title: Hematopoietic stem cell response to acute thrombocytopenia requires signaling through distinct receptor tyrosine kinases

status: Public on Jul 09 2019

city: Dresden

first: Ben

last: Wielockx

address: Fetscherstrasse 74

country: Germany

institute: IKL, Carl Gustav Carus Universitätklinikum Dresden

summary: Although bone marrow (BM) niche cells are essential for hematopoietic stem cell (HSC) maintenance, their interaction in response to stress is not well defined. Here, we used a mouse model of acute thrombocytopenia to investigate the crosstalk between HSCs and niche cells during restoration of the thrombocyte pool. This process required membrane-localized stem cell factor (m-SCF) in megakaryocytes, which was regulated by vascular endothelial growth factor A (VEGF-A) and platelet-derived growth factor-B (PDGF-B) derived from BM endothelial cells. HSCs and multipotent progenitors 2 (MPP2), but not MPP3/4 were subsequently activated by a dual receptor tyrosine kinase (RTK)-dependent signaling event, namely m-SCF/c-Kit and VEGF-A/VEGFR-2, contributing to their selective and early proliferation. Our findings describe a dynamic network of signals in response to the acute loss of a single blood cell type, and reveal the important role of three RTKs in orchestrating the selective activation of HSCs and progenitor cells in thrombocytopenia.

overall_design: Examination of hematopoietic stem cells CD41+ vs. CD41- from control mice and 24h after platelet depletion, biological replicates (cells from 3 mice per sample)

first: Beáta

last: Ramasz

first: Anja

last: Krüger

first: Julia

last: Reinhardt

first: Anupam

last: Sinha

last: Gerlach

first: Alexander

last: Gerbaulet

first: Susanne

first: Andreas

last: Dahl

first: Triantafyllos

last: Chavakis

first: Tatyana

last: Grinenko


title: Mouse lt-hsc single cells - Aging of hematopoietic stem cells is driven by regional specialization of marrow macrophages

status: Public on Jun 10 2019

city: Rochester

first: Laura

last: Calvi

state: New York

address: 601 Elmwood Ave

department: Medicine

country: USA

institute: University of Rochester Medical Center

type: Expression profiling by high throughput sequencing

summary: The human aged hematopoietic system is prone to dysfunction and clonal selection. Aged hematopoietic stem cells (HSCs) have well-defined characteristics, but the contribution of the bone marrow microenvironment (BMME) to HSC ageing is unclear. We identify age-dependent changes in bone-associated (BA) and marrow-associated (MA) cell populations in murine and human marrow, where only aged MA cells induce aged HSC characteristics. MA aged macrophages (Mφs) could impart aged characteristics to both HSC and BMME populations, and demonstrated decreased ability to engulf senescent neutrophils. Moreover, removal of Mφs from young mice rapidly induced aged HSC characteristics. Interleukin-1β (IL-1β), a cytokine that is restrained when Mφs engulf apoptotic cells, was a key mediator of microenvironmental HSC aging. These data define a previously unknown role for aged MA Mφs to orchestrate BMME and HSC changes. Mφs and IL-1β may therefore represent novel targets for preventing or reversing hematopoietic defects due to advanced age.

overall_design: mRNA profiles of  individual long-term hematopoietic stem cells (Lineage-, Sca1+, cKit+, Flt3-, CD48-, CD150+) isoated from bone marrow  generated from young (10 pooled) and aged animals (5 pooled)  by Illumina HiSeq 2500 sequencing.

first: Corey

last: Hoffman

first: Sarah

last: Latchney

first: Mark

last: LaMere

first: Jason

last: Myers

first: John

last: Ashton

first: Allison

last: Li

first: Frank

last: Akwaa

first: Rakhil

last: Rubinova

first: Amanda

last: McCabe

first: Julianne

last: Smith

first: Jane

last: Liesveld

first: Benjamin

last: Frisch

first: Michael

last: Elliott

first: Katherine

last: MacNamara

last: Becker


title: Aging of hematopoietic stem cells is driven by regional specialization of marrow macrophages

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Single-Cell RNA-seq Transcriptome Profiling from Male Germ Cells Isolated from Late Fetal and Neonatal Mouse Testes

status: Public on May 17 2019

city: Pullman

first: Nathan

middle: C

last: Law

state: WA

address: 100 Dairy Road

department: School of Molecular Biology

institute: Washington State University

summary: To better understand the underlying dynamics driving formation of the spermatogonial stem cell (SSC) pool during development, we performed single-cell RNA-sequencing on mouse germ cells isolated from testes during late fetal and early postnatal development. Transcriptome profiling revealed that a subset of prospermatogonia during late fetal development becomes preprogrammed to adopt the SSC fate in postnatal life. Further computational analysis mapped the transcriptional dynamics of the SSC trajectory through developmental time to identify novel pathways and regulators involved in formation of the foundational SSC pool. Paired with in vivo gene expression analysis via a multi-transgenic mouse model and functional assessment of germ cell fate via transplantation, the findings of our study present a model for which stem cell fate is preprogrammed in the spermatogenic lineage.

overall_design: Testicular germ cells from a total of eight different mice across four developmental ages (E16.5, P0, P3, and P6) were used in this study.

first: Jon

middle: M

last: Oatley


title: Prostaglandin E2 inhibits pro-fibrotic function of human pulmonary fibroblasts by disrupting Ca2+-signaling

status: Public on Mar 01 2019

city: La Jolla

first: Paul

middle: A

last: Insel

state: CA

address: 9500 Gilman Drive

department: Pharmacology

institute: UC San Diego

summary:
Purpose: Identification of gene expression in human lung fibroblasts, including analysis of impact of IPF (Idiopathic Pulmonary Fibrosis) as well as TGFβ stimulation, with particular emphasis on prostanoid receptors and related pathways.
Methods: Truseq stranded mRNA sequencing, via Illumina Hiseq 4000. Single reads, 75bp, ~25 million reads per sample. Quantification of gene expression in TPM using Kallisto, followed by Tximport. mRNA isolated via Qiagen RNeasy kit, with on-column DNase1 digestion.
Results: Quantification of gene expression in primary human lung fibroblasts, including quantification of prostanoid GPCRs.

overall_design: Transcriptomes of human lung fibroblasts (HPFs), assayed via RNA-seq for HPFs with/wo TGFβ treatment, from normal donors and patients with IPF; n =3 for each group, with 4 groups.

first: Krishna

last: Sriram

first: Luke

last: Janssen

first: Subhendu

last: Mukherjee


title: The Hox Transcription Factor Ubx stabilizes Lineage Commitment by Suppressing Cellular Plasticity [RNA-seq]

status: Public on May 04 2019

city: Heidelberg

first: Katrin

last: Domsch

address: INF 230

department: COS - Developmental Biology

institute: Heidelberg University

summary: During development cells become gradually restricted in their differentiation potential by the repression of alternative cell fates. While we know that the Polycomb complex plays a crucial role in this process, it still remains unclear how alternative fate genes are specifically targeted for silencing in different cell lineages. We address this question by studying Ultrabithorax (Ubx), a multi-lineage transcription factor (TF) of the Hox class, in the mesodermal and neuronal lineages using sorted nuclei of Drosophila embryos and by interfering with Ubx in mesodermal cells that have already initiated differentiation. We find that Ubx is a key regulator of lineage development, as its mesoderm-specific depletion leads to the de-repression of many genes normally expressed in other lineages. Ubx silences expression of alternative fate genes by interacting with and retaining the Polycomb Group (PcG) protein Pleiohomeotic (Pho) at Ubx targeted genomic regions, thereby setting repressive chromatin marks in a lineage-dependent manner. In sum, our study demonstrates that Ubx stabilizes lineage choice by suppressing the multi-potency encoded in the genome in a lineage-specific manner via its interaction with Pho. This mechanism may explain why the Hox code is maintained throughout the lifecycle, since it seems to set a block to transdifferentiation in many adult cells.

overall_design: Profiling Ubx binding, H3K27ac and H3K27me3 distribution in the mesodermal and neuronal tissue in two developmental stages in wildtype and Ubx protein degradation conditions

first: Julie

last: Carnesecchi

first: Vanessa

last: Disela

first: Jana

last: Friedrich

first: Nils

last: Trost

first: Olga

last: Ermakova

first: Maria

last: Polychronidou

first: Ingrid

last: Lohmann


title: Transcriptome analysis of the larval zebrafish brain

status: Public on Apr 16 2019

city: Tsu

first: Mikiko

last: Yamanaka

state: Mie

address: 2-174 edobashi

department: Department of Systems Pharmacology

country: Japan

institute: Mie University

summary:
We applied zebrafish whole genome microarrays to identify molecular effects of suvorexant, imipramine and a orexin antagonist from natural plant. Behavioral assays were performed to analyze for correlations between altered gene expression with effects on the organism level.
Central nervous system drug induced gene expression in larval zebrafish brain was measured at 3 hours after exposure of 1uM suvorexant, 1uM imipramine, 10uM 8beta-(4'-Hydroxytigloyloxy) costunolide or 100uM 8beta-(4'-Hydroxytigloyloxy) costunolide. Three independent experiments were performed.Gene expression profile of brain tissue of 10uM 8beta-(4'-Hydroxytigloyloxy) costunolide treated larva showed closest similarity with suvorexant, as assumed by behavior profile.

overall_design: Chemical-induced transcriptional changes were measured in 8dpf larval zebrafish. Gene expression in zebrafish brain was measured after exposure for 3hours to 1uM suvorexant, 1uM imipramine, 10uM 8beta-(4'-Hydroxytigloyloxy) costunolide or 100uM 8beta-(4'-Hydroxytigloyloxy) costunolide. Three biological replicates of 10 pooled brain were used for each treatment.

first: Katsuyoshi

last: Masuda

first: Hiroaki

last: Iwata

first: Mitsugu

last: Araki

first: Yasushi

last: Okuno

first: Mina

last: Okamura

first: Junko

last: Koiwa

first: Toshio

last: Tanaka


title: High-throughput single-cell transcriptome profiling of plant cell types

status: Public on May 13 2019

city: Berkeley

first: Benjamin

middle: Jeremy

last: Cole

address: 1, Cyclotron Road

institute: DOE-Joint Genome Institute

summary: Single-cell transcriptome analysis of heterogeneous tissues can provide high-resolution windows into the spatiotemporal dynamics of developmental processes and environmental responses. Here we use the high-hroughput Drop-seq approach to profile the transcriptomes of over 12,000 individual cells from the Arabidopsis root. We identify marker genes for a diversity of cell types, capture cell-type frequency and gene expression alterations in response to sucrose, and illuminate the transcriptome changes that occur across endodermis development.

overall_design: Single-cell transcriptomes were captured from over 12,000 cells, across 10 drop-seq runs (6 independent protoplast preparations)

first: Christine

middle: N

last: Shulse

middle: J

first: Doina

last: Ciobanu

first: Junyan

last: Lin

first: Yuko

last: Yoshinaga

first: Mona

last: Gouran

first: Gina

last: Turco

first: Yiwen

last: Zhu

first: Ronan

last: O’Malley

first: Siobhan

last: Brady

first: Diane

middle: E

last: Dickel


title: The Hox Transcription Factor Ubx stabilizes Lineage Commitment by Suppressing Cellular Plasticity [ChIP-seq]

status: Public on May 02 2019

first: Katrin

last: Domsch

type: Genome binding/occupancy profiling by high throughput sequencing

first: Julie

last: Carnesecchi

first: Vanessa

last: Disela

first: Jana

last: Friedrich

first: Nils

last: Trost

first: Olga

last: Ermakova

first: Maria

last: Polychronidou

first: Ingrid

last: Lohmann


title: Mapping translation in wild-type and METTL5 knockout (KO) HepG2 cells

status: Public on May 19 2021

city: Chicago

first: Caraline

last: Sepich

state: IL

address: 929 E 57th Street

department: Chemistry

institute: University of Chicago

summary: We performed ribosome profiling on wild-type and METTL5 KO HepG2 cells to investigate translation changes due to loss of METTL5.

