title: Chromatin binding profiles of the APC tumor suppressor and changes in gene expression following APC silencing

city: Columbus

first: Joanna

last: Groden

state: OH

address: 986 BRT 460 West 12th Ave.

department: Department of Cancer Biology and Genetics

institute: The Ohio State University, College of Medicine


title: APC ChIP-seq in HCT-116 colon cancer cell line

status: Public on May 24 2018

country: USA

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Anti-APC ChIP-seq data were collected from HCT-116 cells and 3,985 genomic sequences were found to be enriched in both independent biological replicates.

overall_design: Examination by ChIP-seq of chromatin binding profiles for APC in a colon cancer cell line expressing wild-type APC and a degradation-resistant β-catenin that constitutively activates canonical WNT signaling

first: William

last: Hankey

first: Baris

last: Hancioglu


title: B-cell activating factor (BAFF) stimulation of Burkitt Lymphoma cell line [Affymetrix]

status: Public on May 23 2018

city: Goettingen

first: Alexander

last: Wolff

state: Lower Saxony

address: Humboldtallee 32

department: Medical Statistics

country: Germany

institute: UMG

summary:
Microarray profiling of Burkitt Lymphoma cell line (BL2) with B-cell activating factor (BAFF) for 24 hrs .
The Burkitt Lymphoma cell line were either only cultured in cell culture medium supplemented with 10 mM HEPES at 1 × 106 cells/ml  or additionally incubated with B-cell activating factor (BAFF) for 24 hrs

overall_design: Two conditions of  BL2 cells each in 3 replicates:  1. non-stimulated control (BL2),  2. Baff stimulated (BL2Baff)

first: Michaela

last: Bayerlová

first: Dieter

last: Kube

first: Jochen

last: Gaedcke

first: Tim

last: Beißbarth


title: Genome-Wide Identification and Comprehensive Analysis of Conserved MicroRNAs and Phased small Interfering RNAs in Watermelon [miRNA-Seq]

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

country: China

institute: Yunnan Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs involved in the post-transcriptional gene regulation and play a critical role in plant growth, development and stress responses. Watermelon (Citrullus lanatus L.) is one of the important agricultural crops worldwide. Here we carried out computational and experimental analysis of miRNAs and phased small interfering RNAs (phasiRNAs) in watermelon by analyzing 14 small RNA profiles from roots, leaves, androecium, flowers, and fruits, and one published small RNA profile of mixed tissues. To identify the targets of miRNAs and phasiRNAs, we generated a degradome profile for watermelon leaf which is analyzed with the SeqTar algorithm. We identified 97 conserved pre-miRNAs, of which 58 have not been reported previously and 348 conserved mature miRNAs without precursors. We also found 9 novel pre-miRNAs encoding 18 mature miRNAs. One hundred and one 21 nucleotide (nt) PHAS loci, and two hundred and forty one 24 nt PHAS loci were also identified. We identified 120 conserved targets of the conserved miRNAs and TAS3-derived tasiRNAs by analyzing a degradome profile of watermelon leaf. The presented results provide a comprehensive view of small regulatory RNAs and their targets in watermelon.

overall_design: Identification and comprehensive analysis of conserved microRNAs and phased small interfering RNAs in watermelon or whole plant using Illumina HiSeq 2000 sequencer.


title: Genome-Wide Identification and Comprehensive Analysis of Conserved MicroRNAs and Phased small Interfering RNAs in Watermelon

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

overall_design: Refer to individual Series


title: The physiology of Agaricus bisporus in semi-commercial compost cultivation appears to be highly conserved among unrelated isolates

status: Public on May 22 2018

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

country: Netherlands

institute: Centre of fungal biodiversity

type: Expression profiling by high throughput sequencing

summary: The white button mushroom Agaricus bisporus is the most widely produced edible fungus with a great economical value. Its commercial cultivation process is often performed on wheat straw and animal manure based compost that mainly contains lignocellulosic material as a source of carbon and nutrients for the mushroom production. As a large portion of compost carbohydrates are left unused in the current mushroom cultivation process, the aim of this work was to study wild-type A. bisporus strains for their potential to convert the components that are poorly utilized by the commercial strain A15. Growth profiling suggested different abilities for several A. bisporus strains to use plant biomass derived polysaccharides, as well as to transport and metabolize the corresponding monomeric sugars. Six wild-type isolates with diverse growth profiles were compared for mushroom production to A15 strain in semi-commercial cultivation conditions. Transcriptome and proteome analyses of the three most interesting wild-type strains and A15 indicated that the unrelated A. bisporus strains degrade and convert plant biomass polymers in a highly similar manner. This was also supported by the chemical content of the compost during the mushroom production process. Our study therefore reveals a highly conserved physiology for unrelated strains of this species during growth in compost.

overall_design: The aim of the study was to compare the gene expression of different strains of A. bisporus (A. bisporus strain A15, 065 BP-8, 219 30P and 245 AMA-7) at different stages of its life cycle to select for better abilities towards components that are poorly utilized by the commercially cultivated strain A15. The samples were taken at primordial stage and first flush respectively.

first: María Victoria

last: Aguilar-Pontes

first: Aleksandrina

last: Patyshakuliyeva

first: Harm

last: Post

first: Edita

last: Jurak

first: Kristiina

last: Hildén

first: Maarten

last: Altelaar

first: Albert

last: Heck

first: Mirjam

middle: A

last: Kabel

middle: P

first: Miia

middle: R

last: Mäkelä


title: MicroRNA expression profiling of extracellular vesicles derived from human BM-MSC

status: Public on May 21 2018

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

summary:
Human MSC are tissue stem cells that show multiple biological effects. At the present, how BM-MSC exert their effects are not fully understood.
In this study, a novel cell-cell communication mediator, extraxellular vesicles (EV), were examined in the involvement of BM-MSC-mediated biological effects.

overall_design: Human BM samples from healthy adult volunteers were purchased from AllCells (Emeryville, CA, USA). Human BM-MSC were isolated according to our previously published methods (Yao H, Stem Cells 2014;32:2245). EV were isolated from culture supernatant according to the literature with some modifications. NHDF purchased from LONZA (Barzel, Switzerland) were used as a control.

first: Sumie

last: Fujii

first: Yasuo

last: Miura


title: Fgf8 signaling alters the osteogenic cell fate in anterior hard palate

city: New Orleans

first: Yiping

last: Chen

state: LA

address: 6400 Freret

department: CMB

institute: Tulane University

summary: FGF signaling has been implicated in the regulation of osteogenesis in both intramembranous and endochondral ossification. In the developing palate, the anterior bony palate forms by direct differentiation of cranial neural crest-derived mesenchymal cells, but the signals that regulate osteogenic cell fate remains unclear. In the present study, we present evidence that locally activated FGF8 signaling in the anterior palate leads to complete bone loss of the palatine process of the maxilla (ma) and ectopic cartilage formation. This aberrant developmental process was accompanied by significantly elevated level of cell proliferation, which contributes to abnormally thickened ma, and complete inhibition of Osterix expression, which accounts for the lack of bone formation. Consistent with the phenotype, RNA-Sequencing (RNA-Seq) analysis further demonstrated that augmented FGF8 signaling downregulated genes involved in ossification, biomineral tissue development, and bone mineralization, but upregulated genes involved in cell proliferation, cartilage development, and cell fate commitment. Expression validation of selected genes supported the RNA-Seq results. We conclude that FGF signaling functions as a negative regulator of osteogenic fate but promotes chondrogenesis of cranial neural crest cell-derived mesenchyme in the hard palate, which will have implication in directed differentiation of precursor cells for clinical application.

overall_design: Examination of mRNA level in E14.5 and E16.5 anterior hard palatal tissues from control and Shox2-Cre; R26R-Fgf8 mutant.

first: Zhen

last: Huang

first: Jue

last: Xu

first: YiPing


title: Oxidation treated small RNA-seq for studying roles of chicken piRNAs in germ cell development

city: Taipei City

first: Shau-Ping

last: Lin

address: No. 81, Chang-Xing St.

department: Institute of Biotechnology

country: Taiwan

institute: National Taiwan University

summary: We adapted oxidation treatment for the identification of methylated small RNAs, which is an identifiable feature for piRNAs in animal kingdom. Upon obtaining piRNA candidates at blastodermal cells, E7 cultured primordial germ cells (PGCs), E11 gonads, and E14 gonads, we are able to compare and contrast PIWI/piRNA pathway regulation in different germ cell development stages, that include pre-migratory PGCs, PGCs, pro-spermatogonia, and spermatogonia. We found dramatic changes in piRNA features. include length distribution, secondary piRNA features, and genomic association between blastodermal cell piRNAs and embryonic gonadal piRNAs. Such observation reflect stage-dependent transcriptions in piRNA clusters and also imply stage-depndent transcriptional regulation.

overall_design: Small RNA isolated from chicken blastodermal cells, cultured E7 primordial germ cells, E11 male gonads, and E14 male gonads. Periodate oxidation treatments are performed prior small RNA library construction. Total RNA isolated from chicken blastodermal cells, E11 male gonads, and E14 male gonads.

first: Yen-Tzu

last: Tseng

first: Kai-Wei

last: Chang


title: B-cell activating factor (BAFF) stimulation of Burkitt Lymphoma cell line

first: Alexander

last: Wolff


title: Comparison of rectal patient data separated by their event of developing distant metastasis [Agilent]

summary: The rectal cancer patient data set consists of 10 patients from a clinical study at the Surgery department of the University Medical Center Göttingen collected over a longer time. Patients were chosen based on the follow-up time and development of a distant metastasis. First a balanced sample size of five versus five patients with and without  a metastatic event was choosen. This needed to be changed to six versus four.

overall_design: Two conditions of  rectal cancer patient data separates by the event of distant metastasis:  1. good prognosis, no event (4 samples),  2. bad prognosis, event (6 samples)

first: Michaela

last: Bayerlová

first: Dieter

last: Kube

first: Jochen

last: Gaedcke

first: Tim

last: Beißbarth


title: Global expression of sebacous gland carcinoma [mRNA]

city: Whitechapel

first: John

last: Bladen

address: 4 Newark Street

department: Blizard Institute

country: United Kingdom

institute: QMUL

summary:
Samples were taken from patients undergoing cancer excision for pagetoid (wide) sebaceous gland carcinoma (SGC) and different individuals undergoing excision for nodular (local) SGC.
Diifferent individuals who did not have cancer as Control samples, specifically their tarsal plate, were also taken.

overall_design:
Pagetoid SGC vs Nodular SGC vs normal eyelid control.

