title: Tumor Suppressor TSC1 Negatively Regulates Polo-like Kinase Expression and Controls the Balance of Schwann Cell Proliferation and Differentiation

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

summary: Activation of mTOR signaling by Tsc1 ablation during early developmental stages increases SC proliferation and delays radial sorting, while causing hypomyelination in the PNS. However, knockout Tsc1 in myelinating SCs at postnatal stages promotes myelin overgrowth and outfoldings. Sustained mTOR pathway leads to activation of the PLK signaling pathway. mTOR attenuation or pharmacological inhibition of PLK1 could partially rescue myelination defects in Tsc1 mutant sciatic nerves. Our data suggest that TSC1-mTOR maintains the homeostasis of SC proliferation and differentiation in a stage-specific manner.

overall_design: Gene expression profiling of sciatic nerve from P7 control and Tsc1cKO mice

first: Minqing

last: Jiang

first: Qing

middle: R


title: Single Cell and Open Chromatin Analysis Reveals Molecular Origin of Epidermal Cells of the Skin

status: Public on Sep 05 2018

city: Aurora

first: Xiying

last: Fan

state: CO

department: Dermatology

country: USA

institute: University of Colorado Anschutz Medical Campus

type: Expression profiling by high throughput sequencing

summary: Skin and its appendages such as hair follicle and sweat gland are formed by Keratin-5 expressing (Krt5+) epidermal cells that are specified from primitive, Keratin-8 expressing (Krt8+) ectodermal progenitors shortly after gastrulation. Here we show that transcription factor ∆Np63 is required for converting Krt8+ ectodermal progenitors to Krt5+ epidermal progenitors and priming the underlying dermal cells to form dermal condensate by activating the Wnt/ß-Catenin pathway. These findings unearth the molecular cascades during the fate specification of epidermal cells, illuminate the essential role of ∆Np63 in initiating the Wnt signaling in the epidermis and programming the underlying dermal cells and provide new possibilities to harness the intrinsic developmental program for generating the skin and its appendages.

overall_design: Single Cell RNA-seq on early epidermis  isolated from  Ctrl and P63KO mice.

first: Dongmei

last: Wang

first: Jeremy

middle: E

last: Burgmaier

first: Yudong

last: Teng

first: Rose-Anne

last: Romano

first: Satrajit

last: Sinha

first: Rui

last: Yi


title: Expression data from Csf1r deficient rats

status: Public on Sep 06 2018

city: Edinburgh

first: Clare

last: Pridans

address: 47 Little France Crescent

department: University of Edinburgh

country: United Kingdom

institute: Centre for Inflammation Research

summary:
We used microarray to examine changes in gene expression in the absence of Csf1r in the brain and spleen.
Spleen gene expression was compared to BMDM to identify splenic-specific genes.

overall_design: RNA was isolated from spleen, hippocampus, striatum, olfactory bulbs, pituitary glands and bone marrow derived macrophages.

first: David

middle: A

last: Hume


title: HOXA9 Reprograms the Enhancer Landscape During Leukemic Transformation

city: Ann Arbor

first: Yali

last: Dou

state: MI

address: 1301 Catherine Street

department: Pathology Department

institute: University of Michigan

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Expression data of the control and CITED1 OE ESCs

status: Public on Sep 01 2018

city: Shanghai

first: Yanli

last: Xu

state: Shanghai

address: 320 Yue Yang Road

country: China

institute: Shanghai Jiao Tong University School of Medicine

summary:
Trophoblast lineages, as the precursor of placenta, are essential for post-implantation embryo survival. However, the regulatory networks for trophoblast development remains incompletely understood. Here, we identified CITED1 as a regulator to induce trophoblast-like differentiation from mESCs. Overexpression of CITED1 in ESCs prompted differentiation towards trophoblast accompanying with elevated expression of trophoblast marker genes. To evaluate the ability of CITED1 to induce trophoblast differentiation at a genome-wide scale, we compared the global transcriptional profiles between CITED1 overexpressing cells and control ESCs by Affymetrix microarray analysis at day 1 and day 2 after transfection.
We used microarrays to identify genes affected by CITED1 overexpression in mouse ESCs.

overall_design: E14T ESCs were transiently transfected with plasmids expressing CITED1 or empty vector pPy. 8 hours later, ESCs were selected by puromycin at the final concentration of 2 ug/mL, and then collected for RNA isolation. In total, 15 RNA samples were prepared from three independent biological triplicates. Microarray was carried out with the Affymetrix GeneChip® Mouse Genome 430 2.0 Arrays. The procedures including RNA extraction, cDNA synthesis, labeling, hybridization, washing, and scanning were conducted according to the standard Affymetrix protocol by the Shanghai Biotechnology Corporation.

first: Xinlong

last: Luo

first: Hui

last: Li


title: Metformin induces chromosome reorganization and changes in gene expression in normal human fibroblasts

city: Saskatoon

first: Christopher

middle: H.

last: Eskiw

state: SK

address: 51 Campus Drive

department: Food and Bioproduct Science

country: Canada

institute: University of Saskatchewan

summary: We report the effects of metformin treatment on the transcriptome of normal human dermal fibroblasts isolated from foreskin (designated 2DD). We sequenced mRNA from 2 replicates of proliferative (PRO) and 2DD cells treated with two concentrations of metformin (0.5mM and 1.0 mM;5 days exposure). Comparative analyses with PRO transcripts a baseline indicate that fibroblsts exposed to different concentration of metformin result in differnetial transcript profiles.

overall_design: Examination of mRNAs from proliferative and metformin treated (0.5mM and 1.0 mM for 5 days) 2DD normal human dermal/foreskin fibroblasts.

first: Z

last: Gillespie

first: K

last: MacKay

first: A

last: Kusalik

first: C

middle: H


title: Spo11-oligo mapping in S. cerevisiae  red1, hop1, mek1 mutants

city: New York

first: Isabel

last: Lam

state: New York

address: 1275 York Avenue

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

summary: Meiotic recombination starts with the formation of DNA double-strand breaks (DSBs) made by Spo11. In Saccharomyces cerevisiae, the nonrandom distribution of meiotic DSBs along the genome can be attributed to the combined influence of multiple factors on Spo11 cleavage. One factor is higher-order chromatin structure, particularly the loop-axis organization of meiotic chromosomes. Axial element proteins Red1 and Hop1 provide the basis for meiotic loop-axis organization and are implicated in diverse aspects of meiotic recombination. Mek1 is a meiotic-specific kinase associated with Red1 and Hop1. Red1, Hop1, and Mek1 are required for normal DSB levels, but their effects on the DSB distribution has not been examined, and exactly how these proteins influence DSB levels and distribution is unknown. Here, we examined the contributions of Red1, Hop1, and Mek1 to the DSB distribution by deep sequencing and mapping Spo11-associated oligonucleotides from red1, hop1, and mek1 mutant strains, thereby generating genome-wide meiotic DSB maps.

overall_design: Six samples total: two biological replicates each of Spo11-oligo maps of S. cerevisiae SK1 red1, hop1,  and mek1 null mutants

first: Scott

last: Keeney


title: Functional TDP-43 amyloids bind sarcomeric mRNA to direct skeletal muscle formation

first: Aaron

middle: M

last: Johnson

address: 12801 E 17th Ave Research 1 South L18-10402G

department: Biochemistry and Molecular Genetics

institute: University of Colorado Denver

summary: Cytoplasmic aggregates of TDP-43 are found in neuronal and skeletal muscle diseases yet it is not understood how these protein aggregates relate to the biological function of TDP-43. By examining normal skeletal muscle formation, we discovered TDP-43 redistributes from the nucleus into the cytoplasm and forms higher-ordered aggregates. These skeletal muscle TDP-43 aggregates adopt an amyloid-like structure capable of binding RNA. In skeletal muscle, TDP-43 binds UG-rich, sarcomeric mRNAs and oligomerizes on these long mRNA transcripts facilitating amyloid formation. Tissue specific genetic deletion of TDP-43 in skeletal muscle disrupts the formation and maintenance of the sarcomere and mislocalizes sarcomeric mRNAs. Thus, cytoplasmic, amyloid-like TDP-43 aggregates that traffic mRNAs could serve as a precursor to pathological TDP-43 aggregates common in degenerative neuromuscular disease.

overall_design: eCLIP-seq in mouse C2C12 cells

first: Eric

middle: D

last: Nguyen

first: Joshua

last: Wheeler

first: Thomas

middle: O

last: Vogler


title: LIX48 (H37Ra-devR overexpression) versus LIX47 (control strain) and LIX50 (H37Rv-devR overexpression) versus LIX49 (control strain)

status: Public on Aug 31 2018

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

summary: Transcription analysis of M. tuberculosis H37Ra devR overexpressing strain (LIX48) versus empty vector control strain (LIX47);  H37Rv devR overexpressing strain t (LIX50) versus empty vector control strain (LIX49) to study the effect of DevR overexpression

overall_design: Two color Experiment,Organism: Mycobacterium tuberculosis

first: Vandana

last: Malhotra

first: Atul

last: Vashist

first: Gunjan

last: Sharma

first: Jaya

last: Sivaswami Tyagi

first: Josephine

last: Clark-Curtiss


title: Unravelling adaptive mechanisms to H2O2 in Candida glabrata using laboratory adaptive evolution

city: College Station

first: Katy

last: Kao

state: Texas

address: 3122 TAMU Room 200

department: Chemical Engineering

institute: Texas A&M University

summary: Transcriptome analysis of C. glabrata mutants evolved for improved tolerance to H2O2.

overall_design: Both mutant and parental reference were challenged with 1 mM of H2O2 for 30 minutes at 30°C during exponential growth (OD600 between 0.4 and 0.6), two biological replicates per sample, reference is unevolved parent strain for each mutant.

first: Mian

last: Huang

middle: C


title: Whole transcriptome analysis of human macrophages infected with H5N1 and H1N1 influenza viruses reveals the significant up-regulation of RIG-I-like receptor signaling pathway

city: Notre Dame

first: Yunjuan

last: Bao

state: Indiana

address: 1234 Notre Dame Avenue

institute: University of Notre Dame

type: Non-coding RNA profiling by high throughput sequencing


title: DNMTs and SETDB1 function as co-repressors in MAX-mediated repression of germ cell-related genes in mouse embryonic stem cells

city: Sendai

first: Yohei

last: Hayashi

state: Miyagi

address: 4-1 Seiryo-machi, Aobaku

department: Institute of Development, Aging and Cancer

country: Japan

institute: Tohoku University

summary: In embryonic stem cells (ESCs), the expression of development-related genes, including germ cell-related genes, is globally repressed. The transcription factor MAX represses germ cell-related gene expression in ESCs via PCGF6-polycomb repressive complex (PRC)1, which consists of several epigenetic factors. However, we predicted that MAX represses germ cell-related gene expression through several additional mechanisms because PCGF6-PRC1 regulates the expression of only a subset of genes repressed by MAX. Here, we report that MAX associated with DNA methyltransferases (DNMTs) and the histone methyltransferase SETDB1 cooperatively control germ cell-related gene expression in ESCs. Both DNA methylation and histone H3 lysine 9 tri-methylation of the promoter regions of several germ cell-related genes were not affected by knockout of the PRC1 components, indicating that the MAX-DNMT and MAX-SETDB1 pathways are independent of the PCGF6-PRC1 pathway. Our findings provide insights into our understanding of MAX-based repressive mechanisms of germ cell-related genes in ESCs.

