title: Effect of the Hsp70 inhibitor JG-98 on gene expression in MCF7 cells

status: Public on Jan 11 2018

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary:
Hsp70 inhibition affects many signaling pathways. We established how these effects are translated into changes in gene expression.
Hsp70 is a promising anti-cancer target, and several inhibitors of Hsp70 have been recently developed. Interest to Hsp70 inhibitors as drug prototypes is, however, somewhat hampered by potential similarity of their physiological effects to effects of already well-developed Hsp90 inhibitors. JG-98 series of inhibitors is unique in its ability to target an allosteric site in the ATPase domain of Hsp70, which disrupts its interaction with a co-chaperone Bag3 and affects a variety of signaling pathways important for cancer development and survival. Here, we used the Broad Institute Connectivity Map platform to evaluate physiological effects of JG-98, and found that these effects are dissimilar from effects of Hsp90 inhibitors, thus justifying further development of this compound series. Further, using gene expression data and ActivSignal IPAD platform, we identified pathways modulated by JG-98. Some of these pathways were affected by JG-98 in Bag3-dependent and some pathways in Bag3-independent manner, indicating multiple mechanisms of JG-98 action. Using pooled shRNA genetic screen, we established gene sets that modulate the response of cancer cells to JG-98. Based on genetic and gene expression information, we developed approaches to predict potent combinations of JG-98 with known drugs. These predictions were validated by demonstrating that proteasome, RNApol II, Akt and RTK inhibitors synergize with anti-cancer effects of JG-98. Overall, in this study we analyze unique effects of Hsp70 inhibitors of JG-98 series on cell physiology and define potential drug combinations for clinical use of these inhibitors.

overall_design: MCF7 cells were treated with 2 micromoles of JG-98 for 24 hours or left untreated and mRNA levels were assessed by microarrays.

last: Sherman


title: Transcriptomics study of three Blumeria graminis formae speciales

status: Public on Jan 10 2018

city: Zürich

first: Coraline

middle: Rosalie

last: Praz

address: Zollikerstrasse 107

department: Institute of Plant and Microbial Biology

country: Switzerland

institute: University of Zürich

type: Expression profiling by high throughput sequencing

summary: We analyzed the gene expression and especially the expression of effector candidate genes in wheat and rye powdery mildews.

sample_organism:
Secale cereale
Triticum aestivum
x Triticosecale
Blumeria graminis f. sp. secalis
Blumeria graminis f. sp. tritici
Blumeria graminis f. sp. triticale

overall_design: mRNA of wheat, rye and triticale infected with 3 wheat,  2 rye and 2 triticale powdery mildew isolates, respectively. 3 biological replicates of each infection were collected 48 hours after infection.

middle: R

first: Fabrizio

last: Menardo

first: Salim

last: Bourras

first: Beat

last: Keller


title: Mesenchymal Igf2 is a major regulator of pancreatic growth and function

status: Public on Dec 31 2017

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

summary: The genetic mechanisms that determine the size of the adult pancreas are not fully understood. Here we address the importance of the imprinted Igf2 gene for growth and function of the mouse pancreas. We used reporter lines to monitor Igf2 levels during late fetal and postnatal pancreatic development and demonstrate that Igf2 is mostly expressed within the mesenchyme. We manipulated Igf2 levels in vivo in the major pancreas cell types using Cre lines and found that loss of Igf2 from the developing mesenchyme results in pancreatic hypoplasia, associated with loss of acinar and beta-cell mass, postnatal whole-body growth restriction and maternal glucose intolerance during pregnancy. Overexpression of Igf2 directed to the mesenchyme results in pancreatic overgrowth. Importantly, deletion of Igf2 from the developing epithelium has no growth effects. Our findings demonstrate that a major role for Igf2 is the regulation of pancreas size, and reveal an unforeseen key function for mesenchymal IGF signalling in pancreatic growth.

overall_design: We generated mRNA profiles of mesenchymal and non-mesenchymal cells isolated by FACS from P2 pancreata of mice with mesenchymal specific deletion or overexpression of Igf2 and littermate controls

first: Constanze

middle: M

last: Hammerle

first: Ionel

last: Sandovici

first: Marcella

last: Ma

middle: Y

first: Giles

middle: S

last: Yeo

first: Miguel

last: Constancia


title: Next Generation Sequencing Analysis of lung and spleen tissue transcriptomes from Wild Type KrasLA2 and miR-301a-/- Kras mice

status: Public on Jan 17 2018

city: Guangzhou

first: Xiaodong

state: Guangdong

address: Rm406,Building 29, South China Normal University

country: China

institute: South China Normal University

summary:
Purpose: we used next generation sequencing to analyze gene expression profiles of lung and spleen tissues wild-type KrasLA2(WT-KrasLA2) and miR-301a knockout KrasLA2 (miR301aKO-KrasLA2) mice. The goals of this study are to compare the different gene expression profiles of lung tumorigenesis between WT-KrasLA2 and miR301aKO-KrasLA2 mice.
Methods: WT-KrasLA2 and miR301aKO-KrasLA2 mice were sacrificed at 9 weeks and lung and spleen tissue were obtained and total RNA was extracted. mRNA profiles were generated by deep sequencing spleen tissue in single, lung tissue from WT and miR-301a KO mice in single, lung tissue from WT-KrasLA2 and miR301aKO-KrasLA2 mice in duplicate using High-seq 2000 Illumina sequencing platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results: After quality filtering of raw sequencing data, we obtained 47,865,482 (95%) out of 50,579,239 tags of lung, 34,855,916 (96%) out of 36,426,771 tags of spleen from WT-KrasLA2 mice, and 44,632,009 (95%) out of 46,771,631 tags of lung, 44,306,242 (94%) out of 47,032,715 tags of spleen from miR301aKO-KrasLA2 mice. We then mapped these tags to the mouse genome. We identified 1,641 DEGs (1,166 upregulated and 475 downregulated) in lung between WT-KrasLA2 and miR301aKO-KrasLA2 mice with a fold change more than 2.0 (up-regulation) or less than 0.5 (down-regulation).
Conclusions: We identified 1166 up-regulation and 475 down-regulation differentially expressed genes (DEGs) between WT-KrasLA2 and miR301aKO-KrasLA2 mice. Immune system response and cell cycle were major pathways involved in the protection role of miR-301a deletion in lung tumorigenesis. Runx3 activation is an early event identified in miR301aKO-KrasLA2 mice compared to WT-KrasLA2 mice.

overall_design: Lung and spleen mRNA profiles of WT-KrasLA2 and miR301aKO-KrasLA2 mice were generated by deep sequencing, spleen tissue in single, lung tissue from WT and miR-301a KO mice in single, lung tissue from WT-KrasLA2 and miR301aKO-KrasLA2 mice in duplicate using High-seq 2000 Illumina sequencing platform.


title: Expression data from Huh7.5 hepatoma cells transfected with 100 nM miR-7 mimic

status: Public on Dec 20 2017

city: Ottawa

first: John

middle: Paul

last: Pezacki

state: ON

address: 150 Louis-Pasteur Pvt

department: Chemistry and Biomolecular Sciences

country: Canada

institute: University of Ottawa

summary:
Our work demonstrated that PPAR-α regulates miR-7, a microRNA which regulates SREBP1 signaling.
We used microarrays to detail the effect of miR-7 on hepatic gene expression, and, within activated genes, identified an enrichment for genes with SREBP1 binding sites in their promoters.

overall_design: Huh7.5 cells were transfected with miR-7 or control mimics (100 nM), and total RNA was isolated 72 hours post-transfection.

first: Ragunath

last: Singaravelu

middle: P


title: Characterization of PPAR-α regulated miRNAs in HCV infected hepatoma cells

summary: We aimed to characterize changes in hepatic miRNA expression associated with inhibition of PPAR-α signaling.

overall_design: Huh7.5 hepatoma cells were infected with a cell culture adapted JFH1 strain (JFH-1T; MOI = 0.1) of hepatitis C virus.  48 hours post-infection, cells were treated with 25 μM 2-chloro-5-nitro-N-(pyridyl)benzamide (or BA), a PPAR-α antagonist.  24 hours post- drug treatment, cells were lysed.


title: RNA seq of ventral rumen wall of Australian sheep

status: Public on Dec 30 2017

city: St lucia

first: Ruidong

last: Xiang

state: QLD

address: Level 5, QBP, 306 Carmody rd,

country: Australia

institute: CSIRO

summary: Experiment to understand relationships between sheep rumen wall transcriptome and microbial methane emissions

first: Jody

last: McNally

first: Jude

last: Bond

first: Margaret

last: Cameron

first: Alistair

middle: J

last: Donaldson

first: Katie

middle: L

last: Austin

first: Phil

last: Vercoe

first: V

middle: H

last: Oddy

last: Dalrymple


title: Endoplasmic reticulum stress engenders immune-resistant, latent pancreatic cancer metastases

status: Public on Jan 06 2018

city: Cold Spring Harbor

first: Arnaud

last: Pommier

state: NY

address: 1 Bungtown Road

country: USA

institute: Cold Spring Harbor laboratory

summary: Latent pancreatic cancer metastases are created when T cells select disseminated cancer cells in which immune resistance and quiescence have been imposed by endoplasmic stress

overall_design: Comparison by single-cell RNA sequencing of two subpopulation of in vitro pancreatic ductal adenocarcinoma cells

first: Naishitha

last: Anaparthy

first: Nicoletta

last: Memos

first: Z

last: Larkin Kelley

first: Alizée

last: Gouronnec

first: Yan

last: Ran

first: Jean

last: Albrengues

first: Mikala

last: Egeblad

first: Christine

middle: A

last: Iacobuzio-Donahue

first: Scott

middle: K

last: Lyons

first: Douglas

middle: T

last: Fearon


title: High-throughput deep sequence of zebrafish wild-type and ezh2 mutant embryos

status: Public on Feb 06 2018

city: Suzhou

first: Han

last: Wang

state: JIangsu

address: 199 Renai, SIP

department: Center for Circadian Clocks

institute: Soochow University

summary: To determine the molecular basis for the reduced blood cells in circulation in ezh2 mutant zebrafish, we performed high-throughput sequencing at 28 hpf. Results revealed 893 up-regulated genes and 425 down-regulated genes in the ezh2 mutant zebrafish compared with wild-type zebrafish. We found that some hematopoietic genes are down-regulated in ezh2 mutant zebrafish, which was reconfirmed with qRT-PCR.

overall_design: mRNA profiles of 28 hpf wild-type and ezh2 mutant zebrafish were generated by deep sequncing.

first: Yingbin

last: Zhong


title: Role of CXCL12-CXCR4 mediated axis during DNA damage response

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

summary: Analysis of genes in DNA damage induced senescence using BrdU as a DNA damaging agent in HeLa cells which can trigger cellular senescence and identifying effect of CXCL12-CXCR4 axis during this process.