Labeling, hybridization and scanning carried out at UCL Genomics, UCL GOS Institute of Child Health, 30 Guilford Street, London WC1N 1EH

first: Jun

last: Wang

first: Ajanthah

last: Sangaralingam


title: Soluble Neuregulin1 is a negative regulator of myelination

city: Orbassano

first: Elio

last: Grazio

address: Department of Clinical and Biological Sciences, University of Turin, Regione Gonzole 10

country: Italy

institute: University of Turin

summary: Peripheral nerves are characterized by the ability to regenerate after injury. The activity of Schwann cells is fundamental for all steps of peripheral nerve regeneration: immediately after injury they de-differentiate, remove myelin debris, proliferate and repopulate the injured nerve. Neuregulin1 (NRG1) is a factor strongly up-regulated and released by Schwann cells immediately after nerve injury, known to play an important role for their de-differentiation, proliferation and survival. Nevertheless, up to now, the global analysis of the genes regulated by NRG1 was not performed. For this reason, we planned a deep RNA sequencing to generate a transcriptome database and identify all the genes regulated following stimulation of primary adult rat Schwann cells with soluble recombinant NRG1. Interestingly, the gene ontology analysis of the transcriptome shows that NRG1 regulates genes belonging to categories strongly regulated in the peripheral nerve immediately following injury. In particular, NRG1 strongly inhibits the expression of genes involved in myelination and in glial cell differentiation, suggesting that NRG1 plays a fundamental role in the de-differentiation (or “trans-differentiation”) process of Schwann cells from a myelinating to a repair phenotype. Moreover, NRG1 inhibits genes involved in the apoptotic process, therefore promoting cell survival, and up-regulates genes positively regulating the ribosomal RNA processing, thus suggesting that NRG1 actively stimulates new protein expression.  This transcriptome analysis demonstrates that NRG1, which is strongly up-regulated immediately after injury, drives the expression of many important genes, thus playing a major role in the regeneration process.

overall_design: Examination of genes regulated in Schwann cells after 6 hour stimulation with 10nM soluble Neuregulin1beta1

first: Marwa

last: El Soury

first: Benedetta

middle: E

last: Fornasari

first: Michela

last: Morano

first: Giulia

last: Ronchi

first: Danny

last: Incarnato

first: Mario

last: Giacobini

first: Stefano

last: Geuna

first: Paolo

last: Provero

first: Giovanna

last: Gambarotta


title: Comparison of rectal patient data separated by their event of developing distant metastasis

first: Alexander

last: Wolff


title: Transcriptional regulation mediated by H2A.Z via ANP32e-dependent inhibition of protein phosphatase 2A

city: Newark

first: Danish

last: Sayed

state: NJ

address: 185 south orange avenue

department: CBMM

institute: Rutgers-NJMS

summary: The mechanisms that regulate H2A.Z and its requirement for transcription in differentiated mammalian cells remains ambiguous. In this study, we identified the interaction between the C-terminus of ANP32e and N-terminus of H2A.Z in a yeast two-hybrid screen. Knockdown of ANP32e resulted in proteasomal degradation and nuclear depletion of H2A.Z or of a chimeric green florescence protein fused to its N-terminus. This effect was reversed by inhibition of protein phosphatase 2A (PP2A) and, conversely, reproduced by overexpression of its catalytic subunit.  Accordingly, knockdown of ANP32e inhibited phosphorylation of H2A.Z, whereas a mutation of serine-9 proved its requirement for both the protein’s stability and nuclear localization, as did knockdown of the nuclear mitogen and stress-induced kinase 1. Moreover, ANP32e’s knockdown also revealed its differential requirement for cell signaling and gene expression, whereas, genome-wide binding analysis confirmed its co-localization with H2A.Z at transcription start sites, as well as, gene bodies of inducible genes. The data also suggest that H2A.Z restricts transcription, which is moderated by ANP32e after induction of transcriptional activity of inducible and housekeeping genes vs. constitutively-expressed tissue-specific genes during cellular growth. Thus, ANP32e, through inhibition of PP2A, is required for nucleosomal inclusion of H2A.Z and the regulation of gene expression.

overall_design: Methods: Hearts were extracted from from mice subjecetd to Transaortic coarctation or sham operations. The hearts were sent to Active Motif for H2Az- or Anp32e-ChIP-Seq.

first: Maha

last: Abdellatif


title: Gene expression changes after Ctcfl overexpression in undifferentiated and differentiated p19 cells.

status: Public on May 30 2018

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

summary: The two paralogous zinc finger factors CTCF and CTCFL differ in expression such that CTCF is ubiquitously expressed, whereas CTCFL is found during spermatogenesis and in some cancer types. Both factors share the highly conserved DNA binding domain and are bound to DNA sequences with an identical consensus. Here we analyzed the differential gene expression effect mediated by expression of Ctcfl in undifferentiated and differentiated p19 cell.

overall_design: p19 wt cells and p19 cells stably transfected with inducible Ctcfl expression vectors were used for RNA extraction and hybridization on Affymetrix microarrays. We analyzed gene expression in the presence/absence of Ctcfl in undifferentiated as well as as cells differentiated with 10 µM retinoic acid.

first: Rainer

last: Renkawitz

first: Philipp

last: Bergmaier


title: The RhoA guanine nucleotide exchange factor Net1 is required for PyMT mediated mammary gland tumorigenesis and metastasis

city: Houston

first: Jeffrey

last: Chang

address: 6431 Fannin St

institute: University of Texas

summary:
The Net1 RhoGEF has been implicated in invasive behavior in vitro, but its impact on tumorigenesis and metastasis in vivo has not yet been established.
We developed Net1 knockout mice and profiled the transcriptomes of the resulting tumors to assess impact on pathway activation.

overall_design: Expression profiles of breast tumors from MMTV-PyMT mice with Net1+/+ and Net1-/- genotypes.

first: Yan

last: Zuo

first: Arzu

last: Ulu

middle: T

last: Frost


title: InDePTH: Detection of upstream hub genes participating in drug-induced gene expression network development

city: Tokyo

first: Masaru

last: Koido

address: 4-6-1, Shirokanedai, Minato-ku

institute: Institute of Medical Science, The University of Tokyo

summary: It has been difficult to elucidate the structure of gene regulatory networks under anticancer drug treatment. Here, we developed an algorithm to highlight the hub genes that play a major role in creating the upstream and downstream relationships within a given set of differentially expressed genes. The directionality of the relationships between genes was defined using information from comprehensive collections of transcriptome profiles after gene knockdown and overexpression. As expected, among the drug-perturbed genes, our algorithm tended to derive plausible hub genes, such as transcription factors. Our validation experiments successfully showed the anticipated activity of certain hub gene in establishing the gene regulatory network that was associated with cell growth inhibition. Notably, giving such top priority to the hub gene was not achieved by ranking fold change in expression and by the conventional gene set enrichment analysis of drug-induced transcriptome data. Thus, our data-driven approach can facilitate to understand drug-induced gene regulatory networks for finding potential functional genes.

overall_design: Human colon cancer HT-29 cells were selected for RNA extraction and hybridization on Affymetrix microarrays. We examined the gene expression change in cells treated with MYC si-RNA.

first: Yuri

last: Tani

first: Satomi

last: Tsukahara

first: Yuka

last: Okamoto

first: Akihiro

last: Tomida


title: Sema6D reverse signaling controls lipid metabolism for macrophage polarization linking mTOR to PPARγ

status: Public on May 20 2018

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: The goal of this study is to compare downstream genes of Sema6D signaling in both M1 and M2 macrophages.

overall_design: Bone marrow derived macrophage mRNA profiles of 7 weeks of wild type (WT) and Sema6D-/- mice were stimulated by IL-4 for  24 hrs.

first: Sujin

last: Kang

first: Atsushi

last: Kumanogoh


title: Differential gene expression tools exhibit substandard performance for long non-coding RNA-sequencing data

city: Ghent

first: Celine

last: Everaert

address: De Pintelaan 185

country: Belgium

institute: University Ghent

summary: Paired End PolyA-+ RNA-sequencing of NGP cells with and without NGP treatment in 10 replicates.

overall_design: NGP cells treated with and without Nutlin

first: Jo

last: Vandesompele


title: Short-read nascent RNA sequencing from S. pombe

status: Public on May 18 2018

city: Berlin

first: Lydia

last: Herzel

address: Takustr. 6

department: Biology, Chemistry and Pharmacy

institute: Freie Universität

summary: Short-read  sequencing of nascent RNA from exponentially growing S. pombe cells was employed to quantify co-transcriptional splicing and expression levels. Nascent RNA was prepared from the yeast chromatin fraction (Carrillo Oesterreich, Preibisch, Neugebauer, Mol Cell 2010). Single-end Illumina sequencing data were generated from chromatin-associated, non-polyadenylated RNA (nascent RNA) and cytoplasmic mRNA for reference. In an experiment to test for splicing-associated gene expression changes cells were treated with 10mM Caffeine for 15minutes and nascent and mRNA-seq data were generated subsequently.

overall_design: Nascent RNA profiles were generated with short-read cDNA sequencing.

first: Karla

last: Neugebauer


title: A kinome-wide high-content siRNA screen identifies MEK5-ERK5 signaling as critical for breast cancer cell EMT and metastasis

status: Public on May 17 2018

city: Basel

first: Ravi Kiran Reddy

last: KALATHUR

state: Basel

address: Mattenstrasse 28

department: Departement Biomedizin

country: Switzerland

institute: University of Basel

summary: We have employed a high-content microscopy screen in combination with a kinome and phosphatome-wide siRNA library to identify signaling pathways underlying an EMT of murine mammary epithelial cells and breast cancer cells. This screen identified the MEK5-ERK5 axis as a critical player in TGFb-mediated EMT. Suppression of MEK5-ERK5 signaling completely prevented the morphological and molecular changes occurring during a TGFb-induced EMT and, conversely, forced highly metastatic breast cancer cells into a differentiated epithelial state. Inhibition of MEK5-ERK5 signaling also repressed breast cancer cell migration and invasion and substantially reduced lung metastasis without affecting primary tumor growth. The results suggest that the MEK5-ERK5 signaling axis plays an important role in the induction and maintenance of breast cancer cell migration and invasion and thus represents an exploitable target for the pharmacological inhibition of cancer cell metastasis.

overall_design: We performed RNA-sequencing of 3 replicates of 2 different cell lines and 2 replicates of another cell line

first: Simona

last: Pavan

first: Nathalie

last: Meyer-Schaller

first: Ravi

middle: K

last: Kalathur

first: Meera

last: Saxena

first: Gerhard

last: Christofori


title: Long-read nascent RNA sequencing from S. pombe

summary: Long-read SMRT cDNA sequencing of nascent RNA from exponentially growing S. pombe cells was employed to obtain transcription elongation and splicing information from single transcripts. Nascent RNA was prepared from the yeast chromatin fraction (Carrillo Oesterreich, Preibisch, Neugebauer, Mol Cell 2010). The nascent 3’ end was labeled with a 3’ DNA adaptor through ligation. The adaptor sequence served as template for full-length reverse transcription and double-stranded cDNA was obtained in a transcriptome-wide PCR. SMRT DNA sequencing libraries were prepared subsequently.

overall_design: Nascent RNA profiles were generated with long-read SMRT cDNA sequencing.


title: A transcriptionally und functionally distinct PD-1+ CD8+ T cell pool with predictive potential in non-small cell lung cancer treated with PD-1 blockade

first: Andreas

last: Roller

address: Grenzacherstrasse 124

institute: Roche

summary: Evidence from mouse chronic viral infection models suggests that CD8+ T cell subsets characterized by distinct expression levels of the receptor PD-1 diverge in their state of exhaustion and potential for reinvigoration by PD-1 blockade. However, it remains unknown whether T cells in human cancer adopt a similar spectrum of exhausted states based on PD-1 expression levels. We compared transcriptional, metabolic, and functional signatures of intratumoral CD8+ T lymphocyte populations with high (PD-1T), intermediate (PD-1N) and no PD-1 expression (PD-1-) from non-small cell lung cancer patients. We observed that, PD-1T T cells show a markedly different transcriptional and metabolic profile as compared to PD-1N and PD-1- lymphocytes, as well as an intrinsically high capacity for tumor recognition. Furthermore, while PD-1T lymphocytes are impaired in classical effector cytokine production, they produce CXCL13 that mediates immune cell recruitment to tertiary lymphoid structures. Strikingly, the presence of PD-1T cells was strongly predictive for both response and survival in a small cohort of non-small cell lung cancer patients treated with PD-1 blockade. The characterization of a distinct state of tumor-reactive, PD-1 bright lymphocytes in human cancer, which only partially resembles that seen in chronic infection, provides novel potential avenues for therapeutic intervention.

