title: Gene expression profile among undifferentiated iPS cells (Und. iPSCs) , mesoderm cells (KDR+PDGFRα+ (KP)) at day 3(d3) to (d5) , and d5 KP derived-cardiomyocytes (CMs d5-19).

city: Kyoto

first: Jun

last: Yamashita

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

department: Department of Stem Cell Differentiation

institute: Center for iPS Cell Research and Application (CiRA)

summary:
Despite numerous reports of human induced pluripotent stem cell (iPSC)-derived cardiac progenitor cells which potentially differentiate into cardiomyocytes (CMs), defined cellular population which definitively differentiate into CMs under diverse conditions is not reported so far.
To identify cardiomyocyte-fated progenitors (CFPs) which exclusively differentiate into CMs under various culture conditions in vitro, we performed microarray analysis to detect candidate genes related to CFPs by examining the increase of temporal gene expression level during differentiation days 3 to 5.

overall_design: 5 samples were derived from  undifferentiated iPS cells (Und. iPSCs), KDR+PDGFRα+ (KP) cells at differentiation day3, 4, and 5, and purified KP cells at day5 derived cardiomyocytes (CMs).

first: Yasuharu

last: Kanki

first: Masafumi

last: Takeda

first: Akashi

last: Izumi-Taguchi

first: Yusuke

last: Matsui

first: Teppei

last: Shimamura


title: Derivation and functional annotation of human hematopoietic subpopulations from single-cell DNA methylation data

status: Public on Apr 01 2018

city: Vancouver

first: Martin

last: Hirst

state: BC

address: 2125 East Mall

department: Microbiology and Immunology

country: Canada

institute: University of British Columbia

type: Methylation profiling by high throughput sequencing

summary: We report the development of a bisulfite based whole genome protocol suitable for use on single index sorted primary mammalian cells. Application of this protocol to murine and human hematopoietic stem cells provided quantitative DNA methylation measurements of up to 5.7 million CpGs in a single cell. To analyze the resulting datasets we developed a novel analytical approach designed to detect differences at single CpG resolution and identified epigenetically distinct subpopulations within the highly purified and functionally defined stem and progenitor populations. In silico merging of the methylation states from the single cells residing in each subpopulation allowed us to ascribe functional pathways to these epigenetically distinct subpopulations on the basis of their unique epigenetic states.

overall_design:
Single-cell DNA methylation analysis of the heterogeneity within human primary hematopoetic stem cells
RAW DATA was not provided. The lab will be submitting the sequencing data to EGA (https://www.ebi.ac.uk/ega/home).

first: Tony

last: Hui


title: Transcriptional and Epigenomic profile of GSK126 or dox-mediated Ezh2 inhibition in KrasG12D/+;Trp53-/-;Ezh2i-GFP-2A-rTA;Luc lung tumors in vivo

city: Berlin

first: Gaetano

last: Gargiulo

address: Robert-Rössle-Straße 10

department: Molecular Oncology

country: Germany

institute: Max Delbrüch Center

type: Expression profiling by high throughput sequencing

summary:
We wanted to understand the consequences of GSK126-mediated Ezh2 inhibition in an orthotopic model of Kras-driven non-small cell lung cancer (NSCLC). We injected the NSCLC cells with above-mentioned genotype into Nude mice and treated them with GSK126 50mg/kg (daily) or vehicle. As additional control for Ezh2 specificity we treated one tumor with doxycycline that induces shRNA-mediated Ezh2 protein downregulation in those cells. Purified tumour cells were obtained by dissection and FACS sorting based of GFP expression.
This experiment contributes the genome-wide response of NSCLC cells to Ezh2 inhibition in vivo.

overall_design:
We generated mRNA profiles of tumor cells tail vein injected into the lungs of Nude mice by deep sequencing. After FACS purification, RNA extraction and Bioanalyzer analysis, we processed only samples with high quality cellular and RNA profiles. Overall, we compared 10-day GSK126 treated cells (n=4) and up to 30 days GSK126 treated cells (n=3) to Captisol-treated samples (vehicle, n=2), using Illumina Hiseq2000.  FACS sorted cells from individual animals were obtained by GFP expression.

For H3K27ac and H2AK5ac profiling, we used KP primary tumors generated by injection of NSCLC into the tail vein of nude mice. Mice were sacrificed on the onset of shortness of breath and tissues were resuspended in ChIP lysis buffer.

first: Michela

last: Serresi

first: Matteo

last: Cesaroni

first: Iris

last: de Rink

first: Carlos

last: Company


title: Polycomb repressive complex 1 (PRC1) role in skin epithelium development [ChIP-seq Ring1b, Suz12, H3K27me3]

status: Public on Mar 31 2018

city: New Haven

first: Dejian

last: Zhao

state: CT

address: 333 Cedar St

department: Genetics

country: USA

institute: Yale School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Polycomb repressive complexes (PRC) 1 and 2 are essential chromatin regulators of cell identity. PRC1, a dominant executer of Polycomb-mediated control, functions as multiple sub-complexes that possess catalytic-dependent H2AK119 mono-ubiquitination (H2AK119ub) and catalytic-independent activities. Here, we show that despite its well-established repressor functions, PRC1 binds to both silent and active genes.  Through in vivo loss-of-function studies, we show that global PRC1 function is essential for skin development and stem cell (SC) specification.

overall_design: Newborn mouse epidermal cells  were FACS purified from Ring1a-/- Ring1b-/I53A mutants and Controls. Immunoprecipitated chromatin was analyzed by ChIP-seq.

first: Idan

last: Cohen

first: Deyou

last: Zheng

first: Elena

last: Ezhkova


title: Polycomb repressive complex 1 (PRC1) role in skin epithelium development [ChIP-seq Auts2, Bmi1, Rybp]

overall_design: Newborn mouse epidermal progenitor cells  were FACS purified. Immunoprecipitated chromatin was analyzed by ChIP-seq.


title: Polycomb repressive complex 1 (PRC1) role in skin epithelium development [Epi ChIP-seq]


title: Polycomb repressive complex 1 (PRC1) role in skin epithelium development [HF I53A]

overall_design: Newborn mouse epidermal cells  were purified from Ring1a-/- Ring1b-/I53A mutants and control mice. RNA from the sorted cells was analyzed by RNA-seq.


title: Polycomb repressive complex 1 (PRC1) role in skin epithelium development [Epi Eed cKO]

overall_design: Newborn mouse epidermal cells  were purified from Eed knock out and control mice. RNA from the sorted cells was analyzed by RNA-seq.


title: Integrating single-cell transcriptomic data across different conditions, technologies, and species

status: Public on Apr 02 2018

city: Seattle

first: Andrew

last: Butler

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutch Cancer Center

summary: Computational single-cell RNA-seq (scRNA-seq) methods have been successfully applied to experiments representing a single condition, technology, or species to discover and define cellular phenotypes. However, identifying subpopulations of cells that are present across multiple datasets remains challenging. Here, we introduce an analytical strategy for integrating scRNA-seq datasets based on common sources of variation, enabling the identification of shared populations across datasets and downstream comparative analysis. Implemented in our R toolkit Seurat (http://satijalab.org/seurat/), we use our approach to align scRNA-seq datasets of peripheral blood monocytes (PBMCs) under resting and stimulated conditions, hematopoietic progenitors sequenced using two profiling technologies, and pancreatic cell ‘atlases’ generated from human and mouse islets. In each case, we learn distinct or transitional cell states jointly across datasets, while boosting statistical power through integrated analysis. Our approach facilitates general comparisons of scRNA-seq datasets, potentially deepening our understanding of how distinct cell states respond to perturbation, disease, and evolution.

overall_design: Human PBMCs were profiled using ddSeq and bulk RNA-seq.  The ddSeq experiment was performed on unperturbed PBMCs. The bulk RNA-seq experiments were performed on both unperturbed and IFN-beta stimulated PBMC-derived populations (cDCs and pDCs) with three technical replicates.


title: Polycomb repressive complex 1 (PRC1) role in skin epithelium development [ChIP-seq Auts2, Cbx8, Kdm2b, L3mbtl2]


title: PRC1 fine-tunes gene repression and activation to safeguard skin development and stem cell specification

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

overall_design: Refer to individual Series


title: Polycomb repressive complex 1 (PRC1) role in skin epithelium development [Epidermis I53A]


title: Polycomb repressive complex 1 (PRC1) role in skin epithelium development [Epi Ring1a/b dKO]

overall_design: Newborn mouse epidermal cells  were purified from Ring1a/b double knock out and control mice. RNA from the sorted cells was analyzed by RNA-seq.


title: A selection of Saccharomyces cerevisiae promoters for biotechnological applications aiming at the use of synthetic glycerol medium

city: Bremen

first: Ping-Wei

last: Ho

address: College Ring 3

institute: Jacobs University Bremen GmbH

summary: Glycerol offers several advantages as a substrate for biotechnological applications. An important step towards using the popular production host Saccharomyces cerevisiae for glycerol-based bioprocesses have been recent studies in which commonly used S. cerevisiae strains were engineered to grow in synthetic medium containing glycerol as the sole carbon source. In order to boost extensive S. cerevisiae metabolic engineering incentives aiming at the use of glycerol, we realized that promoters with predictable expression levels in synthetic glycerol medium were required. In the current study, we used transcriptome analysis and a yECitrine-based fluorescence reporter assay to select and characterize useful 25 promoters for driving expression of target genes in S. cerevisiae under the given conditions. The promoters of the genes ALD4 and ADH2 showed 4.2- and 3-fold higher activities compared to the well-known strong TEF1 promoter. Moreover, the collection contains promoters with graded activities in synthetic glycerol medium and different degrees of glucose repression. To demonstrate the general applicability of the promoter collection, we successfully used a subset of the characterized promoters with graded activities in order to optimize growth on glycerol in an engineered derivative of CEN.PK, in which glycerol catabolism exclusively occurs via a non-native DHA pathway.

overall_design: Examine one sample of S. cerevisiae's transcriptome during exponential growth in synthetic glycerol medium.

first: Ping-Wie

first: Mathias

last: Klein

first: Matthias

last: Futschik

first: Elke

last: Nevoigt


title: X Chromosome Dosage Modulates Multiple Molecular and Cellular Properties of Mouse Pluripotent Stem Cells Independently of Global DNA Methylation Levels

city: Leuven

first: Vincent

last: Pasque

address: Herestraat 49 bus 804

department: Development and Regeneration

country: Belgium

institute: KU Leuven

summary: During early mammalian development, the two X-chromosomes in female cells are active. Dosage compensation between XX female and XY male cells is then achieved by X-chromosome inactivation in female cells. Reprogramming female mouse somatic cells into induced pluripotent stem cells (iPSCs) leads to X-chromosome reactivation. The extent to which increased X-chromosome dosage (X-dosage) in female iPSCs leads to differences in the molecular and cellular properties of XX and XY iPSCs is still unclear. We show that chromatin accessibility in mouse iPSCs is modulated by X-dosage. Specific sets of transcriptional regulator motifs are enriched in chromatin with increased accessibility in XX or XY iPSCs. We show that the transcriptome, growth and pluripotency exit are also modulated by X-dosage in iPSCs. To understand the mechanisms by which increased X-dosage modulates the molecular and cellular properties of mouse pluripotent stem cells, we used heterozygous deletions of the X-linked gene Dusp9 in XX embryonic stem cells. We show that X-dosage regulates the transcriptome, open chromatin landscape, growth and pluripotency exit largely independently of global DNA methylation. Our results uncover new insights into X-dosage in pluripotent stem cells, providing principles of how gene dosage modulates the epigenetic and genetic mechanisms regulating cell identity.

sample_organism: Mus musculus musculus x Mus musculus castaneus

overall_design:
Transcriptome profiles of early and late passage female induced Pluripotent Stem Cells (XX/XO iPSCs), early and late passage male induced Pluripotent Stem Cells (XY iPCSs), wild-type female Embryonic Stem Cells (WT XX ESCs), wild-type male Embryonic Stem Cells (WT XY ESCs), Dusp9 heterozygous mutants (Dusp9+/- XX ESCs) were  generated by next generation sequencing using Illumina HiSeq 4000. In total, 32 samples were analyzed including: three early XX and three late passage XO iPSC lines, three early and three late passage XY iPSCs lines, three WT XX ESC lines, three WT XY ESC lines and two independent Dusp9 clones. Where indicated, samples originate from two different timepoints of LIF withdrawal differentiation experiment (0h, 24h), and samples are in technical replicate ("b").