overall_design: L3mbtl2-KD was performed in VV3 ESCs. Total RNA (100 ng) was isolated and purified using an RNeasy micro kit (Qiagen). The quality and quantity of purified total RNA were verified by Agilent 2100 Bioanalyzer (Agilent) and NanoDrop ND-1000 (Thermo Fischer Scientific), respectively. DNA microarray analysis was carried out according to manufacturer’s instruction. In brief, cyanine3-labelled cRNA was obtained from 100 ng of purified total RNA using a Low Input Quick Amp Labeling kit (Agilent). The cRNA was purified, fragmented and then hybridized to an Agilent Whole Mouse Genome Oligo DNA Microarray kit, Ver 2.0 (Agilent) containing over 44,000 probe sets for mouse genes. Following hybridization at 65°C for 17h, the arrays were washed and fluorescence signals were scanned using an Agilent DNA microarray scanner. Agilent Feature Extraction software was used to reduce the array images to the intensity of each probe (TXT files). Each cell type was analyzed in four biological replicates.

first: Daiki

last: Tatsumi

first: Mai

last: Endo

first: Hisato

last: Kobayashi

first: Takumi

last: Yoshioka

first: Kohei

last: Kiso

first: Shinichiro

last: Kanno

first: Yuji

last: Nakai

first: Ikuma

last: Maeda

first: Kentaro

last: Mochizuki

first: Makoto

last: Tachibana

first: Haruhiko

last: Koseki

first: Akihiko

last: Okuda

first: Akira

last: Yasui

first: Tomohiro

last: Kohno

first: Yasuhisa

last: Matsui


title: microRNA expression profiling in human brain glioblastoma

city: shanghai

first: chun

last: luo

address: 415# fengyang road

department: neurosurgery

institute: changzheng hospital

summary: The expression profiling of a total of 2085 microRNAs in 5 glioblastoma and 5 normal brain cases, which had been consecutively operated on within a defined short period of time

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: In the study presented here, 5 glioblastoma and 5 normal brain tissues were used to acquire expression profiles of a total of 2085 microRNAs. The same RNA samples were used for the mRNA and lncRNA study (GSE103227).

first: Chun

last: Luo

first: Jingliang

last: Ye


title: Whole transcriptome analysis of human macrophages infected with H5N1 and H1N1 influenza viruses reveals the significant up-regulation of RIG-I-like receptor signaling pathway [mRNA]

first: Yunjuan

last: Bao

summary: We generated an average of 868 million nucleotides and 30 folds coverage per sample. More than 76% of the sequencing reads were mapped to the human genome, and 45.5% of the annotated reference genes were mapped by at least 10 reads. Differential expression quantification showed that H5N1 virus elicits greater changes in host gene expression than the H1N1 virus at nearly all three time points with 1198,273,and 620 up-regulated in H5N1, and 426,285, and 523 in H1N1 compared with mock control (fold-change >= 2.0, and p-value <= 0.05). Pathway over-representation analysis revealed that the up-regulated genes in H5N1 are significantly enriched by genes involved in RIG-I-like receptor signaling pathway at 6-hr post-infection.

overall_design: We studied the whole transcriptome of a highly pathogenic influenza virus H5N1 and a low virulent H1N1 in human monocyte-derived macrophages at 1-, 3-, and 6-hr post-infection to identify the molecular events  leading to virus pathogenesis at early infection stages by comparing with the mock infected cells.

last: Zhang

first: Yun-Juan

first: Amy

last: Tong

first: Lok

last: Si

first: Suki

last: Lee


title: miRNA profiling of small intestinal neuroendocrine tumors defines novel molecular subtypes and identifies miR-375 as a biomarker of patient survival

city: Göteborg

first: Anna

last: Rehammar

address: Chalmers Tvärgata 3

department: Department of Mathematical Sciences

country: Sweden

institute: Chalmers University of Technology

summary: The aim of this study was to define the miRNA profile of SI-NETs and search for novel molecular subgroups and prognostic biomarkers.

overall_design: miRNA profiling was conducted on 42 tumors from 37 patients who underwent surgery for SI-NETs.

first: Yvonne

last: Arvidsson

first: Anders

last: Bergström

first: Ellinor

last: Andersson

first: Christina

last: Swärd

first: Bo

last: Wängberg

first: Erik

last: Kristiansson

first: Ola

last: Nilsson


title: mRNA, lncRNA and microRNA expression profiling in human brain glioblastoma

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


title: NPR1 REGULATES COLD ACCLIMATION VIA NOVEL INTERACTION WITH HSFA1s TRANSCRIPTION FACTOR FAMILY PROTEINS

city: MADRID

first: EMA

middle: YOLANDA

last: OLATE

state: MADRID

address: RAMIRO DE MAEZTU 9

department: MOLECULAR BIOLOGY

country: Spain

institute: CIB-CSIC

summary: We report novel function of NPR1 coactivator that regulates cold acclimation by promoting cold-induced gene expression.

overall_design: Comparison of transcriptomes from Col-0 and npr1-1 plants exposed to low temperature

first: Ema

last: Olate-Rodriguez

first: Jose

last: Jiménez-Gómez

first: Loreto

last: Holuigue

first: Julio

last: Salinas


title: Subtle asymmetry of gene expression in embryonic and foetal human brains

city: Nijmegen

first: Clyde

last: Francks

address: Wundtlaan 1

department: Language & Genetics

country: Netherlands

institute: Max Planck Institute for Psycholinguistics

summary: Note: this project is a combination of the data deposited here in  GEO and data made available by HDBR in ArrayExpress under E-MTAB-4840. Summary: Brain asymmetry in humans, both structurally and functionally, is observed very early during development, and is important for healthy development. Using RNA sequencing, we investigated gene expression profiles of left and right sides of various brain structures in human foetuses aged 5 to 13 weeks post conception. All brain structures showed significant differences between the expression profiles of left and right sides. The differences partly correlated with gene expression changes with age, suggesting left/right differences in maturation rate. In particular on the faster side (right for cerebral cortex, left for all other investigated tissues), different tissues were lateralised for tissue-specific processes. In the youngest forebrain (5.5 weeks), KCTD12, SNAI1 and GATA1 were significantly right-lateralised. SNAI1 is involved in visceral asymmetry in vertebrates, and KCTD12 is important in lateralisation of fish brains. In the youngest midbrain, SOX1 was significantly left-lateralised.

overall_design: For the part of the project for which data are deposited here, six human embryos in Carnegie stage 15 or 16 were studied. Left and right side of the midbrain and left and right side of the forebrain were dissected, and RNA sequenced. Differential expression analysis per tissue to find left/right differences (paired analysis by embryo).

first: Carolien

middle: G

last: de Kovel

first: Steve

middle: N

last: Lisgo

first: Simon

last: Fisher


title: H19 regulates hepatic glucose production by epigenetic modification of Hnf4*

status: Public on Aug 30 2018

city: Farmington

last: Zhang

state: CT

address: 400 Farmington Ave

department: Genetics and Genome Sciences

institute: UConn Health

type: Methylation profiling by high throughput sequencing

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Genome-wide DNA methylation change in mice liver due to overnight fasting

summary: We used Methyl-MiniSeq platform from Zymo Research company to identify genome-wide methylation changes affected by overnight fasting in mice liver. Compared to control mice liver, we observed extensive genome-wide methylation patern changes in fasted mice liver, with some genes showing incresed methylation, others showing decreased methylation, and the rest with no significant change.

overall_design: 12-week-old mice were either untreated or fasted for 12 hr and then sacrificed by ether anesthesia followed by cervical dislocation. Liver samples were collected and snap frozen in liquid nitrogen and stored at -80°C. Genomic DNA was extracted from liver samples and subjected to genome-wide DNA methylation mapping using the platform of an improved version of Reduced Representation Bisulfite Sequencing (RRBS).

first: Karolyn

last: Giang

first: Hunter

last: Chung


title: Expression data from hypothalamus of rats fed omega-3 or omega-6 essential fats

status: Public on Aug 29 2018

city: Guelph

first: David

last: Mutch

state: Ontario

address: 50 Stone Road East

department: Human Health & Nutritional Sciences

institute: University of Guelph

summary:
Omega-3 (n-3) and omega-6 (n-6) polyunsaturated fatty acids (PUFA) have important signalling roles in the hypothalamus, a region of the brain that regulates whole-body energy homeostasis. While evidence suggests that high PUFA intake can impact hypothalamic activity, the underlying molecular mechanisms regulated by essential dietary PUFA (i.e., linoleic acid and alpha-linolenic acid) remain poorly described in this brain region.
To differentiate the roles of essential dietary PUFA on hypothalamic function, we fed male rats high-fat diets (35% kcal/d) containing either safflower (linoleic acid) or flaxseed (alpha-linolenic acid) oil for 2 months. Control rats were fed a low-fat (16% kcal/d) diet containing soybean oil. Hypothalmic gene expression was investigated by microrray.

overall_design: Group comparison


title: Whole Retina RNAseq after injury and Valproic acid (VPA) treatment in zebrafish

city: Mohali

first: Rajesh

last: Ramachandran

state: Punjab

address: Knowledge city, Sector 81, SAS Nagar, Manauli

department: Department of Biological Sciences

institute: Indian Institute of Science Education and Research, Mohali

summary: several genes are being regulated after injury at various time points and after VPA treatment.

overall_design: Examination of uninjured, 12hpi, 4dpi and VPA treated 4dpi retinae with duplicate samples.

first: Soumitra

last: Mitra

first: Simran

last: Kaur


title: Arginine starvation response of Mycobacterium tuberculosis H37Rv ΔargB and ΔargF

city: bronx

first: Sangeeta

last: Tiwari

state: NY

address: 1300 Morris park ave

department: Microbiology and Immunology

institute: Albert Einstein College of Medicine

summary: Time -course transcriptional profiling of arginine starved Mycobacterium tuberculosis H37Rv ΔargB or  ΔargF realtive to day 0 of starvation

overall_design: Two-condition experiment, before starvation vs. either 1 day, 3 days or 6 days after starvation. Biological replicates: 3, one dye flip


title: Histidine-dependent protein methylation is required for compartmentalization of CTP synthase

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

summary:
CTP synthase (CTPS) forms compartmentalized filaments in response to substrate availability and environmental nutrient status. However, the physiological role of filaments and mechanisms for filament assembly are not well understood. Here, we provide evidence that CTPS forms filaments in response to histidine influx during glutamine starvation. CTPS protein levels remained stable in the presence of histidine during nutrient deprivation, followed by rapid cell growth following nutrient replenishment. Tetramer conformation-based filament formation restricted CTPS enzyme activity duringnutrient deprivation.
Furthermore, we demonstrated that filament formation controlled at two levels. Starvation stress/glutamine deficiency activates the GCN2/ATF4/MTHFD2 axis to accelerate the folate cycle in mitochondria for energy homeostasis. In addition, histidine promotes re-methylation of homocysteine by donating one-carbon to the cytosolic folate cycle. CTPS filament formation induced by histidine-mediated methylation maybe a strategy usedby cancer cells to maintain homeostasis and ensure a growth advantage in adverse environments.

