title: Profiling of transcripts expression in Rag2 KO and wild type mice spleen by BeadChip array analysis

summary:
Purpose: The purpose of the study was to investigate the differential expression pattern of genes in Rag2 KO mice spleen compared to its wild type counterpart.
Methods: In this study, we have excised the spleen tissues from three Rag2 KO mice and three wild type mice, and then RNA samples were prepared with the spleen tissues for the analysis of transcriptomic profiles using the Illumina MouseRef-8 v2 Expression BeadChip platforms. The MouseRef-8 v2.0 BeadChip Kit content is derived from the national center for biotechnology information reference sequence (NCBI RefSeq) database (Build 36, Release 22). The content was supplemented with probes derived from the mouse exonic evidence based oligonucleotide (MEEBO) set, as well as standard protein-coding sequences described in the RIKEN FANTOM2 database. As well, the MouseRef-8 v2.0 BeadChip targets approximately 25,600 well-annotated RefSeq transcripts, over 19,100 unique genes, and enables the interrogation of 8 samples in parallel. The MouseRef-8 v2.0 BeadChip Kit uses the DirectHyb assay and is compatible with the iScan, HiScan, and Bead array reader systems.
Result: The genes expression BeadChip array analysis showed that many genes have been expressed differentially between Rag2 KO and wild type  mice spleen. These genes might be involved in the different biological and physiological processes including immune regulations.
Conclusion: The differential genes expression profile will provide important insight about the immune deregulation in Rag2 KO mice.

overall_design: Spleen RNA derived from Rag2 KO and wild type mice were profiled by microarray, in triplicates for each sample, by the Illumina MouseRef-8 v2 Expression BeadChip platforms.


title: SENP6 in OCP maintenance

status: Public on Nov 28 2017

city: Grand Rapids

first: Tao

last: Yang

state: MI

address: 333 Bostwick Ave NE

department: Cancer and Cell Biology

country: USA

institute: Van Andel Research Institute

type: Expression profiling by high throughput sequencing

summary: To understand the role of sumoylation/desumoylation pathway in skeletla development and homeostasis, we compared the transcriptomic profiles of primary rib chondrocytes from WT vs.Dermo1-Cre;Senp6f/f mice.

overall_design: Total RNA were extracted from Dermo1-Cre;Senp6f/f (Mut) and Senp6f/f (WT) mice (n=2), and used for RNAseq service provided by BGI.


title: Control of gene expression in senescence through transcriptional read-through of convergent protein-coding genes [RNA-Seq siRNA H2A.Z]

city: Toulouse

first: Estelle

last: Nicolas

address: 118 route de Narbonne

country: France

institute: INSERM

type: Non-coding RNA profiling by high throughput sequencing

summary: Antisense RNAs are non-coding RNAs, which can regulate their corresponding sense RNAs and are generally produced from specific promoters. By genome-wide approaches and in depth analyses at specific loci in human cells undergoing senescence, we uncover a family of antisense RNAs produced by transcriptional read-through at convergent protein-coding genes. Importantly, these antisense RNAs, that we named STARTs, repress the expression of their corresponding sense RNAs. We found that the elongation rate of RNA pol II is limited downstream of the TTS at START loci in proliferative cells. This allows transcription termination to occur before the RNA pol II reaches the convergent genes, thus preventing antisense RNA production and interference with the expression of the convergent genes. In proliferative cells, STARTs are repressed by the histone variant H2A.Z, whose local occupancy decreases in senescence. Our results thus uncover a novel mechanism of gene expression regulation, relying on the control of the expression of read-through antisense transcripts at convergent genes and underline the functional importance of the epigenetic control of RNA pol II elongation rate at intergenic regions.

overall_design: Strand-specific RNA-seq datasets in si-Ctrl and in siH2A.Z- treated WI38 hTERT RAF1-ER cells (2 replicates).

first: Lisa

last: Muniz

first: Maharshi

last: Deb

first: Marion

last: Aguirrebengoa

first: Didier

last: Trouche


title: Control of gene expression in senescence through transcriptional read-through of convergent protein-coding genes [RNA-Seq PROLIF-SEN]

overall_design: Strand-specific RNA-seq datasets in proliferative cells and in Raf1-induced senescent cells (2 replicates).

first: Sandra

last: Lazorthes


title: Control of gene expression in senescence through transcriptional read-through of convergent protein-coding genes

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Primary Tumor-Derived Liver Cancer Organoids Promote Metastasis in vivo

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: Past studies have identified hepatic tumors with mixed hepatocellular carcinoma (HCC) and cholangiocarcinoma (CC) characteristics which have a more aggressive behavior and a poorer prognosis than classic HCC. Whether this pathological heterogeneity is due to a cell of origin of bipotent liver progenitors or the plasticity of cellular constituents comprising these tumors remains debated. In this study, we investigated the potential acquisition of CC-like traits during advanced development of HCC in mice. We first characterized the primary and rare high-grade HCC developed in a genetic mouse model. We further developed a mouse model of highly efficient HCC invasion and metastasis via orthotopic transplantation of liver cancer organoids (LCOs) propagated from primary tumors in the genetic model. We found invasive/metastatic tumors developed in both models closely recapitulated advanced human HCC, and displayed a striking acquisition of CC-related pathological and molecular features which was absent in the primary HCC tumors. Our study directly demonstrates the pathological evolution of HCC during advanced tumor development, providing the first evidence that tumors with mixed HCC and CC features, or at least a subset of these tumors, represent a more advanced developmental stage of HCC. Lastly, we found LCO-generated high-grade tumors exhibited significantly increased extracellular vesicle (EV) secretion, suggesting that identifying tumor-specific EV proteins in plasma may be a promising tool for liver cancer detection.