Open chromatin profiles of early and late passage female induced Pluripotent Stem Cells (XX/XO iPSCs), early and late passage male induced Pluripotent Stem Cells (XY iPCSs), wild-type female Embryonic Stem Cells (WT XX ESCs), wild-type male Embryonic Stem Cells (WT XY ESCs), Dusp9 heterozygous mutants (Dusp9+/- XX ESCs) were  generated by next generation sequencing using Illumina HiSeq 4000. In total, 20 samples were analyzed including: three early XX and three late passage XO iPSC lines, three early and three late passage XY iPSCs lines, three WT XX ESC lines, three WT XY ESC lines and two independent Dusp9 clones.

first: Juan

last: Song

first: Adrian

last: Janiszewski

first: Natalie

last: De Geest

first: Lotte

last: Vanheer

first: Irene

last: Talon

first: Taeho

last: Oh


title: Polycomb repressive complex 1 (PRC1) role in skin epithelium development [HF]

first: Dejian


title: Widespread Changes in Transcriptome Profile of Human Mesenchymal Stem Cells Induced by Two-Dimensional (2D) Nanosilicates

city: Bryan

first: Irtisha

last: Singh

state: TX

address: 8447 Riverside Pkwy Medical Research and Education Building II

institute: Texas A&M Health Science Center

summary: Two-dimensional (2D) nanomaterials, an ultrathin class of materials such as graphene, nanoclays, transition metal dichalcogenides (TMDs), and transition metal oxides (TMOs), have emerged as a new generation of materials due to their unique properties relative to macroscale counterparts. However, little is known about the transcriptome dynamics following exposure to these nanomaterials. Here we investigate the interactions of 2D nanosilicates, a layered clay, with human mesenchymal stem cells (hMSCs) at the whole transcriptome level by high-throughput sequencing (RNA-seq). Analysis of cell-nanosilicate interactions by monitoring change in transcriptome profile uncovers key biophysical and biochemical cellular pathways triggered by nanosilicates. A widespread alteration of genes is observed due to nanosilicate exposure as more than 4,000 genes are differentially expressed. The change in mRNA expression levels reveal clathrin-mediated endocytosis of nanosilicates. Nanosilicate attachment to cell membrane and subsequent cellular internalization activate stress-responsive pathways such as mitogen activated protein kinase (MAPK), which subsequently directs hMSC differentiation towards osteogenic and chondrogenic lineages. This study provides transcriptomic insight on the role of surface-mediated cellular signaling triggered by nanomaterials and enables development of nanomaterials-based therapeutics for regenerative medicine. This approach in understanding nanomaterial-cell interactions, illustrates how change in transcriptomic profile can predict downstream effects following nanomaterial treatment.

overall_design: Examination of affect of 2D nanosilicates on hMSCs

first: James

middle: K

last: Carrow

first: Lauren

middle: M

last: Cross

first: Akhilesh

last: Gaharwar


title: Microarray expression data from FVB mice with induced hepatoblastoma (liver tumors)

status: Public on Mar 30 2018

city: Pittsburgh

first: Satdarshan

last: Monga

state: PA

address: S-422 SBST, 200 Lothrop Street

department: Pathology

institute: University of Pittsburgh School of Medicine

summary: Hepatoblastoma (HB) is the most common pediatric liver tumor, and there are no targeted therapies available for children with HB. We have previously developed a murine model of HB which is driven by coactivation of the oncogenes YAP1 and β-catenin (CTNNB1) [Tao J, Calvisi D, Ranganathan S, et al. Gastroenterology, 2014 Sep; 147(3): 690–701]. We used the Sleeping Beauty transposase system combined with hydrodynamic tail vein injection to deliver plasmids containing mutant activated forms of YAP1 (YAP S127A) and β-catenin (ΔN90 β-catenin) to a small number of pericentral hepatocytes. We have shown that these few transformed hepatocytes proliferate and dedifferentiate, eventually forming histologically heterogeneous tumors that  resemble various subtypes of human HB (which is also highly heterogeneous), including areas of well-differentiated fetal, crowded fetal, embryonal, and blastemal HB. Our goal was to investigate how coactivation of YAP1 and β-catenin drive the dedifferentiation of hepatocytes into hepatoblast-like tumor cells over time, leading to HB tumors. In order to measure changes in gene expression during tumorigenesis in our model, we used an Affymetrix microarray to analyze isolated RNA from wild type FVB mouse livers and tissue from livers laden with late-stage HB tumors.

overall_design: We extracted RNA from wild type liver tissue from FVB mice (3 biological replicates), and liver tissue from FVB mice laden with late-stage HB liver tumors in our mouse model (3 biological replicates).

first: Junyan

last: Tao

first: Laura

last: Molina

first: Maria

last: Chikina

first: Jianhua

last: Luo


title: Depletion of DNMT1 in differentiated human cells highlights key classes of sensitive genes and an interplay with polycomb repression

city: Coleraine

first: Colum

middle: Patrick

last: Walsh

state: County Londonderry

address: Cromore Road

department: Life and Health Sciences

country: United Kingdom

institute: Ulster University

type: Methylation profiling by genome tiling array


title: Prognostic Model for Stage II/III Colon Cancer Based on Gene Expression Subtypes and KRAS Mutation Status

city: Kobe

first: Yuichiro

last: Yoshida

address: 4-4-4 Takatsukadai Nishi-ku

department: central research laboratories

country: Japan

institute: Sysmex corporation

summary:
The purpose of this study was to establish a new prognostic model for stage II/III colon cancer. Using public DNA microarray data of colon cancer patients, we created an integrated prognostic model for classifying the patients into high- and low-risk groups based on the expression levels of 55 genes and the KRAS mutation status.
For validation, we examined specimens from patients with stage II/III colon cancer who had undergone radical resection at our department, and successfully confirmed prognostic value of our model. We believe that our prognostic model may be clinically helpful to select patients for adjuvant chemotherapy.

overall_design: mRNA from 59 primary colorectal tumor samples were extracted and hybridized to HG-U133Plus 2.0 expression arrays. Each data was normalized with Microarray Suite (MAS) 5.0. The predictor we constructed was then used to classify tumors into subtypes.

first: Kengo

last: Gotoh

first: Eiji

last: Shinto

first: Hideki

last: Ueno

first: Yoshiki

last: Kajiwara

first: Masato

last: Yamadera

first: Ken

last: Nagata

first: Hitoshi

last: Tsuda

first: Junji

last: Yamamoto

first: Kazuo

last: Hase


title: Hepatic phosphorylation of transcription factor SREBP-1a interferes with gene regulation and peroxisomal function

city: Duesseldorf

first: Birgit

last: Knebel

address: Auf'm Hennekamp 65

department: Cinical Biochemistry and Pathobiochemistry

institute: German Diabetes Center

summary: The key lipid metabolism transcription factor sterol regulatory element-binding protein (SREBP)-1a integrates gene regulatory effects of hormones, cytokines, nutrition and metabolites as lipids, glucose or cholesterol via stimuli specific phosphorylation by different MAPK cascades. We have formerly reported the systemic impact of phosphorylation in transgenic mouse models with liver-specific overexpression of the N-terminal transcriptional active domain of SREBP-1a (alb-SREBP-1a) or a MAPK kinase phosphorylation sites deficient variant (alb-SREBP-1a∆P; (S63A, S117A, T426V)), respectively. Here we investigated the molecular basis of the systemic observation in holistic hepatic gene expression analyses and lipid degrading organelles involved in the pathogenesis of metabolic syndrome, i.e. peroxisomes, by 2D-DIGE and mass spectrometry analyses. Although alb-SREBP-1a mice develop a severe phenotype with visceral adipositas and hepatic lipid accumulation featuring a fatty liver, the hepatic differential gene expression and alterations in peroxisomal protein patterns compared to control mice were surprisingly relative low. In contrast, phosphorylation site deficient alb-SREBP-1a∆P mice, protected from hepatic lipid accumulation phenotype, showed gross alteration in hepatic gene expression and peroxisomal proteome. Further knowledge based analyzes revealed that overexpression of SREBP-1a favored mainly acceleration in lipid metabolism and indicated a regular insulin signaling, whereas disruption of SREBP-1a phosphorylation resulted in massive alteration of cellular processes including signs for loss of lipid metabolic targets. These results could be the link to a disturbed lipid metabolism that overall resembles a state of insulin resistance.

overall_design: C57Bl6 (C57Bl6), C57Bl6-TgN alb-HA-hSREBP-1a-NT (alb-SREBP-1a) and C57Bl6-TgN alb-HA-hSREBP-1a∆P-NT (alb-SREBP-1a∆P) [Kotzka  et al. PLoS One. 2012;7(2):e32609. doi: 10.1371/journal.pone.0032609] mice were bred and maintained under standard conditions to until alb-SREBP-1a mice develop fatty liver and adipositas phenotype (24 weeks of age).

first: B

first: J

last: Kotzka

first: D

last: Muller-Wieland


title: Depletion of DNMT1 in differentiated human cells highlights key classes of sensitive genes and an interplay with polycomb repression [methylation]

summary: DNA methylation plays a vital role in the cell, but loss-of-function mutations of the maintenance methyltransferase DNMT1 in normal human cells are lethal, precluding target identification, and existing hypomorphic lines are tumour cells. We generated instead a hypomorphic series in normal hTERT-immortalised fibroblasts using stably integrated short hairpin RNA. Approx 2/3 of sites showed demethylation as expected, with 1/3 showing hypermethylation, and targets were shared between the three independently-derived lines. Enrichment analysis indicated significant losses at promoters and gene bodies with four gene classes most affected: 1)protocadherins, which are key to neural cell identity; 2)genes involved in fat homeostasis/body mass determination; 3)olfactory receptors and 4) cancer/testis antigen (CTA) genes. Overall effects on transcription were relatively small in these fibroblasts, but CTA genes showed robust derepression. Comparison with siRNA-treated cells indicated that shRNA lines show substantial remethylation over time. Regions showing persistent hypomethylation in the shRNA lines were associated with polycomb repression, and were derepressed on addition of an EZH2 inhibitor. Persistent hypermethylation in shRNA lines was in contrast associated with poised promoters. Our results suggest polycomb marking blocks remethylation and indicate the sensitivity of key neural, adipose, and cancer-associated genes to chronic depletion of maintenance methylation activity.