overall_design: Intratumoral CD8+ T cells from 11 non-small cell lung cancer patients that were sub-sorted into PD1-high (PD-1T), PD1-intermediate (PD-1N) and PD1-negative (PD-1-) cells, were sequenced using Illumina HiSeq4000. In addition, peripheral blood effector memory T cells from 4 healthy donors were sequenced using Illumina HiSeq4000.

first: Daniela

last: Thommen

first: Viktor

last: Koelzer

first: Petra

last: Herzig

first: Marcel

last: Trefny

first: Sarah

last: Dimeloe

first: Anna

last: Kiialainen

first: Jonathan

last: Hanhart

first: Catherine

last: Schill

first: Christoph

last: Hess

first: Spasenija

last: Prince

first: Mark

last: Wiese

first: Didier

last: Lardinois

first: Ping-Chih

last: Ho

first: Christian

last: Klein

first: Vaios

last: Karanikas

first: Kirsten

last: Mertz

first: Ton

last: Schumacher

first: Alfred

last: Zippelius


title: Long-read sequencing of nascent RNA in S. pombe reveals coupling among RNA processing events

first: Lydia

last: Herzel

summary:
Splicing and expression profiling of nascent and mRNA by RNA sequencing
This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Inherited DNA methylation primes the establishment of accessible chromatin during genome activation

status: Public on May 16 2018

city: Shanghai

first: Yong

last: Zhang

address: No. 1239, Siping Road

institute: Tongji University

summary: For animals, epigenetic modifications can be globally or partially inherited from gametes after fertilization, but the mechanism underlying how the inherited epigenetic signatures affect transcriptional regulation during zygotic genome activation (ZGA) remains poorly understood. Here, we performed genome-wide profiling of chromatin accessibility during zebrafish ZGA, which is closely related to zygotic transcriptional regulation. The locations of the accessible chromatin at promoters were precisely primed by the enrichment of unmethylated CpGs that were fully inherited from gametes. On the other hand, distal regions with high methylation levels that were inherited from the sperm facilitated the binding of DNA methylation-preferred transcription factors, such as pou5f3 and nanog, which contributed to the establishment of accessible chromatin at these loci. Our results demonstrate a model whereby inherited DNA methylation signatures from gametes prime the establishment of accessible chromatin during zebrafish ZGA through two distinct mechanisms.

overall_design: ATAC-seq to generate accessible chromatins for wild type in five stages of zebrafish development; ATAC-seq for knock down or mRNA rescue at oblong stage; two or three replicates for each sample.

first: Guifen

last: Liu

first: Wen

last: Wang

first: Shengen

last: Hu

first: Xiangxiu


title: Remote memory and cortical synaptic plasticity require neuronal CCCTC-binding factor (CTCF), a central organizer of 3D chromatin architecture

city: Seoul

first: Shim

last: Kyuwon

address: 1, Gwanak-ro,Gwanak-gu

department: Biological Sciences

country: South Korea

institute: Seoul National University

summary: Molecular mechanism of long-term memory has been extensively studied in the context of hippocampus-dependent recent memory examined within several days; however, months-old remote memory maintained in the cortex for long-term has not much been investigated at molecular levels yet. Various epigenetic mechanisms are known to be important for long-term memory, but how 3D chromatin architecture and its regulator molecules contribute to neuronal plasticity and memory consolidation are still largely unknown. To assess memory upon perturbation of 3D chromatin structure, we chose CCCTC-binding factor (CTCF), a seven-zinc finger protein well known for its role as a transcription factor and a chromatin regulator, and created the conditional knockout (cKO) mice, in which CTCF is lost in neurons during adulthood. Our CTCF cKO mice showed normal recent memory in contextual fear conditioning and spatial water maze task. However, they showed remarkable impairments in remote memory in both tasks. Underlying the remote memory-specific phenotypes, we found that loss of CTCF disrupts cortical long-term potentiation (LTP) but not hippocampal LTP. Through RNA-sequencing, we found that CTCF KD cultured cortical neurons have altered the expression of hundreds of genes, some of which we uncovered to be regulated by neuronal activity. These results suggest that remote memory storage in the cortex requires CTCF-mediated chromatin regulation in neurons while recent memory formation in the hippocampus does not.

overall_design: Primary mouse cortical culture with CTCF knockdown(experimental group) and lacZ knockdown(control group) using adeno-associated virus. Gene expression profile of shCTCF and shLAC were compared

first: Somi

last: Kim

first: Nam-Kyung

last: Yu

first: Ji-il

last: Ki

first: Kyu-Won

last: Shim

first: Myung

middle: W

first: Dong

last: Choi

first: Seung-Woo

last: Lee

first: Ja

first: Jae-Hyung

first: Bong-Kiun

last: Kaang


title: TMPRSS2-ERG suppresses PTEN/TP53 alteration-induced cancer lineage plasticity

city: San Antonio

first: Zhenqing

last: Ye

state: TX

address: 8403 Floyd Curl Dr

department: 6Department of Population Health Sciences

institute: UT Health San Antonio

summary: Lineage plasticity is a major mechanism driving prostate cancer progression and antiandrogen therapy resistance. Deletions or mutations in phosphatase and tensin homolog (PTEN) and TP53 tumor suppressor genes have been linked to lineage plasticity in prostate cancer. Fusion-driven overexpression of the E-twenty-six transformation specific (ETS)-related gene (ERG), encoding an oncogenic transcription factor, is observed in approximately 50% of all prostate cancers, yet its role in prostate cell lineage determination remains elusive. Here we demonstrate that transgenic expression of prostate cancer-associated ERG blocks Pten and Trp53 mutation-induced decreased expression of Ar and its downstream target genes and loss of luminal epithelial cell identity in the mouse prostate. Integrative analyses of ERG chromatin-immunoprecipitation sequencing (ChIP-seq) and transcriptome data show that ERG suppresses expression of a subset of cell cycle-promoting genes and RB phosphorylation, which in turn causes repression of E2F1-mediated expression of non-epithelial lineage genes. Xenograft studies show that PTEN/TP53 double mutated prostate tumors are responsive to the cyclin-dependent kinase 4 or 6 (CDK4/6) inhibitor palbociclib, but resistant to the AR inhibitor enzalutamide, while ERG/PTEN/TP53 triple-mutated prostate tumors behave completely opposite. Our studies identify ERG and the repressed cell cycle gene signature as intrinsic inhibitors of PTEN/TP53 double mutation-elicited lineage plasticity in prostate cancer. Our findings also suggest that ERG fusion can be utilized as a biomarker to guide the treatment of PTEN/TP53-mutated, RB1-intact prostate cancer with either antiandrogen or anti-CDK4/6 therapies.

overall_design: Prostate tissue from mice with 1) prostate specific PTEN deletion, p53 R172H mutation with loss of heterozygosity, or 2) prostate specific PTEN deletion, p53 R172H mutation with loss of heterozygosity and transgenic ERG expression were harvested at 4-5 months. RNA was isolated from tissue and RNA-seq experiments were then performed for both genotype samples in triplicates. Differentially expressed genes were identified by comparing genotype #1 and genotype #2.

first: Alexandra

last: Blee

first: Liguo

first: Haojie

last: Huang


title: Genome-wide maps of histone modifications in WT, Dnmt3a-/- and Tet1-/- J1 ES cells.

city: seattle

first: xueqiu

last: lin

state: wa

address: 1100 Fairview Ave N

institute: FRED HUTCHINSON CANCER CENTER

summary: Using ChIP-seq to assess changes of histone modifications in response to Dnmt3a or Tet1 deficiency.

overall_design: Examination of H3K4me3 and H3K27me3 in WT, Dnmt3a-/- and Tet1-/- ES cells.

first: Sean

middle: M

last: Cullen

first: Xueqiu

last: Lin

first: Tianpeng

last: Gu

first: Wei

last: Li

first: Margaret

last: Goodell


first: Daisuke

last: Okuzaki

summary:
Purpose: The goal of this study is to compare downstream genes of Sema6D signaling in LPS plus IFNg stimulated macrophages.
Methods: Bone marrow derived macrophage mRNA profiles of 7 weeks of wild type (WT) and Sema6D-/- mice were stimulated by LPS for 4 hrs.
Results: According to this comparison, we found that 550 genes were downregulated in Sema6D-/- macrophages than WT macrophages in response to LPS.
Conclusions: Our study represents 62 genes were supressed in both M1 and M2 Sema6D-/- macrophage than WT macrophages, suggesting of Sema6D reverse sigaling genes.

overall_design: Bone marrow derived macrophage mRNA profiles of 7 weeks of wild type (WT) and Sema6D-/- mice were stimulated by LPS for 4 hrs, then isolated total RNA by RNeasy kit.

first: Sujin

last: Kang

first: Atsushi

last: Kumanogoh


title: RNA expression profiles from HUVECs overexpressing adenovirally delivered HIF1a and HIF2a proteins

city: Kuopio

first: Minna

middle: U

last: Kaikkonen

department: A.I. Virtanen Institute, Department of Biotechnology and Molecular Medicine

country: Finland

institute: University of Eastern Finland

summary: RNA-Seq analysis was performed from human umbilical vein endothelial cells exposed to constitutively active HIF1a and HIF2a overexpression

first: Nicholas

last: Downes


title: In vivo reprogramming drives Kras-induced cancer development [expression]

first: Yasuhiro

last: Yamada

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

department: Department of Molecular Pathology

institute: University of Tokyo

summary: Accumulation of genetic mutations is thought to be a primary cause of cancer. However, a set of genetic mutations sufficient for cancer development remains unclear in most cancers, including pancreatic cancer. Here, we examined the effect of in vivo reprogramming on Kras-induced cancer development. We first demonstrate that Kras and p53 mutations are insufficient to induce activation of ERK signaling and cancer development in the pancreas. We next show that short transient expression of reprogramming factors (1-3 days) in pancreatic acinar cells results in repression of acinar cell enhancers and reversible loss of acinar cell properties. Notably, the transient expression of reprogramming factors in Kras mutant mice is sufficient to induce robust and persistent activation of ERK signaling in acinar cells and rapid formation of pancreatic ductal adenocarcinoma (PDAC). In contrast, forced expression of acinar cell-related transcription factors inhibits pancreatitis-induced activation of ERK signaling and development of precancerous lesions in Kras-mutated acinar cells.

