title: Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA-sequencing

status: Public on Dec 13 2017

city: Cambridge

first: Karsten

last: Bach

address: Tennis Court Road

department: Department of Pharmacology

institute: University of Cambridge

summary: The mammary gland is a unique organ as it undergoes most of its development during puberty and adulthood. Characterising the hierarchy of the various mammary epithelial cells and how they are regulated in response to gestation, lactation and involution is important for understanding how breast cancer develops. Recent studies have used numerous markers to enrich, isolate and characterise the different epithelial cell compartments within the adult mammary gland. However, in all of these studies only a handful of markers were used to define and trace cell populations. Therefore, there is a need for an unbiased and comprehensive description of mammary epithelial cells within the gland at different developmental stages. To this end we used single cell RNA sequencing (scRNAseq) to determine the gene expression profile of individual mammary epithelial cells across four adult developmental stages; nulliparous, mid gestation, lactation and post weaning (full natural involution). Our data from 25,010 individual cells identifies 8 distinct mammary epithelial cell populations and allows their hierarchical structure across development to be charted. Interestingly, the effect of gestation and lactation appeared to be more pronounced for some cell types. For example, our analysis revealed a cluster of luminal progenitor cells in post involution glands, which is distinct from progenitors found in nulliparous glands. The data also showed that few clusters could be fully characterized by a single marker gene. We argue instead that the epithelial cells – especially in the luminal compartment – should rather be conceptualized as being part of a continuous spectrum of differentiation. This view highlights the plasticity of the tissue and might help to explain some of the conflicting results from lineage tracing studies.

overall_design: We compared the gene expression profile at single-cell level of four adult developmental time-points of the murine mammary gland. Tissues were harvested at gestation day 14.5 (G), lactation day 6 (L) and day 11 post natural weaning of the pups (PI). Tissue from NP females was harvested at 8 weeks of age. Two individual mice per developmental time point were used in the study. Lymph node divested mammary glands (excluding the cervical pair) were dissected from the mice and mechanically dissociated. The finely minced tissue was transferred to a digestion mix consisting of DMEM/F12 (Gibco) + 10 mM HEPES (Gibco) + collagenase (Roche) + 200 U ml-1 hyaluronidase (Sigma) + gentamicin (Gibco) and incubated for 3 hours at 37° C. From the single-cell suspensions, epithelial cells were sorted based on EpCam. Cells that were positive for CD31, CD45 or Ter119 were excluded.

first: Pensa

last: Sara


title: siRNA knockdown of C1GALT1 in AGS cells

status: Public on Dec 04 2017

city: Taipei

first: Min-Chuan

last: Huang

address: No. 1, Sec. 1, Ren-Ai RD, Taipei, Taiwan, R.O.C.

department: Graduate Institute of Anatomy and Cell Biology

country: Taiwan

institute: National Taiwan University

summary: To determine the C1GALT1 regulated gene expression profile in AGS cells.

overall_design: AGS cells were transfected with non-targeting or C1GALT1-specific siRNAs for 48 hours and total RNA were extracted.

first: Min

middle: C


title: Sub-kb resolution Hi-C in D. melanogaster reveals conserved characteristics of TADs between insect and mammalian cells

status: Public on Nov 22 2017

city: Shanghai

first: Qi

last: Wang

state: Shanghai

address: 800 Dong Chuan Rd.

country: China

institute: Shanghai Jiaotong University

type: Expression profiling by high throughput sequencing

summary: Topologically associating domains (TADs) are widely recognized as fundamental elements of the 3D structure of the eukaryotic genome. However, while the structural importance of the insulator protein CTCF together with cohesin at TAD borders in mammalian cells is well established, the absence of such co-localization at most TAD borders in recent Hi-C studies of D. melanogaster is enigmatic, raising the possibility that these TAD border elements are not generally conserved among metazoans. Using in situ Hi-C with sub-kb resolution, we show that the genome of D. melanogaster is almost completely partitioned into more than 4,000 TADs (median size, 13 kb), nearly 7-fold more than previously identified. The overwhelming majority of these TADs are demarcated by pairs of Drosophila-specific insulator proteins, BEAF-32/CP190 or BEAF-32/Chromator, indicating that these proteins may play an analogous role in Drosophila as that of the CTCF/cohesin pair in mammals. Moreover, we find that previously identified TADs enriched for inactive chromatin are predominantly assembled from the higher-level interactions between smaller TADs. In contrast, the closely-spaced small TADs in regions previously thought to be unstructured “inter-TADs” are organized in an open configuration with far fewer TAD-TAD interactions. Such structures can also be identified in some “inter-TAD” regions of the mammalian genome, suggesting that larger assemblages of small self-interacting TADs separated by a “burst” of adjacent small, weakly interacting TADs may be a conserved, basic characteristic of the higher order folding of the metazoan genome.

overall_design: The genome-wide interactome with sub-kb resolution were generated using in-situ Hi-C method in both asychonous Drosophola cell line S2R+ and the cells that were arrest at G1/S

first: Zhifeng

last: Shao


title: RNA-binding proteins Cugbp1 and HuD regulate neocortical projection neuron identities under the translational control of Neurotrophin-3

status: Public on Sep 08 2017

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

country: USA

institute: Rutgers University

summary: Intrinsic molecular pathways in the central nervous system dictate neuronal cell fate during development. However, interplay of RNA binding proteins (RBPs) dictating mRNA translation, and their spatiotemporal extracellular regulators in neocortical neural stem cells during neurogenesis are poorly understood. Using an unbiased RNAseq screen of polysomes between early and mid-neurogenesis, we identified functionally related mRNA groups and their isoforms are regulated translationally in prenatal neocortices, including mRNAs encoding RBPs. Here, we show that isoforms of the RBP, Hu antigen D (HuD), regulate the balance of neocortical glutamatergic neurons in an isoform-specific manner during development. HuD3 promoted a Cdp+ intracortically projecting neuronal fate, while HuD4 promoted a Tle4+ subcortically projecting neuronal fate. In early neurogenic radial glia of the neocortex, HuD transcripts were bound and translationally repressed by another RBP, CUG triplet repeat RNA-binding protein 1 (Cugbp1). Cugbp1 knockdown increased the number of Cdp+ intracortically projecting neurons, while having distinct effects on Tle4+ and Ctip2+ subcortically projecting neurons. Neurotrophin-3 promoted HuD3 mRNA translation and Cdp+ fate, which was reversed by Cugbp1. Thus, our findings reveal a novel post-transcriptional molecular pathway in the developing neocortex that regulates the balance of distinct subpopulations of neocortical projection neurons.

overall_design: Mouse neocortex from E13 and E16 were prepared and loaded onto sucrose density gradients.  Fractions representing total cellular RNA, 40-60-80S, and polysome were sequenced using standard Illumina protocols.

first: Mathew

middle: L

last: Kraushar

middle: P

first: Mladen-Roko

last: Rasin


title: LPS Sensing Mounts an Adaptive MSC Response Enhancing Neutrophil Activation and Wound Healing

status: Public on May 09 2018

city: Ulm

first: Pallab

last: Maity

address: Meyerhofstrasse/James Franck Ring

department: Dermatology

country: Germany

institute: University of Ulm

summary: We here addressed the question whether the unique capacity of mesenchymal stromal/stem cells (MSCs) to re-establish tissue homeostasis depends on their potential to sense pathogen associated molecular pattern (PAMP) and, in consequence, mount an adaptive response in the interest of tissue repair. After injection of MSCs which had been primed with the bacterial wall component LPS into murine wounds, an unexpected acceleration of healing occurred, clearly exceeding that of non-primed MSCs. This correlates with a fundamental reprogramming of the transcriptome in LPS treated MSCs as deduced from RNA-seq analysis and its validation.  A network of genes mediating the adaptive response through the TLR-4 pathway responsible for neutrophil activation (GCP- 2, ENA-78, IL-1β IL-8) and MSC protection (SOX6) profoundly contributes to enhanced wound healing. In fact, silencing of either TRL-4, or IRAK3, a downstream effector of TRL-4, or SOX6 suppressed wound healing most likely due to suppression of neutrophil extracellular trap formation and suppression of the enhanced microbicidal release of reactive oxygen species (ROS), key features of neutrophil activation. This previously unreported results uncover SOX6 which protects MSCs at the wound site from enhanced oxidative stress. This unprecedented findings hold substantial promise to refine current MSC-based therapies for difficult-to-treat wounds.

overall_design: Transcriptome profiling of MSCs

first: Karin

last: Scharffetter-Kochanek


title: Inner stem tissue of V2 seedlings and husks (maize B73)

status: Public on Jul 03 2017

city: Amsterdam

first: Maike

last: Stam

address: Science Park 904

department: Swammerdam Institute for Life Sciences

country: Netherlands

institute: University of Amsterdam

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Genome-wide prediction of transcriptional enhancers in maize B73 using DNase-seq and H3K9ac ChIP-seq.  RNA-seq data was used to associate potential target genes to enhancer candidates.

overall_design:
Examination of DNase I hypersensitivity in 2 tissue types (GSE94291)
Examination of H3K9ac in 2 tissue types (GSE94251)
Examination of gene expression in 2 tissue types (GSE94252)


title: Whole transcriptome sequencing of  WT and PRDM15KO mESCs

status: Public on Jul 24 2017

city: Singapore

first: Jingxian

last: Zhang

state: Singpaore

address: 61 Biopolis Drive Proteos

department: IMCB

country: Singapore

institute: Institute of Molecular and Cell Biology (IMCB), A-Star, Singapore

summary: Examination of transcriptional changes in WT vs. Prdm15 KO mESCs

overall_design: Whole transcriptome sequencing of pluripotent  mESCs comparing PRDM15 WT and PRDM15KO.

first: Slim

last: Mzoughi

first: Heike

last: Wollmann


title: Genome-wide gene expression profile in inner stem tissue of V2 seedlings and husks (maize B73) [RNA-Seq]

summary:
Most cells in a multicellular organism carry the same genetic information; however, they can still differentiate to take up different functions in the organism.  This differentiation process involves tight regulation of gene expressions by regulatory sequences including transcriptional enhancers.  Enhancers can be located distantly from their target genes; this characteristic makes it difficult to identify enhancers only using experimental approaches.
Importantly, enhancers carry characteristic chromatin signatures such as low DNA methylation, high chromatin accessibility and histone modifications such as H3K9ac and H3K27ac.  Computational enhancer identification approaches often use machine learning methods in combination with a number of experimental genome-wide datasets to identify key enhancers features and scans the whole genome.
Limited knowledge on plant enhancers restricts us in available approaches we can use to perform genome-wide enhancer prediction in plant species.  In this work, we have integrated genome-wide low DNA methylation, chromatin accessibility and H3K9ac data from two tissues, inner stem tissue (V2-IST) from seedlings at the V2 stage and husk tissue, in the crop plant Zea mays.  This study identified approximately 1,400 candidate enhancers.
By comparing data from two different tissues, we determined tissue-specificity of the candidate enhancers.  We also have associated putative target genes using gene expression data taking an advantage of having data from two tissues.