overall_design: HeLa cell treatments: Control, 100μM BrdU, CXCL12 200ng/ml, CXCL12 200ng/ml+100μM BrdU for 48 hours

first: Deepak

last: Saini

first: Raji

last: Nair


title: Inhibition of the H3K9 methyltransferase epigenetic regulator G9A attenuates oncogenicity but provokes a survival response via activation of the hypoxia pathway

city: Singapore

first: Kian Leong

last: LEE

state: Singapore

address: #07-21, 8 College Road

department: Duke-NUS Medical School

country: Singapore

institute: National University of Singapore (NUS)

summary: Epigenetic mechanisms play important roles in the regulation of tumorigenesis, and hypoxia-induced epigenetic changes may be key drivers of the adaptation of cancer cells to the hypoxic microenvironment typical of solid tumors. Previously, we showed that loss-of-function or inhibition of the oncogenic H3K9 methyltransferase G9A attenuates tumor growth and constitutes an important strategy for cancer management. However, the mechanisms by which blockade of G9A leads to a tumor suppressive effect remain poorly understood. Here, we show that G9A is highly expressed in breast cancer compared to normal breast tissue and is associated with poor prognosis in patients, where it may function as a potent oncogenic driver in this cancer type. In agreement with this, G9A inhibition leads to increased cell death, impaired cell migration, reduced cell cycle and downregulated anchorage-independent growth. Interestingly, whole transcriptome analysis revealed that a number of previously non-responsive genes become amenable to hypoxia following G9A inhibition, including many targets that drive cancer cell survival. This was accompanied by the upregulation of the hypoxia inducible factors HIF1A and HIF2A during the use of G9A inhibition to curb cancer cell growth even under normoxic conditions. Therefore, we show that G9A is a key mediator of oncogenic processes in breast cancer cells and cancer therapeutics involving G9A inhibition can be used successfully to attenuate oncogenicity. However, cancer cells mount a survival response via activation of the HIF pathway that may necessitate the additional suppression of HIF signaling for improved efficacy in the eradication of the disease.

overall_design: 27 samples consisting of MCF7 human breast cancer cells treated with 6 μM BIX-01294 in 0.1% dimethyl sulfoxide (DMSO) or 0.1% DMSO carrier controls and untreated controls in acute (4 hours) hypoxia, chronic (24 hours) hypoxia (1% O2) or normoxia (21% O2) control conditions in triplicate cultures.

first: Jolene

middle: C

last: Ho

first: Jun

last: Ueda

first: Qing

last: Pang

first: Hiroyuki

last: Kato

first: Sudhakar

last: Jha

first: Henry

last: Yang

first: Lorenz

last: Poellinger

first: Kian

last: Lee


title: TGIF1 loss contributes to progression of KRASG12D-induced pancreatic ductal adenocarcinoma involving HAS2-CD44 activation and PD-L1 upregulation.

status: Public on Jan 22 2018

city: Chiayi

first: Weng

middle: Ching

last: Chieh

address: No.168, Sec. 1, University Rd., Minhsiung

department: Department of Biomedical Sciences

country: Taiwan

institute: National Chung Cheng University

summary: Transcriptional profiling of mouse Pancreatic cancer cells comparing Pdx1-Cre LSL-KrasG12D TGIF1L/L P53L/L cells with Pdx1-Cre LSL-KrasG12D P53L/L cells, and to determine the effects of TGIF1 deletion on  PDAC gene expression.

overall_design: Two-condition experiment, Pdx1-Cre LSL-KrasG12D TGIF1L/L P53L/L cells vs. Pdx1-Cre LSL-KrasG12D P53L/L cellss, 2 KrasG12D and P53L/L mutant replicates and 2 2 KrasG12D, TGIF1 and P53 mutant replicates.

first: Ching-Chieh

last: Weng

first: Mei-Jen

last: Hsieh

first: Chia-Chen

last: Wu

first: Yu-Chun

last: Lin

first: Wen-Chun

last: Hung

first: Li-Tzong

last: Chen

first: Kuang-Hung

last: Cheng


title: Small molecule screen identifies de novo nucleotide synthesis as a vulnerability of cells lacking SIRT3

status: Public on Jan 18 2018

first: Karina

middle: Noemi

last: Gonzalez Herrera

state: MA

address: 240 Longwood Avenue, LHRRB, Haigis Lab, Room 301

department: Cell Biology

institute: Harvard Medical School

summary: Sirtuin 3 (SIRT3) is an NAD+-dependent deacetylase downregulated in aging and age-associated diseases such as cancer and neurodegeneration, and high fat diet (HFD)-induced metabolic disorders. Thus, we performed a small molecule screen and identified an unexpected metabolic vulnerability associated with SIRT3 loss.

overall_design: RNA sequencing in SV40T immortalized SIRT3 WT (triplicates) and SIRT3 KO MEF (duplicates) lines under normal conditions.

middle: N

first: Elma

last: Zaganjor

first: Yoshinori

last: Ishikawa

first: Jessica

middle: B

last: Spinelli

first: Haejin

last: Yoon

first: Jia-Ren

first: F

last: Satterstrom

first: Alison

last: Ringel

first: Stacy

last: Mulei

first: Amanda

last: Souza

first: Joshua

last: Gorham

first: Craig

last: Benson

first: Jonathan

middle: G

last: Seidman

first: Peter

last: Sorger

first: Clary

last: Clish

first: Marcia

last: Haigis


title: The satellite cell niche regulates the balance between myoblast differentiation and self-renewal via p53

city: Liverpool

first: Philipp

last: Antczak

state: Merseyside

address: Crown Street

institute: University of Liverpool

summary: Satellite cells (SCs) are adult muscle stem cells residing in a specialised niche that regulates SC homeostasis. How niche-generated signals integrate to regulate gene expression in SC-derived myoblasts, is poorly understood. We undertook an unbiased approach to study the effect of the SC niche on SC-derived myoblast transcriptional regulation and identified the tumour suppressor p53 as a key player in the regulation of myoblast quiescence. After activation and proliferation, a subpopulation of myoblasts cultured in the presence of the niche upregulates p53 and fails to differentiate. When SC self-renewal is modelled ex vivo in a reserve cell assay, myoblasts treated with Nutlin-3, which increases p53 levels in the cell, fail to differentiate and instead become quiescent. Since both these effects of Nutlin-3 are rescued by siRNA-mediated p53 knockdown we conclude that a tight control of p53 levels in myoblasts regulate the balance between differentiation and return to quiescence.

overall_design: Myofibres were extracted from Male mice and 48h and 72h after isolation collected washed and characterized on Agilent microarrays.

first: Valentina

last: Flamini

first: Rachel

last: Ghadiali

first: Amy

last: Rothwell

first: Jeremy

middle: E

last: Turnbull

first: Addolorata

last: Pisconti


title: Gene expression analysis of multinucleated gian cells

status: Public on Dec 06 2017

city: Freiburg

last: Henneke

address: Breisacher Str. 115

department: MEDICAL CENTER – UNIVERSITY OF FREIBURG

country: Germany

institute: Center for Chronic Immunodeficiency

summary: Bone marrow-derived macrophages can form multinucleated giant cells upon FSL-1 stimulation in vitro, which can be prevented by supplementation with nutlin-3a

overall_design: Bone marrow-derived macrophages, multinucleated giant cells and cells additionally treated with nutlin-3a, to increase levels of active p53 in macrophages, were compared for transcriptionally different gene expression

first: Kourosh

last: Gharun


title: Affymetrix profiling of IMIDIA biobank samples from organ donors and partially pancreatectomized patients [organ donor cohort]

status: Public on Dec 09 2017

city: Lausanne

first: Mark

last: Ibberson

address: Genopode building

department: Vital-IT

institute: SIB Swiss Institute of Bioinformatics

summary: Pancreatic islet beta cell failure causes type 2 diabetes (T2D). The IMIDIA consortium has used a strategy entailing a stringent comparative transcriptomics analysis of islets isolated enzymatically or by laser microdissection from two large cohorts of non-diabetic (ND) and T2D organ donors (OD) or partially pancreatectomized patients (PPP). This work led to the identification of a signature of genes that were differentially expressed between T2D and ND regardless of the sample type (OD or PPP). This signature includes 19 genes, of which 9 have never been previously reported to be differentially expressed in T2D islets. The PPP cohort also includes samples from individuals with impaired glucose tolerance (IGT) or recent onset diabetes associated with a pancreatic exocrine disorder (T3cD). Notably, none of the 19 signature genes of T2D islets were significantly dysregulated in islets of subjects with IGT or T3cD, suggesting that their changed expression reflects beta cell deterioration rather than a deficit preceding it.

overall_design: 206 pancreatic islet samples in total. 103 islet samples from organ donors of which 19 were type 2 diabetic (T2D) and 84 non-diabetic (ND). 103 islet samples from partially pancreatectomized patients of which 36 were T2D, 32 ND, 15 impaired glucose tolerance (IGT) and 20 type 3 diabetic (T3cD). Comparisons comparing T2D (cases) against ND (controls) were performed separately for OD and PPP cohorts

first: Michele

last: Solimena

first: Anke

middle: M

last: Schulte

first: Lorella

last: Marselli

first: Florian

last: Ehehalt

first: Daniela

last: Richter

first: Manuela

last: Rösler

first: Hassan

last: Mziaut

first: Klaus-Peter

last: Knoch

first: Julia

last: Parnis

first: Marco

last: Bugliani

first: Afshan

last: Siddiq

first: Anne

last: Jörns

first: Frédéric

last: Burdet

first: Robin

last: Liechti

first: Mara

last: Suleiman

first: Daniel

last: Margerie

first: Farooq

last: Syed

first: Marius

last: Distler

first: Robert

last: Grützmann

first: Enrico

last: Petretto

first: Aida

last: Moreno

first: Carolin

last: Wegbrod

last: Sönmez

first: Katja

last: Pfriem

last: Friedrich

first: Joern

last: Meinel

first: Claes

last: Wollheim

first: Gustavo

last: Baretton

first: Raphael

last: Scharfmann

first: Everson

last: Nogoceke

first: Ezio

last: Bonifacio

first: Dorotheé

last: Sturm

first: Ugo

last: Boggi

first: Hans-Detlev

last: Saeger

first: Franco

last: Filipponi

first: Mathias

last: Lesche

first: Paolo

last: Meda

first: Andreas

last: Dahl

first: Leonore

last: Wigger

first: Ioannis

last: Xenarios

first: Mario

last: Falchi

first: Bernard

last: Thorens

first: Jürgen

last: Weitz

first: Krister

last: Bokvist

first: Sigurd

last: Lenzen

first: Guy


title: Transcriptome-wide gene expression of the heart of neonatal rats with polygenic cardiac hypetrophy

status: Public on Dec 01 2017

city: Melbourne

first: Francine

last: Marques

state: VIC

address: Level 3, 75 Commercial Rd

institute: Baker IDI Heart and Diabetes

summary: Identification of genes differentially expressed between the  neonatal heart of a genetic rat model of cardiac hypertrophy (the Hypertrophic Heart Rat, HHR) and the control (the Normal Heart Rat, NHR) using Affymetrix GeneChip® Rat Gene 1.0 ST Arrays.

overall_design: Neonatal (day 2) HHR and age-matched NHR were killed with an overdose of pentobarbitone (Lethobarb). The heart was immediately removed, and the ventricles were dissected from the atriums.  The tissues were first preserved in liquid nitrogen and later transferred to a –80C freezer. Microarrays (one per sample, with no pooling) were performed on 8 neonatal HHR (4 male, 4 female) and 8 neonatal NHR (4 male, 4 female).  After extraction of RNA, cRNA was prepared and arrays performed using Affymetrix GeneChip® Rat Gene 1.0 ST Arrays performed at the Ramaciotti Gene Function Analysis facility, University of New South Wales in Sydney, Australia.