overall_design: Stable knockdowns of the maintenance methyltransferase DNMT1 were generated in hTERT-immortalised adult fibroblasts using shRNA. WThTERT-1604 cells were used in triplicate as a control. Genome wide methylation and transriptional levels were assayed using the Illumina 450k BeadChip and HT12 arrays respectively and subsequently analysed using bioinformatic approaches. Genes targets of relevant interest identified through bioinformatic mining were validated using wet lab approaches.

first: Karla

last: O’Neill

first: Rachelle

last: Irwin

first: Sarah-Jayne

last: Mackin

first: Sara-Jayne

last: Thursby

first: Avinash

last: Thakur

first: Ciske

last: Bertens

first: Laura

last: Masala

first: Jayne

last: Loughery

first: Darragh

last: McArt

middle: P


title: GABA regulates release of inflammatory cytokines from peripheral blood mononuclear cells and CD4+ T cells and is immunosuppressive in type 1 diabetes

city: Uppsala

first: Bryndis

last: Birnir

address: Husargatan 3

department: Department of Medical Cell Biology

country: Sweden

institute: Uppsala University

summary: This study compared the transcriptome profiling (RNA-seq) of CD3+ T cells from nondiabetic (ND) individuals and patients with type 1 diabetes (T1D).

overall_design: Total RNA was extracted from CD3+ T cells of 18 nondiabetic individuals and 31patients with type 1 diabetes and subjected to deep sequencing using Illumina HiSeq 2500.

first: Amol

last: Bhandage

first: Yu

last: Pei


title: Impact of ERG and PTEN loss on RNA expression

status: Public on Mar 29 2018

city: New York

first: Brett

last: Carver

state: NY

address: 1275 York Ave

institute: MSKCC

summary: The current study defines the how ERG, PTEN, and AR inteact to regulate the transciptome in established prostate cancers.  Prostate cancer organoids were derived from established prostate cancer in GEM models harboring ERG over-expression and/or loss of PTEN and cultured in vitro using prostate epithelial organoid culture conditions. The established organoids were then isolated as individual clones in triplicate and CRISPR strategies were employeed to knock out ERG and AR.  RNA was isolated under physiologic steady state growth conditions and 24 hour treatment with the AR inhbitor MDV3100 in a subset of ERG-PTEN CRISPR ERG organoids.

overall_design: 18 samples over 6 genotype/conditions with 3 individual clones per genotype/condition

middle: S


title: PARN and TOE1 constitute a 3′ end maturation module for nuclear non-coding RNAs

city: Cheonan-si, Chungcheongnam-do

first: Ahyeon

last: Son

address: 25 Bongjeong-ro, Dongnam-gu

country: South Korea

institute: Soonchunhyang Institute of Medi-bio Science

summary: Poly(A)-specific ribonuclease (PARN) and target of EGR1 protein 1 (TOE1) are nuclear granule-associated deadenylases, whose mutations are linked to multiple human diseases. Here, we applied mTAIL-seq and RNA sequencing (RNA-seq) to systematically identify the substrates of PARN and TOE1 and elucidate their molecular functions. We found that PARN and TOE1 do not modulate the length of mRNA poly(A) tails. Rather, they promote the maturation of nuclear small non-coding RNAs (ncRNAs). PARN and TOE1 act redundantly on some ncRNAs, most prominently small Cajal body-specific RNAs (scaRNAs). scaRNAs are strongly downregulated when PARN and TOE1 are compromised together, leading to defects in small nuclear RNA (snRNA) pseudouridylation. They also function redundantly in the biogenesis of telomerase RNA component (TERC), which shares sequence motifs found in H/ACA box scaRNAs. Our findings extend the knowledge of nuclear ncRNA biogenesis, and they provide insights into the pathology of PARN/TOE1-associated genetic disorders whose therapeutic treatments are currently unavailable.

overall_design: RNA-seq of short non-coding RNAs in siRNA-transfected HeLa cells

first: Jong-Eun

last: Park

first: V. Narry

last: Kim


title: Nuclear localization of intracellular domain of LDL receptor-related protein 1B induced expresion data

city: Gifu

first: Tamotsu

last: Takeuchi

address: Yanagido

department: Pathology and Translational Research

institute: Gifu University School of Medcine

summary:
We have generated a MCF-7 Tet-On model system for inducible nuclear expression of intracellular domain of LRP1b using the pTRE-Tight vector system (Clontech Takara, Ohtsu, Japan).
Expression data of MCF-7 without and with induction of Doxycycline, sample 1 and sample 2, respectively.

overall_design: We have generated a MCF-7 Tet-On model system for inducible expression of intracellular domain of LRP1b using the pTRE-Tight vector system (Clontech Takara, Ohtsu, Japan). Human cDNA, which encoded a intracellular lesion of LRP1B, was amplified by PCR using sense primer 5’-ACCATGGGTAAAAGAAAAAGAAGGACAAAAAC-3’ (underline indicates the introduced start codon) and antisense primer 5’-AGGGATCCTCACTGATTATGCCACTGTCTCTCTTATAC-3’(double underline and underline indicates the introduced BamH1 site and internal stop codon, respectively), cloned to pTarget-T vector (Promega), and subsequently verified by sequencing. Next, Mlu1 and BamH1 fragment, which contained the coding region of intracellular domain of LRP1B was subcloned to Mlu1-BamH1 site of pTRE3G-ZsGreen1 vector (Clontech Takara). After verified by sequencing of the inserted lesion, the vector was designated pTRE3G-ZsGreen1-cLRP1B vector. A stable Tet-On 3G MCF-7 cell line, which was a host for Tet-inducible gene expression systems, was established using a pCMV-Tet3G vector and Xfect transfection reagent (Clontech Takara), subsequently transfected with pTRE3G-ZsGreen1-cLRP1B vector according to the manufacture’s protocol. Finally, a doxycycline (Dox) controlled expression of intracellular domain of LRP1B was established in MCF-7 cells. We established six MCF cell clones, in which intracellular domain of LRP1B was tightly regulated by doxycycline (Dox) at 100ng/ml.

first: Yoshimi

last: Asano


title: MOF forms a positive feedback regulation with ERα to suppress endometrial cancer progression

city: Shenyang

first: Wensu

last: Liu

state: Liaoning

address: 77 Puhe Road, Shenyang North New Area

country: China

institute: China Medical University

summary: MOF is a histone acetyltransferase specific for H4K16 acetylation. It has been demonstrated that MOF is lower expressed in series of human cancers. However, the molecular mechanism underlying the detailed biological function of MOF in endometrial carcinomas (ECa) has not been fully defined. The estrogen receptor α (ERα) action plays a crucial role in endometrial cancer tumorigenesis and progression. Here, our data have demonstrated that estrogen/ERα induces MOF gene transcription, meanwhile MOF stabilizes ERα via acetylating ERα in ECa, indicating that MOF forms a positive feedback loop with ERα. In the whole genome-wide level, RNA microarray analyses have shown that MOF modulates a subset of endogenous ERα-regulated genes, such as apoptosis associated factor DRAM1 and oncogene FXYD3. Knockdown of MOF leads to a G2/M cell cycle arrest and promotes ECa cell growth and proliferation. MOF depletion promotes xenograft tumor growth in mice. In addition, our results have demonstrated that MOF expression is lower in ECa than that in benign endometrial tissues. Importantly, the expression of MOF is positively correlated with that of ERα in clinical samples. Cumulatively, our results suggest a positive feedback regulation involving MOF and ERα is essential for suppression of endometrial cancer.

overall_design: 4 groups: control cells (ctrl) and shMOF cells (sh) with conditions of either  ERα(-) or ERα(+) ; Each group with 3 replicates

first: Yi

last: Wu

first: Kai

last: Zeng

first: Chunyu

last: Wang

first: Shengli

first: Wei

first: Hongmiao

last: Sun

first: Renlong

last: Zou

first: Ge

first: Ning

first: Xue

first: Huijuan

last: Song

first: Tingting

last: Zhou

first: Lin

last: Lin

first: Tao

last: Wen

first: Wenshu

first: Da

last: Li

first: Xiuxia

first: Jumin

last: Niu

first: Shu-yan

last: Cong

first: Liu

last: Cao

first: Feng

first: Yuhua

last: Chen

first: Xin

first: Yue

last: Zhao


title: Ldb1 mediates trans enhancement in mammals

city: Piscataway

first: Kevin

last: Monahan

state: NJ

address: 604 Allison Rd

department: Molecular Biology and Biochemistry

institute: Rutgers University

summary: The monoallelic expression of olfactory receptor (OR) genes is governed by a large number of intergenic enhancer elements that are located in intergenic regions of OR gene clusters. In mature olfactory sensory neurons (OSNs), multiple OR enhancers colocalize in an interchromosomal enhancer hub together with the active OR allele. Here we show that in OSNs OR enhancers are bound by Ldb1, but not general purpose mediators of nuclear architecture (CTCF or the cohesin complex subunit Rad21). Conditional deletion of Ldb1 in OSNs results in the dissolution of long range and interchromosomal contacts between OR Enhancers and in pervasive reductions in OR gene expression.

overall_design: Two types of data are included:  Crosslinked ChIP-Seq data identifies sites bound by CTCF, Rad21, or Ldb1 and RNA-Seq data profiles changes in gene expression in Ldb1 deleted mOSNs, Lhx2 deleted cells, or Enhancer Knockout mOSNs. The number of replicates varies between experiments.

first: Stavros

last: Lomvardas


title: EHEC Tir regulate the expression of  genes in primary macrophages

city: Shanghai

first: ruixue

last: zhou

address: Dong'an Road

institute: Fudan University

summary: Analysis of total RNA extracted from primary macrophages infected with the bacterial strains of EHEC or EHEC∆Tir. The results showed that Tir might regulate the expression of selected genes.

overall_design: four samples are analyzed, and two samples are control samples

first: Ruixue

first: Dapeng

last: Yan


title: Dynamic and integrated transcriptional code orchestrates the angiogenic response [Nanostring]

status: Public on Mar 28 2018

city: Minhang

first: bing

last: zhang

state: Shanghai

address: 800 Dong Chuan Road

department: Shanghai Center for Systems Biomedicine

institute: Shanghai Jiao Tong University

summary: Epigenetic modifications and transcription factors form a chromatin code to regulate gene expression in many physiological and pathological processes. However, little is known about whether the environmental stimuli could interplay with this code and regulate the transcription and biological functions. Here, we interrogated the chromatin state of multiple epigenetic modifications and transcription factors during a time course of VEGF stimulation in the endothelial cells and found a broad change of transcriptome induced by VEGF. At the promoter-proximal regions, a unique epigenetic pattern of bivalent domain preferentially governed the part of transcriptome change by hijacking the EZH1 transcriptional activity. VEGF substantially altered the epigenetic landscape at enhancer regions and transcription factor chromatin occupancy across the genome, which significantly accounted for the change of VEGF-downstream gene expression. Moreover, by integrating a transcription-regulatory network of VEGF pathway, we discovered MAFs as a novel mater transcriptional factor controlling the VEGF transcriptional program and angiogenesis. Collectively, these results revealed the extracellular stimulus of VEGF in fact implements a significant reconfiguration of chromatin code that coordinately regulates the angiogenic response.