overall_design: Cell culture in different medium (DMEM, EBSS and EBSS+Histidine) for 4 h, with two independent experiment

first: Wei-Cheng

last: Lin

first: Archan

last: Chakraborty

first: Pei-Yu

last: Wang

first: Yen-Hsien

first: Chia-Chun

last: Chang

first: Hsiang-Yu

last: Tang

first: Yu-Tsun

first: Chang-Shung

last: Tung

first: Ji-Dung

last: Luo

first: Shih-Chia

last: Huang

first: Tzu-Yang

first: Mei-Ling

last: Cheng

first: Ji-Long

last: Liu

first: Li-Ying

last: Sung

first: Ming-Shi

last: Shiao

first: Jau-Song

last: Yu

first: Yu-Sun

first: Li-Mei

last: Pai


title: mRNA and lncRNA expression profiling in human brain glioblastoma

first: chun

last: luo

summary: The expression profiling of a total of 26109 mRNAs and 30586 lncRNAs in 5 glioblastoma and 5 normal brain cases, which had been consecutively operated on within a defined short period of time.

overall_design: In the study presented here, 5 glioblastoma and 5 normal brain tissues were used to acquire expression profiles of a total of 26109 mRNAs and 30586 lncRNAs. The same RNA samples were used for the miRNA study (GSE103228).

first: Chun

first: Jingliang

last: Ye


title: Genome-wide regulatory architecture maps using ATAC-seq, H3K4me2 ChIP-seq, and PEAT in Drosophila S2 cells and ATAC-seq in whole worms

city: Berlin-Buch

first: Scott

middle: Allen

last: Lacadie

address: Robert-Rössle-Str. 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

summary: To assess the organization of regulatory architecture across organisms, we performed ATAC-seq to identify accessible regions of chromatin, H3K4me2 ChIP-seq to measure regulatory status, and PEAT to measure Transcription start sites of stable transcripts in Drosophila S2 cells. For comparison, ATAC-seq for accessible chromatin measurement was performed in whole stage L3 worms.

sample_organism:
Caenorhabditis elegans
Drosophila melanogaster

first: Uwe

last: Ohler

first: Mahmoud

last: Ibrahim


title: Symbiotic Transcriptome profiling of candidate genes in model legume Arachis hypogaea using Next Generation Sequencing Technology (NGS)

city: Kolkata

first: Maitrayee

last: DasGupta

state: WestBengal

address: 35 Ballygunge Circular Road

department: Biochemistry

institute: University of Calcutta

summary: The Goal of this study is to develop NGS derived Arachis hypogaea root-nodule symbiotic Transcriptome Profile (RNAseq).

overall_design: Differential Gene Expression profile during the progression of symbiosis is generated by deep Sequencing,in triplicate using Illumina HiSeq 2000 platform

last: Dasgupta

first: Fabienne

last: Cartieaux

first: Pierre

last: Czernic

first: Kanchan

last: Karmakar

first: Ahsan Z

last: Rizvi

first: Anindya

last: Kundu

first: Emeric

last: Dubois

first: Sophie

last: Vivier

first: Dany

last: Severac

first: Samia

last: Guendouz

first: Hugues

last: Parrinello

first: Laurent

last: Journot

first: Marine

last: Rohmer

first: Stephanie

last: Rialle


title: Depletion of ZNF185 causes delay of keratinocyte differentiation

status: Public on Aug 26 2018

city: Rome

first: Artem

last: Smirnov

address: Via Montpellier, 1

department: Dept. of Exp. Medicine and Surgery

country: Italy

institute: University of Rome "Tor Vergata"

summary: Development of epidermis includes a complicated program of keratinocyte differentiation. Here we study a new membrane LIM-domain containing Zn-finger protein ZNF185 which is expressed in upper layers of human skin and is up-regulated during keratinocyte differentiation in vitro. Interestingly, depletion of ZNF185 causes delay of keratinocyte differentiation with decreased levels of FLG, LOR, LCEs expression.

overall_design: To study the role of ZNF185 in keratinocyte differentiation, we performed microarray expression profiling to identify the genes which expression is altered. Human normal epidermal keratinocytes (HEKn) we transiently knocked-down by RNA interference and induced for differentiation for 3 days.


title: PTEN deficiency in TNBC provides vulnerability to co-targeting KDM4B and PI3K through over-activation of Unfolded Protein Response pathway

status: Public on Aug 27 2018

city: Singapore

first: Gokce

last: OGUZ

address: 60 Biopolis St, GENOME, #02-01

department: Bioinformatics Consulting and Training Platform

country: Singapore

institute: Genome Institute of Singapore

summary: Analysis of gene expression profiles of three TNBC cell lines (two PTEN deficient, one PTEN wildtype), which are treated with dmso or Methylstat, respectively.

overall_design: Total RNA obtained from three TNBC cell lines (two PTEN deficient, one PTEN wildtype) treated with methylstat are subject to expression microarray analysis using Illumina Gene Expression Sentrix BeadChip HumanHT-12_V4.

first: Wenyu

last: Wang

last: Oguz

first: Puay

middle: L

last: Lee

first: Siti

last: Yatim

first: Qiang

last: Yu


title: ChIP-Seq interscapular brown adipose tissue Prdm16

city: Boston

first: Yi

last: Chen

state: Massachusetts

address: 450 Brookline Ave CLS 11116

institute: Dana-Farber Cancer Institute

summary: We report the binding targets of Prdm16 in interscapular brown adipose tissue

overall_design: ChIp from interscapular brown adipose tissue of C57BL6/J mice with Prdm16 antibody followed by sequencing

first: Zeng

last: Xing

first: Spiegelman

last: Bruce


title: Revealing Mytilus galloprovincialis transcriptomic profile during ontogeny

status: Public on Aug 28 2018

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

institute: University of Padova

summary: Mediterranean mussels are a worldwide spread bivalve species with extraordinary biological success. One of the reasons of this success could be the reproduction strategy of bivalves, characterized by the presence of trochophore larvae. Larval development in bivalves has been a topic of raising interest in the scientific community but it deserves much more attention. The principal objective of this work was to study the transcriptomic profile of the ontogeny of M. galloprovincialis analyzing the gene expression in different developmental stages, from oocytes to seed. For this purpose, after conducting a 454 sequencing of transcriptome of mussel hemocytes, adult tissues and larvae, a new DNA microarray comprising sequences of was designed and developed. The studied developmental stages: unfertilized oocytes, veliger (3 days post fertilization; dpf) and pediveliger (20dpf) larvae, settled juveniles (25dpf) and seed (30dpf), showed very different transcriptomic profiles and clustered in groups defining their characteristic gene expression along ontogeny.

overall_design: Mature mussels were obtained from a commercial shellfish farm in Vigo (NW Spain) during the spawning season. Mussels spawning and larval rearing was performed as detailed in Balseiro et al., 2013. Biological replicates were taken at each developmental stage: oocytes, veliger, pediveliger, settled and seed. Total RNA isolation was conducted following the manufacturer’s specifications in combination with the RNeasy Mini kit (Qiagen) for RNA purification after DNase I treatment. Next, the concentration and purity of the RNA were measured using a NanoDrop ND1000 spectrophotometer. Finally, RNA integrity was tested on an Agilent 2100 Bioanalyzer (Agilent Technologies). Only the samples with high RNA quality and quantity were used for labeling and hybridization. 3 to 5 biological replicates were used for each developmental stage and trochophore samples were discarded due to the low RNA integrity.

first: Milan

last: Massimo

first: Bargelloni

last: Luca

first: Moreira

last: Rebeca

first: Antonio

last: Figueras


title: Gene expression data in MDA231-LM2 breast cancer cells exposed to paclitaxel chemotherapy

city: Heidelberg

first: Jacob

last: Insua-Rodríguez

state: Baden-Württemberg

address: Im Neuenheimer Feld 280

department: Division of Stem Cells and Cancer

institute: German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ)

summary:
In advanced malignancies, cancer cells have acquired capabilities to resist a variety of stress-inducing insults. We show that c-Jun N-terminal kinase (JNK) stress signaling is highly active in cancer cells from patients with late stage breast cancer and promotes tumor growth and metastasis in mouse models. Transcriptomic analysis revealed that JNK activity induces genes associated with extracellular matrix (ECM), wound healing and mammary stem cells. The ECM proteins and niche components osteopontin (SPP1) and tenascin C (TNC) are induced by JNK signaling and promote metastatic colonization of the lungs. Notably, treatment with chemotherapeutic drugs induces JNK activity in breast cancer cells, reinforcing the production of SPP1 and TNC. Inhibition of JNK or reduction of SPP1 or TNC expression sensitizes primary tumors and metastases in mice to chemotherapy.
In order to investigate cancer cell-response to chemotherapy, we exposed MDA231-LM2 breast cancer cells to the chemotherapeutic agent paclitaxel and performed transcriptomic analysis using Affymetrix microarray.

overall_design: MDA231-LM2 cells were treated with a vehicle (DMSO) or 5nM paclitaxel for 48 hours.

first: J

last: Insua-Rodriguez

first: M

last: Pein

first: T

last: Oskarsson


title: Gene expression data in MDA231-LM2 breast cancer cells cultured as oncospheres

summary:
In advanced malignancies, cancer cells have acquired capabilities to resist a variety of stress-inducing insults. We show that c-Jun N-terminal kinase (JNK) stress signaling is highly active in cancer cells from patients with late stage breast cancer and promotes tumor growth and metastasis in mouse models. Transcriptomic analysis revealed that JNK activity induces genes associated with extracellular matrix (ECM), wound healing and mammary stem cells. The ECM proteins and niche components osteopontin (SPP1) and tenascin C (TNC) are induced by JNK signaling and promote metastatic colonization of the lungs. Notably, treatment with chemotherapeutic drugs induces JNK activity in breast cancer cells, reinforcing the production of SPP1 and TNC. Inhibition of JNK or reduction of SPP1 or TNC expression sensitizes primary tumors and metastases in mice to chemotherapy.
We used Affymetrix microarrays to investigate gene expression changes upon culturing metastatic breast cancer cells as oncospheres, in ultra-low adhesive plates in the absence of serum, in contrast to regular monolayer culture conditions.

overall_design: Gene expression in MDA231-LM2 cells grown as oncospheres (seeded on ultra-low adhesive plates under serum-free conditions) was compared to gene expression in the same cells grown as a monolayer. Layer cultures were grown for 48 hours and oncospheres were collected 4 days after seeding.


title: Genes regulated by JNK signaling in MDA231-LM2 breast cancer cells

summary:
In advanced malignancies, cancer cells have acquired capabilities to resist a variety of stress-inducing insults. We show that c-Jun N-terminal kinase (JNK) stress signaling is highly active in cancer cells from patients with late stage breast cancer and promotes tumor growth and metastasis in mouse models. Transcriptomic analysis revealed that JNK activity induces genes associated with extracellular matrix (ECM), wound healing and mammary stem cells. The ECM proteins and niche components osteopontin (SPP1) and tenascin C (TNC) are induced by JNK signaling and promote metastatic colonization of the lungs. Notably, treatment with chemotherapeutic drugs induces JNK activity in breast cancer cells, reinforcing the production of SPP1 and TNC. Inhibition of JNK or reduction of SPP1 or TNC expression sensitizes primary tumors and metastases in mice to chemotherapy.
We used Affymetrix microarrays to analyze the transcriptomic output modulated by JNK activity in a lung metastatic derivative of the MDA-MB-231 breast cancer cell line, MDA231-LM2.