overall_design: Analyzing gene expression profiles in OSKM induced pancreas and stomach

first: Takuya

last: Yamamoto


title: A PAX5-OCT4-PRDM1 Developmental Switch Specifies Human Primordial Germ Cells

city: Bozeman

first: Fang

last: Fang

state: Montana

address: CBB Room 103

department: Cell Biology

institute: Montana State University

summary: Dysregulation of genetic pathways during germ cell development leads to infertility and tumorigenesis. Here, we used high throughput analyses in bona fide human primordial germ cells (hPGCs) to probe the genetics of human germ cell specification and differentiation and uncover redistribution of OCT4 protein occupancy relative to human embryonic stem cells (hESCs).  We demonstrate that the developmental programs from pluripotent stem cell to germ cell formation and differentiation are driven by switching partners with OCT4 protein from SOX2 to PAX5 and PRDM1. Genetic gain- and loss-of-function studies reveal that PAX5 encodes a novel and critical regulator of human germ cell development. Moreover, analysis of epistasis indicates that PAX5 acts upstream, binding to enhancers of OCT4 and PRDM1, to regulate expression during differentiation.  The PAX5-OCT4-PRDM1 proteins form a core transcriptional network that activates germline and represses somatic genetic programs. Broadly, these findings also illustrate the power of combined human gene editing, cell differentiation and engraftment for directly probing the genetics of human developmental stages that have historically been difficult to study.

overall_design: Examination of transcription factor binding in 2 cell types.

first: Renee

last: Reijo Pera


title: Effect of monocyte- and osteoclast-derived extracellular vesicles on adipose tissue-derived mesenchymal stem/stromal cells

city: Helsinki

first: Arjen

middle: WH

last: Gebraad

address: Haartmaninkatu 8, PO box 63

department: Department of Oral and Maxillofacial Diseases

institute: University of Helsinki

summary: Intercellular communication is essential in bone remodelling to ensure that new bone is formed with only temporary bone loss. Monocytes and osteoclasts actively take part in controlling bone remodelling by providing signals that promote osteogenic differentiation of mesenchymal stem/stromal cells (MSCs). Extracellular vesicles (EVs) have attracted attention as regulators of bone remodelling. EVs facilitate intercellular communication by transferring a complex cargo of biologically active molecules to target cells. In the present study, we evaluated the potency of EVs from monocytes and osteoclasts to induce a lineage-specific response in MSCs. We analysed gene expression and protein secretion by both adipose tissue-derived MSCs and bone marrow-derived MSCs after stimulation with EVs from lipopolysaccharide-activated primary human monocytes and (mineral-resorbing) osteoclasts. Isolated EVs were enriched in exosomes (EVs of endosomal origin) and were free of cell debris. Monocyte- and osteoclast-derived EVs were taken up by adipose tissue-derived MSCs. EVs from activated monocytespromoted the secretion of cytokines by MSCs, which may represent an immunomodulatory mechanism. Monocyte-derived EVs also upregulated the expression of genes encoding for matrix metalloproteinases. Therefore, we hypothesize that monocytes facilitate tissue remodelling through EV-mediated signalling. We did not observe a significant effect of osteoclast-derived EVs on gene expression or protein secretion in MSCs. EV-mediated signalling might represent an additional mode of cell-cell signalling during the transition from injury and inflammation to bone regeneration and play an important role in the coupling between bone resorption and bone formation. This article is protected by copyright. All rights reserved.

overall_design:
Microarray analysis was performed on total RNA isolated from adipose tissue-derived mesenchymal stem/stromal cells (AT-MSC) obtained from water-assisted lipotransfer liposuction aspirates from 5 female donors. AT-MSCs were cultured in maintenance medium (MM) containing 10% fetal bovine serum depleted of extracellular vesicles (EVs), supplemented with:
1) EVs isolated from the conditioned medium of CD14+ monocytes obtained from 2 human buffy coats, activated with 10 ng/ml lipolysaccharide (MC-EVs)
2) EVs isolated from the conditioned medium of osteoclasts cultured on tissue culture polystyrene, differentiated from the CD14+ monocytes by M-CSF/RANK-L stimulation (OC TCPS-EVs)
3) EVs isolated from the conditioned medium of osteoclasts, activated for mineral resorption by culture on hydroxyapatite coatings, differentiated from the CD14+ monocytes by M-CSF/RANK-L stimulation (OC HA-EVs)
4) 50 µM L-Ascorbic acid 2-phosphate, 10 µM beta-glycerophosphate disodium salt hydrate, 100 nM dexamethasone (osteogenic differentiation medium, ODM)
EV-depleted MM without supplementation was used as the reference condition.
The RNA was pooled into 3 distinct pools per condition, assembled from 5 donor replicates. The starting amount of total RNA was 100 ng. Complementary DNA (cDNA) was generated using GeneChip®WT Plus Reagent Kit (Affymetrix).  Micorarray analysis was performed using Clariom D Human Arrays (Affymetrix).

first: Roman

last: Kornilov

first: Sippy

last: Kaur

first: Susanna

last: Miettinen

first: Suvi

last: Haimi

first: Hilkka

last: Peltoniemi

first: Bettina

middle: I

last: Mannerström

first: Riitta

last: Seppänen-Kaijansinkko


title: Transcriptional Profiling Reveals Extraordinary Diversity Among Skeletal Muscle Tissues

city: Saint Louis

first: Michael

last: Hughes

state: MO

address: 425 South Euclid Avenue

department: Internal Medicine

institute: Washington University

summary: Skeletal muscles are a diverse family of highly specialized tissues that perform a wide array of physiological activities and maintain whole-body glucose metabolism and energy homeostasis. Functional diversity is a distinctive feature of muscle tissues, which demonstrate remarkable variability in their speed of contraction, metabolic profile, resistance to fatigue, and regenerative capacity.  Unsurprisingly, many disorders of skeletal muscle afflict a remarkably specific subset of tissues, including muscular dystrophies, cancer cachexia, aging sarcopenia, and amyotrophic lateral sclerosis. Taken as a whole, these observations indicate that specific genetic programs establish and maintain physiological specialization of muscle tissues. Elucidating these genetic programs is essential to understanding muscle specialization and propensity for disease. Nevertheless, most global profiling studies performed to-date have not directly addressed intrinsic variability between different muscle tissues. This gap in the literature is particularly glaring for more sophisticated mechanisms of gene expression regulation such as circadian control, post-transcriptional regulation and non-coding RNA expression, despite their well-established roles in many disease mechanisms.   In an effort to understand the variability present within specific skeletal muscles with respect to gene expression, our lab has performed RNA-Seq on a variety of skeletal muscle tissues.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: 126 samples, 17 mouse tissues (all from males), 2 female rat tissues, 2 male rat tissues.  Six replicates for each tissue; each replicate is 3 individual samples pooled.  For mouse tissues, 3 are smooth muscle, 3 are cardiac muscle and 11 are skeletal muscle.  For male & female rat samples, both tissues are skeletal.

first: Erin

last: Terry

first: Xiping

last: Zhang

first: Christy

last: Hoffmann

first: Laura

middle: D

first: Scott

last: Lewis

first: Jiajia

last: Li

first: Lance

last: Riley

last: Lahens

first: Ming

last: Gong

first: Francisco

last: Andrade

first: Karyn

last: Esser


title: The role of DNMT3A and TET1 in regulating promoter epigenetic landscapes

first: xueqiu

last: lin

type: Methylation profiling by high throughput sequencing

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


title: In vivo reprogramming drives Kras-induced cancer development

first: Yasuhiro

last: Yamada


title: Differentially expressed genes between C.elegans with low physical ability and with high physical ability

city: Daegu

first: Hong Gil

last: Nam

address: Techno jungang-daero

department: Center for Plant Aging Research

institute: IBS

summary: Aging is an important risk factor for disease and is accompanied by the decline of many physiological characteristics, including physical performance. One of the most powerful tests of physical ability in elderly humans is the short physical performance battery (SPPB) (Guralnik et al., 1994), an assessment of the maximum exercise capacity of lower extremities over a short period of time. A similar metric of maximum velocity (MV) in a short period (30 s) is proposed as an equally informative measurement in C. elegans (Hahm et al., 2015). MV declines with age, correlates well with longevity, accurately reports movement ability, and importantly, is predictive of future longevity (Hahm et al., 2015). Here, we characterized the differences in gene expression between high MV group and low MV group of the same age in C. elegans. The genes related to nucleosomes and involved in regulatory processes, including transcriptional regulation (chromatin assembly, regulation of RNA metabolic process and regulation of transcription), and neuronal signaling (neurogenesis, axon guidance, and regulation of neurotransmitter levels) were up-regulated in low MV group compared to high MV group. In contrast, genes belonged to metabolic processes and mitochondria were down-regulated in low MV group compared to high MV group.

overall_design: We utilized maximum velocity (MV) assay (Hahm et al., 2015) to divide an aged population of C. elegans into groups of low and high physical ability. Worms grown in growth plates ad libitum (AL) were moved to a physical assay plate with no food on day 7-8 of adulthood to measure their MV. The locomotion of worm was recorded for 30 seconds using a stereomicroscope, a CCD camera. Recorded images were analyzed by ImageJ and wrMTrck (plugin for ImageJ: www.phage.dk/plugins). The peak locomotion velocity observed in the 30 second period was used as the MV. Worms with an MV of less than 0.22 mm/sec, which corresponds to the minimum MV at day 1 of adulthood, were regarded as low physical ability (Hahm et al., 2015), otherwise, regarded as high physical ability. The analysis was carried out with two replicates of each high MV and low MV groups.

first: Hong-Gil

first: Jeong-Hoon

last: Hahm


title: Gastrointestinal Stromal Tumor Enhancers Support a Transcription Factor Network Predictive of Clinical Outcome

city: Worcester

first: Matthew

last: Hemming

state: MA

address: 364 Plantation Street

institute: UMass Medical School


title: Selectively targeting bromodomain and extraterminal proteins for degradation as a novel anti-glioblastoma strategy [RNA-seq]

status: Public on May 15 2018

city: Singapore

first: Phillip

middle: H

last: Koeffler

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute

summary: Purpose: Characterization of mechanism and vulnerability of BET protein dependency in GBM cells.  Methods: ChIP-seq and RNA-seq were performed on GBM cells at different time points following treatment with dBET6, a novel BET protein degrader. The transcriptome responses of parental and JQ1-resistant U87 cells to JQ1 and dBET6 were compared as well.     Result: This study reveals crucial functions of BET proteins and provides the rationale and therapeutic merits of targeted degradation of BET proteins by dBET6 in GBM.

overall_design: RNA-Seq of U87 Parental and JQ1-Resistant cell lines in response to dBET6 and JQ1

first: Liang

last: Xu

first: Ye

last: Chen

first: Anand

last: Mayakonda

first: H


title: Selectively targeting bromodomain and extraterminal proteins for degradation as a novel anti-glioblastoma strategy [ChIP-seq]

overall_design: ChIP-seq of GBM cells following treatment with or without dBET6.


title: Selectively targeting bromodomain and extraterminal proteins for degradation as a novel anti-glioblastoma strategy [RNA-seq (time course)

overall_design: RNA-Seq of U87 cells in response to dBET6 at different time points; RNA-Seq of NNI24 patient-derived GBM propagating cells in response to dBET6.