middle: Z

first: Sean

last: Quarrell

first: Claire

last: Chevalier

first: Vivek

last: Jayaswal

last: Curl

first: Jean

middle: Y

last: Yang

first: Paul

last: Lewandowski

first: Lea

last: Delbridge

first: Stephen

last: Harrap

first: Fadi

last: Charchar


title: Proliferation pause as an early blockade of human cellular reprogramming toward pluripotency

city: Kyoto

first: Kazutoshi

last: Takahashi

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Center for iPS Cell Research and Application

country: Japan

institute: Kyoto University

summary: Human induced Pluripotent Stem cells (iPSCs) can be generated by enforced-expression of OCT3/4, SOX2, KLF4 and c-MYC (OSKM) via intermediate state that is labeled with a surface antigen TRA-1-60.  However the event during conversion of somatic cells to TRA-1-60 positive (+) fate by OSKM is still unclear. Here we show that TRA-1-60 (+) cells emerged from ESRG (+) cells with proliferation independent manner.   Overcoming the proliferation pausing phase is crucial for further progression of reprogramming. Inactivation of RB pathway is associated with the expansion of early TRA-1-60 (+) cells. Indeed, extended RB activation   drastically decreased the proportion of TRA-1-60 (+) cells with marked premature senescence. An RNA-binding protein LIN41 promotes the RB inactivation and facilitates reprogramming efficiency in early stage via   post-transcriptional suppression of cycline dependent kinase inhibitor p21. This LIN41/p21/RB axis was invalidated in immortalized cells which showed a resistance to oncogene-induced senescence. Thus, LIN41-  mediated RB inactivation promotes to bail out of transient quiescence as a major blockade in initial phase of reprogramming.

overall_design: Reprogrammed cells from five different somatic cell lines, N=90  Human dermal fibroblasts expressing various combination of reprogramming factors, N=48  Human induced Pluripotent Stem cells (iPSCs), N=3  Somatic cell lines N=17

first: K

last: Sutou

last: Tanabe

first: M

last: Narita


title: Expression data from liver cancer cell line Hep3B

status: Public on Jan 05 2018

city: GUANGZHOU

first: LIANG

middle: JIAN

last: KAI

state: GUANGDONG

address: NO.74 ZHONGSHAN NO.2 ROAD YUEXIU DISTRICT

department: PHARMACOLOGY

institute: SUN YAT-SEN UNIVERSITY

summary: We used microarrays to detail the global gene expression in cell line with or without M1 virus infection.

overall_design: Hep3B Cell line with or without M1 virus infection were for RNA extraction and hybridization on Affymetrix microarrays.

first: Jiankai

last: Liang


title: Separable functions of the PHD finger protein Spp1 in the Set1 and the meiotic DSB forming complexes cooperate for meiotic DSB formation

status: Public on Nov 30 2017

city: PARIS

first: Valerie

last: Borde

address: 26 rue d'Ulm

country: France

institute: Institut Curie

type: Genome binding/occupancy profiling by array

summary: Histone H3K4 methylation is a feature of meiotic recombination hotspots shared by many organisms including plants and mammals. Meiotic recombination is initiated by programmed double-strand break (DSB) formation that in budding yeast takes place in gene promoters and is promoted by histone H3K4 di/trimethylation. This histone modification is recognized by Spp1, a PHD-finger containing protein that belongs to the conserved histone H3K4 methyltransferase Set1 complex. During meiosis, Spp1 binds H3K4me3 and interacts with a DSB protein, Mer2, to promote DSB formation close to gene promoters. How Set1 complex- and Mer2- related functions of Spp1 are connected is not clear. Here, combining genome-wide localization analyses, biochemical approaches and the use of separation of function mutants, we show that Spp1 is present within two distinct complexes in meiotic cells, the Set1 and the Mer2 complexes. Disrupting the Spp1-Set1 interaction mildly decreases H3K4me3 levels and does not affect meiotic recombination initiation. Conversely, the Spp1-Mer2 interaction is required for normal meiotic recombination initiation, but dispensable for Set1 complex-mediated histone H3K4 methylation. Finally, we provide evidence that Spp1 preserves normal H3K4me3 levels independently of the Set1 complex. We propose a model where Spp1 works in three ways to promote recombination initiation: first by depositing histone H3K4 methylation (Set1 complex), next by “reading” and protecting histone H3K4 methylation, and finally by making the link with the chromosome axis (Mer2-Spp1 complex). This work deciphers the precise roles of Spp1 in meiotic recombination and opens perspectives to study its functions in other organisms where H3K4me3 is also present at recombination hotspots.

overall_design: ChIP-chip experiment in meiotic diploid SK1 yeast cells

first: Valérie


title: Diabetes Impairs Wound-Healing by let-7d-3p-dependent DNMT1 Upregulation in Hematopoietic Stem Cells

status: Public on Nov 20 2017

city: WORCESTER

first: Lyne

last: Khair

address: 368 PLANTATION STREET

department: SURGERY

institute: UMASS MEDICAL SCHOOL

summary:
To identify microRNAs which differentially expressed in hematopoietic stem cells from wt mice and db/db mice
We used microRNA microarrays to identify miroRNAs which can directly regulate dnmt1 expression in hematopoietic stem cells

overall_design: The microRNAs expression in hematopoietic stem cells from wt mice and DB/DB mice were measured

first: J

last: Yan

first: G

last: Tie

first: S

last: Wang

first: L

last: Messina


title: Transcriptional Profiling of Schistosoma mansoni f zfp-1-1(RNAi) parasites

status: Public on Nov 09 2017

city: Dallas

first: James

last: Collins

state: TX

address: 6001 Forest Park

department: Pharmacology

institute: UT Southwestern

summary: We distrupted the expression of the Schistosoma mansoni zfp-1-1 gene using RNA interference and examined the transcriptional effects by illumina sequencing

overall_design: The transcriptional effects of zfp-1-1 RNAi were examined by RNAseq

first: George

last: Wendt


title: RHOQ knock-down Expression data from colorectal cancer cell line HCT-116

status: Public on Nov 13 2017

summary: We used microarrays to detail the global gene expression in cell line with or without RHOQ knock-down.

overall_design: Cell line with NC or siRNA for RHOQ were for RNA extraction and hybridization on Affymetrix microarrays.


title: Histone variant H3.3-mediated chromatin remodeling is essential for paternal genome activation in mouse preimplantation embryos

city: Harbin

first: Xiaolei

last: Zhang

address: No.59 Mucai street

institute: Northeast Agricultural University

summary: H3.3-mediated paternal chromatin remodeling is essential for the development of preimplantation embryos and the activation of the paternal genome during embryogenesis.

overall_design: We collected embryos of WT, mH3.3KD and H3.3-addback at 50h after ICSI (8-cell or 16-cell stage). RNA-seq results confirmed excellent knockdown of both H3.3A and H3.3B mRNAs in mH3.3KD and H3.3-addback embryos.

first: Qingran

last: Kong

first: Laura

last: Banaszynski


title: Affymetrix profiling of IMIDIA biobank samples from organ donors and partially pancreatectomized patients [partially pancreatectomized patient cohort]

first: Mark

last: Ibberson

first: Michele

last: Solimena

first: Anke

last: Schulte

first: Lorella

last: Marselli

first: Florian

last: Ehehalt

first: Daniela

last: Richter

first: Manuela

last: Rösler

first: Hassan

last: Mziaut

first: Klaus-Peter

last: Knoch

first: Julia

last: Parnis

first: Marco

last: Bugliani

first: Afshan

last: Siddiq

first: Anne

last: Jörns

first: Frédéric

last: Burdet

first: Robin

last: Liechti

first: Mara

last: Suleiman

first: Daniel

last: Margerie

first: Farooq

last: Syed

first: Marius

last: Distler

first: Robert

last: Grützmann

first: Enrico

last: Petretto

first: Aida

last: Moreno

first: Carolin

last: Wegbrod

last: Sönmez

first: Katja

last: Pfriem

last: Friedrich

first: Joern

last: Meinel

first: Claes

last: Wollheim

first: Gustavo

last: Baretton

first: Raphael

last: Scharfmann

first: Everson

last: Nogoceke

first: Ezio

last: Bonifacio

first: Dorotheé

last: Sturm

first: Ugo

last: Boggi

first: Hans-Detlev

last: Saeger

first: Franco

last: Filipponi

first: Mathias

last: Lesche

first: Paolo

last: Meda

first: Andreas

last: Dahl

first: Leonore

last: Wigger

first: Ioannis

last: Xenarios

first: Mario

last: Falchi

first: Bernard

last: Thorens

first: Jürgen

last: Weitz

first: Krister

last: Bokvist

first: Sigurd

last: Lenzen

first: Guy


title: Genome-wide maps of Cbfb variants bound regions in E12.5 lineage negative fetal liver cells and adult thymocytes.

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Multi-potent hematopietic progenitors must acquire thymus-homing capacity to initiate T lymphocyte development. Despite its importance, the transcriptional program underlying this process remains elusive. Cbfβ forms transcription factor complexes with Runx proteins, and here we sho that Cbfβ2, encoded by an RNA splice variant of the Cbfb gene, is essential for differentiation of IL7R+PIRhi thymic-homing progenitors in the mouse fetal liver. Cbfβ2 binds to cell-type specific enhancers and induces expression of the principal thymus-homing receptor CCR9. Like in mouse, an alternative splicing event generates Cbfβ2-specific mRNA whose products controls CCR9 expression and thymus homing in zebrafish. Our findings indicate that functional diversification of Runx transcription factor complexes via alternative splicing emerged early in evolution to support a key step in T cell development.

overall_design: Sequencing of Cbfb ChIP-seq from E12.5 lineage negative fetal liver cells and adult thymocytes.

first: Ichiro

last: Taniuchi

first: Satoshi

last: Kojo


title: Smc3 deacetylation by Hos1 facilitates efficient dissolution of sister chromatid cohesion during anaphase

status: Public on Nov 02 2017

city: Dundee

first: Shuyu

last: Li

address: Dow Street

department: School of Life Sciences

institute: University of Dundee

summary: Sister chromatid cohesion relies on cohesins, a group of proteins that forms a ring-shaped complex embracing sister chromatids. Cohesion is established during S phase and is removed when cohesin Scc1 is cleaved by the protease separase at anaphase onset. During this process, the cohesin subunit Smc3 undergoes a cycle of acetylation: Smc3 acetylation by Eco1 in S phase stabilizes cohesin association with chromosomes, and its deacetylation by Hos1 in anaphase allows re-use of Smc3 in the next cell cycle. Here we find that Smc3 deacetylation by Hos1 has a more immediate effect in early anaphase of budding yeast. Without Hos1, sister chromatid separation and segregation are significantly delayed. Smc3 deacetylation facilitates removal of cohesins from chromosomes, without changing the Scc1 cleavage efficiency, thus promoting dissolution of cohesion. This action is probably due to disengagement of Smc1–3 heads, prompted by de-repression of their ATPase activity. We suggest Scc1 cleavage per se is insufficient for efficient dissolution of cohesion in early anaphase, but subsequent Smc3 deacetylation, which is triggered by Scc1 cleavage, is also required.

overall_design: examination of cohesin subunit SMC1 distribution in S.cerevisiae

first: Tomoyuki

last: Tanaka


title: Affymetrix profiling of IMIDIA biobank samples from organ donors and partially pancreatectomized patients

first: Mark

last: Ibberson

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

overall_design: Refer to individual Series


title: Pan-Cancer DNA Hypermethylation Leads to Transcriptional Upregulation of Homeobox Oncogene

city: HOUSTON

first: Jianzhong

last: Su

state: TEXAS

address: 1 Baylor Plaza

institute: Baylor college of Medicine

type: Methylation profiling by high throughput sequencing

summary: Cancers have long been recognized to be not only genetically but also epigenetically distinct from their tissues of origin. Although genetic alterations underlying oncogene upregulation have been well studied, to what extent epigenetic mechanisms, such as DNA methylation, can also induce oncogene expression remains unknown. Here, through pan-cancer analysis of 4,182 genome-wide profiles, including whole-genome bisulfite sequencing (WGBS) data from 30 normal tissues and 35 solid tumors, we discovered a strong correlation between gene-body hypermethylation of DNA methylation canyons (broad under-methylated regions) and overexpression of ~43% homeobox genes, many of which are also oncogenes. To gain insights into the cause-and-effect relationship, we used a newly developed dCas9-SunTag-DNMT3A system to methylate genomic sites of interest. The locus-specific hypermethylation of gene-body canyon, but not promoter, of homeobox oncogene DLX1 and POU3F3, can direct increase its gene expression. Together, our pan-cancer analysis followed by functional validation reveals DNA hypermethylation as a novel epigenetic mechanism for homeobox oncogene upregulation.

