title: Illumina Bead expression array data from Human IgE+ and IgG+ B cell subsets

first: David

middle: Jonathan

last: Fear

address: 5th Floor, Tower Wing, Great Maze Pond

department: Respiratory Medicine and Allergy

institute: Kings College London

summary: Human in-vitro differentiated IgE+ and IgG+ Germinal Centre B cells, plasma blasts and plasma cells were isolated by flow cytometry and subjected to transcriptome analysis using the Illumina HumanHT-12 v4 Expression BeadChip array platform.  B cells derived from 4 donors are submitted for each cell population.

overall_design: Total B  cells were isolated from discarded tonsillar tissue from 4 donors following routine tonsillectomy (following informed consent) and cultured for 10 days in the presence of IL-4 and anti-CD40 stimulation. After 10 days IgE+ and IgG+ germinal centre, plasma blast or plasma cells were isolated  by flow cytometry and total RNA extracted. RNA was then reverse transcribed, amplified and biotin labelled prior to profiling on Illumina Human HT-12 v4 expression arrays.

first: Hannah

last: Gould


title: Skeletal muscle gene expression in WT C57BL/6 versus TLR2-/- mice

status: Public on Sep 01 2017

city: Stockholm

first: Eric

last: Rullman

address: C1:82 Karolinska University Hospital, Huddinge

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

summary: WT C57BL/6 and TLR2-/- mice were used in this study. TLR2-/- mice were on a C57BL/6 background and were kindly provided by Dr S. Akira (Osaka University, Osaka, Japan). WT C57BL/6 mice were purchased from Charles River Laboratories (Wilminton, MA, USA). All the mice used in this study were males and more than 7 weeks old. Animals were kept and bred at Karolinska Institutet animal facility in a specific pathogen-free environment with standard room temperature and a 12-12 hour light/dark cycle. Food and water were provided ad libitum. Mice were killed by rapid neck disarticulation and the flexor digitorum brevis muscles were removed.

overall_design: Total RNA isolated from flexor digitorum brevis muscle in 7-9 weeks old male TLR2-/- C57BL/6  and WT C57BL/6 littermates (n=4+4)

first: Joseph

last: Bruton


title: Simultaneous detection and relative quantification of coding and non-coding RNA using a single sequencing reaction

city: Sherbrooke

first: Michelle

middle: S

last: Scott

state: Quebec

address: 3201 Jean Mignault

department: Biochemistry

country: Canada

institute: University of Sherbrooke

type: Expression profiling by high throughput sequencing

summary: The ability to compare the abundance of one RNA molecule to another is a crucial step for understanding how gene expression is modulated to shape the transcriptome landscape. However, little information is available about the relative expression of the different classes of coding and non-coding RNA or even between RNA of the same class. In this study, we present a complete portrait of the human transcriptome that depicts the relationship of all classes of non-ribosomal RNA longer than sixty nucleotides. The results show that the most abundant RNA in the human rRNA-depleted transcriptome is tRNA followed by spliceosomal RNA. Surprisingly, the signal recognition particle RNA 7SL by itself occupied 8% of the ribodepleted transcriptome producing a similar number of transcripts as that produced by all snoRNA genes combined. In general, the most abundant RNA are non-coding but many more protein coding than non-coding genes produce more than 1 transcript per million. Examination of gene functions suggests that RNA abundance reflects both gene and cell function. Together, the data indicate that the human transcriptome is shaped by a small number of highly expressed non-coding genes and a large number of moderately expressed protein coding genes that reflect cellular phenotypes.

overall_design: RNA was isolated from SKOV3ip1 and INOF human cell lines and selected with different methods. The resulting libraries were multiplexed and paired-end sequenced using Illumina HiSeq.


title: Neuronal EphB1 induces STAT3 activation in astrocytes, which is impaired in ALS models [Hs]

city: Edinburgh

first: Christopher

last: Sibley

address: 1 George Square

country: United Kingdom

institute: University of Edinburgh

summary: Astrocyte  responses to neuronal injury may be beneficial or detrimental to neuronal recovery, but the mechanism that determines these different responses are poorly understood. Transcriptional analysis showed that EphB1 induces a protective inflammatory signature in astrocytes, which is distinct from the response evoked by interleukin (IL)-6, which is known to have both pro- and anti-inflammatory properties. We demonstrate that this beneficial EphB1 induced signaling pathway is disrupted in astrocytes derived from human induced pluripotent stem cells (iPSC) of amyotrophic lateral sclerosis (ALS) patients.

overall_design: Examination of transcriptome-wide gene expression profiles of terminally differentiated and enriched iPSC-derived astrocytes harboring the SOD1 D90A mutation.

first: Giulia

middle: E

last: Tyzack

first: Claire

last: Hall

middle: R

first: Rickie

last: Patani

first: Andras

last: Lakatos


title: H3K4me2 and H3K4me3 profiles in the undifferentiated male germline

city: Kweishan, Taoyuan

first: Shu Yuan

last: Yang

address: Wenhua 1st Rd, No. 259

country: Taiwan

institute: Chang Gung University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Using high-throughput sequencing, we probed the H3K4me2 and H3K4me3 landscape in the bam mutant testes which are enriched with earlier stages of male germline.

overall_design: The H3K4me2 and H3K4me3 profiles of bam- mutant testes were determined.

first: Shu

middle: Y

first: Mark

last: Van Doren


title: Transcriptome analysis of bam- vs. Phf7-,bam- mutant testes, and H3K4me2 and H3K4me3 profiles in the undifferentiated male germline

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

overall_design: Refer to individual Series


title: Neuronal EphB1 induces STAT3 activation in astrocytes, which is impaired in ALS models

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: miRNA expression profile of non-epithelial ovarian tumors

first: Roger

middle: Kae-Jia

last: Chang

address: Karolinska Univ Hospital, R8:04

department: Oncology-Pathology

institute: Karolinska Institute

type: Non-coding RNA profiling by high throughput sequencing

summary: Ovarian cancer is common among women. Cancer in ovaries can arise from three different tissues, epithelial, germ and stromal cells. Majority of ovarian cancer arise from epithelial tissues. However, cancer in the germ cells or stromal cells are histologically, genetically and clinically heterogeneous, which result in a challenge in terms of treatment. In this study, we generated sRNA libraries of germ cell tumors (7 benign and 2 malignant) as well as 3 stromal tumors. In particular, we analyzed the miRNA profile of these tumors and found that malignant ovarian germ cell tumors (OGCT) are genetically distinct from benign OGCT and sex cord-stromal tumors (SCST). We detected several miRNAs that were deregulated in malignant OGCT compared to benign and SCST and fewer deregulated miRNAs between benign OGCT and SCST. However, we were still able to detect several deregulated miRNAs between benign OGCT and SCST.

overall_design: 12 snap frozen tissues, including 3 sex cord-stromal tumors (SCSTs), 7 benign and 2 malignant ovarian germ cell tumors (OGCTs), were subjected to small RNA sequencing using Solexa/Illumina sequencing platform (Illumina 1G Genome Analyzer)

middle: K

first: Weng-Onn

last: Lui


title: DNA replication timing of Arabidopsis thaliana chromosome 4

status: Public on Aug 31 2017

city: Raleigh

first: Linda

last: Hanley-Bowdoin

state: NC

address: 851 Main Campus Drive, Partners III Suite 360

department: Plant and Microbial Biology

country: USA

institute: North Carolina State University

summary: DNA replication programs have been studied extensively in yeast and animal systems, where they have been shown to correlate with gene expression and certain epigenetic modifications. Despite the conservation of core DNA replication proteins, little is known about the replication proteins of plants.  We used flow cytometry and isothermal Nimblegen arrays to profile DNA replication of Arabidopsis chromsome 4 during early, mid and late S phase. Replication timing profiles for early and mid S phase were similar and encompassed the majority of the euchromatin. Late S phase exhibited a distinctly different profile that includes essentially all of the heterochromatin.

overall_design: Replicating DNA of cultured Arabidopsis Col-0 cells was labeled with BrdU for 1 h. After fixation using 1% formaldehyde, nuclei were isolated and flow sorted into Early, Mid and Late S phase based on DNA content (DAPI). Nascent DNA isolated by immunoprecitation to BrdU, amplified and labeled with Cy5/Cy3. Input DNA labeled with Cy5/Cy3 was the reference. Equal amounts of DNA was hybridized to an isothermal Nimblegen array that covered Arabidopsis chromosome 4. Each 2 phase sample has 2 biological replicates with a dye swap serving as a technical replicated for a total of 12 arrays.

first: Tae-Jin

last: Lee

first: Pete

last: Pascuzzi

first: Lorenzo

last: Concia

first: William

middle: F

last: Thompson


title: Neuronal EphB1 induces STAT3 activation in astrocytes, which is impaired in ALS models [Mm]

overall_design: Examination of transcriptome-wide gene expression profiles of purified  murine wildtype astrocyte cultures (untreated and treated with IL-6 or EphB1).


title: Normal karyotype CLL show high rate of SF3B1 mutations and genomic arrays aberrations with impact on time to treatment

city: München

first: Torsten

last: Haferlach

address: Max-Lebsche-Platz 31

country: Germany

institute: MLL Munich leukemia laboratory

summary: Chronic Lymphocytic Leukemia (CLL) is a heterogeneous disease with a variable clinical course strictly dependent on cytogenetic and molecular features. However, in 15-20% of cases both conventional cytogenetic and FISH analyses do not show any kind of abnormality. With the aim to identify dependable molecular prognostic factors in this subgroup, we evaluated 171 CLL patients, without aberrations detected by chromosome banding and FISH analysis. A comprehensive analysis was performed including genomic arrays (CGH+SNP), IGHV status, flow cytometry and a targeted sequencing. By genomic arrays, we detected 73 aberrations in 39 patients (23%). Most frequently, patients had 1 aberration (25/171; 15%), while 14 patients (8%) had at least 2 aberrations. IGHV unmutated status was present in 53/171 (31%) patients. SF3B1 was the most frequently mutated gene (26/171 patients; 15%), followed by NOTCH1 (n=15, 9%), ATM (n=5; 3%); TP53 (n=5; 3%); KLHL6 (n=5; 3%); MYD88 (n=5; 3%) and XPO1 (n=5; 3%). At univariate analysis, an adverse impact on time to treatment (TTT) was evident for SF3B1 mutations, higher white blood cell count, higher CLL cells percentage by flow cytometry, CD38 positivity, IGHV unmutated status and at least 2 genomic array abnormalities. Of them, SF3B1 mutations, CLL cells percentage, IGHV unmutated status and number of genomic array aberrations maintained their impact in multivariate analysis. In conclusion, integrating genomic and molecular data, we identified patients at higher risk for treatment need. Therefore, we suggest to evaluate these factors for a better prognostic stratification of normal karyotype CLL subset.

overall_design: 171 samples were analyzed by CGH + SNP array.