overall_design: Comparing sequencing of ribosome-protected-fragments (RPFs, normalized to input RNA-seq) from wild type and METTL5 KO HepG2.

last: Sepich-Poore

first: Sigrid

last: Nachtergaele

first: Chuan

last: He


title: TAD cliques shape the 4-dimensional genome during dual lineage terminal differentiation

status: Public on Feb 23 2019

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

summary: How genomic information is selectively utilized to direct spatial and temporal gene expression patterns during differentiation remains to be elucidated but it is clear that regulated changes in higher-order genomic architecture plays a fundamental role. Specifically, long range interactions within and between chromosomes and the position of chromosome territories in the nucleus are controlled by TADs and LADs respectively, but the relationship between these genomic organizers remains poorly understood

overall_design: We analyzed the large-scale spatial reorganization of chromatin by generating matched Hi-C and nuclear lamin-chromatin contact datasets throughout a dual adipose/neuronal induction of human primary adipose stem cells.  We have mapped Hi-C (TADs) and lamin-associated domains (LADs) in multiple steps during adipose stem cell differentiation to characterize the spatial and temporal link between genomic architecture and gene expression. We identify a new level of 4D genomic organization involving a long-range clustering of individual TADs or TAD pairs into TAD cliques. LADs appear to regulate their formation. (ASCs). We unveil a lineage-specific dynamic assembly and disassembly of repressive cliques of linearly non-contiguous TADs, and a time course-coupled relationship between TAD clique size and lamina association. Our findings reveal a new level of developmental genome organization and provide an overview of large-scale changes in the 4D nucleome during lineage-specific differentiation.

first: Jonas

last: Paulsen

first: Maxim

last: Nekrasov

first: David

last: Tremethick


title: Dynamic transcriptome profiles within spermatogonial and spermatocyte populations during postnatal testis maturation revealed by single-cell sequencing

status: Public on Feb 26 2019

city: Ithaca

first: Jennifer

middle: K

last: Grenier

state: NY

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

summary: This analysis represents the first comprehensive sampling of germ cells in the developing testis over time, at high-resolution, single-cell depth. From these analyses, we have not only revealed novel genetic regulatory signatures of murine germ cells over time, but have also demonstrated that cell types positive for a single marker gene have the capacity to change dramatically during testis maturation, and therefore cells of a particular “identity” may differ significantly from postnatal to adult life.

overall_design: Single-cell suspensions of mammalian testes ranging from PND6 to adult were processed for single-cell RNAseq (10x Genomics Chromium) and libraries were sequenced on a NextSeq500 (Illumina).

first: Kathryn

last: Grive

first: Yang

last: Hu

first: Paula

last: Cohen


title: Reconstruction of the global neural crest gene regulatory network in vivo

status: Public on Oct 09 2019

city: Oxford

first: Tatjana

last: Sauka-Spengler

state: Oxfordshire

address: Radcliffe Department of Medicine

department: University of Oxford

country: United Kingdom

institute: MRC Weatherall Institute of Molecular Medicine

summary: Precise control of developmental processes is encoded in the genome in the form of gene regulatory networks (GRNs). Such multi-factorial systems are difficult to decode in vertebrates owing to their complex gene hierarchies and transient dynamic molecular interactions. Here we present a genome-wide in vivo reconstruction of the GRN underlying development of neural crest (NC), an emblematic embryonic multipotent cell population. By coupling NC-specific epigenomic and single-cell transcriptome profiling with genome/epigenome engineering in vivo, we identify multiple regulatory layers governing NC ontogeny, including NC-specific enhancers and super-enhancers, novel trans-factors and cis-signatures. Assembling the NC regulome has allowed the comprehensive reverse engineering of the NC-GRN at unprecedented resolution. Furthermore, identification and dissection of divergent upstream combinatorial regulatory codes has afforded new insights into opposing gene circuits t hat define canonical and neural NC fates. Our integrated approach, allowing dissection of cell-type-specific regulatory circuits in vivo, has broad implications for GRN discovery and investigation.

first: Ruth

last: Williams

first: Ivan

last: Candido-Ferreira

first: Emmanouela

last: Repapi

first: Daria

last: Gavriouchkina

first: Upeka

last: Senanayake

first: Jelena

last: Telenius

first: Irving

last: Ling

first: Stephen

last: Taylor

first: Jim

last: Hughes


title: Exon Level Expression Profiling in Kawasaki disease (KD): gene expression profile in healthy control subjects, acute-phase KD subjects and convalescent-phase KD subjects

status: Public on Oct 21 2018

city: Kaohsiung

first: Sung-Chou

last: Li

state: Kaohsiung

address: No.386, Dazhong 1st Rd

department: Department of Medical Education and Research

country: Taiwan

institute: Kaohsiung Veterans General Hospital

summary:
Transcriptome analysis of pooled RNA samples from total WBC collection
The RNA samples from six subjects were evenly pooled into one pooled one, followed by sample preparation and microarray experiment.

overall_design:
We analyzed 3 pooled healthy control RNA samples, 3 pooled acute-phase KD RNA samples and 3 convalescent-phase KD RNA samples.
[contributor] Kaohsiung Chang Gung memorial Hospital, Taiwan

first: Ho-Chang

last: Kuo


title: Gene expression profiling of LSKSLAM cells in mice deficient for cholinergic fibers

status: Public on Jan 25 2019

city: Cambridge

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

institute: University of Cambridge

summary: RNASeq of LSKSLAM cells from Gfra2 WT vs KO mice

overall_design: RNASeq of 30 cell pools of LSKSLAM cells from bone and marrow fraction of Gfra2 WT and KO mice

first: Simón

last: Méndez-Ferrer

first: Claudia

last: Korn

first: Winnie

last: Lau

first: Andrés

last: García-García


title: Maresin 1 attenuates neuroinflammation in a mouse model of perioperative neurocognitive disorders

status: Public on Nov 13 2018

city: Stockholm

first: Souren

last: Mkrtchian

address: Solnavägen 9

department: Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

summary:
Maresin 1 administered to mice prior to orthopedic surgery exerts distinct anti-inflammatory and pro-resolving effects through regulation of MΦ infiltration, NF-κB signaling, and cytokine release.
We used microarrays to detail the global programme of gene expression underlying  Maresin 1 effect on mouse hippocampus and identified distinct classes of dysregulated genes during this process.

overall_design: Mice hippocampi were isolated  72 h after surgery and RNA was extracted for further processing and hybridization on Affymetrix microarray.

first: Niccolo

last: Terrando


title: Genome-wide localisation of histone variants in Toxoplasma gondii implicates variant exchange in transcriptional control by demarcation of functional chromatin regions

status: Public on Apr 30 2019

city: Bronx

first: Kami

last: Kim

address: 1300 Morris Park Avenue

institute: Albert Einstein College of Medicine

type: Genome binding/occupancy profiling by genome tiling array

summary: Chromatin is composed of DNA wrapped around nucleosomes, complexes consisting of highly basic proteins called histones. Histone variants are non-canonical variants of histones that have specific functions. The Apicomplexan parasite Toxoplasma gondii possesses conserved histone variants CenH3, H3.3, H2A.Z, H2A.X, as well as the parasite-specific H2B variant, H2BV (or H2B.Z). We surveyed the genome-wide distribution of T. gondii histone variants by chromatin immunoprecipitation coupled with microarray (ChIP-chip) and next generation sequencing (ChIP-seq). Histone variants have specific localisations in chromosomes and in relation to genomic features. Histones H2BV and H2AZ localise to promoter regions with the transcriptional activation mark H3K4me3. Sites where H2BV, H2AZ and H3K4me3 colocalise are enriched in motifs recognised by AP2 transcription factors, particularly in the nucleosome-free region just upstream of the transcription start site. In contrast, histone variants H3.3 and H2AX are largely absent from promoters but enriched in gene bodies. Consistent with previous biochemical work, the majority of H2AX and H2AZ loci do not overlap, suggesting that they are present in different nucleosomes. In addition, the T. gondii homologue of the centromeric histone CenH3 demarcates centromeric chromatin and appears to be part of a unique centromeric histone complex including H3.3 that localises to centromeric chromatin as detected in proteomic analysis of co-immunoprecipitated CenH3 complexes. Together, these data suggest that the position of variant histones demarcates specific functional regions of chromatin and that exchange of histone variants is an important transcriptional regulatory mechanism in T. gondii.

overall_design: ChIP-chip experiments using antibodies against protein or epitope tagged: H3K4me3 (1 replicate), H2AX (2 replicates), H2AZ (2 replicates)

first: Sheila

last: Nardelli

first: Natalie

last: Silmon de Monerri

first: Xiaonan

last: Wang

first: Maria

last: Carolina Dalmasso

first: Lisa

last: Brown

first: Li-Min

last: Ting

first: William

last: Sullivan Jr

first: Sergio

last: Angel


title: Transcriptome profile of GEN2.2 cell line silenced for SIDT1 and stimulated with ODN2006

status: Public on Jan 11 2019

city: Granada

first: Concepción

last: Marañón

address: Avda Ilustración 114

country: Spain

institute: Genyo Centre

summary: Analysis of expression profile of human GEN2.2 shSIDT1 cell line and their controls cultured in the presence of ODN2006 for different time points.

overall_design: Total RNA was isolated from GEN2.2 WT, shCLT or shSIDT1 cells growing at log phase with High Pure RNA isolation Kit (Roche Diagnostics, Mannheim, Germany), according with the manufacturer´s instructions in triplicate. GEN2.2 cells were stimulated with 1 µM ODN2006 (Life Technologies) for 2h, 6h or 24h. A total of 300 ng of total RNA was processed using Illumina TotalPrep RNA Amplification Kit. Hybridization of human samples was performed on Illumina Human-HT12 Version 4.