overall_design: Nanostring on HUVEC after VEGF stimulation at 0, 1, 4, 12 hours.

first: Shiyan

last: Wang

first: Jiahuan

first: Sara

last: Garcia

first: Xiaodong

last: Liang

first: Fang

last: Zhang

first: Yi

last: Fu

first: Pengyi

first: Huijing

last: Yu

first: Weiting

last: Wei

first: Jingfang

last: wang

first: Huangying

last: Le

first: Zeguang

last: Han

first: Daniel

last: Day

first: Sean

last: Stevens

first: Yan

first: Peter

middle: J

last: Park

first: Kun

first: Guocheng

last: Yuan

first: William

middle: T

last: Pu

first: Bing


title: A SIRT1-centered Circuitry Regulates Breast Cancer Stemness and Metastasis

city: shenzhen

first: Xiaolong

last: Tang

address: 3688 Nanhai Ave, Nanshan District

institute: shenzhen university

summary: Deficiency of deacetylase SIRT1 or its downstream target PRRX1 promotes breast cancer stemness and metastasis. To explore the mechnisms of SIRT1 and its downstream target PRRX1 in breast cancer, we analysed the gene expressions in breast cancer BT549 cells with SIRT1 knockout or PRRX1 knockout or not.

overall_design: The mRNA profiles of breast cancer BT549 cells with SIRT1 knockout or PRRX1 knocknout or not were generated by deep sequencing using Illumina HiSeq x ten

first: Lei

last: Shi

first: Baohua

last: Liu


title: Targets of Bmi1 in HCC pathogenesis

city: Wuhan

first: Yuyuan

last: Chen

address: Hangkong Road

institute: School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Dynamic and integrated transcriptional code orchestrates the angiogenic response [Seq]

first: bing

last: zhang

overall_design: RNA-seq on HUVEC after VEGF stimulation at 0,1,4,12 hours. ChIP-seq of H3K27ac, H3K27me3, H3K4me1, 2, 3, H3K36me3, RNAPII, ETS1, ERG1, FLI, JUN, RBPJ, GATA2, p300 and EZH2 on HUVEC after VEGF stimulation at 0, 1, 4, 12 hour.

first: Shiyan

last: Wang

first: Jiahuan

first: Sara

last: Garcia

first: Xiaodong

last: Liang

first: Fang

first: Yi

first: Pengyi

last: Yan

first: Huijing

last: Sun


title: Gene expression in the liver of Bmi1 knockout mice

summary: To explore the potential targets of Bmi1 in the liver development of hepatic carcinogenesis, we assayed the gene expression level in the liver of Bmi1 knockout mice. We isolated the liver tissue of Bmi1 WT and KO mice around 6-8 weeks. Then we extracted total RNA and run the microarray detection. Gene expression in Bmi1 KO mouse livers was compared with that in Bmi1 WT mouse livers to screen potential targets of Bmi1.

overall_design: Bmi1 gene was knocked out and microarray was used to screen the target genes up-regulated in mouse liver tissues.

first: Chuanrui

last: Xu

first: Bin

last: Li


title: Evolutionary Convergence of Pathway-specific Enzyme Expression Stoichiometry

city: Montreal

first: Jean-Benoit

last: Lalanne

state: QC

address: 5155 Chem. de la Rampe

department: Biochemistry and Molecular Medicine

institute: University of Montreal

summary: Coexpression of proteins in response to pathway-inducing signals is the founding paradigm of gene regulation. Yet, it remains unexplored whether the relative abundance of coregulated proteins requires precise tuning. Here we present large-scale analyses of protein stoichiometry and corresponding regulatory strategies for 21 pathways and 67-224 operons in divergent bacteria separated by 0.6-2 billion years. Using end-enriched RNA-sequencing (Rend-seq) with single-nucleotide resolution, we found that many bacterial gene clusters encoding conserved pathways have undergone massive divergence in transcript abundance and architectures via remodeling of internal promoters and terminators. Remarkably, these evolutionary changes are compensated post-transcriptionally to maintain preferred stoichiometry of protein synthesis rates. Even more strikingly, in eukaryotic budding yeast, functionally analogous proteins that arose independently from bacterial counterparts also evolved to convergent in-pathway expression. The broad requirement for exact protein stoichiometries despite regulatory divergence provides an unexpected principle for building biological pathways both in nature and for synthetic activities.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

sample_organism: Escherichia coli str. K-12 substr. MG1655

sample_organism: Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759

overall_design: Three ribosome profiling datasets (two in Bacillus subtilis and one in Vibrio natriegens). Eighteen Rend-seq data sets (Esherichia coli,  Bacillus subtilis, Vibrio natriegens, and Caulobacter crescentus, including mutants and different library preparations).

first: James

middle: C

last: Taggart

first: Monica

last: Guo

first: Lydia

last: Herzel

first: Ariel

last: Schieler

first: Gene-Wei


title: Dynamic and integrated transcriptional code orchestrates the angiogenic response

first: bing


title: Expression data from heat-damaged MHCC97H treated by HGF

status: Public on Mar 27 2018

first: Rui

last: Zhang

address: Fenglin road of Xuhui district

institute: Zhongshan hospital of Fudan University

summary:
Incomplete heat-damaged MHCC97H ususlly recurred. The mechanism of how residual HCC cells survive sublethal heat stress and develop rapid outgrowth remains poorly understood.
We used microarrays to detail the gene expression and identified distinct classes of up-regulated and downregulated genes under the treatment of HGF at different dosages.

overall_design: Sample from heat-damaged MHCC97H treated by HGF for RNA extraction and hybridization on Affymetrix microarrays. We sought to  identified distinct classes of up-regulated and downregulated genes during this process. To that end, we compared differential genes among three groups:  heat-damaged MHCC97H treated by HGF at 0 ng/ml, 2ng/ml, 10ng/ml.

first: Min

last: Ma

first: Xia-Hui

last: Lin

first: Hua-Hua

first: Jie

first: Jun

first: Dong-Mei

last: Gao

first: Jie-Feng

last: Cui

first: Zheng-Gang

last: Ren

first: Rong-Xin


title: Large differences in small RNA composition between human biofluids - 10 biofluids

city: San Francisco

first: David

last: Erle

state: CA

address: 1550 4th Street, Bldg 19B

institute: University of California, San Francisco

type: Non-coding RNA profiling by high throughput sequencing

summary: One goal of Phase 1 of our project is to produce reference profiles of miRNAs and other small RNAs in a large and diverse set of biofluids using a systemic approach. This study contains samples associated with 10 different biofluids, and all data (sequencing data, full alignments, etc.) is openly available.

overall_design: 10-12 donors each from 12 biofluids using modified TruSeq protocol with randomized adapters

first: Paula

last: Godoy

first: Nirav

middle: R

last: Bhakta

first: Andrea

last: Barczak

first: Prescott

last: Woodruff


title: Analysis of gene expression profile in the control and CHD7-knockdown hiPSC-derived lt-NES cells (scRNA-Seq)

city: Shinjuku-ku

first: Tsukasa

last: Sanosaka

state: Tokyo

address: 35 Shinanomachi

department: Department of Physiology

institute: Keio University School of Medicine

summary: CHARGE syndrome is a congenital disorder caused by mutations in Chromodomain Helicase DNA-binding domain 7 (CHD7) gene. We performed single cell RNA-seq analysis in CTRL and CHD7-knockdown lt-NES cells.

overall_design: Single cell RNA-Seq profiling of control (shCTRL) and CHD7-knockdown (sh410 or sh411) cells.


title: Study of dynamic transcriptome profiling in DNA damage-induced cellular senescence and transient cell-cycle arrest

city: Beijing

first: Zhen

last: Zhao

address: Haidian District

department: Department of Automation

institute: Tsinghua University

summary: For studing dynamic transcriptome profiling in DNA damage-induced cellular senescence and transient cell-cycle arrest, samples were treated with the DNA-damaging agent bleomycin at 0 ug/ml, 2 ug/ml and 40 ug/ml for 2 h. High-resolution time course analysis of gene expression in DNA damage-induced cellular senescence and transient cell-cycle arrest was used to explore the transcriptomic differences between different cell fates after DNA damage response.

overall_design: Examination of IMR90 cells with different levels of DNA damage.

first: Xiaowo

last: Wang


title: Microarray analysis of subcutaneous adipose tissue obtained in 27 moderate obese women

city: paris

first: veronique

last: PELLOUX

address: 50-52 bld Vincent Auriol

department: UMR 1166 eq 6

country: France

institute: INSERM

summary: The mechanisms responsible for weight loss-induced improvement in insulin sensitivity are partially understood. Greater insight can now be achieved through deep phenotyping and data integration. Here, we used an integrative approach to investigate associations between changes in insulin sensitivity and variations in lifestyle factors (diet and physical activity), subcutaneous adipose tissue (sAT) gene expression, metabolomics in serum, urine and feces, and gut microbiota composition after a 6-week calorie restriction period in overweight and obese adults

overall_design: Subcutaneous adipose tissue obtained by needle (BTA), in 27 moderate obese women.(BMI 33.3 ± 3.8 kg / m2). Comparison of two periods: After diet (after 6 weeks VLCD) compared to before diet (J0). Total RNA was amplified and labeled using kit (Ambion, Austin, TX) was used according to the manufacturer's instructions.

first: Maria

last: Pelloux

first: Karine

last: Clement


title: Genome-wide maps of SMAD2-chromatin binding state in TGFbeta-treated vascular smooth muscle cells

city: Cambridge

first: zehua

last: chen

state: Massachusetts

address: 55 Cambridge Parkway

institute: WuXi NextCODE

summary: To further explore the role of these two factors in SMC reprogramming, we treated human aortic smooth muscle (HASMCs) in vitro with TGFβ and mapped binding of Smad2/3, which reflects TGFβ activity, and Pol2-Ser2p, which reflects transcriptional activity, by ChIP-seq analysis. Smad2/3 bound to numerous regulatory regions in the genome differentially regulating expression of numerous genes as demonstrate by alterations in Pol2-Serp2 binding profile and analysis of bulk RNA sequencing. Examination of the top 20 transcription factors identified by sequencing of Smad2/3 binding regulatory regions identified KLF4 gene as one of the most prominently regulated genes. Further analysis showed Smad2/3 binding to multiple KLF4 gene regulatory elements that increased following TGFβ treatment, indicating that KLF4 is a direct target of Smad2/3. At the same time, the amount of bound Pol2-Ser2p decreased, pointing to reduced transcriptional activity. In contrast, Smad2/3 did not bind to KLF2 or KLF5 regulatory elements, demonstrating that these genes are not directly regulated by TGFβ.

overall_design: Examination of the binding of SMAD in chromatin of vascular smooth muscle cell.

first: Pei-Yu

last: Chen

first: Lingfeng

last: Qin

first: Sharvari

last: Gujja

first: Zehua


title: A CLK3-HMGA2 alternative splicing axis impacts human hematopoietic stem cell molecular identity throughout development

status: Public on Apr 05 2018

first: Michael

last: Guo

state: MA

address: 415 Main St

institute: Broad Institute


title: AKBA regulates mRNA expression of mouse epidermis.