overall_design: Modulation of JNK activity in metastatic breast cancer cells MDA231-LM2 was achieved either by overexpression of constitutively active JNK or by exposing the cells to a selective JNK inhibitor. Constitutively active JNK was overexpressed in MDA231-LM2 cells via lentiviral transduction using a pLVX-Puro vector, into which we subcloned the Flag-MKK7B2Jnk1a1 (MKK7-JNK) or the mutated Flag-MKK7B2Jnk1a1(APF) (MKK7-JNK(mut)) fusion genes (Addgene plasmids #19726 and #19730, provided by Roger Davis). Cells transduced with an empty pLVX-Puro vector (Control) or overexpressing MKK7-JNK(mut) were used as controls. Inhibition of JNK activity in MDA231-LM2 breast cancer cells was attained by treating the cells with the second generation ATP-competitive anthrapyrazolone JNK inhibitor CC-401 (JNKi). MDA231-LM2 cells exposed to DMSO (vehicle) were used as controls. For each condition, three biological replicates were analyzed.


title: The effect of anti-S100A11 antibody on cell growth of MPM cell lines

status: Public on Aug 24 2018

city: Okayama

first: Shinichi

last: Toyooka

address: 2-5-1, shikatacho kitaku

department: School of medicine

institute: Okayama University

summary: In this study, we focused on the impact of extracellular S100A11 in MPM and explored the therapeutic potential of a S100A11-targeting strategy. We found that the neutralization of extracellular S100A11 using anti-S100A11 antibody significantly inhibit the cell growth of MPM cell lines. We also showed that the secretion of S100A11 was significantly higher in MPM pleural effusions, compared to others, suggesting the possibility for the use of S100A11 as a biomarker. Our results indicate that extracellular S100A11 plays important roles in MPM and may be a therapeutic target in S100A11-secreting MPM.

overall_design: Altered gene expression induced by anti-S100A11 antibody was examined. Two MPM cell lines (H2052, H2452) were used for this experiment.

first: Hiroki

last: Sato

first: Shuta

last: Tomida


title: Identification of differentially expressed genes in MDV-transformed cells lines treated with sodium butyrate

status: Public on Aug 23 2018

city: Raleigh

first: Julie

last: Hicks

state: NC

address: 120 Broughton Dr

department: Animal Science

institute: NC State University

summary: In order to characterize alterations in cellular regulatory mechanisms associated with MDV reactivation, we employed microarray analysis to identify changes in gene expression in chemically-reactivated MDV transformed cell lines, specifically MSB1, RP2 and CU115. Differentially expressed genes identified in the MDV-transformed cell lines were then compared against differentially expressed genes in the REV-transformed CU91 cell line.  This step was done to reduce the number of false positives (i.e. genes likely responding solely to sodium butyrate rather than MDV reactivation). Multiple cellular pathways are also affected by MDV reactivation, including  those associated with apoptosis, the cell cycle, DNA repair, and immune response.

overall_design: A loop design (one replicate per loop) and a dye swap design scheme was used.  RNA was amplified using an Amino Allyl MessageAmpII aRNA Amplification kit (Ambion), aliquoted into two pools per sample, and each pool was separately labeled with either Cy3 or Cy5 reactive dyes (GE Healthcare).  RNA samples from the same cell line and from a different time-point (either 0 or 12 or 24 hr post-treatment (hpt)) were co-hybridized.  The chicken (20.7 K) oligoarray (GPL6049) was purchased from Steele Children’s Research Centre, Tucson, Arizona.  Two replicates of each cell line and each time-point were used, for a total of 24 slides.

first: Hsiao-Ching

last: Liu

first: Nares

last: Trakooljul


title: Genome-wide DNA accessibility maps and differential gene expression using ChIP-seq, ATAC-seq and RNA-seq for the human secondary fibroblast cell line hiF-T and whole worms with and without knockdown of FACT complex

first: Scott

last: Lacadie

summary: To assess the mechanisms by which FACT depletion leads to increased sensitivity of cells to be reprogrammed, we measured the chromatin accessibility landscape using ATAC-seq following mock treatment, SSRP1 knockdown, or SUPT16H knockdown in human fibroblasts and mock, hmg-3 or hmg-4 knockdown in whole worms, and differential gene expression in hmg-3 knockout mutants or following mock, hmg-4, or spt-16 knockdown by RNAseq.

sample_organism:
Caenorhabditis elegans
Homo sapiens

platform_organism:
Caenorhabditis elegans
Homo sapiens

overall_design: Examination of two FACT complex components in human cells and worms with ChIP-seq, ATAC-seq and RNA-seq

first: Ena

last: Kolundzic

first: Baris

last: Tursun


title: Stress signaling in breast cancer cells induces matrix components that promote chemoresistant metastasis

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

overall_design: Refer to individual Series


title: Evf2 enhancer long non-coding RNA regulation of gene expression in embryonic mouse brain

city: Chicago

first: Jhumku

last: Kohtz

state: Illinois

address: 303 E Chicago

department: Neurology

institute: Northwestern University

summary:
The Evf2 long non-coding RNA regulates genes adjacent and overlapping genes (Dlx5 and Dlx6), but it was not known if long range gene regulation occurs.  In this study, we find that Evf2 regulates genes across a 27Mb region on mouse chromosome 6, and additional genes outside of mosue chromosome 6.
We used microarrays to determine the effects of the Evf2 lncRNA on gene expression at sites of interenuron birth in a specific region of the mouse brain (ventral forebrain, MGE) at E13.5.

overall_design: Embryonic brain tissue from medial ganglionic eminence (MGE) at E13.5 were isolated from Evf2+/+ (wildtype) and Evf2TS/TS (lacking expression of the Evf2 lncRNA).  Total RNA was isolated from pools of 4 MGE's per genotype.  5 pools were made from each genotype.  Males and females were distinguished by Y-specific PCR analysis:  Evf2+/+ n=2  males, n=3 females, Evf2TS/TS n=3 males, n=2 females

first: Ivelisse

last: Cajigas

first: Sean

last: Chen


title: Trabectedin is a novel chemotherapy agent for diffuse large B cell lymphoma

status: Public on Aug 22 2018

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

summary: Assess the efficacy of trabectedin in two DLBCL cell lines

overall_design: GEP analysis of 2 lymphoma cell lines with and without treatment

first: Filippo

last: Spriano

first: Raffaella

last: Gatta

first: Eugenio

last: Gaudio

first: Andrea

last: Rinaldi

first: Luciano

last: Cascione

first: Chiara

last: Tarantelli


title: Sequence context controls the DNA binding and processivity of the T7 DNA primase

city: Durham

first: Raluca

last: Gordan

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

summary: Primases are key enzymes involved in DNA replication. They act on single-stranded DNA, and catalyze the synthesis of short RNA primers used by DNA polymerases. Here, we investigate the DNA-binding and functional activity of the bacteriophage T7 primase using a new workflow called High-Throughput Primase Profiling (HTPP). Using a unique combination of high-throughput binding assays and biochemical analyses, HTPP reveals a complex landscape of binding specificity and functional activity for the T7 primase, determined by sequences flanking the primase recognition site. We identified specific features, such at G/T-rich flanks, which in-crease primase-DNA binding up to 10-fold and, surprisingly, also increase the length of newly formed RNA (2-3 fold). To our knowledge, variability in primer length has not been reported for this primase. We expect that applying HTPP to additional enzymes will reveal new insights into the effects of DNA sequence composition on the DNA recognition and functional activity of primases.

overall_design: HTPP (High-Throughput Primase Profiling) experiments were performed for recombinant T7 primase residue: 1-271. Briefly, the HTPP involved binding of his-tagged primase to single-stranded 180K Agilent microarrays in order to determine their binding specificity in different artificial context. Each sequence represented on the array is present in 6 replicate spots. We report the signal intensity for each spot.

first: Ariel

last: Afek


title: Function of HNRNPC in breast cancer cells by controlling the dsRNA-induced interferon response

city: Beijing

first: Xuerui

last: Yang

address: Haidian District

department: School of Life Sciences

institute: Tsinghua University

summary: Elevated expression of RNA binding protein HNRNPC has been reported in cancer cells, while the essentialness and functions of HNRNPC in tumors were not clear. We showed that repression of HNRNPC in the breast cancer cells MCF7 and T47D inhibited cell proliferation and tumor growth. Our computational inference of the key pathways and extensive experimental investigations revealed that the cascade of interferon responses mediated by RIG-I was responsible for such tumor-inhibitory effect. Interestingly, repression of HNRNPC resulted in accumulation of endogenous double-stranded RNA (dsRNA), the binding ligand of RIG-I. These up-regulated dsRNA species were highly enriched by Alu sequences and mostly originated from pre-mRNA introns that harbor the known HNRNPC binding sites. Such source of dsRNA is different than the recently well-characterized endogenous retroviruses that encode dsRNA. In summary, essentialness of HNRNPC in the breast cancer cells was attributed to its function in controlling the endogenous dsRNA and the down-stream interferon response. This is a novel extension from the previous understandings about HNRNPC in binding with introns and regulating RNA splicing.

overall_design: Cytoplasmic total RNAs were profiled upon HNRNPC knock-down in MCF7 (2 replicates) and T47D cells, NC and LAMN knock-down cells served as controls.

first: Wenwei

last: Zhao

first: Yusheng

last: Wu

first: Yang

last: Liu


title: Global gene expression profiling of SM and the derivatives (DM, D, MYO, SCL, SYN) induced from hiPSCs

city: Kyoto

first: Makoto

last: Ikeya

address: 53 kawahara-cho, shogoin

department: Center for iPS Cell Research and Application(CiRA)

institute: Kyoto University

summary: Global gene expression profiling of human iPSC and the iPSC-derived presomitic mesoderm(PSM), somite(SM), and the derivatives, dermomyotome(DM), dermatome(D), myotome(MYO), sclerotome(SCL) and syndetome(SYN).

overall_design: Total RNA was prepared using the RNeasy Mini Kit (Qiagen). cDNA was synthesized using the GeneChip WT (Whole Transcript) Sense Target Labeling and Control Reagents Kit as described by the manufacturer (Affymetrix, Santa Clara, CA). Hybridization to the GeneChip Human Gene 1.0 ST expression arrays, washing, and scanning were performed according to the manufacturer’s protocol (Affymetrix). Expression values were calculated using the RMA summarization method, and the data obtained were analyzed by GeneSpring GX 14.5 (Agilent Technologies, Santa Clara, CA, USA).

first: Taiki

last: Nakajima


title: Comparison of gene expression between high- and low-Sost/sclerostin expressing osteocytes

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: Single-cell sorted cells from the osteocytic cell line Ocy454 were screened for high- and low-Sost/sclerostin expression to see changes in other gene expressions related to Sost/sclerostin.

overall_design: Ocy454 cells were single cloned and 37 clones were tested for Sost/sclerostin expression after 7 days in culture. 2 clones (12H and 15H) with the highest Sost expression and 3 clones (9L, 4L and 24L) with low Sost expression were selected for microarray analysis.

first: Christopher

last: Dedic

first: Yuhei

last: Uda

first: Paola

last: Pajevic


title: Natural variation affecting allele-specific expression in the Malpighian tubules of Drosophila melanogaster

city: Planegg

first: John

last: Parsch

state: BY

address: Grosshaderner Str. 2

department: Biology II

institute: University of Munich (LMU)

summary: We used RNA-seq to investigate natural variation in gene expression in the Malpighian tubules of three inbred Drosophila melanogaster strains and their F1 hybrids. One of the strains was from a population in the species’ ancestral range (Zambia), while the other two were from a more recently derived population (Sweden).