first: Concepcion

last: Marañon


title: RNA seq analysis of Active TB and treatment after 6 &12 months

status: Public on Nov 14 2018

city: Bangalore

first: Nagasuma

last: Chandra

state: Karnataka

address: C V Raman Road

department: Biochemistry

country: India

institute: IISC

summary: Study to identify putative condition specific biomarkers

overall_design: Whole Blood RNA seq analysis of patient samples

first: Annapurna

last: Vyakarnam

first: Subhash

last: Basu

first: Soumya

last: Swaminathan

first: Abhilash

last: Mohan

first: Awanti

last: Sambarey

first: Abhinandan

last: Devaprasad

first: Asma

last: Ahmed

last: Rath


title: PARCB Project: Reprogramming normal human epithelial tissues to a common, lethal neuroendocrine cancer lineage

status: Public on Oct 05 2018

city: Los Angeles

first: Owen

last: Witte

address: 675 Charles E Young Dr S, 5720 MRL Bldg; MC 729022

department: MIMG

institute: UCLA


title: Reprogramming normal human epithelial tissues to a common, lethal neuroendocrine cancer lineage (RNA-seq)

summary: Small cell carcinomas from different tissues exhibit transcriptional and epigenetic convergence and suggest common vulnerabilities for therapies

overall_design: Convergent neuroendocrine cancer from distinct epithelial tissues

first: Jung

middle: W

last: Park


title: Gene expression data from HepG2 SND1 knockdown stable cell lines after 5-Fu treatment

status: Public on Dec 26 2018

city: Tianjin

first: Xiaoteng

last: Cui

address: NO. 22, Qixiangtai Road, Heping district

country: China

institute: Tianjin Medical University

summary:
SND1 protein is a highly conserved protein of eukaryotic cells and is involved in a group of cellular biological processes, such as gene transcription, pre-mRNA splicing, cell cycle, DNA damage repair, proliferation and programmed cell death degradome, adipogenesis and cancerogenesis. SND1 can promote the metastasis and proliferation of breast cancer cells by down-regulating the miR-127 expression.
Herein, we used microarrays to detail the potential molecular mechanism in the chemotherapy drug-induced HCC apoptosis.

overall_design: HepG2 stable cell lines of shSND1-#1 and pLKO-Vector were treated with 6μg/mL 5-Fu, respectively. 48 h after treatment, total RNA was extracted. cDNA was synthesized and hybridised to Affymetrix microarrays.

first: Xingjie

last: Gao

first: Jie

last: Yang


title: TRPS1 is a lineage-specific transcriptional dependency in breast cancer [Seq]

status: Public on Oct 03 2018

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: We performed an unbiased cell viability-based pooled shRNA screen on 59 cell lines to identify novel epigenetic and transcriptional dependencies of multiple cancer types, including leukemia, neuroblastoma, breast, colorectal, prostate, and rhabdoid tumors. Here, we identified Tricho-Rhino-Phalangeal Syndrome Type I protein (TRPS1) as one of the most significant hits specific for breast cancer cell lines. Downregulation of TRPS1 resulted in cell cycle arrest and apoptosis increase in vitro and impaired tumorigenic capacity in vivo. We characterized TRPS1 genomic targets and protein interactome. We identified GATAD2B as an important partner of TRPS1, uncovering novel epigenetic network crucial for breast cancer cell survival.

overall_design:
Bulk RNA-Seq: Gene expression analysis of 57 cell lines used in the screen and HCC3153 and SUM159 cell lines with TET-inducible shRNA against TRPS1 with the following variables: Two different shRNA labeled sh1 (sh41) and sh2 (sh43), doxycyclin (plus/treatment) and no doxycyclin (minus/control), 3, 4 and 5 days after doxycyclin treatment. All conditions were sequenced without replicates (24 samples).

ChIP-Seq: Examination of H3K27me3, GATAD2A, GATAD2B, H3K27ac, and TRPS1 in three different cell lines, in duplicates. HCC3153 cell line included the following variables: Two different shRNA labeled sh1 (sh41) and sh2 (sh43),  doxycyclin (plus/treatment) and no doxycyclin (minus/control).

Please note that  the 'DFCI_EpiCluster_RNA-Seq.reads.gct' processed data file includes 4 re-analyzed samples, which were submitted as a part of series GSE63582 and the data columns correspond to the following samples;
SUM149PT - GSM1842497 [SUM149_DMSO_12H_R1]
SUM149PT_JQ1R_w_JQ1 - GSM1842493 [SUM149R_DMSO_12H_R1]
SUM159PT - GSM1553156 [SUM159_DMSO_3H_1]
SUM159PT_JQ1R_w_JQ1 - GSM1553147 [SUM159R_DMSO_3H_2]

first: Robert

last: Witwicki

first: Muhammad

middle: B

last: Ekram

first: Xintao

last: Qiu

first: Michalina

last: Janiszewska

first: Shaokun

last: Shu

first: Mijung

last: Kwon

first: Anne

last: Trinh

first: Elizabeth

last: Frias

first: Nadire

last: Cochran

first: Greg

last: Hoffman

first: Yingtian

last: Xie

first: Gregory

last: McAllister

first: Rob

last: McDonald

first: Javad

last: Golji

first: Michael

last: Schlabach

first: Kavitha

last: Venkatesan

first: Antoine

last: deWeck

first: Nicholas

last: Keen

first: Ho

last: Chan

first: David

last: Ruddy

first: Tomas

last: Rejtar

first: Sosathya

last: Sovath

first: Serena

last: Silver

first: William

last: Sellers

first: Zainab

last: Jagani

middle: D

last: Hogarty

first: Ramesh

last: Shivdasani

first: Charles

last: Roberts

first: Myles

last: Brown

first: Kimberly

last: Stegmaier

first: Henry

last: Long

last: Pellman


title: TRPS1 is a lineage-specific transcriptional dependency in breast cancer

first: Kornelia

last: Polyak

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: SAPORIN-EpCAM antibody conjugates for targeted therapy

status: Public on Sep 05 2018

city: Chennai

first: Narayanan

last: Janakiraman

state: Tamil nadu

address: College Road

department: Nanobiotechnology

institute: Vision Research Foundation

summary:
Saporin (SAP) is an Ribosomal inactivation protein (RIP) toxin molecule. Conjugating SAP with EpCAM Antibody will direct the toxin pay loads to the EpCAM positive cancer cells as a targeted therapy
We used microarrays to detail the global gene expression to understand the pathways involved in EpCAM-mediated SAP drug delivery in breast cancer cells.

overall_design: MCF-7 breast cancer cells were cultured and treated with Saporin and Saporin-EpCAM Antibody conjugate for the duration of 24h. RNA was extracted from cells and hybridized onto Affymetrix Human PrimeView arrays. To understand the changes in the transcriptome, we have included untreated MCF-7 cells (Controls; C1, C2- were taken from our own data Accession number:GSE69160) along with treated cells (SAP_1, SAP_2, SAP-CONJ_1, SAP CONJ_2).

first: Prasanna

last: Athyala

first: Srujana

last: Chitipothu


title: PARP1 Stabilizes CTCF Binding and Chromatin Structure to Maintain Epstein Barr Virus Latency Type

status: Public on Jun 27 2018

city: Philadelphia

first: Italo

last: Tempera

state: PA

address: 3307 N. Broad Street, PAHB, Room 206

department: Fels Institute

institute: Temple University

summary: Epstein Barr Virus (EBV) is a potentially oncogenic gammaherpesvirus that establishes a chronic, latent infection in memory B cells. The EBV genome persists in infected host cells as a chromatinized episome and is subject to chromatin-mediated regulation. Binding of the host insulator protein CTCF to the EBV genome has an established role in maintaining viral latency type. CTCF is post-translationally modified by the host enzyme PARP1. PARP1, or Poly(ADP-ribose) polymerase 1, catalyzes the transfer of a poly(ADP-ribose) (PAR) moiety from NAD+ onto acceptor proteins including itself, histone proteins, and CTCF. PARylation of CTCF by PARP1 can affect CTCF’s insulator activity, DNA binding capacity, and ability to form chromatin loops. Both PARP1 and CTCF have been implicated in the regulation of EBV latency and lytic reactivation. Thus, we predicted that pharmacological inhibition with PARP1 inhibitors would affect EBV latency type through a chromatin-specific mechanism. Here, we show that PARP1 and CTCF colocalize at specific sites throughout the EBV genome, and provide evidence to suggest that PARP1 acts to stabilize CTCF binding and maintain the open chromatin landscape at the active Cp promoter during type III latency. Further, PARP1 activity is important in maintaining latency type-specific viral gene expression. The data presented here provide a rationale for the use of PARP inhibitors in the treatment of EBV-associated cancers exhibiting type III latency, and could ultimately contribute to an EBV-specific treatment strategy for AIDS-related or post-transplant lymphomas.

overall_design:
Two biological replicates of LCL FAIRE or just sonicate DNA (input) were used to make ChIP-seq libraries.  For peak calling we compare the FAIRE enrichment to the input signal.
This series includes PARP1 and CTCF ChIP-seq of EBV.

first: Lena

last: Lupey-Green

first: Lisa

last: Caruso

first: Jozef

last: Madzo

first: Kayla

last: Martin

first: Yinfei

last: Tan

first: Michael

last: Hulse


title: Naturally-occurring canine invasive urothelial carcinoma harbors luminal and basal transcriptional subtypes found in human muscle invasive bladder cancer

status: Public on Aug 01 2018

city: West Lafayette

first: Deborah

last: Knapp

address: 625 Harrison Street

institute: Purdue University

summary: RNA-seq was used to identify basal and luminal subtypes in canine bladder cancer. In addition to larger gene-sets, a smaller panel of genes was developed to stratify canine samples into either basal or luminal subtype prospectively. Immune signature patterns were queried in basal and luminal subtypes.

overall_design: Canine normal urothelial cells (n=4) were compared to canine invasive urothelial carcinoma samples (n=29). DEGs were identified, and overlapping genes with those that predict basal and luminal subtypes in human breast cancer were used to identify the subtypes in canine tissues.

first: Deepika

last: Dhawan

first: Noah

last: Hahn

first: José

last: Ramos-Vara


title: RNA-seq from Harpegnathos tissues and brain regions

status: Public on May 24 2018

first: Roberto

last: Bonasio

address: 3400 Civic Center Blvd - SCTR 9-111

department: Cell and Developmental Biology

institute: University of Pennsylvania

summary: Transcriptome sequencing of Harpegnathos ovary, fat body, antenna, non-visual brain, optic lobe, and retina

overall_design: RNA was extracted from the indicated tissue of the ants and sequenced.

first: Emily

last: Shields


title: Staphylococcus aureus TCH1516 response to sub-inhibitory concentrations of Nafcillin in different media conditions

status: Public on Jun 05 2018

city: La Jolla

first: Saugat

last: Poudel

address: 9500 Gilman Dr.

institute: University of California San Diego

summary: Methicillin resistant S.aureus (MRSA) resistance to beta-lactam is dependent on environmental conditions. In physiologically relevant conditions present in RPMI (supplemented with 10% LB for proper growth) the MIC of beta lactam Nafcillin drops more than 20 fold when compared to MIC in bateriological Cation Adjusted Mueller Hinton Broth(CAMHB).  In order to elucidate the underlying mechanism behind this difference, MRSA isolate TCH1516 was grown in each media in presence of varying levels of nafcillin. At 2.5 hour timepoint cells were harvested and expression profile determined with RNA sequencing.

overall_design: S.aureus was grown in two different bacterial conditions CAMHB/ RPMI + 10% LB (R10LB) with varying sub-inhibitory concentrations of Nafcillin – 0.0625 ug/mL and/or 0.5 ug/mL. SRPSRP127172. PRJNA422941


title: Methylomic signatures of platinum re-sensitization in ovarian cancer [Illumina HumanMethylation450 BeadChip]

city: Bloomington

first: Kenneth

last: Nephew

state: IN

institute: Indiana University

summary: Epigenetic changes, particularly DNA methylation aberrations have been implicated in acquired resistance to platinum in ovarian cancer. A multi-institutional randomized clinical trial compared a regimen of a DNA methyl transferase (DNMT) inhibitor guadecitabine and carboplatin to physician’s choice chemotherapy for patients with recurrent platinum resistant ovarian cancer. Tumor biopsies or malignant ascites were collected at day 1 of cycle 1 (pre-guadecitabine) and after two cycles of treatment (post-decitabine). The goal of the current study was to analyze guadecitabine-induced DNA methylation and gene expression changes and correlate pretreatment levels with clinical outcomes. Epigenomic and transcriptomic profiling using the Infinium HumanMethylation450 BeadChip (HM450) and RNA sequencing revealed extensive methylation and gene expression changes induced by guadecitabine in ovarian tumors. Ninety-four gene promoters were significantly hypomethylated after treatment with guadecitabine and 949 genes were differentially expressed in pre vs. post-treatment tumors. Pathways associated with immune reactivation and DNA repair were significantly altered by guadecitabine treatment.  Expression levels of 1155 genes involved in 25 networks on day 1 of cycle 1 correlated with progression free survival. Increased expression of selected genes (e.g. DOK2, miR193a) silenced through promoter methylation restored platinum sensitivity in ovarian cancer cells.  Together, these results support that guadecitabine altered DNA methylation and expression of genes and gene networks correlate with re-sensitization to carboplatin in ovarian cancer patients.