overall_design: RNA-seq is performed at two locations, with three biological replicates per location. Each biological replicate is derived from the tissues of three different plants pooled together

first: Johan

last: Zicola

first: Blaise

last: Weber

first: Rurika

last: Oka

first: Franziska

last: Turck


title: Genome-wide single base resolution profiling of 5-hydroxymethylcytosine in human breast tissue

status: Public on Dec 01 2017

city: Hanover

first: Kevin

middle: Crowley

last: Johnson

state: NH

address: 72 College Street

department: Epidemiology

institute: Geisel School of Medicine at Dartmouth College

summary: Through parallel processing of genomic DNA with oxidative bisulfite treatments on Illumina 450K arrays we resolved both 5mC in human breast tissues.

overall_design: Non-diseased breast tissue (n=18) DNA was subjected to tandem oxidative bisulfite conversion with an input of 4ug per sample using the TrueMethyl® kit v.1.1 (Cambridge Epigenetix) protocol optimized for Illumina HumanMethylation450 arrays.


title: Dnmt3a associates with promoters and enhancers to protect epidermal stem cells from cancer [ChIP-seq]

status: Public on Jun 13 2017

city: Barcelona

first: Lorenzo

last: Rinaldi

state: Spain

address: Carrer Reixac Baldiri 10

department: Oncology

country: Spain

institute: IRB

summary: The de novo DNA methyltransferase Dnmt3a is mutated in human acute myeloid leukemia, and suppresses tumorigenesis in murine models of leukemia and lung cancer. Conversely, deregulation of the other de novo DNA methyltransferase, Dnmt3b, predominantly promotes tumorigenesis. However, the molecular mechanisms underlying the roles of Dnmt3a and Dnmt3b in cancer remain poorly understood. Using conditional knockout mice, here we show that Dnmt3a -- but not Dnmt3b -- strongly protects epidermal stem cells from carcinogen-induced tumor initiation, without affecting the progression of benign lesions to aggressive carcinomas. Only upon combined deletion of Dnmt3a and Dnmt3b, squamous cell carcinomas acquired a more aggressive fate and even became metastatic, indicating that Dnmt3b is tumor-suppressive, rather than pro-tumorigenic, in epidermal neoplasia. Mechanistically, Dnmt3a promotes the expression of epidermal differentiation genes by interacting with their enhancers, and inhibits the expression of lipid metabolism and cell proliferation genes by directly methylating their promoters. Altogether, we demonstrate that Dnmt3a, but not Dnmt3b, is critical for suppressing epidermal tumor initiation, while both enzymes prevent tumor progression.

overall_design: The study was performed to understand the genomic localization bound by Dnmt3a during epidermal tumorigenesis.

first: Alexandra

last: Avgustinova

first: Debayan

last: Datta

first: Guiomar

last: Solanas

first: Neus

last: Prats

first: Salvador

last: Aznar Benitah


title: RNA-sequencing analysis of differentiating wildtype and Ezh2 deficient immature mouse chondrocytes

status: Public on Mar 29 2017

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

summary:
Objective: To evalute the role of Ezh2 in chondrocyte differentiation.
Method: Ezh2 was inactivated in chondrocytes using the Col2a1-Cre driver in vivo. Immature mouse chondrocytes (IMC) were isolated from wildtype and Ezh2 deficient mice, and plated in micromass culture. Chondrocytes were differentiated and RNA was isolated at days 3, 7, and 14 of culture. Isolated RNA was subjected to RNA sequencing analysis.
Results: Ezh2 deficient chondrocytes exhibit enhanced expression of osteogenic genes compared to wildtype cells.

overall_design: Transcriptome analysis of wildtype and Ezh2-deficient chondrocytes at days 3, 7, and 14 of differentiation.

first: Andre

middle: J

last: van Wijnen

first: Emily

middle: T

last: Camilleri


title: Genome-wide maps of SATB1 bound regions in thymocytes and peripheral CD4+ T lymphocytes.

status: Public on May 23 2017

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

summary: T-cell receptor (TCR) signaling by MHC class-I and -II induces thymocytes to acquire cytotoxic and helper fates via induction of Runx3 or and ThPOK transcription factors, respectively. The mechanisms by The mechanisms by which TCR signaling is translated into transcriptional programs for each cell fate remain elusive. It remains elusivewhich how TCR signaling is translated into transcriptional programs for each cell fate remain elusive. We show that a genome organizer, SATB1, activates genes for lineage-specifying factors, including ThPOK, Runx3, CD4, CD8 and Treg factor Foxp3, and Treg factor Foxp3, and CD4, and /CD8, in post-selection thymocytes. Indeed, SATBatb1-deficient thymocytes are partially redirected into inappropriate T lineages after both MHC class-I and -II mediated selection, and fail to generate Treg subset. Despite its essential role in initiating regulatory regions activity in TCR signaled thymocytes. SATBatb1 is becomes dispensable for maintaining ThPOK in CD4+ T cells. Collectively, our findings demonstrate that SATBatb1 shapes the primary T-cell pool by initially directing lineage-specific transcriptional programs in the thymus.

overall_design: Sequencing of SATB1 ChIP-seq and input control from thymocytes and peripheral CD4+ T lymphocytes

first: Ichiro

last: Taniuchi

first: Satoshi

last: Kojo

middle: A

first: Yoshinori

last: Kohwi

first: Terumi

last: Kowhi-Shigematsu


title: Loss of Dnmt3a and Dnmt3b does not affect epidermal homeostasis but promotes squamous transformation through PPAR-γ

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Microarray Analyses of Otospheres Derived from the Cochlea in the Inner Ear Identify Putative Transcription Factors that Regulate the Characteristics of Otospheres

status: Public on Mar 01 2017

city: Kyoto

first: Takehiro

last: Iki

address: 53, Shogoin-Kawahara cho, Sakyo

department: Clinical Application Department

institute: Center for iPS cell research and application, Kyoto University

summary: Stem/progenitor cells of the inner ear can be isolated as so-called otospheres from differentiated cells using a sphere forming assay. Although recent studies have demonstrated the characteristics of otospheres to some extent, most of the features of these cells are unknown. We describe the findings of transcriptome analyses with a cDNA microarray of otospheres derived from the cochleae of the inner ears of neonatal mice in order to clarify the gene expression profile of otic stem/progenitor cells. There were common transcription factors between otospheres and embryonic stem cells, which were supposed to be due to the stemness of otospheres. In comparison with the cochlear sensory epithelium, the otospheres shared characteristics with the cochlea, although several transcription factors specific for otospheres were identified. These transcription factors are expected to be essential for maintaining the characteristics of otospheres, and appear to be candidate genes that promote the direct conversion of cells into otic stem/progenitor cells.

overall_design: A gene expression pattern of otospheres is compared with that of the CSE and embryonic stem cells (ESCs) to clarify the unique transcriptional characteristics of otospheres as tissue-specific stem/progenitor cells.

first: Michihiro

last: Tanaka

first: Tomoko

last: Kita

first: Yuri

last: Kawasaki

first: Shin-ichiro

last: Kitajiri

first: Akifumi

last: Mizukoshi

first: Wataru

last: Fujibuchi

first: Takayuki

last: Nakagawa

first: Tatsutoshi

last: Nakahata

first: Juichi

last: Ito

first: Koichi

last: Omori

first: Megumu

middle: K

last: Saito


title: Glycolytic Enzymes Bind mRNA and Coalesce in G-bodies Essential for Cell Proliferation Under Hypoxic Conditions

status: Public on May 31 2017

city: Baltimore

first: Mallory

middle: Ann

last: Freeberg

state: MD

address: 3400 N Charles St

department: Department of Biology

institute: Johns Hopkins University

type: Non-coding RNA profiling by high throughput sequencing

summary: This experiment aimed to identify the direct RNA targets of G-body components Pfk2, Eno1, and Fba1 in budding yeast.

overall_design: PAR-CLIP-seq was performed on RNAs crosslinked to Pfk2, Eno1, or Fba1.

first: Ting

last: Han

first: Meiyan

last: Jin

first: Daniel

last: Klionsky

first: John

last: Kim


title: Regulation of miRNA-29c and its downstream pathways in preneoplastic progression of triple negative breast cancer

status: Public on Jan 18 2017

city: Houston

first: Isabelle

last: Bedrosian

state: TX

address: 1515 Holcombe Street

department: Breast Surgical Oncology

institute: UT MD Anderson Cancer Center

summary: Little is understood about the early molecular drivers of triple-negative breast cancer (TNBC), making the identification of women at risk and development of targeted therapy for prevention significant challenges. By sequencing a TNBC cell line-based breast cancer progression model we have found that miRNA-29c is progressively lost during TNBC tumorigenesis.   In support of the tumor suppressive role of miRNA 29c, we found that low levels predict poor overall patient survival and, conversely, that ectopic expression of miRNA-29c in preneoplastic cell models inhibits growth.  miRNA-29c exerts its growth inhibitory effects through direct binding and regulation of TGFB-induced factor homeobox 2 (TGIF2), CAMP-responsive element binding protein 5 (CREB5), and V-Akt murine thymoma viral oncogene homolog 3 (AKT3).  miRNA-29c regulation of these gene targets seems to be functionally relevant, as TGIF2, CREB5, and AKT3 were able to rescue the inhibition of cell proliferation and colony formation caused by ectopic expression of miRNA-29c in preneoplastic cells.  AKT3 is an oncogene of known relevance in breast cancer, and as a proof of principle we found that inhibition of phosphoinositide 3-kinase (PI3K) activity, a protein upstream of AKT3, suppressed proliferation in TNBC preneoplastic cells.  We explored additional opportunities for prevention of TNBC by studying the regulation of miRNA-29c and identified DNA methylation to have a role in the inhibition of miRNA-29c during TNBC tumorigenesis.  Consistent with these observations, we found 5 aza-cytadine to relieve the suppression of miRNA-29c.  Together, these results demonstrate that miRNA-29c loss plays a key role in the early development of TNBC.

overall_design: To identify small RNA changes that underlie during TNBC progression.

first: Anjana

last: Bhardwaj

first: Cristian

last: Coarfa

first: Preethi

middle: H

last: Gunaratne

first: Kimal

last: Rajapakshe

first: Harpreet

last: Singh

first: Kazunoshin

last: Tachibana

first: Nivetha

last: Ganesan

first: Yinghong

last: Pan


title: Integrative clustering reveals a novel split in the luminal A subtype of breast cancer with impact on outcome

city: Oslo

first: Miriam

middle: Ragle

last: Aure

address: Ullernchauséen 70

department: Dept. of Cancer Genetics

country: Norway

institute: Oslo University Hospital Radiumhospitalet

summary:
Background: Breast cancer is a heterogeneous disease at the clinical and molecular level. In this study we integrate classifications extracted from five different molecular levels in order to identify integrated subtypes.

Methods: Tumor tissue from 425 primary breast cancer patients of the Oslo2 study was cut and blended before being divided into fractions for DNA-, RNA- and protein isolation, and metabolomics, allowing for representative and comparable molecular data. Patients were stratified into groups based on their tumor characteristics from five different molecular levels, using various clustering methods. Finally, all previously identified and newly determined subgroups were combined in a multilevel classification using a “cluster-of-clusters” approach with consensus clustering.