overall_design: Locus-specific DNA methylation of DLX1 and POU3F3 gene-bodies was conducted using our dCas9-SunTag-DNMT3A system. In brief, doxycycline-inducible lentiviral particles of dCas9-SunTag-p2A-BFP and scFv-sfGFP-DNMT3A were transduced in human embryonic kidney cell line (HEK293T).  The Single clones of idCas9SunTag, idCas9SunTag+iscFvDNMT3A and idCas9SunTag+iscFvDNMT3AE756A was purified. Lentiviral particles of sgDLX1+sgPOU3F3-puromycin and sgPOU3F3-puromycin were also generated and transduced in previously generated inducible dCas9-SunTag-DNMT3A cells. Transduced cells were treated with 2μg/ml puromycin for seven consecutive days and cultured in 2μg/ml doxycycline for another thirty days. SgRNA primers were listed as following: DLX1-F 5’-CACCGGGCGGACTCGGAGAAGAGCA-3’, DLX1-R 5’-AAACTGCTCTTCTC CGAGTCCGCCC-3’, POU3F3-F: 5’-CACCGCGGCGGCGGGGGCGGCGCAG-3’, POU3F3-R: 5’ -AAACCTGCGCCGCCCCCGCCGCCGC-3’. Bisulfite sequencing to identify the loci DNA methylation changes in homeobox gene DLX1 and POU3F3 promoter and gene body using Illumina HiSeq 2000

first: Yung-Hsin

last: Huang


title: Progressive kidney disease is suppressed by a small molecule inhibitor of TRPC5

status: Public on Oct 01 2017

city: Boston

first: Abbe

middle: Rose

last: Clark

state: Massachusetts

address: 4 Blackfan Circle, HIM 534

institute: Harvard, Brigham and Women's Hospital

summary:
Purpose: To characterize the transcriptional responses to TRPC5 inhibition in vivo, we compared gene expression profiles (RNASeq) in isolated glomeruli from wild type (WT) rats, AC1903-treated AT1R transgenic (Tg) rats in the advanced cohort and vehicle-treated, age-matched AT1R controls.
Methods: Glomerular mRNA profiles of WT rats, AC1903-treated AT1R transgenic (Tg) rats in the advanced cohort and vehicle-treated, age-matched AT1R controls were generated by deep sequencing using Illumina. Sequenced reads were mapped by STAR and quanitifed using RSEM. Differential expression analysis and Gene Ontology term enrichment analysis was performed.
Results: We identified 541 differentially expressed genes in AT1R Tg rats compared to WT controls. Interestingly, Gene Ontology (GO) term enrichment analysis revealed ROS-related and ion (cation) channel and transporter activity gene signatures, in line with the hypothesis that Rac1-mediated ROS generation and TRPC5 Ca2+ (cation) mediated signaling lead to disease progression.  After treatment with AC1903, 42 genes were differentially expressed in AC1903-treated versus vehicle-treated AT1R Tg rats. This smaller number of genes is consistent with the notion that AC1903 targets a specific pathway triggered by TRPC5 activity to confer its therapeutic advantage. GO term enrichment analysis revealed cell adhesion and integrin signaling gene sets, consistent with our observations in vivo that AC1903 protects podocytes from attenuations, detachment and loss.
Conclusions: In short, the in vivo gene expression profiles support a Rac1-TRPC5 disease-promoting pathway in proteinuric kidney disease that is reversed by treatment with AC1903.

overall_design: Glomerular mRNA profiles of WT and AC1903-treated AT1R Tg rats in the advanced cohort and vehicle-treated, age-matched AT1R controls were generated by deep sequencing using Illumina HiSeq 2000

middle: R

first: Anna

last: Greka


title: Circulating Exosomal miRNA as a Biomarker for Age-Related Cognitive Decline and Decreased Hippocampal Volume

status: Public on Oct 11 2017

city: Gainesville

first: Thomas

last: Foster

state: FL

address: 1149 S Newell Dr.

department: Neuroscience

institute: University of Florida

type: Non-coding RNA profiling by high throughput sequencing

summary: Neural imaging, genetics, and circulating biomarkers are being developed to differentiate normal aging from diseases that affect cognition. The blood based biomarkers, such as plasma exosome could provide a simple and relatively inexpensive means for tracking the progression of cognitive decline and effectiveness of treatments, as well as providing information on mechanism for cognitive impairment.

overall_design: The study included 97 human subjects, males (n = 58) and females (n = 39) (age range 44-102 years, average 73 years). Plasma exosomal miRNA was used to investigate the expression level associated with cognitive decline.

first: Asha

last: Rani

first: Andrew

last: O’Shea

first: Lara

last: Ianov

first: Ronald

middle: A

last: Cohen

first: Adam

middle: J

last: Woods


title: Gene expression profiling of IL7R+PIR+ and IL7R-PIR- subsets in LIN-c-Kit+ E12.5 mouse fetal liver cells

status: Public on Dec 05 2017

city: Suita

first: Katsuyuki

last: Shiroguchi

state: Osaka

address: 6-2-3 Furuedai

department: Center for Biosystems Dymanics Research

summary: In order to find out taget genes of Runx/Cbfb2 complexes in PIR+IL7R+ subset. In particular, genes that would explain why the size of thymus was small by lack of Cbfb2. Upon finding of decresed IL7R+PIR+ subset, which was reported as thymus-homing progenitor, in Cbfb2 deficient embruos embryos, we focused on these population.

overall_design: Examination of wild type and knock out in 2 cell types.

first: Mari

last: Tenno


title: Genome-wide expression patterns of microRNAs in ground state embryonic stem cells

status: Public on Sep 21 2017

city: Tehran

first: Ali

last: Sharifi-Zarchi

address: Royan Institute, Bani Hashem Sq.

country: Iran

institute: Royan Institute for Stem Cell Biology and Technology

summary: We apply deep small-RNA sequencing technology for high-throughput profiling of microRNAs in ground state embryonic stem cells (ESCs). We provide global expression signatures of microRNAs in ESCs cultured under serum, 2i, and R2i conditions. We report that microRNAs are significantly differentially expressed when ESCs are cultured under different conditions, and that ground state pluripotency features a uniqure microRNA signature which is mainly encoded by microRNA-coding sequences within the developmentally important DLK1-Dio3 locus. Finally, we indicate that microRNA upregulated in ground state pluripotent cells (i.e. 2i/R2i) contribute to the maintenace of ground state pluripotency through stimulating self-renewal and inhibiting multi-lineague differentiation.

overall_design: Comprehensive expression analysis of microRNAs in serum, 2i, and R2i mouse ESCs using small RNA sequencing.

first: Sharif

last: Moradi

last: Sharif-Zarchi

first: Sepideh

last: Mollamohammadi

first: Alexander

last: Stubenvoll

first: Stefan

last: Günther

first: Ghasem

last: Hosseini-Salekdeh

first: Sassan

last: Asgari

last: Braun

first: Hossein

last: Baharvand

first: Amirhossein

last: Ahmadi


title: Whole blood stabilization for the microfluidic isolation and molecular characterization of circulating tumor cells

status: Public on Oct 08 2017

first: David

middle: T

last: Ting

address: 149 E 13th street

department: Cancer Center

institute: Massachusetts General Hospital

summary: We report RNA sequencing data from enriched prostate circulating tumor cells (CTCs) from clinical blood specimens. The goal is to examine the stability of RNA signatures as a function of whole blood preservation. Each blood sample was split into two equal portions; one portion was processed immediately (i.e., 0 hour) for CTC isolation; the other was preserved in 4 deg C, using methods described in this publication, for 24, 48, or 72 hours prior to CTC isolation. CTCs were isolated using the CTC-iChip and processed for RNA sequencing.

overall_design: Blood specimens from a total of four patients were included in this study; for one of the patients, blood was obtained from three different dates and the sample was preserved for different durations. Each patient has a paired 0 hour sample and a preserved sample (indicated as 24, 48, or 72 hours). A total of 12 samples were processed and sequenced.

first: Keith

middle: H

last: Wong

first: Shannon

last: Tessier

last: Miyamoto

first: Kathleen

middle: L

last: Miller

first: Lauren

middle: D

last: Bookstaver

first: Thomas

last: Carey

first: Cleo

last: Stannard

first: Vishal

last: Thapar

first: Eric

last: Tai

first: Kevin

last: Vo

first: Erin

middle: S

last: Emmons

first: Haley

last: Pleskow

first: Rebecca

last: Sandlin

first: Lecia

middle: V

last: Sequist

first: Daniel

last: Haber

first: Shyamala

last: Maheswaran

last: Stott

first: Mehmet

last: Toner


title: Single-base resolution methylomes of Xenopus laevis x Xenopus tropicalis embryos

status: Public on Sep 28 2017

city: Darlinghurst

first: Ozren

last: Bogdanovic

state: NSW

address: 384 Victoria Street

department: Genomics and Epigenetics

institute: Garvan Institute of Medical Research

summary: Genome duplication has played a pivotal role in the evolution of many eukaryotic lineages, including the vertebrates. The most recent vertebrate genome duplication is that in Xenopus laevis, which resulted from the hybridization of two closely related species about 17 million years ago. Here we generated epigenetic profiles and determined gene expression in X.laevis embryos to study the consequences of this duplication at the level of the genome, the epigenome, and gene expression.

overall_design: WGBS profiling of Xenopus tropicalis x Xenopus laevis st.10.5 embryos.

first: Ryan

last: Lister


title: Gene expression of magnetic fluid hyperthermia (MFH) in ovarian cancer cells

city: Houston

first: Sangbae

last: Kim

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

summary: The expression ovarian cancer cell line HeyA8 was studied when the cells were treated with MFH at 43˚C for 30 min, the iron oxide nanoparticles concentration was 0.5 mgFe/ml.

overall_design: Two groups of samples are included: 1. HeyA8 untreated (UT) 2. HeyA8 treated with MFH (MFH). Gene expression profiles of HeyA8 MFH  treated cells were compared to HeyA8 untreated cells.

