title: Evaluation of the interplay between the ADAR editome and immunotherapy in melanoma

city: Geneva

first: Phil

middle: Fang

last: Cheng

address: Rue Gabrielle-Perret-Gentil 4

department: Oncology

institute: Hopitaux universitaires de Geneve

summary: We evaluated the editome of melanoma cell lines generated from patients pre- and post-immunotherapy with immune checkpoint inhibitors by RNAseq. Our results reveal a differential editing in Alu sequences between samples pre-therapy and relapses during therapy with immune checkpoint inhibitors

overall_design: RNA sequencing of 12 immunotherapy naive and 11 immunotherapy relapsed unpaired melanoma cell cultures was analysised for gene expression differences and RNA editome differences.

first: Marina

last: Tusup

first: Steve

last: Pascolo


title: ecDNA hubs drive cooperative intermolecular oncogene expression

status: Public on Nov 25 2020

city: Stanford

first: Howard

middle: Y

last: Chang

state: CA

address: CCSR 2130, 269 Campus Drive

department: Center for Personal Dynamic Regulomes

country: USA

institute: Stanford University

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Mechanical injury to murine femoral head epiphyseal or hip cartilage significantly modulates the transcriptome of articular chondrocytes in wildtype and MAPK9 knockout mice

status: Public on Nov 01 2020

city: Sheffield

first: Heba

last: Ismail

address: Firth Court, University of Sheffield, Western Bank, Sheffield

department: Infection, Immunity and Cardiovascular disease.

country: United Kingdom

institute: University of Sheffield

summary: To identify the gene expression profile of hip cartilage post injury in wild type C57BL6 and MAPK9 knockout mice.

overall_design: Total RNA obtained from femoral head epiphyseal cartilage of murine hips before and after 4 hours post injury induction


title: RNA-sequencing comparison of pneumonectomy and bleomycin reveals novel anti-fibrotic mechanisms and regulators

status: Public on Nov 13 2020

city: Austin

first: Qi

last: Tan

state: MN

address: 801 16th Ave NE

department: The Hormel Institute

institute: Univesity of Minnesota

summary: Fibroblast activation is transient in successful wound repair, but persistent in fibrotic pathologies. Understanding fibroblast deactivation during successful wound healing may provide new approaches to therapeutically reverse fibrogenic cell activation. To characterize the gene programs that accompany fibroblast activation and reversal during lung fibrosis resolution, we used RNA-seq analysis of flow-sorted Col1α1-GFP positive and CD45, CD31, and CD326 negative cells isolated from the lungs of young mice exposed to bleomycin and pneumonectomy. We compared fibroblasts isolated from controls to those isolated at days 14 and 30 after bleomycin exposure, as well as at 14 days after pneumonectomy, representing the peak of extracellular matrix deposition, early stage of fibrosis resolution, and non-fibrotic lung repair respectively.

overall_design: RNA-seq of Co11a1-GFP fibroblasts in D14 bleomycin, D30 Bleomycin, D14 pneumonectomy, and control groups.

first: Jeffrey

middle: A

last: Meridew

first: Giovanni

last: Ligresti

first: Daniel

middle: J

last: Tschumperlin

first: Jack

last: Wellmerling


title: Glia-specific nuclei isolation and single cell transcriptomics inform astrocyte pathology in human temporal lobe epilepsy

status: Public on Oct 29 2020

city: NEW YORK

first: Nadejda

middle: M

last: Tsankova

state: NY

address: 1425 MADISON AVE ICAHN BUILDING FLOOR 9, 9-20B

department: Pathology

institute: Icahn School of Medicine at Mount Sinai

summary: The role of human glia in many neurological disorders is still poorly understood due to the lack of tools that reliably isolate specific glial subpopulations from bulk tissue, directly from their native niche. To better understand the contributions of glial pathology in human epilepsy, we developed and validated a novel sorting strategy that simultaneously isolates nuclei populations of astrocytes (PAX6+), oligodendroglial progenitors (OPCs) (OLIG2+) and neurons (NEUN+) from non-pathological fresh-frozen human postmortem temporal neocortex brain tissue (TL Control) and then employed it, in combination with single cell RNA-seq, to characterize the cell-type specific transcriptome alterations in epilepsy temporal neocortex derived from fresh surgical material in patients with medically refractory temporal lobe epilepsy (TLE).

overall_design: Analysis of cell-type specific transcriptome changes in human temporal lobe epilepsy generated from cell-type-specific nuclei populations and single cells

first: German

last: Nudelman

first: Elena

last: Zaslavsky

first: Jessica

last: Tome-Garcia


title: ESRRB regulates glucocorticoid gene expression in mice and patients with acute lymphoblastic leukemia

status: Public on Jul 20 2020

city: Worcester

first: Julie

last: Zhu

state: MA

address: 364 Plantation Street

department: Molecular Cellular and Cancer Biology

institute: UMass Medical School

summary: Synthetic glucocorticoids (GCs), such as dexamethasone and prednisone, remain key components of therapy for patients with lymphoid malignancies. For pediatric patients with acute lymphoblastic leukemia (ALL), response to GCs remains the most reliable prognostic indicator; failure to respond to GC correlates with poor event-free survival. To uncover GC resistance mechanisms, we performed a genome-wide, survival-based short hairpin RNA screen and identified the orphan nuclear receptor estrogen-related receptor-? (ESRRB) as a critical transcription factor that cooperates with the GC receptor (GR) to mediate the GC gene expression signature in mouse and human ALL cells. Esrrb knockdown interfered with the expression of genes that were induced and repressed by GR and resulted in GC resistance in vitro and in vivo. Dexamethasone treatment stimulated ESRRB binding to estrogen-related receptor elements (ERREs) in canonical GC-regulated genes, and H3K27Ac Hi-chromatin immunoprecipitation revealed increased interactions between GR- and ERRE-containing regulatory regions in dexamethasone-treated human T-ALL cells. Furthermore, ESRRB agonists enhanced GC target gene expression and synergized with dexamethasone to induce leukemic cell death, indicating that ESRRB agonists may overcome GC resistance in ALL, and potentially, in other lymphoid malignancies.

overall_design:
RNA-seq:  The effects of dexamethasone treatment on gene expression in mouse T-ALL cells. We examine how the gene expression response changes with repression of NR3C1 and ESRRB.

HiChIP:  H3K27ac HiChIP analysis in mouse T-ALL cells to analyze active chromatin-chromatin interactions after treatment with DMSO or DEX
Cells were crosslinked with formaldehyde for 10 min.  DNA was enriched by chromatin-immunoprecipitation (ChIP), tagmented with Tn5 and analyzed by BGISeq500.  HiChIP was performed using an antibody against H3K27ac Antibody  (ABCAM, ab4729).

first: Kayleigh

last: Gallagher

first: T

middle: K

first: S

middle: H

last: Sanda

first: M

last: Kelliher


title: The response of intestinal microbiota and immunity to increasing dietary iron in piglets

status: Public on Sep 20 2020

city: Changsha

first: Shuai

last: CHEN

state: Hunan

address: Yuandaer Road 644

country: China

institute: Institute of Subtropical Agriculture, Chinese Academy of Sciences

summary: Iron is an essential metal for both animals and microbiota, and neonates and infants of humans and animals, in general, are at the risk of iron insufficient. However, excess dietary iron usually causes negative impacts on the host and microbiota. This study aimed to investigate over-loaded dietary iron supplementation on growth performance, the distribution pattern of iron in the gut lumen and the host, intestinal microbiota, and intestine gene expression profile of piglets. Sixty healthy weaning piglets were randomly assigned to six groups: fed with diets supplemented with ferrous sulfate monohydrate at the dose of 50ppm (Fe50 group), 100ppm (Fe100 group), 200ppm (Fe200 group), 500ppm (Fe500 group), and 800ppm (Fe800) for three weeks. The results indicated that increasing iron had no effects on growth performance but increased diarrheal risk and iron deposition in intestinal digesta, tissues of intestine and liver, and serum. High iron also reduced serum iron-binding capacity, apolipoprotein, and immunoglobin A. The RNA-sequencing analysis revealed that iron changed colonic gene expression profile, such as interferon gamma-signal transducer and activator of transcription 2 based anti-virus and bacteria gene network. Increasing iron also shifted cecal and colonic microbiota, such as reducing alpha diversity, Clostridiales and Lactobacillus reuteri, and increasing Lactobacillus and Lactobacillus amylovorus. Collectively, this study demonstrated that high dietary iron increased diarrheal incidence, changed intestinal immune response-associated gene expression, and shifts gut microbiota. The results would enhance our knowledge of iron effects on the gut and microbiome in piglets, and further contribute to understanding these aspects in humans.

overall_design: Sixty healthy weaning piglets (Duroc × Landrace × Landrace, 21 days old, average body weight 6.58kg)were randomly assigned to six groups: Fe50, Fe100, Fe200, Fe500, and Fe800 groups. The piglets in Fe50 group were fed on a corn and soybean meat-based diet supplemented with 50 ppm ferrous sulphate, while the diets of piglets in Fe100, Fe200, Fe500, and Fe800 were fed our formula supplemented with 100, 200, 500, and 800 ppm ferrous sulfate monohydrate, separately. This experiment was last for 21 days. The piglets were sacrificed on the day21 for collection of blood, liver tissue, intestinal tissue (including duodenum, jejunum, ileum, and colon), and digesta of cecum and colon.Ten colonic samples from Fe50 group (five samples) and Fe800 group (five samples)were set to RNA-Seq-based reference transcriptome analysis.

first: Xin

last: Wu

first: Xia

last: Wang

first: Yirui

last: Shao

first: Huansheng

last: Yang

first: Jie

last: Yin

first: Yulong


title: Comparison of macrophages that have or have not received mitochondria from adipocytes in vivo

status: Public on Sep 04 2020

city: St. Louis

first: Brian

last: DeBosch

state: Missouri

address: 660 South Euclid Avenue

department: Pediatrics and Cell Biology & Physiology

institute: Washington University School of Medicine

summary: Epididymal white adipose tissue from adipocyte-specific mitochondria reporter (MitoFat) mice was harvested, and the stromal vascular fraction was isolated. Live CD45+ F4/80+ CD64+ mtD2- and live CD45+ F4/80+ CD64+ mtD2+ macrophages were sort-purified directly into lysis buffer, followed by RNA sequencing.

overall_design: mtD2- and mtD2+ eWAT macrophages were compared pair-wise from n=4 male MitoFat mice on a normal chow diet. There are a total of 8 samples.

first: Jonathan

middle: R

last: Brestoff

first: Steven

middle: L

last: Tietelbaum


title: CircRNA preofiles in mock-infected and human cytomegalovirus (HCMV) infected human embryonic lung fibroblasts (HELF) cells

status: Public on Sep 05 2020

city: Shenyang

first: Jingui

last: Deng

state: Liaoning

address: No.36 Sanhao Street, Heping District

department: Virus Laboratory

institute: the Affiliated Shengjing Hospital, China Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: In this study, RNA-seq analysis was performed to generally understand the circRNA profiles of mock-infected and HCMV-infected HELF cells. Totally, 27,409 and 35,515 host circRNAs were identified in mock-infected and HCMV-infected HELF cells by RNA-seq respectively. Among them, 278 circRNAs were significantly modified filtrating by a threshold value of >2 (or <-2) fold-change and q-value <0.05. GO and KEGG pathway enrichment analysis suggested that the remarkably changed circRNAs might play important roles in viral entry, cell proliferation, and inhibition of apoptosis. Verification of four selected circRNAs ( circSP100, circMAP3K1, circTRIO, and circPLEKHM1) was performed using RT-PCR and Sanger sequencing. Moreover, further verification of circSP100 was performed using northern blotting and RT-qPCR and proteins binding directly to circSP100 were purified using RNA antisense purification (RAP).