Results: Based on DNA copy number data, tumors were scored into three groups according to the complex arm aberration index. mRNA expression profiles divided tumors into five molecular subgroups according to PAM50 subtyping, and clustering based on microRNA expression revealed four subgroups. Reverse-phase protein array data divided tumors into five subgroups. Hierarchical clustering of tumor metabolic profiles revealed three clusters. Combining DNA copy number and mRNA expression classified tumors into seven clusters based on pathway activity levels, and using integrative clustering, tumors were classified into ten subtypes. The final consensus clustering incorporating all the aforementioned subtypes revealed six major groups. Five corresponded well with the mRNA subtypes, while a sixth group resulted from a split of the luminal A subtype where these tumors belonged to distinct microRNA clusters. Gain-of-function studies using MCF-7 cells showed that microRNAs differentially expressed between the luminal A clusters were important for cancer cell survival. These microRNAs were used to validate the split in luminal A tumors in four independent breast cancer cohorts. In two cohorts the microRNAs divided tumors into subgroups with significant different outcome, and in another a trend was observed.

Conclusions: The herein identified six integrated subtypes confirm the heterogeneity of breast cancer and show that finer subdivisions of subtypes are evident. Increasing the knowledge of the luminal A subtype heterogeneity may add pivotal information guiding therapeutic choices, evidently bringing us closer to more personalized treatment for this largest subgroup of breast cancer.

overall_design: The mRNA expression profiling of  breast cancer samples was performed using the SurePrint G3 Human GE 8x60K one-color microarrays from Agilent (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling, v.6.5, May 2010). For each sample, 100 ng of RNA was amplified and hybridized on the array. Scanning was performed with Agilent Scanner G2565A, using AgilentG3_GX_1Color as profile. Signals were extracted using FE v.10.7.3.1 and protocol GE1_107_Sep09 (Agilent Technologies). Arrays were log2-transformed, quantile normalized and hospital-adjusted by subtracting from each probe value the mean probe value among samples from the same hospital.

middle: R

first: Valeria

last: Vitelli

first: Sandra

last: Jernström

first: Marit

last: Krohn

first: Eldri

middle: U

last: Due

first: Tonje

last: Haukaas

first: Suvi-Katri

last: Leivonen

first: Hans

last: Vollan

first: Surendra

last: Kumar

first: Torben

last: Lüders

first: Einar

last: Rødland

first: Charles

last: Vaske

first: Wei

last: Zhao

first: Elen

last: Møller

first: Silje

last: Nord

first: Guro

middle: F

last: Giskeødegård

first: Tone

last: Bathen

first: Carlos

last: Caldas

first: Trine

last: Tramm

first: Jan

last: Alsner

first: Jens

last: Overgaard

first: Jürgen

last: Geisler

first: Ida

last: Bukholm

first: Bjørn

last: Naume

first: Ellen

last: Schlichting

first: Torill

last: Sauer

first: Gordon

middle: B

last: Mills

first: Rolf

last: Kåresen

first: Gunhild

middle: M

last: Mælandsmo

first: Ole

last: Lingjærde

first: Arnoldo

last: Frigessi

first: Vessela

middle: N

last: Kristensen

first: Anne-Lise

last: Børresen-Dale

first: Kristine

last: Sahlberg


title: Time series of Escherichia coli BL21(DE3) growth curve, tiling arrays

status: Public on Jan 13 2017

city: Seoul

first: Sung Ho

last: Yoon

address: 120 Neungdong-ro, Gwangjin-gu

department: Department of Bioscience and Biotechnology

country: South Korea

institute: Konkuk University

type: Expression profiling by genome tiling array

summary: Experimentally mapped transcriptome structure of Escherichia coli BL21(DE3) by hybridizing total RNA (including RNA species <200 nt) to genome-wide high-density tiling arrays (60 mer probes tiled every 10 nt).

overall_design: Five samples were taken from batch fermentations in complex LB medium (two exponential phases and one stationary phase) and minimal MR medium (one exponential phase and one stationary phase).

first: Sung


first: Miriam

last: Aure

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


title: Identification of ice plant (Mesembryanthemum crystallinum L.) microRNAs using RNA-Seq and analysis of the response to high salinity at seedling stage

status: Public on Dec 31 2016

city: Taichung

first: Hungchen

middle: Emilie

last: Yen

address: 250 Kuo Kwang Rd

department: Life Sciences

institute: National Chung Hsing University

summary:
Background:   The halophyte Mesembryanthemum crystallinum (ice plant) is a model for studying salt tolerance. The morphology, physiology, metabolism, and gene expression of ice plant have been studied for over 40 years. Although the complete genome sequence has not been revealed, large-scale analyses of gene expression profiling have drawn an outline of salt tolerance in ice plant. Despite ample information in the transcriptome, miRNA information has not been documented.
Results:   We examined responses to a sudden increase in salinity in ice plant seedlings. Using a fluorescent dye to detect Na+, we found that ice plant roots respond to an increased flux of Na+ by either secreting or storing Na+ in specialized cells. High-throughput sequencing was used to identify small RNA profiles in three-day-old seedlings treated with or without 200 mM NaCl. Totally 132 conserved miRNAs belonging to 22 families were found. The hairpin precursor of 19 conserved mcr-miRNAs and 12 novel mcr-miRNAs were identified. Target genes are involved in a broad range of biological processes: transcription factors that regulate growth and development, enzymes that catalyze miRNA biogenesis for the most conserved mcr-miRNA, and proteins that are involved in ion homeostasis and drought-stress responses for some novel mcr-miRNAs. After 6 h of salt stress, the expressions of most mcr-miRNAs were down-regulated, whereas the expressions of their corresponding target genes were up-regulated. Analyses of the functions of target genes revealed that cellular processes, including growth and development, metabolism, and ion transport activity were up-regulated in roots under salt stress.
Conclusions:   Analyses of small RNA profile of ice plant seedlings identified many conserved miRNA families and several novel miRNAs. The expression of ten conserved miRNAs and three novel miRNAs were reciprocally correlated to predicted targets hourly after salt stress. Based on the expression pattern of miRNA and target genes in combination with the observation of Na+ distribution, we suggest that ice plant roots respond effectively to increased salinity by using Na+ as an osmoticum for cell expansion and guard cell opening. Excessive Na+ could either be secreted through root epidermis or stored in specialized leaf epidermal cells. These responses are partially regulated at the miRNA-mediated post-transcriptional level.

overall_design: miRNA profile of three-day-old dark-grown ice plant seedlings (control) or 200 mM NaCl (salt) treated for 6 h.

first: Chih-Pin

last: Chiang

middle: E


title: Gene expression in liver-specific insulin receptor knockout (LIRKO) and IR/FoxO1 double knockout (LIRFKO) mice

status: Public on Jun 16 2017

city: Chicago

first: Terry

last: Unterman

state: Illinois

address: 820 South Damen Avenue

department: Medical Research Unit

institute: University of Illinois at Chicago and Jesse Brown VA

summary: Gene expression was analyzed by gene array in liver RNA collected from 11-12 week old male IR floxed, LIRKO, IR/FoxO1 floxed and LIRFKO mice either a) following an overnight 24 hr fast, b) 60 min after dextrose (2 g/kg ip) was administered to overnight fasted mice, or c) 6 hr after fasted mice were allowed to refeed on standard chow.

overall_design: LIRKO and and LIRFKO mice were created on a mixed background by crossing C57bl/6 IR floxed (R. Kahn), FVB/N FoxO1 floxed (R. DePinho) and C57Bl/6 albumin-Cre mice (Jackson Lab) and verified by genotyping tail DNA, and PCR and western blotting of liver extracts. Mice were fasted and refed or treated with glucose prior to tissue collection.

middle: G

first: InSug

last: O-Sullivan


title: miRNA expression during fracture healing in diabetic rats

status: Public on Jan 15 2017

city: Kamakura

first: Satoshi

last: Kondo

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: The association between DM and impaired fracture healing including delayed union and nonunion has been documented in clinical and experimental settings. We examine miRNA expression specific for impaired fracture healing in diabetic rat.

overall_design: 12w, male, Sprague–Dawley rats were divided into two groups. As a model for impaired fracture-repairing ability, diabetic rats were created by a single intravenous injection of 40 mg/kg streptozotocin. Control rats were injected with sodium chloride as a sham treatment. Closed transverse femoral shaft fractures were created in both groups. Briefly, a 1.25-mm diameter K-wire was inserted retrograde into the right femoral intramedullary canal and a closed transverse femoral shaft fracture was produced using a three-point bending apparatus with a drop weight. Five animals from each group were euthanized at post-fracture days 5 and 11 respectively for microarray analysis. At the each time points, the newly generated specific tissues, that is, the fracture callus, were harvested.

first: Shunsuke

last: Takahara

first: Sang

middle: Y

last: Lee

first: Takahiro

last: Niikura

first: Takashi

last: Iwakura

last: Waki

first: Ryosuke

last: Kuroda

first: Masahiro

last: Kurosaka


title: QKI's function in neural stem cells (NSCs) and pre-malignant NSCs (PM-NSCs) and transcriptome of Nestin-CreERT2 PtenLoxP/LoxP p53LoxP/LoxP QKILoxP/LoxP (QPP) mouse glioblastoma

status: Public on Nov 10 2016

first: Jian

last: Hu

state: Texas

address: 1881 East Rd

department: Department of Cancer Biology, Division of Basic Sciences

institute: The University of Texas MD Anderson Cancer Center

summary: This study is to determine the impact of QKI deletion on transcriptomes of mouse NSC and PM-NSC and to analyze the transcriptomic profiles of Nestin-CreERT2 PtenLoxP/LoxP p53LoxP/LoxP QKILoxP/LoxP (QPP) mouse glioblastoma and to determine which subtypes these tumors belong to

overall_design: NSCs of different genetic background (Nestin-CreERT2 QKI+/+, Nestin-CreERT2 QKILoxP/LoxP, Nestin-CreERT2 PtenLoxP/LoxP p53LoxP/LoxP and Nestin-CreERT2 PtenLoxP/LoxP p53LoxP/LoxP QKILoxP/LoxP) were isolated from postnatal day one SVZs and then treated with either EtOH or 4OHT for two days. Nestin-CreERT2 PtenLoxP/LoxP p53LoxP/LoxP QKILoxP/LoxP (QPP) mice were treated with tamoxifen at day8-10, and mouse brain tumors were collected. The total RNAs of NSCs, PM-NSCs and brain tumors were extracted by Rnasey kit and sent for sequencing with llumina HiSeq2000 Sequencer.

last: Shingu


title: QKI deficiency maintains stemness of glioma stem cells in suboptimal environment by downregulating endolysosomal degradation

status: Public on Nov 09 2016


title: Sequencing data of Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) of QKI-5 and QKI-6

summary: This study was designed to look for the RNAs that directly bind with QKI

overall_design: HA tagged QKI-5 and QKI-6 were overexpressed in QPP GSCs and were applied to PAR-CLIP protocol. RNAs were exacted and sent for sequencing with Illumina HiSeq2000 Sequencer.


title: Gene expression profiling of pediatric adrenocortical tumors of patients treated on the Children's Oncology Group XXX protocol.