overall_design: comparing normal liver, organoids and  primary tumor from mice

first: Liyuan

last: Li

first: Maoxiang

last: Qian

first: Arzu

last: Onar-Thomas

first: Melissa

last: Johnson

first: Christopher

last: Calabrese

first: Armita

last: Bahrami

first: Jun

middle: J

first: Dolores

middle: H

last: Lopez-Terrada

first: Liqin

last: Zhu


title: Gene expressions of BMDC with or without Rbpj

status: Public on Nov 27 2017

city: Tokushima

first: Koji

last: Yasutomo

address: 3-18-15 Kuramoto-cho

department: Graduate school of Biomedical Sciences

country: Japan

institute: Tokushima University

summary: cDNA microarray data of Bone marrow-derived dendritic cells (BMDC) with or without Rbpj gene

overall_design: Bone marrow cells from Rbpj fl/fl (RFF) or Rbpj fl/fl x CD11c-cre (RFF11) mice were cultured to differentiate into dendritic cells. CD11c+ cells were isolated and subjected to cDNA microarray analysis


title: Gene expression changes associated with high density collagen microenviroment in cancer cells

status: Public on Nov 26 2017

city: La Jolla

first: Daniel

last: Ortiz

state: California

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California San Diego

summary: We report RNA sequencing data from 2 cancer cell line (fibrosarcoma, HT1080 and Breast cancer, MDA-MB-231) and one non-canceours cell line (human foreskin fibroblast HFF) embbeded in two different 3D collagen matrix environements. The topographical organization of collagen within the tumor ECM has been implicated in guiding cancer cell migration and independently predicts progression to metastasis. Here, we show that collagen matrices with small pores and short fibers, but not Matrigel, trigger a conserved transcriptional response and subsequent motility switch in cancer cells that results in formation of multicellular network structures. The response is not mediated by hypoxia, matrix stiffness, or bulk matrix density, but by matrix architecture and beta1 integrin upregulation. The transcriptional module associated with network formation is enriched for migration and vasculogenesis-associated genes that predicted survival in patient data across nine distinct tumor types. Evidence at the protein level of this gene module is found in patient tumors displaying a vasculogenic mimicry (VM) phenotype. Our findings link a collagen matrix-induced migration program to VM, and suggest that this process may be broadly relevant to metastatic progression in solid human cancers.

overall_design: Total RNA extraction and mRNA sequencing of 3 diiferent cell lines cultured in 2 different collagen matrix conditions.

first: Stephanie

last: Fraley


title: Control of gene expression in senescence through transcriptional read-through of convergent protein-coding genes [ChIP-Seq]

first: Estelle

last: Nicolas

overall_design: ChIP-seq H2A.Z and H3 datasets in proliferative and in senescent WI38 hTERT RAF1-ER cells.

first: Lisa

last: Muniz


title: Transcription Rate Strongly Affects Splicing Fidelity and Co-transcriptionality in Budding Yeast

status: Public on Nov 25 2017

city: Edinburgh

first: Vahid

last: Aslanzadeh

address: Mayfield Road

department: Wellcome Trust Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

summary: The functional consequences for alternative splicing of altering the transcription rate have been the subject of intensive study in mammalian cells but less is known about effects on splicing of changing the transcription rate in yeast. We present several lines of evidence showing that slow RNA polymerase II elongation increases both co-transcriptional splicing and splicing efficiency and faster elongation reduces co transcriptional splicing and splicing efficiency in budding yeast, suggesting that splicing is more efficient when co-transcriptional. Moreover, we demonstrate that altering RNA polymerase II elongation rate in either direction compromises splicing fidelity, and we reveal that splicing fidelity depends largely on intron length together with secondary structure and splice site score. These effects are notably stronger for the highly expressed ribosomal protein coding transcripts. We propose that transcription by RNA polymerase II is tuned to optimise the efficiency and accuracy of ribosomal protein gene expression, while allowing flexibility in splice site choice with the nonribosomal protein transcripts.

overall_design: Examination of pre-mRNA splicing in RNAPII elongation mutants.  All experiments were performed in duplicate.