overall_design: circRNA profiles of mock-infect and HCMV-infected HELF cells were generated by deep sequencing using Illumina Hiseq 2500

first: Juigui

first: Yunjing

last: Huang

first: Qiang

last: Ruan


title: Small RNA sequencing of brain-derived extracellular vesicles from post-mortem brain tissue of controls and Alzheimer's disease patients with different APOE genotypes

status: Public on Oct 20 2020

city: Baltimore

first: Kenneth

middle: W.

last: Witwer

state: MD

address: 733 N. Broadway

department: Department of Molecular and Comparative Pathobiology

institute: Johns Hopkins University School of Medicine

summary: Using a recently optimized method for separation of brain-derived EVs (bdEVs) from post-mortem tissues, we obtained bdEVs of 23 AD patients with different APOE genotypes and 7 controls. RNA was extracted from brain homogenate, an intermediate ("10K") EV fraction, and more purified EVs and subjected to small RNA sequencing. Numerous RNA species varied with AD pathology and APOE genotypes. Dysregulation of some of these molecules has been implicated in amyloid processing, neurodegeneration and metabolic functions. Molecular differences of bdEVs may thus reflect or play a role in modulating AD progression.

overall_design: Total RNA was extracted from brain tissue (BH), 10K, and EVs of 23 AD patient with different APOE genotypes, as well as from 7 control brains.

first: Yiyao

first: Tom

last: Driedonks

first: Andrew

middle: F

last: Hill

first: Lesley

last: Cheng

first: Andrey

last: Turchinovich

middle: W


title: Multimodal Mapping of the Tumor and Peripheral Blood Immune Landscape in Human Pancreatic Cancer

status: Public on Oct 01 2020

city: Ann Arbor

first: Marina

last: Pasca Di Magliano

state: MI

address: 1500 E Medical Center Dr.

institute: University of Michigan

summary: This is a human single cell sequencing repository of pancreatic cancer tumor tissue and PBMCs of pancreatic cancer patients.  The goal of this study was to thorough map the immune landscape of pancreatic ductal adenocarinoma patient tumors and peripheral blood.

overall_design:
This repository contains 16 PDA tissue samples, 3 adjacent normal pancreas samples, 16 PBMC samples isolated from human PDA patients, and 4 PBMC samples isolated from healthy volunteers. Tissues  were  mechanically  minced  and  enzymatically  digested  with  collagenase  P  (1mg/mL DMEM) and subsequently filtered through a 40μm mesh to obtain single cells. Dead cells were removed using MACS®Dead Cell Removal Kit (Miltenyi Biotec Inc.). Single-cell cDNA libraries were  prepared  and  sequenced  at  the  University  of  Michigan  Sequencing  Core  using  the  10x Genomics  Platform.  Samples  were run  using  paired  end  50  cycle  reads  on  HiSeq  4000  or the NovaSeq 6000 (Illumina) to a depth of 100,000 reads. The raw data were processed and aligned by the University of Michigan DNA Sequencing Core. Cellranger count version 3.0.0 with default settings was used, with an initial expected cell count of 10,000.
Submitter states the raw data is deposted in the dbGaP: accession number phs002071.v1.p1

middle: P

last: di Magliano


title: Transcriptomic analysis of of hepatocellular carcinoma cells Hep G2 overexpressing EFTUD2

status: Public on Jul 15 2020

city: Guangzhou

first: Chen

last: Qu

state: Guangdong

address: #601 West Huangpu Road

institute: Jinan University

summary: We performed RNA-sequencing to detect the effects of overexpressing EFTUD2 in Hep G2 cells on gene expression.

overall_design: Hep G2 cells were infected with empty lentivirus vector or lentivirus expressing EFTUD2 gene to establish Hep G2 cells stably expressing empty vector or EFTUD2 gene. The total RNA of Hep G2 cells with or without EFTUD2 overexpression were isolated using Trizol reagent. The transcriptome profiles of these cells were generated by RNA sequencing using BGISEQ-500.


title: Ion AmpliSeq transcriptome analysis of atypical hepatocytes

status: Public on Jul 03 2020

city: Itabashi-ku

first: Mitsuhiko

last: Moriyama

state: Tokyo

address: Oyaguchi Uemachi 30-1

country: Japan

institute: Nihon University School of Medicine

summary: We  compared transcriptome between atypical and non-atypical hepatocytes by RNA-seq

overall_design: mRNA profiles of atypical and non-atypical hepatocytes which were obtained by laser capture microdisection (LCM) of FFPE

first: Tatsuo

last: Kanda

first: Kazumichi

last: Kuroda


title: Developmental GABA polarity switch and neuronal plasticity in Bioengineered Neuronal Organoids

status: Public on Jul 02 2020

city: Esch-sur-Alzette

first: Rashi

last: Halder

address: 7, Avenue des Hauts-Fourneaux

country: Luxembourg

institute: Luxembourg Center for Systems Biomedicine

summary: Brain organoids are promising tools for disease modelling and drug development. For proper neuronal network formation excitatory and inhibitory neurons as well as glia need to co-develop. Here we report the directed differentiation and self-organization of induced pluripotent stem cells in a collagen hydrogel towards a highly interconnected neuronal network in a macroscale tissue format. Bioengineered Neuronal Organoids (BENOs) comprise interconnected excitatory and inhibitory neurons as well as supportive astrocytes and oligodendrocytes. Giant depolarizing potential (GDP)-like events observed within 20-40 days of BENO culture mimic early network activity of the fetal brain. The switch from excitatory to inhibitory GABA activity, and reduced GDPs at >40 day BENO cultures indicate progressive neuronal network maturation. BENOs demonstrate expedited complex network burst development after two months of culture and provide the first evidence for long-term potentiation and plasticity in brain organoids. BENOs exhibit structural and functional properties similar to the fetal brain and thus may be explored as a model to study the development of neuronal plasticity.

overall_design: Bioengineered neuronal organoid RNA was analyzed at different time points of directed cortical differentiation in a collagen hydrogel. 3-6 organoids were used as biological replicates for each time point. Organoids derived from 2 independent differentiation experiments.

first: Maria

last: Zafeiriou

first: Andre

last: Fischer

first: Wolfram

last: Zimmermann


title: Long noncoding RNA and mRNA expression profile in brainstem of DBA/1 and C57BL/6 mouse

status: Public on Jun 23 2020

city: Chengdu

first: Ling

last: Liu

state: Sichuan

address: Wai Nan Guo Xue Lane 37 #

department: Department of neurology

institute: West China Hospital, Sichuan University

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

summary: Our study reveals that many lncRNAs and mRNAs were differentially expressed between the brainstem of DBA/1 and C57BL/6 mouse

overall_design: Microarray analysis were conducted to investigate long non-coding RNAs (lncRNAs) and mRNA expression profile in the brainstem of DBA/1(n=4) and C57BL/6 (n=4) mice. C57BL/6 mice were enrolled as control groups.

first: Lina

last: Zhu


title: IPF Cell Atlas

status: Public on May 12 2020

city: New Haven

first: Naftali

last: Kaminski

state: CT

address: 300 Cedar Street

department: PCCSM

institute: Yale School of Medicine

summary: Single Cell RNAseq of Whole Lung Dissociates from IPF, COPD and control lungs

overall_design: Exploratory analysis of disease and healthy lung cell populations

first: Taylor

last: Adams

first: Jonas

last: Schupp

first: Ivan

last: Rosas


title: Analysis of DNA methylation-based tumor immune microenvironment patterns in metastatic melanoma

status: Public on Mar 25 2020

city: Lund

first: Göran

middle: B

last: Jönsson

address: Scheelevägen 2

department: Clinical Sciences

country: Sweden

institute: Lund University

type: Methylation profiling by genome tiling array

summary: We subjected 196 melanoma tumors to genome-wide methylation analysis using the Illumina Infinium MethylationEPIC BeadChip array.

overall_design: Bisulphite converted DNA from 196 melanoma tumors were hybridized using Illumina Infinium MethylationEPIC BeadChip array

first: Shamik

last: Mitra

first: Martin

last: Lauss


title: Social network architecture of human immune cells in ZIKV-infected patients highlights a unique role of plasmacytoid dendritic cells

status: Public on Mar 05 2020

city: Cambridge

first: Ce

last: Gao

address: 400 Technology Square

institute: Ragon Institute of MGH, MIT and Harvard

summary: Zika virus (ZIKV) is an emerging mosquito-borne pathogen with increasing public health significance. To characterize interconnected immune responses to ZIKV, we here examined transcriptional signatures of CD4 and CD8 T cells, B cells, NK cells, monocytes, myeloid dendritic cells (mDCs), and plasmacytoid dendritic cells (pDCs) from three individuals with naturally-acquired ZIKV infection. While gene expression patterns from most cell subsets displayed signs of impaired antiviral immune activity, pDCs showed a highly distinct transcriptional response marked by an activation of innate immune recognition and type I interferon signaling pathways, combined with a downregulation of key host factors known to support ZIKV replication steps. At the same time, pDCs exhibited a unique expression pattern of gene modules that were tightly correlated with alternative cell populations, suggesting highly collaborative interactions between pDCs and other immune cells. Together, these results point towards a discrete but integrative role of pDCs in the human immune response to ZIKV infection.

overall_design: 3 ZIKV infected patients and 3 age and gender matched healthy donors were used as control, in addition, we also performed cell subsets analysis of 3 healthy donor infected with ZIKV in vitro.

first: Stephane

last: Hua

first: Xiaoming

last: Sun

first: Jane

middle: E

last: Blackmer

first: Zhengyu

last: Ouyang

first: Kevin

last: Ard

first: Andrea

last: Ciaranello

first: Sigal

last: Yawetz

first: Paul

last: Sax

first: Eric

middle: S

last: Rosenberg

first: Mathias

last: Lichterfeld

first: Xu

middle: G

last: Yu


title: Single cell and bulk RNA sequencing of Enteroendocrine cells from human hormone reporter organoids

status: Public on May 13 2020

city: Utrecht

first: Jens

last: Puschhof

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Enteroendocrine cell subpopulations were sorted by positivity for endogenous knock-in reporters in different hormones. Unbiased and biased FAC sorting was performed and coupled to single cell sorting by the SortSeq protocol (Muraro et al., 2016) and bulk sequencing.

overall_design: Enteroendocrine cell differentiation was induced through overexpression of Neurogenin 3. After 5 days of differentiation, cells were collected by FACS and subjected to single cell and bulk RNA sequencing.