overall_design: 146 samples are analyzed, including tumor, ascites samples collected from patients with platinum resistant ovarian cancer before and after treated by guadecitabine, as well as HOSE (human normal ovarian surface epithelium cells), used as normal control

first: Fang

last: Fang

middle: P

first: Daniela

last: Matei


title: Gene expression profile of human colorectal carcinoma

status: Public on Apr 24 2018

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

summary: Despite steady progress in the diagnosis and treatment of colorectal cancer (CRC), overall therapeutic outcomes remain unsatisfactory. Therefore, a better understanding of the molecular mechanisms of CRC is urgently needed. Fourteen pairs of cancerous and matched non-cancerous tissues (at least 5 cm away) were obtained from CRC patients undergoing surgical resection. Affymetrix human GeneChip primeview array was conducted to identify differentially expressed genes (DEGs) between CRC tissues and matched adjacent normal tissues. cDNA microarray analysis of cancerous and paired noncancerous tissues from CRC patients revealed 1,868 DEGs, of which 778 in primary lesions were up-regulated and 1,090 were down-regulated.

overall_design: Samples from fourteen colorectal cancer patients who had undergone surgical resection of colorectal cancer were collected. No patients had received radio- or chemotherapy prior to surgery. To identify molecular signatures of CRC, we examined the DEGs in fourteen pairs of CRC primary lesions and non-cancerous surrounding tissue.

first: Aling

last: Shen


title: RNA-seq from Camponotus and Harpegnathos ants for genome annotation

sample_organism:
Camponotus floridanus
Harpegnathos saltator

overall_design:
Refer to individual Series

The RNA-seq was performed for a study that reports PacBio-based reassembly for our two ant genomes. However, those versions of the assemblies are not in a database yet. The records will be updated with the proper links to the assembly records once available.


title: Whole body RNA-seq from developmental stages of Harpegnathos ants

summary: RNA from Harpegnathos embryos, instar 1 larvae, instar 4 larvae, early pupae, late pupae, adult workers, and males was sequenced to look for gene expression changes throughout development.

overall_design:
RNA was extracted from the whole body of the ants and sequenced.

The RNA-seq was performed for a study that reports PacBio-based reassembly for our two ant genomes. However, those versions of the assemblies are not in a database yet. The records will be updated with the proper links to the assembly records once available.


title: Transcriptional changes in glioma cells following treatment with 1-Benzyl-3-cetyl-2-methylimidazolium iodide (NH125), Tunicamycin, and 0.1% DMSO (in media)

status: Public on Mar 02 2018

first: Saad

last: Sheikh

address: Bldg 421 8-169, 3400 Civic Center Blvd

department: Radiation Oncology

institute: University of Pennsylvania, Perelman School of Medicine

summary:
Purpose: Evaluate transcriptional changes in glioma derived stem cells, U251, and normal human astrocytes following treatment with NH125, Tunicamycin, or 0.1% DMSO
Methods: Glioma derived stem cells, U251 and Normal Human Astrocytes were plated in individual dishes and treated with either 2.5 micromolar NH125, 1.0 mcg/mL Tunicamycin, or 0.1% DMSO (vehicle) for twenty-four hours followed by total RNA extraction, library preparation and next generation sequencing
Results: Using our analysis pipeline we mapped our sequence reads to the reference genome GRCh38.   Following read count normalization and differential expression of NH125 and tunicamycin treated samples to vehicle treated controls we found that NH125 and tunicamycin treatment lead to activation of similar signalling pathways
Conclusions: We present an optimized workflow for analysis of transcriptional changes in drug treated glioma derived stem cells, glioblastoma cells and normal human astrocytes

overall_design: Three cell lines (one patient derived) underwent three separate treatments followed by total RNA isolation, library preparation and next generation sequencing

first: Rodrigo

last: Gier


title: Effect of ROQUIN2(Y691F) expression on mRNA levels upon BCR stimulation

status: Public on Apr 27 2018

summary: Roquin2, and its paralog Roquin1, are key regulator of mRNA decay. Roquin proteins recognize mRNAs containing a 3’-UTR stem-loop motif, called constitutive decay element (CDE), through the ROQ domain. Upon target engagement, Roquin proteins recruit the CCR4-CAF1-NOT complex, mediating mRNA deadenylation and destabilization. To study the effect of  Roquin2 stabilization, we sought out to identify the relevant Roquin2 mRNA targets in human DLBCL. To this purpose, we measured differential gene expression via RNA-seq analysis in U-2932 cells expressing Roquin2 or non-degradable Roquin2 upon BCR crosslinking.

overall_design: U-2932 stably expressin Roquin2(WT) or Roquin2(Y691F) were treated with F(ab')2-IgM at 10 µg/ml for 12 hours. RNA was collected from three independent biological replicates per condition.

first: Luca

last: Busino

first: Jaewoo

last: Choi


title: Genome-wide localisation of histone variants in Toxoplasma gondii implicates variant exchange in transcriptional control by demarcation of functional chromatin regions (ChIP-seq)

status: Public on Mar 01 2018

first: Kami

last: Kim

department: Medicine

summary: Chromatin is composed of DNA wrapped around nucleosomes, complexes consisting of highly basic proteins called histones. Histone variants are non-canonical variants of histones that have specific functions. The Apicomplexan parasite Toxoplasma gondii possesses conserved histone variants CenH3, H3.3, H2A.Z, H2A.X, as well as the parasite-specific H2B variant, H2BV (or H2B.Z). We surveyed the genome-wide distribution of T. gondii histone variants by chromatin immunoprecipitation coupled with microarray (ChIP-chip) and next generation sequencing (ChIP-seq). Histone variants have specific localisations in chromosomes and in relation to genomic features. Histones H2BV and H2AZ localise to promoter regions with the transcriptional activation mark H3K4me3. Sites where H2BV, H2AZ and H3K4me3 colocalise are enriched in motifs recognised by AP2 transcription factors, particularly in the nucleosome-free region just upstream of the transcription start site. In contrast, histone variants H3.3 and H2AX are largely absent from promoters but enriched in gene bodies. Consistent with previous biochemical work, the majority of H2AX and H2AZ loci do not overlap, suggesting that they are present in different nucleosomes. In addition, the T. gondii homologue of the centromeric histone CenH3 demarcates centromeric chromatin and appears to be part of a unique centromeric histone complex including H3.3 that localises to centromeric chromatin as detected in proteomic analysis of co-immunoprecipitated CenH3 complexes. Together, these data suggest that the position of variant histones demarcates specific functional regions of chromatin and that exchange of histone variants is an important transcriptional regulatory mechanism in T. gondii.

overall_design: Localization of histone variants in Toxoplasma gondii by ChIP-chip and ChIP-seq

first: Sheila

last: Nardelli

first: Natalie

last: Silmon de Monerri

first: Xiaonan

last: Wang

first: Maria

last: Dalmasso

first: Lisa

last: Brown

first: Li-Min

last: Ting

first: William

last: Sullivan

first: Sergio

last: Angel


title: Whole body RNA-seq from developmental stages of Camponotus ants

first: Roberto

last: Bonasio

summary: RNA from Camponotus embryos, instar 1 larvae, instar 4 larvae, early pupae, late pupae (minor and major), adult workers, and males was sequenced to look for gene expression changes throughout development.

first: Emily

last: Shields


title: Dissecting the Variations of Ripening Progression and Flavonoid Metabolism in Grape Berries Grown under Double Cropping System

status: Public on Oct 01 2017

city: Beijing

first: Jun

state: Beijing

address: No. 17 Tsinghua East Road, Beijing, 100083, China.

department: College of Food Science and Nutritional Engineering

institute: China Agricultural University

summary: A double cropping system has been commercially adopted in subtropical regions in southern China, where there is abundant sunshine and heat resources. In this viticulture system, the first growing season normally starts as a summer cropping cycle; then, the vine is pruned and forced by hydrogen cyanamide, resulting in a second crop in January of the next year. Due to climate differences between the two growing seasons, flavonoid content and composition varies greatly. In this study, changes in the transcriptome of flavonoid-associated pathways were compared in berries grown under the double cropping system; in addition, the accumulation of flavonoid compounds was compared. Specific alterations in MYB transcription factors occurred in winter cropping berries around veraison. Then, the winter cropping cycle distinctly induced the flavonoid metabolic pathways while triggering the ripening-associated pathways. Notably, the climate conditions in winter cropping positively affected flavonoid biosynthesis, while the summer season took a major toll on anthocyanin accumulation. In addition, the three classes of flavonoid compounds responded differently to the changing climate; the anthocyanins and flavonols were promoted several fold, whereas no consistent increase was found for flavan-3-ols. Conclusively, flavonoid biosynthesis in grapes grown under a double cropping system showed seasonal or climatic-specific accumulation patterns.

overall_design: Total RNA obtained from deseed grape berries of of Cabernet Sauvignon and Riesling at three developmental stages (E-L 35, 36 and 38) in winter cropping compared to summer control crops.

first: Weikai

last: Chen

first: Xianjin

last: Bai

first: Muming

last: Cao

first: Fei

last: He

first: Changqing

last: Duan


title: Distinct changes in transcriptional profiles and epigenetic patterns mediated by EZH2 inhibitors in sensitive and insensitive prostate cancer cells

status: Public on Sep 01 2017

city: San Antonio

first: Kexin

last: Xu

state: TX

address: 7703 Floyd Curl, MC 8257

department: Molecular Medicine

institute: UT Health Science Center at San Antonio


title: OXR1A deficient male mouse displays fatty liver associated with impaired transcription regulation of hormone response and lipid metabolism

status: Public on Aug 24 2017

city: Oslo

first: Mingyi

last: Yang

address: Sognsvannsveien 20

department: Department of Microbiology, Rikshospitalet

institute: Oslo University Hospital

summary:
Purpose: The Oxidation Resistance gene 1 (Oxr1) protects cells against oxidative stress and involves in transcription regulation. Here we generated the brain specific isoform A knockout mice (Oxr1A-/-). Unexpectedly, the male mice developed fatty liver with large number of lipid-droplets at 12 months. To understand the mechanism of the phenotype,  we investigated the transcriptome profile of Oxr1A-/- mice liver both in male and female by RNA sequencing and compared to wild type.

