedlings overexpressing AtERF#111 with wildtype seedlings. Experiment 2: Wounding response after 3 hr of wildtype and AtERF#111 knockout lines. Experiment 3: Identification of direct target genes for AtERF#111 in leaf protoplasts.

first: Judith

last: Bäumler


title: Industrial trans fatty acids stimulate SREBP2-mediated cholesterogenesis and promote non-alcoholic fatty liver disease [3T3-L1]

status: Public on Aug 27 2019

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: Scope: Consumption of industrial trans fatty acids unfavourably alters plasma cholesterol and has been linked to NAFLD. However, the mechanisms underlying these deleterious effects of trans fatty acids are unclear. Here, we aim to investigate the molecular mechanisms of action of industrial trans fatty acids. Methods & Results: Hepa1-6 hepatoma cells were incubated with elaidate, oleate, or palmitate. C57Bl/6 mice were fed diets rich in trans-unsaturated, cis-unsaturated or saturated fatty acids. Transcriptomics analysis of Hepa1-6 cells showed that elaidate but not oleate or palmitate induced expression of genes involved in cholesterol biosynthesis. Induction of cholesterogenesis by elaidate was mediated by increased SREBP2 and dependent on SCAP, yet independent of LXR and UBXD8. Elaidate decreased intracellular free cholesterol levels and repressed the anti-cholesterogenic effect of exogenous cholesterol. In mice, the trans-unsaturated diet increased the ratio of liver to gonadal fat mass, steatosis, hepatic cholesterol levels, ALT activity, and fibrosis markers, suggesting enhanced NAFLD, compared to the cis-unsaturated and saturated diets. Conclusion: Elaidate induces cholesterogenesis in vitro via activation of the SCAP-SREBP axis, likely by lowering intracellular free cholesterol and attenuating cholesterol-dependent repression of SCAP. This pathway potentially underlies the increase in liver cholesterol and NAFLD by industrial trans fatty acids.

overall_design: 3T3-L1 pre-adipocytes were incubated with 3 different fatty acids and control for 24hrs, whereafter gene expression profiling was performed.

first: Antwi-Boasiako

last: Oteng

first: Anke

last: Loregger

first: Michel

last: van Weeghel

first: Noam

last: Zelcer

first: Sander

last: Kersten


title: mRNA expression in CD4+ T cells of malignant pleural effusion (MPE) from WT and IL-10 knock out mice

city: Beijing

first: Yuan

last: Yang

address: 8 Gongti Nanlu, Chaoyang District

institute: Beijing Chaoyang Hospital, Capital Medical University

summary: The interactions between tumor cells and the host vasculature and immune cells results in increased net fluid production via enhanced plasma extravasation into the pleural space.Understanding the regulatory mechanism of IL-10 in MPE formation is essential both for deciphering how IL-10 acts in regulating tumor immunity and for discovering key molecular targets for intervention in advanced cancers.

overall_design: We investigate the characteristic of  mRNA in CD4+ T cells in IL-10 induced murine MPE. Identifing the distinct classes of up-regulated and down-regulated mRNAs during this process.

first: Xin-Yu

last: Shi

first: Kan

last: Zhai

first: Huan-Zhong


title: Industrial trans fatty acids stimulate SREBP2-mediated cholesterogenesis and promote non-alcoholic fatty liver disease

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

overall_design: Refer to individual Series


title: A circadian clock is essential for homeostasis of group 3 innate lymphoid cells in the gut

first: Gregory

last: Putzel

state: NY

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

summary: Interleukin (IL)-2 is a pleiotropic cytokine that is necessary to prevent chronic inflammation in the gastrointestinal tract.  The protective effects of IL-2 involve the generation, maintenance and function of regulatory T cells (Tregs), and low-dose IL-2 has emerged as a potential therapeutic strategy in inflammatory bowel disease (IBD) patients.  However, the cellular and molecular pathways that control the production of IL-2 in the context of intestinal health are undefined.  Here we identify that IL-2 is acutely required to maintain Tregs and immunologic homeostasis throughout the gastrointestinal tract.  Strikingly, lineage-specific deletion of IL-2 in T cells could recapitulate these phenotypes in the large intestine, but not in the small intestine.  Unbiased analyses revealed that group 3 innate lymphoid cells (ILC3) are the dominant cellular source of IL-2 in the small intestine, which is selectively induced by IL-1β.  Macrophages produce IL-1β in the small intestine and activation of this pathway involves MyD88- and Nod2-dependent sensing of the microbiota.  Loss-of-function studies defined that ILC3-derived IL-2 is essential to maintain Tregs, immunologic homeostasis and oral tolerance to dietary antigens uniquely in the small intestine.  Furthermore, ILC3 production of IL-2 was significantly reduced in the small intestine of Crohn’s disease patients, and this correlated with diminished Tregs.  Collectively, these results reveal a previously unappreciated pathway whereby a microbiota- and IL-1β-dependent axis promotes ILC3 production of IL-2 to orchestrate immune regulation in the small intestine.

overall_design: RNAs of ILC2s were  sorted as CD45+CD3-CD5-CD8-NK1.1-CD11b-CD11c-B220-CD90.2+CD127+KLRG1+ (ILC2) from 3 wild type mice.

first: Lei

last: Zhou

last: Sonnenberg


title: Obesity tuning human Sperm RNA Chromatin remodeler cofactors, RNA interactors, Writers and Erasers

city: Detroit

first: Grace

middle: Michelle

last: Swanson

state: MI

address: 275 E. Hancock, C.S. Mott Center room 271

institute: Wayne State University

summary: This study was designed to identify the population of sperm RNAs responding to obesity as measured by BMI.