first: Karem

last: Court

first: Anil

last: Sood

first: Ju-Seog

last: Lee


title: Transcriptome analysis of HCMV infected tissues

status: Public on Sep 19 2017

city: Jerusalem

first: Yiska

last: Weisblum

address: Kiryat Hadassah

country: Israel

institute: Hadassah Hebrew University Medical Center

summary: We report the application of RNA sequencing for transcriptome analysis of HCMV infected tissues, enabling the study of tissue responses to infection

overall_design: Transcriptome analysis of infected and uninfected tissues

first: Esther

last: Oiknine-Djian

first: Zichria

last: Zakay-Rones

first: Olesya

last: Vorontsov

first: Ronit

last: Haimov-Kochman

first: Yuval

last: Nevo

first: David

last: Stockheim

first: Simcha

last: Yagel

first: Amos

last: Panet

first: Dana

middle: G

last: Wolf


title: Thiol-linked alkylation for the metabolic sequencing of RNA [Small RNA sequencing in wildtype and Xpo5 knockout mES cells]

status: Public on Sep 23 2017

city: Vienna

first: Brian

last: Reichholf

address: Doktor-Bohr-Gasse 3

country: Austria

institute: IMBA

summary: Gene expression profiling by high-throughput sequencing reveals qualitative and quantitative changes in RNA species at steady-state but obscures the intracellular dynamics of RNA transcription, processing and decay. We developed thiol(SH)-linked alkylation for the metabolic sequencing of RNA (SLAM-seq), an orthogonal chemistry-based epitranscriptomics-sequencing technology that uncovers 4-thiouridine (s4U)-incorporation in RNA species at single-nucleotide resolution. In combination with well-established metabolic RNA labeling protocols and coupled to standard, low-input, high-throughput RNA sequencing methods, SLAM-seq enables rapid access to RNA polymerase II-dependent gene expression dynamics in the context of total RNA. When applied to mouse embryonic stem cells, SLAM-seq provides global and transcript-specific insights into pluripotency-associated gene expression. We validated the method by showing that the RNA-polymerase II-dependent transcriptional output scales with Oct4/Sox2/Nanog-defined enhancer activity; and provides quantitative and mechanistic evidence for transcript-specific RNA turnover mediated by post-transcriptional gene regulatory pathways initiated by microRNAs and N6-methyladenosine. SLAM-seq facilitates the dissection of fundamental mechanisms that control gene expression in an accessible, cost-effective, and scalable manner.

overall_design: Total RNA was extracted from wiltype mouse embryonic stem (mES) cells, clonal mES cells that had been transfected with non-targeting control guide RNAs (ctr), or Exportin-5 depleted (Xpo5KO) mES cells. Total RNA from Arabidopsis thaliana unopened floral buds was added as spike-in prior to small RNA library preparation.

first: Veronika

last: Herzog

first: Tobias

last: Neumann

first: Philipp

last: Rescheneder

first: Pooja

last: Bhat

first: Thomas

last: Burkard

first: Wiebke

last: Wlotzka

first: Arndt

last: von Haeseler

first: Johannes

last: Zuber

first: Stefan

last: Ameres


title: The RNA Binding Protein EWS Is Broadly Involved in the Regulation of Pri-miRNA Processing in Mammalian Cells

status: Public on Sep 04 2017

city: La Jolla

first: Xiang-Dong

last: Fu

state: CA

address: 9500 Gilman Drive, Room 231

department: CMM

institute: UC San Diego

summary: The Ewing Sarcoma protein (EWS) is a multifaceted RNA binding protein (RBP) with established roles in transcription, pre-mRNA processing, and DNA damage response.  By generating high quality EWS-RNA interactome, we uncovered its specific and prevalent interaction with a large subset of primary microRNAs (pri-miRNA).  Depletion of EWS reduced, while overexpression enhanced, the expression of its target miRNAs.  Biochemical analysis revealed that multiple elements in target pri-miRNAs, including the sequences flanking the stem-loop region, contribute to EWS binding and sequence swap between target and non-target demonstrated that the flanking sequences provide the specificity for enhanced pri-miRNA processing by the Microprocessor Drosha/DGCR8.  Interestingly, as previously reported and we confirmed, EWS appears to repress Drosha expression, and we further demonstrated that EWS is able to enhance the recruitment of Drosha to the chromatin.  Together, these findings suggest that EWS may positively and negatively regulate miRNA biogenesis, but via distinct mechanisms, thus providing a new foundation to understand the function of EWS in development and disease.

overall_design: EWS CLIP-seq

first: Huiwu

last: Ouyang

first: Kristi

last: Fox-Walsh

first: Yu

last: Zhou


title: Biotin tagging of MeCP2 reveals contextual insights into the Rett syndrome transcriptome

status: Public on Sep 18 2017

city: Old Westbury

first: Ying-Tao

last: Zhao

address: Riland building, Room 024 Northern Boulevard, P.O. Box 8000

department: Biomedical Sciences

institute: New York Institute of Technology

summary: Mutations in MECP2 cause Rett syndrome (RTT), a X-linked neurological disorder characterized by the regressive loss of neurodevelopmental milestones and acquired intellectual disability and motor impairments. However, the cellular heterogeneity of the mammalian brain impedes our understanding of how MECP2 mutations disrupt neuronal function and contribute to RTT. In response, we developed cell type-specific biotin tagging in mice bearing RTT-associated mutations and profiled nuclear transcriptomes in WT and mutant neurons. Although individual gene expression changes are largely specific to each mutation and cell type, higher-level transcriptional features remain conserved and correlate with RTT phenotypic severity. Furthermore, subcellular RNA populations support post-transcriptional compensation as a basis for the upregulation of long genes previously reported in RTT mutant neurons. Finally, we overcame the genetic mosacism associated with female RTT mouse models and identified functionally distinct gene expression changes in neighboring WT and mutant neurons, which altogether provide key contextual insights into RTT.

overall_design: Nuclear total RNA-seq of two types of neurons of male and female RTT mice and GRO-seq of the cortex

first: Zhaolan

last: Johnson

first: Maria

last: Fasolino


title: Expression data of S. pombe wild-type and subtelomere-deleted strains

status: Public on Aug 27 2017

first: Junko

last: Kanoh

address: 3-1 Yamadaoka

department: Institute for Protein Research

institute: Osaka University

summary: Gene expression is regulated by various mechanisms. One is gene silencing, which is caused by highly condensed heterochromatin structures. S. pombe genome contains 4-6 subtelomeres adjacent to the telomeres. In order to investigate the roles of subtelomeres,  we analyzed the effect of subtelomere deletion in global gene expressions.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: S. pombe cultures(wild-type and subtelomere-deleted strains) at log phase were collected and global mRNAs were analyzed.

first: Sanki

last: Tashiro

first: Kazuto

last: Kugou

first: Kunihiro

last: Ohta


title: Expression data from individual MEF2A isoform knockdown in neonatal rat ventricular myocytes (NRVMs)

status: Public on Sep 08 2017

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary:
Regulation of homeostasis and development of cardiac muscle tissues is controlled by a core set of transcription factors. The MEF2 family plays a critical role in these processes.
We knocked down expression of MEF2 isoforms in a primary cell culture model of cardiomyocytes and assessed global expression pattern changes between MEF2 knockdowns, and with a negative control.

overall_design: NRVMs were transduced with shRNA viral vectors to knockdown expression of individual MEF2 proteins. Cells were harvested 2 days post-transduction for Affymetrix global gene expression analysis. Each array represents a single biological replicate, and treatments were done in triplicate (3 arrays per treatment, each a single biological sample).

first: Cody

last: Desjardins

first: Frank

last: Naya


title: Dysregulated gene expression in cardiac chambers of adult Mef2a knockout mice

status: Public on Oct 25 2017

summary: In this study, we have identified MEF2A-sensitive genes in atrial and ventricular chambers of the adult heart. MEF2A is a member of the myocyte enhancer factor 2 (MEF2) family of transcription factors. MEF2 proteins are expressed in skeletal and cardiac muscle tissues and are conserved across many mammalian species, but the gene programs regulated by MEF2A in adult cardiac chambers are largely unknown. We compared gene expression profiles between WT and Mef2a knockout atria and ventricles from adult mice, and the results identified distinct and overlapping sets of genes sensitive to the loss of MEF2A in the adult heart.

overall_design: Total RNA from atrial and ventricular cardiac tissue were pooled into four groups: WT atria (N=7), KO atria (N=7), WT ventricles (N=7), and KO ventricles (N=7). Global gene dysregulation was analyzed via microarray by comparing KO to WT atria, and KO to WT ventricles. Additionally, transcript enrichment in cardiac chambers was analyzed by comparing WT atria to ventricles. Mice were at 2 months of age, and both male and female mice were used.

first: Jose

last: Medrano

first: Francisco


title: mRNA-Seq profile of gene expression in tip and stalk compartments of ureteric epithelium in developing mouse kidney

status: Public on Aug 15 2017

city: Los Angeles

first: Andrew

middle: P

last: McMahon

state: California

address: 1425 San Pablo St, BCC 312

department: Stem Cell Biol & Regen Med

institute: University of Southern California

summary: Morphogenesis of cellecting duct system within developing mouse kidney is driven by growth at the tips of ureteric epithelium. To characterize the transcription program within the tip compartment, here we performed mRNA-Seq of tip cells (Wnt11RFP+;Hoxb7+ cells) and stalk cells (Wnt11RFP-;Hoxb7GFP+ cells) obtained from mouse embryonic kidney through FACS. We identified tip-specific genes from these data, and verified with in situ hybridization and followed up with mechanistic study for some of the intersting targets.

overall_design: Examination of two cell types within the ureteric bud of the developing mouse kidney

first: Benazet

last: Jean-Denis

first: Rutledge

last: Elisabeth

first: McMahon

last: Andrew


title: Genomic binding for cAMP responsive transcription factors, CRP (Rv3676) and Cmr (Rv1675c) in TB complex mycobacteria

status: Public on Oct 26 2017

city: Albany

first: Kathleen

last: McDonough

state: NY

address: 120 New Scotland Ave

institute: Wadsworth Center, NYSDOH

summary: We identified the genome-wide binding sites of CRP/FNR family transcription factors CRP and Cmr in M. bovis BCG using ChIP-seq, and cross-referenced these binding sites to orthologous regions in M. tuberculosis.  Selected binding sites for each transcription factor were further characterized for their importance to gene regulation.

sample_organism: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2

overall_design:
Chromatin immunoprecipitation was performed in M. bovis BCG Pasteur strain using antibodies to CRP or Cmr.  Genome-wide binding profiles for each transcription factor were compared with and without elevated levels of cAMP.  CRP studies were performed with native CRP expression levels, while Cmr binding was analyzed in the presence of cmr overexpression using the tuf promoter.  cAMP levels were elevated exogenously by addition of dibutyryl cAMP treatment, or endogenously by expression of the Rv1264 catalytic domain.  Bacteria were analyzed in late log phase during growth in ambient air (21% O2) or hypoxia (1.3% O2) supplemented with 5% CO2.
Please note that polyclonal antisera were generated in New Zealand white rabbits against CRP, as described in Bai et al. 2007. Infect Immun 75(11): 5509-5517, and against Cmr, as described in Ranganathan et al. 2016. Nucleic Acids Res 44(1):134-151.

first: Sridevi

last: Ranganathan


title: AKT activation directs LPA-induced invasion of ovarian cancer cells through HIF1α-ETS-1 axis

city: Kolkata

first: Sib

middle: Sankar

last: Roy

state: West Bengal

address: 4, Raja S. C. Mullick Road

department: Cell Biology and Physiology

institute: CSIR-Indian Institute of Chemical Biology

summary: We sequenced the global transcriptome of human ovarian cancer cell line treated Vs untreated to identify the pathways and genes that are regulating the metabolite-induced invasion in ovarian cancer cells.

overall_design: Ovarian cancer cells were treated with LPA and in one set treatment was not given (Con). Total RNAs were isolated from the cellls and then sequenciung of the transcriptome was performed.

first: Upasana

last: Ray


title: Role of epigenetics in adaptive evolution of an asexual snail (Lake Washington)

status: Public on Aug 18 2017

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

summary: We examined adaptive morphological divergence and epigenetic variation in genetically impoverished asexual populations of a freshwater snail, Potamopyrgus antipodarum from distinct environments.  These populations exhibit environment-specific adaptive divergence in shell shape and significant genome wide DNA methylation differences among differentially adapted lake and fast water flow river populations. The epigenetic variation correlated with adaptive phenotypic variation in rapidly adapting asexual animal populations. This provides one of the first examples of environmentally-driven differences in epigenetics that associates with adaptive phenotypic divergence.