title: In vivo reprogramming drives Kras-induced cancer development [ChIP-seq]

overall_design: Analyzing H3K27ac in promoter and enhancer of the pancreas of with or without OSKM induction/ Caerulein treatment

first: Hirofumi

last: Shibata

first: Tomoyo

last: Ukai

first: Takuya

last: Yamamoto


title: Selectively targeting bromodomain and extraterminal proteins for degradation as a novel anti-glioblastoma strategy NA-seq (time course)  May 15, 2018   approved  TSV


title: A systems biology approach in understanding oncogenic cooperation between TAL1 expression and PTEN deletion in T-cell acute lymphoblastic leukaemia

city: Leuven

first: Sofie

last: Demeyer

address: Herestraat 49 / bus 912

department: Center for Cancer Biology

institute: KULeuven / VIB

summary: T-cell acute lymphoblastic leukemia (T-ALL) is caused by the accumulation of multiple mutations combined with the ectopic expression of transcription factors. However, how these transcription factors cooperate with oncogenic mutations has been difficult to assess due to a lack of robust T cell model systems. Here we utilize a new ex vivo pro-T cell model to study oncogenic cooperation. Using a systems biological approach we dissect the pro-T cell signaling network driven by interleukin-7, stem cell factor (Scf) and Notch1 and identify downstream Akt, Stat, E2f and Myc genetic signaling networks. Furthermore, we demonstrate that ectopic expression of the TAL1 transcription factor and PTEN deletion are bona-fide cooperating events leading to Scf addiction and metabolic reprogramming, partially through upregulation of the lactate transporter Mct4. This ex vivo pro-T cell system is a powerful new model system to understand transforming events and the identification of new therapeutic targets in T-cell malignancies.

overall_design: This study consists of 36 samples, i.e. 3 replicates for 12 conditions. Unstimulated and GFP-empty are reference conditions.

first: Simon

last: Bornschein

first: Rocco

last: Stirparo

first: Olga

last: Gielen

first: Ellen

last: Geerdens

first: Bart

last: Ghesquiere

first: Stein

last: Aerts

first: Jan

last: Cools

first: Charles

last: de Bock


title: Expression data from C57/Bl6 Wt mice CD4+ T cells after activation with anti-CD3 plus Wt APC or OX40L-Tg APC

city: HOUSTON

first: Xiaolong

last: Zhang

state: Texas

address: 6670 Bertner Avenue, R7-211

department: Immunobiology & Transplant Research Center

institute: Houston Methodist Research Institute

summary:
OX40 is a T cell costimulatory molecule in the tumor necrosis factor receptor (TNFR) superfamily. Unlike other costimulatory molecules, OX40 is not expressed by naive T cells, but its expression is rapidly induced following T cell activation, and OX40 costimulation plays a critical role in cell survival, proliferation, and generation of memory cells.
We used microarrays to detail the global programme of gene expression of activated CD4 T cells underlying OX40 costimulation and identified distinct classes of up-regulated genes after OX40 costimulation.

overall_design: Naive CD4+ T cells (CD62LhighCD44lowFoxp3−) were sorted from C57/Bl6 Foxp3-eGFP reporter mice, and activated in vitro with soluble anti-CD3 mAb and mitomycin C-treated Wt APCs or OX40L-Tg APCs in 96-well round bottom tissue-culture plates. Forty-eight hours later, living CD4+ T cells were sorted from cultures by flow cytometry. Total RNA was extracted with RNeasy mini kit (Qiagen). Complementary DNAs (cDNAs) were then synthesized using Superscript III kits (Invitrogen), hybridization of the samples with Affymetrix mouse arrays was then performed at the Harvard Medical School Facility according to the manufacturer's protocol.

first: Xiang

last: Xiao


title: peakC: a flexible, non-parametric peak calling package for 4C and Capture-C data

status: Public on May 14 2018

city: Utrecht

first: Geert

last: Geeven

state: Utrecht

address: Uppsalalaan 8

department: Biomedical Genomics

institute: Hubrecht Institute

summary: High-resolution methods such as 4C and Capture-C enable the study of chromatin loops such as those formed between promoters and enhancers or CTCF/cohesin binding sites. An important aspect of 4C/CapC analyses is the identification of robust peaks in the data for the identification of chromatin loops. Here we present an R package for the analysis of 4C/CapC data. We generated 4C data for 10 viewpoints in 2 tissues in triplicate to test our methods. We developed a non-parametric peak caller based on rank-products. Sampling analysis shows that not read depth but template quality is the most important determinant of success in 4C experiments. By performing peak calling on single experiments we show that the peak calling results are similar to the replicate experiments, but that false positive rates are significantly reduced by performing replicates.

overall_design: 4C-seq was performed with either 3 or 6 replicates on a range of viewpoints in ES 14 embryonic stem cells (IB10) and e14.5 fetal liver cells

first: Hans

last: Teunissen

first: Wouter

last: de Laat

first: Elzo

last: de Wit


title: Genome-wide profiling of active regulatory elements in dentate gyrus of WT and MBD1 KO mice

city: Madison

first: Xinyu

last: Zhao

state: WI

address: 1500 HIGHLAND AVE, T513 Waisman Center

department: Department of Neuroscience

institute: University of Wisconsin-Madison

summary: We report the genome-wide active regulatory elements in mouse dentate gyrus with or without presence of MBD1.

overall_design: Examination of  genome-wide differential active regulatory elements in dentate gyrus of Mbd1 KO mice.

first: Yu

last: Gao

first: Brian

last: Eisinger


title: Differential expression of oral cancer cell line UM1 and UM2

city: Chicago

first: Xiaofeng

last: Zhou

state: Illinois

address: 801 S Paulina Street

institute: University of Illinois at Chicago

summary: UM1 and UM2 are paired cell lines generated from a oral cancer patient [Nakayama, et al Invas. Metast., 18 (1998), pp. 219–228].  UM1 is highly invasive and exhibits elevated metastatic potential as compared to UM2.

overall_design:
We use microarray to identify differentially expressed gene in UM1 and UM2 cells.
Cells were grown with standard procedure, and total RNA was isolated with Qiagen kit, and then hybridized to the Affymetirx arrays.

first: Anxun

last: Wang


title: Extracellular matrix remodeling regulates glucose metabolism through TXNIP destabilization

status: Public on May 12 2018

city: Los Angeles

first: William

middle: Juster

last: Sullivan

state: California

address: 354-06 BSRB, 615 Charles E. Young Drive S

department: Biological Chemistry

institute: University of California, Los Angeles

summary: The metabolic state of a cell is influenced by cell-extrinsic factors, including nutrient availability and growth factor signaling.  Here, we present extracellular matrix (ECM) remodeling as another fundamental node of cell-extrinsic metabolic regulation. Unbiased analysis of glycolytic drivers identified the hyaluronan-mediated motility receptor as among the most highly correlated with glycolysis in cancer. Confirming a mechanistic link between the ECM glycosaminoglycan hyaluronan and metabolism, treatment of both cells and xenograft tumors with hyaluronidase (HAase) triggers a robust increase in glycolysis. This is largely achieved through rapid receptor tyrosine kinase-mediated induction of mRNA decay factor ZFP36, which targets TXNIP transcripts for degradation. Since TXNIP promotes internalization of the glucose transporter GLUT1, its acute decline enriches GLUT1 at the plasma membrane. Functionally, induction of glycolysis by HAase is required for concomitant acceleration of cell migration. This interconnection between ECM remodeling and metabolism is exhibited in dynamic tissues states including tumorigenesis and embryogenesis.

overall_design:
Total RNA was extracted from LiSa-2 liposarcoma cells treated with either PBS control (24h) or bovine testicular hyaluronidase (HAase; 400ug/mL; 6h and 24h). All groups were performed in triplicate.

CEL files were analyzed directly with the GSEA software from the Broad institute: http://software.broadinstitute.org/gsea/index.jsp. Sample tables were generated from the provided CHP files for public use but were not used in the submitter's analysis.

middle: J

first: Peter

last: Mullen

first: Ernst

last: Schmid

first: Aimee

last: Flores

first: Milica

last: Momcilovic

first: Mark

middle: S

last: Sharpley

first: David

last: Jelinek

first: Andrew

last: Whiteley

first: Matthew

middle: B

last: Maxwell

first: Blake

last: Wilde

first: Utpal

last: Banerjee

first: Hilary

last: Coller

last: Shackelford

first: Daniel

last: Braas

first: Donald

last: Ayer

first: Thomas

middle: Q

last: de Aguiar Vallim

last: Lowry

first: Heather

last: Christofk


title: Wnt-signaling pathways are dysregulated in female cerebellum following an early methyl donor deficiency in a rat nutritional model

status: Public on May 11 2018

city: Vandoeuvre-lès-Nancy

first: Sebastien

last: Hergalant

address: Faculté de Médecine. 9 avenue de la forêt de Haye

department: Bioinformatics

country: France

institute: INSERM

summary: Early methyl donor –especially B9 and B12 vitamins- deficiency (MDD) is involved in birth defects and brain development retardation. Molecular mechanisms that take place in response to MDD still remain not well understood. In this study we took advantage of a rat nutritional MDD model and performed a microarray analysis on female cerebellum, in order to identify which genes and molecular pathways are disrupted in response to MDD. We found that cerebellum development is altered, with a decrease of the granular cell layer thickness in cerebellum at P21. Furthermore, we investigated the involvement of Wnt-signaling pathway –a major molecular pathway involved in neuronal development but also later in synaptic assembly and neurotransmission. We found that Wnt canonical and Ca2+ pathways are disrupted following early MDD. Notably, we identified GSK3β as a pivotal player affected by MDD, affecting synaptic assembly and signaling. These results could explain the structural brain defects previously observed in response to early MDD and identify new genes and a new molecular pathway that is affected following nutritional methyl donor deprivation.

overall_design: One month before pregnancy,  female rats were either fed with a standard diet (control - CTRL), or with a diet deficient in folate and vitamin B12 and lowered in choline (methyl donor deficiency - MDD). These diets were maintained until the offspring was weaned at postnatal day 21. Rat pups were euthanized at postnatal day 21, cerebellums were harvested and constituted biological replicates for both CTRL and MDD models.

first: Jérèmy

last: Willekens

first: Natacha

last: Dreumont

first: Sébastien


title: Fnip1 null kidney versus wildtype kidney RNAseq data

city: Seattle

first: Brian

last: Iritani

state: WA

address: 1959 NE Pacific Street

department: Comparative Medicine

institute: University of Washington

summary: This RNAseq data was generated by comparing kidney tissue from Fnip1 null mice versus Wildtype Mice

overall_design: RNA was extracted from kidney tissue from 3 independent Fnip1 null mice and 2 independent wildtype mice. Fnip1 null mice were generated by ENU mutagenesis (See Park et al., Immunity 2012)

first: Ryan

last: Centini


title: A critical role for nucleoporin 358 (Nup358) in transposon silencing and piRNA biogenesis in Drosophila

city: Charleston

first: Vamsi

last: Gangaraju

address: 173 Ashley Ave

institute: Medical University of South Carolina

overall_design: Refer to individual Series


title: Resistance to pentamidine is mediated by AdeAB, regulated by AdeRS, and influenced by growth conditions in Acinetobacter baumannii ATCC 17978

status: Public on May 13 2018

city: Adelaide

first: Felise

last: Adams

state: SA

address: Bedford Park

country: Australia

institute: Flinders University

summary: The goal of this study was to assess the role of the AdeRS two component signal transduction system in Acinetobacter baumannii ATCC 17978 and its impact on the virulence potential of this bacterial organism. Specific gene deletion strains targeting the adeRS system were generated and compared to wildtype for a number of phenotypic in vitro assays as well as transcriptomic profiling via RNA-sequencing.