status: Public on Mar 24 2018

first: Jing

last: Bai

address: 280# South Chongqing Road

department: School of Medicine

summary: The goal of this study was to determine the effects of AKBA on mRNA expression of mouse epidermis.

overall_design: mRNA of AKBA gel treated and blank gel treated mouse epidermis were sequenced using Illumina Hiseq.

first: Honglin


title: Inhibitors of LSD1 target demethylase-independent activity to induce differentiation in acute myeloid leukemia [anti-H3K9 ac, anti-H3K27, RCOR1, SPI1, and MLL4 ChIP-Seq]

city: Manchester

first: Tim

last: Somervaille

state: Lancashire

address: Wilmslow Road

institute: Cancer Research UK Manchester Institute

summary: To determine whether changes in histone modifications directly correlate with changes in transcription, THP1 AML cells were treated with a potent and selective LSD1 inhibitor (OG86, 250nM) and then subjected to concomitant RNA sequencing (RNAseq) and ChIP sequencing (ChIPseq) for histone acetylation modifications, RCOR1, SPI1 and MLL4.

overall_design: THP1 AML cells were treated with 250nM OG86 or DMSO vehicle for 24 hours in RPMI with 10% fetal bovine serum.


title: Multi-environment fitness landscapes of a tRNA gene

status: Public on Mar 23 2018

city: Stanford

first: Chuan

last: Li

address: 327 Campus Drive

department: Biology

institute: Stanford University

type: Genome variation profiling by high throughput sequencing

summary: A fitness landscape (FL) describes the genotype-fitness relationship in a given environment.  To explain and predict evolution, it is imperative to measure the FL in multiple environments because the natural environment changes frequently.  Using a high-throughput method that combines precise gene replacement with next-generation sequencing, we determine the in vivo FL of a yeast tRNA gene comprising over 23,000 genotypes in four environments.  Although genotype-by-environment interaction (G×E) is abundantly detected, its pattern is so simple that we can transform an existing FL to that in a new environment with fitness measures of only a few genotypes in the new environment.  Under each environment, we observe prevalent, negatively biased epistasis between mutations (G×G).  Epistasis-by-environment interaction (G×G×E) is also prevalent, but trends in epistasis difference between environments are predictable.  Our study thus reveals simple rules underlying seemingly complex FLs, opening the door to understanding and predicting FLs in general.

overall_design: We constructed a library of more than 100,000 yeast strains, each carrying a tR(CCU)J gene variant at its native genomic location.  Three to five parallel competitions of this strain pool were conducted in each of four environments: 30°C in the rich medium YPD, 23°C in YPD, 37°C in YPD, and 30°C in YPD with 3% DMSO added.

first: Jianzhi

last: Zhang


title: Genome-wide map of H3K27me3 before and after AKBA treatment in HaCaT cells

status: Public on Mar 22 2018

first: Hong

middle: Lin

address: 280 Chongqing South Road

summary: The goal of this study was to compare the distribution of H3K4me3 before and after AKBA treatment to understand how small molecule AKBA affects the epigenetic state. To do this we performed ChIP-seq with an H3K27me3 antibody.

overall_design: We compared genome-wide H3K27me3 profiles generated by Next Generation Sequencing (NGS) between +AKBA and -AKBA conditions after 12 hours in HaCaT cells.


title: Chemical Inhibition of Ezh2 Alters Ex Vivo B cell Differentiation and Gene Expression Dynamics

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: To understand the role of Ezh2 in B cell differentiation B cells were stimulated ex vivo with LPS, Il2, and Il5 in the presence of DMSO or the selective Ezh2 inhibitor GSK343.  Following 3 days culture, activated B cells and Plasmablasts were FACS isolated and RNA-seq was performed to identify the molecular effects of Ezh2 inhibition on B cell subsets during differentiation.

overall_design: RNAseq on ex vivo differentiated B cell subsets treated with GSK343 or DMSO

first: C

middle: D

first: J

last: Boss


title: Gene chip analysis of NPCs with and without cocultured with ASCs

first: Zhihua Han

last: Han

state: Please select region, state or province

address: Xin Songjiang Road 650

department: Orthopedic Traumatology, Shanghai Trauma and Emergency Center

institute: Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University

summary: We used microarrays to detail the global programme of gene expression underlying the coculturing of degenerate NPCs and ASCs and identified distinct classes of altered genes and ncRNAs during this process.

overall_design: We used 3 samples (after coculturing) with 3 control (without coculturing), then compare the genes and ncRNAs.

first: Zhihua

first: Jianhong

last: Wu


title: DNA methylation inhibitor in HCT116

city: Chikusa-ku

first: Hitoshi

last: Ohtani

state: Nagoya

address: Furo-cho

department: Graduate School of Bioagricultural Sciences

institute: Nagoya University


title: Expression data from mouse bone marrow myeloid dendritic cells (classical DCs) and classical dendritic cells in spleen

status: Public on Mar 21 2018

city: St. Louis

first: Daniel

last: Link

state: MO

address: 660 South Euclid Avenue

department: Internal Medicine

institute: Washington University in St Louis

summary:
Classical dendritic cells may be found in mouse bone marrow and spleen. Due to the differences in their local environment, two populations may express different genes and potentially carry different functions
We used microarrays to compare the gene expression profiles between myeloid dendritic cells and classical dendritic cells in spleen. Our data supported the hypothesis that bone marrow myeloid dendritic cells are enriched for the expression of certain sets of genes that may play specific functions in the bone marrow microenvironment

overall_design: Myeloid dendritic cells and classical dendritic cells from bone marrow and spleen were FACS sorted from four mice. RNA were extracted from these sorted cells and processed for microarray using Affymetrix mogene 1.0 ST chip. Cells from one mouse represent one sample

first: Jingzhu


title: Expression data of control and adult-induced Bcl11b mutant dentate gyrus granule cells 4 weeks after induction.

city: Ulm

first: Ruth

last: Simon

address: Albert-Einstein-Allee 11

department: Institute of Molecular and Cellular Anatomy

institute: University of Ulm

summary:
Bcl11b plays an important role in postnatal dentate gyrus development and adult neurogenesis. To determine its role in adult neurogenesis independant from postnatal development the Bcl11b mutation was induced at the age of 2 months.
Microarray analysis was performed on RNA isolated 4 weeks after the induction of the Bcl11b mutation to determine Bcl11b target genes.

overall_design: Control and mutant dentate gyrus (DG) granule cells were isolated by laser capture microdisection and RNA isolated. Transcriptome analysis was performed by BRB-ArrayTools.

first: Karlheinz

last: Holzmann


title: Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities

city: Copenhagen N

first: Robin

last: Andersson

address: Ole Maaloes Vej 5

country: Denmark

institute: University of Copenhagen

summary: Sequencing of 5' ends of RNA molecules from control and exosome-depleted S2 cells.

overall_design: CAGE library construction from RNA extracted from control and exosome-depleted cells.


title: Epigenomics analysis of a fibrosarcoma with ESCC case

status: Public on Mar 20 2018

city: Shantou

first: Qian

last: Yang

state: Guangdong

address: Xinling 22 Road

institute: Medical College of Shantou University

summary: We detected DNA methylation of a fibrosarcoma with ESCC sample and the corresponding normal sample to identify the aberrant DNA methylation status in this rare disease.

overall_design: Bisulphite converted DNA from the 2 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Jian-Zhong

last: He

first: En-Min

first: Li-Yan

last: Xu


title: RNA-Seq of fibrosarcoma with ESCC case

summary: Analysis of a fibrosarcoma with ESCC case at transcriptome level

overall_design: RNA-Seq of normal esophageal tissue and esophageal squamous cell carcinoma from the same individual.


title: Snai2 influences breast cancer evolution in a non-cell autonomous manner

city: Salamanca

first: Jesús

last: Pérez Losada

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

country: Spain

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

summary: SNAI2 is a transcription factor involved in multiple processes in both physiology and pathology, including apoptosis, epithelial-mesenchymal transition and tumorigenesis. The effects of SNAI2 on the epithelial compartment have been interpreted as an effect of its expression and action in that compartment. In this work, we demonstrated that the absence of Snai2 in other compartments has repercussions in different aspects of the behavior of the epithelial cells of luminal breast tumors, developed by MMTV-ErbB2/Neu transgenic mice that do not express SNAI2 in the epithelial component. The absent of SNAI2 in the stroma of these tumors is accompanied by different characteristics at histopathological and molecular levels than those having functional SNAI2. These results indicate that the expression of SNAI2 in the tumor niche contributes to the luminal tumor development and behavior.

overall_design: Mice were housed at the Animal Research Core Facility of the University of Salamanca. FVB/N-Tg(MMTVneu)202Mul/J, carrying the ErbB2 protooncogene (Guy et al., 1992) were obtained from the Jackson Laboratory. B6;129S1-Snai2tm2Grid/J Snai2-deficient mice were generated by Dr. Gridley (Jiang et al., 1998) To generate the parous cohort, Snai2 WT ERBB2+ and Snai2 KO

first: Lourdes

last: Hontecillas-Prieto

first: Adrián

last: Blanco-Gómez

first: Andrés

last: Castellanos-Martín

first: María

last: del Mar Sáez-Freire

first: Diego

last: Alonso-López

first: Mar

last: Lorente

first: Ana

last: García-Casas

first: Begoña

last: García-Cenador

first: Javier

last: García-Criado

last: Abad

last: de las Rivas

first: Jian-Hua

last: Mao

first: Thomas

last: Gridley

last: Pérez-Losada

first: Sonia

last: Castillo-Lluva


title: Chromosome loop control of oncogenic MYC produces a common vulnerability in diverse cancers [HiChIP]

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: The majority of human cancers become highly dependent on a deregulated MYC oncogene, thus identifying a common mechanism underlying MYC regulation could provide valuable targets for therapy. We show here that diverse tumor-specific super-enhancers acquired throughout the 3Mb MYC insulated neighborhood functionally interact with a single conserved site occupied by CTCF protein in the MYC promoter. CRISPR-mediated deletion analysis shows that this common CTCF site is required for super-enhancer looping to the MYC promoter, high MYC expression and rapid cell proliferation in multiple cancers. Targeted methylation of the MYC enhancer anchor by a dCAS9-DNMT3A-3L fusion protein abrogates CTCF binding with consequent loss of MYC expression, suggesting a common vulnerability and a novel approach for therapeutic targeting of aggressive cancers.

overall_design: Evaluation of SMC1 loops in human colorectal cancer cell line

first: Jurian

last: Schuijers


title: Cell-free DNA modification dynamics in abiraterone acetate-treated prostate cancer patients

city: Vilnius

first: Algimantas

last: Krisciunas

address: Sauletekio al. 7

country: Lithuania

institute: Vilnius University

summary:
Purpose: Primary resistance to abiraterone acetate (AA), a key medication for the treatment of metastatic castration-resistant prostate cancer, occurs in 20-40% of the patients. We aim to identify predictive biomarkers for AA-treatment response and understand the mechanisms related to treatment resistance.

Experimental Design: We used the Infinium Human Methylation 450K BeadChip to monitor modification profiles of cell-free circulating DNA (cfDNA) in 108 plasma samples collected from 33 AA-treated patients.