status: Public on Dec 14 2016

city: Memphis

first: Stanley

last: Pounds

state: TN

address: 262 Danny Thomas Place

department: Biostatistics

institute: St. Jude Children's Research Hospital

summary:
We have previously observed that expression of HLA genes associate with histology of adrenocortical tumors (PMID 17234769).
Here, we used gene expression microarrays to associate the diagnostic tumor expression of these genes with outcome among 34 patients treated on the COG ARAR0332 protocol.

overall_design:
We used microarrays to explore the expression profiles of a large group of uniformly-treated pediatric adrenocortical carcinomas.
Specimens were harvested during surgery and snap frozen in liquid nitrogen to preserve tissue integrity.

first: Emilia

last: Pinto

first: Carlos

last: Rodriguez-Galindo

first: Raul

last: Ribeiro

first: Gerard

middle: P

last: Zambetti


title: Next Generation Sequencing Facilitates Quantitative Analysis of Human Primary and Pluripotent Stem Cell-Derived Epicardial Cell Transcriptomes

status: Public on Dec 05 2016

city: West Lafayette

first: Xiaoping

last: Bao

state: Indiana

address: 480 Stadium Mall Drive

department: Chemical Engineering

institute: Purdue University

summary: Next-generation sequencing (NGS) has significantly advanced the elucidation of developmental signaling mechanisms that are important for different cell lineage formation from human pluripotent stem cells (hPSCs). We report here the application of RNA-sequencing technology for transcriptome profile of human primary and hPSC-derived epicardial cell, and compare to those of other cell lineages including hPSCs, mesoderm, cardiomcyotyes. Eight epicaridal cell samples from four different hPSC lines and four different donors were performed in IIIumina HiSeq2500. The resulting sequence reads (about 20 million reads per sample) were mapped to human genome (hg19) using HISAT, and the RefSeq transcript levels (RPKMs) were quantified using the python script rpkmforgenes.py. Our RNA-seq data confirmed the stable expression of key epicardial cell markers including WT1, TBX18, TCF21, ALDH1A2 and ZO1, and the gene set enrichment analysis (GSEA) showed enrichment in extracellular matrix related pathways and keratinocyte (epithelial) differentiation. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to epicardial function. This study represents the first detailed analysis of epicardial transcriptomes generated by RNA-seq technology, providing insight into the mechanisms underlying the differentiation of hPSCs into epicardial cells.

overall_design: Epicardial transcriptome profiles of 8 different samples from 4 hPSC lines and donors were generated by RNA-seq technology using IIIumina HiSeq2500

first: Sean

last: Palecek


title: Carbon black nanoparticles induce biphasic inflammatory responses in the lungs of C56BL/6 mice following single intratracheal instillation

city: Ottawa

first: Mainul

last: Husain

address: 50 Colombine Driveway

country: Canada

institute: Health Canada

summary: Carbon black nanoparticles (CBNP) are the most widely produced nanomaterial and are thus a concern for occupational exposures. CBNPs are known to cause inflammation upon inhalation; however, detailed time course data to evaluate the changing nature of inflammatory responses have not been evaluated. In this study, we investigate the short- and longer-term effects of CBNP following a single intratracheal exposure. Female C57BL/6BomTac mice were exposed to CBNPs (printex 90) via a single intratracheal instillation of 162 µg/mouse alongside vehicle controls. Mice were examined 3 hours (hrs), and 1, 2, 3, 4, 5, 14, and 42 days (d) post-exposure. Global gene expression was assessed using DNA microarrays in parallel with analysis of pulmonary inflammation assessed as bronchoalveolar lavage (BAL) cell counts and DNA strand breaks assessed by the comet assay. Pulmonary inflammation in terms of increased neutrophil influx was obverved at all time points. Increased levels of DNA strand breaks were observed in BAL cells 3 hrs post exposure and in lung tissue 2-5 d post exposure. Approximately 2600 significant differentially expressed genes (±1.5 fold; p ≤0.05) across all of the time-points in the lungs of exposed mice were identified upon comparison to time-matched controls. Transcriptional alterations were enriched for genes involved in common respiratory infectious diseases. The perturbed biological processes and pathways were primarily related to immune-inflammatory responses and acute phase responses, consistent with the BAL inflammatory profiles. Gene and pathway analysis revealed a biphasic inflammatory response, with changes occurring as early as 3 hrs post-exposure and declining to base-levels by 3 d post-exposure, but with inflammatory pathways increasing in response again at 14 d and persisting to 42 d post-exposure. Other perturbed pathways included DNA repair and apoptosis, cell cycle regulation, and muscle contraction. Single CBNP exposure induced a biphasic inflammatory response that lasted until 42 d post-exposure. Such persistent inflammatory response raises concerns over the chronic effects of CBNP exposure since the administered dose corresponds to pulmonary deposition in mice during nine 8-hour working days at the current occupational exposure limit for carbon black.

overall_design: This experiment consists of one dose of CBNP (162 ug) and one control. There are 8 time points (3 hours, and 1, 2, 3, 4, 5, 14, and 42 days) for each treatment and control group. Each dose or time point has 5-6 biological replicates. There are total 76 samples (arrays).

first: Zdenka

middle: O

last: Kyjovska

first: Julie

last: Bourdon-Lacombe

first: Anne

middle: T

last: Saber

first: Keld

last: Jensen

first: Nicklas

last: Jacobsen

first: Andrew

last: Williams

first: Håkan

last: Wallin

first: Sabina

last: Halappanavar

first: Ulla

last: Vogel

first: Carole

middle: L

last: Yauk


title: Genome-wide binding of MYCN protein in MYCN-amplified neuroblastoma cell lines

status: Public on Aug 02 2017

city: Philadelphia

first: John

last: Maris

state: Pennsylvania

address: 3501 Civic Center Blvd, CTRB

institute: Children's Hospital of Philadelphia

summary: The MYCN locus is amplified in about half of high-risk neuroblastoma tumors. To identify genomic loci occupied by MYCN protein in the MYCN-amplified neuroblastoma cell lines NGP, Kelly and NB-1643, we performed chromatin immunoprecipitation coupled with Next-Generation Sequencing (ChIP-seq) using an anti-MYCN antibody.

overall_design: Identification of  MYCN occupancy throughout the genome of MYCN-amplified neuroblastoma cells.

first: Robyn

last: Sussman

first: Komal

middle: S

last: Rathi


title: Capture-C reveals preformed chromatin interactions between HIF-binding sites and distant promoters.

status: Public on Sep 14 2016

city: Oxfors

first: James

last: Platt

address: Roosevelt Drive

country: United Kingdom

institute: University of Oxford


title: Lifespan extension by diet restriction in DNA repair deficient progeroid Ercc1Δ/- mice [mRNA]

status: Public on Sep 09 2016

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

institute: Natl. Inst. Public Health & Environment

summary: DNA repair-deficient Ercc1Δ/- mice show premature cell death, senescence and numerous accelerated aging features limiting lifespan to 4-6 month. Simultaneously they exhibit a ‘survival response’, which suppresses growth and enhances maintenance, resembling the anti-aging response induced by dietary restriction (DR). Here we report that subjecting these progeroid, dwarf mutants to actual dietary restriction (DR) resulted in the largest lifespan increase recorded in mammals. Thirty percent DR tripled median and maximal remaining lifespan, and drastically retarded numerous aspects of accelerated aging, e.g. DR animals retained 50% more neurons and maintained full motoric function. The DR response in Ercc1Δ/- mice resembled DR in wild type animals including reduced insulin signaling. Interestingly, ad libitum Ercc1Δ/- liver expression profiles showed preferential extinction of expression of long genes, consistent with genome-wide accumulation of stochastic, transcription-blocking lesions, which affect long genes more than short ones. DR largely prevented this decline of transcriptional output, indicating that DR prolongs genome function. Our findings strengthen the link between DNA damage and aging, establish Ercc1Δ/- mice as powerful model for identifying interventions to promote healthy aging, reveal untapped potential for reducing endogenous damage, provide new venues for understanding the molecular mechanism of DR, and suggest a counterintuitive DR-like therapy for human progeroid genome instability syndromes and DR-like interventions for preventing neurodegenerative diseases.

overall_design: 20 samples (4 groups with 5 replicates each) analyzed on Affymetrix genechips

first: Martijn

last: Dollé

first: Akos

last: Gyenis

first: Wilbert

last: Vermeij


title: Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing [CLIP-seq]

status: Public on Sep 02 2016

city: Pasadena

first: Chun-Kan

last: Chen

state: CA

address: 1200 E California Blvd

institute: California Institute of Technology

summary: Xist orchestrates X chromosome inactivation, a process that entails chromosome-wide silencing and remodeling of the 3-dimensional structure of the X chromosome. Yet, it remains unclear whether these changes in nuclear structure are mediated by Xist and whether they are required for silencing. Here we show that Xist directly interacts with the Lamin B Receptor (LBR), an integral component of the nuclear lamina, and that this interaction is required for Xist-mediated silencing. We show that this interaction recruits the inactive X to the nuclear lamina and by doing so enables Xist to spread to actively transcribed genes across the X. Our results demonstrate that lamina recruitment changes the accessibility of DNA thereby enabling Xist, and its silencing proteins, to spread across the X to silence transcription.

overall_design: We identified the binding sites of SHARP, LBR, and PTBP1 on Xist lncRNA using cross-linking immunoprecipitation (CLIP) of target proteins and sequenced the RNA fragments bound to the target proteins in UV-crosslinked male mouse ES cells where the endogenous Xist promoter is replaced by a tet-inducible one (pSM33).

first: Mario

last: Blanco

first: Mitch

last: Guttman


title: Capture-C reveals preformed chromatin interactions between HIF-binding sites and distant promoters. [ChIP-Seq]

summary: Hypoxia inducible factor (HIF) directs an extensive transcriptional cascade that transduces numerous adaptive responses to hypoxia. Pan-genomic analyses, using chromatin immunoprecipitation and transcript profiling, have revealed large numbers of HIF-binding sites that are generally associated with hypoxia-inducible transcripts, even over long chromosomal distances. However, these studies do not define the specific targets of HIF-binding sites and do not reveal how induction of HIF affects chromatin conformation over distantly connected functional elements. To address these questions we deployed a recently developed chromosome conformation assay that enables simultaneous high-resolution analyses from multiple viewpoints. These assays defined specific long-range interactions between intergenic HIF-binding regions and one or more promoters of hypoxia-inducible genes, revealing the existence of multiple enhancer-promoter, promoter-enhancer and enhancer-enhancer interactions.