overall_design: Examination of ∆adeRS mutant derivative compared to wildtype A. baumannii ATCC 17978 from bacterial cells grown in Mueller-Hinton broth which were grown to 0.6 OD600. Total RNA was isolated in triplicate samples over three biological replicates. RNA-sequencing was undertaken on pooled RNA. The overall aim was to assess the global transcriptional profile of the A. baumannii ATCC 17978  ∆adeRS two component system deletion strain in comparison to the transcriptome of wildtype A. baumannii ATCC 17978.

middle: G

first: Uwe

last: Stroeher

first: Karl

middle: A

last: Hassan

first: Shashikanth

last: Marri

first: Melissa

last: Brown


title: Recombination map of male germline cell for a single Holstein bull

city: Wuhan

first: Yang

last: Zhou

state: Hubei

address: Shizishanjie #1

department: College of animal science

institute: Huazhong Agricultural University

type:
Other
Genome variation profiling by SNP array

summary: Using Illumina® BovineHD Genotyping BeadChip assay, we applied single sperms genotyping from one single Holstein bull to preliminarily describe its recombination map. We received 56 single sperms with qualified genotype information and totally detected 1,526 autosomal crossovers.

overall_design: Sperm cells were obtained from a single Holstein bull. The active single sperms were picked up by pipetting into a reaction tube under micromanipulator. Whole genome amplification was performed according to the protocol of Single Cell Whole Genome Amplification Kit (Yikon Genomics, Shanghai, China) based on the MALBAC (Multiple Annealing and Looping Based Amplification Cycles) technology.PCR products were purified and sent to Neogen/GeneSeek (Lansing, MI, USA) for genotyping by the Illumina® BovineHD Genotyping BeadChip assay.  Heterozygous SNPs (hetSNPs) of the semen donor (the bull) were phased to two haploids (paternal and maternal) based on the genotypes of two parents. We applied the Viterbi algorithm in hidden Markov model (HMM) in R to identify crossovers in the sperm haplotype as a transition between paternal and maternal status.

first: George

middle: E

last: Liu


title: GTSF-1 is required for the formation of an RNA-dependent RNA Polymerase complex in C. elegans

city: Mainz

first: Emil

last: Karaulanov

address: Ackermannweg 4

institute: Institute of Molecular Biology

summary: In every domain of life, Argonaute proteins and their associated small RNAs regulate gene expression. Despite great conservation of Argonaute proteins throughout evolution, there are not many other conserved proteins involved in small RNA pathways. Gametocyte-specific factor 1 (Gtsf1) proteins, characterized by two tandem CHHC zinc fingers and an unstructured, acidic C-terminal tail, represent one such conserved small RNA pathway component. In fly and mouse, they are required for fertility and have been shown to interact with Piwi clade Argonautes. We identified T06A10.3 as the Caenorhabditis elegans Gtsf1 homolog and named it gtsf-1. Given its conserved nature and roles in Piwi-mediated gene silencing, we sought out to characterize GTSF-1 in the context of the small RNA pathways of C. elegans. Surprisingly, we report that GTSF-1 is not required for Piwi-mediated gene silencing. Instead, gtsf-1 mutants lack a class of endogenous small RNAs, known as 26G-RNAs, and fully phenocopy mutants lacking RRF-3, the RNA-dependent RNA Polymerase that synthesizes 26G-RNAs. Like its homologs, GTSF-1 is required for normal fertility. We show, both in vivo and in vitro, that GTSF-1 specifically and robustly interacts with RRF-3 via its tandem CHHC zinc fingers. Furthermore, we demonstrate that GTSF-1 is required for the assembly of a larger RRF-3 and DCR-1-containing complex, also known as ERIC, thereby allowing for 26G-RNA generation. Interestingly, while a GTSF-1-RRF-3 complex exists in the adult, ERIC appears to assemble primarily in embryos, suggesting that 26G-RNA biogenesis mostly occurs after fertilization. We propose that GTSF-1 homologs may similarly act to drive the assembly of larger complexes that subsequently act in small RNA production and/or in imposing small RNA-mediated silencing activities.

overall_design: Small RNA-seq profiling of wild-type and gtsf-1 mutant worms in triplicates using 3 different library preparation conditions (direct cloning, TAP or oxidation treatment).

first: Miguel

middle: V

last: Almeida

first: René

middle: F

last: Ketting


title: Effect of aging on the global gene expression profiles of mouse olfactory neuroepithelium

city: Chiba

first: Shigeyuki

last: Shichino

address: 2641, Yamasaki, Noda-shi

department: Department of Molecular regulation of Inflammatory and Immune Diseases

institute: Tokyo University of Science

summary: The olfactory system is a part of the mammalian central nervous system and is characterized by neurogenesis and replacement of degenerated neurons. Clinically, it has been reported that the elderly has a high incidence of olfactory impairment. However, the molecular mechanisms underlying aging-associated defect of olfaction have yet been unclear. To elucidate this problem, we performed micoarray analysis against murine olfactory epithelium and compared the transcriptome of them between young-adult and aged mice.

overall_design: Gene expression of olfactory epihtelium from young-adult (8 weeks of age) and aged (16 months of age) male C57BL/6 mice was measured. Each total RNA sample pooled from 5 biological replicates (two experimental replicate) was analyzed using microarray.

first: Rumi

last: Ueha

first: Satoshi

first: Kenji

last: Kondo

first: Shu

last: Kikuta

first: Hironobu

last: Nishijima

first: Francis

last: Wm Shand

first: Kouji

last: Matsushima

first: Tatsuya

last: Yamasoba


title: Microarray gene-expression data to validate a 17-gene biomarker obtained from excessive meta-analysis to test its PDAC specificity in the presence of pancreatitis tissues.

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

summary: Clinical signs and radiographic findings of PDAC and pancreatitis are often indistinguishable, highlighting the need of a PDAC biomarker to be insensitive to pancreatitis. Therefore we validated a biomarker signature of 17-genes in this gene expression data containing PDAC, non-tumor pancreatic and pancreatitis of fresh-frozen and formalin-fixed paraffin-embedded tissues.

overall_design: Total RNA was obtained from 3 FF and 1 FFPE non-tumor pancreatic, 3 FF and 3 FFPE PDAC,  4 FFPE non-tumor pancreatic, and 10 FFPE pancreatitis tissues. Data was quantile normalized and manufactor IDs were matched to unique Entrez IDs using the probe with the largest interquartile range. Subsequently, classification performance of the biomarker genes were tested by distinguishing between PDAC and non-tumor (adjacent pancreas and pancreatitis) tissues.

first: Melanie

last: Boerries

first: Hagen

last: Klett


title: A conserved RNA-binding protein Celf1 controls cell differentiation in vertebrate eye development

city: Newark

first: Deepti

last: Anand

state: Delaware

address: 351 Wolf Hall, University of Delaware

department: Biological Sciences

institute: University of Delaware

summary: Celf1 germline or conditional deletion mouse mutants exhibit fully penetrant lens defects including cataract. To gain insight into gene expression changes underlying these lens defects, microarray comparison was performed for lenses obtained from wild-type and Celf1 conditional deletion mutant mice. At ±2.0 fold-change cut-off (p<0.05), 102 genes were identified to be differentially expressed in Celf1 conditional mutant lenses

overall_design: Microarray comparison of lenses from mixed background (C57BL/6J, FVB) wild-type and mutant (Celf1cKO/lacZKI; Pax6GFPCre) mice was performed

first: Salil

last: Lachke

first: Atul

last: Kakrana


title: The transcription factor Bhlhe40 is a switch of inflammatory versus anti-inflammatory Th1 cell fate determination

status: Public on May 10 2018

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

summary: Type 1 T helper (Th1) cells play a critical role in host defense against intracellular pathogens and in autoimmune diseases by producing a key inflammatory cytokine interferon (IFN)-γ; some Th1 cells can also be anti-inflammatory through producing IL-10. However, the molecular switch for regulating the differentiation of inflammatory and anti-inflammatory Th1 cells is still elusive. Here we show that Bhlhe40-deficient CD4 Th1 cells produced less IFN-γ but substantially more IL-10 than wild type Th1 cells. Bhlhe40-mediated IFN-γ production was independent of transcription factor T-bet regulation. Mice with conditional deletion of Bhlhe40 in T cells succumbed to Toxoplasma gondii infection and blockage of IL-10 signaling during infection rescued these mice from death.  Thus, our results demonstrate that transcription factor Bhlhe40 is a molecular switch for determining the fate of inflammatory and anti-inflammatory Th1 cells.

overall_design: RNA-Seq analysis of gene expression in WT stimulated TH1 cells and in Bhlhe40 conditional KO stimulated TH1 mice.

first: Yu

last: Fang

first: Sharma

last: Suveena

first: Jankovic

last: Dragana

first: Gurram

last: Rama Krishna

first: Su

last: Pan

first: Hu

last: Gangqing

first: Li

last: Rao

first: Rieder

last: Sadiye

first: Zhao

last: Keji

first: Sun

last: Bing

first: Zhu

last: Jinfang


title: Sp8 and Sp9 Coordinately Promote Striatal Medium Spiny Neuron Production through Activating Six3 Expression

city: Shanghai

first: Qifei

last: Liang

address: 138 Yi Xue Yuan Road

institute: Fudan University

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


title: Gene expression analysis in PKP2mut cardiomyocytes

city: Munich

first: Gianluca

last: Santamaria

state: Germany

address: Ismaninger Strasse 22

department: Department of Medicine I

institute: Klinikum rechts der Isar – Technical University Munich

summary: In the present study, genome-wide expression profiling was carried out to identify genes dysregulated in PKP2mut-iPSCs-derived cardiomyocytes.

overall_design: mRNA from 3-month-old wild-type and PKP2mut iPSC-derived cardiomyocytes from 3 independent differentiation experiments was isolated, pooled and hybridized to the Agilent SurePrint G3 Human GE Microarray chips.

first: Harold

last: Ayetey

first: Alessandra

last: Moretti


title: Microarray gene-expression data to identify a robust biomarker signature in PDAC and validate it in formalin-fixed paraffin-embedded tissue material.

first: Hauke

last: Busch

summary: To identify a robust diagnostic biomarker for PDAC, we used FF samples in a meta-analysis with five other publicly available data sets. The identified biomarker genes were subsequently validated in the remaining samples to test the detection performance of FFPE samples.

overall_design: Total RNA was obtained from 31 fresh-frozen tissue samples; 18 with pancreatic tumor and 13 non-tumor panreatic tissue samples. Furthermore, total RNA was extracted from 12 formalin-fixed paraffin-embedded tissue samples; 6 with pancreatic tumor and 6 non-tumor pancreatic tissues. Gene expression was analyzed using the Illumina HumanHT-12v4 expression beadchip. Data was quantile normalized and manufactor IDs were matched to unique Entrez IDs using the probe with the largest interquartile range. Subsequently, data was split into fresh-frozen samples that were used to identify a robust biomarker gene signature for PDAC, and FFPE samples that were used to validate the biomarker signature in FFPE material.

first: Melanie

last: Boerries

first: Hagen

last: Klett


title: Utility and validation in placental DNA methylation profiling of preeclampsia and intrauterine growth restriction [discovery cohort]

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

country: Canada

institute: University of British Columbia

type: Methylation profiling by genome tiling array

summary:
Preeclampsia (PE), a maternal hypertensive disorder, and intrauterine growth restriction (IUGR), pathologically poor fetal growth, often co-occur and are associated with placental insufficiency (PI). PI is more common in early-onset PE (EOPE) than late-onset PE (LOPE). However, the relationship between these disorders remains unclear. While DNA methylation (DNAm) alterations have been previously identified in PE and IUGR, few studies validated the findings in an independent cohort. This study aims to identify altered DNAm in EOPE, LOPE, and normotensive IUGR, validate these alterations, and use the findings to better understand the relationships between these related disorders.