Methods: The OXR1A knockout mice were generated by gene trap approach to targeted on OXR1 isoform A specific exons. Total RNA was pooled from triplicate liver samples of male and female mice at 12 months old in knockout and control groups  and performed RNA sequencing on an Illumina HiSeq 2500 platform. The sequence reads that passed quality filters were analyzed at gene level. The GOseq program was used to generate gene ontology (GO) annotation of differentially expressed genes (DEGs). The pathway enrichments were identified by KEGG Pathway Enrichment Analysis. qRT–PCR validation was performed using SYBR Green assays.

Results: We identified total 724 differentially expressed genes (DEGs) between OXR1A-/- and wild type in male mice,  while only 169 DEGs were identified in female. For the male, OG analysis revealed that a subset of 22 DEGs involved in fatty acid metabolism and transport, while 24 DEGs involved in hormone response and 164 DEGs involved in immune response.

Conclusions: Enrichment of differentially expressed genes (DEGs) in the liver of male Oxr1A-/- mice associated with hormone response, fatty liver metabolism and immune response.

overall_design: The differential expression profiles were generated by comparsion in the liver tissues between wild type and OXR1A difficent mice.

first: Xiaolin

last: Lin

first: Filip

last: Segers

first: Rajikala

last: Suganthan

first: Gunn

last: Hildrestrand

first: Per

last: Aas

first: Elise

last: Kristiansen

first: Arne

last: Klungland

first: Luisa

last: Luna

first: Lars

last: Eide

first: Bente

last: Halvorsen

first: Pål

last: Aukrust

first: Magnar

last: Bjoras


title: Gemone-wide changes of epigenetic mark H3K27 trimethylation (H3K27me3) and AR in prostate cancer cells upon the treatment of EZH2 inhibitors [ChIP-seq]

summary: Our initial data showed different responses of abl and DU145 cells to EZH2 inhibitors, therefore we detected the chromatin binding signals of H3K27me3 in both cell lines in the presence of the compounds. We found that genome-wide changes in H3K27me3 levels were not associated with the inhibitor-mediated transcriptional programs or biological effects. Since the gene expression profiles upon the compound treatment indicated an important role of AR signaling in mediating the inhibitory action of the drugs in abl cells, we them mapped AR chromatin binding patterns in the presence or absence of EZH2 inhibitors. It was interesting to detect a dramatic decline in AR binding intesities at regulatory regions of the regulated target genes.

overall_design: Detection of the changes in chromatin binding intesities/signals of H3K27me3 and AR upon EZH2 inhibitors in prostate cancer cells

first: Chen-Hao

last: Chen


title: Systematic transcriptomics reveals a biphasic mode of sarcomere morphogenesis in flight muscles regulated by Spalt

status: Public on Dec 01 2017

city: Kansas City

first: Maria

middle: Lynn

last: Spletter

state: MO

address: 5009 Rockhill Rd

department: Biological and Biomedical Systems

institute: University of Missouri Kansas City

summary: Muscles organise a pseudo-crystalline array of actin, myosin and titin filaments to build force-producing sarcomeres. To study how sarcomeres are built, we performed mRNA-sequencing of developing Drosophila flight muscles and identified 40 distinct expression profile clusters. Strikingly, two clusters are strongly enriched for sarcomeric components. Temporal gene expression together with detailed morphological analysis enabled us to define two distinct phases of sarcomere development, both of which require the transcriptional regulator Spalt major. During the first sarcomere formation phase, 2.0 µm long immature sarcomeres assemble myofibrils that spontaneously contract. In the second sarcomere maturation phase, sarcomeres grow to their final 3.2 µm length and 1.5 µm diameter and acquire stretch-sensitivity. Interestingly, the final number of myofibrils per flight muscle fiber is determined at the onset of the first phase and remains constant. Together, this defines a biphasic mode of sarcomere and myofibril morphogenesis – a new concept which may also apply to vertebrate muscle or heart development.

overall_design: Part I: An 8-point timecourse of wild-type flight muscle development in Drosophila melanogaster was analyzed with duplicates/triplicates for each timepoint Part II: A Mef2-Gal4 x salmIR timecourse in duplicate at 4 timepoints was compared to wild-type flight muscle

middle: L

first: Frank

last: Schnorrer

first: Assa

last: Yeroslaviz

first: Alexander

last: Stark

first: Bianca

last: Habermann


title: Brain RNA-seq one day after knockdown of the corazonin receptor in Harpegnathos ants

status: Public on Aug 10 2017

first: Roberto

last: Bonasio

summary: This experiment aimed at determining the immediate (d1) transcriptional consequences of knockding down the corazonin receptor in the ant brain.

overall_design: Dueling Harpegnathos individuals were removed from the transition colony and injected with corazonin receptor or GFP siRNAs to perform mRNA knockdown

first: Janko

last: Gospocic

first: Emily

last: Shields


title: EZH2 inhibitor-mediated transcriptional profiling in prostate cancer cells [RNA-seq]

first: Kexin

last: Xu

summary: We reported here the gene expression profiles that were mediated upon the treatment of EZH2 inhibitor in two hormone-refractory prostate cancer cell lines: the sensitive, AR-positive abl cells and the insensitive, AR-null DU145 cells.

overall_design: We treated both types of prostate cancer cells with two different EZH2 inhibitors (GSK126 or EPZ-6438) at final concentrations of 5 uM for 60-72 hrs, and then collected RNAs for gene expression profiling.


title: Genome-wide high resolution map of transcription start sites across the life cycle of Oikopleura dioica

status: Public on Feb 05 2018

city: Bergen

first: Eric

last: Thompson

address: Thormøhlensgt. 55

institute: Sars International Centre for Marine Molecular Biology

summary: The selection and activity of transcription start sites (TSSs) are central to gene regulation and depend on sequence and chromatin features within a core promoter region. We present, at single-bp resolution, the TSS landscape of Oikopleura dioica, a marine chordate in the sister group to vertebrates and relate dynamics of promoter usage, and their architectures, across its life cycle, to chromatin features. TSS selection grammars include a genome-wide shift during spermatogenesis to promoters with a novel, position-specific, core promoter element, present in >70% of male-specific promoters. Differential promoter usage in spermatogenesis includes the activation of cryptic internal promoters within polycistronic operons, alternative TSS selection within promoters of genes expressed in earlier development and the exclusion of trans-splice sites. In contrast, maternal promoters, which are active in endocycling nurse nuclei in O. dioica, lack position-specific motifs, have dispersed TSS usage, ordered nucleosomes around the TSS and typical histone modifications associated with broad promoters. Furthermore, our results indicate that the cell cycle regulator, E2F1, acts as a master regulator of these maternally expressed genes. Zygotic promoters are also predominantly broad and the vertebrate maternal to zygotic switch in mode of TSS-selection is absent. DNA methylation in gene bodies is an ancient property of eukaryotic genomes and is thought to repress alternative TSSs. We report a strong association between gene body DNA methylation, H3K4me3-depletion and TATA-dependent sharp promoters in O. dioica. Core promoter features may therefore determine the subset of gene bodies that are methylated in this invertebrate genome.

overall_design: RNA was extracted from 6 key stages of development, depleted of trans-spliced transcripts and TSSs profiled using DeepCAGE.

first: Gemma

last: Danks

first: Pavla

last: Navratilova

first: Boris

last: Lenhard


title: RNA-seq in heads from Monomorium pharaonis nurses and foragers

summary: Replicate pools of heads from 10 individual Monomorium pharaonis workers, collected in the act of nursing larvae or foraging for food, each from a separate replicate colony

overall_design: Replicate colonies contained ~300-400 workers, ~300-400 brood, and 10 queens; nurse and forager workers were collected in the act of nursing larvae or foraging for food

first: Timothy

last: Linksvayer

middle: S

last: Mikheyev


title: Brain RNA-seq during the worker-gamergate transitions in Harpegnathos ants

summary: Harpegnathos workers were induced to transition to reproductive gamergates and mRNA from their brains was sequenced to determine changes in gene expression at different time points (0, 6, 13, and 110 days after transition onset)

overall_design: Ants were removed from their original colony at d0 and placed in boxes lacking a dominant reproductive. Dueling was monitored and the top three individuals displaying the most dueling were collected 6 and 13 days later. Pre-transfer individuals (d0) and stable gamergates at d110 were also harvested. Whole brains (including optic lobes) were dissected and processed for RNA-seq.

first: Juergen

last: Liebig


title: Brain RNA-seq one day intra-head injection of corazonin or control peptide in Harpegnathos ants.

summary: This experiment aimed at determining the immediate (d1) transcriptional consequences of corazonin in the brain.

overall_design: Six dueling Harpegnathos individuals were removed from the transition colony and injected with corazonin or control peptide.


city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

summary: To identify a microRNA profile of human medullary thyroid cancer (MTC), we performed a miRNA microarray analysis exploiting 8 primary tumours and 9 paired neck nodes metastases in comparison with 3 non-neoplastic thyroid tissues.

overall_design: Eight sporadic MTC patients were selected for the miRNA microarray analysis. A total of 17 MTC (P = primary tumour, M = nodal metastasis) and 3 non-neoplastic thyroid (N) formalin-fixed paraffin-embedded (FFPE) surgical specimens were obtained. The primary tumours and the matched nodal metastases were obtained from the initial surgery or from a subsequent lymphadenectomy. Referring to the matched primary tumour, 6 of the nodal metastases were synchronous and 3 were metachronous (one patient had both metastasis types included in the array). Non-neoplastic thyroid samples were obtained from patients with pathologies other than thyroid cancer. For each specimen haematoxylin and eosin-stained sections and calcitonin-stained sections were evaluated by an experienced pathologist to confirm the histological diagnosis and to select areas in which tumour cells represented at least the 80% of the total cells.

first: Paola

last: Romeo

first: Angela

last: Zanframundo

first: Antonella

last: Aiello

last: Carcangiu

first: Loris

last: De Cecco

last: Greco

first: Laura

last: Locati

middle: G

last: Borrello


title: Global Methylation Profiles in Buccal Cells of Long-Term Smokers and Moist Snuff Consumers

city: Winston-Salem

first: Gaddamanugu

last: Prasad

state: NC

institute: RAI Services Company

summary: Alternations in gene methylation and other epigenetic changes regulate normal development as well as drive disease progression. Chronic cigarette smoking causes hyper- and hypo-methylation of genes that could contribute to smoking-related diseases. It is unclear whether consumers of non-combustible tobacco, such as moist snuff, also exhibit such perturbations in their methylome. Here, we present global methylation changes relative to non-tobacco consumers in buccal cells collected from smokers (SMK) and moist snuff consumers (MSC). Generally healthy adult male study subjects were recruited into SMK, MSC and Non-Tobacco Consumer (NTC) cohorts (40 subjects/cohort). Global methylation profiling was performed on the Illumina 450K methylation array using buccal cell DNA. A total of 1,252 loci were found to be significantly differentially methylated in tobacco consumers relative to non-tobacco consumers. Overall, the SMK cohort exhibited larger qualitative and quantitative changes relative to MSC. Approximately half of the total number of gene loci, classified as Combustible Tobacco-Related signatures, and a third of the changes, termed Tobacco-Related signatures, were commonly detected in the tobacco consumers. Very few differences were detected between MSC and NTC, and hierarchical clustering of the top 50 significant gene loci suggested that MSC and NTC co-cluster. Consistent with physiological functions of AhR, combustible tobacco drives profound changes in buccal cell methylation status, principally impacting cell development and immune response pathways. These results aid in placing combustible and non-combustible tobacco products along a risk continuum and provide additional insights into the effects of tobacco consumption.