overall_design: To examine the association between this adaptive divergence and epigenetic differences, we sampled at least 30 individuals from a “river” site characterized by constantly fast water current speeds due to input from underground springs (Ritter Island, Snake River, ID) and from a “lake” site with no water current (Lake Washington, Seattle, WA).  Shell spire height and aperture length were measured as an index of adaptive foot size and shell shape differences. On these same samples, we dissected foot tissue from individuals for the analysis of epigenetic variation.

first: Jennifer

middle: M

last: Thorson

first: Mark

last: Smithson

first: Daniel

last: Beck

first: Ingrid

last: Sadler-Riggleman

first: Eric

last: Nilsson

last: Dybdahl


title: ChIP-Seq based analysis of THAP1 binding in mouse ES cells

status: Public on Aug 11 2017

city: New York

first: Chengguo

last: Wei

address: 1428 Madison Ave1468 Madison Ave

department: Medicine

institute: Icahn School of Medicine at Mount Sinai

summary: Genome binding/occupancy by wild type THAP1 was profiled by high throughput sequencing in wild type mouse ES cells derived from C57Bl/6 blastocysts

overall_design: ChIP Seq was performed by standard methods using a commercial antibody (ProteinTech) in untreated cells in the pluripotent state

first: Michelle

middle: E

last: Ehrlich


title: Thiol-linked alkylation for the metabolic sequencing of RNA [RNA-seq and Cap-seq of wildtype mES cells]

first: Brian

last: Reichholf

overall_design:
Total RNA from wildtype mouse embryonic stem cells (mES cells) was extracted. Stranded RNA-seq libraries (NEBNext Ultra Directional RNA Library Prep Kit for Illumina®, NEB) were prepared according to the manufacturer's protocol. Cap-seq libraries were prepared as previously described (Mohn et al., Cell, 2014, PMID: 24906153). Upon library generation, RNA-seq and Cap-seq samples were subjected to high-throughput sequencing.

Please note that there is processed data file for the Cap-seq samples. The Cap-seq data was used for example screenshots from the genome browser in the associated manuscript.

first: Veronika

last: Herzog

first: Tobias

last: Neumann

first: Philipp

last: Rescheneder

first: Pooja

last: Bhat

first: Thomas

last: Burkard

first: Wiebke

last: Wlotzka

first: Arndt

last: von Haeseler

first: Johannes

last: Zuber

first: Stefan

last: Ameres


title: Transcriptomic Profiling of Posterior Polymorphous Corneal Dystrophy

status: Public on Aug 17 2017

first: Anthony

middle: J.

last: Aldave

address: 200 Stein Plaza DSERC 3-143

department: Ophthalmology

institute: Stein Eye Institute, UCLA

summary: To investigate the molecular basis of posterior polymorphous corneal dystrophy (PPCD) by examining the transcriptome in affected individuals and the effect of decreased ZEB1 expression on corneal endothelial gene expression.

overall_design: Cornea endothelial tissue from two patients with PPCD, ages 15 (P5) and 5 (P6), were obtained when the patients underwent a Descemet membrane endothelial keratoplasty (P5) or a penetrating keratoplasty (PK) (P6) . The Descemet membrane and endothelium were placed onto a piece of filter paper and submerged in TRI Reagent (Thermo Fisher, Waltham, MA) for RNA isolation. Human cornea tissue from two age-matched donors, ages 6 and 17, were obtained from commercial eye banks. Descemet’s membrane and corneal endothelium were stripped from the donor corneas using a published technique and placed into TRI Reagent for RNA isolation.     To assess the effect of decreased ZEB1 protein on gene expression in primary human corneal endothelial cells (pHCEnC), confluent pHCEnC cultures were transfected with 10nM anti-ZEB1 siRNA                                                                                (rGrGrCrCrUrArCrArArUrArArCrUrArGrCrArUrUrUrGrUTG) or scrambled siRNA (OriGene Technologies, Rockville, MD) using Lipofectamine LTX (Life Technologies) per the manufacturer’s instructions. Performed in triplicates at 24,48, 72 and 96 hours post-transfection, the transfected cells were lysed in either Tri Reagent (Sigma-Aldrich, St. Louis, MO, USA), or radioimmunoprecipitation assay (RIPA) buffer for RNA and protein isolation, respectively. RNA from 24 hr and 72 hrs post-transfection with ZEB1 siRNA (n=3) was sequenced by RNAseq. RNA from pHCEnC transfected with CNTL (scramble) siRNA at 24 hours post-tranfection (n=3) was also collected and processed for RNAseq.

first: Doug

last: Chung

first: Ricardo

middle: F

last: Frausto

first: Evenlyn

last: Hanser


title: Deep sequencing of transcript levels in pluripotent stem cells and their differentiated derivatives in all three germ layers

status: Public on Sep 22 2017

city: Athens

first: Stephen

last: Dalton

state: GA

address: 500 D.W. Brooks Dr

department: Biochemistry and Molecular Biology Department

institute: Univeristy of Georgia

summary: Human pluripotent stem cells (hESCs) are an excellent model to dissect the transcriptional changes that direct cell fate decisions and lineage specification during development. Utilizing directed differentiation protocols to derive definitive endoderm, splanchnic mesoderm, neural progenitor cells (NPCs), and pre-neural crest stem cells (NCSCs) from hESCs. Transcriptional profiling via RNA-seq on hESCs and cells differentiated to all three germ layers revealed lineage specific transcriptional networks that remodeled many cell processes, including epigenetic status, cell surface markers, cell cycle profiles, metabolic flux, and cellular signaling pathways. From this data we were able to verify that metabolic flux within NPCs and pre-NCSCs are regulated in a lineage specific manner that is distinct from endoderm and mesoderm formation.

overall_design: Profiles of mRNA transcripts levels were generated for 5 cell types by deep sequencing, in duplicate, on a Illumina Hisec 2500 platform.  Cell types analyzed were WA09 human embryonic stem cells (hESCs), as the control sample, and 4 WA09 hESC-derived cell types: definitive endoderm (DE), splanchnic mesoderm (MESO), neural progenitor cells (NPCs) and pre-neural crest cells (NCSCs).

first: Tianming

last: Wu

first: Tim

last: Cliff


title: Comparative analysis of shoot and root in response to salinity stress in camelina sativa

status: Public on Aug 10 2017

city: Saskatoon

first: Dwayne

last: Hegedus

state: SK

address: 107 Science Place

institute: Agriculture and Agri-Food Canada

summary: Soil salinity presents a notable challenge to agriculture and to increasing the use marginal lands for farming. Here we provide a detailed analysis of the physiology, chemistry and gene expression patterns in roots and shoots of Camelina sativa in response to salt stress.  Salt treatment reduced shoot, but not root length.  Root and shoot weight were affected by salt, as was photosynthetic capacity.  Salt treatment did not alter micro-element concentration in shoots, but increased macro-element (Ca and Mg) levels.  Gene expression patterns in shoots indicated that salt stress may have led to shuttling of Na+ from the cytoplasm to the tonoplast and to an increase in K+ and Ca+2 import into the cytoplasm. In roots, gene expression patterns indicated that Na+ was exported from the cytoplasm by the SOS pathway and that K+ was imported in response to salt.  Genes encoding proteins involved in chelation and storage were highly up-regulated in shoots, while metal detoxification appeared to involve various export mechanisms in roots.  In shoots, genes involved in secondary metabolism leading to lignin, anthocyanin and wax production were up-regulated, probably to improve desiccation tolerance.  Partial genome expression partitioning was observed in roots and shoots based on the expression of homeologous genes from the three C. sativa genomes.  Genome I and II were involved in the response to salinity stress to about the same degree, while about 10 % more differentially-expressed genes were associated with Genome III.  This study has provided valuable information and insight into the response of camelina to salt stress.  Examination of this data and comparison to similar studies in more halophytic species will allow development of even more salt-tolerant varieties of this emerging industrial crop.

overall_design: Camelina roots and shoots, with or without salt treatment, were analyzed.  3 replicates of each (root after salt treatment, root without salt treatment, shoot after salt treatment, shoot without salt treatment) were compared.

first: Zohreh

last: Heydarian

first: Min

last: Yu

first: Margaret

last: Gruber

first: Cathy

last: Coutu

first: Steven

last: Robinson


title: Malaria Host Pathogen Interaction Center Experiment 03: Host and parasite gene transcript abundance measures from whole blood for Macaca mulatta infected with Plasmodium coatneyi Hackeri strain from 7 time points over a 101 day study

status: Public on Sep 01 2017

city: Atlanta

first: Mary

last: Galinski

address: 954 Gatewood Road

department: Vaccine Center at Yerkes

institute: Emory University

summary: This project is part of the Malaria Host-Pathogen Interaction Center (MaHPIC) - a transdisciplinary malaria systems biology research program initially supported by an NIH/NIAID contract (# HHSN272201200031C, 2012-2017; see http://www.systemsbiology.emory.edu). The MaHPIC continues with ongoing support from the Defense Advanced Research Project Agency (DARPA) and others. The MaHPIC generates many data types (e.g., clinical, hematological, parasitological, metabolomics, functional genomics, lipidomics, proteomics, immune response, telemetry) and mathematical models, to iteratively test and develop hypotheses related to the complex host-parasite dynamics in the course of malaria in non-human primates (NHPs), and metabolomics data via collaborations with investigators conducting clinical studies in malaria endemic countries, with the overarching goal of better understanding human disease, pathogenesis, and immunity. Curation and maintenance of all data and metadata are the responsibility of the MaHPIC:  Mary Galinski mary.galinski@emory.edu (MaHPIC Program Director), Jessica Kissinger jkissinger@uga.edu (MaHPIC Co-Program Director), and Alberto Moreno alberto.moreno@emory.edu (MaHPIC Co-Program Director).

sample_organism:
Macaca mulatta
Plasmodium coatneyi

platform_organism:
Macaca mulatta
Plasmodium coatneyi

overall_design: Malaria-naive male rhesus macaques (Macaca mulatta), approximately four years of age, were inoculated intravenously with salivary gland sporozoites produced and isolated at the Centers for Disease Control and Prevention from multiple Anopheles species (An. dirus, An. gambiae, and An. stephensi) and then profiled for clinical, hematological, parasitological, immunological, functional genomic, lipidomic, proteomic, and metabolomic measurements. The experiment was designed for 101 days, and pre- and post-101 day periods to prepare subjects and administer curative treatments respectively. The anti-malarial drug artemether was subcuratively administered to all subjects at the initial peak of infection, one out of the five macaques received four additional subcurative treatments for subsequent recrudescence peaks.  The experimental infection in one subject was ineffective but the macaque was followed-up for the same period of 101 days. The different clinical phases of the infection were clinically determined for each subject.  Blood-stage curative doses of artemether were administered to all subjects at the end of the study.  Capillary blood samples were collected daily for the measurement of CBCs, reticulocytes, and parasitemias. Capillary blood samples were collected every other day to obtain plasma for metabolomic analysis. Venous blood and bone marrow samples were collected at seven time points for functional genomic, proteomic, lipidomic, and immunological analyses. The seven-time point collections were used to generate these results.  This dataset was generated from whole blood samples from 5 individuals collected 7 times over the 101-day experiment. A total of 35 samples were collected. Within the MaHPIC, this project is known as ‘Experiment 03’.  This dataset was produced by Dr. Steven E. Bosinger, Nirav Patel and Greg Tharp at the Emory University Yerkes Genomics Core. To access other publicly available results from E03 and other MaHPIC Experiments, including clinical results (specifics on drugs administered, diet, and veterinary interventions), and other omics, visit http://plasmodb.org/plasmo/mahpic.jsp .  This page will be updated as datasets are released to the public.  The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC). These results are a product of a consortium of researchers known as the Malaria Host Pathogen Interaction Center (MaHPIC).  For more information on the MaHPIC, please visit http://www.systemsbiology.emory.edu/.