overall_design: We utilised ChIP-seq to study the histone marks and CTCF binding in MCF7 cells in normoxia and hypoxia

first: David

last: Mole


title: Unprecedented life- and healthspan extension and genome preservation by diet restriction in DNA repair deficient progeroid Ercc1 Δ/- mice

city: Rotterdam

address: Wytemaweg 80

department: Genetics

institute: ERASMUS MC

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

platform_organism:
Mus musculus
synthetic construct

overall_design: Refer to individual Series

first: J

first: M

first: A

first: W

last: Hoeijmakers


title: The aryl hydrocarbon receptor in keratinocytes is essential for murine skin barrier integrity

status: Public on Aug 31 2016

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

institute: University of Duesseldorf

summary: The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor involved in adaptive cell functions, and highly active in the epidermis. AhR-ligands can accelerate keratinocyte differentiation, but a precise role for AhR in the skin barrier is unknown. We here show that transepidermal water loss (TEWL), a parameter of skin barrier integrity, is high in AhR-deficient (AhR-KO) mice. Experiments with conditionally AhR-deficient mouse lines identified keratinocytes as the major responsible cell population for high TEWL. Electron microscopy showed weaker inter-cellular connectivity in the epidermis of keratinocytes in AhR-KO mice, and gene expression analysis identified many barrier-associated genes as AhR targets. Moreover, AhR-deficient mice had higher inter-individual differences in their microbiome. Interestingly, removing AhR-ligands from the diet of wild-type mice mimicked AhR-deficiency regarding the impaired barrier. Vice versa, re-addition of the plant-derived ligand indole-3-carbinol (I3C) rescued the barrier deficiency even in aged mice. Our results suggest that functional AhR expression is critical for skin barrier integrity and that AhR represents a molecular target for the development of novel therapeutic approaches for skin barrier diseases, including dietary intervention.

overall_design: Three AhR-deficient and wild-type littermates were used for each time point after mechanical stress (i.e. tape stripping). Timepoints were 0 hours (before tape-stripping), 6 hours, 24 hours after tape-stripping.

first: Katharina

last: Haas

first: René

last: Deenen

last: Köhrer

first: Jean

last: Krutmann

first: Charlotte

last: Esser


title: Changes in Bacillus anthracis CodY regulation under host-specific environmental factor deprived conditions

status: Public on Aug 12 2016

city: Ansan

first: Se Kye

last: Kim

state: GYOENGGI-DO

address: 55 Hanyangdaehak-ro

department: Molecular and Life Science

institute: Hanyang University ERICA

summary: Using RNA-seq, we report here that CodY regulation is hierarchically regulated in response to environmental starvation.

overall_design: Examination of codY null Bacillus anthracis Sterne in three environmentally deprived conditions, generated by deep sequencing on an Illumina HiSeq 2000 (101 cycles PE lane).

first: Young Gyu

last: Chai

first: Kyoung Hwa

last: Jung


title: RNA-Seq of Escherichia coli after anaerobic-aerobic transition

status: Public on Jul 01 2016

city: Stuttgart

first: Joachim

last: von Wulffen

address: Waldburgstr. 19

department: Institute for System Dynamics

institute: University of Stuttgart

summary: E. coli K12 strain W3110 was used in this study. Cells were grown anaerobically in defined medium at pH7 and 37°C in a stirred 3-liter bioreactor until the culture reached an OD (600nm) of 3. At that point the first sample was drawn and aeration was started subsequently at 1l/min. 0.5, 1, 2, 5, and 10 min after the onset of aeration additional samples were drawn.

overall_design: 3 replicates of anaerobic culture and 0.5, 1, 2, 5, and 10 min after aeration

first: Günter

last: Jäger

first: Vanessa

last: Vosseler

first: Karin

last: Schäferhoff

first: Ronny

last: Feuer


title: Gene expression profiling of pediatric adrenocortical tumors collected by the International Pediatric Adrenocortical Tumor Registry (IPACTR).

first: Stanley

last: Pounds

summary:
We have previously observed that expression of HLA genes associate with histology of adrenocortical tumors (PMID 17234769).
Here, we supplement that data with gene expression data on N additional tumors.
This submission includes the data from the original study and N additional tumors.

overall_design:
We used microarrays to explore the expression profiles of a cohort of heterogenously treated pediatric adrenocortical carcinomas with histology.
Specimens were harvested during surgery and snap frozen in liquid nitrogen to preserve tissue integrity.

first: Emilia

last: Pinto

first: Carlos

last: Rodriguez-Galindo

first: Raul

last: Ribeiro

first: Gerard

last: Zambetti


title: Integrative analysis of methylome and transcriptome in human blood identifies extensive sex and immune cell-specific differentially methylated regions [methylation]

city: Haifa

first: Ariel

last: Miller

address: Efron 1

department: Medicine

country: Israel

institute: Technion

type: Methylation profiling by genome tiling array

summary: DNA methylation has an impact on regulation of gene expression, however the relation between the two is complex. By performing an integrative analysis of the methylome and transcriptome of the four main circulating immune cell-subsets from healthy females, namely B cells, monocytes, CD4 and CD8 T cells, the relation between the two was characterized. In addition, in light of the known sex bias in the prevalence of several immune-mediated diseases, the female datasets were compared with similar public available male datasets. Immune subset-specific differentially methylated regions (DMRs) were found to be highly similar between males and females; however numerous sex-specific DMRs shared by the four leukocytes subsets were identified, most located on autosomal chromosomes. This provides a list of highly interesting candidate genes to be studied in diseases with sexual dimorphism like autoimmunity. Immune cell-specific DMRs were mainly located in the gene body and intergenic region, distant from CpG islands but overlapping with enhancer elements, thus indicating the importance of distal regulatory elements in leukocyte subsets. In contrast; sex-specific DMRs were over-represented in CpG islands, suggesting some difference in regulation between sex and immune-cell specificity. Both positive and negative correlations between cell-specific expression and methylation were observed, with negative correlation being more frequent. Our acquired immune cell- and sex- specific methylome and transcriptome profiles provide novel insight on their complex regulatory interactions, and may particularly contribute to research of immune-mediated diseases.

overall_design: DNA purified from isolated 5 cell subsets (monocyte, B cells, CD4 T cells, CD8 T cells and PBMCs) obtained from 6 healthy female donors

first: Shimrat

last: Mamrut

first: Nili

last: Avidan

first: Elsebeth

last: Staun-Ram

first: Elizabeta

last: Ginzburg

first: Frederique

last: Truffault

first: Sonia

last: Berrih-Aknin


title: Integrative analysis of methylome and transcriptome in human blood identifies extensive sex and immune cell-specific differentially methylated regions [expression]

overall_design: RNA purified from isolated 5 cell subsets (monocyte, B cells, CD4 T cells, CD8 T cells and PBMCs) obtained from 6 healthy female donors


title: Integrative analysis of methylome and transcriptome in human blood identifies extensive sex and immune cell-specific differentially methylated regions


title: Whole genome transcription and DNA methylation analysis of peripheral blood mononuclear cells identified aberrant gene regulation pathways in systemic lupus erythematosus [expression]

status: Public on Jun 01 2016

city: Dallas

first: yun

last: lian

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: Our study has demonstrated that significant number of differential genes in SLE was involved in IFN, TLR signaling pathways and inflammatory cytokines. The enrichment of differential genes has been associated with aberrant DNA methylation, which may be relevant to the pathogenesis of SLE. Our observations laid the groundwork for further diagnostic and mechanistic studies of SLE and LN.

overall_design: We performed whole genome transcription and DNA methylation analysis in PBMC of 30 SLE patients, including 15 with LN (SLE LN+) and 15 without LN (SLE LN-), and 25 normal controls (NC) using HumanHT-12 Beadchips and Illumina Human Methy450 chips. The serum pro-inflammatory cytokines were quantified using Bio-plex human cytokine 27-plex assay.

first: Honglin

last: Zhu

first: Wentao

last: Mi

first: Hui

last: Luo

first: Tao

last: Chen

first: Shengxi

last: Liu

first: Xiaoxia

last: Zuo

first: Quan-zhen

last: Li


title: Genome-wide mapping of H4K20me3 in proliferating and senescent IMR90 cells.

status: Public on May 27 2016

city: Glasgow

first: Peter

last: Adams

address: Switchback Rd, Bearsden

institute: University of Glasgow, Beatson Institute for Cancer Research

summary: Cellular senescence is a stable proliferation arrest and tumor suppressor mechanism. Abundance of histone modification, H4K20me3, has been reported to increase in senescent cells. Generally, H4K20me3 promotes formation of compacted transcriptionally silent constitutive heterochromatin, but its specific role in senescence is unknown. Here, we show that in senescent cells H4K20me3 is enriched at specific families of gene repeats (ZNFs, Olfactory Receptors, Protocadherins), and DNA sequences contained within senescence-associated heterochromatin (senescence-associated heterochromatin (SAHF)). Furthermore, in senescent cells, but not proliferating cells, H4K20me3 is also markedly enriched at bodies of repressed genes, including proliferation-promoting genes. Ectopic expression of SUV420H2, responsible for deposition of H4K20me3, reinforces senescence-associated proliferation arrest, and slows proliferation of transformed cells and tumorigenesis in vivo. These results indicate a dedicated role for H4K20me3 in control of nuclear organization and gene expression in senescent cells and stable senescence-associated proliferation arrest and tumor suppression.

overall_design: ChIP-seq of H4K20me3 in proliferating (PD32) and replicative senescent (PD86) IMR90 cells was performed using two different H4K20me3 antibodies. In total, four samples are included in the dataset.

first: David

last: Nelson

first: John

middle: J

last: Cole

middle: D


title: PML regulates NF-κB transcriptional activity

first: Ruaidhri

last: Carmody

address: Sir Graeme Davies Building, 120 University Place

department: Institute of Infection, Immunity and Inflammation

institute: University of Glasgow

summary: The transcription factor NF-κB is the master regulator of the immune response but also regulates gene expression to influences cell survival, proliferation and differentiation. Inducible site-specific phosphorylation of NF-κB is critical for its activity and appears to be important in gene specific transcriptional control. Promyelocytic Leukemia (PML) is a nuclear protein that forms sub-nuclear structures termed nuclear bodies associated with transcriptionally active genomic regions. We demonstrate that PML promotes NF-κB- induced transcriptional responses by promoting the phosphorylation of NF-κB p65 at key regulatory sites. Our findings demonstrate a critical role for PML in promoting NF-κB transcriptional activity through signal induced post-translational modifications.

overall_design: WT and PML-/- MEFs were analysed for gene expression analysis. Total of 12 samples, inlcluding triplicates were utilized. WT MEFs and PML-/- were stimulated with TNFα for three hours and analysed for gene expresison using unstimulated WT MEFs as control.

first: Abrar

last: Ahmed

first: Ruaidhrí


title: Whole genome transcription and DNA methylation analysis of peripheral blood mononuclear cells identified aberrant gene regulation pathways in systemic lupus erythematosus

status: Public on Jun 03 2016


title: Effects of MYCN knockdwon on miRNA expression in neuroblastoma cells

status: Public on May 16 2016

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

institute: National Taiwan University Hospital

summary: Global miRNAs expression profilling of SK-N-BE(2)-C cells after dsRNA-mediated knockdown of MYCN

overall_design: To identify MYCN-associated miRNAs, we carried out a small RNA-seq on MYCN knockdown in SK-N-BE(2)-C cells to profile the miRNA expression.