first: Jean

middle: D

last: Beggs


title: Global unleashing of transcription elongation waves in response to genotoxic stress restricts somatic mutation rate

city: Vari

first: Maria

last: Fousteri

address: 34 Fleming Street

department: Institute for Fundamental Biomolecular Research

country: Greece

institute: Biomedical Sciences Research Center "Alexander Fleming"

summary: Complex molecular responses preserve gene expression accuracy and genome integrity in the face of environmental perturbations. Here we report that, in response to UV-irradiation, RNA Polymerase II (RNAPII) molecules are dynamically and synchronously released from promoter-proximal regions to promote uniform and accelerated scanning of the whole transcribed genome. The maximised influx of de novo released RNAPII correlates with increased sensing of damaged sites, as confirmed by RNAPII accumulation at dipyrimidine sites and by the average slow-down of elongation rates in gene bodies. By triggering this transcription elongation ‘safe’ mode, endangered cells guarantee an efficient DNA repair regardless of damage location, gene size and transcription level. Accordingly, in clinically-relevant samples we detect low and homogenous rates of mutational signatures associated with UV-irradiation or cigarette-smoke across all active genes. Together, our data highlight a novel functional advantage associated with regulation of promoter-proximal pausing and provide unanticipated insights into the mechanism underlying the central role of active transcription in shaping the mutagenic landscape of cancer genomes.

overall_design:
ChIP-seq,  Nascent RNA-seq, mRNA-seq and in-house developed CPDIP-seq experiments were performed in human VH10 cells before and following DNA damage induced by low doses (8 or 20 J/m2) of UV-C irradiation. Inhibitor of transcription DRB were used as indicated in the protocols section.
Please note that the input sample INPUT_0_NO was used to normalize with ser2P, ser5P and hypo samples generating 3 different bigWig files;
C6D06ACXX_M_V5095_2_15s010830-1-1_Fousteri_lane3VNOUVtheoI_sequence.merged_norm_ser2P.bigWig
C6D06ACXX_M_V5095_2_15s010830-1-1_Fousteri_lane3VNOUVtheoI_sequence.merged_norm_ser5P.bigWig
C6D06ACXX_M_V5095_2_15s010830-1-1_Fousteri_lane3VNOUVtheoI_sequence.merged_norm_hypo.bigWig

first: Matthieu

last: Lavigne

first: Dimitris

last: Konstantopoulos

first: Katerina

last: Ntakou-Zamplara


title: Cartilage microRNA dysregulation during the onset and progression of mouse osteoarthritis is independent of aggrecanolysis and overlaps with candidates from end-stage human disease

status: Public on Nov 30 2017

city: Melbourne

first: John

last: Bateman

address: Flemington Road

department: Skeletal Biology

country: Australia

institute: Murdoch Childrens Research Institute

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


title: Elevated HuR in Pancreas Promotes a pancreatitis-like Inflammatory Microenvironment that Facilitates Tumor Development

city: Wynnewood

first: Janet

middle: A

last: Sawicki

state: PA

address: 100 Lancaster Ave.

institute: Lankenau Institute for Medical Research

summary:
Gene expression in pancreas of 6 month-old C mice bearing Pdx1/Cre transgene having normal pancreas  was compared to that of pancreas of 6 week old TC mice in which HuR protein was specifically overexpressed in the pancreas.
We used microarrays to identify gene expression changes associated with HuR overexpression-induced fibro-inflammatory response in the pancreas.

overall_design: Histologic, metabolic, and gene expression Affymetrix analyses of HuR overexpressing pancreas in mice were performed and shown to elicit a fibro-inflammatory reaction characteristic of chronic pancreatitis.

first: Weidan

last: Peng

first: Narumi

last: Furuuchi

first: Ludmila

last: Aslanukova

first: Yu-Hung

last: Huang

first: Wei

last: Jiang

first: Sankar

last: Addya

first: Vikalp

last: Vishwakarma

first: Erika

last: Peters

first: Jonathan

middle: R

last: Brody

first: Dan

last: Dixon

first: Samantha

middle: Z

last: Brown


title: Intervals of unmethylated DNA spatially co-segregate in cis and in trans [WGBS]

status: Public on Nov 24 2017

city: HOUSTON

first: Jianzhong

last: Su

state: TEXAS

address: 1 Baylor Plaza

institute: Baylor college of Medicine

type: Methylation profiling by high throughput sequencing

summary: High order chromatin structure and DNA methylation are implicated in multiple development processes and diseases. Despite the recent developments of methods studying high order chromatin interactions, how DNA methylation is associated with high order chromatin structure is not clear. Currently, it is believed that the insulator protein CTCF binding is blocked by DNA methylation, occurring in its core binding site. Thus the disruption of CTCF binding will result in the ectopic assessment of enhancer in the isolated neighborhood. However, not all CTCF bears CpG sites in its core binding site and no integrated analysis has been applied to discover the relationship between DNA methylation and high order chromatin structure utilizing the DNA methylome data. Here we found the lowly methylated DNA methylation canyon are interacting with each other specifically in CD34+ CD38- hematopoietic stem and progenitor cells (HSPC) but not its differentiated progenitors. The DNA methylation canyon interactions are enriched for H3K27me3 mark and represent a different category of interactions other than looped domain mediated by CTCF extrusion mechanism. We also found these canyons are contributing to the active HOX gene expression acting as scaffolds for gene expression rather enhancers. Disruption of canyon interaction with CTCF deletion and whole canyon deletion result in a great compromise of self-renewal ability of HSPC and the decrease of expression of active HOXA/B gene.