overall_design: Analysis of sperm RNA alterations in response to increasing BMI

first: Molly

last: Estill

first: Michael

last: Diamond

first: Richard

last: Legro

first: Christos

last: Coutifaris

first: Kurt

last: Barnhart

first: Hoa

last: Huang

first: Karl

last: Hansen

first: J

last: Trussell

first: R

last: Coward

first: Heping

last: Zhang

first: Robert

last: Goodrich

first: Stephen

middle: A

last: Krawetz


title: Industrial trans fatty acids stimulate SREBP2-mediated cholesterogenesis and promote non-alcoholic fatty liver disease [Hepa1-6 cells]

first: Guido

last: Hooiveld

overall_design: Hepa1-6 cells were incubated with 3 different fatty acids and control for 24hrs, whereafter gene expression profiling was performed.

first: Antwi-Boasiako

last: Oteng

first: Anke

last: Loregger

first: Michel

last: van Weeghel

first: Noam

last: Zelcer

first: Sander

last: Kersten


title: Industrial trans fatty acids stimulate SREBP2-mediated cholesterogenesis and promote non-alcoholic fatty liver disease [liver]

overall_design: Mice were fed diets enriched in trans-unsaturated, cis-unsaturated or saturated fatty acids for 7 weeks whereafter livers were subjected to gene expression profiling.


title: Effect of Bile Acids on C. difficile Growth

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

institute: Institut Pasteur

summary: Clostridium difficile epidemic strain R20291 was grown in presence of the two main bile acids, Deoxycholate and Cholate.

overall_design: Total RNA was extracted from 4 independent biological replicates of the R20291 C. difficile strain with 0.5 mM Deoxycholate or 5 mM Cholate or DMSO.

first: Joe

last: Sorg

first: Marc

last: Monot


title: CTCF orchestrated enhancer hijacking accelerated tumorigenesis through remodeling 3D chromosomal architecture in NTS locus [ChIP-seq]

city: Shanghai

first: Peiwei

last: Chai

state: Shanghai

address: No.833 Zhizaoju Road

department: Opthalmology

institute: Shanghai Ninth people's hospital

summary: We identified aberrant CTCF binding lead to a 3D chromosomal interactional driver in NTS locus that accelerates tumorigenesis of uveal melanoma. Both enhancer deletion and abolishing CTCF binding lead to the loss of chromosomal looping and triggered therapeutic efficacy in inhibiting tumorigenesis. Our study shed light on a functional chromosomal architecture induced enhancer hijacking, thereby provide novel concept of 3D-chromosomal conformation exploration.

overall_design: We performed CTCF ChIP-Seq in melanoma cells and RNA-seq in 2 types of ocular melanoma cells with or without NTS promoter deletion

first: Xianqun

last: Fan


title: Enterovirus 71 oncolysis of malignant gliomas

city: Wuhan

first: Xiaowei

state: Hubei province

address: Xiao Hong Shan No.44

institute: Wuhan Institute of Virology, Chinese Academy of Sciences

summary: This study finds that EV71 has oncolytic activity against experimental human malignant gliomas. RNA-seq analysis of infected glioma cells reveals transcriptional up-regulation, notably genes in apoptosis pathways. Application of virus targeting based on brain-specific microRNA-124 enhances the safety profile. Oncolysis with EV71 may be a potentially novel treatment for malignant gliomas.

overall_design: To investigate the impact of EV71 infection on glioma cells at the molecular level, we carried out transcriptome analyses (RNA-seq). Total RNA samples from CCF-STTG1 glioma cells after EV71 or mock infection were used for RNA-seq analysis by using Illumina HiSeqTM 2000 System.

first: Hanzhong

last: Wang


title: Dach1 downregulation marks a lymphoid-primed progenitor in early haematopoiesis (2X96 cells)

city: Cambridge

first: Luyi

last: Tian

address: 415 main st Cambridge

institute: Broad institute

summary: A classical view of blood cell development is that multipotent haematopoietic stem and progenitor cells (HSPCs) become lineage-restricted at defined stages. The Lin–c-kit+Sca1+Flt3+ stage, termed lymphoid-primed multipotent progenitors (LMPPs), have lost megakaryocyte and erythroid potential but are heterogeneous in their fate. Through single cell RNA-sequencing, we identify heterogeneous expression of Dach1 and associated genes in this fraction where it co-expressed with myeloid/stem genes but inversely correlated with lymphoid genes. Through generation of Dach1-GFP reporter mice, we identify a transcriptionally and functionally unique Dach1– subpopulation within LMPPs with lymphoid potential but devoid of myeloid potential. We term these ‘lymphoid-primed progenitors’, or LPPs. These findings define the earliest branch point of lymphoid development in haematopoiesis and a means for their prospective isolation.

overall_design: Mouse HSPCs were isolated from bone marrow and sorted into 384 PCR plate, with library generated using the in-house CEL-seq protocol.

first: Daniela

last: Amann-Zalcenstein

first: Jaring

last: Schreuder

first: Shalin

middle: H

last: Naik


title: Transcriptional profiling of neurons in the mouse cortex-amygdala transition zone (CxA)

city: New York

first: Laura

last: Kus

address: 1230 York Avenue # 260

department: Heintz Laboratory

institute: The Rockefeller University

summary: TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain.  Using this technique we obtained RNA-Seq data from actively translating transcripts present in neurons in the cortex-amygdala transition zone (CxA) of adult Lypd1-EGFP/Rpl10a (OI82) mice.  This work was supported by a grant from the National Institute on Drug Abuse P30DA035756 to N.H.

overall_design: TRAP-Seq of neurons in the cortex-amygdala transition zone (CxA) of three adult Lypd1-EGFP/Rpl10a (OI82) control mice.

first: Cuidong

first: Nathaniel

last: Heintz


title: Glucocorticoids delay RAF-induced senescence promoted by EGR1 [ChIP-seq]

city: Gif sur Yvette

first: Jean-Yves

last: Thuret

address: CEA Saclay Bat 142

institute: CEA

summary: Analysis of the differential binding of EGR1 to chromatin in human fibroblasts entering oncogene-induced senescence, with and without clobetasol.

overall_design: BJ-hTert-B-RAF-V600E human cells treated for 24 hours with doxycycline to induce B-Raf-V600E expression were simultaneously treated with clobetasol or DMSO before harvest. Three replicates per condition. Differential peak-calling with MACS2.