first: Calogero

last: Vetro

first: Claudia


title: Transcriptome differences during blebbishield emergency program and between cell lines that differ in tumorigenecity

city: Houston

first: Goodwin

middle: G

last: Jinesh

state: TX

address: 1515 Holecombe Blvd.,

department: Urology

institute: UT MD Anderson Cancer Center

summary: Blebbishields and spheres (transformed) from blebbishields after apoptosis were compared for gene expression changed from live RT4P cells. Highly tumorigenic cells RT4v6, PBSHMS, RT4P-BSE2 were compared for gene expression differences from RT4P cells

overall_design: Total RNA isolated were subjected to gene expression analysis using Illumina human HT chip version-4

first: Ashish

middle: M

last: Kamat


title: ZIKV infection of monocytes activates inflammasome pathways

city: Reno

first: Subhash

middle: C

last: Verma

state: NV

address: 1664 N Virginia Street, MS 320

department: Microbiology and Immunology

institute: University of Nevada, Reno

summary: The objective of this assay was to determine the effect of ZIKV on host cellular pathways

overall_design: Purified human CD14+ monocytes were infected with two strains of ZIKV (PR and NIG) and RNA was subjected for differential gene expression by next generation sequence analysis.

first: Stephen

last: St. Jeor


title: Transcriptomic profiles of CD4+ T lymphocytes from RhoA wild type (WT) and RhoA G17V mice were generated by deep sequencing in duplicate, using Illumina poly-A RNA seq.

city: New York

first: Stuart

middle: Aidan

last: Quinn

state: NY

address: 1130 St Nicholas Ave

department: Institute for Cancer Genetics

institute: Columbia University

summary: The goal of this study is to identify transcriptomic effects of RhoA G17V expression in mouse CD4+ T lymphocytes. To this end, mice conditionally expressing RhoA G17V were generated by replacing exon 3 of RhoA with a minigene containing RhoA exons 3 to 6 flanked by loxP sites followed by a neomycin selection cassette and a mutant Rhoa exon 3 encoding the G17V substitution. These mice were then crossed with the CD4CreERT2 line (Tg(Cd4-cre/ERT2)11Gnri, Jackson Laboratories), which expresses a 4-hydroxi-tamoxifen-inducible form of the Cre recombinase under the control of the mouse Cd4 promoter to generate conditional inducible CD4 specific RhoA G17V mice (Rhoaco-G17V/+ CD4CreERT2).  Mice were treated with vehicle only or Tamoxifen to induce expression of the RhoA G17V in CD4+ T cells. CD4CreERT2 mice were included as a negative control. CD4+ T cells were isolated from single cell suspensions of spleen by negative selection using the mouse naive CD4+ T Cell Isolation Kit (Milteny#130-104-453) according to the manufacturer’s protocol. Total RNA was extracted and standard Illumina poly-A RNA seq was performed. Naive mouse CD4+ T cells expressing RhoA G17V displayed an enrichment in a Tfh gene expression program.

overall_design: Transcriptomic profiles of CD4+ lymphocytes from wild type (WT) and RhoAG17V mice were generated by deep sequencing in duplicate, using Illumina poly-A RNA seq.

first: J

last: Cortes

first: A

first: T

last: Palomero


title: Profiling of small RNA populations in uninucleate microspores and bicellular pollen of rice

city: Chengdu

first: Wei

last: Liu

address: Wangjiang Road 29

department: college of life sciences

country: China

institute: Sichuan university

summary: There are multiple types of small RNAs that may affect rice pollen’s development. To investigate the small RNA populations’ change during rice pollen development, 13-40 nt RNA were extracted from uninucleate microspores (UNM) and bicellular pollen (BCP) for high throughput sequencing. Together with our laboratory’s previous published rice tricellular pollen (TCP) small RNA sequencing data (GSM722128), sharp increase of tRNA fragments (tRFs) in BCP stage and a slightly decreased tRFs in TCP were found. Among which, new lengths of tRFs were also discovered. Our work accomplished the knowledge about tRFs in rice pollen development.

overall_design: Spores from 3 stages of pollen development (UNM: uninucleate microspore, BCP: bicellular pollen; TCP: tricellular pollen) were isolated using a sucrose gradient-based method and the small RNA fraction for either sample was isolated and sequenced by Illumina technology.

first: Fosheng

last: Li

first: Yong'ao

last: Tong

first: Qingwei

last: Wang

first: Qiang

last: Mao

first: Hua

last: Peng

first: Fengxue

last: Luo

first: Shuhua

last: Zhu

first: Fang

last: Xia

first: Shenghua


title: 3D genome landscape of Epstein-Barr Virus oncoproteins and virus activated NF-kB in lymphoblastoid cells

city: Boston

first: Sizun

last: Jiang

state: MA

address: 3 Blackfan Circle

institute: BIDMC/Harvard

summary: Epstein-Barr Virus (EBV) encoded Nuclear Antigens (EBNAs) and virus activated NF-kB subunits mostly bind to enhancers in EBV transformed lymphoblastoid cells lines (LCLs). Using LCL 3D genome organization map that links EBV enhancers to promoters, we built the most comprehensive virus regulome. EBV regulome contained 1992 genes and enhancers directly linked to them. ~30% of genes essential for LCL growth were linked to EBV enhancers. CRISPR knock out of EBNA2 sites significantly reduced their target gene expression. Additional EBV super-enhancer (ESE) targets including MCL1, IRF4, and EBF were identified. MYC ESEs looping to MYC TSS was dependent on EBNAs. CRISPR deletions of MYC ESEs greatly reduced MYC expression and LCL growth. EBNA3A/3C altered CDKN2A/B spatial organization to suppress senescence. EZH2 inhibition decreased the looping at the CDKN2A/B loci and reduced LCL growth. This study defines the most comprehensive host-pathogen interactions on the spatial organization of chromatin during infection and cancer.

overall_design: Purified human primary B cells was infected with EBV using the B95-8 strain and the P3HR1 strain. ATAC-seq was performed at Days 0, 1, 2, 5 and 7 (B95-8 only).

first: Bo

last: Zhao


title: Characterization of a clival chordoma xenograft model reveals inherent tumor genomic instability

city: Homburg (Saar)

first: Marc

last: Remke

state: Saarland

address: Kirrberger Straße 100, Gebäude 9

department: Pediatric Translational Oncology Lab

institute: Universitätsklinikum des Saarlandes

summary: Patient-derived xenografts retain the genotype of the parent tumors more readily than tumor cells maintained in culture. The two reported clival chordoma xenografts are derived from recurrent tumors after radiation. In order to study the genetics of clival chordoma in the absence of prior radiation we sought to establish a patient-derived xenograft at primary resection of a clival chordoma.

overall_design: Copy number analysis of primary tumor and 2 PDX passages using Affymetrix SNP6 arrays

first: Roberto

middle: J

last: Diaz

first: Daniel

last: Picard

first: James

middle: T

last: Rutka


title: Transcriptomics of drought tolerance in barley

city: Katowice

first: Miroslaw

last: Kwasniewski

state: silesia district

address: Jagiellonska 28

country: Poland

institute: University of Silesia in Katowice

summary: Plant survival in adverse environmental conditions requires a substantial change in the metabolism, which is reflected by the extensive transcriptome rebuilding upon the occurrence of the stress. Therefore, transcriptomic studies offer an insight into the mechanisms of plant stress responses. Here, we present the results of global gene expression profiling of roots and leaves of two barley genotypes with contrasting ability to cope with drought stress. Our analysis suggests that drought tolerance results from a certain level of transcription of stress-influenced genes that is present even before the onset of drought. Genes that predispose the plant to better drought survival play a role in the regulatory network of gene expression, including transcripts for several transcription factors, translation regulators and structural components of ribosomes. Important group of genes is involved in signaling mechanisms, with significant contribution of hormone signaling pathways and an interplay between ABA, auxin, ethylene and brassinosteroid homeostasis. Signal transduction in drought tolerant genotype may be more efficient through the expression of genes required for environmental sensing that are active already during normal water availability and are related to actin filaments and LIM domain proteins, which may function as osmotic biosensors. Better survival of drought may also be attributed to more effective processes of energy generation and more efficient chloroplasts biogenesis. Interestingly, our data suggest that several genes from photosynthesis process are required for the establishment of effective drought response not only in leaves, but also in roots of barley. Thus, we propose a hypothesis that root plastids may turn into the anti-oxidative centers protecting root macromolecules from oxidative damage during drought stress. Specific genes and their potential role in building up a drought-tolerant barley phenotype is extensively discussed with special emphasis on processes that take place in barley roots. When possible, the interconnections between particular factors are emphasize to draw a broader picture of the molecular mechanisms of drought tolerance in barley.

overall_design: Water-deficiency conditions related gene expression analysis was performed in barley in two genotypes: a German semidwarf cultivar Maresi and a Syrian breeding line Cam/B1/CI08887//CI05761 (CamB), adapted to dry environments; in two time points: (1) control conditions, (2) water stress; in two organs: roots and leaves no. 2; analyses were performed in three biological replicates.

first: Agnieszka

last: Janiak


title: Exploring the occupancy and interaction with FXR2, STAT1/3 and H3K4me3 at genomic level of FXR1 in H358 and AGS cell line by ChIP-seq

city: Shanghai

first: Bin

last: Xiang

address: Building 3, 4218 Jinke Road, Pudong

institute: novartis institutes for biomedical research

summary: The chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) was conducted in the human cancer cell lines H358 and AGS using FXR1, FXR2, STAT1/3 and H3K4me3 specific antibodies on the platform Illumina HiSeq 2000. ChIP-seq data quality was analyzed using FastQC. Target protein binding genomic regions (called ChIP-seq peaks) were identified by Model-based Analysis of ChIP-Seq (MACS) algorithm using the default p-value cutoff of 1e-5.

overall_design: ChIP-seq using antibodies against FXR1/FXR2/STAT1/STAT3/H3K4me3 in H358 and AGS cells

first: Yichao

last: Fan

first: Chun

last: Ma

first: Vickie

last: Yao Wang

first: Yingxiang

first: Youjia

last: Hua

first: Zhiping

last: Wen


title: Transcriptome analysis reveals molecular anthelmintic effects of procyanidins in C. elegans

city: Muenster

first: Jochen

last: Seggewiss

address: Roentgenstr. 21

department: Integrated Functional Genomics

institute: University of Muenster

summary: Worldwide, more than 1 billion people are affected by infestations with soil-transmitted helminths and also in veterinary medicine helminthiases are a severe thread to livestock due to emerging resistances against the common anthelmintics. Proanthocyanidins have been increasingly investigated for their anthelmintic properties, however, except for an interaction with certain proteins of the nematodes, not much is known about their mode of action.   To investigate the anthelmintic activity on a molecular level, a transcriptome analysis was performed in Caenorhabditis elegans after treatment with purified and fully characterized oligomeric procyanidins (OPC). The OPCs had previously been obtained from a hydro-ethanolic (1:1) extract from the leaves of Combretum mucronatum, a plant which is traditionally used in West Africa for the treatment of helminthiasis, therefore, also the crude extract was included in the study.  Significant changes in differential gene expression were observed mainly for proteins related to the intestine, many of which were located extracellularly or within cellular membranes. Among the up-regulated genes, several hitherto undescribed orthologues of structural proteins in humans were identified, but also genes that are potentially involved in the worms’ defense against tannins. For example, T22D1.2, an orthologue of human basic salivary proline-rich protein (PRB) 2, and numr-1 (nuclear localized metal responsive) were found to be strongly up-regulated. Down-regulated genes were mainly associated with lysosomal activity, glycoside hydrolysis or the worms’ innate immune response. No major differences were found between the groups treated with purified OPCs versus the crude extract. Investigations using GFP reporter gene constructs of T22D1.2 and numr-1 corroborated the intestine as the predominant site of the anthelmintic activity.