Placental samples from a discovery cohort (43 controls, 22 EOPE, 18 LOPE, 11 IUGR) and validation cohort (15 controls, 22 EOPE, 11 LOPE) were evaluated using the Illumina HumanMethylation450 array. To minimize gestational age (GA) effects, EOPE samples were compared to pre-term controls (GA <37 weeks), while LOPE and IUGR were compared to term controls (GA >37 weeks). Linear regression identified 1703 differentially methylated (DM) sites (FDR<0.05, ∆β>0.1) in EOPE, 5 in LOPE, and 0 in IUGR. Of the 1703 sites associated with EOPE in the discovery cohort, 599 were validated in the second cohort. These sites cluster samples from both cohorts into 3 distinct methylation clusters. Interestingly, LOPE samples diagnosed between 34-36 weeks and had co-occurring IUGR clustered with the EOPE methylation cluster. DNAm profiling may provide an independent tool to refine clinical diagnoses into subgroups with more uniform pathology. The challenges in reproducing genome-wide DNAm studies are also discussed.

DNA methylation data of the validation cohort can be found at GSE98224.

overall_design: Placental samples from a discovery cohort (43 controls, 22 EOPE, 18 LOPE, 11 IUGR and 8 techical replicates) were evaluated using the Illumina HumanMethylation450 array.  To minimize gestational age (GA) effects, EOPE samples were compared to pre-term controls (GA <37 weeks), while LOPE and IUGR were compared to term controls (GA >37 weeks).

first: Samantha

middle: L

last: Wilson

first: Katherine

last: Leavey

first: Brian

last: Cox

middle: P


title: Microarray analysis of adipocyte co-culture with SKOv3ip1 cells

status: Public on May 09 2018

first: Andras

last: Ladanyi

address: 820 S. Wood St.

department: OB/GYN

institute: UIC

summary: Analysis of gene expression in SKOv3ip1 cells with and without co-culture of human primary adipocytes. Hypothesis is that adipocyte co-culure changes lipid metabolism pathways in ovarian cancer cells.

overall_design: SKOV3ip1 ovarian cancer cells were cultured alone or with human primary adipocytes that were extracted from healthy omental tissue for 16hrs. Total RNA was collected and gene expression analyzed with Illumina microarray.

first: Lengyel

last: Lab


title: Intact interleukin-10 receptor signaling protects from hippocampal damage elicited by experimental neurotropic virus infection of SJL mice

city: Braunschweig

first: Michael

last: Beckstette

state: Lower Saxony

address: Inhoffenstrase 7

department: Molecular Infection Biology

institute: Helmholtz Centre for Infection Research

summary:
Differential interleukin-10 (IL-10) expression is suspected to contribute to strain specific differences in the course of Theiler's murine encephalomyelitis virus infection in mice. To determine the expression kinetics of IL-10 and related genes, RNA-based next generation sequencing (RNA-seq) was performed with brain cells obtained from infected SJL mice.
Methods: 5-week old, female SJL mice were infected with the BeAn strain of TMEV and sacrificed 4, 7 or 14 days post infection (dpi). RNA was isolated from transversal sections of brain tissue at the level of the hippocampus. RNA-seq was performed on an Illumina HiSeq2500 system. Genes involved in Interleukin-10 (IL-10) signalling were analyzed and transcript levels were compared during the course of infection.
Results: A significant upregulation of Interleukin-10 (Il10), Interleukin-10 receptor subunit α (ll10rα), Janus kinase 1 (Jak1) and signal transducer and activator of transcription 3 (Stat3) was detected 7 days post infection (dpi) compared to 4 dpi. Same genes showed a significant downregulation at 14 dpi compared to 7 dpi. Suppressor of cytokine signaling 3 (Socs3) was significantly downregulated at 14 dpi compared to 7 dpi. No differences were detected between transcript levels of interleukin-10 receptor subunit β (Il10rβ) and tyrosine kinase 2 (Tyk2).
Conclusion: IL-10 pathway gene expression is transiently upregulated following TMEV-infection of SJL-mice.

overall_design: RNA-seq of brain tissue derived from TMEV-infected SJL mice. 3 different timepoints post infection with 5 animals per timepoint.

first: Ann-Kathrin

last: Uhde

first: Andreas

last: Beineke

first: Malgorzata

last: Ciurkiewicz


title: Genome-wide microarray analysis to identify the differentially expressed patterns of lncRNAs of cholesteatoma tissues compared with matched normal skin tissues.

city: Beijing

first: Hua

last: Yang

address: Department of Otolaryngology, Peking Union Medical College Hospital, Beijing, 100730, China

institute: Peking Union Medical College Hospital

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

summary: We performed genome-wide microarray analysis to identify the differentially expressed patterns of lncRNAs in cholesteatoma. Our data indicated that lncRNA expression profiles were significantly altered in cholesteatoma compared with normal skin tissues. A total of 787 lncRNAs were identified (fold change ≥2.0, P < 0.05), consisting of 181 upregulated and 606 downregulated lncRNAs.

overall_design: A genome-wide analysis was performed to profile differences in lncRNA expression between 4 paires of cholesteatoma and matched normal skin samples. Two female and 2 male patients aged 18-year-old to 32-year-old who underwent unilateral middle ear cholesteatoma surgerieswere enrolled in this study.

first: Juanjuan

last: Gao


title: In vitro study of role of Sigma B in pathogenesis of Avian Reovirus

city: Bareilly

first: Deepak

last: Kumar

state: UP

address: IVRI Road

department: Division of Veterinary Biotechnology

country: India

institute: Indian Veterinary Research Institute

summary: Using microarray technology, we aim to identify in vitro host gene expression for understanding the crosstalk of signaling pathways that leads to the joint pathogenesis in Avian orthoreovirus infection.

overall_design: Chicken Embryo Fibroblast cells were collected after 48hr of Avian Reovirus infection and sigma B (σB) transfection to identify the global gene expression changes vis - a - vis the control in the host.

first: M

middle: R

last: Praharaj

first: T

last: Chauhan

first: S

last: Saxena

first: A

last: Sahoo

first: R

middle: K

last: Gandham

first: K

last: Dhama

first: P

last: Goswami

first: Bina

last: Mishra

first: B

first: D


title: APT1 regulates the asymmetric partitioning of Notch and Wnt signaling during cell division

city: Philadelphia

first: Eric

last: Witze

state: PA

address: 421 Curie Blvd.

department: Cancer Biology

country: USA

institute: University of Pennsylvania School of Medicine

summary: Asymmetric cell division results in two distinctly fated daughter cells to generate cellular diversity. A major molecular hallmark of an asymmetric division is the unequal partitioning of cell-fate determinant proteins.  We have previously established that growth factor signaling promotes protein depalmitoylation to foster polarized protein localization, which in turns drives migration and metastasis. Here, we report protein palmitoylation as a key mechanism for the asymmetric partitioning of the cell-fate determinants Numb (Notch antagonist) and β-catenin (canonical Wnt regulator) through the activity of a depalmitoylating enzyme, APT1. Using point mutants, we show specific palmitoylated residues on proteins, such as Numb, are required for asymmetric localization. Furthermore, by live-cell imaging, we show that reciprocal interactions between APT1 and CDC42 regulate the asymmetric localization of Numb and β-catenin to the plasma membrane. This in turn restricts Notch and Wnt transcriptional activity to one daughter cell.  Moreover, we show altering APT1 expression changes the transcriptional signatures to those resembling that of Notch and β-catenin in MDA-MB-231 cells.  We also show loss of APT1 depletes the population of CD44+/CD24lo/ALDH+ tumorigenic cells in colony formation assays. Together, the findings of this study demonstrate that palmitoylation, via APT1, is a major mechanism of asymmetric cell division regulating Notch and Wnt-associated protein dynamics, gene expression, and cellular functions.

overall_design: Gene expression by RNAseq of MDA-MB-231 triple receptor negative breast cancer cells expressing scramble control vector, shAPT1 knockdown, and APT1wt performed in triplicate. Total of 9 samples were analyzed.

first: Ewa

last: Stypulkowski

first: Irfan

last: Asangani


title: Deficiency in class III PI3-kinase induces intestinal epithelial damage and inflammatory bowel disease like phenotype in zebrafish

city: Guangzhou

first: Shaoyang

last: Zhao

state: Guangdong

address: 190 Kaiyuan Avenue

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

summary: PIK3C3 and its product phosphatidylinositol 3-phosphate (PI(3)P) play critical roles in autophagy as well as vesicular trafficking. To fully compare the gene expression differences between wild-type and pik3c3 KO zebrafish, we performed RNAseq at 6dpf, 7dpf and 8dpf before mutant died. We found that homologs of barrier-function related human IBD susceptibility genes are suppressed while the inflammation response genes are stimulated in mutant, while genes involved in bacterial sensing and autophagy pathways are not affected. Thus, the pik3c3 mutant may serve as a valuable model for epithelial injury induced IBD.

overall_design: mRNA profiles of wild type and pik3c3 KO zebrafish at indicated stages were generated by deep sequencing, using Illumina NextSeq500.

first: Duanqing

last: Pei

first: Xiaodong

last: Shu


title: RNA-seq analysis of sow mammary gland tissue from late pregnancy to farrowing.

city: Campobasso

first: Valentino

last: Palombo

address: via Francesco De Sanctis

department: Dipartimento Agricoltura Ambiente e Alimenti

institute: Università degli Studi del Molise

summary: To further delineate the genes and transcription regulators implicated in the control of the transition from colostrogenesis to lactogenesis, we applied RNA-seq analysis of swine mammary gland tissue from late-gestation to farrowing.

overall_design: Mammary tissue was collected on days 14, 10, 6 and 2 before (-) parturition and on day 1 after (+) parturition from three 2nd parity sows with the highest colostrum yield.

first: Mariasilvia

last: D'Andrea

first: Juan

last: Loor

first: Mario

last: Vailati-Riboni

first: Khuram

last: Shahzad

first: Klaus

last: Krogh

first: Peter

last: Theil


title: Expression data in U2OS cells transfected with control-, DBP5-, GLE1- or IPPK-siRNA

city: Kyoto City

first: Masumi

last: Okamura

state: Kyoto Prefecture

address: Kitashirakawa Oiwakechou

institute: Kyoto University

summary:
GLE1, DBP5 and inositol hexakisphosphate (IP6) function in mRNA export at the cytoplasmic face of the NPC in eukaryotic cells. It is believed that these three factors have a major and consistent role for the mRNA export. We performed RNA microarray analysis to detect the effect and function of DBP5, GLE1 and IPPK (IP6 synthetic enzyme) on the mRNA expression. The expression of some mRNA subsets (e.g. cell cycle, DNA replication) was similarly suppressed.
However, GLE1 knockdown specifically attenuates the mRNA expression of factors participated in Sonic hedgehog signaling. On the other hand, several factors function to immunoresponse was downregulated in DBP5 or IPPK knocked-down cells. These results imply that DBP5, GLE1 and IP6 have a conserved and individual function in the mRNA expression.