overall_design: Whole genome bisulfite sequencing of human Erythroid progenitor cell using Illumina Nextseq500.

first: Mira

last: Jeong

first: Margaret

last: Goodell


title: The somatically generated T cell receptor  CDR3a contributes to the MHC allele specificity of the T cell receptor

city: Denver

first: Philippa

last: Marrack

state: CO

address: 1400 Jackson St

department: Biomedical Research

institute: National Jewish Health

summary: Mature T cells bearing ab T cell receptors react with foreign antigens bound to alleles of major histocompatibility complex proteins (MHC) that they were exposed to during their development in the thymus, a phenomenon known as positive selection.  The structural basis for positive selection has long been debated.  Here, using mice expressing one of two different T cell receptor b chains and various MHC alleles, we show that positive selection-induced MHC bias of T cell receptors is affected both by the germline encoded elements of the T cell receptor a and b chain and, surprisingly, dramatically affected by the non germ line encoded CDR3 of the T cell receptor a chain.  Thus, in addition to determining specificity for antigen, the non germline encoded elements of T cell receptors may help the proteins cope with the extremely polymorphic nature of major histocompatibility complex products within the species.

overall_design: Naïve CD4 T cells were isolated from mice expressing a single T cell receptor b chain and one of 3 different alleles of MHCII.  The T cell receptor a chains on these cells were sequenced and their sequences compared.  Comparisons were also made in the use of different elements, the TRAVs, TRAJs and non germ line encoded CDR3 of the T cell receptor alpha chains.

first: Sai

last: Krovi

first: Daniel

last: Silberman

first: Janice

last: White

first: Eleanora

last: Kushnir

first: Maki

last: Nakayama

first: James

last: Crook

first: Thomas

last: Danhorn

first: Sonia

middle: M

last: Leach

first: Randy

last: Anselment

last: Scott-Browne

first: Laurent

last: Gapin

middle: W

last: Kappler


title: DNA methylation state is associated with the formation of loops and links in hematopoietic stem cells


title: Transcriptome profile of liver, adipose tissue, muscle and PBMC in genetically fat and lean chicken lines submitted to high-fiber and high-fat diet versus standard high-starch diet [Muscle]

status: Public on Nov 23 2017

city: Rennes

first: Colette

last: DESERT

address: 65 Rue de St Brieuc

institute: Agrocampus INRA UMR1348 PEGASE

summary: The aim of this study was to evaluate the responses of meat-type chicken to changes in dietary energy sources by comparing high-fiber high-fat vs. standard high-starch diets and using a transcriptomic approach in three major metabolic tissues - liver, adipose tissue and muscle - as well as in circulating blood cells.

overall_design: 48 broilers from two experimental lines divergently selected on abdominal fat content (fat and lean lines) were fed with two different diets (high-fiber and high-fat diet (HF) versus standard high-starch (LF) diet).

first: C

last: Désert

first: E

last: Baeza

first: M

last: Aite

last: Boutin

first: A

last: Le Cam

first: J

last: Montfort

last: Houee-Bigot

first: Y

last: Blum

first: P

middle: F

last: Roux

last: Hennequet-Antier

last: Berri

first: S

last: Metayer-Coustard

last: Collin

last: Allais

last: Le Bihan-Duval

first: D

last: Causeur

first: F

last: Gondret

last: Duclos

last: Lagarrigue


title: Transcriptome profile of liver, adipose tissue, muscle and PBMC in genetically fat and lean chicken lines submitted to high-fiber and high-fat diet versus standard high-starch diet [Adipose tissue]

last: DESERT

last: Désert

last: Baeza

last: Aite


title: Transcriptome profile of liver, adipose tissue, muscle and PBMC in genetically fat and lean chicken lines submitted to high-fiber and high-fat diet versus standard high-starch diet [Liver]

last: Boutin

last: Le Cam

last: Montfort

last: Houee-Bigot


title: Gene expression patterns define the hepatocyte-like cells derived by different strategies [ChIP-seq]

city: Shanghai

first: Xiaoran

last: zhang

address: Yueyang Road 320

department: Shanghai Institutes for Biological Sciences

country: China

institute: Chinese Academy of Sciences

summary: We analyzed the active H3K27 acetylation (H3K27ac) histone marker in hiPSC-Heps and hiHeps.The genome-wide H3K27ac occupancy analysis exhibited different patterns among these 4 types of cells. In accordance with the RNA-seq clustering results, the H3K27ac modifications of genes in seven clusters matched well with the active gene expressions in different cell types.

overall_design: Examination of H3K27 acetylation(H3K37ac) and input in 3 cell types.

first: Yimeng

last: Gao

last: Zhang

first: Ying

last: Li

first: Gang

last: Wei

first: Lijian

last: Hui


title: Gene expression patterns define the hepatocyte-like cells derived by different strategies


status: Public on Nov 21 2017

first: ai

middle: ping

last: jiang

address: No.151, Libing Rd., Zhangjiang Hi-tech Park, Pudong

institute: Shanghai Biotechnology Corporation

summary: To further identify the most significantly changed miRNA resulting from the different expression levels of TWIST2 in cervical cancer cells, we used a miRNA microarray to identify the miRNA expression profiles among SiHa, SiHa-tw2 and SiHa-shtw2. The significantly deregulated miRNAs (changes of more than 2-fold in expression) included miR-23b-5p, miR-221-3p, miR-502-3p, miR-221-5p, miR-15a-5p, miR-1227, miR-93-5p and miR-4257.