first: Joep

last: Beumer

first: Julia

last: Bauzá-Martinez

first: Adriana

last: Martínez-Silgado

first: Rasa

last: Elmentaite

first: Kylie

last: James

first: Alexander

last: Ross

first: Delilah

last: Hendriks

first: Benedetta

last: Artegiani

first: Georg

last: Busslinger

first: Bas

last: Ponsioen

first: Amanda

last: Andersson-Rolf

first: Aurelia

last: Saftien

first: Charel

last: Boot

first: Kai

last: Kretzschmar

first: Maarten

last: Geurts

first: Yotam

last: Bar-Ephraim

first: Cayetano

last: Pleguezuelos-Manzano

first: Yorick

last: Post

first: Harry

last: Begthel

first: Franka

last: van der Linden

first: Carmen

last: Lopez-Iglesias

first: Willine

last: van de Wetering

first: Reinier

first: Peter

last: Peters

first: Albert

last: Heck

first: Joachim

last: Goedhart

first: Hugo

last: Snippert

first: Matthias

last: Zilbauer

first: Sarah

last: Teichmann

first: Wei

last: WU

first: Hans

last: Clevers


title: Transdifferentiation of tumor infiltrating innate lymphoid cells during progression of colorectal cancer

status: Public on Dec 29 2019

city: Beijing

first: Pengyan

last: Xia

state: Beijing

address: 15, Datun Road, Chaoyang district

department: The CAS key Laboratory of Infection and Immunity, Institute of Biophysics

institute: Institute of biophysics, Chinese Academy of Sciences

summary: Innate lymphoid cells (ILCs) reside in mucosal surfaces to potentiate immune responses, sustain mucosal integrity and maintain tissue homeostasis. However, how tumor infiltrating ILCs modulate tumor development and progression is unclear. Here we profiled tumor infiltrating ILCs during colorectal cancer (CRC) progression by single-cell RNA sequencing. We identified six clusters of tumor infiltrating ILCs with unique features. ILC1s expressed inhibitory receptors and underwent inhibitory functional conversion at the late stage of CRC. ILC2s were classified into three subsets (called ILC2-A, -B, -C), ILC2-C subset could facilitate tumor progression. HS3ST1 and PD1 were highly expressed in ILC2s of late stage CRC tumors and deficiency of HS3ST1 or PD1 in ILC2s suppressed tumor growth. Moreover, ILC3s transdifferentiated into ILCregs during CRC progression and ILCregs promoted tumor growth. Of note, TGF- signaling initiated the conversion of ILC3s to ILCregs and blockade of TGF- signaling could disrupt the ILCreg transdifferentiation and inhibited tumor growth as well. Thus intervention of ILC conversions might be a potential strategy for CRC immunotherapy.

overall_design: Colon tumor infiltrating ILCs during colorectal cancer (CRC) progression were profiled by single-cell RNA sequencing

first: Shuo

last: Wang


title: Multi-omics analysis reveals divergent epigenetic regulation of gene expression and drivers of esophageal squamous cell carcinoma (WGBS)

status: Public on Apr 30 2020

city: San Francisco

last: Wu

address: 600 16th street

department: Department of Medicine

institute: University of California, San Franciso

type: Methylation profiling by high throughput sequencing

summary: Purpose: Epigenetic landscapes can shape physiologic and disease phenotypes. We used whole genome bisulfite sequencing, RNAseq, and ChIP-seq technologies to understand the methylome profiling, gene expression and regulation via epigenetic alterations on esophageal sequamouse carcinoma comparing to adjacent non-tumor tissues.

overall_design: Methods:  Frozen surgical removed specimens of ten matched normal and tumor samples were used for DNA.

last: Cao

first: HanYan

last: Lee

first: Aubhishek

last: Zaman

first: Sean

last: McCorkle

first: Ming

last: Yan

first: Justin

last: Chen

first: Qinghe

last: Xing

first: Nasa

last: Sinnott-Armstrong

first: Hongen

last: Xu

last: Sailani

first: Wenxue

last: Tang

first: Yuanbo

last: Cui

first: Jia

last: Liu

first: Hongyan

last: Guan

first: Pengju

last: Lv

first: Xiaoyan

last: Sun

first: Lei

first: Pengli

last: Han

first: Yanan

last: Lou

first: Jing

last: Chang

first: Jinwu

first: Yuchi

last: Gao

first: Jingcheng

last: Guo

first: Gundolf

last: Schenk

first: Alan

last: Hunter Shain

first: Fred

last: Biddle

first: Eric

last: Collisson

first: Michael

last: Snyder

first: Trever

last: Bivona


title: Mitochondrial Pyruvate Carrier 1 (MPC1) promotes peripheral T cell quiescence through metabolic regulation of thymic development

status: Public on Dec 30 2019

city: Salt Lake City

first: Ryan

last: O'Connell

state: UT

address: Emma Eccles Jones, Medical Research Building, 15 North Medical Drive East

department: Pathology, Microbiology & Immunology

institute: University of Utah

summary: The transporter which uptakes pyruvate into the mitochondria during pyruvate oxidation, called the Mitochondrial Pyruvate Carrier (MPC), was only recently identified. While the MPC has been studied in a variety of cell types, including cancer cells and stem cells, very little is known about the importance of MPC in immune cells. Here, we delete MPC from hematopoietic cells and measure its impact on thymocyte gene expression by 10X Genomics scRNA-seq.

overall_design: DAPI negative cells were FACS sorted from homogenized and RBC lysed thymi of 6-10 week old Female MPC1fl/fl (WT) and Vav-Cre MPC1fl/fl (KO). Single cell data.

first: Andrew

last: Ramstead

first: Jared

last: Wallace


title: A human single cell atlas of the substantia nigra reveals novel cell specific pathways associated with the genetic risk of Parkinson’s disease and neuropsychiatric disorders

status: Public on Jan 07 2020

city: Cardiff

first: Caleb

last: Webber

address: Hadyn Ellis Building, Maindy road

department: School of Medicine

institute: Cardiff University

summary: We describe the first human single-nuclei transcriptomic atlas for substantia nigra (SN), generated by sequencing ~ 17,000 nuclei from matched cortical and SN samples.  We show that common genetic risk for Parkinson’s disease (PD) is associated with dopaminergic neuron (DaN)-specific gene expression including mitochondrial functioning, protein folding and ubiquitination pathways. We also identified a distinct cell-type association between PD risk and oligodendrocyte-specific expression implicating metabolic and gene expression regulation networks. Beyond PD, we find SN DaNs and GABAergic neurons to be associated with different neuropsychiatric disorders, particularly schizophrenia (SCZ) and bipolar disorder (BP). We identified distinct cortex/SN associations with SCZ genetic risk for both excitatory (synaptic functioning) and dopaminergic neurons (mitochondrial functioning and synaptic signalling). Conditional analyses shows that independent sets of loci associate distinct neuropsychiatric disorders with the same neuronal types. This atlas guides our aetiological understanding by associating SN cell-type expression profiles with specific disease risk.

overall_design: Single nuclei were extracted and isolated from 3mm2 blocks that were manually dissected from the substantia nigra and cortex of 5 control (4 males & 1Female)de-identified post-mortem human donors, totaling to 12 matched samples, including 2 SN replicates and sequenced using the 10X chromium system (V2)

first: Devika

last: Agarwal

first: Cynthia

last: Sandor

first: Viola

last: Volpato

first: Tara

last: Caffrey

first: Rory

last: Bowden

first: Javier

last: Alegre-Abarrategui

first: Richard

last: Wade-Martins


title: Genome-wide methylation analysis of gastric mucosae using Infinium HumanMethylation 450 BeadChip

status: Public on Dec 23 2019

city: Chuo-ku

first: Satoshi

last: Yamashita

address: Tsukiji 5-1-1

institute: National Cancer Center Research Institute

summary: DNA methylation in gastric mucosae

overall_design: A picture of epigenetic alterations in gastric mucosae with and without Helicobacter pylori infection was characterized.

first: Sohachi

last: Nanjo

first: Takao

last: Maekita

first: Emil

last: Rehnberg

first: Hideyuki

last: Takeshima

first: Toshikazu

last: Ushijima


title: Genome-wide analysis upon ZBTB18 expression and/or CTBP2 silencing in Glioblastoma

status: Public on Dec 01 2019

city: Freiburg

first: Maria Stella

last: Carro

address: Breisacherstraße 64

country: Germany

institute: Freiburg University Medical Center

summary: We have identified the CTBP2 protein as a new ZBTB18 interactor. Here we have evaluated transcriptomic changes upon CTBP2 knockdown in the GBM cell line SNB19. Moreover, we have analyzed whether CTBP2 is required for ZBTB18-mediated gene repression.

overall_design: Total RNA obtained from SNB19 cells transduced with eith control vectors (EV and shctr), ZBTB18, shCTBP2 or ZBTB18 and shCTBP2

first: Maria

first: Roberto

last: Ferrarese


title: Inflammatory Cytokines shape a Changing DNA Methylome in Monocytes Mirroring Disease Activity in Rheumatoid Arthritis (in vitro)

status: Public on Dec 31 2019

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

summary: Genome wide DNA methylation profiling of CD11b+CD33+ cells after treatment with different cytokines. The Illumina Infinium MethylationEPIC Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpGs in CD11b+CD33+ cells isolated from PBMCs treated in vitro for 4 days with TNF-alpha, IFN-alpha, IFN-gamma or control.

overall_design: Bisulphite converted DNA from the 12 samples were hybridised to the Illumina Infinium MethylationEPIC Beadchip.

last: Rodríguez-Ubreva

first: Carlos

last: de la Calle-Fabregat

first: Tianlu

last: Li

first: Laura

last: Ciudad

first: Francesc

last: Català-Moll

first: Octavio

last: Morante-Palacios

first: Antonio

last: García-Gómez

first: Raquel

last: Celis

first: Frances

last: Humby

first: Alessandra

last: Nerviani

last: Martín

first: Constantino

last: Pitzalis

first: Juan

middle: D

last: Cañete


title: Histone H3 lysine 56 acetylation is required for formation of normal levels of meiotic DNA breaks in S. cerevisiae

status: Public on Dec 25 2019

city: Debrecen

first: Lorant

last: Szekvolgyi

address: Egyetem ter 1.

department: Department of Pharmacy

country: Hungary

institute: University of Debrecen

type: Genome binding/occupancy profiling by genome tiling array

summary: Genomic profiling of (1) histone H3K56 acetylation and (2) meiotic DSBs flanked by replication protein A (RPA). The major goal was to reveal the genome-wide distribution DSBs when the H3K56 residue was mutated to alanine (H3K56A).

overall_design: Meiotic DSBs were mapped in control (H3 ctrl) and H3K56A mutant plasmid shuffle strains using the replication protein A (RPA) ChIP approach (Borde V et al. 2009 (PMID 19078966)) at 4 hours after the induction of sporulation. H3K56 acetylation were mapped by ChIP-chip using a specific antibody agains this histone modification.

first: Lóránt

last: Székvölgyi


title: Geographical distribution and molecular insights into abamectin and milbemectin cross-resistance in European field populations of Tetranychus urticae

status: Public on Mar 17 2020

city: Ghent

first: Wannes

last: Dermauw

address: Coupure Links 653

department: Crop Protection

country: Belgium

institute: University Ghent

summary: Macrocylic lactones, milbemectin and abamectin, are compounds that are frequently used for the control of the two-spotted spider mite Tetranychus urticae. The development of abamectin resistance in this major pest has become an increasing problem worldwide, potentially compromising the use of milbemectin. In this study, gene expression profile differences between abamectin/milbemectin resistant T. urticae populations (ES1, IT2 and UK6) and a susceptible T. urticae population (RO1 and IT3) were compared using Illumina RNAseq.

overall_design: In total, 20 RNA-seq samples (5 populations, 4 biological replicates per population) from Tetranychus urticae were generated. RNA was collected from adult T. urticae females. For each sample, Illumina mRNA-seq libraries were constructed and stranded, paired-end 125 bp (RO1, IT2, IT3 and ES1) or 150 bp (UK6) RNA-seq Illumina reads were generated. The obtained reads were used to quantify gene expression in each sample.