overall_design: 15 samples in total, 5 groups, 3 replicates each

first: Verena

last: Spiegler

first: Andreas

last: Hensel

first: Milena

last: Lubisch

first: Eva

last: Liebau


title: Transcriptome analysis by RNA-seq of ovarian cancer derived from the Cancer Institute Hospital of Japanese Foundation for Cancer Research.

city: Tokyo

first: Norio

last: Tanaka

address: Ariake 3-8-31, Koto

country: Japan

institute: Japanese Foundation Cancer Research

summary:
We performed the RNA-seq experiments for mRNA of ovarian cancer tissue.
Raw data not provided. Institutional Review Board (IRB) does not allow submitters to disclose raw data to the public

overall_design: Messenger RNA were extracted from primary tumor of 58 ovarian cancer patients, prepared with Ilumina TruSeq Stranded mRNA  Library Prep Kit and sequenced  on the Illumina HiSeq

first: Kazuyoshi

last: Kato


title: Transcriptome analysis of bam- vs. Phf7-,bam- mutant testes

first: Shu Yuan

last: Yang

summary: High-throughput sequencing was used to determine the RNA profiles of the designated genotypes to identify genes with significant expression changes upon deletion of the male germline gene Phf7 in the fruit fly testis.

overall_design: Transcriptomes of testes from newly-eclosed bam- and Phf7-bam- flies were generated by high-throughput sequencing in biological replicates on the Illumina platform.

first: Shu

first: Mark

last: Van Doren


title: Term Amniotic Fluid: An Unexploited Reserve of Mesenchymal Stromal Cells for Reprogramming and Potential Cell Therapy Applications

city: Lund

first: Niels-Bjarne

last: Woods

address: BMC A12

department: Molecular Medicine and Gene Therapy

institute: Lund University

summary: Mesenchymal stromal cells (MSC) are currently being evaluated in numerous preclinical and clinical cell-based therapy studies. Furthermore, there is an increasing interest in exploring alternative uses of these cells in disease modelling, pharmaceutical screening and regenerative medicine by applying reprogramming technologies. However, the limited availability of MSCs from various sources, restricts their use. Term amniotic fluid has been proposed as an alternative source of MSCs. Previously, only low volumes of term fluid and its cellular constituents have been collected, and current knowledge of the MSCs derived from this fluid is limited. In this study, we collected amniotic fluid at term using a novel collection system and evaluated amniotic fluid MSC content and their characteristics, including their feasibility to undergo cellular reprogramming.

overall_design: Two replicates of cord blood endothelium are compared to two replicates of amniotic fluid cells


title: The Elongation Factor and Histone Chaperone Spt6 Maintains ESC Pluripotency by Controlling Super-Enhancers and Counteracting Polycomb Repressive Complex 2

city: Bethsda

first: Vittorio

last: Sartorelli

state: MD

address: 50 South Dr.

department: NIAMS

institute: NIH

summary: Spt6 coordinates nucleosome dis- and re-assembly, transcriptional elongation and mRNA processing. Here, we report that depleting Spt6 in ESCs reduced expression of pluripotency factors, increased expression of cell lineage-affiliated developmental regulators, and induced cell morphological and biochemical changes indicative of ESC differentiation. Selective down-regulation of pluripotency factors upon Spt6 depletion may be mechanistically explained by its enrichment at ESC super-enhancers where Spt6 controlled H3K27 acetylation and methylation, and super-enhancer RNA transcription. In ESCs, Spt6 interacted with the PRC2 core subunit Suz12 and prevented H3K27me3 accumulation at ESC super-enhancers and associated promoters. Biochemical as well as functional experiments revealed that Spt6 could compete for binding of the PRC2 methyltransferase Ezh2 to Suz12 and reduce PRC2 chromatin engagement. Thus, in addition to serving as histone chaperone and transcription elongation factor, Spt6 counteracts repression by opposing H3K27me3 deposition at critical genomic regulatory regions.

overall_design: Examination of genome-wide distribution of Spt6 in mouse embryonic stem cells and 3 different histone modifications in control or Spt6 KD ESCs.

first: A

middle: H

last: Wang

first: Aster

last: Juan

first: Kyung

middle: D

last: Ko

first: Pei-Fang

last: Tsai

first: Hossein

last: Zare

first: Stefania

last: Dell’Orso


title: A map of human circular RNAs in clinically-relevant tissues

city: Berlin

first: Petar

last: Glazar

address: Robert Rössle Str. 10 (H. 87)

department: Systems Biology of Gene Regulatory Elements

institute: Max Delbrück Center for Molecular Medicine

summary: Cellular circular RNAs (circRNAs) are generated by head-to-tail splicing and are present in all multicellular organisms studied so far. Recently, circRNAs have emerged as large class of RNA which can function as post-transcriptional regulators. It has also been shown that many circRNAs are tissue- and stage specifically expressed. Moreover, the unusual stability and expression specificity make circRNAs important candidates for clinical biomarker research. Here, we present a circRNA expression resource of twenty human tissues highly relevant to disease-related research: vascular smooth muscle cells (VSMCs), human umbilical vein (HUVECs), artery endothelial cells (HUAECs), atrium, vena cava, neutrophils, platelets, cerebral cortex, placenta, and samples from mesenchymal stem cell differentiation. In eight different samples from a single donor, we found highly tissue-specific circRNA expression. Circular-to-linear RNA ratios revealed that many circRNAs were higher expressed than their linear host transcripts. Among the 65 validated circRNAs, we noticed potential biomarkers. In adenosine deaminase-deficient, severe combined immunodeficiency (ADA-SCID) patients and in Wiskott-Aldrich-Syndrome (WAS) patients’ samples, we found evidence for differential circRNA expression of genes that are involved in the molecular pathogenesis of both phenotypes. Our findings underscore the need to assess circRNAs in mechanisms of human disease.

overall_design: To explore circRNA expression patterns in human tissues, we performed rRNA-depleted RNA sequencing and circRNA detection in twenty clinically relevant samples.

first: Philipp

last: Maass

last: Glažar

first: Sebastian

last: Memczak

first: Gunnar

last: Dittmar

first: Irene

last: Hollfinger

first: Luisa

last: Schreyer

first: Aisha

middle: V

last: Sauer

first: Okan

last: Toka

first: Alessandro

last: Aiuti

first: Friedrich

last: Luft

first: Nikolaus

last: Rajewsky


title: Analysis of Genes with Alternatively Spliced Transcripts in the Leaf, Root, Panicle and Seed of Rice using RNA Sequencing

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

summary:
Purpose: RNA-Sequencing was applied to differentiate transcriptomes among the leaf, root, 1-cm panicle and young seed.
Methods: All four organs in this study were prepared from Oryza sativa L. cv. Ilmi. Leaves and roots were harvested separately at 14 days after sowing in soil. Flowers before pollination were collected in the range of 0.5-1.5-cm panicles (P1cm). Seeds at 20-30 days after pollination (S21DAP) were collected at the internal ripening stage of the grains. Total RNA was isolated from tissues using Hybrid-RTM (GeneAll, Korea) extraction following the manufacturer’s manual.  mRNA was purified using the TruSeq RNA sample preparation kit (http://www.illumina.com/) following the company’s protocol. Following purification, the mRNA was fragmented, and first-strand cDNA was generated using reverse transcriptase and random primers. Second-strand cDNA synthesis was then performed using DNA polymerase I and RNase H. These cDNA fragments were subjected to an end-repair process, the addition of a single A base, and adaptor ligation. The products were purified and enriched by polymerase chain reaction (PCR) to create a cDNA library in a bridged amplification reaction that occurred on the surface of the flow cell. A flow cell containing millions of unique clusters was loaded into a HiSeq 2000 for automated cycles of extension and imaging. Each sequencing cycle was carried out in the presence of all four nucleotides, generating a series of images with each representing a single base extension at a specific cluster. Libraries were constructed for the leaf, root, P1cm, and S21DAP. Repetitions were performed for all samples, except roots. In the initial sequencing, 2.7-0 Gb was sequenced at each end. These results generated 16-43 X 106 paired-end reads.
Results: Programs such as TopHat, Cufflinks and HTSeq were used to process sequence reads. Differential exon usage was examined with the DEXseq package in Bioconductor. Briefly, the rice genome sequence (IRGSP-1.0_2014-06-25) in the RAP database (http://rapdb.lab.nig.ac.jp) was indexed using Bowtie 2 with an FM Index based on the Burrows-Wheeler transform (Langmead et al., 2009). Reads in FASTQ files were aligned using TopHat (v2.0.4) with default parameters (Kim et al., 2013). TopHat aligned the RNA-Seq reads to genomes using the short read aligner Bowtie 2 and then analyzed the mapping results to identify splice junctions between exons. In the program, samtools (version 1.2) was used for indexing and sorting of bam and sam files. For transcriptome assembly and isoform quantitation from the RNA-Seq reads, Cufflinks was used and tested for comparison (Trapnell et al., 2012). Prior to statistical analysis of exons using the DEXseq package, per-gene read counts were performed with htseq-count in HTSeq-0.6.1 using the annotated gtf file (Anders et al., 2015). To extract exons among transcripts, non-overlapping exonic regions were defined with dexseq_prepare_annotation.py, and then the per-exon read counts were extracted with the script dexseq_count.py in the DEXSeq package (Anders et al., 2012). For each exon of each gene, the data contain the number of reads in each sample that overlap with the exon. If an exon’s boundary is not the same in all transcripts, the exon is separated into two or more parts, referred to as ‘‘counting bin’’. A read that overlaps with several counting bins of the same gene is counted for each of these. The program returned one file for each biological replicate with the exon counts. Finally, differential exon usage was assessed with the DEXseq package in Bioconductor (http://bioconductor.org). In the package, generalized linear models (GLMs) for model read counts and parameters are calculated from a negative binomial (NB) distribution of these count data (McCullagh and Nelder 1989).
Conclusions: In this study, rice RNA-Seq was applied to differentiate alternatively spliced transcripts between representative rice organs, including the leaf, root, panicle at 1 cm, and young seed. Transcripts were classified according to organ enrichment, and the results are collectively explained in terms of evolutionary pressure. The portion of loci with multiple transcripts due to alternative splicing was higher among constitutively expressed genes than organ-preferential loci. The allowance of alternative splicing is maximized by avoiding expression of the other alternative splicing transcript under unwanted circumstances. Among loci, transcripts with a longer CDS tended to be more highly expressed than those with a shorter CDS. These genome-wide technologies might be useful for studying transcriptomes and their biological significance with regard to pre-mRNA splicing.

first: Songhwa

last: Chae


title: Myocardial glycolysis and gene expression in the adult mouse heart

city: Louisville

first: Bradford

last: Hill

state: KY

address: 580 S. Preston St.