last: Bosinger

first: Monica

last: Cabrera-Mora

first: Jung-Ting

last: Chien

first: Jeremy

last: DeBarry

middle: R

first: Trenton

last: Hoffman

first: Jay

middle: C

last: Humphrey

first: Jianlin

last: Jiang

first: Regina

last: Joice-Cordy

first: Chester

last: Joyner

first: Jessica

last: Kissinger

first: Stacey

last: Lapp

first: Nicolas

last: Lackman

first: Esmeralda

last: Meyer

first: Alberto

last: Moreno

first: Mustafa

last: Nural

first: Suman

middle: B

last: Pakala

first: Nirav

last: Patel

first: Hannah

last: Stealey

first: Greg

last: Tharp


title: Comprehensive miRNA expression profiling in human T-cell acute lymphoblastic leukemia by small RNA-sequencing

city: Gent

first: Annelynn

last: Wallaert

address: De Pintelaan 185

country: Belgium

institute: UGent

summary: We profiled the full miRNA expression profile of 48 T-ALL patient samples from different subtypes by means of small RNA-sequencing, identifying for the first time subtype specific miRNA signatures. In addition we also profiled T-ALL cell lines by small RNA-sequencing, recapitulating the subtype specific miRNAs. Furthermore, profiling of CD34+ and CD4+CD8+ healthy donor thymocytes identified several novel potential oncogenic miRNAs or miRNAs with a tumor suppressive role in T-ALL. With these datasets, we complement the mRNA and lncRNA T-ALL subtype specific expression signatures with miRNAs, leading to the full transcriptomic profile of T-ALL subtypes.

overall_design: Small RNA-seq of 48 patient samples, 2 CD34+ thymocyte subsets, 2 CD4+CD8+ thymocyte subsets and 7 T-ALL cell lines

first: Jean

last: Soulier

first: Tom

last: Taghon

first: Frank

last: Speleman

first: Pieter

last: Van Vlierberghe


city: Lund

first: Ingrid

last: Hedenfalk

address: Medicon Village

department: Div of Omcology & Pathology, Dept of Clinical Sciences

country: Sweden

institute: Lund University

summary:
Assessment of tumor pathological and transcriptional biomarkers in pre- and on-treatment core biopsies predictive of response and outcome after neoadjuvant chemotherapy plus Bevacizumab in patients with HER2-negative breast cancer: Results from a multi-center, single-arm, phase 2 study (the PROMIX trial)
Global gene expression profiling was performed on samples from 3 time points (baseline, after 2 cycles and  surgery) from women with breast cancer receivcing neoadjuvant chemotherapy with bevacizumab in a phase 2 trial

overall_design: Multi-center, single-arm, phase 2 study of neoadjuvant anthracycline (epirubicin) plus taxane (docetaxel) with the addition of bevacizumab (avastin) for women with large operable and locally advanced HER2-negative breast cancer.

first: Siker

last: Kimbung

first: Ida

last: Johansson

first: Judith

last: Bjöhle

first: Tobias

last: Lekberg

first: Anna

last: von Wachenfeldt

first: Edward

last: Azavedo

first: Ariel

last: Saracco

first: Jonas

last: Bergh

first: Mats

last: Hellström

first: Arne

last: Östman

first: Srinivas

last: Veerla

first: Eric

last: Paquet

first: Pär-Ola

last: Bendahl

first: Mårten

last: Fernö

first: Niklas

last: Loman

first: Thomas

last: Hatschek


title: LMO1 Synergizes with MYCN to Promotes Neuroblastoma Initiation and Metastasis

status: Public on Jul 31 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

summary: High levels of LMO1 expression synergizes with MYCN to accelerate neuroblastomagenesis, enhance disease penetrance and promote widespread metastasis in zebrafish. Transcriptomic analysis of human neuroblasotma cells with programed expression of LMO1 vs vector control or neuroblastoma cells with differential endogenous LMO1 expression revealed that gene signitures affecting tumor cell-extracellular matrix interaction are significantly associated with high levels of LMO1 expression. Our findings provide compelling evidence for a major pathogenic role of LMO1 in MYCN-driven neuroblastoma.

overall_design: Examination of transcriptiome profiles in LMO1 overexpression neuroblastoma cells

first: Shizhen

last: Zhu


title: Gene expression in murine alveolar macrophage: effect of aging and influenza infection

status: Public on Aug 01 2017

city: New Haven

first: Koji

last: Sakamoto

state: CT

address: 300 Cedar Street

department: Internal Medicine

institute: Yale University

summary: Alveolar macrophages maintain lung homeostasis and are critical for host defense to respiratory pathogens, including influenza virus. Yet how aging impacts alveolar macrophages remains unclear. Here, we found that aging reduces the proliferation and concentration of alveolar macrophages under basal conditions in mice. Transcriptomic analysis revealed that aging induces a down regulation in cell cycling pathways in alveolar macrophages. Functionally, aging impaired the capacity of alveolar macrophages to phagocytose in vivo, and also increased influenza virus-induced lung damage, morbidity and mortality. Depleting alveolar macrophages indicated that these cells were critical for accelerated mortality during influenza viral lung infection with aging. Adoptive transfer experiments demonstrated that aging impaired the ability of alveolar macrophages to reduce lung damage after influenza viral infection. Thus, our study has revealed that aging impairs alveolar macrophages to resolve damageand increases mortality after influenza viral infection.

overall_design: Six replicated lung alveolar macrophage samples isolated from single-cell suspension using FACS from either young or advanced-aged C57BL/6 mice lungs after intranasal challenge with influenza virus or control PBS.

first: Christine

last: Wong

first: Candice

last: Smith

first: Naftali

last: Kaminski

first: Jonathan

last: Koff

first: Daniel

last: Goldstein


status: Public on Jul 12 2017

city: Davis

first: John

last: Harada

address: One Shields Avenue

department: Plant Biology

institute: University of California

summary: LEAFY COTYLEDON1 (LEC1), an atypical subunit of the NF-Y CCAAT binding transcription factor, is a central regulator that controls many aspects of seed development including the maturation phase during which seeds accumulate storage macromolecules and embryos acquire the ability to withstand desiccation.    To define the gene network and developmental processes controlled by LEC1, genes regulated directly by and downstream of LEC1 were identified.   In order to identify the genes bound by LEC1 in soybean embryos, we used two antibodies specific for soybean LEC1 (GmLEC1) and performed chromatin immunoprecipitation followed by sequencing (ChIP-Seq) using chromatin isolated from soybean embryos at the cotyledon, early maturation and mid-maturation stages.

overall_design: Identification of LEC1 binding sites in soybean embryos at 3 developmental stages (cotyledon, early maturation and mid-maturation), using two distinct antibodies directed against soybean LEC1 (GmLEC1). ChIP and total chromatin controls (input) were obtained for two biological replicates for each stage/antibody combinations.  A total of 16 samples were sequenced using the Illumina HiSeq2000 platform.

first: Julie

last: Pelletier

first: Russell

last: Baden

first: Alexandro

last: Cagliari

first: Robert

last: Golberg

middle: J


title: Expression data from SKBR3 cells

city: chengdu

first: Tao

last: Liu

address: 24th,yihuan road

institute: Sichuan University

summary:
Long noncoding RNA plays a significant role in gene regulation. Long noncoding RNA TMS1AS negatively regulates the sense strand gene TMS1 in breast cancer cells SKBR3. TMS1 is invovled in cell growth and apoptosis through regulating its target genes.
We used microarrays to detail the global programme of gene expression upon TMS1AS knockdown or TMS1 knockdown and analyzed the specifity of TMS1AS regulating TMS1.

overall_design: SKBR3 cells were infected with shNC, shTMS1AS or shTMS1 for RNA extraction and hybridization on Affymetrix microarrays. We sought to identify the genes regulated by TMS1AS or/and TMS1 and analyzed the specifity of TMS1AS regulating TMS1.

first: Ling


title: Identification of LEC1 binding sites in Arabidopsis bent cotyledon stage seeds

summary: LEAFY COTYLEDON1 (LEC1), an atypical subunit of the NF-Y CCAAT binding transcription factor, is a central regulator that controls many aspects of seed development including the maturation phase during which seeds accumulate storage macromolecules and embryos acquire the ability to withstand desiccation.    To define the gene network and developmental processes controlled by LEC1, genes regulated directly by and downstream of LEC1 were identified. In this part of the study, we identified the genes bound by LEC1 in Arabidopsis bent cotyledon stage seeds.  We expressed a GFP-tagged form of LEC1 under the control of its native promoter and terminator in lec1 null mutant seeds.  Using an anti-GFP antibody (NeuroMab 75-131) , we performed chromatin immunoprecipitation followed by sequencing (ChIP-Seq) using chromatin isolated from bent cotyledon stage seeds to identify the genes bound by LEC1.

overall_design: Plants homozygous for both the lec1-1 mutation and the LEC1:LEC1-GFP:LEC1 transgene were used to isolate chromatin from bent cotyledon-stage seeds.  Anti-GFP antibodies (Neuromab 75-131) were used to immunoprecipitate LEC1-bound DNA fragments and compared to total fragmented chromatin from the same biological materials.  Two biological replicates per conditions were analyzed.

first: Meryl

last: Hashimoto

first: Jiong

last: Fei


title: Biofumigation effects of wild Brassica oleracea on beneficial soil invertebrates

status: Public on Jul 06 2017

city: Loughborough

first: Neil

last: Graham

state: Leicestershire

address: Sutton Bonington Campus

department: Plant and Crop Sciences

institute: University of Nottingham

summary: The aim of the experiment was to identify the transcriptional changes between wild Brassica oleraceae lines (Winspit) and 2 cultivated lines (purple sprouting broccoli and savoy cabbage) that show different biofumigation phenotypes. Fully expanded leaves were compared from 8 week old plants.

overall_design: Comparison of leaf samples taken from 4 different Winspit lines and 4 replicates of 2 different cultivated cultivars of Brassica oleracea

first: Diana

last: Zuluaga

first: Elaine

last: van Ommen Kloeke

first: Ruud

last: Verkerk

first: Wilfred

last: Roling

first: Jacintha

last: Ellers

first: Dick

last: Roelofs

first: Mark

last: Aarts


title: Derivation of ground-state female ESCs maintaining gamete-derived DNA methylation

status: Public on Jul 27 2017

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

institute: University of Tokyo

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

overall_design: Refer to individual Series


title: Identifying Genes Associated with the Molecular Scleractinian Coral Calcification Process (Stylophora pistillata study case)

status: Public on Jun 29 2017

city: Ramat-Gan

first: Hiba

last: Waldman Ben-Asher

address: Ramat-Gan

department: Life-Sciences

institute: Bar-Ilan University

summary: Increasing seawater’s calcium concentration has shown to increase reef building (scleractinian) coral’s calcification rates. In this way the expression of the genes that are associated with the calcification process also altered and, thus can be identified. Needless to say that the overall gene repertoire that participate in the coral calcification process and its molecular mechanisms have not yet been revealed, although sporadic genes that are related to the process have been discovered and investigated. In this study, nubbins of the Red Sea scleractinian coral, Stylophora pistillata were treated with increased calcium concentrations seawater (addition of 100 gm/L) and the genes that have been up-regulated were compared to the genes expression profile of corals with natural seawater calcium concentration. Measurements of AT were taken at mid-day (11:00) and in nighttime (23:00), to record the calcification rates of coral individuals under normal and increased calcium seawater concentrations. In order to reveal the gene involved in the calcification process, S. pistillata fragments of normal and of increased calcium concentrations were sampled for microarray RNA transcriptional profiling at two time-points (mid-day and nighttime).Results of this study have revealed that Smad genes may play a role in the coral skeletal growth apparatus. This study show that the calcification molecular mechanism is conserved Among identified genes are large group of genes that are characterized in the TGF-b/BMP signal transduction pathways which have been revealed in other organisms to participate in bone and cartilage tissue development molecular processes.