first: HF

last: Juan

first: CL


title: DNA-methylation profiling of monocyte genomic DNAs collected from participants of  Diabetes Control and Complications Trial/Epidemiology of Diabetes Interventions and Complications (DCCT/EDIC) study

status: Public on May 15 2016

city: Duarte

first: Nancy

address: 1500 Duarte Road

department: Diabetes

institute: City of Hope

summary: Study the association of DNA-methylation and metabolic memory by examing DNA-methylation alternation  between cases (received conventional therapy in DCCT  and showing retinopathy or albuminuria progression at EDIC year-10)  and Controls(in DCCT intensive treatment group  and did not have retinopathy or nephropathy progression during EDIC]

overall_design:
Bisulphite converted DNA from the 61 monocyte samples (31 Cases and 30 Controls) were hybridised to the Illumina Infinium HumanMethylation450 Beadchip arrays.
Please note that the same samples were used on histone-modification profilling in PMID:24458354

first: Zhuo

first: Rama

last: Natarajan


title: DNA-methylation profiling of Whole blood genomic DNAs collected at EDIC baseline and monocytes at EDIC years 16/17 yrs from participants of DCCT/EDIC study

summary:
DNA-methylation profiling of Whole blood genomic DNAs collected at EDIC baseline and monocytes at EDIC years 16/17 years from participants of Diabetes Control and Complications Trial/ Epidemiology of Diabetes Interventions and Complications (DCCT/EDIC) study
This SuperSeries is composed of the SubSeries listed below.


title: Mapping H4K20me3 onto the chromatin landscape of senescent cells indicates a function in control of cell senescence and tumor suppression through preservation of genetic and epigenetic stability.

summary: Histone modification H4K20me3 and its methyltransferase SUV420H2 have been implicated in suppression of tumorigenesis. The underlying mechanism is unclear, although abundance of H4K20me3 increases during cellular senescence. Cellular senescence is a stable proliferation arrest and tumor suppressor process, triggered by diverse molecular cues, including activated oncogenes. Here, we set out to better understand the function of H4K20me3 in senescence and tumor suppression.

overall_design: ChIP-seq of H4K20me3 in RAS induced senescence and associated controls in IMR90 cells was performed. In total, four samples are included in the dataset which associates with a dataset that includes H4K20me3 ChIP in proliferating (PD32) and replicative senescent (PD87) samples.

first: Farah

last: Jaber-Hijazi

first: Neil

middle: A

last: Robertson


title: Screening of differentially expressed genes after IMB5046 treatment

status: Public on Mar 08 2016

city: Beijing

first: Yanbo

last: Zheng

address: 1# Tiantan Xili

institute: Institute of Medicinal Biotechnology

summary: To investigate the effects of IMB5046 treatment on cells, we used the gene expression microarray to compare the  difference between the IMB5046-treated cells and control cells.  A431 cells were treated with 100 nM IMB5046 or 0.1% DMSO (vehicle) for 24 hr. A total of 441 genes were down-regulated and 383 genes were up-regulated by at least 2-fold between IMB5046-treated and control cells.The most obviuos changes in Gene Ontology biolocial process classification were related to cell death and immune response.

overall_design: A431 cells were treated with 100 nM IMB5046 or (0.1% DMSO) vehicle for 24 h. Then, total RNA was extracted from cells using TRIzol reagent and analyzed.

first: Yan-bo


title: DNA-methylation profiling of Whole blood genomic DNAs collected from participants of  Diabetes Control and Complications Trial/Epidemiology of Diabetes Interventions and Complications (DCCT/EDIC) study

summary: Study the association of DNA-methylation and metabolic memory by examing DNA-methylation alternation between cases (received conventional therapy in DCCT  and showing retinopathy or albuminuria progression at EDIC year-10)  and Controls (in DCCT intensive treatment group  and did not have retinopathy or nephropathy progression during EDIC).

overall_design: Bisulphite converted DNA from the 63 whole blood samples (32 Cases and 31 Controls) were hybridised to the Illumina Infinium HumanMethylation450 Beadchip arrays.

first: Feng

last: Miao


title: The acetyllysine reader BRD3R promotes human nuclear reprogramming and regulates mitosis

status: Public on Mar 01 2016

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

summary: It is well known that both recipient cells and donor nuclei demonstrate a mitotic advantage as observed in the traditional reprogramming with somatic cell nuclear transfer (SCNT). However, It is not known whether a specific mitotic factor plays a critical role in reprogramming. Here we identify an isoform of human bromodomain-containing 3 (BRD3), BRD3R (BRD3 with Reprogramming activity), as a reprogramming factor. BRD3R positively regulates mitosis during reprogramming, upregulates a large set of mitotic genes at early stages of reprogramming, and associates with mitotic chromatin. Interestingly, a set of the mitotic genes upregulated by BRD3R constitutes a pluripotent molecular signature. The two BRD3 isoforms display differential binding to acetylated histones. Our results suggest a molecular interpretation for the mitotic advantage in reprogramming, and show that mitosis may be a driving force of reprogramming.

overall_design: Human BJ cells transduced with lentiviral particles of the conventional reprogramming factors (OCT3/4, SOX2 and KLF4) were used as controls. Two types of controls were used: 1) BJ transduced with OSK (OCT4, SOX2 and KFL4) viruses; 2) BJ cells transduced with OSK plus GFP viruses. Experimental treatment was BJ cells transduced with OSK plus BRD3R viruses. RNA was extracted from cells at day 3 of reprogramming because the reprogramming cells are still homogeneous and transgenes are well expressed at this time point.

first: Zhicheng

last: Shao

first: Michael

last: Crowley

last: Crossman

first: Kejin

last: Hu


title: Gene expression in a 3-dimensional reconstructed human corneal epithelial tissue after near-infrared irradiation simulating solar near-infrared radiation that reaches human tissues on the Earth’s surface

status: Public on Jan 05 2016

city: Matsumoto

first: Yohei

last: Tanaka

state: Nagano

department: Plastic Surgery

institute: Clinica Tanaka

summary: To clarify the effects of near-infrared radiation, we assessed DNA microarray after water-filtered broad-spectrum near-infrared (1100-1800 nm together with a water-filter that excludes wavelengths 1400-1500 nm) irradiation.

overall_design: We performed 5 rounds of near-infrared irradiation (at 10 J ⁄cm2) using 2 sets of transparent polycarbonate plates, one to block UV and the other to block both UV and near-infrared.

first: Jun

last: Nakayama


title: Role of Fibroblast Growth Factor-5 on the Proliferation of Human Tonsil-derived Mesenchymal Stem Cells

status: Public on Jan 28 2016

city: Changwon

first: Gi Cheol

last: Park

address: Samsung Changwon Hospital, 158, Paryong-ro, MasanHoewon-Gu

department: Otolaryngology-Head and Neck Surgery

institute: Samsung Changwon Hospital, Sungkyunkwan University School of Medicine

summary:
Filtering differentially expressed gene probes between samples (A1-4, B1-4, T1-4) - Fold change, LPR test    A:Adipose tissue-derived mesenchymal stem cells, B: bone marrow-derived MSC, T: palatine tonsil-derived MSC)
Hierarchical clustering (Eudlidean method, complete Linkage), venn-diagrm

overall_design: Total RNA obtained from 12 MSCs (4 T-MSCs, 4 A-MSCs, 4 BM-MSCs) to compared the gene expression level ( T-MSC vs A-MSC, T-MSC vs BM-MSC)

first: Byung-Joo

last: Lee

first: Ji-Sun

last: Song


title: Genome-wide transcriptional profiling of Legionella Pneumophila-infected A549 cells transfected with siRNA against TNFAIP2

status: Public on Apr 13 2016

city: Berlin

first: Brian

last: Caffrey

address: Ihnestrasse 63-73

institute: Max Planck Institute for molecular Genetics

summary:
In this study we transfected A549 cells with siRNA against TNFAIP2, infected them with L. pneumophila and performed transcriptional profiling. We found enrichment of genes in pro-inflammatory
pathways by Pathway Over-respresentation analysis upon infection. There was no significant change in gene expression that we could attribute specifically to the knockdown of TNFAIP2.

overall_design: Examination of the transcriptional response of A549 cells to Legionella infection with concomitant TNFAIP2 knockdown

first: Annalisa

last: Marsico


title: The circular RNA (circRNA)  expression profiles in human aortic vascular smooth muscle cells (HAVSMCs)

city: shi jia zhuang

first: shaoguang

last: sun

state: Hebei

address: zhong shan dong lu 361

department: biochemistry and molecular biology

institute: Hebei medical university

summary: To explore the potential involvement of circRNAs in the vascular smooth muscle cell (VSMC) proliferation, we conducted circRNA profiling in three pairs of proliferative HAVSMCs and quiescent HAVSMCs by microarray. Our results showed that circRNAs were aberrantly expressed in proliferative HAVSMCs compared with quiescent HAVSMCs, and provided potential targets for novel insights into VSMC proliferation or vascular remodeling diseases.

overall_design: The circRNA expression profiles of three paired proliferative HAVSMCs and quiescent HAVSMCs were analyzed using the microarry platform.

first: Shaoguang

last: Sun

first: Xin

last: Xu

first: Shanhu

last: Cao

first: Fangfang

last: Li

first: Mei

last: Han


title: SK-NEP-1 treated with LBH589

status: Public on Dec 30 2015

city: suzhou

first: Jian

last: Pan

address: Jingde road 303

department: Department of Hematology and Oncology

institute: Children's Hospital of Soochow University

summary: Wilms tumor (WT) is an embryonic kidney cancer, for which histone acetylation might be a therapeutic target. LBH589, a novel targeted agent, suppresses histone deacetylases in many tumors. This study investigated the antitumor activity of LBH589 in SK-NEP-1 cells. LBH589 inhibited cell proliferation of SK-NEP-1  cells in a dose-dependent manner. Annexin V, Tunel and Hochest 33342 staining analysis showed that LBH589-treated cells showed more apoptotic features compared with the control. LBH589 treatment inhibited the growth of SK-NEP-1 xenograft tumors in nude mice. Arraystar Human LncRNA Array analysis of genes and lncRNas regulated by LBH589 identified 6653 mRNAs and 8135 lncRNAs in LBH589-treated SK-NEP-1 cells. The most enriched gene ontology terms were those involved in nucleosome assembly. KEGG pathway analysis identified cell cycle proteins, including CCNA2, CCNB2, CCND1, CCND2, CDK4, CDKN1B and HDAC2, etc. Ingenuity Pathway Analysis identified important upstream molecules: HIST2H3C, HIST1H4A, HIST1A, HIST1C, HIST1D, Histone H1, Histone H3, RPRM, HSP70 and MYC.

overall_design: SK-NEP-1 cells were treated with 100nM LBH589 and control group cells were treated with the same volume of DMSO 24 hours later. Human LncRNA Array analysis was performed by KangChen Bio-tech, Shanghai P.R. China. Briefly, RNA purified from total RNA after removal of rRNA was amplified and transcribed into fluorescent cRNA and cDNA was labeled and hybridized to the Human LncRNA Array v3.0 (8660 K, Arraystar). 30,586 LncRNAs and 26,109coding transcripts which collected from the most authoritative databases such as RefSeq, UCSC Knowngenes, Ensembl and many related literatures can be detected by the microarray.