overall_design: DNA extraction and global methylation profiling was performed by Expression Analysis on Illumina Infinium HumanMethylation450 BeadChip arrays. All data were normalized using Illumina recommended normalization method to reduce the effects of experimental variation. This normalization procedure included background estimation using negative control probes and normalization of intensities to the housekeeping genes with no CpG sites. Beta values (β), which are used to estimate the methylation level of the CpG locus using the ratio of intensities between methylated and un-methylated alleles, were exported from Illumina Genome Studio software and all analyses were performed using the SAS® statistical software package.   For normally distributed beta values, we analyzed the data by modeling each individual methylation locus by linear regression with age and race as independent variables.

first: Walter

last: Jessen

first: Michael

middle: F

last: Borgerding

first: Gaddamangu


title: Conserved DNA methylation combined with differential frontal cortex and cerebellar expression distinguishes C9orf72-associated and sporadic ALS, and implicates SERPINA1 in disease.

status: Public on Aug 14 2017

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

type: Methylation profiling by high throughput sequencing

summary: We previously found C9orf72-associated (c9ALS) and sporadic amyotrophic lateral sclerosis (sALS) brain transcriptomes comprise thousands of defects, among which, some are likely key contributors to ALS pathogenesis. We have now generated complementary methylome data and combine these two data sets to perform a comprehensive “multi-omic” analysis to clarify the molecular mechanisms initiating RNA misregulation in ALS. We found that c9ALS and sALS patients have generally distinct but overlapping methylome profiles, and that the c9ALS- and sALS-affected genes and pathways have similar biological functions, indicating conserved pathobiology in disease. Our results strongly implicate SERPINA1 in both C9orf72 repeat expansion carriers and non-carriers, where expression levels are greatly increased in both patient groups across the frontal cortex and cerebellum. SERPINA1 expression is particularly pronounced in C9orf72 repeat expansion carriers for both brain regions, where SERPINA1 levels are strictly down regulated across most human tissues, including the brain, except liver and blood, and are not measurable in E18 mouse brain. The altered biological networks we identified contain critical molecular players known to contribute to ALS pathology, which also interact with SERPINA1. Our comprehensive combined methylation and transcription study identifies new genes and highlights that direct genetic and epigenetic changes contribute to c9ALS and sALS pathogenesis.

overall_design: Examination epigenetic methylation profiles in c9orf72-associated ALS, sporadic ALS and healthy control

first: Veronique

middle: V

last: Belzil


title: Caste-specific gene expression in ants

first: Roberto

last: Bonasio

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

sample_organism:
Camponotus floridanus
Monomorium pharaonis
Harpegnathos saltator

overall_design: Refer to individual Series


title: Brain RNA-seq 120 days after worker-gamergate transitions in Harpegnathos ants

summary: Harpegnathos workers were induced to transition to reproductive gamergates and 120 days later mRNA from their brains was sequenced to determine changes in gene expressioin

overall_design: Ants were removed from their original colony at d0 and placed in boxes lacking a dominant reproductive. After 120 days individuals were scored for reproductive status by inspecting their ovaries and brains (minus optic lobes) were dissected and processed for sequencing.

first: Janko

last: Gospocic

first: Emily

last: Shields


title: Whole-body RNA-seq from Camponotus floridanus workers and queen

summary: RNA-seq from whole bodies of workers (major and minor) and queen from C. floridanus to increase replicate number from 2010 genome study

overall_design: Two workers (one major and one minor) and one queen were snap frozen and the whole body processed for RNA-seq


title: ChIP-seq for Polycomb repressive complex 2 in wild type and mutants in Arabidopsis

status: Public on Jul 31 2017

summary: We performed ChIP-seq for the Polycomb protein FIE using anti-FIE antiserum in germinated wild-type and double class I BPC and C1-2iD transcruption factor family knockdown seedlings of Arabidopsis thaliana.

overall_design: Three biological replicates for each condition and three biological replicate for input

first: Jun

last: Xiao

first: Doris

last: Wagner


title: Genome-wide screening of HNF1b binding sites identifies transcriptional regulation of the Kir4.1/Kir5.1 potassium channel

status: Public on Aug 01 2017

city: Nijmegen

first: Andreas

last: Kompatscher

state: Gelderland

address: Geert Grooteplein Zuid 30

department: Physiology

country: Netherlands

institute: Radboud Institute for Molecular Life Sciences

summary: chIP-seq was used to provide a genome-wide screening of transcription factor HNF1B binding sites to further elucidate its effect on cyst formation, diabetes and electrolyte handling in patients. A highly specific dataset for Hnf1b binding was constructed for an immortalized murine DCT cell line (mpkDCT4a).

overall_design: 1 transcription factor and 1 histone modification in 1 cell type

first: Jeroen

middle: H

last: de Baaij

first: Anke

last: Hoefnagels

first: Gertjan

last: Veenstra

first: Rene

last: Bindels

first: Joost

last: Hoenderop


title: ChIP-seq for Polycomb and associated transcription factors in Arabidopsis

summary: We performed ChIP-seq for H3K27me3, the Polycomb protein FIE, and two associated transcription factor (AZF1 and BPC1) using epitope tags expressed in germinated seedlings of Arabidopsis thaliana.

overall_design: Three biological replicates for each mark/factor and three biological replicate for corresponding input (C24 or Col strain for FIE, AZF1, and BPC1, and H3 for H3K27me3)


title: Microgravity effect on C. elegans N2/VC (CERISE, 4 days)

status: Public on Aug 31 2016

city: Tsukuba

first: Akira

last: Higashibata

state: Ibaraki

department: Department of Space Biology and Microgravity Sciences

institute: Japan Aerospace Exploration Agency

summary: Microgravity effect on C. elegans gene expression was analysed by whole genome microarray. The worms were cultivated under microgravity for 4 days in the Japanese Module of the International Space Station.

overall_design: C. elegans N2 was exposed microgravity for 4 days. The worms synchronously were cultivated from L1 larvae to adult. There are two control groups, onboard 1G and ground 1G control.

first: Toko

last: Hashizume


title: Next Generation Sequencing Facilitates Quantitative Analysis of Normoxia and Hypoxia Macrophage Transcriptomes

status: Public on Jul 25 2017

city: Kyoto

first: Koichi

last: Murata

state: Kyoto

address: 54, Kawahara-cho, Shogoin, Sakyo-ku

department: Orthopaedics

institute: Kyoto University

summary: To test in an unbiased manner for hypoxia effect, we performed a transcriptomic analysis using high throughput RNA sequencing.

overall_design: Homo Sapiens Macrophage gene expression


title: Genome-wide DNA methylation profiling reveals epigenetic adaptation of stickleback to sea and freshwater conditions

status: Public on May 30 2017

city: Vienna

first: Artem

last: Artemov

address: Spitalgasse 4

department: Center for Brain Research

country: Austria

institute: Medical University of Vienna

summary: Three-spined stickleback (Gasterosteus aculeatus) represents a convenient model to study microevolution - adaptation  to freshwater environment. While genetic adaptations to freshwater are well-studied, epigenetic adaptations attracted little attention. In this work, we investigated the role of DNA methylation in the adaptation of marine stickleback population to freshwater conditions. DNA methylation profiling was performed in marine and freshwater populations of sticklebacks, as well as in marine sticklebacks placed into freshwater environment and freshwater sticklebacks placed into seawater. For the first time, we demonstrated that genes encoding ion channels kcnd3, cacna1fb, gja3 are differentially methylated between marine and freshwater populations. We also showed that after placing marine stickleback into fresh water, its DNA methylation profile partially converges to the one of a freshwater stickleback. This suggests that immediate epigenetic response to freshwater conditions can be maintained in freshwater population. Interestingly, we observed enhanced epigenetic plasticity in freshwater sticklebacks that may serve as a compensatory regulatory mechanism for the lack of genetic variation in the freshwater population. Some of the regions that were reported previously to be under selection in freshwater populations also show differential methylation. Thus, epigenetic changes might represent a parallel mechanism of adaptation along with genetic selection in freshwater environment.

overall_design: The following sample groups were studied: 1) marine sticklebacks kept in marine water, their natural habitat (M@M); 2) freshwater sticklebacks kept in freshwater (F@F); 3) marine sticklebacks incubated in fresh water for 4 days (M@F); 4) freshwater sticklebacks incubated in marine water for 4 days (F@M). In each gruop, 3 individual fish were profiled.

first: Nikolai

last: Mugue

first: Sergey

middle: M

last: Rastorguev

first: Alexander

last: Mazur

first: Svetlana

last: Tsygankova

first: Eugenia

last: Boulygina

last: Nedoluzhko

first: Yulia

middle: A

last: Medvedeva

first: Egor

last: Prokhortchouk


title: Transcription of the human 5-Hydroxytryptamine receptor 2B (HTR2B) gene is under the regulatory influence of the transcription factors NFI and RUNX1 in human uveal melanoma

status: Public on Sep 15 2016

city: Québec

first: Karine

last: Zaniolo

state: Québec

address: 1050 Chemin Sainte-Foy

department: CUO-Recherche

country: Canada

institute: Centre de recherche du CHU de Québec

summary: Introduction: Uveal melanoma (UM) is the most common type of primary intraocular tumor in the adult population. UM will propagate to the liver as the first metastatic site. Once this organ is invaded, survival becomes a matter of months for the patient as no treatment has proved effectiveness. Among the candidates from the class II gene signature, the serotonin receptor-encoding gene HTR2B appears to be the most discriminating as its expression strongly increases in the tumors of UM patients that will progress toward liver metastases. Our study aims at characterizing the molecular mechanisms that lead to this aberrant expression of HTR2B in metastatic UM cell lines.Materials and Methods: Expression of HTR2B was monitored by microarrays and validated by Western blot in a variety of UM cell lines. A 2 Kbp segment covering both the promoter and 5 '-flanking region of the HTR2B gene was cloned upstream the CAT reporter gene in the plasmid pCATbasic (to yield the -2000/HTR2B construct). Deletion mutants were generated by double digestion of the -2000/HTR2B construct with restriction enzymes and transfected, along with the parental -2000/HTR2B construct, in UM cell lines. The genomic areas of interest were 5’ end-labeled and used as probes in electrophoretic mobility shift assays (EMSAs). DMS methylation footprinting was also used to precisely position the DNA target sites for transcription factors (TFs) that bind the HTR2B regulatory regions.Results and Discussion: Transfection analyses revealed that the upstream regulatory regions of HTR2B promoter is made up of a combination of alternative positive and negative regulatory elements. Repressive regions have an abnormally elevated number of target sites for the TFs NFI. EMSA analyses provided evidence that both the NFI isoforms NFIC and NFIX could interact with the promoter and the upstream negative regulatory element from the HTR2B gene. In addition, the TF RunX1 was shown by DMS methylation interference footprinting to bind a target site from the distal silencer element.Conclusion: This project will help understand better the molecular mechanisms accounting for the abnormal expression of the HTR2B gene in uveal melanoma. In the long term, this study will allow us to identify new potential targets that could help screening patients at risk of progressing to liver metastasis formation.

overall_design: Primary culture of humal uveal melanoma cell lines (T97, T98, T108, T111, T128, T131, T132, T142, T143, T151, T157) were analyzed by gene profiling on microarrays at low culture passages (between passage 2 to 7). and their transcriptome analyzed by gen profiling.