overall_design: 2-condition experiment: in two time points, mid-day (11:00) and night (23:00), coral fragments of S. pistillata were sampled after treated with seawater added with calcium concentration of 100mg/L (T11 and T23). In addition, control treatment for the two time points were sampled (C11 and C23), and free swimming larvae (plan). Data from three to five biological replicates were used (except the palnulla which have 1 replicate).

first: Eldad

last: Gutner-Hoch

middle: W

last: Ben-Asher

first: Ruth

last: Yam

first: Aldo

last: Shemesh

first: Oren

last: Levy


title: Aldosterone-Sensing Neurons in the NTS Exhibit State-Dependent Pacemaker Activity and Drive Sodium Appetite via Synergy with Angiotensin II Signaling.

status: Public on Aug 09 2017

city: Boston

first: John

middle: N

last: Campbell

address: Center for Life Science, room 7-717

institute: Beth Israel Deaconess Medical Center

summary: Single cell sequencing of Hsd11b2-expressing neurons in the NTS from mice fed standard chow or low sodium diet.

overall_design: Single-cell RNA-seq was performed on Cre-dependent tdTomato+ cells that were manually isolated from dissociated NTS of Hsd11b2-Cre mice

first: Jon

last: Resch


title: Derivation of ground-state female ESCs maintaining gamete-derived DNA methylation [gene expression]

summary: Preimplantation embryos undergo a transient wave of genome-wide demethylation with the exception of imprinted genes that are critical for fetal development. Here we show that the derivation of female mouse embryonic stem cells (ESCs) in the presence of inhibitors of MEK1/2 and Gsk3 (2i-ESCs), known as ‘2i’ or “ground-state” culture conditions, results in a widespread loss of DNA methylation including a massive erasure of genomic imprints. In this study, we analyzed global gene expression profile and global DNA methylation status in 2i-ESCs and 2i-ESCs derived differentiated cells. S-ESCs are ESCs established under serum-containing medium. 2i_S_ESCs are ESCs established in 2i-containing medium, followed by maintenance in serum-containing medium.

overall_design: Analyzing gene expression profiles in 2i-ESCs, S-ESCs, 2n-2i-MEFs, 4n-2i-MEFs, and control MEFs

first: Takuya

last: Yamamoto


title: The RNA-seq (miRNA and mRNA) analysis of three human osteosarcoma cells

status: Public on Jun 13 2017

city: Hefei

first: Liang

last: Wang

state: Anhui

address: Huanhu Road 107#

department: West Branch/Anhui Cancer Hostpital

institute: Anhui Provincial Hospital

summary: RNA-seq analysis was performed by BGI-Tech of China, and RNA-seq library preparation and sequencing were performed by BGI (Shenzhen, China).

overall_design:
Following purification, the RNA was fragmented using divalent cations at an elevated temperature, and first-strand cDNA was synthesized using random hexamer primers and Superscript TMIII (Invitrogen™, Carlsbad, CA, USA). Second-strand cDNA was synthesized using buffer, dNTPs, RNaseH, and DNA polymerase I. Short fragments were purified with a QiaQuick PCR extraction kit (Qiagen) and resolved with EB buffer for end repair and poly (A) addition. The short fragments were subsequently connected using sequencing adapters.
After agarose gel electrophoresis, suitable fragments were used as templates for PCR amplification. During the QC steps, an Agilent 2100 Bioanalyzer and an ABI StepOnePlus Real-Time PCR System were used for the quantification and qualification of the sample library. Finally, the library (200 bp insert) was sequenced using an Illumina HiSeq 2000 (Illumina Inc., San Diego, CA, USA).
The single-end library was prepared following the protocol of the Illumina TruSeq RNA Sample Preparation Kit (Illumina)


title: DNA methylation profiling of primary medulloblastoma samples

city: Toronto

first: Florence

middle: M G

last: Cavalli

state: Ontario

address: PGCRL, 686 Bay Street

department: Developmental and Stem Cell

institute: The Hospital for Sick Children

summary: Genome wide DNA metylation of 763 primary medulloblastoma samples

overall_design: Bisulphite converted DNA from 763 fresh frozen primary medulloblastoma samples were hybridized to the Illumina Infinium HumanMethylation450 BeadChips according to manufacturer’s instructions.

first: Marc

last: Remke

first: Michael

middle: D

last: Taylor


title: Gene expression profiling of a transplantable model of preneoplastic progression in mice using p53-null mammary epithelial cells

status: Public on Jun 04 2017

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: We show that macrophages are recruited to ductal hyperplasias that have a high tumor-forming potential where they are differentiated and polarized toward a tumor-promoting phenotype. These studies suggest that therapeutic targeting of tumor-promoting macrophages may not only be an effective strategy to block tumor progression and metastasis, but may also have critical implications for breast cancer prevention. To investigate mechanisms that drive tumorigenesis in early breast cancer progression, we employed a transplantable model of preneoplastic progression. Transplantation of p53-null mammary epithelial cells into the cleared mammary fad pads of syngeneic wildtype mice led to the formation of several premalignant lines that histologically and genetically recapitulated the various subtypes of human breast cancer. Two of these lines, PN1a and PN1b, were derived from contralateral outgrowths from the same mouse, and tissue from these outgrowths was serially transplanted for over 10 generations to confirm stability. At 16 weeks post-transplantation, PN1a lesions develop a poorly differentiated, lobuloalveolar morphology with multifocal regions of atypical cells in solid nests, while PN1b lesions remain low grade, ductal hyperplasia.

overall_design: hyperplasia I (PN1a) group and hyperplasia 2 (PN1b) group

first: Yiqun

last: Zhang

first: Heather

last: Machado


title: The marine natural product honaucin A attenuates inflammation by activating the Nrf2-ARE pathway

status: Public on Jun 12 2017

city: La Jolla

first: Samantha

last: Mascuch

address: 8622 Kennel Way

department: CMBB

institute: Scripps Institution of Oceanography

overall_design: mRNA profiles were generated from untreated and honaucin A-exposed RAW 264.7 macrophages in the presence of LPS  (Illumina Hiseq2000)

first: Lena

last: Gerwick


title: Comparaison of left and right cervical motoneurons transcriptome

status: Public on Jun 08 2017

city: Lyon

first: joel

last: lachuer

address: 8 avenue rockefeller

institute: university Lyon1

summary:
Left and Right phrenic nerves, which innervate the left and right diaphragm muscles, exhibit different innervation patterns. This left/right (L/R) asymmetry is established at the onset of innervation by a developmental program that requires Nodal. Phenotype analysis suggests that the cervical motoneurons, which innervate the diaphragm, have a L/R imprint that contributes to set the L/R asymmetries of innervation.
We used microarray to analyze the expression profile of left and right cervical motoneurons before diaphragm innervation

overall_design: Left and right cervical motoneurons pools were collected from E11.5 HB9::GFP mice embryos. Left and right pools were collected from the same sections to allow paired analysis. The three embryos were from the same litter to minimize expression changes due to variation of the developmental stages.

first: Julien

last: Falk

first: Muriel

last: Bozon

first: Valerie

last: Castellani

first: Catherine

last: Rey

first: Séverine

last: Croze

first: Joel

last: Lachuer


title: mRNA profiles of hematopoieitc stme cells treated with interferon gamma and/or vitronectin

status: Public on Jun 01 2017

city: Kumamoto

first: Terumasa

last: Umemoto

address: 2-2-1, Honjo, Chuo-Ku

institute: Kumamoto University

summary:
Purpose: The goals of this study are to elucidate the influence of integrin β3 signaling on STAT1-dependnet gene expression in IFNγ-treated HSCs.
Methods: Wild type (WT) HSCs were cultured with or without IFNγ and/or VN in the presence of stem cell factor (SCF) plus thrombopoietin (TPO). Subsequently, cultured HSC fraction (CD48- c-kit+ Sca-1+ Lineage-) were sorted, followed by mRNA sequence using Ion Proton (n>4).  Moreover, to extract genes whose expression were changed via STAT1 in the presence of IFNγ, mRNA profiles of STAT1-/- HSCs treated with or without IFNγ were also generated by the same way. The sequence reads that passed quality filters were analyzed by CLC genomic workbench.
Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm10) with CLC genomic workbench.  Indeed, hierarchical clustering analysis showed that IFNγ-treated STAT1-/- HSCs was categorized to the group including Wt HSCs cultured in the absence of IFNγ rather than HSCs treated with IFNγ. Furthermore, gene set enrichment analysis (GSEA) showed that STAT1-dependent upregulated gene sets were significantly enriched within genes whose expression was enhanced in HSCs treated with VN and IFNγ. In contrast, integrin β3 signaling in the absence of IFNγ appears to not influence the expression of IFNγ/STAT1-dependent genes, as evidenced by the observation that VN treatment was statistically and significantly independent of the enrichment of gene sets that were both up-regulated by STAT1
Conclusions: Our study represents that STAT1 plays a central role in IFNγ-mediated HSC responses and integrin β3 signaling in HSCs promotes STAT1-dependent gene expression in the presence of IFNγ.

overall_design: After HSCs derived from wild type (WT) and STAT1-/- mice were treated with IFNg and/or vitronectin for 5 days, mRNA profiles were generated by deep sequencing using Ion Proton system (n>4).

first: Masako

last: Fujita

first: Yoshiko

last: Shiratsuschi

first: Takayuki

last: Yoshimoto


first: Yasuhiro

last: Yamada

summary:
Inhibitors of MEK1/2 and Gsk3b, known as '2i' culture conditions, enhance the derivation of embryonic stem cells (ESCs) and promote ground-state pluripotency in rodents 1,2. Here we show that the derivation of female mouse ESCs in the presence of 2i (2i-ESCs) results in a widespread loss of DNA methylation including a massive erasure of genomic imprints. Despite this global loss of DNA methylation, the early-passage 2i-ESCs efficiently differentiate into somatic cells and this process requires genome-wide de novo DNA methylation. However, the majority of imprinting control regions (ICRs) remain unmethylated in the 2i-ESC-derived differentiated cells. Consistently, 2i-ESCs exhibit impairment of autonomous embryonic and placental development by tetraploid embryo complementation and nuclear transplantation. We identified the derivation conditions of female ESCs that display 2i-ESC-like transcriptional signatures while preserving gamete-derived DNA methylation and autonomous developmental potential. Upon prolonged culture, however, female ESCs exhibit ICR demethylation, regardless of culture conditions. Our results provide insights into derivation of female ESCs reminiscent of ICM of preimplantation embryos.

S-ESCs are ESCs established under serum-containing medium. 2i_S_ESCs are ESCs established in 2i-containing medium, followed by maintenance in serum-containing medium.

overall_design: Analyzing DNA methylation profiles and transcriptional profiles in 2i-ESCs, 2i-S-ESCs, 2i-MEFs, S-ESCs, t2i-ESCs, a2i-ESCs and MEFs for molecular analysis and 2n/4n injection and nuclear transfer for developmental assay for ESCs.

first: Takuya

last: Yamamoto