first: Cyril

last: Carvalho

first: Regis

last: Courbeyrette

last: Denby-Wilkes

first: Carl

last: Mann


title: Glucocorticoids delay RAF-induced senescence promoted by EGR1

summary: Analysis of the transcriptional response to treatment with glucocorticoids in human fibroblasts entering oncogene-induced senescence.

overall_design: BJ-hTert-B-RAF-V600E human cells treated for 24-120 hours with doxycycline to induce B-Raf-V600E expression were treated with clobetasol or compound A for 2 hours before harvest or during the entire time with doxycycline. At least three replicates per sample. Differential expression with clobetasol assessed against control with DMSO (vehicle).

first: Celine

last: Derbois

first: Robert

last: Olaso

first: Jean-François

last: Deleuze


title: Transcriptomic responses to Ivacaftor and prediction of Ivacaftor clinical responsiveness

city: Pittsburgh

first: Wei

last: Chen

state: PA

address: 4401 Penn Ave., Rangos Research Building, Room 9125

department: Division of Pulmonary Medicine, Allergy and Immunology, Department of Pediatrics

institute: Children’s Hospital of Pittsburgh of UPMC

summary:
Rationale: Ivacaftor is a recently FDA-approved drug for the treatment of cystic fibrosis (CF) patients with at least one copy of the G511D mutation in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. The transcriptomic effect of Ivacaftor in CF patients remains unclear.
Objectives: We aim to examine if and how the transcriptome of patients is influenced by Ivacaftor treatment and to determine if these data allow prediction of Ivacaftor responsiveness.
Methods: We performed RNA-sequencing (RNA-seq) on PBMCs from CF patients and compared the transcriptomic changes before and after Ivacaftor treatments. Consensus clustering method is employed to stratify patients into sub-groups based on clinical responses post treatment, and determined differences in baseline gene expression. A random forest model is built to predict Ivacaftor responsiveness.
Measurement and Main Results: We identified 239 genes that were significantly influenced by Ivacaftor in PBMC. The functions of these genes relate to cell differentiation, microbial infection, inflammation, Toll-like receptor signaling, and metabolism. We classified patients into “good” and “moderate” responders based on clinical response to Ivacraftor. We identified a panel of signature genes and built a statistical model for predicting CFTR modulator responsiveness. Despite a limited sample size, adequate prediction performance was achieved with an accuracy of 0.92.
Conclusions: For the first time, the present study demonstrates profound transcriptomic impacts of Ivafactor in CF patients PBMCs and successfully built a statistical model for predicting the clinical responsiveness to Ivacaftor prior to treatment.

overall_design: before- and after-Ivacaftor treatment RNA-seq samples from CF subjects

first: Tao

last: Sun

first: Jay

last: Kolls

first: Kong


title: Global gene expression analysis of MGAS10870 serotype of Group A Streptococcus (Streptococcus pyogenes/GAS) in the absence or presence of 100 µM Manganese

city: Houston

first: Muthiah

last: Kumaraswami

state: TX

address: 6670 Bertner Ave

department: Infectious Diseases

institute: Houston Methodist Research Institute

summary: The goal was to perform global transcriptome analysis on MGAS10870 serotype to investigate and compare the gene expression alterations between ΔmtsR mutant to WT or WT grown in the presence or absence of 100 µM Manganese (MnCl2) to WT grown in the presence of 100µM Manganese (MnCl2)

overall_design: There were 3 strains analyzed, each in triplicate replicates: 1) WT GAS grown to late exponential growth phase in the absence of 100 µM MnCl₂; 2) WT GAS grown to late exponential growth phase in the presence of 100 µM MnCl₂; 3) ΔmtsR mutant strain grown to late exponential growth phase in the presence of 100µM MnCl₂

first: Hackwon

last: Do

first: Nishanth

last: Makthal


title: CSF1R and BTK inhibitions as novel strategies to disrupt   the dialogue between mantle cell lymphoma and macrophages

city: Nantes

first: David

last: Chiron

address: 8 quai Moncousu

institute: CRCI2NA, INSERM_U1307, CNRS_6075, Nantes_Université

summary: The microenvironment strongly influences mantle cell lymphoma (MCL) survival, proliferation and chemoresistance. However, little is known regarding the molecular characterization of lymphoma niches. We focused on the interplay between MCL cells and associated monocytes/macrophages.

overall_design: RNA was extracted using the RNeasy Kit (Qiagen, Hilden, Germany). Biotinylated cRNA was amplified with a double in vitro transcription and hybridized to the human U133 2.0 plus GeneChips, according to the manu- facturer’s instructions (Affymetrix, Santa Clara, CA, USA). Fluorescence intensities were quantified and analyzed using the GECOS software (Affymetrix).

first: Antonin

last: Papin

first: Benoit

last: Tessoulin

first: Céline

last: Bellanger

first: Anne

last: Moreau

first: Yannick

last: Le Bris

first: Hervé

last: Maisonneuve

first: Philippe

first: Cyrille

last: Touzeau

first: Martine

last: Amiot

first: Catherine

last: Pellat-Deceunynck

first: Steven

last: Le Gouill


title: Selective Disruption of Core Regulatory Transcription [single cell RNA-seq]

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

summary: Activation of identity determining transcription factors (TFs), or core regulatory TFs, is governed by cell-type specific enhancers, an important subset of these being super enhancers (SEs). This mechanism is distinct from constitutive expression of housekeeping genes. The characterization of drug-like small molecules to selectively inhibit core regulatory circuitry is of high interest for treatment of cancers, which are addicted to core regulatory TF function at SEs. Surprisingly, we find histone deacetylases (HDAC) to be an indispensable component of SE-driven transcription. While histone acetylation is a marker for active genes, over accumulation of acetylation selectively halts core regulatory transcription. We show this conundrum may in part be explained by a SE-specific need for resetting histones to maintain SE boundaries, to facilitate enhancer-promoter looping and high levels of transcription.