overall_design: Cytoplasmic RNA was prepared in U2OS cells transfected with control-, DBP5-, GLE1- or IPPK-siRNA and analyzed by gene expression array.

first: Yuhko

last: Kobayashi

first: Issei

first: Seiji

last: Masuda


title: Aristolochic acid nephropathy induced by aristolochic acid type I in C57BL/6 mice

city: Tainan

first: Bu-Miin

last: Huang

address: No. 1, University Rd.

department: Cell Biology and Anatomy

institute: National Cheng Kung University

summary: Aristolochic acid (AA) is a nephrotoxic carcinogen responsible for acute kidney injury, chronic renal failure, and associated urothelial cancers. This study aims to determine the genes in xenobiotic metabolism pathway regulated by AA and clarify the molecular mechanism underlying their action.

overall_design: Six-week-old female and male C57BL/6 mice were used. AAI (Sigma-Aldrich, St. Louis, MO, USA) was dissolved by corn oil and administered by i.p. injection at a dose of 2 mg/kg/day (male) or 5 mg/kg/day (female), 5 days per week for 3 weeks. Total liver RNA was isolated from four groups of animals, AAI- or corn oil-treated female and male WT mice, using RNeasy Mini Kits (Qiagen Inc., Valencia, CA, USA). In each group, pooled RNA was prepared by mixing the same amount total RNA from 5 mice. The microarray hybridization was performed by Welgen Biotech, Co., Ltd. (Taipei, Taiwan) using Agilent SurePrint Microarray (Agilent Technologies, USA). After microarrays were scanned with an Agilent microarray scanner (Agilent Technologies, USA) for fluorescent signal intensities, scanned images were analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA). Raw signal data was normalized by quantile normalization for differentially expressed gene discovery.

first: Ming-Min

last: Chang

first: Yi-Ming

last: Chen


title: Transcriptome analysis of Bcl11b-deficient CD4+ T-cells during Th2 immune response

city: Gainesville

first: Kyle

middle: James

last: Lorentsen

state: FL

address: 1345 Center Drive, MSB M350

department: Medicine

institute: University of Florida

summary: Naïve CD4+ T-helper cells differentiate into Th2 effector cells during asthma and helminth (worm) infection. Here, we report that mice lacking the transcription factor Bcl11b in mature CD4+ T-cells are incapable of mounting an effective Th2 response in asthma and worm infection, with a major reduction of Th2 cytokine secretion and GATA3 expression. We found that Bcl11b exerts its role in Th2 differentiation through several avenues: (1) association with intronic regions at the Gata3 locus, sustaining GATA3 expression; (2) binding to and restricting chromatin accessibility at the Il4 silencer, located at hypersensitivity site (HS) IV; and (3) restricting Runx3 expression by association with a regulatory region 5’ of Runx3. Thus, in the absence of Bcl11b, the reduction in GATA3 levels combined with increased Runx3 levels and activity at Il4 HS IV silencer and consequently diminished IL-4 expression. This results in reduced chromatin opening at the Th2 locus control region (LCR), Il13 and Il5 promoters, subsequently preventing expression of Th2 cytokine genes and Th2 differentiation. Our results establish a novel role for Bcl11b in the regulatory loop critical for licensing the Th2 program in vivo.

overall_design: Examination of changes to transcriptome resulting from removal of Bcl11b from the mature CD4+ T-cells of mice infected with Heligmosomoides polygyrus

first: Dorina

last: Avram


title: Genome wide mapping of accessible chromatin in CD4+ T-cells during Th2 immune responses

overall_design: Examination of the changes caused to chromatin accessibility during allergic asthma by the removal of Bcl11b


title: CD4+ T-cells during Th2 immune responses

overall_design: Refer to individual Series


title: Mapping of Bcl11b binding in CD4+ T-cells during Th2 immune response

overall_design: Examination of Bcl11b binding in CD4+ T-cells from mice infected with Heligmosomoides polygyrus


title: Chronophin regulates metabolic and transcriptomic features of glioblastoma stem-like cells

city: Regensburg

first: Markus

last: Schulze

address: Franz-Josef-Strauss Allee 11

department: Neuropathology

country: Germany

institute: University Hospital Regensburg

summary: High throughput sequencing of poly-A RNA

overall_design: Two-condition experiment: Control- and Chronophin shRNA (CIN/PDXP) in glioblastoma stem-like cells

first: M

last: Riemenschneider


title: Genome-wide maps of Tet1 binding in [WT, Tet1-Flag] and [Dnmt3a-/-, Tet1-Flag] J1 ES cells

city: seattle

first: xueqiu

last: lin

state: wa

address: 1100 Fairview Ave N

institute: FRED HUTCHINSON CANCER CENTER

summary: In order to assess Tet1 binding, we first generated a Flag tagged Tet1 ES cells and then knocked out Dnmt3a in the [WT, Tet1-Flag] cells. By Tet1 ChIP and Flag ChIP, we showed that Tet1 binding was complementary to Dnmt3a. And Tet1 binding was not affected or slightly increased at majority of its targets.

overall_design: ChIP-seq with anti-Tet1 or anti-Flag in [WT, Tet1-Flag] and [Dnmt3a-/-, Tet1-Flag] ES cells

first: Xueqiu

last: Lin

first: Tianpeng

last: Gu

first: Wei

last: Li

first: Margaret

last: Goodell


title: The LetA/S two-component system is essential for the survival of Legionella pneumophila in water

city: St-Anne-de-Bellevue

first: Sebastien

last: Faucher

state: QC

address: 21,111 Lakeshore

department: Natural Resource Sciences

institute: McGill University

summary:
Surviving the nutrient-poor aquatic environment for extended periods of time is important for transmission of various water-borne pathogen to the host, including Legionella pneumophila (Lp). Lp is a leading cause of community-acquired and nosocomial pneumonia called Legionnaires’ disease. The remarkable ability of the bacterium to survive in water for periods ranging from several months to years under starvation conditions alludes to regulatory pathways that mediate adaptation to the water environment. In the present study, we investigated a potential role for the LetA/LetS signal transduction system in the successful survival of Lp in water. During infection of host cells, the LetA/LetS two-component system controls the transition from the replicative phase to the transmissive phase in response to nutrient deprivation.
In accordance with previous work, the letS mutant used in the present study is defective for pigment production and contributed to cell size reduction in the post-exponential phase. LetS also contributed to cell size reduction when Lp was exposed to water. Importantly, absence of the sensor kinase resulted in a significantly lower survival rate in water at various temperatures, as well as an increase sensitivity to heat shock. Transcriptomic analysis indicated that a general transcriptomic downshift of major pathways is orchestrated by LetA/LetS upon water exposure leading to better survival, suggesting a potential link with the stringent response. However, the expression of the LetA/S regulated small regulatory RNAs RsmY and RsmZ was not changed in a relAspoT mutant, which indicates that the stringent response and the LetA/S response are two distinct regulatory systems important for the survival of Lp in water.

sample_organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1

overall_design: Legionella pneumophila strains KS79 (WT), ∆letS, induced ∆letS+pletS (ON) and uninduced ∆letS+pletS (OFF) were grown on CYE plates. Each strain was suspended in Fraquil at an OD600 of 1 and washed 3 times. 10ml aliquots of each strain were incubated at 42oC in triplicate. After 2 hours, RNA was extracted from samples.

first: N

last: Mendis

first: P

last: McBride

first: S


title: Lnc-31 acts as a molecular scaffold to control the Rock1 mRNA translation

city: Rome

first: Mariangela

last: Morlando

address: P.le Aldo Moro, 5

department: Dept. of Biologi and Biotechnology "C. Darwin"

institute: Sapienza Unoversity of Rome

summary: Cytoplasmic long non coding RNAs have been shown to act at many different levels to control post-transcriptional gene expression; though their role in translational control is still poorly understood. Here we show that lnc-31 is a translational activator of Rock1, a negative regulator of myogenesis which prevents the exit of myoblasts from the cell cycle. This activity well correlates with the described role of lnc-31 in supporting myoblast proliferation. We show that lnc-31 binds the translational regulator YB-1 and targets the Rock1 mRNA by direct base pair interaction. We present evidences that lnc-31 stabilizes YB-1 on the Rock1 mRNA; this effect would in turn allow the YB-1-dependent remodelling of the Rock1 5’UTR and the promotion of its translation.

overall_design: High-throughput sequencing of total RNA from proliferating C2C12 cells treated with si-scr and si-lnc31. High-throughput sequencing of total RNA from lnc-31 pull down experiments performed using specific and aspecific (lacZ) biotinylated antisense probes.

first: Irene

last: Bozzoni

first: Dacia

last: Dimartino

first: Alessio

last: Colantoni

first: Monica

last: Ballarino

first: Davide

last: Mariani

first: Julie

last: Martone

first: Sama

last: Shamloo

first: Gunter

last: Meister


title: Consensus molecular subtypes classification of colorectal cancer as a predictive factor for chemotherapeutic efficacy against metastatic colorectal cancer

status: Public on May 08 2018

city: Sendai

first: Akira

last: Okita

state: Miyagi

address: 4-1, Seiryomachi, Aobaku

institute: Tohoku University Hospital

summary: Gene expression profile from 193 formalin-fixed and paraffin embedded primary tumor samples.

overall_design: This retrospective study analyzed the associations between the consensus molecular subtypes and the efficacies of standard chemotherapies in 193 patients with metastatic colorectal cancer.

first: Shin

last: Takahashi


title: Expression profilings of fission yeast strains (RNA-seq data set)

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

summary: We report gene expression profiling in the fission yeast Schizosaccharomyces pombe. We performed high-throughput sequencing of RNA isolated from wild-type, clr6-1, ago1∆, red1∆, rrp6∆, clr4∆, ccr4∆, ccr4∆fep1, wild-type cells treated with an iron chelator (2,2′-bipyridyl; DIP) grown at 30°C or 18°C and ccr4∆fep1 cells treated with DIP at 18C. We find that many stress response genes, transmembrane transporters, and non-coding RNAs are up-regulated in cells cultured at 18°C.  Our analyses concluded that Clr4 and Ccr4 are important for controlling transcript levels at 18°C and uncovered a role for iron homeostasis in adaptive genome control.

overall_design: RNA sequencing in wild-type, clr6-1, ago1∆, red1∆, rrp6∆, clr4∆, ccr4∆, ccr4∆fep1, wild-type cells treated with an iron chelator (2,2′-bipyridyl; DIP) grown at 30°C or 18°C and ccr4∆fep1 cells treated with DIP at 18C. Two biological replicates for wild-type strains grown at 30°C and 18°C.

first: Pamela

last: Gallagher

first: David

last: Wheeler

first: Gobi

last: Thillainadesan

first: Jothy

last: Dhakshnamoorthy

first: Vanivilasini

last: Balachandran

first: Christopher

last: Wellman

middle: I