overall_design: mRNA expression profiles of Drosophila melanogaster Malpighian tubules from adult females of 3 parental and 3 F1 hybrid genotypes (2 biological replicates per genotype)

first: Amanda

last: Glaser-Schmitt

first: Aleksandra

last: Zecic


title: Nuclear receptor Nur77 limits the macrophage inflammatory response by reprogramming mitochondrial metabolism (RNA-seq)

status: Public on Aug 21 2018

city: Amsterdam

first: Carlie

last: de Vries

address: Meibergdreef 15

department: Medical Biochemistry

institute: Academic Medical Center, University of Amsterdam

summary: Activation of macrophages by inflammatory stimuli leads to reprogramming of mitochondrial metabolism to support the production of pro-inflammatory cytokines. Hallmarks of this metabolic rewiring are downregulation of α-ketoglutarate formation via isocitrate dehydrogenase (IDH) and accumulation of glutamine-derived succinate, which enhances the inflammatory response via the activity of succinate dehydrogenase (SDH). Here, we identify the nuclear receptor Nur77 (Nr4a1) as a key regulator of the pro-inflammatory metabolic switch in macrophages. Nur77-deficient macrophages fail to downregulate IDH expression and accumulate higher levels of succinate and other downstream TCA cycle metabolites in response to an inflammatory stimulus. Consequently, these macrophages produce more nitric oxide and pro-inflammatory cytokines in an SDH-dependent manner. In vivo, bone marrow Nur77 deficiency exacerbates atherosclerosis development and leads to increased systemic succinate levels. In conclusion, Nur77 supports an anti-inflammatory metabolic state in macrophages that protects against chronic inflammatory diseases such as atherosclerosis.

overall_design: Gene expression profiling by RNA-seq was performed in triplicate in RAW264.7 mouse macrophage stable cell lines with doxycycline-inducible overexpression of HA-tagged NUR77 or GFP as control.

first: Duco

middle: S

last: Koenis

first: Yongsoo

last: Kim

first: Lodewyk

last: Wessels

first: Wilbert

last: Zwart

middle: J


title: H3.V and H4.V

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

sample_organism:
Trypanosoma brucei brucei
other sequences


title: Nuclear receptor Nur77 limits the macrophage inflammatory response by reprogramming mitochondrial metabolism


title: MicroRNA Regulation in Blood Cells of Renal Transplanted Patients with Interstitial Fibrosis/Tubular Atrophy and Antibody-Mediated Rejection

status: Public on Aug 20 2018

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

summary: We performed small RNA-Seq and compared expression levels of microRNAs of whole blood cells isolated from patients after kidney transplantation with stable graft function (SGF), antibody-mediated rejection (ABMR) and T cell-mediated rejection (TCMR).

overall_design: Whole blood cells were isolated from 6 patients with stable graft function, 6 patients with histologically verified antibody-mediated graft rejection episode and 4 patients with histologically verified T cell-mediated graft rejection after kidney transplantation. Total RNA was extracted and cDNA libraries for small RNA sequencing were generated using "TruSeq® small RNA library Prep" kit (Illumina, San Diego, CA, USA).

first: Mareen

last: Matz

first: FrederiK

last: Heinrich

first: Christine

last: Lorkowski

first: Kaiyin

last: Wu

first: Qiang

last: Zhang

first: Nils

last: Lachmann

first: Klemens

last: Budde

first: Mir

middle: F

last: Mashreghi


title: Genome-wide maps of RNA polymerase II occupancy and transcriptome profile in response to expression of ectopic MYC proteins in immortalized MEF cells

city: Lebanon

first: Michael

middle: David

last: Cole

state: NH

address: One Medical Center Drive

department: Genetics

institute: Geisel School of Medicine at Dartmouth


title: Nuclear receptor Nur77 limits the macrophage inflammatory response by reprogramming mitochondrial metabolism (ChIP-seq)

overall_design:
Nur77 binding site profiling by ChIP-seq was performed in triplicate in RAW264.7 mouse macrophage stable cell line with doxycycline-inducible overexpression of HA-tagged NUR77.
Third-party reanalysis of raw input control sequencing data obtained from GSM1232949 and GSM1559473 .


title: Transcriptional profiling reveals functional dichotomy between human slan+ non-classical monocytes and myeloid dendritic cells

city: Lund

first: Kristina

last: Lundberg

address: Medicon Village building 406, Scheelevägen 8

department: Immunotechnology

institute: Lund University

summary: Abstract: Human 6-sulfo LacNac (slan)+ cells have been subject to a paradigm debate. They have previously been classified as a distinct dendritic cell (DC) subset. However, evidence has emerged that they may be more related to monocytes than to DC. To gain deeper insight into the functional specialization of slan+ cells, we have compared them with both conventional myeloid DC subsets (CD1c+ and CD141+) in human peripheral blood. Using genome-wide transcriptional profiling as well as extensive functional tests, we clearly show that slan+ cells form a distinct, non-DC-like, population. They cluster away from both DC subsets and their gene expression profile evidently suggests involvement in distinct inflammatory processes. An extensive comparison with existing genomic data sets also strongly confirmed the relationship of slan+ with the monocytic compartment rather than with DC. From a functional perspective, their ability to induce CD4+ and CD8+ T cell proliferation is relatively low. Combined with the finding that ‘antigen presentation by MHC class II’ is at the top of under-represented pathways in slan+ cells, this points to a minimal role in directing adaptive T cell immunity. Rather, the higher expression of complement receptors on their cell surface, together with their high secretion of IL-1β and IL-6, imply a specific role in innate inflammatory processes, which is consistent with their recent identification as non-classical monocytes. This study extends our knowledge on DC/monocyte subset biology under steady state conditions and contributes to our understanding of their role in immune-mediated diseases and their potential use in immunotherapeutic strategies.

overall_design: Genome-wide transcriptional analysis of slan+ cells and both conventional myeloid CD1c+ and CD141+ DC subsets in human peripheral blood.

first: Nathalie

last: van Leeuwen-Kerkhoff

first: Theresia

last: Westers

first: Shahram

last: Kordasti

first: Hetty

last: Bontkes

first: Tanja

last: de Gruijl

first: Malin

last: Lindstedt

first: Arjan

middle: A

last: van de Loosdrecht


title: Genome-wide maps of RNA polymerase II occupancy in immortalized MEF cells [ChIP-seq]

summary: We report the application of ChIP-seq using an anti-RNA pol II antibody to determine changes in RNAP II occupancy patterns genome-wide. We found that as a result of MYC expression, RNAP II levels increased at both the promoter and gene body regions. This suggests that MYC increases the amount of both the initiation and elongation steps of trasncription globally.

overall_design: Examination of RNA polymerase II genome occupancy comparing the effect of the absence of Myc to two full length versions of Myc

first: Dustin

last: Elwood

first: Charles

middle: Y

last: Lin


title: Discordant molecular subtype classification of muscle-invasive bladder cancer and matched lymph-node metastases occurs preferentially in the Basal/Squamous-like subtype.

first: Pontus

last: Eriksson

state: Select:

address: Scheelevägen 2

department: Department of Clinical Sciences

summary: By combining molecular pathology, mRNA profiling, and exome-sequencing we describe muscle-invasive bladder tumors and matched lymph-node metastases.

overall_design: Data from 307 FFPE embedded bladder cancers (availabe in GSE83586) and 28 lymph node metastasis were generated using the GeneChip Human Gene 1.0 ST Arrays (Affymetrix). Total RNA was extracted using the High Pure FFPET RNA isolation kit (Roche), assessed for quality using Nanodrop ND-1000, and labeled using SensationPlus FFPE Amplification and WT labeling kit. The full dataset of 335 CEL files were normalized using RMA by labeling batches. Batches were combined and RMA normalized. The data was filtered for probes with signal intensity less than the median of negative control probes for >80% of the values. Gene symbols and EntrezID were appended using Bioconductor (hugene10stprobeset.db Version 8.3.1). Probes not mapping to a gene symbol were removed. The probes were median merged by gene symbol and log-transformed. Batch correction was performed using ComBat. The 28 lymph node samples and the 28 matched tumors (available in GSE83586) were used in this cohort. These 56 samples were median centered and used for subtype classification and pair-wise t tests.

first: G

last: Sjödahl

first: P

first: F

last: Liedberg

first: M

last: Höglund


title: Immunological differences between primary and metastatic breast cancer

city: New Haven

first: Lajos

last: Pusztai

state: CT

address: 300 George St., Suite 120

institute: Yale University

summary: Little is known about how the immune microenvironment of breast cancer evolves during disease progression. The goal of this project was to examine immune gene mRNA expression in primary tumors (P) and metastatic lesions (M). The expression of 730 immune-related genes was measured using the Nanostring PanCancer Immune Gene Panel.

overall_design: Expression of 730 immune-related genes were measured in 31 P and 17 M, including 10 paired cases.

first: Borbala

last: Szekely

first: Xiaotong

last: Li


title: AR-V7 Targets in Castration-Resistant Prostate Cancer (CRPC) Cell Line

status: Public on Aug 16 2018

city: Miami

first: Kerry

last: Burnstein

state: FL

department: Molecular and Cellular Pharmacology

institute: University of Miami

summary: In order to define the genes responsible for the growth and survival of a human castration-resistant prostate cancer cell line, a short term (doxycycline inducible) knockdown system was developed and utilized. Three independent 22Rv1 cell isolates were derived for each of the following doxycycline-inducible shRNAs (shGFP, shAR3, and shVav3) (AR3 = AR-V7). The cells were grown in androgen depleted conditions, plus or minus doxycycline, for three days. RNA from the 18 samples was then sent to the University of Miami Genetics Core for RNA Integrity Number (RIN) evaluation and microarray analysis. Genes differentially regulated by AR-V7 knock-down or VAV3 knock-down were explored as downstream targets of AR-V7 or VAV3, respectively.

overall_design: Stable 22Rv1 cell lines were established for each doxycycline-inducible shRNA (tet-pKLO.1-shGFP, tet-pKLO.1-shAR3, and tet-pKLO.1-VAV3). Cells were grown in androgen depleted conditions (10% CSS) plus or minus doxycycline for three days, three replicates per condition. Knockdown was confirmed by parallel protein harvest. RNA was isolated and analyzed on Affymetrix Human Gene 1.0 ST Arrays v1. Arrays were analyzed using R (3.3.1, https://cran.r-project.org/), the Bioconductor suite (https://www.bioconductor.org/), and the oligo package(1.36.1). Arrays were rma normalized. Limma (3.28.21) was used to calaculate differential gene expression upon doxycycline induced knock-down.

first: Eric

middle: R

last: Bray

first: Fiorella

last: Magani

first: Stephanie

last: Peacock


title: Copy number alteration burden is a pan-cancer prognostic factor associated with metastasis and death in conservatively treated prostate cancer: TAPG1 CNA cohort aCGH data

status: Public on Aug 18 2018

city: New York

first: Haley

last: Hieronymus

state: New York

address: 1275 York Ave.

institute: Memorial Sloan Kettering Cancer Center

type: Genome variation profiling by genome tiling array

summary: The level of copy number alteration (CNA), or CNA burden, in cancer genomes is associated with recurrence and metastasis in prostate cancer. As clinical genomic analysis of tumors and tumor biopsies becomes widespread, there is a growing need to understand the prognostic factors captured by genomic features, especially in prostate cancer where conservative treatment approaches are increasingly common. Here we analyze the CNA landscape of conservatively treated prostate cancer in a prostate cancer biopsy and transurethral resection cohort. We find that CNA burden is prognostic for metastasis and cancer-specific survival, independent of clinical prognostic factors such as Gleason and CAPRA score, in conservatively treated prostate cancer.