overall_design: Single cell RNA-seq data for FP-RMS cells treated with Entinostat.

first: Walton

last: Ashley

first: Gryder

last: Berkley

first: Xinyu

last: Wen


city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

institute: Yunnan Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs are small non-coding RNAs that are critical in post-transcriptional regulation. According to the latest miRBase (v22), there are 617 annotated pre-miRNAs in Macaca mulatta, which is much less than 1917 in human, although both of these two species are primates. To improve the annotation of miRNAs in Macaca mulatta, we generated 12 small RNA profiles from 8 tissues and perform comprehensive analysis of these profiles. We identified 613 conserved pre-miRNAs that have not been reported in Macaca mulatta and 25 novel miRNAs. Furthermore, we identified 996 editing sites with significant editing levels from 250 pre-miRNAs after analyzing the 12 self-generated and 58 additional published sRNA-seq profiles from different types of organs or tissues. Our results show that the distribution of different miRNA editing types in Macaca mulatta is different from that in human brains. Particularly, there are much more small indel events in miRNAs of Macaca mulatta than in human brains. These results significantly increase our understanding of miRNAs and their editing events in Macaca mulatta.

overall_design: Identifying microRNAs and their editing sites in Macaca mulatta using Illumina HiSeq 2000 sequencer.


title: DNA accessibility is not the primary determinant of chromatin-mediated gene regulation (yeast III)

first: Razvan

middle: V.

last: Chereji

state: Maryland

address: 6 Center Drive, Room 2A14

department: NICHD

institute: National Institutes of Health

summary: DNA accessibility is thought to be of major importance in regulating gene expression. We test this hypothesis using a restriction enzyme as a probe of chromatin structure and as a proxy for transcription factors. We measured the digestion rate and the fraction of accessible DNA at all genomic AluI sites in budding yeast and mouse liver nuclei. Hepatocyte DNA is more accessible than yeast DNA, consistent with longer linkers between nucleosomes, and indicating that DNA accessibility is primarily determined by nucleosome spacing. Remarkably, AluI sites in inactive mouse promoters are accessible in some cells. Furthermore, euchromatin and heterochromatin have very similar accessibilities. Cell-to-cell heterogeneity in DNA accessibility has implications for chromatin models of gene regulation: a transcription factor binding site is blocked in some cells, but not in all cells, guaranteeing neither activation nor repression.

overall_design: 44 samples

middle: V

first: Peter

middle: R

last: Eriksson

first: Josefina

last: Ocampo

first: David

last: Clark


title: Quantitative MNase-seq accurately maps nucleosome occupancy levels

summary: Chromatin mapping using micrococcal nuclease (MNase) has been the standard tool for mapping nucleosomes for >40 years. When coupled with DNA sequencing, MNase-seq can provide base-pair-resolution nucleosome maps. However, determining nucleosome occupancy using MNase-seq has been hampered by its aggressive endo-/exo-nuclease activities, whereby cleavages within linker regions produce oligo- and mono-nucleosomes whereas cleavages within nucleosomes destroy them. Here we introduce a theoretical framework for predicting nucleosome occupancies and an experimental protocol with appropriate spike-in normalization that confirms our theory and provides accurate occupancy levels over an MNase digestion time-course. As expected, DNaseI hypersensitive sites and transcription units are digested by MNase at elevated rates, and the apparent deficiency of nucleosomes at 3’ ends of Drosophila genes is an artifact of MNase preference for AT-rich DNA. Surprisingly, we observed no overall differences between Drosophila euchromatin and heterochromatin, which implies that heterochromatin compaction does not render nucleosomal DNA less accessible than euchromatin.

overall_design: Quantitative MNase-Seq of Drosophila S2 and Kc167 cells, 6 digestion levels

first: Terri

last: Bryson

last: Henikoff


title: Expression data from uninfected and pneumococcus-infected wt and PGLYPR4-KO primary alveolar macrophages

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

summary:
Streptococcus pneumoniae is the most frequent cause of community-acquired pneumonia. Endogenous antimicrobial proteins such as PGLYRP4 might participate to the course of the disease. PGLYRP4 is expressed in different cell types but is downregulated in alveolar epithelial after stimulation with Streptococcus pneumoniae. Interestingly, mice lacking PGLYRP4 displayed an enhanced bacterial clearance in the lungs and less mice develop a bacteremia. We investigated the gene expression in alveolar macrphages and found most top 50 up- and down-regulated genes to be not annotated. Genes which could be annotated seem unlikely to play a major role in the phenotype of PGLYRP4-KO mice.
We implemented microarray analysis of infected primary alveolar macrophage cells to identify possible regulated genes by PGLYPR4-deficency, which contribute to the seen phenotype.

overall_design: We isolated primary alveolar macrophages cells from untreated and S. pneumoniae-infected 10-16 week old BALB/c wt and PGLYRP4-deficient mice. We used three mice of each strain and performed three indipendant experiments.

first: Alexander

middle: N

last: Dabrowski

first: Anshu

last: Shrivastav

first: Claudia

last: Conrad

first: Kassandra

last: Komma

first: Markus

last: Weigel

first: Kristina

last: Dietert

first: Achim

last: Gruber

first: Wilhelm

middle: G

last: Bertrams

first: Bernd

last: Schmeck

first: Katrin

last: Reppe

last: N'Guessan

first: Sahar

last: Aly

first: Norbert

last: Suttorp

first: Torsten

last: Hain

first: Janine

last: Zahlten


title: Synergy of Nras mutation and Nup98-Hoxa10HD gene fusion efficiently preserves the stemness of single hematopoietic stem cells after feeder-free culture

city: chengdu

first: Yong

last: Dong

state: sichuan

address: Xindu road 783, Xindu district

department: Immunology

institute: Chengdu medical college

summary: Hematopoietic stem cell (HSC) gives rise to all the hematopoietic cells. The stemness of HSC is strictly controlled by some transcription factors. Here we show that both of  Nras mutation (NrasG12D) and Nup98-Hoxa10HD (NA) improve the transplantation competition ability of HSC. Pathways and differential expression genes analysis show that NrasG12D and NA proteins enhance the competitiveness of HSCs via distinct signaling mechanisms.