first: Wenxin

last: Xue

first: Simon

last: Snoeck

first: Thomas

last: Van Leeuwen


title: Copper and MTF1: New roles for a classic metal sensing transcription factor in myogenesis

status: Public on Oct 04 2019

city: Pittsburgh

first: Sarah

last: Hainer

state: PA

address: 4249 Fifth Ave

department: Department of Biological Sciecnes

institute: University of Pittsburgh

summary: MTF1 is a highly conserved metal-binding transcription factor in eukaryotes. MTF1 binds to DNA sequence motifs, termed metal response elements (MREs) to induce the expression of genes involved in metal and oxidative stress homeostasis. MTF1 is responsive to both metal excess and deprivation, and can also protect cells from oxidative and hypoxic stresses. Disruption of metal homeostasis leads to the development of several pathological states. Despite its roles in these processes , MTF1 has been shown to be required for developmental processes such as embryonic liver formation.  In this study, we used multiple strategies to understand the mechanism by which MTF1 functions in skeletal muscle differentiation and to determine the role cellular copper (Cu) status plays in this process. We provide the functional relationships between MTF1, Cu, myogenic gene promoters, and MyoD, an specific component of the myogenic transcriptional machinery in differentiating primary myoblasts derived from mouse satellite cells. We found that MTF1 is induced and translocated to the nucleus upon initiation of myogenesis. Consistent with previous studies from our laboratory , addition of non-toxic concentrations of Cu promote myogenesis and enhanced MTF1 expression. CRISPR/Cas9-mediated depletion of MTF1 demonstrated that MTF1 is essential for proper development of skeletal muscle, as partial Mtf1 knockdown leads to apoptosis to differentiating myoblasts. MTF1 was also found to bind Cu at a carboxy-terminal tetra-cysteine cluster, which may contribute to the mobilization of Cu to the nucleus during myogenesis. ChIP-seq and ChIP-qPCR analyses showed that MTF1 binds at the promoter regions of myogenic genes as part of a complex with MyoD, the master transcriptional regulator of the myogenic lineage. These results have the potential to initiate a new area of research in MTF1 function and in the regulation of myogenesis. Furthermore, these studies set the basis to understand the role of Cu at the transcriptional level, affects growth and development and will contribute to the largely unexplored are of muscular phenotypes observed in human pathologies associated to Cu misbalance, such as Menkes’ and Wilson’s diseases.

overall_design: ChIP-seq profiling of MTF1 in the presence or absence of CuSO4:  24plusCu is presence of CuSO4.  24noICu and 24plusI are absence of CuSO4.

first: Cristina

last: Tavera-Montañez

first: Daniella

last: Cangussu

first: Yao

last: Xiao

first: Pablo

last: Reyes-Gutierrez

first: Yeonsoo

last: Yong

first: Jaime

last: Rivera-Perez

first: Anthony

middle: N

last: Imbalzano

last: Navea

last: Fazzio

first: Teresita

last: Padilla-Benavides


title: Inflammatory cytokines and organ dysfunction associate with the aberrant DNA methylome of monocytes in sepsis

status: Public on Oct 03 2019

first: Esteban

last: Ballestar

summary: Genome wide DNA methylation profiling of monocytes from healthy donors, systemic inflammatory response syndrome (SIRS) and septic patients. The Illumina Infinium MethylationEPIC Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpGs in CD14+CD66bneg monocytes isolated from PBMCs of 11 healthy donors, 4 SIRS and 14 septic patients.

overall_design: Bisulphite converted DNA from the 29 samples were hybridised to the Illumina Infinium MethylationEPIC Beadchip.

first: Clara

last: Lorente-Sorolla

first: Antonio

last: García-Gómez

first: Francesc

last: Català-Moll

first: Victor

last: Toledano

first: Laura

last: Ciudad

first: José

last: Avendaño-Ortiz

first: Charbel

last: Maroun-Eid

first: Alejandro

last: Martín-Quirós

first: Mónica

last: Martínez-Gallo

first: Adolfo

last: Ruiz-Sanmartín

first: Álvaro

last: García del Campo

first: Ricard

last: Ferrer-Roca

middle: C

last: Ruiz-Rodriguez

first: Damiana

last: Álvarez-Errico

first: Eduardo

last: López-Collazo


status: Public on Feb 07 2020

city: Birmingham

first: Thanh

middle: Minh

last: Nguyen

state: AL

address: 1670 University Blvd, Volker Hall G094

department: Department of Biomedical Engineering

institute: University of Alabama at Birmingham

summary: This is the dataset used in the paper: Zhang et al. Identifying the Key Regulators that Promote Cell-cycle Activity in the Hearts of Early Neonatal Pigs after Myocardial Injury. PloS One.

first: Jaym

last: Zhang


title: Stat1-induced NAMPT sustains glycolysis to regulate gene expression in classically activated macrophages

status: Public on Oct 01 2019

first: Ryan

last: O'Connell

summary: Single Cell RNA Sequencing is used to profile in vivo responses by immune cells lacking the Nampt NRE1 region to melanoma challenge, finding multiple defects in macrophages and other myeloid APCs. We analyzed B16F10 melanoma tumor infiltrating immune cells from mice specifically lacking NRE1 in hematopoietic cells, finding inflammatory and metabolic defects in APC populations within tumors, correlating with trends toward defective control of malignant growth.

overall_design: 500,000 B16F10 cells (from Mingnan Chen lab) injected subcutaneously into NRE1 fl/fl VavCre(-) or NRE1 fl/fl VavCre(+) male mice. Tumors were excised at the endpoint, pooled and digested with Accumax to liberate single cells. Cells were stained with APC-CD45 (1:200) for 15 min on ice and sorted via flow cytometer (HCI Aria) after spiking 1:100 DAPI (1x final). CD45+DAPI- cells were obtained (860,000 cells from WT, 1,0260,00 cels from KO), and subjected to Single Cell RNA Sequencing.

middle: M

first: Thomas

last: Huffaker

first: H

middle: A

last: Ekiz

first: Warren

last: Voth


title: Tumour Cell Heterogeneity Instructs Fibroblast Diversity and Reciprocal Signalling

status: Public on Sep 30 2019

city: Macclesfield

first: Claus

last: Jorgensen

state: Lancs

address: Alderley Park

institute: Cancer Research UK Manchester Institute

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

overall_design: Refer to individual Series


title: Tumour Cell Heterogeneity Instructs Fibroblast Diversity and Reciprocal Signalling [dataset 2]

summary:
We investigated changes to murine pancreatic fibroblast gene expression in response to co-culture with 8 murine pancreatic tumour cell sub-populations.
Tumours are complex ecosystems where phenotypically diverse tumour cells are embedded in a heterocellular environment. Using an in vitro model of intra-tumoral heterogeneity, we show that clonal tumour cell populations establish distinct interactions with stromal fibroblasts to expand phenotypic diversity across tumour and stromal cell populations. Heterocellular interactions drive differential engagement of tumour cell reciprocal signalling pathways, resulting in normalisation of cell-autonomous differences in MAPK signalling but diversification of AKT signalling.  Consequently, tumour cell clones display differential cell-autonomous and non-cell autonomous dependencies. These results demonstrate that tumour-stroma interactions amplify tumour cell autonomous diversity and that our existing perspective on tumour cell heterogeneity underestimates functional diversity.

overall_design: RNA sequencing of fibroblasts after direct co-culture with tumour sub-clones

first: Amy

last: McCarthy


title: Tumour Cell Heterogeneity Instructs Fibroblast Diversity and Reciprocal Signalling [dataset 1]

summary:
We investigated changes to gene expression in 8 murine pancreatic tumour sub-clones response to co-culture with fibroblasts.
Tumours are complex ecosystems where phenotypically diverse tumour cells are embedded in a heterocellular environment. Using an in vitro model of intra-tumoral heterogeneity, we show that clonal tumour cell populations establish distinct interactions with stromal fibroblasts to expand phenotypic diversity across tumour and stromal cell populations. Heterocellular interactions drive differential engagement of tumour cell reciprocal signalling pathways, resulting in normalisation of cell-autonomous differences in MAPK signalling but diversification of AKT signalling.  Consequently, tumour cell clones display differential cell-autonomous and non-cell autonomous dependencies. These results demonstrate that tumour-stroma interactions amplify tumour cell autonomous diversity and that our existing perspective on tumour cell heterogeneity underestimates functional diversity.

overall_design: RNA sequencing of tumour 8 sub-clones from mono-culture or isolted from direct co-culture with fibroblasts.


title: Comparison of RNA Isolation Methods in Yeast on RNA-Seq: Implications for Differential Expression and Meta-Analyses

status: Public on Aug 07 2019

city: Fayetteville

first: Jeffrey

middle: A.

last: Lewis

state: AR

address: 850 W. Dickson St.

department: Biological Sciences

institute: University of Arkansas

summary: Based on the different chemistries of phenol extraction of RNA versus commercial kits, we hypothesized that certain species of mRNA may be preferentially extracted depending upon method, which could masquerade as differential expression in downstream RNA-seq experiments. We tested this using Saccharomyces cerevisiae samples that only differ in the RNA isolation method: a "standard" hot phenol extraction, versus two different commercial RNA isolation kits. While the kits had comparable relative mRNA abundances, samples isolated with hot phenol  had higher relative abundance of mRNAs encoding membrane proteins. We hypothesize that hot phenol better solubilizes mRNAs associated with cellular membranes. We then compared the effects of each RNA isolation method on the ability to identify differentially expressed transcripts, using the yeast heat shock response a test case. The method of RNA isolation had little effect on the ability to identify differentially expressed transcripts. Thus, experiments within a single lab are unlikely to be affected by the choice of RNA isolation method as long as the same method is used throughout an experiment. For meta-analyses however, researchers should be cautious if trying to compare experiments where the RNA isolation methods differ.

overall_design: We performed RNA-seq comparing the effects of RNA isolation method on relative transcript abundance and the ability to detect differential expression.

first: Amanda

last: Scholes


title: In vivo Firre and Dxz4 deletion elucidates roles for autosomal gene regulation

status: Public on Nov 15 2019

city: Munich

first: Daniel

last: Andergassen

address: Biedersteiner Straße 29

institute: Technical University Munich

summary: Recent evidence has determined that the conserved X chromosome “mega-structures” controlled by the Firre and Dxz4 alleles are not required for X chromosome inactivation (XCI) in cell lines. Here we determined the in vivo contribution of these alleles individually and in combination and found that mutant mice are viable, fertile and show no defect in random or imprinted XCI. However, the lack of these elements results in many dysregulated genes on autosomes in an organ-specific manner, suggesting that these X-linked loci are involved in autosomal gene regulation rather than XCI biology.

overall_design: RNA-seq from Firre and/or Dxz4 deletion mouse strains (embryonic, extraembryonic and adult organs)

first: Alexander

last: Meissner

first: John

last: Rinn


title: Expression data from D. melanogaster whole guts or intestinal progenitor cells isolated from flies mock infected or infected with wild type Vibrio cholerae (C6706) or type VI secretion system deficient Vibrio cholerae (C6706ΔvasK)

status: Public on Aug 21 2019

city: Edmonton

first: Edan

last: Foley

state: Alberta

address: 114th St and 87th ave

department: Medical Microbiology and Immunology

country: Canada

institute: University of Alberta

summary: We used RNA-seq to determine transcriptional profiles of whole guts or IPCs isolated from guts infected with wild type or type VI secretion system deficient Vibrio cholerae. We found significant differences between guts and progenitor cells infected wild type or type VI secretion system deficient Vibrio cholerae.

overall_design: Newly eclosed female flies were raised for 5 days at 29C and then mock infected (with sterile bacterial growth media) or infected with wild Vibrio cholerae (C6706) or type VI secretion system deficient Vibrio cholerae for 24 hours. After 24 hours guts were dissected. The transcriptome of whole guts or intestinal progenitor cells only was sequenced.