overall_design: Genome-wide copy number profiles of 107 primary prostate cancers from TAPG1 cohort, as determined by Agilent aCGH. Human prostate cancer samples (DNA from macrodissected FFPE sections) versus Promega male reference DNA (catalog number G1471). 107 biological samples from 107 patients.

first: Barry

last: Taylor

last: Sawyers


title: Genome wide expression change by SMURF1 knocking down in MCF-7 cells

status: Public on Aug 14 2018

city: Shenzhen

first: Qiangzu

last: Zhang

address: Nan Hai Da Dao Chuang Shi Ji Bin Hai Hua Yuan Building9 9A , Nanshan District, Shenzhen City, Guangdong Province

institute: Lemondata BioTechnology Limited

summary: We aim to the investigate the role of SMURF1 in breast cancer progression. MCF-7 cells were used as the model and SMURF1 was silenced by siRNA.

overall_design: The MCF-7 cells were treated with 50nM stramble siRNA and siSMURF1. After 48 hours, cells were harvested and the total RNA was extacted by Qiagen kit. The RNA sample was sent to BGI for RNA expression anaylsis.

first: J

last: Zhu


title: Expression data from two rat strains comparing naïve vs 24h picornavirus infection.

city: Nedlands

first: Anya

last: Jones

state: Western Australia

address: Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue

country: Australia

institute: Telethon Kids Institute, The University of Western Australia

summary: Allergic (Th2high immunophenotype) asthmatics have a heightened susceptibility to common respiratory viral infections such as human rhinovirus. Evidence suggests that the innate interferon response is deficient in asthmatic/atopic individuals, whilst other studies show no differences in antiviral response pathways. Unsensitized and OVA-sensitized/challenged Th2high (BN rats) and Th2low immunophenotype (PVG rats) animals were inoculated intranasally with attenuated mengovirus (vMC0). Sensitized animals were exposed/unexposed during the acute viral response phase. Cellular and transcriptomic profiling was performed on bronchoalveolar lavage cells. In unsensitized PVG rats, vMC0 elicits a prototypical antiviral response (neutrophilic airways inflammation, upregulation of Th1/type I interferon-related pathways). In contrast, response to infection in the Th2high BN rats was associated with a radically altered intrinsic host response to respiratory viral infection, characterized by macrophage influx/Th2-associated pathways. In sensitized animals, response to virus infection alone was not altered compared to unsensitized animals. However, allergen exposure of sensitized animals during viral infection unleashes a notably exaggerated airways inflammatory response profile orders of magnitude higher in BN versus PVG rats despite similar viral loads. The coexposure responses in the Th2high BN incorporated type I interferon/Th1, alternative macrophage activation/Th2 and Th17 signatures. Similar factors may underlie the hyper-susceptibility to infection-associated airways inflammation characteristic of the human Th2high immunophenotype.

overall_design: A total of n=12 samples were profiled by microarray comparing naïve vs virus infected at 24 hours in two strains of rats. The samples included 4 groups: BN naïve (n=3), BN virus at 24 hours (n=3), PVG naïve (n=3), PVG virus at 24 hours (n=3).

first: Jean-François

last: Lauzon-Joset

first: Kyle

middle: T

last: Mincham

first: Jenny

last: Thomas

first: Louis

last: Rosenthal

first: Anthony

last: Bosco

first: Patrick

last: Holt

first: Deborah

middle: H

last: Strickland


title: SIRT6 haploinsufficiency induces BRAFV600E melanoma cell resistance to MAPK inhibitors via IGF signaling

first: Emily

last: Bernstein

state: NY

address: 1470 Madison Avenue, 6th floor Rm 302

department: Oncological Sciences

institute: Mount Sinai School of Medicine

summary: Through integrated transcriptomic, epigenomic and proteomic analyses, we identified IGFBP2, an insulin growth factor (IGF) binding protein, as a direct SIRT6 target gene. We further show that SIRT6 haploinsufficiency, but not complete knock out of SIRT6 promotes IGFBP2 expression via increased H3K56 acetylation at the IGFBP2 locus allowing melanoma cell survival in the presence of MAPK signaling inhibitors (MAPKi).

overall_design: We examine three melanoma cell lines (L-C-B (WT for SIRT6), SIRT6.2-7 (SIRT6 happloinsufficient cells) and SIRT6.1-1 (SIRT6 KO cells)) for transcriptional changes upon MAPK signaling inhibtion to identify SIRT6 targets/pathways whose inhibition might prevent resistance to MAPKi by correlating those with changes in histone modifications at SIRT6 targets

first: Thomas

last: Strub

first: Dan

last: Hasson


title: ARID2 promotes clear cell renal cell carcinoma in the absence of functional PBRM1 [microarray]

first: David

middle: Aaron

last: Schoenfeld

address: 20 York Street

department: Medical Oncology

institute: Yale Cancer Center

summary: Subunits of SWI/SNF chromatin remodeling complexes are frequently mutated in human malignancies. The PBAF complex is composed of multiple subunits, including the putative tumor suppressor proteins PBRM1 (BAF180) and ARID2 (BAF200) that are unique to this SWI/SNF complex. PBRM1 is mutated in various cancers, with a high mutation frequency in clear cell renal cell carcinoma (ccRCC). Here, we integrate RNA-seq, ARID2 and histone mark ChIP-seq, and ATAC-seq data to show that PBAF acts to enhance or repress gene expression depending on the genomic context. At baseline, ARID2 binds to areas of open chromatin at both active enhancers and promoters. Depletion of PBRM1 leads to attenuated and redistributed ARID2 chromatin binding that correlates significantly with gene expression changes. At enhancers, ARID2 binding loss leads to diminishment of the histone mark H3K4me1 and gene downregulation. Alternatively, at a subset of promoters, ARID2 binding loss derepresses gene expression. Interestingly, ARID2, which remains bound to other PBAF subunits after loss of PBRM1, is essential for many of the pro-tumorigenic transcriptional changes observed after loss of PBRM1, whereas other core SWI/SNF components are dispensable. Upon loss of PBRM1, ARID2 positively regulates cancer-related genes and pathways, including the cancer stem cell marker ALDH1A1 and EGF signaling, to stimulate tumor cell growth. Therefore, ARID2 is crucial for maintaining the transformed state of PBRM1-deficient ccRCC cells. In total, this study suggests a novel mechanism of transcriptional control by PBRM1, whereby its loss alters the chromatin distribution of the residual PBAF complex leading to altered transcription that promotes tumorigenesis.

overall_design: We isolated murine embryonic fibroblasts (MEFs) from conditional Pbrm1 mice we had generated, where Cre-mediated recombination caused a frame-shift mutation of the Pbrm1 allele and loss of Pbrm1 expression. We then performed microarray analysis on 3 matcheds of MEFs with or without Pbrm1 expression to investigate gene expression differences.

first: Sakellarios

last: Zairis

first: William

last: Su

first: Nicole

last: Steinbach

first: Deepti

last: Mathur

first: Asif

last: Chowdhury

first: Bertilia

last: Tavarez

first: Raul

last: Rabadan

first: Ramon

last: Parsons


title: MDA-MB-231 gene expression upon IRE1 RNase inhibition with MKC-8866

status: Public on Aug 15 2018

city: Galway

first: Afshin

last: Samali

address: Newcastle Road, Dangan

department: Biomedical Sciences

country: Ireland

institute: Apoptosis Research Centre

summary:
The IRE1 Rnase domain has been implicated in the pathology of triple negative breast cancer (TNBC), a disease with limited treatment options. The IRE1 Rnase mediates it's effects on the transcriptome via activation of the trancription factor XBP1s and via direct cleavage of mRNA through a process called RIDD. The processes through which the RNase domain contributes to TNBC is not fully understood.
We used a novel small molecule inhibitor of the IRE1 Rnase to find novel targets of IRE1 in TNBC, in an effort to elucidate how it contributes to the disease.

overall_design: A TNBC cell line MDA-MB 231 was treated with the IRE1 Rnase inhibitor for 4, and 24h in normoxic and hypoxic (1% O2) conditions. We aimed to determine effects of inhibiting IRE1 on an early and a later timepoint to have a broader uderstand how IRE1 Rnase effects cells. Recent reports suggest that XBP1s plays a role in controlling the hypoxic stress response in TNBC cells. To find novel hypoxia-specific functions for IRE1 we inhibited the RNase under hypoxic condditions.

first: Eoghan

last: McGrath

first: Susan

last: Logue


title: ARID2 promotes clear cell renal cell carcinoma in the absence of functional PBRM1 [ARID2 ChIP-seq]

overall_design: ARID2 ChIP-seq was performed in the the human clear cell renal cell carcinoma cell line 786-O in which PBRM1 had been stably knocked down with two different lentiviral vectors containing shRNA targeting PBRM1 (sh1 or sh2), or with a lentiviral vector containing an off-target control shRNA (control).


title: ARID2 promotes clear cell renal cell carcinoma in the absence of functional PBRM1 [ATAC-seq]

overall_design: ATAC-seq was performed in the the human clear cell renal cell carcinoma cell line 786-O in which PBRM1 had been stably knocked down with two different lentiviral vectors containing shRNA targeting PBRM1 (sh1 or sh2), or with a lentiviral vector containing an off-target control shRNA (control).


title: Global Profiling of hnRNP A2/B1-RNA Interactions on Chromatin Suggests Additional Roles Outside of Splicing

city: Aurora

first: Aaron

middle: M

last: Johnson

state: CO

address: 12801 E 17th Ave Research 1 South L18-10402G

department: Biochemistry and Molecular Genetics

institute: University of Colorado Denver

summary: Long noncoding RNAs (lncRNAs) often carry out their functions through associations with adaptor proteins. We recently identified heterogeneous ribonucleoprotein (hnRNP) A2/B1 as an adaptor of the human HOTAIR lncRNA. hnRNP A2 and B1 are splice isoforms of the same gene. Spliced HOTAIR preferentially associates with the B1 isoform, which may contribute to a mechanism matching lncRNAs with RNA transcripts of target genes. In this study we used enhanced cross-linking immunoprecipitation (eCLIP) to map the complete set of direct interactions between A2/B1 and RNA in breast cancer cells. We identified multiple additional sites of isoform specificity that correlate with differences in binding motif enrichment. Surprisingly, a strong A2/B1 binding site occurs in the third intron of HOTAIR, which interrupts a known RNA-RNA interaction hotspot and is retained at a higher frequency than other HOTAIR introns. In vitro eCLIP experiments suggest that A2/B1 may redistribute to exonic binding sites once this intron is spliced. A2/B1 associates with multiple lncRNAs at regions that may contribute to downstream regulation and function of the lncRNA. Finally, we performed cellular fractionation experiments to characterize the pattern of RNA association of A2/B1 in chromatin, nucleoplasm, and cytoplasm and find that a majority of interactions occur on chromatin, even those that do not contribute to co-transcriptional splicing. Our data characterize the multiple functions of a repurposed splicing factor, including isoform-biased interactions, and highlight that the vast majority of these functions occur on chromatin-associated RNA.