department: Medicine

institute: University of Louisville

summary: The heart uses primarily fatty acids and glucose for deriving energy.  The majority of energy in the healthy heart derives from fat utilization, with the remainder coming primarily from the catabolism of glucose.  Classical studies by Randle and colleagues describe the ability of the heart to switch its mode of utilization facilely and reversibly between glucose and fatty acids (myocardial glucose-fatty acid cycle or Randle cycle). However, under conditions of pathological stress, reliance of the heart on fatty acids decreases with a concomitant increase in reliance on glucose.  It is unclear how such changes in metabolism regulate gene expression in the heart. Therefore, we examined how regulation of glycolysis at the level of phosphofructokinase modulates gene expression in the heart.  We performed transcriptomic analysis of hearts from mice expressing either kinase-deficient phosphofructokinase 2 (GlycoLo) or phosphatase-deficient phosphofructokinase 2 (GlycoHi) under the control of the α-MHC promoter, which restricted expression of the transgenes to the heart. Phosphofructokinase 2 only controls the ability of the myocyte to regulate abundance of a single metabolite, F-2,6-P2, which is an allosteric regulator of the rate-limiting and committed step in glycolysis. Parallel radiometric and metabolomic studies showed the expected increases or decreases in glycolytic flux along with diametrically opposite changes in fat metabolism, which is consistent with the myocardial glucose-fatty acid cycle.  Transcriptomic analyses showed remarkable changes in gene transcription in these hearts, which indicates that glucose and/or fatty acid metabolism is a driver of transcriptional programs in the heart.  Furthermore, glycolytic activity coordinately regulated numerous genes in the heart, including genes important for cardiac remodeling as well as genes regulating gluconeogenic and ancillary biosynthetic pathway activity. These findings reveal that glycolytic rate is a critical regulator of gene expression in the heart and can coordinate programs that modulate cardiac metabolism, growth, and hypertrophy.

overall_design: Mouse genome array was performed on hearts from adult, male WT mice and mice expressing either kinase-deficient or phosphatase-deficient phosphofructokinase 2 in the heart. n = 3 mice per group

first: Paul

middle: N

last: Epstein

first: Shizuka

last: Uchida


title: PAF1 regulation of promoter-proximal pause release via enhancer activation

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

summary: Gene expression in metazoans is regulated by RNA Polymerase II (Pol II) promoter-proximal pausing and its release. Previously, we identified that Pol II-associated factor 1 (PAF1) modulates the release of paused Pol II into productive elongation. Here, we find that PAF1 occupies transcriptional enhancers and restrains hyperactivation of a subset of these enhancers. Enhancer activation as the result of Paf1 loss releases Pol II from paused promoters of nearby PAF1 target genes. Knockout of PAF1-regulated enhancers attenuates the release of paused Pol II on PAF1 target genes without major interference in the establishment of pausing at their cognate promoters. Thus, a subset of enhancers can primarily modulate gene expression by controlling the release of paused Pol II in a PAF1-dependent manner.

overall_design: ChIP-seq and different types of RNA-seq in in human cell lines targeted by PAF1 or scramble shRNA or ChIP-seq in cells depleted for PAF1 using the auxin-inducible degron system.

first: Fei

middle: X

last: Chen

first: Clayton

last: Collings


title: Identification of gene targets of the transcription factor SALL4 in undifferentiated spermatogonia

city: CLAYTON

first: Robin

middle: Mark

last: Hobbs

state: VIC

address: 27-31 Wright Street

department: Centre for Reproductive Health

country: Australia

institute: Hudson Institute of Medical Research

summary: Sustained spermatogenesis in adult males and recovery of fertility following germ cell depletion are dependent on undifferentiated spermatogonia with self-renewal potential. We have previously demonstrated a critical role for the transcription factor Spalt-like 4 (SALL4) in spermatogonial differentiation. However, it remains unclear whether SALL4 has broader roles within the spermatogonial pool despite its ability to co-regulate genes with PLZF, a transcription factor required for undifferentiated cell maintenance. To identify genes regulated by SALL4 in the male germline, we established cultures of undifferentiated spermatogonia from a Sall4 inducible knockout mouse model. Cells were treated with vehicle (as control) or tamoxifen to induce gene deletion, then cells harvested and analysed by microarray to identify genes mis-expressed upon loss of SALL4.

overall_design: Three independently derived Sall4flox/flox Ubc-CreER (Sall4TAM-KO) cultured undifferentiated spermatogonia were treated with vehicle (CTRL) or 4-hydroxytamoxifen (TAM) and harvested 4 days later.

first: Ai-Leen

last: Chan

first: Hue

last: La

first: Julien

last: Legrand

first: Michael

last: Eichenlaub

first: Juho-Antti

last: Mäkelä

first: Mia

last: De Seram

first: Mirana

last: Ramialison


title: The nucleoid occlusion factor Noc controls DNA replication initiation in Staphylococcus aureus [Tn-seq]

first: Ting

last: Pang

address: 4 Blackfan Circle

department: MBIB

institute: Harvard Medical School

summary: Successive division events in the spherically shaped bacterium Staphylococcus aureus are oriented in three alternating perpendicular planes. The mechanisms that underlie this relatively unique pattern of division and coordinate it with chromosome segregation remain largely unknown. Thus far, the only known spatial regulator of division in this organism is the nucleoid occlusion protein Noc that inhibits assembly of the cytokinetic ring over the chromosome. However, Noc is not essential in S. aureus, indicating that additional regulators are likely to exist. To search for these factors, we screened for mutants that are synthetic lethal with Noc inactivation. Our characterization of these mutants led to the discovery that S. aureus Noc also controls the initiation of DNA replication. We show that cells lacking Noc over-initiate and mutations in the initiator gene dnaA suppress this defect. Importantly, these dnaA mutations also partially suppress the division problems associated with ∆noc. Reciprocally, we show that over-expression of DnaA enhances the over-initiation and cell division phenotypes of cells lacking Noc. Thus, a single factor both blocks cell division over chromosomes and helps to ensure that new rounds of DNA replication are not initiated prematurely. This degree of economy in coordinating key cell biological processes has not been observed in rod-shaped bacteria and may reflect the challenges posed by the reduced cell volume and complicated division pattern of this spherical pathogen.

sample_organism: Staphylococcus aureus subsp. aureus NCTC 8325

overall_design: Tn-seq experiments were performed on wild type and mutant cells of Staphylococcus aureus RN4220 (Nair et al,PMID: 21378186 ) growing in tryptic soy broth (TSB) at 30°C with aeration.

first: T

last: Bernhardt

first: D

middle: Z

last: Rudner


title: The nucleoid occlusion factor Noc controls DNA replication initiation in Staphylococcus aureus [WGS-Seq]

platform_organism: Staphylococcus aureus subsp. aureus NCTC 8325

overall_design: Whole Genome Sequencing experiments were performed on wild type and mutant cells of Staphylococcus aureus RN4220 (Nair et al,PMID: 21378186 ) and HG003 (Herbert et al, 2010 PMID: 20212089) derivatives grown in tryptic soy broth (TSB) at 37°C with aeration.


title: Gene expression data from MCF7 cells overexpressing RAF1

city: Rochester

first: Alexey

middle: Aleksandrovich

last: Leontovich

state: MN

address: 200 First street

department: Health Science Research

institute: Mayo Clinic

summary: In this study we performed gene transcription analysis of parental MCF7 cells and MCF7 engineered to overexpress oncoprotein RAF1. We demonstrate that overexpression of RAF1 leads to development of ivasive phenotype.

overall_design: Total RNA was extracted from culturued cells or from nude mice xenografts.

first: Antonino

last: D'Assoro

middle: A

first: Jeffrey

middle: L

last: Salisbury

first: James

last: Ingle

first: Evanthia

last: Galanis

first: Amy

last: Degnim


title: Expression data from draining lymph node of mice immunized with AS01 or its components

city: Rixensart

first: Margherita

last: Coccia

address: Rue de l'Institut 89

country: Belgium

institute: GSK Vaccines

summary: Immunization with adjuvanted antigen results in coordinate changes in gene expression. Combination adjuvants exploit the interplay between different immunostimulants to promote immune response to vaccination. The Adjuvant System 01 (AS01) is a liposome-based combination adjuvant which contains two immunostimulants, MPL and QS-21   Here, we assess the contribution of the components of AS01 on its immunogenicity by comparing the transcriptional response induced in the draining lymph node by AS01, MPL and QS-21 at 2,4 or 6h after intramuscolar (i.m.) immunization

overall_design: C57BL/6 mice (6-8 weeks old) were immunized in both hind limbs, in the gastrocnemius (gcm) muscles and in a volume of 50 µl/muscle with AS01b (100mg/ml QS-21 + 100mg/ml MPL) or QS-21 (100mg/ml) or MPL (100mg/ml), all formulated in liposomes. Ileac lymph nodes were identified as draining in setup experiments. Total RNA was isolated by homogenizing pooled dLN in Tripure reagent (1 ml/100 mg tissue; Roche Applied Science) and then extracted with chloroform followed by RNeasy™ Minikit (Qiagen) according to the manufacturer’s protocol. A DNAse treatment was applied on the RNeasy column to avoid genomic DNA contamination. RNA was concentrated by ethanol precipitation, and quantified by RiboGreen™ (Life Technologies). 1 g of each RNA sample was used for target preparation,using a one-cycle cDNA synthesis kit, and hybridized to GeneChip_ Whole Mouse Genome 430 2.0 arrays (Affymetrix). Data acquisition was performed using GeneChip Operating Software (Affimetrix). For each condition, 6 mice were treated. dLN from 2 mice were pooled for each hybridization. 3 replicate chips were analysed per condition.

first: Catherine

last: Collignon

first: Caroline

last: Herve

first: Aurelie

last: Chalon

first: Iain

last: Welsby

first: Sophie

last: Detienne

first: Mary

last: van Helden

first: Katrijn

last: Van Deun

first: Age

middle: K

last: Smilde

first: Patricia

last: Bourgignon

first: Sandra

last: Morel

first: Robert

last: Van den Berg

first: Bart

last: Lambrecht

first: Stanislas

last: Goriely

first: Robbert

last: Van der Most

first: Arnaud

last: Didierlaurent


title: Gene expression in the hippocampus of Mef2c-HET mice

status: Public on Aug 30 2017

city: Irvine

first: Vivek

last: Swarup

state: CALIFORNIA

address: 3400 Bio Sci 3

department: Neurobiology and Behavior

institute: University of California Irvine

summary:
Gene expression of Mef2c-het mice vs. WT littermates in hippocampus
Total RNA isolated from hippocampus of P1 and P30 aged Mef2c-HET and WT mice using QIAGEN miRNeasy mini kit (QIAGEN; Cat #217004) were processed on an Illumina mouse Ref8 v2 beadchip microarrays following the manufacture’s protocol.  Microarray data analysis was performed using R and Bioconductor packages. Raw expression data were log2 transformed and normalized by quantile normalization. Probes were considered robustly expressed if the detection P value was 0.01 for at least half of the samples in the data set.

overall_design: Hippocampus of P1 and P30 aged Mef2c-HET and WT mice were used for the study

first: Swarup

last: Vivek

first: Nakanishi

last: Nobuki

first: Daniel

last: Geschwind


title: The nucleoid occlusion factor Noc controls DNA replication initiation in Staphylococcus aureus

first: Ting

last: Pang

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

overall_design: Refer to individual Series


title: MiR-1287-5p has inhibitory effects on breast cancer growth mediated by interaction with phosphoinositide 3-kinase CB

city: Graz

first: Martin

last: Pichler

address: Auenbruggerplatz 15

department: Internal medicine, Division of Oncology

country: Austria

institute: Medical University of Graz

summary:
Background: Non-coding RNAs and especially microRNAs have been discovered as master regulators of cancer initiation and progression. The aim of our study was to discover and characterize the function of yet uncharacterized microRNAs in human breast carcinogenesis.
Methods:
In an unbiased approach, we made use of a commonly used model system for breast cancer (BC) stem cells (“mammospheres”) to identify whole miRNome alterations with a special focus on previously uncharacterized miRNAs in BC. We further characterized the influence of microRNA-1287-5p, a yet uncharacterized microRNA in BC, in patient samples (n=1262) and on several hallmarks of cancer in vitro and in vivo with a special focus on triple negative BC. The molecular mode of action was further characterized using whole transcriptome analysis, in silico prediction tools, miRNA-interaction luciferase assays and pheno-copy assays.
Results:
We identified miR-1287-5p among many others as differentially expressed in mammospheres. Clinical validation indicated that miR-1287-5p is significantly downregulated in human BC and associated with poor prognosis. This clinical finding can be explained by miR-1287-5p mediated growth inhibitory effects, G1 cell cycle arrest, decreased anchorage-independent growth and tumor growth in vivo. Finally, we identified PIK3CB as a direct molecular interactor of miR-1287-5p and a pheno-copy factor for miR-1287-5p. Finally, targeting PI3K-signaling pathway with chemical inhibitors together with miR-1287-5p mimics increased the pharmacological growth inhibitory potential.
Conclusion:
In conclusion, our data identified for the first time an involvement of miR-1287-5p in human BC and suggest a potential for therapeutic interventions in hardly to treat triple negative BC.