overall_design: SiHa-tw2 cells overexpressed TWIST2 and SiHa-shtw2 cells down-expressed TWIST2 in SiHa cells.

first: Wei

last: Wang


title: Gene expression patterns define the hepatocyte-like cells derived by different strategies [RNA-seq]

summary: We performed genome-wide gene profiling in hiPSC-Hep and hiHep and compared gene expression patterns in these two types of hepatocyte-like cells.Genes involving in fat digestion and absorption and metabolism enzymes were induced in both hiHeps and hiPSC-Heps. There were also hepatic genes not expressed in either hiPSC-Heps or hiHeps, including cytochrome P450-based metabolism genes and coagulation complements. Interestingly, when genes were clustered based on their hepatic functions, we found that for each hepatic function there were always a few genes not fully induced in either hiPSC-Heps or hiHeps.

overall_design: mRNA profiles of 4 cell types (UCF,hiHep,hiPSC-Hep,PHH) were generated by deep sequencing, UCF have 2 replications,hiHep and hiPSC-Hep have 4 replications,PHH have 3 replications, using Illumina Hiseq 2000.


title: iMEF SDHC-loss RRBS time course

city: Rochester

first: John

middle: Andrew

last: Smestad

state: Minnesota

address: 200 1st St. SW

department: Biochemistry and Molecular Biology

institute: Mayo Clinic

summary: We have developed a tet-inducible immortalized mouse embryonic fibroblast (iMEF) cell culture model of SDH-loss paraganglioma/pheochromocytoma in which silencing gene rearrangement of the Sdhc floxed allele is driven by doxycycline-dependent expression of cre-recombinase from a tet-inducible promoter (R26M2rtTA/+;TetOcre;Sdhcfl/fl).  Using this model and an isogenic Sdhc wt control line (R26M2rtTA/+;TetOcre;Sdhcfl/wt), we have characterized the time-course of Sdhc gene rearrangement, protein loss, and succinate accumulation following induction with doxycycline.  Using reduced representation bisulfite sequencing (RRBS), we have quantified changes in the genome-wide distribution of cytosine/5’-methyl-cytosine due to succinate accumulation using our Sdhc -/- cell line.  Through a time-course experimental design, we have grown R26M2rtTA/+;TetOcre;Sdhcfl/fl (experimental) and R26M2rtTA/+;TetOcre;Sdhcfl/wt (control) iMEFs in standard DMEM media containing 10% FBS and quantified DNA methylation changes in these cells as a function of time after triggering SDHC gene rearrangement via doxycycline exposure.

overall_design: Included in this dataset are single replicate RRBS time course data for experimental (R26M2rtTA/+;TetOcre;Sdhcfl/fl) and control (R26M2rtTA/+;TetOcre;Sdhcfl/wt) cell lines at days 0, 5, 9, 12,16, and 20 after induction with doxycycline.

first: Louis

last: Maher


title: The white adipose tissue is a hub for memory T cells and promotes memory responses

city: BETHESDA

first: abdel

middle: G

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

summary: The white adipose tissue represents 15% of healthy mammalian hosts and bridges body organs. In addition to serving as a scaffold for the lymphatic and blood vasculature, this compartment plays a fundamental role in the control of host metabolism. To which extent the adipose tissue also contributes to immune surveillance and long-term protective defense remains largely unknown. Here, we show that under steady state conditions, the white adipose tissue is home to abundant and diverse memory lymphocyte populations. Following infection, the adipose tissue accumulates large numbers of pathogen-specific memory T cells, including tissue-resident (TRM) cells. Memory T cells found in the adipose tissue express a distinct metabolic profile and are characterized by heightened proliferative and effector capacity. As such, adipose tissue from previously infected mice is sufficient to protect from lethal challenge. Local reactivation of adipose tissue memory T cells leads to rapid responses with local impacts on both immune and metabolic pathways, including direct responses by adipocytes. Notably, induction of recall responses within the adipose tissue is associated with the collapse of lipid metabolism in favor of antimicrobial responses. Thus, our results propose that the white adipose tissue, a compartment that interfaces with all body organs, may represent a unique immune compartment, able to provide early warning and potent effector memory responses. Together, these results uncover the adipose tissue as a dominant reservoir of memory T cells endowed with long-term protective functions, positioning this compartment as a potential major contributor of immunological memory.