Results: Thirty cytosines showed significant modification differences (FDR q < 0.05) between the AA-sensitive and AA-resistant patients during the treatment, of which 21 cytosines were differentially modified prior to treatment. In addition, the AA-sensitive patients, but not AA-resistant patients, lost interindividual variation of cfDNA modification shortly after starting AA-treatment, but such variation returned to initial levels in the later phases of treatment.

Conclusions: Our findings provide a list of potential biomarkers for prediction of AA-treatment response, highlight the prognostic value of using cytosine modification variance as biomarkers, and shed new insights into the mechanisms of prostate cancer relapse in AA-sensitive patients.

overall_design: 181 (120 unique samples + 61 technical replicates) cell free DNA samples were collected from 33 patients undergoing abiraterone acetate (AA) treatment. Bisulphite converted cell free DNA was hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.2. Patients classified to 'Sensitive' and 'Resistant' to treatment based on PSA change over the course of treatment. Samples marked as outliers were identified as described in the paper.

first: Juozas

last: Gordevicius

first: Daniel

middle: E

last: Groot

first: Steven

last: Yip

first: Miki

last: Susic

first: Andrew

last: Kwan

first: Rafal

last: Kustra

first: Anthony

last: Joshua

first: Kim

middle: N

last: Chi

first: Art

last: Petronis

first: Gabriel

last: Oh


title: Genome-wide occupancy of LSD1 in differentiating and differentiated C2C12 myoblasts.

status: Public on Mar 19 2018

city: Kumamoto

first: Kotaro

last: Anan

state: Kumamoto

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

department: Department of Medicall Cell Biology

institute: Kumamoto University

summary: ChIP-seq analysis of LSD1 in C2C12 cells. We found that LSD1 directly regulates the expression of fiber and metabolism genes during myogenesis. Results provide insight into the metabolic prgramming mechanisms of myogenesis.

overall_design: Examination of LSD1/DNA interaction in C2C12 myoblasts 48 h (day 2) and 120 h (day 5) post-differentiation.

first: Shinjiro

last: Hino

first: Mitsuyoshi

last: Nakao


title: Mitochondrial retrograde signaling in mammals is mediated by the transcriptional cofactor GPS2 via direct mitochondria-to-nucleus translocation [GRO-seq]

city: Boston

first: Valentina

last: Perissi

address: 72 E. Concord St

institute: Boston University

summary: As most of the mitochondrial proteome is encoded in the nucleus, mitochondrial functions critically depend on nuclear gene expression and bidirectional mito-nuclear communication. However, mitochondria-to-nucleus communication pathways are incompletely understood. Here, we identify G-Protein Pathway Suppressor 2 (GPS2) as a mediator of mitochondrial retrograde signaling and a key transcriptional activator of nuclear-encoded mitochondrial genes in mammals. GPS2 regulated translocation from mitochondria to nucleus is essential for the transcriptional activation of the nuclear stress response to mitochondrial depolarization and for supporting basal mitochondrial biogenesis in differentiating adipocytes and in brown adipose tissue from mice. In the nucleus, GPS2 recruitment to target gene promoters regulates histone H3K9 demethylation and RNA Polymerase II (POL2) activation through inhibition of Ubc13-mediated ubiquitination. These findings, together, reveal an unexpected layer of regulation of mitochondrial gene transcription, uncover a novel direct mitochondria-nuclear communication pathway and indicate that GPS2 retrograde signaling is a key component of the mitochondrial stress response in mammals.

overall_design: The changes in the gene expression profiles were investigated by RNA-seq, GRO-seq, and ChIP-seq, after the knock-down of GPS2 .

first: Maria

last: Cardamone

first: Bogdan

last: Tanasa


title: Genome-wide distribution of methylated H3K4 in LSD1-inhibited C2C12 myoblasts.

summary: ChIP-seq analysis of methylated H3K4 in LSD1-inhibited C2C12 cells. We found that LSD1 widely regulates the methylation levels of H3K4. Results provide insight into the molecular mechanisms of regulation of histone modification in myogenesis.

overall_design: Examination of H3, H3K4me1, H3K4me2 and H3K4me3/DNA interaction in LSD1-inhibited C2C12 myoblasts 48 h (day 2) post-differentiation.


title: Intratumoral CpG-B promotes anti-tumoral neutrophil, cDC, and T cell cooperation without reprograming tolerogenic pDC

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

summary: Cancer immunotherapies utilize distinct mechanisms to harness the power of the immune system to eradicate cancer cells. Therapeutic vaccines, aimed at inducing active immune responses against an existing cancer, are highly dependent on the immunological microenvironment, where many immune cell types display high levels of plasticity and, depending on the context, promote very different immunological outcomes. Among them, plasmacytoid dendritic cells (pDC), known to be highly immunogenic upon inflammation, are maintained in a tolerogenic state by the tumor microenvironment. Here we report that intratumoral (i.t.) injection of established solid tumors with CpG oligonucleotides-B (CpG-B) inhibits tumor growth. Interestingly, control of tumor growth was independent of tumor-associated (TA) pDC, which remained refractory to CpG-B stimulation and whose depletion did not alter the efficacy of the treatment. Instead, tumor growth inhibition subsequent to i.t. CpG-B injection depended on the recruitment of neutrophils into the milieu, resulting in the activation of conventional dendritic cells (cDC), subsequent increased anti-tumor T cell priming in draining lymph nodes, and enhanced effector T cell infiltration in the tumor microenvironment. These results reinforce the concept that intratumoral delivery of TLR9 agonists alters the tumor microenvironment by improving the anti-tumor activity of both innate and adaptive immune cells.

overall_design: mRNA profiles of tumor-associated plasmacytoid and conventional dendritic cells after intratumoral injection of CpG-B were generated by RNAseqencing, using Illumina HiSeq, 3-4 replicates per condition were used

first: Marion

last: Humbert

first: Leslie

last: Guéry

first: Dale

last: Brighouse

last: Lemeille

first: Stéphanie

last: Hugues


title: Genome-Wide DNA methylation analysis of tumor and adjacent normal prostate tissues

city: London

first: Bekim

last: Sadikovic

state: Ontario

address: 800 Commissioners Rd E

department: Pathology and Laboratory Medicine

institute: University of Western Ontario

summary: Archival formalin-fixed paraffin-embedded tissues were collected. The slides were reviewed by a pathologist to identify representative tumor tissue blocks. Enrichment of tumor cells was performed by tissue macro-dissection of predetermined areas, as outlined by Haemotoxylin and Eosin staining. Seven-micron thick sections in isolated areas of interest with at least 50% tumor cellularity were dissected to be used as tumor samples. Normal prostate samples were obtained from the adjacent tissues demonstrating no tumor involvement. Genomic DNA extraction was conducted using the Illumina FFPE DNA recovery kit. Following bisulfite conversion, DNA methylation analysis of the samples was performed using the Illumina Infinium methylation 450k bead chip array (San Diego, CA), according to the manufacturer’s protocol. Both tumor and normal samples were assayed in one experiment to avoid batch effect. The resulting methylated and unmethylated signal intensity data were imported into R 3.4.2 for analysis. Normalization was performed using Illumina normalization method with background correction using the minfi package in R 3.4.2.

overall_design: Bisulfate converted DNA, extracted from 47 FFPE prostate tissues (31 tumors and 16 adjacent normal), were hybridized to illumina infinium methylation 450k array.

first: Erfan

last: Aref-Eshghi


title: Twin DNA methylation profiling reveals flare-dependent interferon signature and B-cell promoter hypermethylation in systemic lupus erythematosus

city: Evry

first: Jorg

last: Tost

address: 2 rue Gaston Cremieux

institute: CEA-Institut de Genomique, Centre National de Genotypage

summary: Objective: Systemic lupus erythematosus (SLE) has limited monozygotic (MZ) twin concordance, implying a role for other pathogenic factors than genetic variation, such as epigenetic changes. Using the disease discordant twin model, we investigated genome-wide DNA methylation changes in sorted CD4+ T-cells, monocytes, granulocytes and B-cells in twin pairs with at least one SLE-affected twin. Methods: Peripheral blood from 15 SLE twin pairs (six MZ, nine dizygotic (DZ)) was processed using gradient density centrifugation for the granulocyte fraction. CD4+ T-cells, monocytes and B-cells were further isolated using magnetic beads. Genome-wide DNA methylation was analysed using Infinium HumanMethylation450K BeadChips. Probes with a p-value <0.01 between SLE twins and co-twins were considered statistically significant and a median DNA methylation difference >7% biologically relevant. Findings were validated using pyrosequencing and replicated in an independent case-control sample. Results: In paired analyses of discordant SLE twins restricted to the gene promoter and start region, we identified 55, 327, 247 and 1628 genes with differentially methylated CpGs in CD4+ T-cells, monocytes, granulocytes and B-cells, respectively. All cell types displayed marked hypomethylation in interferon-regulated genes, such as IFI44L, PARP9 and IFITM1, which was more pronounced in twins with flare within the past two years. In contrast to the other cell types, differentially methylated CpGs in B-cells were predominantly hypermethylated, where the most important upstream regulators included TNF and EP300. Conclusion: Hypomethylation of interferon-regulated genes occurs in all major cellular compartments in SLE twins. The observed B-cell promoter hypermethylation is a novel finding with potential significance for SLE pathogenesis.

overall_design: Fifteen Danish twin pairs were included in the study, 13 twin pairs are submitted to GEO (excluding two concordant twin pairs).

first: Constance

last: Ulff-Møller

first: Fazila

last: Asmar

first: Yi

last: Liu

first: Anders

last: Svendsen

first: Florence

last: Busato

first: Kirsten

last: Grønbæk

first: Jörg

first: Søren

last: Jacobsen


title: IGF2BP1 enhances an aggressive tumor cell phenotype by impairing miRNA-directed downregulation of oncogenic factors [HUH-7 small RNA]

city: Halle

first: Markus

last: Glaß

address: Kurt-Mothes-Str. 3a

department: Institute of Molecular Medicine

institute: Martin Luther University Halle-Wittenberg

summary: The oncofetal IGF2 mRNA binding protein (IGF2BP) family modulates tumor cell properties but IGF2BP paralogue-specific roles remain poorly understood. We demonstrate that phenotypic roles of IGF2BPs vary in a cancer cell-dependent manner. However, only IGF2BP1 shows oncogenic potential in all cancer cells analyzed. Consistently, only IGF2BP1 expression is associated with poor prognosis in ovarian carcinoma and promotes all oncogenic properties analyzed in ovarian cancer-derived tumor cells. Despite a substantial overlap of candidate target mRNAs of IGF2BP paralogues proposed by CLIP analyses, the paralogue-specific depletion of IGF2BPs induces strikingly distinct deregulation of mRNA abundance. Transcripts decreased by IGF2BP1 depletion or knockout are enriched for IGF2BP1- as well as AGO-CLIP hits conserved in distinct cell lines, are prone to targeting by highly abundant miRNAs and comprise significantly longer 3’UTRs. Downregulation of target mRNAs upon IGF2BP1 depletion is abrogated when miRNAs are expressed at low levels or depleted by DICER/DROSHA knockdown. Strikingly, the depletion of all 12 randomly selected miRNA-prone target mRNAs impairs at least one analyzed IGF2BP1-modulated tumor cell property. These findings indicate that IGF2BPs serve distinct roles in cancer-derived cells and suggest that IGF2BP1’s main role is the post-transcriptional, miRNome-dependent enhancement of factors promoting oncogenic tumor cell properties.