overall_design: Comparison af adherent growing breast cancer cell lines versus mammospheres under ultra-low attachment and serum-free conditions

first: Daniela

last: Schwarzenbacher

first: Verena

last: Stiegelbauer

first: Stefanie

last: Cerk

first: Barbara

last: Pasculli

first: Beate

last: Rinner

first: Michael

last: Karbiener

first: Cristina

last: Ivan

first: Raffaela

last: Barbano

first: Hui

last: Ling

first: Annika

last: Wulf-Goldenberg

first: Anna-Maria

last: Pehserl

first: Jan

middle: B

last: Adiprasito

first: Gabriel

last: Rinnerthaler

first: Margit

last: Resel

first: Herbert

last: Stoeger

first: Thomas

last: Bauernhofer

first: Johannes

last: Haybaeck

first: Gerald

last: Hoefler

first: Stephan

last: Jan

first: Paola

last: Parrella

first: George

last: Calin


title: Concentration dependent transcriptome responses of zebrafish embryos after exposure to cadmium, cobalt and copper.

city: Aachen

first: Laura

last: Sonnack

address: Forckenbeckstr. 6

institute: Fraunhofer IME

summary: Environmental metals are known to cause harmful effects to fish of which many molecular mechanisms still require elucidation. Particularly concentration dependence of gene expression effects is unclear. Focusing on this matter, zebrafish embryo toxicity tests were used in combination with transcriptomics. Embryos were exposed to three concentrations of copper (CuSO4), cadmium (CdCl2) and cobalt (CoSO4) from just after fertilization until the end of the 48 hpf pre- and 96 hpf post-hatch stage. The RNA was then analyzed on Agilent’s Zebrafish (V3, 4x44K) arrays. Enrichment for GO terms of biological processes illustrated for cadmium that most affected GO terms were represented in all three concentrations, while for cobalt and copper most GO terms were represented in the lowest test concentration only. This suggested a different response to the non-essential cadmium than cobalt and copper. In cobalt and copper treated embryos, many developmental and cellular processes as well as the Wnt and Notch signaling pathways were found significantly enriched. Also, different exposure concentrations affected varied functional networks. In contrast, the largest clusters of enriched GO terms for all three concentrations of cadmium included responses to cadmium ion, metal ion, xenobiotic stimulus, stress and chemicals. However, concentration dependence of mRNA levels was evident for several genes in all metal exposures. Some of these genes may be indicative of the mechanisms of action of the individual metals in zebrafish embryos.

overall_design: Zebrafish embryos exposed to 0.9 (C1), 1.8 (C2) and 3.3 mg/L (C3) cadmium treatment; 0.5 (C1), 1.4 (C2) and 3.6 mg/L (C3) cobalt treatment; 1.7 (C1), 2.5 (C2) and 6.1 µg/L (C3) copper treatment with additional ISO water controls (C0); Two developmental stages 48 hpf and 96 hpf; 48 hpf three replicates and 96 hpf four replicates

first: Thorsten

last: Klawonn

first: Ralf

last: Kiehuber

first: Henner

last: Hollert

first: Christoph

last: Schäfers

first: Martina

last: Fenske


title: Dynamic Control of X-Chromosome Conformation and Repression by a Histone H4K20 Demethylase

city: Berkeley

first: Barbara

middle: J.

last: Meyer

state: CA

address: 16 Barker Hall #3204

department: MCB

institute: HHMI/UCB

summary: Chromatin modification and higher-order chromosome structure play key roles in gene regulation, but their functional interplay in controlling gene expression is elusive. We discovered the machinery and mechanism underlying the dynamic enrichment of histone modification H4K20me1 on hermaphrodite X chromosomes during C. elegans dosage compensation and demonstrated H4K20me1's pivotal role in regulating higher-order chromosome structure and X-chromosome-wide gene expression. Structure and activity of dosage-compensation-complex (DCC) subunit DPY-21 defined a novel Jumonji demethylase subfamily that converts H4K20me2 to H4K20me1 in worms and mammals. Selective inactivation of demethylase activity eliminated H4K20me1 enrichment in somatic cells, elevated X-linked gene expression, reduced X-chromosome compaction, and disrupted X-chromosome conformation by diminishing formation of topologically-associating domains (TADs). Unexpectedly, DPY-21 also associates with autosomes of germ cells in a DCC-independent manner to enrich H4K20me1 and trigger chromosome compaction. Our findings demonstrate the direct link between chromatin modification and higher-order chromosome structure in long-range regulation of gene expression.

overall_design:
The chromatin modification H4K20me1 becomes enriched on the dosage-compensated X chromosomes of C. elegans hermaphrodites.  We explored the machinery and mechanism underlying the enrichment of H4K20me1 on X chromosomes and discovered H4K20me1's pivotal role in regulating higher-order chromosome structure and X-chromosome gene expression.  Through X-ray crystallography and biochemical assays, we found that the DPY-21 subunit of the C. elegans dosage compensation complex defines a new subfamily of Jumonji C (JmjC) histone demethylases that converts H4K20me2 to H4K20me1 and is widely conserved from worms to mammals. ChIP-seq and immunofluorescence studies showed that inactivation of JmjC activity in vivo by genome editing abrogated H4K20me1 enrichment on X.  Hi-C studies showed loss of demethylase activity reduced X-chromosome compaction and disrupted X-chromosome topology by weakening TAD boundaries.  RNA-seq studies showed that loss of demethylase activity elevated X-linked gene expression, demonstrating a key role for H4K20me1 in DC. Unexpectedly in germ cells, DPY-21 associates with autosomes, but not X chromosomes, in a DCC-independent manner to enrich H4K20me1 and facilitate chromosome compaction. Thus, DPY-21 is an adaptable chromatin regulator that is harnessed during development for distinct biological functions. In both somatic cells and germ cells, H4K20me1 enrichment modulates 3D chromosome architecture, demonstrating the direct impact of chromatin modification on establishing higher-order chromosome structure.

To examine the genome-wide distribution of H4K20me1 in C. elegans at high resolution and determine the effect of dpy-21 demethylase mutations on H4K20me1 enrichment, we performed ChIP-seq in mixed-stage embryos from wild-type, dpy-21(y607 JmjC), and dpy-21(e428 null) mutant strains. We were able to compare directly the levels of H4K20me1 in wild-type and dpy-21 mutant embryos, because we used wide-type C. tropicalis embryos as a spike-in control to normalize the read enrichment.  Two biological replicates were examined for each genotype.

To assay the effect of H4K20me1 on the regulation of X-chromosome gene expression, we performed RNA sequencing (RNA-seq) on three different dpy-21(JmjC) demethylase mutant strains that prevented the conversion of H4K20me2 to H4K20me1 on X chromosomes and compared the expression of genes on X and autosomes with that in wild-type strains and strains with reduced activity of set-1, the methyltransferase that converts H4K20me to H4K20me1 and set-4, the methyltransferase that converts H4K20me1 to H4K20me2/me3.  Mixed-stage embryos were assayed from 3 biological replicates of dpy-21(y607 JmjC), 3 replicates of dpy-21(y618 JmjC), 3 replicates of dpy-21(y622 JmjC), 7 replicates of dpy-21(e428 null), 7 replicates of the wild-type (N2) strain, 2 replicates of the wild-type (N2) strain grown on control RNAi bacteria (L4440), 3 replicates of set-1(RNAi), and 3 replicates of set-4(n4600).

To assess the effect of H4K20me1 enrichment on X-chromosome topology, we performed genome-wide chromosome conformation capture (Hi-C) experiments on mixed-stage wild-type (N2) and dpy-21(y607 JmjC) mutant embryos by combining a previously published Hi-C protocol with in-nucleus ligation (Crane et al., 2015; Rao et al.,

first: Katjuša

last: Brejc

first: Qian

last: Bian

first: Satoru

last: Uzawa

first: Bayly

middle: S

last: Wheeler

first: Erika

last: Anderson

first: David

last: King

first: Philip

last: Kranzusch

first: Christine

middle: G

last: Preston


title: Serum microRNA profile of Her2 positive metastatic breast cancer patients

city: Guangzhou

first: Jiang

last: Liu

address: 107 Yanjiang West Road

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

summary: Some HER2 positive breast cancer  patients are refractory to trastuzumab therapy. MicroRNAs have been used to predict therapeutic effects for various cancers, and our study suggests that the serum-based miRNA signature can effectively distinguish HER2+ MBC patients who are sensitive to trastuzumab from those are resistant.

overall_design: We collected the serum samples of HER2+ metastatic breast cancer patients before receiving first-line chemotherapy with trastuzumab for miRNA analysis, then we used miRNA microarray to obtain microRNA profile from 103 patients randomly selected from 254 patients as the training group, with 61 of them responding to the treatment while the rest 42 were resistant.

first: Huiping

last: Li


title: Expression of Hox transcription factors in Drosophila S2 cells

city: Marseille

first: Andrew

middle: J

last: Saurin

address: Campus de Luminy

country: France

institute: IBDM / CNRS


title: The nucleoid occlusion factor Noc controls DNA replication initiation in Staphylococcus aureus [ChIP-Seq]

city: Boston

first: Ting

last: Pang

overall_design: ChIP-seq experiments were performed on wild type and mutant cells of Staphylococcus aureus HG003 (Herbert et al, 2010 PMID: 20212089), and Bacillus subtilis PY79 (Youngman et al 1983, PMID: 6300908) growing in tryptic soy broth (TSB) and CH, separately, at 37°C with aeration.

first: T

last: Bernhardt

first: D

last: Rudner


title: Genome-wide analysis between murine invariant NKT cells and CD4+ T cells

status: Public on Aug 29 2017

city: Seoul

first: Yeon Duk

last: Woo

address: 103 Daehak-ro, Jongno-gu

department: Department of Biomedical Sciences

institute: Seoul National University, College of Medicine

summary: Analysis between two different types of T cells

overall_design: Invariant NKT cells and CD4+ T cells were isolated from mouse lymph nodes via magenetic cell sorting or flourescence cell sorting techniques. Total RNA was isolated from each sample and used for microarray analysis

first: SJ

last: Oh

first: Doo Hyun

last: Chung


title: Gene expression profiling of hepatocarcinogenesis in a mouse model of chronic hepatitis B

city: Yoshida-gun

first: Takuto

last: Nosaka

state: Fukui

address: 23-3 Matsuoka, Eiheiji-cho

department: Second Department of Internal Medicine

institute: University of Fukui

summary:
BACKGROUND: Hepatocellular carcinoma (HCC) is a common complication of chronic viral hepatitis. In support of this notion, we have reported that hepatitis B surface antigen (HBsAg)-specific CD8+ T lymphocytes critically contribute to inducing chronic liver cell injury that exerts high carcinogenic potential in a hepatitis B virus (HBV) Tg mouse model. The dynamics of the molecular signatures responsible for hepatocellular carcinogenesis are not fully understood. The current study was designed to determine the serial changes in gene expression profiles in a model of chronic immune-mediated hepatitis.