first: David

last: Fast


title: ATAC-Sequencing of human fetal PreProB and ProB progenitors.

status: Public on Aug 06 2019

city: Oxford

first: Sorcha

last: O'Byrne

state: Oxford

address: MRC MHU and WIMM, John Radcliffe Hospital

department: Department of Paediatrics

institute: University of Oxford

summary: Human lymphopoiesis is a dynamic life-long process that starts in utero at 6 weeks gestation; however developmental pathways defining fetal lymphopoiesis are largely unexplored. While the first committed B-progenitor in normal human bone marrow (BM) is a CD10+ve ProB-progenitor, the identification of a CD10-ve B-progenitor (Pre/ProB progenitor) in cord blood suggests there may be a second B-lymphoid development program in fetal life. Here, we provide a comprehensive analysis of the  fetal B-cell developmental hierarchy and report the presence of both PreProB- and ProB-progenitors in fetal tissues and describe their ontogeny, molecular and functional characteristics. PreProB- and ProB-progenitors appear early in the first trimester in fetal liver, followed by a sustained second wave of B-progenitor development in fetal BM, where together they form >40% of the total HSC/progenitor pool. Unexpectedly, one-third of the B-progenitors (13±1% of lin-CD34+ cells) are CD10-ve PreProB-progenitors while, by contrast, PreProB-progenitors are virtually undetectable in adult BM. Single-cell transcriptomics and functional assays place PreProB- upstream of ProB-progenitors, identifying them as the first B-lymphoid restricted progenitor in human fetal life. Fetal BM PreProB- and ProB-progenitors both give rise solely to B-lineage cells yet they are transcriptionally distinct.  PreProB- unlike ProB-progenitors, continue to express a number of key myeloid and stem cell genes and share some transcriptomic signatures with CD10-ve B-progenitor infant acute lymphoblastic leukemia blast cells. Our data identify PreProB-progenitors as the earliest B-lymphoid restricted progenitor in human fetal life, and suggest that this fetal-restricted committed B-progenitor might provide a permissive cellular context for prenatal B-progenitor leukemia initiation.

overall_design: Comparison of chromatin accesibility between two committed B progenitors. Three biological replicates are included in addition to one positive control (Lin+ MNC)


title: Fetal specific human B-cell developmental programs


title: Candida albicans Sfp1 participates in the regulation of multiple antioxidative systems

status: Public on Jun 20 2019

city: Hsinchu

first: Hsueh-Fen

last: Chen

address: No. 101, Section 2, Kuang-Fu Road

country: Taiwan

institute: National Tsing Hua University

summary: To investigate the roles of Sfp1, we used a whole-genome DNA microarray to compare gene expression patterns between the sfp1-deleted and wild-type strains. Among the upregulated genes, a subset of genes is involved in oxidative stress response, including CAP1, SSK1, and SHO1. The CAP1 gene product is a bZip transcription factor involving in regulation of antioxidant gene expression. The SSK1 and SHO1 gene encodes a response regulator of two-component system and an adaptor protein in the Hog1 MAPK signaling pathway, respectively. Moreover, the sfp1-deleted mutant also exhibited an upregulation of genes encoding various antioxidants and enzymes controlling the cellular redox state, especially components of the glutathione system. Noticeably, 8 of the 21 upregulated glutathione-related genes (GCS1, GTT11, YCF1, CYS3, CIP1, EBP1, IFD6, and OYE32) are controlled by Cap1. This result raises a possibility that Sfp1 is involved in C. albicans oxidative stress response and somehow coordinately regulates these glutathione-related genes with Cap1.

overall_design: DNA microarray analysis to compare the gene expression profiles from the WT and sfp1-deleted strains in exponential phase. Two independent experiments were performed.

first: Shao-Yu

last: Lee

first: Chung-Yu

last: Lan


title: Bulk (100cell) RNA-Sequencing of human fetal haematopoietic stem, progenitor and B cells

overall_design: Comparison of human fetal haematopoietic stem and progenitor cells according to their transcriptome (n=3 for each population, 100 cells sorted per population)


title: Complement C5a/C5a receptor 1 induces renal injury in diabetic kidney disease via mitochondrial metabolic reprogramming

status: Public on Jul 01 2019

city: Melbourne

first: Mark

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

summary: In mice, complement C5a and its receptor C5aR1 elicit systemic and local inflammation and drive tissue injury in diabetic kidney disease via altered metabolic flexibility, which can be attenuated by therapy with a specific orally active inhibitor of C5aR1.

overall_design: Bulk RNA-seq was performed to understand gene expression changes in the mouse kidney due to diabetes and treatment with a C5a inhibitor (oral). There were four sample groups (1) non-diabetic mice given the vehicle; (2) STZ diabetic mice given the vehicle; (3) non-diabetic mice given C5a inhibitor PMX-53; and (4)  STZ diabetic mice given the  C5a inhibitor PMX-53.

first: Sih

last: Tan

first: Vicki

last: Thallas-Bonke

first: Matthew

last: Snelson

first: Scott

middle: T

last: Baker

first: George

last: Jerums

first: Alison

last: Skene

last: Power

first: Richard

middle: J

last: MacIsaac

first: Rick

last: Wetsel

first: Peter

last: Meikle

first: Assam

last: El-Osta

first: Josephine

last: Forbes

last: Cooper

first: Elif

middle: I

last: Ekinci

first: Trent

last: Woodruff

first: Melinda

last: Coughlan


title: A variant erythroferrone disrupts iron homeostasis in SF3B1-mutated myelodysplastic syndrome (RNA-Seq)

status: Public on Jun 18 2019

city: Paris

first: Olivier

last: KOSMIDER

address: 27 Rue du faubourg Saint Jacques

country: France

institute: Institut Cochin

summary: Myelodysplastic syndromes (MDS) with ring sideroblasts are hematopoietic stem celldisorders with erythroid dysplasia and mutations in the SF3B1 splicing factor gene. MDS patientswith SF3B1 mutations often accumulate excessive tissue iron, even in the absence oftransfusions, but the mechanisms that are responsible for their parenchymal iron overload areunknown. Body iron content, tissue distribution, and the supply of iron for erythropoiesis arecontrolled by the hormone hepcidin, which is regulated by erythroblasts through secretion of theerythroid hormone erythroferrone (ERFE). Here, we identified an alternative ERFE transcript inMDS patients with the SF3B1 mutation. Induction of this ERFE transcript in primary SF3B1-mutated bone marrow erythroblasts generated a variant protein that maintained the capacity tosuppress hepcidin transcription. Plasma concentrations of ERFE were higher in MDS patientswith a SF3B1 gene mutation than in patients with SF3B1 wild-type MDS. Thus, hepcidinsuppression by a variant erythroferrone is likely responsible for the increased iron loading inpatients with SF3B1-mutated MDS, suggesting that ERFE could be targeted to prevent ironmediated toxicity. The expression of the variant ERFE transcript that was restricted to SF3B1-mutated erythroblasts decreased in lenalidomide-responsive anemic patients, identifying variantERFE as a specific biomarker of clonal erythropoiesis.

overall_design: RNAseq analysis of healthy controls (n=5) and MDS patients (n=27) divided into wildtype and mutated SF3B1 patients.

first: Sabrina

last: Bondu

first: Anne-Sophie

last: Alary

first: Carine

last: Lefèvre

first: Alexandre

last: Houy

first: Grace

last: Jung

first: Thibaud

last: Lefebvre

first: David

last: Rombaut

first: Ismael

last: Boussaid

first: Abderrahmane

last: Bousta

first: François

last: Guillonneau

first: Prunelle

last: Perrier

first: Samar

last: Alsafadi

first: Michel

last: Wassef

first: Raphaël

last: Margueron

first: Alice

last: Rousseau

first: Nathalie

last: Droin

first: Nicolas

last: Cagnard

first: Sophie

last: Kaltenbach

first: Susann

last: Winter

last: Kubasch

first: Didier

last: Bouscary

first: Valeria

last: Santini

first: Andrea

last: Toma

first: Mathilde

last: Hunault

first: Aspasia

last: Stamatoullas

first: Emmanuel

last: Gyan

first: Thomas

last: Cluzeau

first: Uwe

last: Platzbecker

first: Lionel

last: Adès

first: Hervé

last: Puy

first: Marc-Henri

last: Stern

first: Zoubida

last: Karim

first: Patrick

last: Mayeux

first: Elizabeta

last: Nemeth

last: Park

first: Tomas

last: Ganz

first: Léon

last: Kautz

last: Kosmider

first: Michaëla

last: Fontenay


title: Reverse gene-environment interaction approach to identify variants influencing body mass index in humans

status: Public on Jun 17 2019

city: Princeton

first: Kristina

middle: Marie

last: Garske

email: kmgarske@ucla.edu, kg8086@princeton.edu

state: New Jersey

address: Carl Icahn Lab, South Drive, Princeton University

department: Lewis-Sigler Institute for Integrative Genomics; Ecology & Evolutionary Biology

institute: Princeton University

summary: Here we derive candidate gene-environment interaction (GxE) variants from promoter-enhancer interacting regions that respond to dietary fatty acid challenge through altered chromatin accessibility in human primary adipocytes, and demonstrate that molecular genomics data produced in physiologically relevant contexts can illuminate new functional GxE mechanisms in humans and identify variants for GxE testing in large biobanks.

overall_design: Assay for transposase accessible chromatin (ATAC) -seq libraries were produced from human primary preadipocytes (PAd), in vitro differntiated human adipocytes (Ad), and in vitro differentiated human adipocytes that were exposed to 200 uM palmitic acid, 200 uM oleic acid, or BSA control (all with n=3 independent replicates). Promoter Capture Hi-C libraries were produced from in vitro differentiated human white adipocytes that were exposed to 200 uM palmitic acid, 200 uM oleic acid, or BSA control (all with n=2 independent replicates).

first: Päivi

last: Pajukanta


title: A variant erythroferrone disrupts iron homeostasis in SF3B1-mutated myelodysplastic syndrome

first: Olivier

last: KOSMIDER


title: Stat1-induced NAMPT sustains NAD levels to regulate gene expression in classically activated macrophages

status: Public on Apr 30 2019

city: Salt Lake City

first: Ryan

last: O'Connell

address: Emma Eccles Jones, Medical Research Building, 15 North Medical Drive East

institute: University of Utah

summary: We identify gene regulation patterns that influence inflammation and metabolism during interferon treatment in the presence of NAD salvage synthesis inhibitors and products

overall_design: RNA Sequencing of Bone Marrow Macrophages treated in triplicate with IFNg, FK-866 and/or NMN

last: Huffaker

first: Warren

last: Voth


title: Cell-specific expression and function patterns of microRNA-150-5p in liver fibrogenesis

status: Public on Mar 01 2019

city: Beijing

first: Wei

last: Chen

address: No. 95 Yong’an road, Xicheng District

department: Beijing Friendship Hospital

institute: Capital Medical University

summary: MicroRNAs (miRNAs) are endogenous and small non-coding RNA molecules that mediate post-transcriptional gene suppression by incomplete matches with their host mRNAs. Recent studies have highlighted that miRNAs are involved in the pathology of liver lipid metabolism, metabolic inflammation, oxidative stress, chronic liver injury, regeneration and fibrogenesis. During liver fibrosis, miRNAs are simply categorized into pro-fibrotic or anti-fibrotic miRNAs according to their expression alterations in one liver cell type especially hepatic stellate cells (HSCs). Our current study observed a miRNA, termed miR-150-5p, exhibited cell-specific expression pattern in liver fibrosis. Although the expression level of miR-150-5p in fibrotic liver tissues or hepatocytes was significantly enhanced, it was notably down-regulated in HSCs in the context of liver fibrosis. Perturbation of miR-150-5p evidently affected the cell viability of HSCs but had no obvious effect on hepatocytes. While overexpression of miR-150-5p could sensitize the apoptosis of hepatocytes in the presence of pro-apoptotic factors. Further investigations revealed that miR-150-5p mimic treatment had a larger influence on the transcriptomic stability of HSCs but a minor effect on hepatocytes. The genes related to anti-apoptosis or pro-proliferation were decreased and genes associated with pro-apoptosis or anti-proliferation were increased after miR-150-5p overexpression, which might be the potential targets of miR-150-5p overexpressed in HSCs. Collectively, our study provide a strong supporting evidence that some miRNAs may express or function in a cell-specific pattern in the backdrop of liver fibrosis.