first: Tao

last: Fang

first: Pan

last: Jian


title: Development of gene signatures of human unipotent megakaryocyte progenitor and other hematopoietic stem and progenitor populations

status: Public on Feb 02 2016

city: Fukuoka

first: Kohta

last: Miyawaki

address: 3-1-1, Maidashi, Higashi-ku

institute: Kyushu University

summary: We newly identified prospectively-isolatable unipotent megakaryocyte progenitor population (MegP) as the major source of megakaryocytes, which emerges directly from early stage of hematopoiesis bypassing megakaryocyte-erythroid lineage bifurcation and contributes to physiological and pathological human megakaryopoiesis. To explore gene expression signature of hematopoietic stem/progenitor populrations miroarry-based whole transcriptome analysis was performed. As a result, gene expression signature of MegP clearly reflected its differentiation potential.

overall_design: Gene expression profile of megakaryocyte progenitor and other hematopoietic stem and progenitor populations (Manz et al., PNAS, 2002), which were derived from bone marrow aspirates, were analyzed.


title: Expression profiling of long noncoding RNAs and mRNAs in mouse plasma

status: Public on Dec 31 2015

first: Qinghua

last: Cui

address: 38 Xueyuan Road

institute: Peking University

summary: Long noncoding RNA profile in the mouse plasma after ischemia-reperfusion injury (IRI).

overall_design: In the study presented here, we mixed the plasma from three mouse after IRI and identified the genome-wide expression level of lncRNAs.

first: Cui

last: Qinghua

first: Yang

last: Jichun


title: The miRNA Transcriptome directly Reflect the Physiological and Biochemical Differences between Red, White and Intermediate Muscle Fiber Types

status: Public on Dec 23 2015

city: Yaan

first: jideng

last: Ma

address: Xinkang road

institute: Sichuan Agricultural University(SICAU),

summary: MicroRNAs (miRNAs) are small non-coding RNAs that can regulate the expression of their target genes at post-transcriptional level. Skeletal muscle comprises different ﬁber types that can be broadly classified as red, intermediate and white fiber types. Recently, a set of miRNAs were identified to be expressed on a fiber type-specific manner between red and white fiber types. Nonetheless, an integral explanation of the miRNA transcriptome differences in all three fiber types is long overdue. Herein, we collected 15 kinds of porcine skeletal muscles from different anatomic locations, which were then clearly divided into red, white and intermediate fiber type based on the hierarchical clustering analysis for the ratios of myosin heavy chain (MHC) isoforms. We further illustrated that three muscles, which typically represented each muscle fiber type (i.e. red: peroneal longus (PL), intermediate: psoas major muscle (PMM), white: longissimus dorsi muscle (LDM)), have distinct metabolic patterns of mitochondrial and glycolytic enzyme levels. In addition, we constructed the small RNA libraries for PL, PMM and LDM using deep sequencing approach. Results showed that, the differentially expressed miRNAs were mainly enriched in PL and played a vital role in myogenesis and energy metabolism. Overall, this comprehensive analysis will contribute to a better understanding of the miRNA regulatory mechanism for the phenotypic diversity of skeletal muscles.

overall_design: 3 sample

first: Jideng

first: Hongmei

last: Wang


title: A consolidated analysis of the physiological and molecular responses induced under acid stress in the legume symbiont model soil bacterium Sinorhizobium meliloti

status: Public on Oct 29 2015

city: La Plata

first: Antonio

last: Lagares

state: Bs As

department: Ciencias Biológicas

country: Argentina

institute: IBBM

summary: Abiotic stresses disturb and limit nitrogen-fixing symbioses between rhizobia and their host legumes. In particular, the effect of extracellular acidity on rhizobia has been taken as a model example for analysis because of the economic impact and worldwide distribution of these symbionts in agricultural countries. Except for valuable molecular-biological studies on different rhizobia, no consolidated models have been formulated to describe the central physiologic changes that occur in acid-stressed bacteria. We present here an integrated analysis entailing the main cultural, metabolic, and molecular responses of the model bacterium Sinorhizobium meliloti growing under controlled acid stress in a chemostat. A stepwise extracellular acidification of the culture medium had indicated that S. meliloti stopped growing at ca. pH 6.0–6.1. Under such a limiting acid stress the rhizobia increased the O2 consumption per cell by more than 5-fold. This phenotype, together with an increase in the transcripts for several membrane cytochromes, entails a remarkably higher aerobic-respiration rate in acid-stressed rhizobia. Changes in the transcripts encoding enzymes for lipid biosynthesis were also observed, consistent with previous data on rhizobial pH-dependent membrane remodelling. Together with increased energy demands under acidity, proteomic and transcriptomic data revealed that while at pH 7.0 the transport and biosynthesis of cellular compounds were quite active processes, under acid stress most overexpressed markers were associated with protein biosynthesis, macromolecular degradation and/or recycling, and energy metabolism. Within this context, the pentose-phosphate pathway exhibited increases in several transcripts, enzymes, and metabolites. Moreover, multivariate analysis of global metabolome data (more than 60 compounds) served to unequivocally correlate the specific-metabolite profiles with the extracellular pH for growth, with strikingly sensitive variations being observed in the rhizobial metabolomes upon extracellular-pH changes of less than 0.5 units. Except for a ca. 120-kb DNA stretch within the pSymA no specific genomic regions were associated with the observed acid-stress responses. Further practical analyses should be focussed on the phenotypic impact and time course of the observed changes during the acid-stress perception and on the search for common responses during the previously described sublethal acid-adaptive processes in rhizobia

overall_design: pH 6.1 vs pH 7

first: Walter

last: Draghi


title: Microarray study of human adrenal zona glomerulosa (ZG), zona fasciculata (ZF) and aldosterone-producing adenomas (APA)

status: Public on Sep 15 2015

city: Cambridge

first: Junhua

last: Zhou

state: Cambridgeshire

address: CPU, Level 6, ACCI, Addenbrooke’s Hospital

institute: University of Cambridge

summary: Learn about the transcriptome profiling of zona glomerulosa (ZG), zona fasciculata (ZF) and aldosterone-producing adenomas (APA) in human adrenals

overall_design: 21 pairs of zona fasciculata (ZF) and zona glomerulosa (ZG), and 14 paired aldosterone-producing adenomas (APAs) from 14 Conn’s syndrome patients and 7 phaeochromocytoma patients were assayed on the Affymetrix Human Genome U133 Plus 2.0 Array. Laser capture microdissection was used to acquire samples of ZF, ZG and APA as previously described (Azizan EA, et al. J Clin Endocrinol Metab. 2012;97:E819-E829). For differentiation of ZG from ZF, sections were stained with cresyl violet using the LCM Staining Kit (AM1935, Ambion, USA). Data processing and analysis was performed using AffymetrixGeneChip Command Console Software and PartekGenomicSuite 6.5 (Partek Inc., St. Louis, MO). Gene expressions were portrayed as the summarized log-signal of the Robust Multichip Average (RMA) with quantilenormalisation and median polish for probe set summarisation. Validation by qPCR was performed on genes >10 fold up-regulated in zona glomerulosa (compared to zona fasciculata) and >10 fold up-regulated in aldosterone-producing adenomas (compared to zona glomerulosa).

first: Morris

last: Brown

first: Elena

last: Azizan


title: Targeting Focal Adhesion Kinase Renders Pancreatic Cancers Responsive to Checkpoint Immunotherapy

status: Public on Nov 21 2015

city: Saint Louis

first: David

last: DeNardo

state: MO

address: 425 S. Euclid Avenue

institute: Washington University in St. louis

summary: Single-agent immunotherapy has achieved limited clinical benefit to date in patients with pancreatic ductal adenocarcinoma (PDAC). This may be a result of the presence of a uniquely immunosuppressive tumor microenvironment (TME). Critical obstacles to immunotherapy in PDAC tumors include a high number of tumor-associated immunosuppressive cells and a uniquely desmoplastic stroma that functions as a barrier to T cell infiltration. We identified hyperactivated focal adhesion kinase (FAK) activity in neoplastic PDAC cells as an important regulator of the fibrotic and immunosuppressive TME. We found that FAK activity was elevated in human PDAC tissues and correlated with high levels of fibrosis and poor CD8+ cytotoxic T cell infiltration. Single-agent FAK inhibition using the selective FAK inhibitor VS-4718 substantially limited tumor progression, resulting in a doubling of survival in the p48-Cre;LSL-KrasG12D;Trp53flox/+ (KPC) mouse model of human PDAC. This delay in tumor progression was associated with markedly reduced tumor fibrosis and decreased numbers of tumor-infiltrating immunosuppressive cells. We also found that FAK inhibition rendered the previously unresponsive KPC mouse model responsive to T cell immunotherapy and PD-1 antagonists. These data suggest that FAK inhibition increases immune surveillance by overcoming the fibrotic and immunosuppressive PDAC TME and renders tumors responsive to immunotherapy.

overall_design: We treated KP orthotopic tumor-bearing mice with vehicle and FAK inhibitor (FAKi) for 14 days, then extracted total RNA from tumor tissues.

first: Hong

last: Jiang

first: Samarth

last: Hegde

first: Brett

last: Knolhoff

first: Yu

last: Zhu

first: John

last: Herndon

first: Esther

last: Leu

first: William

last: Hawkins

first: Irina

last: Shapiro

last: Weaver

first: Jonathan

last: Pachter

first: Andrea

last: Wang-Gillam


title: Evaluation of DNA array sensitivity to detect viruses in clinical samples following propidium monoazide treatment

status: Public on Nov 02 2015

city: St-Hyacinthe

first: Christian

last: Bellehumeur

address: 3200 Sicotte

institute: Université de Montréal

summary: Pan-viral DNA array (PVDA) and high-throughput sequencing (HTS) are useful tools to identify novel virus of emerging diseases. However, both techniques have difficulties to identify viruses in clinical samples because of host genomic DNA (hgDNA) contamination. Both propidium monoazide (PMA) and ethidium bromide monoazide (EMA) have the capacity to bind free DNA but are cell membrane-impermeable and thus are unable to bind protected DNA and RNA such as viral genomic material. DNA modified by EMA or PMA is not amplifiable by polymerase. In order to assess the capacity of EMA or PMA to lower hgDNA, serum or lung tissue homogenates were spiked with porcine reproductive and respiratory virus (PRRSV) and were processed with different combination of treatment: with or without ultracentrifugation and incubation with or without different concentration of EMA or PMA. PVDA and HTS were used to evaluate the capacity of both techniques to detect the presence of PRRSV from each sample. Negative results were obtained by PVDA and low amount of PRRSV specific reads were obtained by HTS with untreated samples or samples treated only by ultracentrifugation. An increase capacity of PRRSV detection was observable by PVDA in EMA and PMA treated samples but PVDA best results were obtained following PMA treatment, with or without ultracentrifugation. HTS sensitivity was also improved by a treatment with EMA or PMA, but the number of reads was significantly higher in PMA treated samples. These results support the use of PMA as a treatment to increase sensitivity of PVDA and HTS.