overall_design: small RNA-Seq of HUH-7 cells. One replicate.

first: Simon

last: Müller

first: Nadine

last: Bley

first: Bianca

last: Busch

first: Vanessa

last: Rousseau

first: Danny

last: Misiak

first: Tommy

last: Fuchs

first: Marcell

last: Lederer

first: Stefan

last: Hüttelmaier


title: IGF2BP1 enhances an aggressive tumor cell phenotype by impairing miRNA-directed downregulation of oncogenic factors

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

overall_design: Refer to individual Series


title: Leukemia reconstitution in vivo is driven by cells in early cell cycle and low metabolic state

status: Public on Mar 18 2018

city: Padova

first: Luca

last: Trentin

address: Via Giustiniani, 3

department: Department of Women's and Children's Health

country: Italy

institute: University of Padova

summary: To characterize LICs in ALL irrespective of surface markers expression, we investigated leukemia initiating activities of cellular subfractions of patient-derived xenograft BCP-ALL cells sorted according to different cell cycle phases (i.e. G0/G1 and G2/M) followed by transplantation onto NOD/SCID mice. All cell fractions led to leukemia engraftment indicating LIC activity irrespective of cell cycle stage. Most importantly, cells isolated from G0/G1 cell cycle phases led to early leukemia engraftment in contrast to cells from late cell cycle (G2/M). To further characterize cells with different engraftment potential in vivo, we analyzed the gene expression profiles of early (G1b early) and late (G2/M) engrafting cells.

overall_design: Gene expression was measured using  Affymetrix platform in 8 BCP-ALL patient derived xenograft samples sorted according to cell cycle annotations

first: Lueder-Hinrich

last: Meyer


title: Expression data of E7.5 primary germ layers

status: Public on Mar 17 2018

city: Jinan

first: Xukun

last: Lu

address: No. 44 Wenhua West Road

institute: Shandong University


title: Emory University African American Microbiome in Pregnancy Cohort

first: Anna

last: Knight

state: Georgia

address: 101 Woodruff Circle NE

institute: Emory University


title: RppH can faithfully replace TAP to allow cloning of 5’-triphosphate carrying small RNAs

city: Mainz

first: René

last: Ketting

address: Ackermannweg 4

institute: Institute of Molecular Biology

summary: RNA interference was first described in the nematode Caenorhabditis elegans. Ever since, several new endogenous small RNA pathways have been described and characterized to different degrees. Much like plants, but unlike Drosophila and mammals, worms have RNA-dependent RNA Polymerases (RdRPs) that directly synthesize small RNAs using other transcripts as a template. The very prominent secondary small interfering RNAs, also called 22G-RNAs, produced by the RdRPs RRF-1 and EGO-1 in C. elegans, maintain the 5’ triphosphate group, stemming from RdRP activity, also after loading into an Argonaute protein. This creates a technical issue, since 5’PPP groups decrease cloning efficiency for small RNA sequencing. To increase cloning efficiency of these small RNA species, a common practice in the field is the treatment of RNA samples, prior to library preparation, with Tobacco Acid pyrophosphatase (TAP). Recently, TAP production and supply was discontinued, so an alternative must be devised. We turned to RNA 5’ pyrophosphohydrolase (RppH), a commercially available pyrophosphatase isolated from E. coli. Here we directly compare TAP and RppH in their use for small RNA library preparation.

overall_design: A single RNA sample was divided into 6 technical replicates. Three of these technical replicates were treated with Tobacco Acid Phosphatase (TAP, Epicentre) and the other three, with RNA 5’Pyrophosphohydrolase (RppH, New England Biolabs, #M0356S).

first: Miguel

last: Vasconcelos Almeida

first: António

last: de Jesus Domingues

first: Hanna

last: Lukas

first: Maria

last: Mendez-Lago

middle: F


title: Whole-transcriptome splicing profiling of embryonic day (E)7.5 mouse primary germ layers [RNA-seq]

summary: Alternative splicing (AS) and alternative promoter (AP) usage expand the repertories of mammalian transcriptome profiles and thus diversify gene functions. However, our knowledge about the extent and functions of AS and AP usage in mouse early embryogenesis remains elusive. Here, by performing whole-transcriptome splicing profiling with high-throughput next generation sequencing, we report that AS extensively occurs in embryonic day (E) 7.5 mouse primary germ layers, and may be involved in multiple developmental processes. In addition, numerous RNA splicing factors are differentially expressed and alternatively spliced across the three germ layers, implying the potential importance of AS machinery in shaping early embryogenesis. Notably, AP usage is remarkably frequent at this stage, accounting for more than one quarter (430/1648) of the total significantly different AS events. Genes generating the 430 AP events participate in numerous biological processes, and include important regulators essential for mouse early embryogenesis, suggesting that AP usage is widely used and might be relevant to mouse germ layer specification. Our data underline the potential significance of AP usage in mouse gastrulation, providing a rich data source and opening another dimension for understanding the regulatory mechanisms of mammalian early development.

overall_design: The alternative splicing patterns were captured and compared between the three germ layers from E7.5 mouse

first: Lei

last: Li


title: Base editing with a Cpf1–cytidine deaminase fusion

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

summary: The targeting range of CRISPR-Cas9 base editors (BEs) is limited by their G/C-rich PAM sequences. To overcome this limitation, we developed a CRISPR/Cpf1-based BE by fusing the rat cytosine deaminase APOBEC1 to a catalytically inactive version of Lachnospiraceae bacterium Cpf1. The base editor recognizes a T-rich PAM sequence and converts C to T in human cells with low levels of indels, non-C-to-T substitutions and off-target editing.

overall_design: Examination of indels and base substitutions induced by the CRISPR/Cpf1 base editors

first: Jia

last: Chen

first: Xingxu

last: Huang

first: Bei

first: Ying

last: Wang

first: Xiaosa


title: Spontaneous mutations in CYC8 and MIG1 suppress the short chronological lifespan of budding yeast lacking SNF1/AMPK

city: New York

first: Ryan

last: Fine

state: NY

address: 435 E 30th Street

department: Center for Human Genetics and Genomics

institute: NYU Langone

summary: Chronologically aging yeast cells are prone to adaptive regrowth, whereby mutants with a survival advantage spontaneously appear and re-enter the cell cycle in stationary phase cultures. Adaptive regrowth is especially noticeable with short-lived strains, including those defective for SNF1, the homolog of mammalian AMP-activated protein kinase (AMPK). SNF1 becomes active in response to multiple environmental stresses that occur in chronologically aging cells, including glucose depletion and oxidative stress. SNF1 is also required for the extension of chronological lifespan (CLS) by caloric restriction (CR) as defined as limiting glucose at the time of culture inoculation. To identify specific downstream SNF1 targets responsible for CLS extension during CR, we screened for adaptive regrowth mutants that restore chronological longevity to a short-lived snf1∆ parental strain. Whole genome sequencing of the adapted mutants revealed missense mutations in TPR motifs 9 and 10 of the transcriptional co-repressor Cyc8 that specifically mediate repression through the transcriptional repressor Mig1. Another mutation occurred in MIG1 itself, thus implicating the activation of Mig1-repressed genes as a key function of SNF1 in maintaining CLS. Consistent with this conclusion, the cyc8 TPR mutations partially restored growth on alternative carbon sources and significantly extended CLS compared to the snf1∆ parent. Furthermore, cyc8 TPR mutations reactivated multiple Mig1-repressed genes, including the transcription factor gene CAT8, which is responsible for activating genes of the glyoxylate and gluconeogenesis pathways. Deleting CAT8 completely blocked CLS extension by the cyc8 TPR mutations on CLS, identifying these pathways as key Snf1-regulated CLS determinants.

overall_design: 24 RNA-seq cDNA libraries consisting of 3 timepoints taken from  WT, snf1 null, and snf1 supressor strains.

first: Nazif

last: Maqani

first: Mehreen

last: Shahid

first: Mingguang

first: Elisa

last: Enriquez-Hesles

first: Jeffrey

last: Smith


title: Neural Stem Cell Extracellular Vesicle-Treated Microglia and Transcriptional Response

status: Public on Mar 15 2018

city: Clemson

first: David

middle: Matthew

last: Feliciano

state: South Carolina

address: 132 Long Hall

department: Biological Sciences

institute: Clemson University

summary: Extracellular vesicles (EVs) were isolated from primary cultures of neural stem cells (NSCs) and used to treat microglia.

overall_design: EVs were isolated by serial centrifugation from primary NSCs cultured from the subventricular zone of CD1 mice. Cultured microglia were then subjected to control or EV treatments and RNA isolated by Trizol extraction. Library preparation was performed with an NEBNext Ultra RNA Library Preparation Kit according to the manufacturer’s protocol (New England Biolabs). 2 x 150 base pair reads were generated at a depth of 56-84 million reads per sample on an Illumina HiSeq 4000.


first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: Single cell transcriptomic analysis of human CD25+ CD127- CD4+ Treg cells and CD25- CD127+ CD4+ Tconv cells isolated from peripheral blood from two different donors

overall_design: Single cells were sorted by flow cytometry for single cell RNAseq library preparation (InDrops)

last: Zemmour

first: Christophe

last: Benoist


title: Different neuronal activity patterns induce different gene expression programs

status: Public on Mar 16 2018

first: Kelsey

last: Tyssowski

address: 77 Ave Louis Pasteur

department: Genetics


title: Whole blood gene expression in adolescent Chronic Fatigue Syndrom (CFS) by RNA-Seq

city: Lørenskog

first: Vegard

last: Wyller

address: Sykehusveien 20

country: Norway

institute: Akershus University Hospital

summary: This study compared whole blood gene expression in CFS adolescent and healthy controls, and explored associations between gene expression and neuroendocrine markers, immune markers and clinical markers within the CFS group.

overall_design:
Whole blood samples from 29 CFS patient samples and 18 control samples of the Nor Capital project were extracted and their RNA were subjected to RNASeq to measure global gene expression

>>>Raw data are not available for this series due to patient privacy concerns<<<

first: Chinh

middle: B

last: Nguyen


title: The Ultraconserved Long Noncoding RNA, T-UCstem1, controls proliferation and safeguards self-renewal of embryonic stem cells

city: Parma

first: Guidantonio

last: Malagoli Tagliazucchi

address: Via Gramsci 14

department: Division of Research and Innovation

institute: Hospital of Parma

summary: We reported RNA-seq transcriptome profiling of Control and T-UCstem1 KD ESCs (TBV2) grown in FBS/Lif and in optimal culture conditions (feeder cells/high density) using the Illumina HiSeq platform. Whole-genome expression revealed an enrichment in genes involved in regulation of cell proliferation, positive regulation of development and cell differentiation in T-UCstem1 depleted cells compared to N.T. A large number (~50%) of all the developmental regulatory genes that are up-regulated in T-UCstem1 KD ESCs are bivalent domains-associated genes. RNAseq data and validation both at RNA and protein level provide new evidences that T-UCstem1 is required to preserve self-renewal and transcriptional identity of ESCs.