overall_design: To analyzes the transcriptome of NA, NrasG12D and wild type (Ctr) mice HSC, one thousand HSCs of each cell type are sorted for RANseq analysis referred to published protocol (PMID:20203668)

first: Jinyong

last: Wang


title: DNA accessibility is not the primary determinant of chromatin-mediated gene regulation (yeast II)

first: Razvan

last: Chereji

overall_design: 8 samples

first: Peter

last: Eriksson

first: Josefina

last: Ocampo

first: David

last: Clark


title: Genome-wide analysis of enhancer-related DNA methylation in myelofibrosis reveals ZFP36L1 as a potential tumor suppressor gene

city: PAMPLONA

first: Marien

last: Pascual

state: NAVARRA

address: AVDA. PIO XII, 55, LAB 1.04

department: Hemato-Oncology

country: Spain

institute: CIMA, Universidad de Nacarra

type: Methylation profiling by genome tiling array

summary: In this study we have interrogated the DNA methylome of myelofibrosis (MF) patients using high-density DNA methylation arrays. Interestingly, primary and secondary MF showed no differences in DNA methylation profiles, whereas a total of 35,238 differentially methylated CpGs (DMC) corresponding to 10,904 genes were detected between MF patients and healthy controls. Remarkably, the majority of DMCs were located outside gene promoter regions and significantly associated with enhancer regions. This enhancer aberrant hypermethylation showed a negative correlation with the expression of 27 genes in the MF patient cohort. Of these, we focused on ZFP36L1 gene and validated its decreased expression and enhancer DNA hypermethylation in an independent cohort of MF patients and myeloid cell-lines. In vitro reporter assay and 5’ azacitidine treatment confirmed the functional relevance of the intronic-enhancer hypermethylation of ZFP36L1. Finally, in vitro rescue of ZFP36L1 expression had an impact in cell proliferation and induced apoptosis in SET-2 cell line indicating a possible role of ZFP36L1 as a tumor suppressor gene in MF. Overall, we describe for the first time the MF DNA methylation profile, showing enhancer DNA hypermethylation as a potential functional mechanism playing an important role in silencing of a tumor suppressor gene in this disease.

overall_design: Samples and patient data were provided by the Biobank of the University of Navarra and were processed following standard operating procedures approved by the local Ethics & Scientific Committee. All patients consented prior to sample extraction and for the use of stored material for research purposes. MF patient samples cohort (n=39) was composed of either bone marrow (BM) or peripheral blood (PB) total mononuclear cells. Among the MF cohort there were primary MF (n=22), MF post-ET (n=7) or MF post-PV (n=10). PB total mononuclear cells from healthy donors (n=6) were used as control samples in this study. All patients were diagnosed using the 2008 version of the World Health Organization (WHO) classification system of hematological malignancies.

first: Nicolás

last: Martínez-Calle

first: Raquel

last: Ordoñez

first: Xabier

last: Agirre

first: Felipe

last: Prosper


title: DNA accessibility is not the primary determinant of chromatin-mediated gene regulation (mouse)

overall_design: Nuclei were prepared from homogenised liver and digested with increasing amounts of the restriction enzyme AluI.


title: DNA accessibility is not the primary determinant of chromatin-mediated gene regulation

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

sample_organism:
Saccharomyces cerevisiae
Mus musculus

platform_organism:
Saccharomyces cerevisiae
Mus musculus

overall_design: Refer to individual Series


title: Cynomolgus macaques treated with Divalent-siRNA (Di-siRNA) targeting Huntingtin gene

status: Public on Aug 26 2019

city: Worcester

first: Paul

last: Yan

state: MA

address: 368 Plantation Street

department: RNA Therapeutics Institute

institute: University of Massachusetts Medical School

summary: Examine potential off-target effects of HTT targeting siRNA in cynomologus macaque brains.

overall_design: RNA-seq of brain punches from HTT targeting siRNA treated and non-treated cynomolgus macaques (N=4 per group). Three brain punches were taken from each animal and processed/sequenced as separate samples. Reads were processed and combined for analysis.

first: Athma

last: Pai

first: Julia

middle: F

last: Alterman

first: Anastasia

last: Khvorova


title: Developmental gene expression in Clonorchis sinensis using Custom-fabricated 12K oligonucleotide microarray

city: Seoul

first: Sung-Jong

last: Hong

address: Heukseok-ro

department: Dept. of Medical Environmental Biology

institute: Chung-Ang University

summary: Developmental gene expression patterns (9812 genes) of juvenile and adult C. sinensis were analyzed using a 12K oligonucleotide microarray (a total of 11617 genes). A number of significantly differentially expressed genes having more than 2-fold difference were observed in adult stage compared to juvenile stage. This finding suggests that the expression levels of different gene sets are controlled in C. sinensis for adaptation to environmental change, such as developmental stages.

overall_design: This study was conducted to analyze developmental gene expression profile of 9812 genes between four newly excysted juveniles and three adult worms in C. sinensis using a custom-fabricated 12K oligonucleotide microarray to elucidate how C. sinensis adapts to the mammalian host.

first: Won

last: Yoo

first: Tae

last: Kim


title: Long noncoding RNA profiling in HUVEC stimulated with IL-1β.

city: Toronto

first: Jason

last: Fish

state: ON

address: 101 College Street

country: Canada

institute: University Health Network

summary: The purpose of this study was to identify long noncoding RNAs (lncRNAs) that are dysregulated during vascular inflammation and contribute to mRNA regulation. Previous studies have suggested that many lncRNAs interact with protein complexes to regulate their neighboring mRNAs. Therefore, we performed the Human LncRNA Expression Microarray V3.0 (Arraystar) to simultaneously profile the expression of lncRNAs and mRNAs under basal conditions and upon stimulation with IL-1β in human umbilical vein endothelial cells (HUVECs). Following, we identified neighboring IL-1β mRNA-lncRNA pairs and found them to be highly correlation in expression. This observation was particularly true when the pairs were found within the same chromatin neighborhood. We also observed mRNA-lncRNA pairs to be mainly divergent transcribed and share common regulatory elements.