overall_design: A non specific DNA probe is used as a negative hybridization control. Also, specifics probes targeting pUC19 plasmid DNA is used as a DNA array positive control as well as a localization control. Finally, there are 34 probes of 70 nucleotides spotted in duplicate were selected to target PRRSV conserved regions. A total of 80 different tests were done by DNA array in order to evaluate different treatments conditions with EMA or PMA, with or without ultracentrifugation. A total of 58 samples were tested on specific lung tissue homogenates spiked with different concentration of PRRSV and 12 samples were serum samples spiked with one concentration of PRRSV. Finally. A total of six samples

first: Brian

last: Boyle

first: Steve

last: Charette

first: Josee

last: Harel

first: Yvan

last: L'Homme

first: Luke

last: Masson

first: Carl

last: Gagnon


title: Lactobacilli modulate epithelial cytoprotection through the Nrf2 pathway [Microarray]

status: Public on Sep 01 2015

city: Atlanta

first: Rheinallt

last: Jones

state: Georgia

address: 615 Michael

department: Pediatrics

institute: Emory Univeristy

summary: We report that cellular ROS enzymatically generated in response to contact with lactobacilli in both mice and Drosophila has salutary effects against exogenous insults to the intestinal epithelium via the activation of Nrf2 responsive cytoprotective genes.

overall_design: RNA was isolated from 40 3rd instar larvae of sterile PBS or L. plantarum treated drosophila melanogaster, combined into two samples and gene expression measured by microarray

first: Andrew

last: Neish


title: Lactobacilli modulate epithelial cytoprotection through the Nrf2 pathway [RNA-Seq]

overall_design: RNA was isolated from the colons of untreated, PBS, E. coli, and LGG innoculated germ free mice and RNA-seq performed to identify the gene expression in response to each condition


title: The olfactory transcriptome and progression of sexual maturation in homing chum salmon Oncorhynchus keta

status: Public on Aug 27 2015

city: Leiden

first: Ron

last: Dirks

address: Sylviusweg 74

institute: Future Genomics Technologies BV

summary: This study aimed at providing insights into the hypothesized functional link between olfactory sensing of the spawning ground and final sexual maturation. We have therefore assessed the presence and expression levels of olfactory genes by RNA sequencing (RNAseq) of the olfactory rosettes in homing chum salmon Oncorhynchus keta Walbaum from the coastal sea to 75 km upstream the rivers at the pre-spawning ground. RNAseq revealed the expression of 75 known and 27 unknown salmonid olfactory genes of which 13 genes were differentially expressed between fish from the pre-spawning area and from the coastal area, suggesting an important role of these genes in homing. Olfactomedins and ependymin are candidates among the differentially expressed genes that may connect olfactory reception to the expression of sgnrh to regulate final maturation.

overall_design: Deep-sequencing transcriptome analysis of twelve chum salmon olfactory rosette RNA samples: three females and three males from the pre-spawning area and three females and three males from the coastal area.

first: Arjan

last: Palstra

first: Josep

middle: V

last: Planas

first: Hiroshi

last: Ueda


title: Cancer associated SF3B1 hotspot mutations induce cryptic 3' splice site selection through use of a different branch point

status: Public on Sep 08 2015

first: Silvia

last: Buonamici

state: MA

address: 300 Technology Square #5

institute: H3 Biomedicine

summary: Recurrent mutations in the spliceosome are observed in several human cancers but their functional and therapeutic significance remain elusive. SF3B1, the most frequently mutated component of the spliceosome in cancer, is involved in the recognition of the branch point sequence (BPS) during selection of the 3’ splice site (ss) in RNA splicing. Here, we report that common and tumor-specific splicing aberrations are induced by SF3B1 mutations and establish aberrant 3’ ss selection as the most frequent splicing defect. Strikingly, mutant SF3B1 utilizes a BPS that differs from that used by wild-type SF3B1 and requires the canonical 3’ ss to enable aberrant splicing during the second step. Approximately 50% of the aberrantly spliced mRNAs are subjected to nonsense-mediated decay resulting in downregulation of gene and protein expression. These findings ascribe functional significance to the consequences of SF3B1 mutations in cancer.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 72 samples, including two sets of patient data and cell lines with two additional technical replicates each

first: Michael

last: Seiler


title: Lactobacilli modulate epithelial cytoprotection through the Nrf2 pathway

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

sample_organism:
Drosophila melanogaster
Mus musculus

platform_organism:
Drosophila melanogaster
Mus musculus

overall_design: Refer to individual Series


title: Knockdown and Overexpression of FMR4 in HEK293T cells at 6 and 24 hours

city: Miami

first: Veronica

last: Peschansky

state: FL

address: 1501 NW 10th Ave

institute: University of Miami

summary: CGG repeat expansions in the Fragile X mental retardation 1 (FMR1) gene are responsible for a family of associated disorders characterized by either intellectual disability and autism (Fragile X Syndrome, FXS), or adult-onset neurodegeneration (Fragile X-associated Tremor/Ataxia Syndrome, FXTAS). However, the FMR1 locus is complex and encodes several long noncoding RNAs (lncRNAs), whose expression is altered by repeat expansion mutations.    The role of these lncRNAs is thus far unknown; therefore we investigated the functionality of FMR4, which we previously identified. “Full”-length expansions of the FMR1 triplet repeat cause silencing of both FMR1 and FMR4, thus we are interested in potential loss-of-function that may add to phenotypic manifestation of FXS. Since the two transcripts do not exhibit cis-regulation of one another, we examined the potential for FMR4 to regulate target genes at distal genomic loci using gene expression microarrays.  We identified FMR4-responsive genes, and further investigated their function related to human neural precursor cells. We therefore propose that FMR4’s function is as a gene-regulatory lncRNA and that this transcript may function in normal development. Closer examination of FMR4 increases our understanding of the role of regulatory lncRNA and the consequences of FMR1 repeat expansions.

overall_design: Study design includes 2 timepoints (6 and 24 hrs post-transfection) x 4 conditions (knockdown & control, overexpression & control) x 3 biological replicates. 3 technical replicates were pooled to creat each biological replicate.


title: PAT-seq: a simple approach to digital gene expression, the measure of poly(A)-tail length and its position in eukaryotic transcriptomes

status: Public on Aug 19 2015

city: Clayton

first: Traude

last: Beilharz

state: VIC

address: Wellington Rd

department: Biomedicine Discovery Institute

country: Australia

institute: Monash University

summary: The Poly(A)-Tail focused RNA-seq, or PAT-seq approach, is an affordable and efficient tool for the measure of 3’UTR dynamics. We show here that PAT-seq returns (i) digital gene expression, (ii) polyadenylation site usage within and between samples, including alternative adenylation, and (iii) the polyadenylation-state the transcriptome. PAT-seq differs from previous 3’ focused RNA-seq methods in that it strictly depends on native 3’ adenylation within total RNA samples and thus removes the need for ribosome depletion and, that the full native poly(A)-tail is included in the sequencing libraries. Limited RNase digestion combined with size selection and directional sequencing mean that deep-sequencing reads map to within ~50-100 bases of adenylation sites and run from unique sequence into adenosine homopolymers. Here, total RNA samples from budding yeast cells were analyzed to highlight the changes in gene expression and adenylation-state of the transcriptome in response to loss of the deadenylase Ccr4. Furthermore, concordant changes to gene expression and adenylation-state were demonstrated in a classic Crabtree-Warburg metabolic shift. Because all adenylated RNA are interrogated by the PAT-seq approach, alternative adenylation sites, long noncoding RNA and other non-coding RNA and RNA decay intermediates were also identified.

overall_design: Analysis of 3'UTR dynamics in yeast cells responding to the loss of the major cytoplasmic deadenylase or a change in carbon source

first: Paul

middle: F

last: Harrrison

middle: H


title: Transcriptome analysis of cyclic AMP (cAMP) response in bovine cumulus cells

status: Public on Jul 01 2015

city: Quebec

first: Daulat Raheem

last: Khan

state: QC

address: 2425, rue de l'Agriculture, Pavillon Paul-Comtois

department: Sciences Animales

institute: Université Laval

summary: Study the effect of forskolin, dipyridamol and IBMX (here called FID) supplementation in the in vitro maturation medium for an incubation of 6 hrs on the transcriptomics of bovine cumulus cells.

overall_design: 3 biological replicates of cumulus cells derived from cumulus oocyte complexes (COCs) supplemented with FID (CC-FID) vs. cumulus cells without FID (Ct-6H, REFERENCE) were contrasted. Each replicate was subjected to a dye-swap procedure.

first: Daulat

middle: R

first: Christine

last: Guillemette

first: Marc-André

last: Sirard

first: François

last: Richard


title: Transcriptome analysis of bovine cumulus cells during first 6 hrs of in vitro maturation

summary: Study the effect of in vitro maturation system on the transcriptomics of bovine cumulus cells during incubation of first 6 hrs.

overall_design: 3 biological replicates of cumulus cells derived from cumulus oocyte complexes (COCs) after 6 hrs of in vitro matutaion(Ct-6H) vs. cumulus cells before maturation (Ct-0H, REFERENCE) were contrasted. Each replicate was subjected to a dye-swap procedure.


title: Comparative analysis of transcriptome profiles of a lintless-fuzzless mutant XinWX and its near-isogenic line linted-fuzzless mutant XinFLM during fiber initiation development stages

city: Nanjing

first: Wang

middle: Li

last: Man

address: Weigang N0.1

institute: Nanjing Agricultural University

summary: To gain novel insights into the molecular mechanisms of fiber initiation development,transcription profiling of the lintless-fuzzless mutant (XinWX) and its near-isogenic line,XinFLM (fuzzless-linted mutant) were compared using cDNA microarray technology. The expression profiling was performed at 3 developmental time points: -1, 0, and 1 dpa. fiber initiation development related genes were identified by differentially expressed gene analysis. And these genes could be used as potential candidate genes for manipulation to improve fiber yield.

overall_design: Cotton plants were grown under field condition. Flowers were tagged and cotton bolls were collected during Fiber initiation stages. Total RNA was isolated from ovule and fiber mixtures of XinWX and XinFLM at -1, 0, and 1 dpa. A total of 9 hybridizations with three biological replicates including a swap-dye experiment for each fiber developmental stage were employed.

first: Wangzhen

last: Guo


title: Global DNA methylation landscape reveals roles of DNA methylation involved in the regulation of drug metabolizing enzyme

status: Public on Jun 16 2015

city: Yahaba-Cho, Shiwa-Gun

first: Wataru

last: Habano

state: Iwate

address: 2-1-1 Nishitokuta

department: Pharmacodynamics and Molecular Genetics

institute: Iwate Medical University


title: Global DNA methylation landscape reveals roles of DNA methylation involved in the regulation of drug metabolizing enzyme [I]

summary: In order to elucidate the role of DNA methylation in the DME gene regulation, global DNA methylation and mRNA expression profiles of human tissues and cell lines were examinde by HumanMethylation450 Bead Chip and SurePrint G3 Human Gene Expression 8×60K v2. We demonstrated DNA methylation landscape of the DME genes in human tissues. Although a fraction of DME genes can be regulated by their DNA methylation, the variable DNA methylation status probably affects drug metabolism and response.

overall_design: Total RNA was isolated from 2 human tissues (liver and small intestine) and 3 human hepatoma cells that were treated with or without 5-aza-2’-deoxycytidine, and used for mRNA expression analysis.