overall_design: Microarray data were generated for whole murine mesenteric adipose tissues to determine the physiological tissue response to antigen rechallenge

first: Arielle

last: Glatman Zaretsky

first: Abdel

first: Seong-Ji

last: Han

first: Yasmine

last: Belkaid


title: Elevated p53 Activaties Restrict Differentiation Potential of microRNA-deficient Pluripotent Stem Cells

first: Hu

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

summary: Pluripotent stem cells (PSCs) deficient for microRNAs (miRNAs), such as Dgcr8-/- or Dicer-/- embryonic stem cells (ESCs), contain no mature miRNA and cannot differentiate into somatic cells. How miRNA deficiency causes differentiation defects remains poorly understood. Here, we report that miR-302 is sufficient to enable neural differentiation of differentiation-incompetent Dgcr8-/- ESCs. Our data showed that miR-302 directly suppresses the tumor suppressor p53, which is modestly upregulated in Dgcr8-/- ESCs and serves as a barrier restricting neural differentiation. We demonstrated that direct inactivation of p53 by SV40 large T antigen, a short hairpin RNA against Trp53, or genetic ablation of Trp53 in Dgcr8-/- PSCs enables neural differentiation, while activation of p53 by the MDM2 inhibitor nutlin-3a in wild-type ESCs inhibits neural differentiation. Together, we demonstrate that a major function of miRNAs in neural differentiation is suppression of p53 and that modest activation of p53 blocks neural differentiation of miRNA-deficient PSCs.

overall_design: Total RNAs extracted from three independent biological samples of Dgcr8-/--shctrl or Dgcr8-/--302 ESCs were submitted for microarray analysis

first: Rui

last: Zhao


title: Transcriptome profile of liver, adipose tissue, muscle and PBMC in genetically fat and lean chicken lines submitted to high-fiber and high-fat diet versus standard high-starch diet

first: Colette

last: DESERT

overall_design: Refer to individual Series


title: iMEF SDHC-loss RNA-seq time course

summary: We have developed a tet-inducible immortalized mouse embryonic fibroblast (iMEF) cell culture model of SDH-loss paraganglioma/pheochromocytoma in which silencing gene rearrangement of the Sdhc floxed allele is driven by doxycycline-dependent expression of cre-recombinase from a tet-inducible promoter (R26M2rtTA/+;TetOcre;Sdhcfl/fl).  Using this model and an isogenic Sdhc wt control line (R26M2rtTA/+;TetOcre;Sdhcfl/wt), we have characterized the time-course of Sdhc gene rearrangement, protein loss, and succinate accumulation following induction with doxycycline.  Using RNA-seq, we have quantified changes in gene expression due to succinate accumulation using our Sdhc -/- cell line.  Through a time-course experimental design, we have grown R26M2rtTA/+;TetOcre;Sdhcfl/fl (experimental) and R26M2rtTA/+;TetOcre;Sdhcfl/wt (control) iMEFs in standard DMEM media containing 10% FBS and quantified transcriptional changes in these cells as a function of time after triggering SDHC gene rearrangement via doxycycline exposure.

overall_design: Included in this dataset are single replicate RNA-seq time course data for experimental (R26M2rtTA/+;TetOcre;Sdhcfl/fl) and control (R26M2rtTA/+;TetOcre;Sdhcfl/wt) cell lines at days 0, 5, 9, 12, and 20 after induction with doxycycline.  We also include biological triplicate data for both experimental and control cell lines at day 16 after induction with doxycycline.


title: Transcriptome profile of liver, adipose tissue, muscle and PBMC in genetically fat and lean chicken lines submitted to high-fiber and high-fat diet versus standard high-starch diet [PBMC]

first: C

last: Désert

first: E

last: Baeza

first: M

last: Aite

last: Boutin

first: A

last: Le Cam

first: J

last: Montfort

last: Houee-Bigot

first: Y

last: Blum

first: P

last: Roux

last: Hennequet-Antier

last: Berri

first: S

last: Metayer-Coustard

last: Collin

last: Allais

last: Le Bihan-Duval

first: D

last: Causeur

first: F

last: Gondret

last: Duclos

last: Lagarrigue


title: DNA methylation in children from The Gambia

city: London

first: Matt

last: Silver

address: Keppel Street

institute: London School of Hygiene and Tropical Medicine

summary: Genome-wide DNA methylation profiling of 251 whole-blood samples from children aged 2 years from the ENID mother-child cohort in The Gambia.

overall_design: Bisulphite converted DNA from the 251 samples were hybridised to the Illumina Infinium HumanMethylation 450k Beadchip. An additional 6 samples were included as technical replicates.

first: Ayden

last: Saffari


title: LRPPRC-mediated folding of the mitochondrial transcriptome [PAR-CLIP MEF]

city: Perth

first: Stefan

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

institute: The Kids Research Institute Australia

summary: The roles of RNA-binding proteins as chaperones in the lifecycles of mRNAs are not well understood. The mammalian mitochondrial genome has been compressed over evolution to a size of just 16 kb, nevertheless the expression of its genes requires transcription, RNA processing, translation and RNA decay, much like the more complex chromosomal systems, providing an opportunity to use it as a model system to understand the fundamental aspects of gene expression. Here we combine RNase footprinting with PAR-CLIP at unprecedented depth to reveal the importance of RNA-protein interactions guided by the LRPPRC/SLIRP complex in dictating RNA folding within the mitochondrial transcriptome. We show that LRPPRC, in complex with its protein partner SLIRP, binds throughout the mitochondrial transcriptome, with a preference for mRNAs, and its loss affects the entire secondary structure and stability of the transcriptome. We demonstrate that the LRPPRC/SLIRP complex is a global RNA chaperone that stabilizes RNA structures to expose the required sites for translation, stabilization and polyadenylation. Our findings reveal a general mechanism where extensive RNA-protein interactions ensure that RNA is accessible for its biological functions.