overall_design: MiR-150-5p mimics or controls were transfected into LX-2 and QSG cells (n=2 for each group) for 48 hours. Total RNA was isolated using Trizol reagent (Invitrogen, USA). Agilent 2100 Bioanalyzer (Agilent Technologies, USA) was used to evaluate the RNA quality. One μg RNA was used to generate cDNA library based on TruSeq RNA Sample Prep Kit v2 (Illumina, USA) according to the manufacturer’s instructions. Then the cDNA libraries were sequenced on the Illumina HiSeq 2500 System (Illumina, USA) with 100 nucleotide paired-end reads, per the standard manufacturer’s protocol. The RNA-Seq reads were aligned to human reference genome (hg38) using Tophat (version 2.0.10) with default parameters. Read counts were scaled to reads per kilo-base of exon model per million mapped reads (RPKM).

first: Hong

last: You


title: MYC Recruits SPT5 to RNA Polymerase II to Promote Processive Transcription Elongation

status: Public on Mar 27 2019

city: Kiel

first: Elmar

last: Wolf

state: Schleswig-Holstein

address: Rudolf-Höber-Str. 1

department: Biochemical Institute

institute: Christian-Albrechts-University Kiel

summary: The MYC oncoprotein binds to promoter-proximal regions of virtually all transcribed genes and is expressed in a strictly growth factor-dependent manner in non-tumor cells. Here we show that MYC directly binds SPT5, a subunit of the RNA polymerase II (POL2) elongation factor DSIF. MYC recruits SPT5 to genes and enables the CDK7-dependent transfer of SPT5 onto POL2. Consistent with known functions of SPT5, MYC is required for fast and processive transcription elongation. In addition, MYC increases the directionality of promoters by stimulating sense transcription and suppressing the synthesis of antisense RNAs. Our results argue that MYC controls the productive assembly of POL2 with general elongation factors to form processive elongation complexes. The high levels of MYC that are expressed in tumors sequester SPT5 into non-functional complexes, slows transcription at growth-suppressive genes and promotes uncontrolled cellular growth.

overall_design: 4sUDRB Seq, 4sU Seq, ChIPSeq (SPT5,Total Pol2 & Ser2 Pol2) in various levels of MYC or SPT5

first: Apoorva

last: Baluapuri

first: Julia

last: Hofstetter

first: Susanne

last: Walz

first: Martin

last: Eilers


title: Single cell RNAseq analysis of murine fetal growth plate chondrocytes and perichondrial cells

status: Public on Feb 26 2019

city: Houston

first: Noriaki

last: Ono

state: Texas

department: School of Dentistry

institute: University of Texas Health Science Center at Houston

summary: We revealed a single cell transcriptional landscape of fetal growth plate chondrocytes and perichondrial cells.

overall_design: tdTomato+ cells were FACS-isolated from embryonic day 13.5 (E13.5) hind limbs of Col2a1-cre; R26R-tdTomato+ mice. 18,000 cells were loaded onto 10X Genomic Chromium Single Cell Expression Solution version 2. platform. cDNA was sequenced by Illumina HiSeq4000.


title: Gene expression microarray analysis on the dentate gyrus of mice chronically treated with fluoxetine

status: Public on Feb 25 2019

city: Toyoake

first: Hideo

last: Hagihara

address: 1-98 Dengakugakubo, Kutsukake-cho

department: Institute for Comprehensive Medical Science

institute: Fujita Health University

summary: The gene expression patterns in the dentate gyrus of wild-type mice treated with fluoxetine (15 mg/kg/day for 3 weeks) or vehicle were examined using Affymetrix GeneChip arrays.

overall_design: Dentate gyrus RNA isolated from wild-type mice (C57BL/6J) treated with fluoxetine (n = 8) or vehicle (n = 8).


title: Exogenous miRNAs from Moringa oleifera Lam. recover a dysregulated lipid metabolism (mouse)

status: Public on Jan 19 2019

city: Rome

first: Valentina

last: Roglia

address: Via della Ricerca Scientifica, 1

department: Biology

country: Italy

institute: University of Rome "Tor Vergata"

summary: The efficacy of a traditional remedy was tested, based on an aqueous extract of Moringa oleifera Lam. seeds (MOES). Then, the small RNAs have been extracted from the MOES (mol-miR pool) and used for the treatments. Two tissues, in particular, were analyzed: the liver and the adipose tissue, both in vitro (HepG2 and 3T3-L1) and in vivo (C57BL/6J mice) models.

overall_design: It has been recently demonstrated that miRNAs contained in plants can regulate human mRNA translation, similarly to mammalian ones, in a cross-kingdom manner.  Starting from this knowledge, this work focuses on the effects of Moringa oleifera Lam. miR pool on disrupted lipid metabolism.

first: Marina

last: Potestà

first: Antonella

last: Minutolo

first: Carla

last: Montesano


title: The developing mouse dentate gyrus

status: Public on Jan 29 2019

summary: The gene expression patterns in the dentate gyrus of wild-type mice during postnatal development were examined using Affymetrix GeneChip arrays.

overall_design: Dentate gyrus RNA isolated from wild-type mice (C57BL/6J × BALB/cA background) of different postnatal days (PD8, 11, 14, 17, 21, 25, and 29).

first: Hagihara

last: Hideo


title: Gene expression of wild-type or LysM-St18flox M-CSF-derived macrophage or osteoclast

status: Public on Dec 31 2018

city: Tsukuba

first: Yutaro

last: Kumagai

state: Ibaraki

address: Central 5-41, Higashi 1-1-1

department: BRD

institute: AIST

summary: To assess the role of a transcription factor St18 in LPS response, M-CSF-derived macrophage (MDM) or osteoclast (OC) from wild-type or LysM-St18flox mice were prepared and gene expressions were compared.

overall_design: MDM or OC were prepraed from wild-type or LysM-St18flox mice and gene expressions were compared.

first: Kenta

last: Maruyama


title: Exogenous miRNAs from Moringa oleifera Lam. recover a dysregulated lipid metabolism (human)

summary: The efficacy of a traditional remedy was tested, based on an aqueous extract of Moringa oleifera Lam. seeds (MOES). Then, the miRNAs have been extracted from the MOES (mol-miR pool) and used for the treatments. Two tissues, in particular, were analyzed: the liver and the adipose tissue, both in vitro (HepG2 and 3T3-L1) and in vivo (C57BL/6J mice) models.


title: Quantitative Analysis of Worms after P. aeruginosa Infection

status: Public on Oct 11 2018

city: kunming

first: Yi-Cheng

last: Ma

email: 290361200@qq.com, mayc@ynu.edu.cn

state: yunnan

address: NO.2 North Cuihu Road

institute: Yunnan University

summary: To clarify the mechanisms of innate immune responses mediated by epithelial barrier disruption. Reveal the host’s broad transcriptional response to P. aeruginosa infection during disruption of the intestinal barrier. We used RNA-Seq analysis to study the transcriptomic profiles of wt worms were exposed to either P. aeruginosa PA14 or E. coli OP50  for 24 hours, and the transcriptomic profiles of egl-44(MT2247) mutants fed E. coli OP50 for 24 hours. Differential expression analysis was performed by comparing wt worms exposed to PA14 versus wt worms exposed to  E. coli OP50, and egl-44(MT2247) mutants fed E. coli OP50 versus WT worms fed E. coli OP50.

overall_design: Young adult wt worms were exposed to either P. aeruginosa PA14 or E. coli OP50  for 24 hours, and young adult egl-44(MT2247) mutants fed E. coli OP50 for 24 hours. Bacteria were removed and worms were natural precipitation by M9 buffer , flash frozen on dry ice. The transcriptional profiles of those samples were generated by deep sequence, in triplicate, using Illumina Novaseq™.

first: Cheng-Gang

last: Zou


title: Gene expression microarray analysis on the medial prefrontal cortex and dentate gyrus of wild-type mice

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

overall_design: Refer to individual Series


title: Tumor & Tumor-Adj Gene Expression in the Nurses' Health Study Cohorts

status: Public on Jan 08 2019

city: Boston

first: Rulla

last: Tamimi

state: MA

address: 181 Longwood Avenue

department: Medicine

institute: Brigham and Women's Hospital

summary: Gene expression data from the Nurses' Health Study

overall_design: Total of 1577 samples which includes 882 tumor and 695 tumor-adjacent tissues from participants of the Nurses' Heath Study I and II diagnosed with invasive breast cancer. This deposit contains 467 files; remaining 1110 files are in GSE93601.

first: Kevin

middle: H

last: Kensler

first: Venkat

last: Sankar

first: Jun

last: Wang

first: Xuehong

last: Zhang

first: Christopher

last: Rubadue

first: Gabrielle

last: Baker

first: Joel

last: Parker

first: Katherine

last: Hoadley

first: Andreea

middle: L

last: Stancu

first: Michael

last: Pyle

first: Laura

last: Collins

first: David

last: Hunter

first: A

last: Eliassen

first: Susan

last: Hankinson

first: Yujing

last: Heng


title: Global transcriptional regulation by small non-coding RNAs is required for the response to injury of a filamentous fungus

status: Public on Dec 05 2018

city: Irapuato

first: Manuel

last: Villalobos-Escobedo

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-León Irapuato

department: Ingeniera Genetica

country: Mexico

institute: cinvestav

summary: The ability to respond to injury is essential for the survival of an organism and involves analogous mechanisms in animals and plants. Such mechanisms integrate coordinated genetic and metabolic reprogramming events requiring fine tuned regulation by small RNAs for adequate healing of the wounded area. We previously reported that in response to injury, the filamentous fungus Trichoderma atroviride uses molecular mechanisms very similar to those of plants and animals. These processes lead to the formation of new hyphae and the development of asexual reproduction structures (conidiophores). Here we show that regulation by sRNAs of nitrogen metabolic processes and the cellular redox balance is necessary to carry out the correct response to injury. We further discover microRNA-like RNAs (milRNAs) related with the development of conidiophores. Finally, using a loss-of-function and transcriptomic approach, we demonstrate that a milRNA plays a central role in growth and hyphal regeneration in the filamentous fungus T. atroviride, which regulates signaling and cell proliferation at the transcriptional level. Although many classes of small RNAs have been profiled in fungi, and showed to be important for contending with different types of stress, this is the first report showing a physiological function of a milRNA in fungi.

overall_design: The messenger RNA of three mutants and the WT strain of the fungus Trichoderma atroviride were sequenced, both in vegetative growth and in response to injury. In addition, the small RNAs of the WT strain and the mutant of the dcr2 gene were sequenced.