overall_design: RNA-seq transcriptome profiling of Control and T-UCstem1 KD ESCs (TBV2) grown in FBS/Lif and in optimal culture conditions (feeder cells/high density).

first: Alessandro

last: Fiorenzano

first: Emilia

last: Pascale

first: Miriam

last: Gagliardi

first: Sara

last: Terreri

first: Mariarosaria

last: Papa

first: Gennaro

last: Andolfi

first: Marco

last: Galasso

first: Cristian

last: Taccioli

first: Eduardo

last: Patriarca

first: Amelia

last: Cimmino

first: Maria

last: Matarazzo

first: Gabriella

last: Minchiotti

first: Annalisa

last: Fico


title: MicroRNAs mediate liver transcriptome changes upon soy diet intervention in mice

city: Cluj-Napoca

first: Simona

last: Visan

state: Cluj

address: 34-36 Republicii

department: Functional Genomics, Proteomics and Experimental Pathology

country: Romania

institute: The Oncology Institute “Prof Dr. Ion Chiricuta”,

summary: Soy-based diets have triggered the interest of the research community due to their beneficial effects on a wide variety of pathologies like breast and prostate cancer, diabetes, and atherosclerosis. However, the molecular details underlying these effects are far from being completely understood and several recent attempts have been made to elucidate the soy-induced liver transcriptome changes in different animal models. Here we used Next Generation Sequencing to identify a set of two microRNAs specifically modulated by short-term soy-enriched diet in young male mice and estimate their impact on the liver transcriptome assessed by microarray. Clustering and topological community detection (CTCD) network analysis of STRING generated interactions of transcriptome data led to the identification of five topological communities of genes characteristically altered and putatively targeted by microRNAs upon soy diet intervention.

overall_design: One-color microarray study was performed to measure gene expression changes in the liver of mice fed for 4 weeks a soy-enriched diet compared to controls (the liver of mice fed for 4 weeks a regular food). Each group consisted of three biological replicates (mice).

first: Edward

last: Seclaman

first: Andrei

last: Anghel

first: Cristina

last: Bejinar

first: Ovidiu

last: Balacescu

first: Loredana

first: Mihai

last: Udrescu

first: Catalin

last: Marian

first: Ioan

middle: O

last: Sirbu


title: Developmental history provides a roadmap for the emergence of tumor plasticity

city: West Haven

first: Ryan

last: Chow

state: CT

address: 850 West Campus Drive

institute: Yale University

summary: Sox2 binding was assessed in lung epithelial cells, in the presence or absence of Nkx2-1.

overall_design: Examination of Sox2 ChIP-seq binding in lung epithelial cells, with or without Nkx2-1.

first: Purushothama

last: Tata


title: Different neuronal activity patterns induce different gene expression programs [RNA-Seq]

status: Public on Mar 14 2018

first: Kelsey

last: Tyssowski

summary: A vast number of different neuronal activity patterns could each induce a different set of activity-regulated genes. Mapping this coupling between activity pattern and gene induction would allow inference of a neuron's activity-pattern history from its gene expression and deepen our mechanistic understanding of activity pattern-dependent synaptic plasticity. In genome-scale experiments comparing brief and sustained activity patterns, we reveal that activity-pattern history can indeed be inferred from gene expression state. We find that brief activity selectively induces a small subset of the activity-regulated gene program that corresponds to the first of three temporal waves of genes induced by sustained activity. These first-wave genes are mechanistically distinct from genes in the later waves because their induction requires MAPK/ERK signaling but does not require de novo translation. Thus, the same mechanisms that establish the multi-wave temporal structure of gene induction also enable different gene sets to be induced by different activity patterns.

overall_design: Gene expression profiles of neurons in the presence/absense of MEK inhibition and neuronal activity.

middle: M


title: The roles of CSE1L in epigenetic silencing

city: Beijing

first: Zhuqiang

last: Zhang

address: 15 Datun Road, Chaoyang District.

institute: Institute of Biophysics, CAS

summary: Epigenetic silencing can be mediated by various mechanisms and many regulators remain to be identified. We identified CSE1L as a factor essential for silencing of the reporter gene and a fraction of endogenous methylated genes. CSE1L depletion did not cause DNA demethylation or increase of global histone acetylation. Nevertheless, these methylated genes derepressed by CSE1L depletion largely overlapped with methylated genes that were also reactivated by treatment of histone deacetylase inhibitors (HDACi).

overall_design: We measured DNA methylation by MeDIP and expression profiles by RNA-seq in B2-1 HEK293 cells and serveral Knockdown/treatment cells.

first: Qiang

last: Dong

first: Xiang

last: Li

first: Cheng-Zhi

last: Wang

first: Shaohua

last: Xu

first: Gang

last: Yuan

first: Wei

last: Shao

first: Hua

last: Huang

first: Yong

last: Zheng

first: Hailin

first: Xiaoguang

last: Lei

first: Bing

last: Zhu


title: Next Generation Sequencing Facilitates Quantitative Analysis of transcriptomes of human cord blood CD34+ cells treated with HDAC5 inhibitor

city: Indianapolis

first: Xinxin

state: IN

address: 950 W. Walnut St R2 304

department: Microbiology and Immunology

institute: Indiana University School of Medicine

summary: We have used RNA-seq based transcriptome characterization to analyze differentiated gene expression in human cord blood CD34+ cells treated with vehicle control or HDAC5 inhibitor LMK235

overall_design: Examination of mRNA profiles in in human cord blood CD34+ cells treated with vehicle control or HDAC5 inhibitor LMK235

first: Bin

last: Guo

first: Sheng

last: Liu

first: Jun

last: Wan

first: Hal

last: Broxmeyer


title: Dissecting the Functional Consequences of de Novo DNA Methylation Dynamics in Human Motor Neuron Differentiation and Physiology

city: Munich

first: Michael

middle: Johannes

last: Ziller

address: Kraepelinstrasse 2-10

department: Translational Psychiatry

institute: Max Planck Institute of Psychiatry

summary: DNA methylation is a well studied, yet still incompletely understood component of the multi-layered epigenome. The somatic DNA methylation landscape is established early in development, but remains highly dynamic within focal regions that tend to overlap with gene regulatory elements. The functional significance of these dynamic changes remains unresolved. Here we utilized a powerful human ESC differentiation model for the generation of motor neurons (MNs) in combination with genetic mutations in the de novo DNA methylation machinery to dissect the role of DNA methylation in directing somatic cell fate. We quantitatively and in high-resolution measure the molecular and functional consequences of epigenetic perturbation. We find defects in neuralization and MN development. We also observe decreased dendritic arborization and altered electrophysiological properties in DNMT3A KO MNs. Our work provides a specific list of epigenetically deregulated targets and a mechanistic link between de novo DNA methylation, cellular differentiation and human MN function.

overall_design:
We performed whole genome bisulfite sequencing and RNA-Seq on 3 time points during in vitro differentiation of human embryonic stem cells towards spinal motor neurons at day 0, day 6 and day 14 in three conditions, WT, DNMT3A and DNMT3B knockout backround in 3-5 replicates each. In addition, we also performed  single cell RNA-Seq on the same conditions and time point 6 and 14 as well as bisulfite amplicon sequencing.

Please note that raw data is to be made available through dbGaP (controlled access) due to privacy concerns.

first: Evangelos

last: Kiskinis

first: Alexander

last: Meissner


title: PU.1 represses and activates gene expression in early T cells by redirection of transcription factor ensembles [RNA-Seq]

city: Isehara

first: Hiroyuki

last: Hosokawa

state: Kanagawa

address: 143 Shimokasuya

department: Department of Immunology

institute: Tokai University School of Medicine

summary: Transcription factors normally regulate gene expression through their action at sites where they bind to DNA. However, the balance of activating and repressive functions that a transcription factor can mediate is not completely understood. Here, we show that PU.1 regulates gene expression in early stages of T-cell development both by recruiting partner transcription factors to its own binding sites and by depleting them from the binding sites that they may prefer when PU.1 is absent. Importantly, the loss of partner factors Satb1 and Runx1 occurs primarily from sites where PU.1 itself does not establish any detectable local binding. Genes linked to sites of partner factor ‘theft’ are enriched for considerable subsets of the genes PU.1 represses both in a model cell-line system and in normal T-cell development. Thus, system-level competitive recruitment dynamics permit PU.1 to affect gene expression both through own target sites and through action at a distance.

overall_design: RNA-seq; Total RNA was isolated from 300,000 cells using an RNAeasy MicroKit (Qiagen).  Libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (E7530, NEB) from ~1 μg of total RNA following manufacturer’s instructions.  Libraries were sequenced on Illumina HiSeq2500 in single read mode with the read length of 50 nt.

first: Jonas

last: Ungerbäck

first: Xun

first: Sarah

last: Cohen

first: Masaki

last: Matsumoto

first: Keiichi

middle: I

last: Nakayama

first: Tomoaki

last: Tanaka


title: Droplet based single cell RNA sequencing profiles of a murine model of type-1 diabetes

city: Melbourne

first: Mark

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

summary: Diabetic kidney disease remains the leading cause of end-stage renal disease, affecting ~30% of patients with long-standing type 1 and type 2 diabetes, and is characterized by proteinuria and gradual loss of kidney function. There is intense interest in understanding the responses of the many cell types present in the kidney to the diabetic milleu. In this study, we present single cell transcriptomes of renal cortex samples of wild-type and diabetic (C57BL/6-Ins2Akita/J) mice using Drop-Seq.

overall_design: Renal cortex samples from wild type and diabetic Akita mice (n=2 per group) underwent dissociation and Drop-seq.

first: Scott

last: Maxwell

first: Karly

last: Sourris

first: Keith

last: Al-Hasani

first: Assam

last: El-Osta


title: RNA-seq analysis of colorectal cancer cell line (CRC) SW1116 overexpressed POLR1D

status: Public on Mar 13 2018

city: guangzhou

first: wenbo

last: niu

address: shatai road 1023

institute: southern medical university

summary: Gene expression profiles were generated for CRC cell line SW1116 overexpressed POLR1D and empty vector to explore the effect of POLR1D on colorectal cancer cell line SW1116.

overall_design: SW1116 cells were infected with lentivirus overexpressing POLR1D and negative control lentivirus. After 72h, the GFP-positive cells were isolated by FACS. POLR1D overexpression was confirmed by RT-PCR and Western blotting. Then, the total RNA of POLR1D overexpression cells and negative control cells was extracted by Trizol reagent and sequenced using Illumina HiSeqTM4000 according to the manufacturer’s instructions.

first: Mingqing

last: Wang

first: Wenbo

last: Niu


title: Comparison of expression data from DLD-1 subpopulations

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

country: Germany

institute: University Medical Center Hamburg-Eppendorf

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

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

overall_design: Refer to individual Series


title: Comparison of expression data from DLD-1 subpopulations I

summary:
The function of cell-cell contact for radiochemosensitivity is unclear. Here, we investigate the role of the E-cadherin/catenin complex proteins under more physiological three-dimensional (3D) cell culture conditions in a panel of CRC cell lines.
To gain further insights, differential gene expression was investigated in DLD-1 subpopulations showing distinct morphology and invasion in 3D collagen type I.

overall_design: RNA extracted from DLD-1 subpopulations grown in 3D collagen type I (n=3 per subpopulation) was used for Affymetrix microarrays.

first: Nils

last: Cordes