overall_design: RNA was extracted from human umbilical vein endothelial cells (HUVECs) that have either been left unstimulated or have been stimulated with IL-1β (10ng/ml) for 4 hours or 24 hours or for 24 hours followed by a period 24 hour cytokine withdraw. Reverse transcription was performed to obtain cDNA from 1ug of RNA. The cDNA was than hybridized to the Human LncRNA Expression Microarray V3.0 (Arraystar) which has probes for approximately 30,586 lncRNAs and 26,109 coding transcript.

first: J

middle: E

first: N

last: Khyzha


title: DNA accessibility is not the primary determinant of chromatin-mediated gene regulation (yeast)

first: Razvan

last: Chereji

summary: DNA accessibility is thought to be of major importance in regulating gene expression. Here we test this hypothesis, using a restriction enzyme as a probe of chromatin structure and as a proxy for transcription factors. We measured the digestion rate and the fraction of accessible DNA at all genomic AluI sites in budding yeast and mouse liver nuclei. Hepatocyte DNA is more accessible than yeast DNA, consistent with longer linkers between nucleosomes. Remarkably, AluI sites in inactive mouse promoters are accessible in some cells. Furthermore, heterochromatin and euchromatin have very similar accessibilities. Cell-to-cell heterogeneity in DNA accessibility has implications for chromatin models of gene regulation: a transcription factor binding site is blocked in some cells, but not in all cells, guaranteeing neither activation nor repression.

overall_design: Nuclei were prepared from the cells and digested with increasing amounts of the restriction enzyme AluI.  Sample 77P_1_gDNA represents genomic DNA digested overnight with 20U AluI.

first: Peter

last: Eriksson

first: Josefina


title: Digitoxin Inhibits Epithelial-to-Mesenchymal-Transition in Hereditary Castration Resistant Prostate Cancer

first: Clifton

middle: Lee

last: Dalgard

address: 4301 Jones Bridge Road B2038

department: Anatomy Physiology & Genetics

institute: Uniformed Services University

summary: We have previously reported that the cardenolide drug digitoxin blocks TNFα/NFκB-driven proinflammatory signaling. We therefore hypothesized that digitoxin might break the collaborative process between NFκB and TGFβ by also inhibiting expression of TGFBR2. We therefore tested whether TGFβ-driven EMT and resulting metastases would be suppressed.

overall_design: Digitoxin-treated and vehicle-only treated rats were stratified on the basis of serum IL-6 and serum CINC-1.  High serum marker control animals and low serum marker digitoxin-treated animals were used as subjects for differential expression profiling of micropunched primary tumor tissue by mRNA-seq profiling and analysis.

middle: L

first: Harvey

last: Pollard


title: Astrocyte morphogenesis is dependent on BDNF signaling via astrocytic TrkB.T1

city: Blacksburg

first: Michelle

middle: L.

last: Olsen

state: VA

address: 970 Washington Street SW

department: School of Neuroscience

institute: Virginia Polytechnic and State University

summary: Astrocytic morphogenesis and maturation are critical steps in CNS development. The time window of astrocyte morphological development is well defined, but the molecular underpinnings are still unclear. BDNF is a critical growth factor involved in the development of the CNS, including synapse refinement. Here we demonstrate the BDNF receptor at Ntrk2  is enriched in astrocytes relative to all CNS cell populations. RNA sequencing indicates Ntrk2 falls in the top 0.001% of all gene transcripts expressed in juvenile astrocytes, almost exclusively due to truncated TrkB.T1. Astrocyte complexity is increased in the presence of BNDF in vitro, which is dependent upon the presence of TrkB.T1. Furthermore, deletion of TrkB.T1 in vivo revealed astrocytes with significantly reduced volume and branching complexities. Indicating a role for functional astrocyte maturation via BDNF/TrkB.T1 signaling, TrkB.T1 KO  astrocytes do not support normal excitatory synaptogenesis. Together, these data suggest a significant role for BDNF/TrkB.T1 signaling in astrocyte morphogenesis and indicate this signaling may contribute to astrocyte regulation of neuronal synapse development.

overall_design: Wild-type (WT) males were bred with heterozygous Mecp2tm1.1Jae/+ (Jaenisch) female mice. Astrocytes were acutely isolated from whole cortex as previously described (Holt and Olsen, 2016)) from WT males ranging from postnatal days 25-31. An n of 5 biological replicates were used. For RNA-Sequencing, 2 technical replicates were run per biological replicate.

first: Natasha

last: Pacheco


title: Dynamics of mitochondrial DNA methylation in oocytes, embryos and granulosa cells

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

institute: Université Laval

summary: Comparison of mitochondrial DNA (mtDNA) methylation patterns in oocytes, blastocysts and ovarian granulosa cells indicates hitherto unsuspected dynamics. Oocytes and blastocysts recovered from animals subjected to ovarian stimulation and from abattoir ovaries were analyzed using bisulphite transformation of DNA followed by whole genome sequencing. The number of mtDNA copies is quite high in oocytes (200–400,000) and early embryos, resulting in very high coverage (> 3000 X) and very low p values for each of 716 cytosine-based nucleosides. Methylation was lowest in oocytes, following by blastocysts then granulosa cells and was not restricted to CpG sites but found also at CHG and CHH sites not distributed randomly. Analysis of the corresponding genomic DNA also revealed numerous methylated CHG and CHH sites, particularly in oocytes. In association with ovarian stimulation, mtDNA methylation was lower in oocytes than in blastocysts, suggesting a developmental function. RNA analysis of mitochondria encoded genes showed a significant inverse correlation between methylation and expression level for all sequences. Methylation was more extensive in mature animals than in pre-pubertal animals and the profile in granulosa cells differed strikingly from those in oocytes and blastocysts. Although preliminary, the results suggest that mtDNA methylation might play a role during gametogenesis and might be subject to regulation according to animal environment and/or age.