sample_organism:
Homo sapiens
synthetic RNA

platform_organism:
Homo sapiens
synthetic RNA

overall_design: eCLIP-seq in human MCF7 and MCF10A cells

first: Eric

middle: D

last: Nguyen


title: ARID2 promotes clear cell renal cell carcinoma in the absence of functional PBRM1 [Histone modification native ChIP-seq]

overall_design: Native ChIP-seq for the histone modifications H3K4me3, H3K4me1, K3K27ac, and H3K9ac was performed in the the human clear cell renal cell carcinoma cell line 786-O in which PBRM1 had been stably knocked down with two different lentiviral vectors containing shRNA targeting PBRM1 (sh1 or sh2), or with a lentiviral vector containing an off-target control shRNA (control).

first: Emily

last: Bernstein


title: Transcriptional profile comparing poorly diffentiated HCC nodules to well-differentiated HCC nodules arising in HCC/LECT2-KO mice

status: Public on Aug 13 2018

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

summary: The aim of this project is to determine the differential expression of genes between poorly differntiated HCC tumor compared to differntiated tumor arising in  HCC/LECT2-KO mice

overall_design: HCC/LECT2-KO mice harboring differentiated and poorly differentiated nodules were selected according to HE staining from liver frozen sections

first: Jean-Pierre

last: Couty

first: Antoine

last: L'Hermitte

first: Sébastien

last: Jacques


title: Transcriptional profile of HCC nodules and their infiltrating monocytes

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

overall_design: Refer to individual Series


title: Transcriptional profile comparing murine monocytes infiltrating HCC tumors in the absence/presence  of LECT2 expression in the liver

summary: The aim of this project is to determine the differential expression of genes between monocytes infiltrating HCC nodules in the absence versus in the presence of LECT2

overall_design: Inflammatory monocytes were extracted from tumor livers (+/-LECT2 expression) and cell-sorted according to specific markers by flow cytometry


title: DNA methylation profiling of neuron and glia for the dissection of cell type, age and Alzheimer’s disease-specific changes in the human brain

status: Public on Aug 12 2018

city: Saarbruecken

first: Pavlo

last: Lutsik

institute: Saarland University

summary: Alzheimer’s disease (AD) is a progressive brain disorder caused by altered neuronal and glial cell functions. Illumina 450K profiling of cells (nuclei) sorted from post- mortem human brains allowed us assigning cell type- specific epigenetic changes to aging and AD progression. Among a few thousand cell type-specific differentially methylated CpGs (DMCGs) changing with age we identify prominent clusters in the AD genes, CLU, SYNJ2, ANK1 and MCF2L. A distinct set of age independent AD-specific DMCGs shows strong cell specific changes in the genes TOLLIP, BACE2, PKAR1B, PDE9A, ROBO2, FERMT2, UGT8, SPON1, INPP5D, LNFG and SRPK2. Some AD-specific DMCGs even reveal incremental changes with advancing BRAAK stages. In summary we observe a striking presence of DMCGs in major LOAD genes establishing novel connections between genetic and epigenetic contributions to AD. In addition the cell-specific association allows to functionally discriminate epigenetic effects of aging from those related to AD in the human brain.

overall_design: Bulk and cell sorted post-mortem frontal cortex samples

first: Gilles

last: Gasparoni

first: Sebastian

last: Bultmann

first: Theo

last: Kraus

first: Julia

last: Vlcek

first: Vanessa

last: Dietinger

first: Martina

last: Steinmaurer

first: Matthias

last: Riemenschneider

first: Hans

last: Kretzschmar

first: Armin

last: Giehse

first: Heinrich

last: Leonhardt

first: Jörn

last: Walter


title: BRWD1 orchestrates epigenetic landscape of late B lymphopoiesis

status: Public on Aug 11 2018

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

country: USA

institute: University of Illinois at Chicago

summary: Transcription factor (TF) networks determine cell fate in hematopoiesis. However, how TFs cooperate with other regulatory mechanisms to instruct transcription remains poorly understood. We demonstrate in small pre-B cells, that the lineage restricted epigenetic reader BRWD1 closes early development enhancers and opens the enhancers of late B lymphopoiesis to TF binding. BRWD1 differentially regulated over 7000 genes including repressing proliferative and inducing differentiation programs. However, BRWD1 did not regulate expression of transcription factors required for B lymphopoiesis. Hypogammaglobulinemia patients with BRWD1 mutations had B cell transcriptional profiles and enhancer landscapes similar to those observed in Brwd1-/- mice. These data indicate that in both mice and humans, BRWD1 is a master orchestrator of enhancer accessibility that cooperates with TF networks to drive late B cell development.

overall_design: 59 samples from mouse and human: 12 ATAC-seq samples from both mouse and human; 21 RNA-seq samples from human; 6 RNA-seq samples from mouse; 6 ChIP-seq samples from mouse, 2 input controls for the ChIP-seq samples from mouse. Mouse samples available in duplicate. Human samples are classified into one of three genotypic backgrounds, with varying number per group.

first: Malay

last: Mandal

first: Patrick

last: Maffucci

first: Margaret

last: Veselits

first: Domenick

middle: E

last: Kennedy

first: Kaitlin

middle: C

last: McLean

first: Michael

middle: K

last: Okoreeh

first: Charlotte

last: Cunningham-Rundles

first: Marcus

last: Clark


title: Identification of small RNAs expressed in Caulobacter crescentus in response to DNA damage

first: Konrad

last: Förstner

summary: RNA-based regulation of gene expression is substantially contributing to the ability of bacteria to rapidly adapt to changing environmental conditions. This study employs RNAseq to define the transcriptome of Caulobacter in response to treatment with the DNA-crosslinking agent mitomycin C.  We identify a small, regulatory RNA ChvR synthesized under the control of the conserved ChvIG two-component system which represses production of a TonB-dependent receptor, ChvT, in Caulobacter crescentus. ChvR significantly reduces ChvT expression under different physiological conditions, including the response to DNA damage and growth in minimal medium. Full regulation requires the formation of two distinct base-pairs between the sRNA and its cognate mRNA target, and occurs independent of the ubiquitous RNA chaperone, Hfq.

overall_design: Global analysis of gene expression in wild-type Caulobacter crescentus in response to the DNA-damaging agent mitomycin C

first: Kathrin

last: Fröhlich


title: Gene expression profiling of Dox-activable K-ras mutation in human primary bronchial epithelial cell line

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: We constructed a primary lung cell model to permit regulated expression of KRASG12D. To do this, we leveraged a non-transformed, immortalized, human primary bronchial epithelial cell line (HBEC; hTert, CDK4, TP53 knockdown) that remains anchorage dependent and do not develop tumors when implanted into mice. We next modified these cells by stably integrating a regulatable KRASG12D allele, iKRASG12D, such that physiological expression of mutant KRAS is activated upon addition of doxycycline. The HBEC-iKRAS (WT) cell line and HBEC-iKRASG12D  (MUT)  cell line were propagated with or without Doxycycline (500ng/ml) respectively. RNA profiling of HBEC-iKRASG12D and HBEC-iKRASWT cells revealed widespread changes for HBECs harboring the activated KRAS allele in the presence of Dox. Within the KRASG12D-induced genes, the Molecular Signatures Database identified the oncogenic RAS signature as a top-enriched gene set. Upregulation of Ras signaling in Dox-treated HBEC-iKRASG12D cells was also supported by a significant overlap with a KRAS signature previously characterized by Singh et al.

overall_design:
Gene expression microarray analyses were performed on Dox vs. no Dox in HBEC-iKRAS (WT) cell line and HBEC-iKRASG12D  (MUT) cell line.
multiple group comparisons

first: Ken

last: Scott

first: Fengju

last: Chen


title: Ssd1 and Gcn2 suppress global translational efficiency in replicatively aged yeast, while their activation in young cells extends lifespan

status: Public on Aug 10 2018

first: Bo

last: Xia

address: 6670 Bertner Ave, R10-414D

institute: Houston Methodist

summary: Using ribosome profiling, we find globally reduced translation efficiency during mitotic / replicative aging in budding yeast. Two mechanisms contribute to this: Firstly, the mRNA binding protein Ssd1 is induced during aging, sequestering mRNAs to P-bodies and stress granules that are abundant in old cells. Indeed, overexpression of Ssd1 reduced protein synthesis in young cells and extended lifespan, while loss of Ssd1 reduced the translational deficit of old cells and shortened lifespan. Secondly, the Gcn2 kinase is activated in old cells, phosphorylating and inactivating the translational initiation factor eIF2α. Accordingly, deletion of GCN2 reduced the translational defect of old cells. Furthermore, overexpressing an uncharged tRNA to fully activate Gcn2, or overexpression of its downstream mediator, Gcn4, extended replicative lifespan in a manner that was mostly dependent on autophagy without inhibiting the TOR pathway. As such, Ssd1 induction, activation of the integrated stress response or autophagy are favorable TOR-independent therapeutic targets for lifespan extension.

overall_design: Examination of transcription and translational efficiency in replicative lifespan analysis with RNA-seq and Ribo-seq with 3 replicates at 3 different timepoints

first: Zheng

last: Hu

first: Alin

last: Tomoiaga

first: Kaifu

first: Jessica

last: Tyler


title: Novel roles for NKX family members and innate immunity genes in cardiac remodeling

city: Pacific Grove

first: Luke

last: Gardner

state: California

address: 120 Ocean View Blvd, Hopkins Marine Station

institute: Stanford University

summary: Here we used RNAseq in juvenile pink salmon (Oncorhynchus gorbuscha) exposed to crude oil at different concetrations  to identify molecular changes associated with cardiac defects.

overall_design: Compare differentail expression between juvenile pink salmon exposed to crude oil at 4 different concetrations and unexposed control animals

first: Karen

last: Peck

first: Giles

middle: W

last: Goetz

first: Tiffany

middle: L

last: Linbo

first: James

last: Cameron

first: Nathaniel

last: Scholz

first: Barbara

last: Block

first: John

middle: P

last: Incardona


title: Base resolution methylome profiling of Branchiostoma lanceolatum embryos and adult tissues

city: Darlinghurst

first: Ozren

last: Bogdanovic

state: NSW

address: 384 Victoria Street

department: Genomics and Epigenetics

institute: Garvan Institute of Medical Research

summary: To be able to fully comprehend the contribution of the epigenome to embryonic development, it is important to understand how various components of the epigenome evolved. To date, a number of studies have thoroughly described various epigenetic mechanisms in both vertebrates and invertebrates, however there is currently a lack of high resolution epigenomic data corresponding to animals that form the invertebrate-vertebrate boundary. To that end, we have sequenced the genome of the European amphioxus (Branchiostoma lanceolatum) and explored various layers of its epigenome. Our whole genome bisulfite sequencing (MethylC-seq) approach revealed that amphioxus displays invertebrate-like, mosaic DNA methylation patterns. Nevertheless, we found significant DNA methylation remodeling events taking place during tissue differentiation, mostly consisting of developmental hypomethylation. This developmental loss of DNA methylation temporally coincides with the activation of the Tet protein orthologue in the amphioxus genome, suggestive of active demethylation. Furthermore, comparisons with chromatin accessibility data (ATAC-seq) demonstrate that this demethylation event affects cis regulatory elements, as previously described in vertebrates. Altogether, our study provides a rich developmental resource for studying epigenome evolution and demonstrates for the first time the existence of embryonic DNA methylation remodeling in an invertebrate chordate.

overall_design: MethyC-seq in amphioxus embryos and adult tissues; RRBS of amphioxus adult tissues

first: Ksenia

last: Skvortsova

first: Ryan

last: Lister


title: Queuosine modification protects cognate tRNAs against ribonuclease cleavage