first: Manel

last: Benhassine

first: Sylvain

last: Guérin


title: Potential Epigenetic Biomarkers of Obesity Related Insulin Resistance in Human Whole Blood

status: Public on Oct 01 2016

city: Tempe

first: Samantha

middle: Elaine

last: Day

state: AZ

address: University Dr. and Mill Ave.

institute: Arizona State University

summary: Obesity is a critical health concern, and identifying new biomarkers has become essential for better understanding the progression to disease such as type 2 diabetes. DNA methylation has become a useful epigenetic biomarker in part due to its susceptibility to disease influence. Detecting methylation changes in blood is important as it is an easily accessible, compared to the insulin responsive tissue skeletal muscle. The aim of our study was to identify methylation changes in whole blood that were strongly associated with obesity associated insulin resistance. Whole blood was obtained from lean (n=10; BMI= 23.6±0.7 kg/m2) and obese (n=10; BMI= 34.4±1.3 kg/m2) participants in combination with euglycemic hyperinsulinemic clamps to assess insulin sensitivity. We performed the next generation technique, reduced representation bisulfite sequencing (RRBS) on isolated genomic DNA. There were 49 significantly altered differentially methylated cytosines (DMCs; q<0.05). Of these, solute carrier family 19 member 1 (SLC19A1) was also identified using a differentially methylated region approach. The sites for this gene were significantly correlated (P<0.05) with body mass index, body fat percent, and the clamp Rd. Moreover, the decrease in SLC19A1 methylation was similar to the change previously found in skeletal muscle. Pyrosequencing confirmed the changes in methylation at Chr.21:46,957,915 in both tissues. These results demonstrate that the methylation status of SLC19A1 provides a new potential epigenetic biomarker for obesity related insulin resistance.

overall_design: Whole blood were obtained  in  PAXgene tubes from lean (n=10) and obese (n=10) participants in combination with euglycemic hyperinsulinemic clamps to assess insulin sensitivity. We performed reduced representation bisulfite sequencing next generation methylation analysis on DNA isolated from whole blood.

first: Dawn

last: Coletta

first: Richard


title: Interleukin-21 limits inflammation and the viral reservoir in ART-treated, SIV-infected rhesus macaques

status: Public on Feb 28 2017

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: Interleukin-21 treatment during ART was able to decrease residual immune activation and viral burden in SIV-infected rhesus macaques

overall_design: total PBMCs at pre-ART and during ART treatment were used to generate RNA-seq data

first: Luca

last: Micci

first: Emily

last: Ryan

first: Remi

last: Fromentin

first: Steven

last: Bosinger

first: Justin

last: Harper

first: Tianyu

last: He

first: Sara

last: Paganini

first: Kirk

last: Easley

first: Ann

last: Chahroudi

first: Clarisse

last: Benne

first: Sanjeev

last: Gumber

first: Colleen

last: McGary

first: Kenneth

last: Rogers

first: Claire

last: Deleage

first: Carissa

last: Lucero

first: Siddappa

last: Byrareddy

first: Cristian

last: Apetrei

first: Jacob

last: Estes

first: Jeffrey

last: Lifson

first: Michael

last: Piatak Jr

first: Nicolas

last: Chomont

first: Francois

last: Villinger

first: Guido

last: Silvestri

first: Jason

last: Brenchley

first: Mirko

last: Paiardini


title: Epigenomic remodeling of the PAX8 cistrome in high grade serous ovarian cancer [ChIP-Seq]

status: Public on Aug 08 2016

city: Boston

first: Kevin

middle: Meyer

last: Elias

address: 75 Francis Street

department: OB/GYN

institute: Brigham and Women's Hospital

summary: We report mapping of the PAX8 cistrome in three high grade serous ovarian cancer cell lines (KURAMOCHI, OVSAHO, and JHOS4) compared to three benign immortalized fallopian tube cell lines (FT33, FT194, and FT246). We identified a highly conserved PAX8 binding pattern common across benign fallopian tube cell lines that was distinct from the unique PAX8 binding patterns seen in each cancer cell line.

overall_design: Comparison of benign and malignant Mullerian cell lines.


title: Epigenomic remodeling of the PAX8 cistrome in high grade serous ovarian cancer


title: Genome-wide DNA methylation analysis in hepatocellular carcinoma

status: Public on Sep 15 2015

city: Kyotofu Kyotoshi

first: Kohichiroh

last: Yasui

address: Kamigyoku Kajicho 465

department: Molecular Gastroenterology and Hepatology

institute: Kyoto Prefectural University of Medicine Graduate School of Medical Science

summary: Genome wide DNA methylation profiling of primary HCC tumors and their non-tumor tissue counterparts. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in 20 paired tumor and non-tumor tissues which were obtained from HCC patients who underwent surgery.

overall_design: Bisulphite converted DNA from the 20 paired samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

first: Nobuhisa

last: Yamada


title: Epigenomic remodeling of the PAX8 cistrome in high grade serous ovarian cancer [RNA-Seq]

overall_design: Comparison of benign and malignant Mullerian cell lines with and without PAX8 knockdown. For each cell line, three distinct siRNAs targeting PAX8 plus a pool of all three siRNAs were examined and compared to both a non-transfected control as well as a control transfected with a non-targeting siRNA.


title: Response to herbicide treatment in wild type and gcn2 at the transcription and translation level in Arabidopsis thaliana

status: Public on Dec 01 2015

city: Knoxville

first: Albrecht

last: von Arnim

state: TN

address: M407 Walters Life Science Building

department: Biochemistry, Cellular and Molecular Biology

institute: The University of Tennessee

summary:
To understand the role of GCN2 in stress response, the total transcript and translation state were compared between Arabidopsis thaliana wild type (ecotype Landsberg erecta)  and gcn2 (Genetrap line GT8359, Cold Spring Harbor Laboratory)  seedlings with or without herbicide chlorosufuron treatment
RNA was fractionated using sucrose gradients into polysomal and nonpolysomal RNAs. We also determined overall total transcript levels.  We used Affymetrix ATH1 microarrays.

overall_design: wild type and gcn2 mutant were compared in their transcription and translation response to herbicide treatment to identify the  role of GCN2 in stress response and translational regulation. RNA was fractionated using sucrose gradients into nonpolysomal, small polysomal and large polysomal RNAs.   The sucrose gradient fractions and the total RNA were analyzed using Affymetrix ATH1 microarrays (platform  GPL198).

first: Ju

last: Guan


title: The activation of IL-1-induced enhancers depends on TAK1 kinase activity and NF-kappaB p65 II

status: Public on Dec 17 2014

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

summary: The inflammatory gene response requires activation of the protein kinase TAK1, but it is currently unknown how TAK1-derived signals coordinate transcriptional programs in the genome. We determined the genome-wide binding of the TAK1-controlled NF-κB subunit p65 in relation to active enhancers and promoters of transcribed genes by ChIP-seq experiments. Out of 35,000 active enhancer regions, 410 H3K4me1-positive enhancers show interleukin (IL)-1-induced H3K27ac and p65 binding. Inhibition of TAK1, IKK2 or depletion of p65 blocked inducible enhancer activation and gene expression. As exemplified by the CXC chemokine cluster located on chromosome 4, the TAK1-p65 pathway also regulates the recruitment kinetics of the histone acetyltransferase CBP, of NF-κB p50 and of AP-1 transcription factors to both, promoters and enhancers. This study provides a high resolution view of epigenetic changes occurring during the IL-1 response and allows the first genome-wide identification of a novel class of inducible p65 NF-κB-dependent enhancers in epithelial cells.

overall_design: Two sets of experiments were performed as biological replicate series (rep1 and rep2) each comprising 5 dual-color microarray hybridizations. The two series were performed with inverted Cy-Dye allocation (Dye-swap). Human epithelial KB cells were treated with Interleukin-1-alpha (10ng/µl) for 0.5h, 1h, 3h or 24h, or, were left untreated. An individual set of samples was treated identically with IL1a but after an initial preincubation for 1h with PD98059 (50 micromol/l). Each dual-color microarray represents a direct comparison of samples preincubated or not with PD98059.

first: Liane

last: Jurida

first: Johanna

last: Soelch

first: Helmut

last: Mueller

first: Katja

last: Handschick

first: Doris

last: Newel

first: Axel

last: Weber

first: Oliver

last: Dittrich-Breiholz

first: Heike

last: Schneider

first: Sabin

last: Bhuju

first: Vera

last: Saul

first: Lienhard

last: Schmitz

last: Kracht


title: Hedgehog pathway analysis in both CD138+ and B-cells obtained from newly diagnosed Multiple Myeloma patients

status: Public on May 31 2016

city: Bologna

first: Carolina

last: Terragna

address: Via Massarenti, 9

department: Department of Experimental, Diagnostic and Specialty Medicine - DIMES

institute: Institute of Hematology "L.A.Seràgnoli"

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

overall_design: Refer to individual Series


title: The in vivo responses elicited by Clostridium difficile in response to the gut commensal B. thetaiotaomicron and diet

status: Public on Aug 13 2015

city: Stanford

first: Justin

last: Sonnenburg

state: CA

address: Fairchild D315

department: Microbiology and Immunology

institute: Stanford University

summary: Analysis of Clostridium difficile (Cd) from the cecal contents of germ-free mice or Bacteroides thetaiotaomicron (Bt)-monocolonized mice on a standard, polysaccharide rich diet or polysaccharide deficient diet 5 days after infection. Results identify genes that are involved in the Cd response to diet, in vivo colonization and in interactions with Bt.

sample_organism:
Bacteroides thetaiotaomicron
Clostridioides difficile

platform_organism:
Bacteroides fragilis NCTC 9343
Clostridioides difficile 630

overall_design:
In vitro transcriptional profiles of Clostridium difficile obtained from cecal contents of germ-free or Bt-monocolonized mice on a standard, polysaccharide rich or polysaccharide deficient diet. 4 samples/group. 2 control genomic DNA samples for Clostridium difficile and 2 reference genomic DNA samples for Bacteroides thetaiotaomicron

Please note that 4 control samples (genomic DNA) were used to determine whether the genomic DNA correctly bound to the probes and thus, were not included in data processing (i.e no processed/normalized data).

first: Jessica

last: Ferreyra

first: Bart

middle: C

last: Weimer


title: BABY BOOM (BBM) ChIP-seq in Arabidopsis somatic embryo tissue

city: Wageningen

first: Kim

last: Boutilier

address: Droevendaalsesteeg 1

institute: Plant Research International

summary: After fertilization, a plant's life relies on progression through embryogenesis and maintenance of the stem cell niches from which all post-embryonic organs arise. BABY BOOM (BBM) and other members of the AINTEGUMENTA-LIKE (AIL)/PLETHORA (PLT) clade of the AP2-type transcription factor family play important roles controlling these processes in Arabidopsis thaliana (Arabidopsis). Development of the plt2/bbm double mutant is blocked at during early embryogenesis (Galinha et al., 2007), and combinations of bbm with plt1 and plt3 lead to short roots as a result of meristem differentiation. In contrast, overexpression of BBM in Arabidopsis seedlings induces the formation of somatic embryos on cotyledons and leaves (Boutilier, 2002), showing that BBM is a key regulator of cell identity and proliferation. Although the functions of BBM and other AIL genes have been well described, the molecular mode of action of these transcription factors has not been well examined (reviewed in Horstman et al., 2013). Our previous study provided the first insight into BBM molecular function by identifying BBM targets through a microarray-based approach (Passarinho, 2008), but only a few BBM targets have been functionally characterized. To obtain a better understanding of BBM function, we identified direct BBM targets using a chromatin immunoprecipitation (ChIP) combined with massively-parallel DNA sequencing (ChIP-seq) approach.