overall_design: Six samples were analysed in a single replicate with the OPU and Old condidered as good conditions and the abattoir and young as less optimal conditions.


title: Quantitative Analysis of Telomeric Nucleosomal Compaction following ATRX Depletion

city: New york

first: Jihye

last: Paik

address: 1300 York Ave.

department: Pathology

institute: Weill Cornell Medical College

summary: The goal of this experiment is to determine the effect of ATRX depletion on telomeric chromatin compaction. We adapted the ATAC-seq to quantify telomere chromatin accessibility. By scoring the ratio of sequence reads that contained 3 - 12 tandem telomeric repeats over the total number of reads in wild-type and ATRX deplted cells, our analysis revealed that CRISPR/Cas9-mediated ATRX depletion induces a progressive telomere de-compaction.

overall_design:
ATACseq profiles of wild-type control and ATRX-depleted human IMR90 or BJ fibroblast cells were generated by deep sequencing, in duplicate, using Illumina NEXTSeq 500. The sequence reads that contained 3 - 12 tandem telomeric repeats in wild-type and respective ATRX deplted cells were scored. The ratio of telomere reads over the total number of reads were used to quantify the telomereic nucleosomal compaction.
-----------------------------------------------
Authors state "The processed data is what we used for generating the figure of our manuscript. It is telomeric repeat sequence that cannot be processed in the form or wig, bedgraphs or peak files. Only useful data files in fact fastq and excel files we provided."

first: Fei

last: Li

first: Hongwu

last: Zheng


title: Glioblastoma multiforme cancer stem cells from different patients exhibit consistent gene expression and mechanical phenotypes across distinct states in culture

city: Dresden

first: Andreas

last: Androutsellis-Theotokis

address: Fetscherstr. 74

department: Department of Internal Medicine III

institute: University Hospital Carl Gustav Carus at the Technische Universität Dresden

summary: Cancer stem cells are responsible for the regenerative properties of tumors, manifested as recurrence and metastasis. They can adopt different states, some of which may not be sensitive to current therapies. Modeling distinct states in culture will contribute towards efficient drug discovery. We previously demonstrated that putative cancer stem cells from multiple glioblastoma patients can be efficiently maintained under different signal transduction states by means of different culture conditions; each state is marked by different levels of STAT3 phosphorylation and Hes3 expression. Here we perform global gene expression and mechanical analyses on three primary cell lines to better characterize each state and to address their broad relevance. We report consistent gene expression profiles and mechanical phenotypes among the three lines across different states. Our data argues for the use of specific culture conditions to model distinct states, all of which may be useful in therapeutic design.

overall_design: RNA-seq data from triplicated samples of different human glioblastoma multiforme primary cancer stem cell lines grown under three different culture conditions.

first: Steven

last: Poser

first: Mathias

last: Lesche

last: Dahl

first: Yan

last: Ge

first: Carlo

last: Cannistraci


title: The Molecular Landscape of ETMR at Diagnosis and Relapse [gene expression]

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

institute: German Cancer Research Center DKFZ

summary: ETMRs are aggressive pediatric embryonal brain tumors with universally dismal outcome. We collected 193 ETMR samples and an additional 23 matched relapses to investigate the genomic landscape of this distinct entity. We found that patients having tumors without C19MC amplification, the proposed driver, frequently harbor DICER1 germline mutations or other miRNA-related aberrations such as somatic miR-17-92 miRNA cluster amplifications. Despite these distinct genetic aberrations, no molecular subgrouping was observed. Whole-genome sequencing revealed an overall low recurrence of SNVs, but prevalent R-loop-associated chromosomal instability, of which we show that this can be induced by loss of DICER1 function. Comparing primary tumors and matched relapses revealed a strong conservation of SVs but low conservation of SNVs. Moreover, many newly acquired SNVs are associated to a new cisplatin treatment related mutational signature. Finally, we show that targeting R-loops with topoisomerase and PARP inhibitors might be an effective treatment strategy for this deadly disease.

overall_design: RNA was extracted from fresh frozen tumor material of 28 different ETMR patients and profiled on Affymetrix Human Genome U133 Plus 2.0 arrays to study the general gene expression patterns defining ETMRs and to compare this to other entities.

first: Sander

last: Lambo


title: The Molecular Landscape of ETMR at Diagnosis and Relapse


title: CNV Polymorphisms Modulate the Expression of GST Subtypes in the Human Small Airway Epithelium and Alveolar Macrophages

city: New York

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

department: Department of Genetic Medicine

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

summary: The glutathione S-transferase (GST) gene family codes for enzymes that detoxify xenobiotics by catalyzing the conjugation of xenobiotics to glutathione. Based on reports that inherited copy number variations (CNV) in the genome modulate some GST expression levels and with the knowledge that cigarette smoke contains >3000 xenobiotics, and that the small airway epithelium and alveolar macrophages are involved early in the pathogensis of smoking-induced lung disease, we asked: do germline CNVs modulate GST expression level in the small airway epithelium and alveolar macrophages? Affymetrix HG U133 Plus 2.0 microarrays were used to survey GST gene expression in the small airway epithelium and alveolar macrophages obtained by bronchoscopic brushings from current smokers (n=35) and nonsmokers (n=35). The CNV genotypes of these 70 subjects were determined by Affymetrix Human SNP array 5.0 chips. Sixteen % of subjects had deletions of both GSTM1 alleles. These deletions were associated with reduced GSTM1 mRNA levels in both the small airway epithelium (p<10-7) and alveolar macrophages (p<0.05). Thirty % of subjects had homozygous deletions of GSTT1 with concomitant reduced mRNA levels in both small airway epithelium and alveolar macrophages (p<10-7). In contrast, genes flanking the CNV regions of both GST genes showed no difference in expression level among subjects with and without the GST deletions (p>0.3). Interestingly, GSTT2B, a duplicate gene of GSTT2, exhibited homozygous deletion in blood in 27% of subjects and was not expressed in small airway epithelium in the remainder of subjects  but was expressed in alveolar macrophages of heterozygotes and wild type subjects, proportionate to genotype (p<10-3). These data demonstrate that highly prevalent CNV deletions of  genes critical to ameliorating smoking-associated xenobiotic-induced damage in the lung can result in significant modulation of the gene expression levels, with the linear relationship of genotype to expression level suggesting minimal compensation of gene expression levels in heterozygotes consistent with GST polymorphisms playing a role in the risk for development of smoking-induced lung disease.