METHODS: Three-month-old HBV Tg mice were immunologically reconstituted with bone marrow cells and splenocytes from syngeneic nonTg donors. Liver tissues were obtained every three months until 18 months at which time all mice developed multiple liver tumors. Nitrative DNA lesions and hepatocyte turnover were assessed immunohistochemically. Gene expression profiles were generated by extracting total RNA from the tissues and analyzing by microarray.

RESULTS: The nitrative DNA lesions and the regenerative proliferation of hepatocytes were increased during the progression of chronic liver disease. In a gene expression profile analysis of liver samples, the chemokine- and T cell receptor (TCR)-mediated pathways were enhanced during chronic hepatitis, and the EGF- and VEGF-mediated pathways were induced in HCC. Among these molecules, the protein levels of STAT3 were greatly enhanced in all hepatocyte nuclei and further elevated in the cytoplasm in HCC tissue samples at 18 months, and the levels of phosphorylated TP53 (p-p53-Ser 6 and -Ser 15) were increased in liver tissues.

CONCLUSIONS: HBV-specific immune responses caused unique molecular signatures in the liver tissues of chronic hepatitis and triggered subsequent carcinogenic gene expression profiles in a mouse model. The results suggest a plausible molecular basis responsible for HBV-induced immune pathogenesis of HCC.

overall_design: The comprehensive gene expression profiles in the mouse livers, five immunologically reconstituted HBV Tg mice were sacrificed on day 7 and every three months until 18 months. The comparison combinations used in this analysis were the average values of log-ratios against Tg mix of Tg7d, Tg1M, Tg3M, Tg6M, Tg9M, Tg12M, Tg15M, Tg18M, and tumor (Tg18M) and the log ratios of Tg18M/Tg mix and tumor (Tg18M)/ Tg mix.

first: Tatsushi

last: Naito

first: Katsushi

last: Hiramatsu

first: Masahiro

last: Ohtani

first: Tomoyuki

last: Nemoto

first: Hiroyuki

last: Marusawa

first: Ning

last: Ma

first: Yusuke

last: Hiraku

first: Shosuke

last: Kawanishi

first: Taro

last: Yamashita

first: Shuichi

last: Kaneko

first: Yasunari

last: Nakamoto


title: Reduced Slc1a1 expression is associated with neuroinflammation and impaired sensorimotor gating and cognitive performance in mice: implications for schizophrenia

city: Syracuse

first: Frank

last: Middleton

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

summary: We characterized the in vivo and in vitro consequences of reduced expression of Slc1a1 in mice. Heterozygous (HET) Slc1a1+/- mice, which model the hemi-deletion we found in human subjects with schizophrenia, were examined in a series of behavioral, anatomical and biochemical assays. Knockout (KO) mice were also included in the behavioral studies for comparative purposes. Both HET and KO mice exhibited evidence of increased anxiety-like behavior, impaired working memory, decreased exploratory activity and impaired sensorimotor gating, but no changes in overall locomotor activity compared to wildtype (WT) mice. The magnitude of changes was approximately equivalent in the HET and KO mice suggesting a dominant effect of the haploinsufficiency. Whole transcriptome RNA-Seq analysis detected expression changes of genes and pathways involved in cytokine signaling and synaptic functions in both brain and blood of the HET mice compared to WT mice.

overall_design: mRNA profiles of the whole brain and whole blood of young adult wild type (WT) Slc1a1 +/+ and heterozygous (HET) Slc1a1 +/- mice were generated by stranded RNA-seq, with n = 5 per genotype per tissue, using an Illumina NextSeq500.

first: Parisa

last: Afshari


title: Normal gastric mucosa from gastric cancer cases and healthy controls exhibit methylome-wide changes associated with current and past Helicobacter pylori infection and cancer risk

city: Lyon

first: Zdenko

last: Herceg

address: 25 avenue Tony Garnier CS 90627

department: EGM

institute: IARC

summary:
Aim: We aimed to investigate the impact of H. pylori on the epigenome in normal gastric mucosa and whether these changes constitute cancer risk.
Method: The Infinium HumanMethylation450 BeadChip Kit  was used to assess methylation
Results: We found 1924 differentially methylated positions (DMPs) and 438 differentially methylated regions (DMRs) associated with H. pylori infection, most of which were hypermethylated. Significant methylation alterations identified in the initial sample set were replicated in a second validation set. The H. pylori-associated DMP/Rs showed marked stability after H. pylori clearance. Furthermore, we found 152 DMRs associated with cancer risk, regardless of H. pylori status. A methylation score derived using three biomarkers was a strong predictor of GC, with an area under the curve of 0.765.

overall_design: Normal gastric mucosa samples from GC cases (n = 42) and controls (n = 42), nested in a large case-control study and stratified by H. pylori status, were subjected to genome-wide methylation profiling and genotyping. A validation set of gastric mucosa samples (n=180) was used in the replication phase

first: Hae

last: Woo

first: Nora

last: Fernandez-Jimenez

first: Akram

last: Ghantous

first: Davide

last: Degli Esposti

first: Cyrille

last: Cuenin

first: Vincent

last: Cahais

first: Il

last: Choi

first: Young-Il

last: Kim

first: Jeongseon


title: Dynamic regulation of T Follicular Regulatory (Tfr) cell responses by IL-2 during influenza infection

city: Birmingham

first: Andre

last: Ballesteros-Tato

state: AL

address: 1825 University Blvd

department: Medicine, Division of Clinical Immunology and Rheumatology

institute: The University of Alabama at Birmingham

summary: We found that approximately 2,000 genes were differentially expressed between conventional Treg and Tfr cells following influenza virus infection

overall_design: We conducted an RNA-seq analysis on sorted conventional Treg cells (FoxP3+CD69hiPD1loCXCR5loCD25hi) and Tfr cells (FoxP3+CD69hiPD1hiCXCR5hiCD25lo) obtained from the mediastinal lymph node (mLN) of day 30 infected B6.FoxP3-DTR/GFP mice. This analysis was performed to identify and quantify differentially-expressed genes and differentially-enriched signaling pathways between the two T cell subsets.

last: Botta

first: Michael

last: Fuller

first: Tatiana

middle: T

last: Marquez-Lago

first: Holly

last: Bachus

first: John

middle: E

last: Bradley

first: Amy

last: Weinmann

first: Allan

last: Zajac

first: Troy

last: Randall

first: Frances

last: Lund

first: Beatriz

last: Leon


title: Expression data of A549 cells treated with 2 µM of HCI-2509 for 48 h

city: Cologne

first: Iris

middle: Felicitas

last: Macheleidt

address: Kerpenerstr. 63

department: Institute for Pathology

institute: University Hopsital Cologne

summary:
Inhibition of LSD1 is a novel option for treatment of lung  cancer. Using HCI-2509, a specific inhibitor of LSD1, results in a cell cycle arrest as wel as a shift in global histone 3 lysine 4 and lysine 9 dimethylation pattern.
Using microarrays we aim to illucidate the changed transcriptome upon treatement of HCI-2509 in lung adenocarcinoma cell line A549.

overall_design: A549 cells were treated with either DMSO as control or 2 µM HCI-2509 for 48 h. RNA was exctraced using the automated isolation kit AS-1280 (Promega) in the Maxwell-16 (Promega) with subsequent microarray hybridization.

first: Margarete

last: Odenthal


title: Gene expression profile of colorectal cancer HCT116 cells treated with single (2Gy) or fractionated (5 x 2Gy) doses of ionizing radiation.

city: Vilnius

first: Vaidotas

last: Stankevicius

state: Lithuania

address: Santariskiu 1

country: Lithuania

institute: National Cancer Institute

summary: Radiotherapy remains a standard treatment for colorectal cancer. The clinical significance of the conventional treatment is based on accumulated dose and usually consists of single daily irradiations of 1.8 - 2 Gy fractions. However the repopulation of cancer cells during and/or after the treatment suggests that the surviving fraction of cells acquire the radioresistance to cancer therapy. It has been determined a number of radioresistance markers, but only limited data exist on the acquisition of the resistance to fractionated radiation therapy. This research provides the genomic data of gene expression changes in colorectal cancer cell HCT116 line following single and multiple fractions of irradiation, aiming to identify particular genes associated with the effect of fractionated radiotherapy.

overall_design: RNA was harvested from colorectal cancer cell line HCT116 4h after treatment of single (2 Gy) or fractionated (5x2 Gy) ionizing radiation dose. The non-irradiated cells served as a control.

first: V

first: E

last: Strainiene


title: Gene expression profiling of S2 cells and S2 cells expressing AbdA

first: Andrew

last: Saurin

summary: We sought to determine the genes regulated by the Drosophila Hox protein AbdA in a homogenous cell system. S2-DRSC cells that have no Hox expression were stably transfected with HA-tagged AbdA under the control of a metallothionein promoter.

overall_design: S2-DRSC cells are stably transfected with HA-tagged AbdA (S2-DRSC:AbdA). S2 and S2-AbdA cells are analysed for gene expression in the absence (S2-DRSC) and presence (S2-DRSC-HA::AbdA) of AbdA

first: Amel

last: Zouaz

first: Ankush

last: Auradkar

first: Marie

middle: C

last: Delfini

first: Meiggie

last: Macchi

first: Marine

last: Barthez

first: Serge

last: Akoa

first: Leila

last: Bastianelli

first: Stuart

last: Levine

first: Yacine

last: Graba


title: Microarray gene expresion analysis for early and advanced gastric adenocarcinoma vs normal adjacent tissue.

city: Bucuresti

first: Mihaela

last: Chivu-Economescu

state: Bucuresti

address: Mihai Bravu 285 Ave, sector 3

department: Cellular and Molecular Pathology

country: Romania

institute: Stefan S. Nicolau Institute of Virology

summary: The study aimed to understand gradual biological variations during gastric tumorigenesis, and to identify the candidate genes that are involved in tumor progression and metastasis. cDNA microarray data were obtained from 10 pair of cancerous and normal adjacent tissue from gastric adenocarcinoma patients. As a results, we found that 136 genes were up-regulated and 96 genes were down-regulated by at least four-fold in tumor tissue. The analysis of gene clusters revealed a complex remodelling of normal gastric epithelium morphology and function associated with the tumorigenesis and metastasis. A large number of proteases are being overexpressed, together with keratins, genes associated with morphogenesis and anti-apoptosis. Between the most significant down-regulated genes, were genes involved gastric motility and synthesis, genes related to metabolic and pro-apoptotic processes. We report also, the identification of seven genes, significant up-regulated, that seems to be associated with tumor progression: KRT17, COL10A1, KIAA1199, SPP1, IL11, S100A2, and MMP3. Conclusions. Our cDNA microarray study identified several genes that appeared to meet the criteria of a good biomarker, and may therefore be especially useful for the development of diagnostic tools, for the early detection, or for the prediction of tumor progression.