overall_design: Somatic embryo tissue was used for the ChIP-seq experiments with the native BBM promoter (pBBM::BBM-YFP), with a line expressing nuclear-localized GFP from the same BBM promoter (pBBM::NLS-GFP) as a negative control. Whole, embryogenic seedlings of the 35S::BBM-GFP line were used for the 35S::BBM-GFP ChIP-seq experiments, with 35S::BBM embryogenic seedlings serving as a negative control. Both experiments were performed once, making a total of 4 samples.

first: Anneke

last: Horstman

first: Jose

last: Muino


title: Evolutionary comparison reveals that diverging CCCTC-binding factor (CTCF) sites are signatures of ancestral topological associating domains borders

status: Public on May 18 2015

city: Seville

first: Carlos

last: Gómez

state: Seville

address: Crta Utrera  km 1

institute: Centro Andaluz de Biologia del Desarrollo

summary: Comparison of conserved TAD boundaries reveals that diverging CTCF sites is an evolutionary conserved signature associated with TAD borders

sample_organism:
Strongylocentrotus purpuratus
Danio rerio
Mus musculus

overall_design: 4C-seq samples for six gene family  promoters in different samples:  E9.5  and E14.5 mouse embryos ; 24hpf, 48hpf, 80%epiboly and Dome zebrafish embryos ; 48hpf S.purpuratus embryos

last: Gómez-Marín

first: Juan

middle: J

last: Tena

first: Rafael

last: Domínguez-Acemel

first: Silvia

last: Naranjo

first: Ignacio

last: Maeso

first: Elisa

last: De la Calle-Mustienes

first: Leonardo

last: Beccari

first: Erika

last: Vielmas

first: Macarena

last: López-Mayorga

first: Paola

last: Bovolenta

first: Jaime

last: Carvajal

first: José

last: Gómez-Skarmeta


title: Affymetrix SNP array data from BM-CD138+, obtained from newly diagnosed Multiple Myeloma patients

first: Carolina

last: Terragna

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

summary: The iperactivation of self-renewal mechanisms, like Hedgehog (HH) pathway, which govern the refuel of Multiple Myeloma neoplastic clone, is critical to relapse events. The bulk of current knowledge is mainly based on the CD138+ cells molecular characterization, but in the light of the recent evidences, which attributed growing relevance to immature precursor clones, we become aware that multiple myeloma disease heterogeneity have more deepen roots.   Here, we report on a high-throughput transcriptome study of gene expression profiles in newly diagnosed MM patients analyzed both in the CD138+ plasmacell fraction and in the CD19+ B cells compartment. Resulted data demonstrated that Hedgehog pathway, and in particular, a 10 HH-genes signature was heterogeneously expressed among MM patients, both in mature plasmacells and also in B cells at transcriptional level. Interestingly, this signature divide patients in two subgroups, and it seems that exists a sort of “ying-yang effect” between mature and immature cell compartments that are tightly regulate in order to express this relevant self-renewal pathway according to their maturation state.

overall_design: Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved diagnostic CD138+ cell fractions obtained from bone marrow samples.

first: Flores

last: Dico

first: Marina

last: Martello


title: The activation of IL-1-induced enhancers depends on TAK1 kinase activity and NF-kappaB p65 I

first: Marek

last: Bartkuhn

overall_design: Two sets of experiments were performed as biological replicate series (rep1 and rep2) each comprising of the following 4 conditions: Human epithelial KB cells were 1) left untreated or were 2) treated with Interleukin-1-alpha (10ng/µl) for 1 hour, 3) treated for 1.5h with the TAK1 inhibitor 5Z-7-oxozeaenol (1µM) or were 4) treated with 5Z-7-oxozeaenol for 30 minutes followed by Interleukin-1-alpha for 1 hour.

first: Liane

last: Jurida

first: Johanna

last: Soelch

first: Helmut

last: Mueller

first: Katja

last: Handschick

first: Doris

last: Newel

first: Axel

last: Weber

first: Oliver

last: Dittrich-Breiholz

first: Heike

last: Schneider

first: Sabin

last: Bhuju

first: Vera

last: Saul

first: Lienhard

last: Schmitz

first: Michael

last: Kracht


title: The activation of IL-1 induced enhancers depends on TAK1 kinase activity and NF-KB p65

status: Public on Dec 16 2014

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


title: PAR-CLIP for JARID2 before and after differentiation of mouse embryonic stem cells

status: Public on Aug 20 2014

city: Philadelphia

first: Roberto

last: Bonasio

state: PA

address: 3400 Civic Center Blvd - SCTR 9-111

department: Cell and Developmental Biology

institute: University of Pennsylvania

summary: This experiment was designed to indentify RNAs making direct contact JARID2 as mouse ESCs differentiate

overall_design: E14 WT were left untreated or differentiated with 2 µM RA for 24 hrs. In both cases, ceslls were pulsed with 4-SU, irradiated with UV, and subjected to JARID2 immunoprecipitation.

first: Syuzo

last: Kaneko

first: Danny

last: Reinberg


title: Expression data from BM-CD138+, BM B cells and PBL B cells obtained from newly diagnosed Multiple Myeloma patients

first: Carolina

last: Terragna

summary:
The iperactivation of self-renewal mechanisms, like Hedgehog (HH) pathway, which govern the refuel of Multiple Myeloma neoplastic clone, is critical to relapse events. The bulk of current knowledge is mainly based on the CD138+ cells molecular characterization, but in the light of the recent evidences, which attributed growing relevance to immature precursor clones, we become aware that multiple myeloma disease heterogeneity have more deepen roots.
Here, we report on a high-throughput transcriptome study of gene expression profiles in newly diagnosed MM patients analyzed both in the CD138+ plasmacell fraction and in the CD19+ B cells compartment. Resulted data demonstrated that Hedgehog pathway, and in particular, a 10 HH-genes signature was heterogeneously expressed among MM patients, both in mature plasmacells and also in B cells at transcriptional level. Interestingly, this signature divide patients in two subgroups, and it seems that exists a sort of “ying-yang effect” between mature and immature cell compartments that are tightly regulate in order to express this relevant self-renewal pathway according to their maturation state.

overall_design: 144 samples have been analyzed: 126 BM-CD138+, 7 BM-B cells and 11 PBL-B cells; the homogeneity of samples has been ensured by the immunomagnetic enrichment procedure: only >90% pure cells have been employed.

first: Marina

last: Martello

first: Flores

last: Dico


title: The RNA binding protein Arrest (Aret) regulates myofibril maturation in Drosophila flight muscle

status: Public on Dec 23 2014

city: Kansas City

first: Maria

last: Spletter

address: 5009 Rockhill Rd

institute: University of Missouri Kansas City

summary: In Drosophila, fibrillar flight muscles (IFMs) enable flight, while tubular muscles mediate other body movements. Here, we use RNA-sequencing and isoform-specific reporters to show that spalt major (salm) determines fibrillar muscle physiology by regulating transcription and alternative splicing of a large set of sarcomeric proteins. We identify the RNA binding protein Arrest (Aret, Bruno) as downstream of salm. Aret shuttles between cytoplasm and nuclei, and is essential for myofibril maturation and sarcomere growth of IFMs. Molecularly, Aret regulates IFM-specific transcription and splicing of various sarcomeric targets, including Stretchin and wupA (TnI), and thus maintains muscle fiber integrity. As Aret and its sarcomeric targets are evolutionarily conserved, similar principles may regulate mammalian muscle morphogenesis.

overall_design: 9 samples from Drosophila melanogaster were analyzed in duplicate: control dissected wildtype flight muscle at 30h APF, 72h APF and 0 day adult, jump muscle and whole leg from 1d adult and RNAi/mutant conditions for salm (1d flight muscle) and aret (30h, 72h and 1d flight muscle)

first: Frank

last: Schnorrer

first: Daniel

last: Gerlach

first: Alexander

last: Stark

first: Assa

last: Yeroslaviz

first: Bianca

last: Habermann


title: In vivo proximity labeling and sequencing (IPL-seq) for SNRPN70 in 293T-Rex

status: Public on Oct 24 2014

summary: This proof-of-principle experiment was designed to demonstrate the feasibility of proximity labeling for RNA–protein interactions

overall_design: IPL-seq on 293T-Rex expressing MSA-SNRPN70 (sample) or NFH-SNRPN70 (control)

first: David

last: Beck

first: Varun

last: Narendra


title: The activation of IL-1 induced enhancers depends on TAK1 kinase activity and NF-KB p65 [ChIP-Seq]

first: Marek

last: Bartkuhn

overall_design: ChIP-seq in KB cells with 5 different antibodies under different treatment conditions


title: ChIP-seq for SCML2 and SCML2 mutants in 293T-REx and K562 cells

status: Public on Jul 02 2014

summary: Polycomb repressive complex-1 (PRC1) is essential for the epigenetic regulation of gene expression. SCML2 is a mammalian homolog of Drosophila SCM, a Polycomb-group protein that associates with PRC1. Here, we show that SCML2A, an SCML2 isoform tightly associated to chromatin, contributes to PRC1 localization and also directly enforces repression of certain Polycomb target genes. SCML2A binds to PRC1 via its SPM domain and interacts with ncRNAs through a novel RNA-binding region (RBR). Targeting of SCML2A to chromatin involves the coordinated action of the MBT domains, RNA binding, and interaction with PRC1 through the SPM domain. Deletion of the RBR reduces the occupancy of SCML2A at target genes and overexpression of a mutant SCML2A lacking the RBR causes defects in PRC1 recruitment. These observations point to a role for ncRNAs in regulating SCML2 function and suggest that SCML2 participates in the epigenetic control of transcription directly and in cooperation with PRC1.

overall_design: This is the ChIP-seq part of the study

first: Emilio

last: Lecona


title: ChIP-seq and RIP-seq for SCML2 and SCML2 mutants in 293T-REx and K562 cells


title: The activation of IL-1 induced enhancers depends on TAK1 kinase activity and NF-KB p65 [RNA-Seq]

overall_design: RNA-seq of KB cells either untreated or treated with IL-1 alpha

first: Michael

last: Kracht


title: RIP-seq for SCML2 and SCML2 mutants in 293T-REx and K562 cells

first: Roberto

last: Bonasio

overall_design: This is the RIP-seq part of the study


title: Muscle in beef steers with low vs. high residual feed efficiency

status: Public on Apr 11 2014

city: College Station

first: Robert

middle: Neil

last: Vaughn

address: 0965 Agronomy

department: Soil and Crop Sciences

institute: Texas A&M University

summary: Transcriptional profiling of bovine skeletal muscle comparing metabolically efficient steers to metabolically inefficient steers to ascertain what expression differences can be found in muscle tissue that might help explain differences in this economically significant phenotype.

overall_design: Two condition experiment, efficient versus inefficient animals. 8 efficient and 8 inefficient samples were used representing 16 unique individual animals.

middle: N

first: Kelli

last: Kochan

first: Penny

middle: K

last: Riggs


title: Cyclin-dependent kinase 6 is a chromatin-bound cofactor for nuclear factor kappaB-dependent gene expression

status: Public on Dec 31 2013


title: Interactions between JARID2 and noncoding RNAs regulate PRC2 recruitment to chromatin

status: Public on Dec 25 2013