first: JosÃ©

first: Pablo

last: González De la Rosa

first: Pedro

last: Martínez-Hernández

first: Cei

last: Abreu-Goodger


title: RNA seq from liver samples of C57BL/6 mice to study the gene expression synchrony of Plasmodium stages with host circadian cycle.

status: Public on Jun 01 2018

city: Worcester

first: Ricardo

middle: Tostes

last: Gazzinelli

state: Massachusetts

address: 364 Plantation Street

country: USA

institute: University of Massachusetts Medical School

summary: The Plasmodium life cycle parasites differentiate and proliferate synchronously, paralleling the vertebrate host's circadian rhythm. Here we report that expression of carbohydrate metabolism and inflammatory genes in IFNγ-primed leukocytes and liver cells from infected mice are boosted in P. chabaudi-infected mice. In addition, a rhythmic gene expression of PPARG and TNFα, which are key regulators of glucose metabolism, parallel blood glucose levels across the circadian cycle in infected mice.

overall_design: Liver fragments from C57BL/6 mice were collected at different time points: 12 am; 6 am; 12 pm and 6 pm from mice at day 8 post-infection with P. chabaudi or uninfected control.


title: Human post-mortem brain gene expression from various brain regions from alcoholic and non-alcoholic subjects

status: Public on Oct 18 2018

city: Indianapolis

first: Jeanette

middle: Nance

last: McClintick

state: IN

address: 635 Barnhill Dr.

department: Biochemistry & Molecular Biology

institute: Indiana University School of Medicine

summary:
4 samples from 9 brain regions
Brain tissue from the New South Wales Tissue Resource Centre, 9 brain regions, 4 samples each: 1 male alcoholic, 1 female alcoholic, 1 male control, 1 female control. Brain regions: pre-frontal cortex, cerebral cortex, visual cortex,  thalamus, hippocampus, amygdala, caudate nucleus, putamen, cerebellum

overall_design: 4 samples from 9 brain regions

first: Howard

last: Edenberg


title: Genome-wide methylation analysis reveals methylation subtypes of Barrett's Esophagus and Esophageal Adenocarcinoma

status: Public on Jan 01 2019

city: Seattle

first: Sean

last: Maden

state: WA

address: 1100 Fairview Ave N

department: Clinical Research

institute: Fred Hutch

summary: Methylation-based subtypes were identified in nondysplastic Barrett's Esophagus (BE) from BE-only patients (n=62) and Esophageal Adenocarcinoma (n=23) using RPMM-based clustering on methylation data at probes with the most variant Beta-values on the HM450 platform. Samples in these methylation-based subtypes were further identified in the TCGA EAC dataset, and subtypes were characterized using integrated analysis of methylation, sequencing, and expression data.

overall_design: Bisulphite-converted DNA from 89 samples (n=23 EAC; n=62 BE from BE-only patients; n=7 BE from EAC patients) was processed using the HM450 platform. In the EAC subset, the 1515 Infinium probes with most variant Beta-value methylation were used in RPMM clustering to identify methylation-based subtypes. Methylation at these MVPs and RPMM-clustering was also used to identify subtypes in the subset of BE samples from BE patients. Methylation-based subtypes in EAC were further identified in EAC samples from the Cancer Genome Atlas and the cohort published by Krause et al 2016 (GSE72872), the molecular characteristics of the subtypes in EAC and BE were assessed using sequence and expression data, and a six-CpG probe panel was designed to identify HM and non-HM samples.

first: Ming

last: Yu

first: Matthew

last: Stachler

first: Andrew

last: Kaz

first: Tai

last: Heinzerling

first: Rachele

last: O'Leary

first: Xinsen

last: Xu

first: Adam

last: Bass

first: Amitabh

last: Chak

first: Joseph

last: Willis

first: Sanford

last: Markowitz

first: William

last: Grady


title: Proteotranscriptomic profiling of potential E6AP targets in prostate cancer cells

status: Public on Nov 27 2017

first: Franco

last: Caramia

state: Victoria

address: 305 Grattan Street

institute: Peter MacCallum Cancer Centre

summary: Prostate cancer is a common cause of cancer-related death in men. E6AP, an E3 ubiquitin ligase and a transcription cofactor, is elevated in a subset of prostate cancer patients. Genetic manipulations of E6AP in prostate cancer cells expose a role of E6AP in promoting growth and survival of prostate cancer cells in vitro and in vivo. However, the effect of E6AP on prostate cancer cells is broad and it cannot be explained fully by previously identified tumour suppressor targets of E6AP, promyelocytic leukemia protein and p27. To explore additional players that are regulated downstream of E6AP, we combined a transcriptomic and proteomic approaches. We identified and quantified 16,130 transcripts and 7,209 proteins in castration resistant prostate cancer cell line, DU145. A total of 2,763 transcripts and 308 proteins were significantly altered upon knockdown of E6AP. Pathway analyses supported the known phenotypic effects of E6AP knockdown in prostate cancer cells and in parallel exposed novel potential links of E6AP with cancer metabolism, DNA damage repair and immune response. Changes in expression of the top candidates were confirmed using real-time polymerase chain reaction. Of these, clusterin, a stress-induced chaperone protein, commonly deregulated in prostate cancer, was pursued further. Knockdown of E6AP resulted in increased clusterin transcript and protein levels in vitro and in vivo. Concomitant knockdown of E6AP and clusterin supported the contribution of clusterin to the phenotype induced by E6AP. Overall, results from this study provide insight into the potential biological pathways controlled by E6AP in prostate cancer cells and identifies clusterin as a novel target of E6AP.

overall_design: Examination of candidate targets regulated by E6AP at transcript level

first: Twishi

last: Gulati

first: Ygal

last: Haupt

first: Caramia

last: Franco


title: Expression analysis of Thermococcus onnurineus NA1 KCTC10859 and an Frh-deficient mutant, Frh overexpression mutant and TON_0282 deletion mutant in a T. onnurineus NA1 strain.

status: Public on Feb 19 2018

city: Busan

first: LEE

middle: SEONG

last: HYUK

address: Haeyang-ro

department: Department of Marine Biotechnology

country: South Korea

institute: Korea Institute of Ocean Science and Technology

summary:
Investigation of whole genome gene expression level changes in an Frh-deficient mutant, Frh overexpression mutant and TON_0282 deletion mutant, compared to the wild-type strain.
In this study, as a first step to assess the role of the frhAGB-encoding hydrogenases and TON_0282 gene, we constructed three mutants by deleting each gene in a T. onnurineus NA1.

overall_design: A custom microarray was manufactured by Roche NimbleGen. Unique six 60-mer oligonucleotides for all of the predicted 1,986 open reading frames (ORFs) in the annotated genome of T. onnurineus NA1 were designed and synthesized. Examined Wildtype, Frh-deficient mutant, Frh overexpression mutant and TON_0282 deletion mutant in T. onnurineus NA1 strain.

first: Seong

last: Lee

first: Min

middle: S

last: Kim

first: Yun

first: Tae

middle: W

first: Sung

last: Kang

first: Hyun


title: Gene expression profiling of mouse macrophages following IRF2 knockdown

status: Public on Nov 18 2017

city: Birmingham

first: Huachun

last: Cui

state: Alabama

institute: University of Alabama at Birmingham

summary: We applied next-generation sequencing to investigate the gene expression profiles in mouse bone-marrow derived macrophages with or without IRF2 knockdown. We identified a number of differentially regulated genes in cells with IRF2 knockdown.

overall_design: Mouse bone-marrow derived macrophages were transfected with control siRNA or IRF2 specific siRNAs. 48h after transfection, total RNA was isolated and subjected to high-throughput sequencin (RNA-seq), using Illumina GAIIx. Gene expression profiles were compared between two groups.

first: Gang

last: Liu


title: Spatially uniform establishment of chromatin accessibility in the early Drosophila embryo

status: Public on Oct 30 2017

city: Berkeley

first: Jenna

middle: E

last: Haines

state: CA

address: 151 Koshland Hall

department: Molecular and Cellular Biology

institute: University of California Berkeley

summary: As the Drosophila embryo transitions from the use of maternal RNAs to zygotic transcription, domains of “open” chromatin, with relatively low nucleosome density and specific histone marks, are established at promoters and enhancers involved in patterned embryonic transcription. However it remains unclear whether open chromatin is a product of activity - transcription at promoters and patterning transcription factor binding at enhancers - or whether it is established by independent mechanisms. Recent work has implicated the ubiquitously expressed maternal factor Zelda in this process. To assess the relative contribution of activity in the establishment of open chromatin , we have probed chromatin accessibility across the anterior-posterior axis of early Drosophila melanogaster embryos by applying a transposon based assay for chromatin accessibility (ATAC-seq) to anterior and posterior halves of hand-dissected, cellular blastoderm embryos. We find that genome-wide chromatin accessibility is remarkably similar between the two halves. Promoters and enhancers that are active in exclusively one half of the embryo have open chromatin in the other half, demonstrating that chromatin accessibility is not a direct result of activity. However there is a small skew at enhancers that drive transcription exclusively in either the anterior or posterior half of the embryo, with greater accessibility in the region of activity. Taken together these data support a model in which regions of chromatin accessibility are defined and established by ubiquitous factors, and fine tuned subsequently by activity.

overall_design: We perfomed ATAC-seq on 20 anterior and 20 posterior stage 5 Drosophila melanogaster (OregonR) embryos that were frozen and sliced in half with a razor blade.

first: Michael

middle: B

last: Eisen


title: Polycomb Repressive Complex 1 regulates transcription of active genes [RNAseq]

status: Public on Jun 28 2017

city: Saint Louis

first: Dale

last: Dorsett

state: MO

address: 1100 South Grand Boulevard

department: Biochemistry and Molecular Biology

institute: Saint Louis University School of Medicine

summary: RNA expression was measured using RNA-seq

overall_design: RNA levels in Mock-treated control Drosophila cells were compared to RNA levels in cells RNAi depleted for Ph, Sce, and Pc

first: Michelle

last: Pherson


title: Polycomb Repressive Complex 1 regulates transcription of active genes [NTseq]

summary: RNA nascent transcription was measured using NT-seq

overall_design: RNA nascent transcript levels in Mock-treated control Drosophila cells were compared to those in cells RNAi depleted for Ph and Sce


title: Polycomb Repressive Complex 1 regulates transcription of active genes


title: Molecular profiling of dorsal raphe nucleus Vgat and VGLUT3-expressing neurons

status: Public on Jun 09 2017

city: New York

first: Alexander

middle: R

last: Nectow

state: New York

address: 630 W 168th St., Physicians and Surgeons

institute: Columbia University

summary: Hunger, driven by negative energy balance, elicits the search for and consumption of food. In mammals, this is orchestrated principally through the activity of neurons in the hypothalamus, direct manipulation of which can potently drive food intake. However, the neural circuits outside of the hypothalamus that control feeding are poorly understood. Here, we identify two functionally opponent cell types within the dorsal raphe nucleus (DRN), marked by the vesicular transporters for GABA (Vgat) or glutamate (VGLUT3), that project to many known feeding centers and rapidly control feeding. We find that DRNVgat neurons drive, while DRNVGLUT3 neurons suppress, food intake. Furthermore, through the development and application of cell type-specific molecular profiling technologies, we identify many differentially expressed transmembrane receptors, which may represent unique druggable targets. Local application of agonists for these receptors potently modulates feeding, recapitulating the effects of cell-specific manipulations. Together, these data establish a key role for the DRN in controlling food intake and add an important anatomic site that controls energy balance.