overall_design: Small airway epithelium (from 35 healthy nonsmokers and 35 healthy smokers) and alveolar macrophages (from a subset of the 70 subjects: 22 nonsmokers and 34 smokers) were collected at bronchoscopy, and in conjunction with their blood samples, were used to assess the influence of common heritable copy number polymorphisms in glutathione S-transferase (GST) genes, on microarray and RT-PCR-assessed GST gene expression in human tissues that are relevant to the pathogenesis of smoke-induced lung disease.

first: Marcus

middle: W

last: Butler

first: Neil

last: Hackett

first: Jacqueline

last: Salit

first: Ronald

last: Crystal


title: Small RNA sequencing in cell and extracellular vesicles (EVs) of breast cancer 4T1 and 4TO7 cells

status: Public on Aug 25 2019

city: Kowloon

first: Minh

middle: TN

last: Le

state: Hong Kong

address: Tat Chee Avenue, Kowloon Tong

department: Biomedical Sciences

institute: City University of Hong Kong

summary: RNA was purified from 4T1 and 4TO7 cells and their EVs

overall_design: Small RNA were compared in 4 samples, 2 cellular RNAs and 2 EV RNAs


title: mRNA gene expression profiling in a human AML cell line treated with small molecule inhibitors that impact different RNA polymerase transcription complexes, or their combination, in comparison to a global DNA-damaging anthracycline compound

city: Grattan St.

first: Gretchen

last: Poortinga

state: Victoria

department: Division of Cancer Research

institute: Peter MacCallum Cancer Centre

summary: Our results confirmed that CX-5461, a Pol I inhibitor, does not significantly impact mRNA expression at 6 hrs, while I-BET151 alone, known to inhibit MYC and expression of other oncognes, resulted in widespread changes in select gene expression programs as previously demonstrated (Dawson et al., 2011). Interestingly, the combination of CX-5461 and I-BET151 demonstrated no further gene expression changes from I-BET151 alone, suggesting that their mechanism of synergy is more likely directly associated with the CX-5461-mediated DNA damage response. Further, the mRNA gene expression changes following drug combination treatment are distinct from those following doxorubicin treatment, supporting that the synergistic effects of the novel combination of CX-5461 and I-BET151 do not rely on global DNA damage.

overall_design:
Comparative gene expression profiling of the acute myeloid leukemia (AML) MV4-11 cells treated with the novel small molecule inhibitor CX-5461 (Pol I-mediated transcription inhibitor) or I-BET151 (BET protein inhibitor) or their combination, in comparison to treatment with the DNA damaging anthracycline doxorubicin.
We use 3' gene expression profiling to characterise transcriptional programs associated with acute response (6 hour) to treatment with the single agents CX-5461 and I-BET151, representing inhibitors of Pol I and Pol II transcription, respectively, or their combination in the p53 wt MV4-11 acute myeloid leukaemia (AML) cell line. This was in comparison to 2 hr treatment with IC90 doxorubicin, a DNA damaging agent representing the anthracycline class of drug used in standard AML treatment.

first: Sornkom

last: Jirawas

first: Poortinga

last: Gretchen


title: High-throughput sequencing reveals change of microRNA expression caused by allopolyploidization in Cucumis

city: Nanjing

first: Xiaqing

last: Yu

address: Weigang No.1

institute: Nanjing Agricultural University

summary: Allopolyploidy is long recognized as an essential driving force in plant evolution. Recent studies have demonstrated that small RNAs, including microRNAs (miRNAs), play important roles in the process of allopolyploidy. However, the question that how the distinct parent-of-origin miRNAs are maintained in allopolyploids and how these small RNAs affect gene expression and phenotypes remain to be answered. Therefore, we investigated the miRNA expression profiles of a synthesized allotetraploid, Cucumis ×hytivus and its parents. The different developmental stages of leaves of C. ×hytivus showing contrasting leaf colour were compared as well. Following high-throughput sequencing, 546 conserved and 287 novel miRNAs were identified. The expression levels of nine miRNAs obtained by quantitative real-time PCR were consistent with the sequencing results. We detected that 15 miRNAs were divergently expressed between the parent species, and 23 miRNAs were differentially expressed in C. ×hytivus compared to either of its parents or both, which suggests the significant effect of allopolyploidization on miRNAs accumulation. Additionally, 26 conserved and 13 novel miRNAs differed in expression between the young and mature leaves of C. ×hytivus, indicating an essential role of miRNA-mediated regulation of leaf development following allopolyploidization. This study enriches the context of allopolyploidy effect on miRNAs and lays a foundation for the elucidation of the miRNA-mediated regulatory mechanism in phenotypic variation in allopolyploids.

sample_organism:
Cucumis sativus
Cucumis hystrix
Cucumis x hytivus

overall_design: This study enriches the context of allopolyploidy effect on miRNAs and lays a foundation for the elucidation of the miRNA-mediated regulatory mechanism in chlorophyll biosynthesis.

first: Zaobing

last: Zhu

first: Tinglin

last: Zhang

first: Ji

last: Li

first: Chunyan

last: Cheng

first: Qunfeng

last: Lou

first: Carl-Otto

last: Ottosen

first: Jinfeng

last: Chen