overall_design: Examination of Lrpprc-bound sites on RNA from mouse embryonic fibroblasts.

first: Aleksandra

last: Filipovska

first: Oliver

last: Rackham


title: LRPPRC-mediated folding of the mitochondrial transcriptome [RNA-seq]

overall_design: Lrpprc knockout and control mice were sequenced, in quadruplicate, and analysed for differential gene expression and mitochondrial poyladenylation with RSEM and DESeq2.


title: LRPPRC-mediated folding of the mitochondrial transcriptome [PAR-CLIP HeLa]

overall_design: Examination of Lrpprc-bound RNA coverage from HeLa cells.


title: ‘Naïve’ ESRRB+ iPSCs with the capacity for rapid neural differentiation

status: Public on Nov 20 2017

city: Tokyo

first: Seiji

last: Shiozawa

address: 35 Shinanomachi, Shinjuku-ku

institute: Keio University, School of Medicine

summary: Several groups have reported the existence of a form of pluripotency that resembles that of mouse embryonic stem cells (mESCs), i.e., a naïve state, in human pluripotent stem cells; however, the characteristics vary between reports. The nuclear receptor ESRRB is expressed in mESCs and plays a significant role in their self-renewal, but its expression has not been observed in most naïve-like human induced pluripotent stem cells (hiPSCs). In this study, we modified several methods for converting hiPSCs into a naïve state through the transgenic expression of several reprogramming factors. The resulting cells express the components of the core transcriptional network of mESCs, including ESRRB, at high levels, which suggests the existence of naïve-state hiPSCs that are similar to mESCs. We also demonstrate that these cells differentiate more readily into neural cells than do conventional hiPSCs. These features may be beneficial for their use in disease modeling and regenerative medicine.

overall_design: RNA-seq of primed and naïve-like hiPSCs in 3 biological replicates respectively.

first: Fumihiko

last: Kisa

first: Hideyuki

last: Okano


title: Sono-Seq analysis of contextual fear conditioning

city: Spokane

first: Lucia

last: Peixoto

state: WA

address: PO Box 1495

department: College of Medicine

institute: Washington State University, Spokane

summary: This dataset constitutes the first Sono-Seq study of chromatin accessibility following contextual fear conditioning in the mouse hippocampus.

overall_design: 8 total samples were analyzed, including 4 animals trained in a contexual conditioning paradigm (FC) and 4 controls. After 3 days of daily handling, tissue was collected at 30 minutes after FC.  Animals that were handled but not FC were dissected at the same time of day to control for variations in gene expression due to circadian rhythms (HC). The protocol was repeated over the course of 4 days to obtain 4 animals (2 hippocampi) per group, so that 4 independent FC experiments were represented in each time point and all animals for each group were dissected at exactly the same time of day. Testing of additional control animals was performed at 24 hours after training over a 5-minute interval, to confirm the effectiveness of the FC protocol.

first: Ted

last: Abel

first: John

last: Koberstein

first: Bruce

last: Gomes


title: Next Generation Sequencing  Quantitative Analysis of Tshz1GFP/+ and Tshz1GFP/RA purified amygdalar ITCs

city: Cincinnati

first: Jeff

last: Kuerbitz

state: OH

address: 3333 Burnet Ave

department: Developmental Biology

institute: Cincinnati Childrens Hospital

summary: RNA sequencing was performed on the transcriptomes of amygdalar ITCs from Tshz1 GFP/+ embryonic mice (controls) and Tshz1GFP/RA  embryonic mice (knockouts) in order to identify genes functioning downstream of Tshz1 in the development of these cells.

overall_design: ITC mRNA profiles of E16.5 Tshz1 GFP/+ embryonic mice (controls) and Tshz1GFP/RA  embryonic mice (knockouts) were generated by deep sequencing, in triplicate, using Illumina HiSeq2500

first: Kenneth

last: Campbell

first: Jeffrey


title: N6-methyladenosine RNA modification regulates embryonic neural stem cell self-renewal through histone modifications.

city: Cambridge

first: Yue

last: Li

state: Massachusetts

address: 32 Vassar Street, 32-D528

institute: Massachusetts Institute of Technology

summary: Internal N6-methyladenosine (m6A) modification is widespread in messenger RNAs(mRNAs) and catalyzed by heterodimers of methyltransferase-like protein 3 (Mettl3) andMettl14. To understand the role of m6A in development, we deleted Mettl14 in embryonicneural stem cells (NSCs) in a mouse model. Phenotypically, NSCs lacking Mettl14 displaymarkedly decreased proliferation and premature differentiation, suggesting m6Amodification enhances NSC self-renewal. Decreased NSC pool led to decreased numberlate-born neurons during cortical neurogenesis. Mechanistically, we discovered a genomewide increase in specific histone modifications in Mettl14 knockout vs. control NSCs. Thesechanges correlated with altered gene expression and observed cellular phenotypes,suggesting their functional significance. Finally, we showed that m6A regulates histonemodification in part by destabilizing transcripts encoding histone-modifying enzymes. Ourstudy demonstrated an essential role of m6A in development and revealed m6A-regulatedhistone modifications as a novel gene regulatory mechanism in mammalian cells.