overall_design: Methodology: cDNA microarray data were obtained from 10 pair of cancerous and normal adjacent tissue from gastric adenocarcinoma patients. The samples were divided in primary and advanced gastric adenocarcinoma with lymph node metastasis. Validation of the microarray data was accomplished by quantitative RT-PCR on aditional 41 samples. The significantly modified genes were grouped in clusters according to   their functional annotation, and comparison was done regarding molecular mechanisms involved tumor progression.

first: Irinel

last: Popescu


title: Indian Hedgehog suppresses a stromal cell driven intestinal immune response

city: Amsterdam

first: Barbara

middle: Florien

last: Westendorp

state: Noord-Holland

address: Meibergdreef 69-71

department: Tytgat Institute for Liver and Intestinal Research

country: Netherlands

institute: Academic Medical Center


title: Temporal expression profiling of Arterial Remodeling in Rats

city: Sao Paulo

first: Vinicius

last: Bassaneze

state: SP

address: Av. Dr. Eneas de Carvalho Aguiar, 44

department: Cardiopneumology

country: Brazil

institute: Heart Institute

summary: We explored the global expression profile of the arterialized rat jugular vein to identify candidate genes and cellular pathways underlying the arterialization remodeling process.

overall_design: CodeLink Rat Bioarrays were assayed according to the manufacturer’s instruction on total RNA extracted from arterialized vein segments. They were collected at 3 days (n=3) and 28 days (n=3) after surgery. Normal jugular veins (n=5) and carotid arteries (n=2) were used as controls (references of heathy tissues).

first: Ayumi

last: Miyakawa

first: Vinicus

first: Nubia

last: Duarte

first: Thais

last: Girao-Silva

first: Monica

middle: N

last: Bizerra

first: Julliana

last: Campos

first: Jose

last: Krieger


title: The WNT target SP5 negatively regulates WNT transcriptional programs in human pluripotent stem cells

city: La Jolla

first: Theresa

last: Gaasterland

address: 9600 Gilman Drive MS 0202

department: Scripps Institution of Oceanography

institute: University of California San Diego

summary: The WNT/β-catenin signaling pathway is a prominent player in many developmental processes, including gastrulation, anterior-posterior axis specification, organ and tissue development and homeostasis. Here, we use human pluripotent stem cells (hPSCs) to study the dynamics of the transcriptional response to exogenous activation of the WNT pathway. We describe a mechanism involving the WNT target gene SP5 that leads to termination of the transcriptional program initiated by WNT signaling. Integration of gene expression profiles of wildtype and SP5 mutant cells with genome-wide SP5 binding events reveals that SP5 acts to diminish expression of genes previously activated by the WNT pathway. Furthermore, we show that activation of SP5 by WNT signaling is most robust in cells with developmental potential, such as stem cells. These findings indicate a mechanism by which the developmental WNT signaling pathway reins in expression of transcriptional programs.

overall_design: Time series analysis of Wnt3a-treated human embryonic stem cells, including knock-out of SP5 target transcription factor.

first: Terry

first: Karl

middle: H

last: Willert


title: BACH2 in human plasma cell fate decision

city: Rennes

first: Nicolas

last: HIPP

state: France

address: 2 Av. du Pr Léon Bernard

institute: INSERM-

summary: We report here the broad transcriptomic program regulated by BACH2 transcription factor.   We used a well suited in vitro model of B cell differentiation to evaluate transcriptomic program governed by BACH2 leading to Plasmocyte (PC) differentiation.  In this model B cells were cultured with anti-BCR, CpG, CD40L and Interleukin-2 (IL2). This Interleukin triggers PC differentiation by directly repressing BACH2 expression. We artificially inhibit BACH2 expression by siRNA and found that this condition is sufficient to trigger PC differentiation without IL2.   To understand global changes induced by enforced BACH2 downregulation we compared Chip-Sequencing data between activated B Cells  and BACH2 deficient B cells (siBACH2). We found that BACH2 binds more than 3000 genes across the human genome. RNAsequencing comparing IL2 drivent committed cells and siBACH2 committed cells highlighs a large common trasncriptional program shared by  both conditions and involved in B cell destiny.  This study provides evidence that BACH2 is a guardian of B cell fate.

overall_design: Differential gene expression data between 3 conditions (RNAsequencing in triplicate) : Uncomitted, comitted, and BACH2-deficient B cells integrated with BACH2 ChipSequencing on human activated B cells versus BACH2 deficient B cells as control.

last: Hipp

first: Céline

last: Delaloy


title: Gene expression profile of colorectal cancer HCT116_p53minus cells treated with single (2Gy) or fractionated (5 x 2Gy) doses of ionizing radiation.

first: Vaidotas

last: Stankevicius

summary: The clinical significance of conventional treatment is based on an accumulated dose and usually consists of single daily irradiations of 1.8 - 2 Gy fractions. The most important molecule mediating DNA damage response (DDR) is the transcription factor p53. When activated, p53 mediates processes which are important for the cellular response to the clinical irradiation. These processes can be altered in cells having non-functional p53 that decrease cancer cell sensitivity to the fractionated irradiation. Therefore, the ongoing investigation of genomic scale expression changes in colorectal cancer cell line HCT116 with non-functional gene p53 following single and multiple fractions of irradiation provide researchers with essential data studying and incorporating novel therapies in the cancer treatment.

overall_design: RNA was harvested from colorectal cancer cell line HCT116_p53minus 4h after the treatment of single (2 Gy) or fractionated (5x2 Gy) ionizing radiation dose. Non-treated cells were used as a control.

first: V

first: E

last: Strainiene


title: ChIP-seq of UNC-30 and UNC-55 in C.elegans

status: Public on Aug 28 2017

city: Hefei

first: Ge

last: Shan

state: Anhui

address: 443 Huangshan Road

department: School of Life Sciences

institute: University of Science and Technology of China

summary: We performed ChIP-seq for GFP fusion protein of UNC-30 and UNC-55 with endogenous expression

overall_design: Examination of 2 different Transcription Factors

first: Bin

last: Yu


title: The whole human genome expression data from MIHA cells.

status: Public on Aug 26 2017

city: Beijing

first: SHUAI

last: HUANG

address: Nanwei Road NO2

institute: Institute of Materia Medica,Chinese Academy of Medical Sciences/Peking Union Medical College

summary:
Botanic drug CA regulated the genes expression in tumor cells.
We used microarrays to detail the differentiation genes expression treated with CA or not.

overall_design: The MIHA cells were treated with 50 μM,100 μM of CA for 24 hrs.

first: Huang

last: Shuai

first: Han

last: Yan-Xing


title: Increased interleukin-11 and stress genes in human endothelial and human bronchial epithelial cell lines by silver nanoparticles

first: Jiyoung

last: Jang

state: Seodaemungu

address: 50-1 Yonseiro

department: Microbiology

institute: Yonsei university

summary:
Because of their small size, nanoparticles that enter the human body can easily penetrate biological barriers and can be circulated throughout the entire body, ultimately reaching the vascular endothelium. In this study aimed to identify cell reponses by distinguishing endothelial cell and exposing them to silver nanoparticles. The study also assesseed several gene expression levels that increased significantly in the microarray assay. We verified through microarray that 5 nm silver nanoparticles affect the variation of gene expression in cells, and a noticeable increase in the expression of interleukin (IL)-8 and IL-11 genes in early time was also verified. This study found that the variation on oxidative stress related genes in early time, amd among them the variation of metallothionein(MT), heme oxygenase 1(HO1), and heat shock 70kDa protein(HSP70) expression, was noticeable.
This study finds that intracellular genes specifically respond to exposure to silver nanoparticles and that the expression of IL-11 among cytokines is noticeable.

overall_design: cDNA for microarray analysis was collected after 6h of exposure to silver nanoparticles at near the LD50 concentration, in order to detec changes in gene expression at a dose that dose not produce obvious cell damage. (Gene expression was screened using cDNA microarray analysis and confirmed by quantitative RT-PCR.)

first: In-Hong

last: Choi


title: Genome-wide maps of m6A circRNAs identify widespread and cell-type-specific methylation patterns that are distinct from mRNAs

first: Chan

last: Zhou

state: Massachusetts

address: 55 Fruit Street

department: gastroenterology

institute: Mass General Hospital, Harvard Medical School

summary: We performed N6-methyladenosine (m6A) immunoprecipitation of ribosome-depleted RNA to identify m6A-circRNAs

overall_design: Total RNA was isolated from human embryonic stem cells (hESCs) and HeLa cells. Total RNA was depleted of ribosomal RNA and libraries were prepared for sequenceing before and after m6A immunoprecipitation (RIP).

first: Benoit

last: Molinie

first: Cosmas

last: Giallourakis

first: Alan

last: Mullen


title: Gene expression assessed by genome wide hybridization bead array in T84 polarized tight monolayers after challenge with  celiac disease-associated bacteria and gluten [A grav, Bmix Bmix glut]

city: Umeå

first: Marie-Louise

last: Hammarström

address: Peter Lestadius väg

department: Clinical Microbiology

country: Sweden

institute: Umeå universitet

summary: Analysis of the influence of celiac disease-associated bacteria and gluten on intestinal epithelial cells

overall_design: Stimulation with CD-associated bacteria and gluten was done from the apical side of polarized tight monolayers of T84 cells by replacing the medium in the upper chamber with 0.5 mL challenge medium containing 5x10^7 bacteria with or without 1 mg trypsin-treated gluten/mL. For each stimulant three parallel wells were used to carry out the experiment and wells treated with challenge medium only served as experimental controls. The challenge was done under anaerobic condition and at 37°C for 4 hours. The bacteria mix includes Prevotella jejuni (three isolates) + P. melaninogenica + P. histicola + Lachnoanaerobaculum umeaense + Actinomyces graevenitzii in ratio 1:1:1:1:1:1:1. Gluten = tryptic digest of wheat gluten.

first: Grzegorz

last: Pietz


title: Enhanced base editing by co-expression of free uracil DNA glycosylase inhibitor

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

summary: Even the latest generation of base editor (BE3) causes unwanted indels and non-C-to-T substitutions, compromising the fidelity of base editing outcome. Here we report a enhanced base editing system. The enhanced base edting system decreased the formation of unintended indels and C-to-A/C-to-G substitutions, and increased the frequency of desired C-to-T substitution, thereby improving both the accuracy and efficiency of base editing.