overall_design: Paired - Inputs and IPs; Unpaired for Vgat/VGLUT3 comparison

first: Jeffrey

last: Friedman


title: IL-2 therapy restores regulatory T cell dysfunction induced by calcineurin inhibitors

status: Public on May 24 2017

city: London

first: MARC

last: MARTINEZ-LLORDELLA

address: 3rd Floor Cheyne Wing, Denmark Hill

department: Liver Science Department

country: United Kingdom

institute: King's College London

summary:
CNIs drastically modify the Treg specific transcriptional program in vivo in an IL-2 dependent manner
CD4+CD25+FOXP3+ regulatory T cells (Tregs) constitute a heterogeneous lymphocyte subpopulation essential for establishing peripheral immune tolerance. Interleukin-2 (IL-2) plays a critical role in maintaining immune homeostasis promoting optimal development, survival and function of Tregs. Because of their suppressive properties, manipulation of Tregs represents a clear target to modulate immune responses in transplantation and autoimmunity. However, the specific effects of adjunctive immunosuppressive drugs to the maintenance and function of the different Treg subsets remain unclear. Calcineurin inhibitors (CNIs), which are the mainstay immunosuppressants in transplantation, are the most effective agents in controlling alloreactive effector T cells, but also hamper Treg activity. In this study we sought to investigate the differential effects of CNIs on the homeostasis of Treg subsets, and the extent to which these effects are dependent on the overall availability of IL-2.

overall_design: 30 total samples were analyzed and classified in 8 different groups (at least 3 replicates per group): Treg and Teff from mouse treated with PBS (CN), tacrolimus (TAC), IL2 and combination of tacrolimus and IL-2 (TAC+IL-2). Treg specific signature was identified by comparing Tref-CN vs Teff-CN. The genes were ranked based on FDR and the TOP50 were selected as Treg-related genes. To assess the transcriptional effect of tacrolimus and IL-2 to Tregs, the gene expression of the different Treg isolated from the treated mice were compared to Teff-CN or Treg-CN.

first: Marc

last: Martinez-Llordella

first: Alberto

last: Sanchez-Fueyo

first: Elizabeth

last: Gray

first: Juanjo

last: Lozano


title: Human monocyte-derived macrophage (MDM) cell transcriptome response to infection with H1N1, H3N2, and H5N1 influenza virus.

status: Public on May 05 2017

city: La Jolla

first: Max

last: Chang

address: 9500 Gilman Drive

institute: University of California, San Diego

summary: Human monocyte-derived macrophages (MDM) serve as a model for resident alveolar macrophages (AM) in the human respiratory tract. mRNA-Seq analysis was used to profile the cellular transcriptome of MDM cells at multiple time points in response to infection with influenza A/California/04/09 (H1N1), A/Wyoming/03/03 (H3N2), and A/Vietnam/1203/04 (H5N1) HALo virus.  The Influenza A/Vietnam/1203/04 (H5N1) HALo mutant virus is an attenuated H5N1 virus generated from wild-type Influenza A/Vietnam/1203/04 (H5N1) virus as described in Steel, J., et al. J Virol. 2009 Feb; 83(4):1742-53.

overall_design: Human monocyte-derived macrophages (MDM), obtained from healthy donor blood, were infected with influenza A/California/04/09 (H1N1), A/Wyoming/03/03 (H3N2), or A/Vietnam/1203/04 (H5N1) HALo virus. Infected samples and time-matched mock-infected samples were collected in duplicates at 3, 6, 12, and 18 hrs post infection for mRNA-Seq analysis.

first: Matthew

last: Urbanowski

first: Megan

last: Shaw

first: Sven

last: Heinz

first: Chris

last: Benner

first: Lars

last: Pache

first: Randy

last: Albrecht

first: Adolfo

last: Garcia-Sastre


title: Gene expression in the anterior cingulate cortex in mice treated with ketamine (3mg/kg) or sleep deprivation (SD) during 12 hrs., and saline as the control group.

status: Public on Apr 10 2017

city: Ciudad de México

first: Ricardo

last: Orozco-Solis

state: TLALPAN

address: Periférico Sur 4809, Arenal Tepepan

institute: Instituto Nacional de Medicina Genomica

summary: Both, sleep deprivation and ketamine treatments are efficient and fast-acting antidepressants acting within the first 12-24 hr. post-treatment.  This experiment was designed to identify if common transcriptional responses are elicited by both treatments

overall_design: Mice were divided into 3 groups and administered either:  A) KT (3mg/kg i.p at ZT5; B) saline [100 μl/0.03kg i.p.] at ZT 5; (control) or C) SD (animals were kept awake from ZT 0 to ZT 12). All groups were euthanized at ZT 13.

first: R

first: P

last: Sassone-Corsi


title: Experimental evolution of a hyperthermophilic archaeon on carbon monoxide enhanced hydrogen productivity through novel mechanisms associated with genome, transcriptome and epigenome changes

status: Public on Feb 09 2017

first: LEE

last: HYUK

summary: A hyperthermophilic archaeon Thermococcus onnurineus NA1 can grow and produce H2 on a variety of CO-containing feed stocks such as by-product gas generated from steel-mill process. In this study we applied a long-term adaptive evolution to enhance H2 productivity. Through serial transfer of cell cultures with carbon monoxide (CO) as an energy source, we observed physiological changes in cell density, CO consumption rate and H2 production rate. To understand the underlying mechanism for the changes, we performed systems analysis of genomic, transcriptomic and epigenomic data. Genomic analysis of an evolved strain, designated as 156T, revealed that single or multiple bases were substituted, deleted or inserted in the sequence of the parental strain. A single point mutation in a putative transcriptional regulator (TON_1525) seemed to play a pivotal role in changing cellular phenotypes by increasing the expression level of genes of a CO dehydrogenase-hydrogenase gene cluster. Additionally, a mutation in an aromatic amino acid permease (TON_0820) contributed to increasing cell growth. Transcriptomic analysis revealed that genes belonging to the categories of transcription, translation and energy metabolism in archaeal Clusters of Orthologous Genes (arCOGs) were significantly changed. In particular, genes involved in energy conservation via CO oxidation were highly upregulated. Epigenomic analysis suggested that methylation change might be a way of gene regulation in a hyperthermophilic archaeon. The evolved 156T strain showed highly enhanced hydrogen productivity with CO at high flow rates of 800 ml min-1 and above, indicating the adaptation rendered the strain less sensitive to high CO. The 156T strain was demonstrated to be appropriate for H2 production by using synthetic gas obtained by coal gasification. This study is the first example to show that evolutionary engineering is very effective in enhancing H2 productivity of a hyperthermophilic archaeon on CO

overall_design: RNA expreesion profile of adaptive T. onnurineus NA1 genes in CO-containing media, using Illumina HiSeq 2500

first: Seong

last: Lee

first: Min

last: Kim

first: Jae

first: Tae

first: Seung

last: Bae

first: Sung

middle: M

first: Hae

middle: C

last: Jung

last: Yang

first: Ae

last: Choi

first: Yong

last: Cho

first: Jung

first: Kae

middle: K

last: Kwon

first: Hyun

middle: G

last: Kang


title: Sex differences in DNA methylation of the cord blood are related to sex-bias psychiatric diseases

status: Public on May 01 2017

city: Campinas

first: Mariana

last: Maschietto

state: São Paulo

address: Rua Márcia Mendes, 619

department: Research Center

country: Brazil

institute: Boldrini Children's Hospital

summary: Gender differences in the prevalence of psychiatric disorders are well documented in epidemiological studies. Exposure to stress during gestation impacts differentially between females and males. Environmental or biological factors can alter DNA methylation and affect the development of neurodevelopmental diseases. In this study, we explored gender-specific DNA methylation in regarding their potential connection to psychiatric outcomes. We assessed the methylation of cord blood of 39 females and 32 males born at term and with appropriate weight at birth. Mothers between 18 and 48 years of age (median: 28 years) were interviewed to gather information about environmental factors (gestational exposure) that can potentially interfere with the methylation profiles in the newborns. Bisulphite converted DNA was hybridized to Illumina HumanMethylation450 BeadChips. After exclusion of XYS probes, there were 2,332 differentially methylated CpG sites (DMS) between sexes, with an overlap of 890 (38%) CpG sites with an a cohort submitted to gestational stress exposition. Using externals datasets, we found that the DMSs were enriched within brain modules of co-methylated CpGs during gestation and were also differentially methylated in the brain comparing boys and girls during brain development. Genes associated to the DMSs were enriched for neurodevelopmental disorders. Accordingly, we described an enrichment of the DMSs among the differentially methylated CpG sites in brain tissue between schizophrenics and controls. Here, we suggest that gender changes methylation in the autosomes working as a primary driver to stress exposition which potentially contributes for  gender differences found in psychiatric outcomes.

overall_design: Bisulphite converted DNA from the 71 samples were hybridized to the Illumina HumanMethylation450 BeadChip following manufacture's protocols.

first: Helena

last: Brentani


title: High throughput quantitative whole transcriptome analysis of adult mouse distal lung mesenchyme

city: Stanford

first: Mark

last: Krasnow

state: Ca

address: Beckman Center, B400 279 W. Campus Dr.

institute: Stanford University

summary: We used microfluidic single cell RNA-seq on 47 individual mouse lung mesenchymal cells at adulthood to measure the transcriptional state. We were able to classify these cells into distinct populations as well as map their signaling interactions with the distal lung epithelium and endothelium. In this manner, single cell RNA-seq can be used to unbiasedly determine the signals the dictate construction and maintenance of the alveolus.

overall_design: 47 single-cell transcriptomes from adult mouse lung mesenchyme were analyzed in total and one 200-cell bulk control sample; All single cell and control samples contain 92 external RNA spike-ins; In a single adult timepoint, 47 transcriptomes were isolated; In addition, a 200-cell bulk control sample was prepared for this adult timepoint;All single cell samples were processed on the microfluidic platform, 200-cell-bulk control sample was processed in microliter volumes in PCR tubes.

first: Douglas

last: Brownfield


title: Genome wide expression analysis of Caenorhabditis elegans cdk-8(tm1238) null mutants (vs. WT N2 worms)

status: Public on Dec 29 2015

city: Vancouver

first: Stefan

last: Taubert

state: BC

address: 950 W 28th Ave, CMMT Room 2024

department: Medical Genetics

institute: UBC

summary: CDK-8 is the catalytic subunit of the Mediator complex and is known to regulate specific gene programs in yeast and in cultured mammalian cells; because no study has yet identified CDK-8 regulated genes in an in vivo animal model, we performed genome wide expression profiling on cdk-8 null mutant C. elegans worms to identify CDK-8 regulated genes and developmental and/or physiological gene programs.

overall_design: We grew developmentally synchronized wild-type and mutant worms to the L4 larval stage and harvested them for RNA extraction. L4 was chosen to avoid contamination from embryonic mRNA present in adult worms and to allow best comparison to previous Mediator subunit expression profiling done at the same stage (GSE9720ID).

first: Rebecca

last: Barbeau

first: Chris

last: Eisley

first: Andrea

last: Barczak

first: David

last: Erle


title: Anaerobic cysteine catabolism, sulfide production, and their regulation in Escherichia coli and Salmonella enterica

status: Public on Jun 13 2017

city: Richardson

first: Zhenyu

last: Xuan

state: TX

address: 800 West Campbell

institute: UT Dallas

summary: Gene expression in E coli W3110 strains with either ybaO over-expression (W3110/pcutR) or ybaO deletion (W3110/ΔcutR) were measured with cysteine challenge.

overall_design:
Strains: E coli W3110
Medium: Luria-Bertani (LB)
Treatment: 1mM cysteine
Time: 30 minutes

first: Melissa

last: Loddeke

first: Larry

last: Reitzer