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

summary: Eukaryotic transfer RNAs (tRNA) contain on average 13 modifications that perform a wide range of roles in translation and in the generation of tRNA fragments that regulate gene expression. Queuosine (Q) modification occurs in the wobble anticodon position of tRNAs for amino acids His, Asn, Tyr, and Asp. In eukaryotes, Q modification is fully dependent on diet or on gut microbiome in multi-cellular organisms. Despite decades of study, cellular roles of Q modification remain to be fully elucidated. Here we show that in human cells, Q modification specifically protects its cognate tRNAHis and tRNAAsn against cleavage by ribonucleases. We generated cell lines that contain completely depleted or fully Q-modified tRNAs. Using these resources, we found that Q modification significantly reduces angiogenin cleavage of its cognate tRNAs in vitro. Q modification does not change the cellular abundance of the cognate full-length tRNAs, but alters the cellular content of their fragments in vivo in the absence and presence of stress. Our results provide a new biological aspect of Q modification and a mechanism of how Q modification alters small RNA pool in human cells.

overall_design: Comprehensive comparative analysis of high throughput sequencing data to determine queuosine-mediated tRNA fragments

first: Xiaoyun

last: Wang

first: Zaneta

last: Matuszek

first: Yong

last: Huang

first: Marc

last: Parisien

first: Wesley

last: Clark

first: Michael

last: Schwartz

first: Qing

last: Dai


title: Retinoic acid suppresses MYB in adenoid cystic carcinoma [ChIP-seq]

city: Boston

first: Leonard

last: Zon

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

summary: Translocations that drive overexpression of the oncogenic transcription factor MYB are molecular hallmarks of adenoid cystic carcinoma (ACC), a malignant salivary gland tumor. Surgical resection, whenever possible, is the standard therapy for ACC, but there are no available therapeutic options available if surgery fails. Here we performed a chemical genetic screen using a zebrafish embryo culture system and identified retinoic acid agonists as potent suppressors of c-myb. Retinoic acid treatment strongly decreased c-myb gene expression in U937 cells and suggested a direct transcriptional mechanism of regulation. Retinoic acid agonists strongly inhibited tumor growth in vivo in different ACC patient derived xenograft models. Analysis of the xenografts revealed a significant decrease in MYB binding at translocated enhancers, thereby disrupting the MYB positive feedback loop that drives ACC. Our findings identify an important role of retinoic acid in MYB regulation and as a potential new effective therapy for ACC.

overall_design: ChIP-seq analysis of myb, RAR, and H3K27ac in ACC xenograft samples treated with vehicle or ATRA

first: Joseph

last: Mandelbaum

middle: I


title: Analysis of genes regulated by IKKb (Ird5) in the presence or absence of CrPV (Cricket paralysis virus) infection in Drosophila S2 cells

city: Strasbourg Cedex

first: Jean-Luc

last: Imler

address: 2, Allée Konrad Roentgen

department: IBMC

institute: CNRS

summary: This DNA microarray analysis (agilent) helps to identify candidate genes regulated by IKKb (Ird5) on Non-infected condition and after CrPV infection (2h and 6h).

overall_design: S2 cells were knocked down for dsGFP (as negative control) and IKKb (Ird5) by dsRNA soaking. DNA microarray was performed on Non infection, 2h & 6h after CrPV infections.

first: Akira

last: Goto

first: Laurent

last: Troxler


title: Analysis of IKKb (Ird5) regulated genes in control and hemizygote IKKb (Ird5) null mutant adult flies after DCV (Drosophila C virus) infection

summary: This DNA microarray analysis (agilent) help to identify candidate genes induced by DCV infection and regulated by IKKb (Ird5) in control (Df/+) and hemizygote IKKb (Ird5) null mutant (Dr/Ird5[1]) adult flies.

overall_design: Control and hemizygote IKKb (Ird5) null mutant flies were generated by crossing with Df(3R)Exel7328 and wild-type (cnbw) or IKKb (Ird5)[1] flies, respectively. They are then infected by DCV (500 pfu/fly) for 3 days. Tris injected flies for each genotype were used as control.


title: Precision oncology probe set for nomination of biomarker driven intervention opportunities in lung cancer

status: Public on Aug 09 2018

city: Dallas

first: Elizabeth

last: McMillan

state: Tx

address: 6000 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: Diversity in the genetic lesions that drive cancer initiation and progression is extreme. In consequence, a pressing challenge is the development of pharmaceuticals that selectively target disease mechanisms within the appropriate cancer patients. To help delineate the landscape of opportunities that can address this challenge, we have employed a chemistry-first discovery paradigm for de novo identification of druggable targets linked to robust patient selection hypotheses. To do this, a 200,000 compound diversity-oriented chemical library was profiled across a heavily annotated test-bed of >100 cell models representative of the somatic lesions detected in lung cancer. 171 distinct chemical/genetic associations, exploiting disease-selective mechanistic vulnerabilities within a diverse array of biological systems, were discovered. These corresponded to both novel and known oncogenotypes detectable within significant patient populations that lack effective therapy. Chemically addressab  le addictions to ciliogenesis in TTC21B mutants and GLUT8-dependent serine biosynthesis in KRAS/KEAP1 double mutants are prominent examples. These observations indicate a wealth of actionable opportunities within the complex molecular etiology of cancer. One chemical in the screen corrected with high expression levels of the positive regulator of the TLR pathway, PELI2, and high expression of PELI2 was predictive of chemical sensitivities outside the training set. SW151511 was thus selected for delineation of global changes in gene expression pattern in response to chemical perturbation. In this experiment, two SW151511-sensitive cells (H596 and H2122) and two SW151511-resistant cells (H661, HCC366) were treated for 24 hours with 10 uM of either chemical or DMSO. After which, microarray expression profiles were determined using Illumina BeadArray V4 and normalized with lumi in R bioconductor.

overall_design: All cells were seeded in 6-well plates at 300,000 cells/well in 2 mL standard culture media (RPMI, 5%FBS, penicillin/streptomycin) and allowed to adhere overnight.  The media was discarded and replaced with 1.5 mL treatment media containing either 0.1% DMSO vehicle control, or 10 uM of SW compound. After 24 hrs of treatment, total RNA was harvested using the miRNeasy Qiagen kit according to the manufacturer's instructions.

last: White

first: Hyunseok

last: Kim


title: Lineage dynamics of pancreatic development at single cell resolution

city: San Francisco

first: Jeremy

last: Reiter

address: 555 Mission Bay Boulevard South

institute: UCSF

summary: A developmental, single-cell transcriptional timecourse analysis was performed on murine pancreas from embryonic days 12, 14, and 17. Whole embryonic murine pancreas tissue was dissociated to single cells, stained with a dead-cell indicator, and subjected to fluorescence activated cell sorting (FACS) to select all live cells.  Single cell RNA-sequencing libraries were then subsequently generated for 4,631 cells at E12, 9,028 cells at E14 (comprised of two independent batches), and 4,635 cells at E17.  Cells were sequenced at a depth of ~60,000 reads/cell (E14 Batch 1) or ~30,000 reads/cell (E12, E14, and E17 Batch 2). Identification of a novel epithelial progenitor population and multiple novel mesenchymal populations showcases the power of single cell RNA-sequencing to uncover previously uncharacterized cell types, and highlights the dynamic cellular heterogeneity of the developing pancreas.

overall_design:
Data set 1: Single cell sequencing of embryonic Swiss Webster murine pancreatic tissue using the HiSeq 2500. Live cells were collected from E12.5, E14.5, and E17.5 whole pancreata and prepared using the 10x Single Cell instrument and v1 10X single cell kits according to standard protocol. The first batch consisted of 1 E14.5 litter and was run on 1 well of the 10X instrument. The second batch consisted of 1 well each of E12.5, E14.5, and E17.5 pancreata.

Data set 2: Single-cell RNA-sequencing was performed on embryonic Swiss Webster or Fev-Cre;ROSA26mTmG murine pancreatic tissue using the NovaSeq. Live cells were collected from E12.5, E14.5, and E17.5 (Swiss Webster) and E14.5 (Fev-Cre;ROSA26mTmG) whole pancreata and prepared using the 10x Single Cell instrument (10X Genomics) and the v2 10X single cell kits according to manufacturer's instructions.

first: Lauren

last: Byrnes

first: Daniel

last: Wong

first: Meena

last: Subramaniam

first: Nathaniel

last: Meyer

first: Caroline

last: Gilchrist

first: Sarah

last: Knox

first: Aaron

last: Tward

first: Chun

middle: J

last: Ye

first: Julie

middle: B

last: Sneddon


title: Retinoic acid suppresses MYB in adenoid cystic carcinoma

first: Leonard

last: Zon

state: MA


title: Characterizing the molecular changes of Basal Cell Carcinoma during vismodegib treatment

status: Public on Aug 08 2018

city: South San Francisco

first: Robert

last: Piskol

state: CA

address: 1 DNA Way

department: gRED Computational Sciences

institute: Genentech Inc.


title: Profiling of untreated and residual murine BCC after Hedgehog Pathway Inhibitor

summary:
RNA was isolated from laser capture micro-dissected (LCM) tumour nests from fresh frozen skin of K14Cre-ER; Ptch1fl/fl; p53fl/fl mice either before (untreated) or after (treated) 28 days of twice a day vismodegib dosing at 75mg/kg body weight by oral gavage.
The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech.
The ID of this project in Genentech's ExpressionPlot database is PRJ0014355

overall_design: Gene expression profiling of tumour cells from BCC mice before and after 28 days of vismodegib treatment

first: Brian

last: Biehs


title: Gene expression kinetics in 3T3L-1 Cells following treatment with Serotonin and Cortisol separately as well as together: 3T3L-1 cells co-cultured with Raw264.7 cells vs. 3T3L-1 cells cultured alone with the treatment conditions

city: Bhubaneswar

first: Biswaranjan

last: Pradhan

state: ODISHA

address: Jatni

department: Biological Sciences

institute: National Institute of Science Education and Research Bhubaneswar

summary: Gene expression kinetics in 3T3L-1 cells on treatment with Serotonin and Cortisol separately as well as together

overall_design: Twelve conditions of the expriment, 3T3L-1 cells co-cultured with Raw264.7 cells vs. 3T3L-1 cells cultured alone with the treatment conditions for 3 time points.

first: Priyadarshini

last: Sushri

first: Pradhan

last: Biswaranjan

first: Aich

last: Palok


title: Gene expression in 3T3L-1 and Raw264.7 Cells following treatment with Serotonin and Cortisol separately as well as together for 48 hours: 3T3L-1 or Raw264.7 cells co-cultured together vs. Reference (Equal mixture of total RNA from all samples)

overall_design: Eight conditions of the expriment, 3T3L-1 cells or Raw264.7 cells Vs. Reference (Equal mixture of total RNA from all samples).


title: Enterococcus faecalis rpoN mutant gene expression changes

city: Miami

first: Vijayalakshmi

middle: S

last: Iyer

state: Florida

address: 1600 NW 10th Avenue, RMSB 2048

institute: University of Miami, Miller School of Medicine

summary: E. faecalis, wildtype, rpoN deletion mutant and rpoN complement strains were grown in colony biofilms on a defined medium with glucose. Gene expression differences were recorded.

overall_design: Mutant strains were grown overnight, spotted onto permeable membranes on an agar surface to form colony biofilms, grown again overnight and then membranes were transferred to fresh media prior to harvest for RNA.

first: Matthew

last: Ramsey