overall_design: Examination of indels and base substitutions induced by the enhanced base editing system

first: Jia

last: Chen

first: Bei

first: Wei

last: Xue

first: Lijie

last: Wang

first: Lei

last: Yan


title: Genome-wide analysis of bacterial determinants of plant growth promotion and induced systemic resistance by Pseudomonas fluorescens

city: Wageningen

first: Desalegn

middle: W

last: Etalo

state: Gelderland

address: Droevendaalsesteeg 10

department: Microbial Ecology

institute: Netherlands Institute of Ecology

summary:
Pseudomonas fluorescens strain SS101 (Pf.SS101) promotes growth of Arabidopsis thaliana, enhances greening and lateral root formation, and induces systemic resistance (ISR) against the bacterial pathogen Pseudomonas syringae pv. tomato (Pst). Here, targeted and untargeted approaches were adopted to identify bacterial determinants and underlying mechanisms involved in plant growth promotion and ISR by Pf.SS101. Based on targeted analyses, no evidence was found for volatiles, lipopeptides and siderophores in plant growth promotion by Pf.SS101. Untargeted, genome-wide analyses of 7,488 random transposon mutants of Pf.SS101 led to the identification of 21 mutants defective in both plant growth promotion and ISR. Many of these mutants, however, were auxotrophic and impaired in root colonization. Genetic analysis of three mutants followed by site-directed mutagenesis, genetic complementation and plant bioassays revealed the involvement of the phosphogluconate dehydratase gene edd, the response regulator gene colR and the adenylsulfate reductase gene cysH in both plant growth promotion and ISR. Subsequent comparative plant transcriptomics analyses strongly suggest that modulation of sulfur assimilation, auxin biosynthesis and transport, steroid biosynthesis and carbohydrate metabolism in Arabidopsis are key mechanisms linked to growth promotion and ISR by Pf.SS101.
Comparative transcriptome analysis of Arabidopsis treated with Pf. SS101, a growth and ISR promoting rhizobacteria and plants treated with cysH mutant of Pf.SS101 that fails to induce the afformentioned phenotypes

overall_design: Arabidopsis plants (col-0) were grown in half strenght MS-medium and one week seedlings were inoculated with 2 µl Pf.SS101 cell suspensions, 2 µl of the cysH mutant (20H12) and in the control treatement seedlings were inoculated with 2 µl of 10 mM MgSO4. The shoot of the plants receiving different treatment were harvested after 18 d of growth and imediately frozen in liquid nitrogen and kept at -80 0C until further use. Four biological replicates with 30 plants per replicate were used for each treatment.

first: Jos

middle: M

last: Raaijmakers


city: shanghai

first: ql

last: zheng

address: xiangyin

institute: immunity

summary: DDX46 is identified to be required at the early step of pre-spliceosome assembly,but whether DDX46 could regulate antiviral transcripts isoform splicing in the nucleus remain elusive.

overall_design: Transcriptome sequencing analyses of  WT and DDX46+/- macrophages from mouse peritoneal macrophages infected with VSV for 8 h.

first: Qingliang

last: Zheng

first: jin

last: Hou


title: The dynamics of cellular response to therapeutic perturbation using multiplexed quantification of the proteome and transcriptome at single-cell resolution

city: Cambridge

first: Kelvin

last: Zhang

address: 35 CambridgePark Drive, Suite 500

institute: Codiak Biosciences

summary: We developed a scalable assay permitting the simultaneous quantification of hundreds of proteins and the full transcriptome in thousands of individual cells from samples where cell number is limiting.  The RNA Expression and Protein Sequencing assay (REAP-seq) uses DNA-labeled antibodies to permit DNA sequencing of both mRNA and antibodies in a single workflow using droplet microfluidics. We describe the development and validation of REAP-seq in human PBMCs, and use the assay to assess the costimulatory effects of an anti-CD27 agonist antibody in naïve CD8+ lymphocytes. Protein quantification using REAP-seq was more sensitive than parallel mRNA measurements and differentiated cell states with fewer analytes. Unbiased profiling of single cells without prior selection enabled identification and characterization of an unexpected cell type that would have been missed with population-averaged profiling methodologies.

overall_design: The RNA Expression and Protein Sequencing assay (REAP-seq) which uses DNA-labeled antibodies to permit DNA sequencing of both mRNA and antibodies in a single workflow using droplet microfluidics was developed and validated in human PBMCs and naïve CD8+ T cells that were costimulated with either 1) aCD3 and aCD28 or 2) aCD3, aCD28 and aCD27.

first: Vanessa

last: Peterson


title: The TNF receptor super family - NF-κB axis is critical to maintain effector regulatory T cells in lymphoid and non-lymphoid tissues

city: Clayton

last: Shi

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

institute: Monash University

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

overall_design: Refer to individual Series


title: Gene expression profile related to rice internode growth under two nitrogen management practices

status: Public on Aug 25 2017

city: Guangzhou

first: Junliang

last: Zhao

address: 29 Jinying Road, Tianhe District

institute: Guangdong Academy of Agricultural Science

summary:
In order to investigate the gene expression profile related to rice internode growth under different nitrogen management practices, Agilent two color microarray chips were used to profile the differentially expressed genes of rice first internode between two nitrogen management.
A rice cultivars Yin-Jing-Ruan-Zhan was used as material.
First basal internode of YJRZ was taken at 30 days after transplanting, and RNA was extracted for microarray assay. Materials from OPT were label by Cy5 and FFP by Cy3.

overall_design: Two nitrogen management practice treatments were applied in the main field: the farmers’ N-fertilizer management practice (FFP treatment) and optimized nitrogen applicationapproach (OPT treatment). Two channels microarray assays were conducted between rice first nodes from OPT and FFP.

first: Junfeng

last: Pan

first: Yanzhou

last: Liu

first: Nongrong

last: Huang

first: Ka

last: Tian

first: Xuhua

last: Zhong

first: Bin


title: Effect of 20% fructose feeding and dietary salt on RNA expression in the renal cortex of rats

city: Cleveland

first: Ulrich

last: Hopfer

state: Ohio

address: 10900 Euclid Ave.

department: Physiology&Biophysics

institute: Case Western Reserve University

summary: Elevated fructose consumption has been associated with metabolic and renal diseases. It is controversial whether kidney problems are a result of systemic metabolic disease or stem, at least in part, from changes due to local fructose metabolism. To study the short-term effect of fructose on genetic programs in renal proximal tubules, the diet for rats in experimental groups was supplemented for 7 days with 20% fructose in the drinking water. Two sets of 8 rats each on different baseline rodent diets were used in this study. 4 animals of each set received fructose in the drinking water while the other 4 served as controls. Animals were sacrificed after the experimental period of 7 days and slices of superficial kidney cortex were used for total RNA extraction. The RNA was analyzed with Affymetrix  RaGene-2_0-st.

overall_design: A total of 16 male Sprague-Dawley rats weighing ~150 grams were divided in four dietary groups. Rats were housed in pairs under normal rat housing conditions with a 12-hour light cycle and access to food and fluids ad libitum. One set of 8 rats were fed the normal salt rodent chow Prolab® Isopro® RMH 3000, another set of 8 received the high salt (4% NaCl) chow Harlan TD.92034. 4 rats in each set received a solution of 20% fructose for 7 days, while the other 4 served as controls. In other words, Control group (CNS) received tap water and the normal salt rodent chow, Fructose (FNS) group received a solution of 20% fructose as fluid and the normal salt rodent chow, High-Salt group (CHS) received tap water and the high salt rodent chow, and High-Salt Fructose (FHS) group received a solutiion of 20% fructose and the high salt rodent chow. For tissue collection, rats were anesthetized with ketamine and xylazine, and given 2 IU heparin (IP). After sacrifice, the kidneys were cooled and a ~1 mm-thick slice of superficial cortex taken on a sagittal cut. Total RNA was extracted using miRNeasy Mini Kit (Qiagen; #217004) and the RNA was analyzed using the Affymetrix microarray RaGene-2_0-st.

first: Agustin

last: Gonzalez-Vicente

first: Jeffrey

last: Garvin


title: Enhancer connectome in primary human cells reveals target genes of disease-associated DNA elements

city: Stanford

first: Howard

middle: Y

last: Chang

address: 269 Campus Drive

institute: Stanford University

summary: The imprecision of linking intergenic mutations to target genes has limited molecular understanding of diverse human diseases. Here, we show H3K27ac HiChIP generates high-resolution contact maps of active enhancers and target genes in rare primary human T cell subtypes and coronary artery smooth muscle cells. Differentiation of naïve T cells to either T helper 17 cells or regulatory T cells create subtype-specific enhancer-promoter interactions, specifically at regions of shared DNA accessibility. We provide an atlas for assigning molecular functions to autoimmune and cardiovascular disease risk variants, linking hundreds of noncoding variants to putative gene targets. HiChIP target genes are supported by CRISPR interference and activation of enhancers, expression quantitative trait loci, and allele-specific enhancer loops in patient-derived primary cells. The majority of disease-associated enhancers contact genes beyond the nearest gene in the linear genome, leading to a four-fold expansion of target genes for autoimmune and cardiovascular diseases.

sample_organism:
Homo sapiens
Mus

platform_organism:
Homo sapiens
Mus

overall_design: Low cell number titration H3K27ac HiChIP in mESC. H3K27ac HiChIP and ATAC-seq in primary sorted Naïve, Th17, and Treg cells. H3K27ac HiChIP in GM12878, K562, My-La, and phased HCASMC cells.

first: Maxwell

middle: R

last: Mumbach

first: Ansuman

last: Satpathy

first: Evan

middle: A

last: Boyle

first: Chao

last: Dai

first: Benjamin

last: Gowen

first: Seung-Woo

last: Cho

first: Michelle

last: Nguyen

first: Adam

last: Rubin

last: Granja

first: Katelynn

last: Kazane

first: Yuning

last: Wei

first: Trieu

first: Peyton

last: Greenside

first: Michael

last: Corces

first: Josh

last: Tycko

first: Dimitre

last: Simeonov

first: Nabeela

last: Suliman

first: Rui

last: Li

first: Jin

last: Xu

first: Ryan

last: Flynn

first: Anshul

last: Kundaje

first: Paul

last: Khavari

first: Alexander

last: Marson

first: Jacob

last: Corn

first: Thomas

last: Quertermous

first: William

last: Greenleaf


title: Novel Interactions between Gut Microbiome and Host Drug-processing Genes Modify the Hepatic Metabolism of the Environmental Chemicals PBDEs

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary:
Purpose: Next-generation sequencing (NGS) has been utilized for systems-based analysis of all liver samples. The goals of this study were to compare the hepatic transcriptome and PBDE metabolism between conventional (CV) and germ-free (GF) mice.
Methods: Livers from vehicle (corn oil), BDE-47, or BDE-99 treated adult male CV and GF mice were used for RNA-Seq (biological replicates: n=3 for CV corn oil, n=4 for CV BDE-47, n=2 for CV BDE-99, n=3 for GF corn oil, n=3 for GF BDE-47, and n=3 for BDE-99) using a HiSeq 2000 sequencer. The sequence reads that passed quality filters were mapped to the mouse reference genome (mm10) using HISAT v 0.1.6 beta; transcript abundance and differential expression were determined using Cufflinks (CuffDiff) v 2.2.1.
Results: Using an optimized data analysis workflow,RNA-Seq generated approximately 47 to 68 million reads per sample, among which approximately 40 to 60 million reads were uniquely mapped to the mouse reference genome (NCBI GRCm/38/mm10). And we identified 393 drug processing genes in the livers of WT and hCAR-TG with  with HISAT workflow. RNA-seq data confirmed that among all the 393 DPGs with known important functions in xenobiotic biotransformation, 90 DPGs were not expressed in livers of any groups (threshold: average FPKM < 1 in all treatment groups); whereas a total of 303 genes were expressed in livers of at least one groups, among which 258 DPGs were differentially regulated by mCAR or hCAR activation in either Day 5 or Day 60 (FDR-BH<0.05), and 45 genes were stably expressed among all treatment groups.
Conclusions: Our study has unveiled a novel interaction between gut microbiome and the hepatic biotransformation of PBDEs, demonstrating that germ-free conditions modified the hepatic oxidation of PBDEs as well as the expression of relevant drug-processing genes in liver.

overall_design: CV and GF male mice at the age of 9-weeks were treated with corn oil, BDE-47 (100umol/kg), or BDE-99 (100umol/kg) once daily for 4 consecutive days,  and tissues were collected 24h after the final dose. Total RNAs were isolated from livesr using RNA zol bee reagent, and were subjected to RNA-Seq using a HiSeq 2000 sequencer.

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