overall_design: We perform high-throughput sequencing of mouse neural progenitor cell (NPC) with or without deletion of Mettl14 to profile RNA expression, m6A methylated RNA profile, H3K27ac, H3K27me3 histone modifications. Each condition (i.e., wiltype, homozygous knockout, heterozygous deletion) is assayed in two or more biological replicates. For the RNA-seq experiments, we performed 3 batches of sequencing experiments in different biological replicates to account for the technical variation

first: Yang

last: Wang

first: Jing

middle: C

last: Zhao


title: Small RNAs from 11 Drosophila species

city: Stanford

first: Jaaved

last: Mohammed

state: CA

address: 265 Campus Drive

department: Chemical and Systems Biology

institute: Stanford University

summary: Annotation of small RNAs from 11 Drosophila species for the purpose of non-coding RNA annotation and comparative genomics assessment.

sample_organism:
Drosophila ananassae
Drosophila erecta
Drosophila grimshawi
Drosophila mojavensis
Drosophila persimilis
Drosophila pseudoobscura
Drosophila sechellia
Drosophila simulans
Drosophila virilis
Drosophila yakuba
Drosophila willistoni

overall_design: Small RNA samples from 11 Drosophila species.

first: Alex

middle: S

last: Flynt

first: Eric

last: Lai


title: Characterization and metabolic synthetic lethal testing in a new model of SDH-loss familial pheochromocytoma and paraganglioma

last: Smestad

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


title: LRPPRC-mediated folding of the mitochondrial transcriptome

first: Stefan

last: Siira

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Kdm2b regulates somatic reprogramming through variant PRC1 complex dependent function [ChIP-seq, MeDIP-seq]

status: Public on Nov 19 2017

city: GuangZhou

first: Jiangping

last: He

address: Kai yuan avenue 190

institute: Guangzhou Institutes of Biomedicine and Health (GIBH), CAS

summary: Polycomb repressive complex 1 (PRC1) plays essential roles in cell fate determination. Recent studies have found that the composition of mammalian PRC1 is particularly varied and complicated, whereas the function of such variant PRC1 complexes on cell fate determination remains unknown. Here we show that Kdm2b, which recruits a variant PRC1 complex (PRC1.1) to CpG islands (CGIs), elevates Oct4 induced somatic reprogramming. Interaction with PRC1 is critical for Kdm2b’s promotion on the process of induced pluripotency. Furthermore, we find that bone morphogenetic proteins (BMPs) repress Oct4/Kdm2b induced somatic reprogramming selectively. Mechanistically, BMP-Smad pathway attenuates PRC1.1 occupation and H2AK119 ubiquitination on development genes, resulting in the release of meso-endoderm factors such as Sox17 and suppression of somatic reprogramming. These observations reveal that PRC1.1 participates in the establishment of pluripotency as well as cellular differentiation and identify BMP signal as a modulator of PRC1.1 function.

overall_design: We analyzed the gene expression profiles and PRC1.1 occupation on chromatin  during the Oct4/Kdm2b induced reprogramming process by RNA-seq and ChIP-seq. We  performed ChIP-seq of KDM2B,H2AK119ub, H3K36me2, H3K27me3 and 5mC-MeDIP-seq in Oct4/DR(ODR), Oct4/Kdm2a(OA), Oct4/Kdm2b(OB) mediated reprogramming cells at day14. We  also performed ChIP-seq of KDM2B,H2AK119ub and RING1B in Oct4/Kdm2b/Id1(OBD) mediated reprogramming cells at day9.


title: Baf53a is involved in survival of mouse ES cells, which can be compensated by Baf53b.

status: Public on Nov 16 2017

city: Kanazawa

first: Shin-ichi

last: Horike

state: Ishikawa

address: 13-1 Takaramachi

department: Research Center for Experimental Modeling of Human Disease

institute: Kanazawa University

summary: The human Baf (Brg1/Brm associated factor) complex, also known as the mammalian SWI/SNF chromatin-remodeling complex, is involved in a variety of cellular processes. The pluripotency and self-renewal abilities are major characteristics of embryonic stem (ES) cells and are regulated by the ES cell-specific BAF (esBAF) complex. Baf53a is one of the subunits of the esBAF complex. Here, we found that growth of Baf53a-deficient ES cells was repressed, and expression of p53, p21, and cleaved Caspase 3 was increased. Interestingly, Baf53b, a homologue of Baf53a, rescued cell death of Baf53a-deficient ES cells. Baf53a-deficient ES cells overexpressing exogenous Baf53a or Baf53b remained in the undifferentiated state and proliferated. In summary, our findings suggest that Baf53a is involved in the survival of ES cells, and that Baf53b is able to compensate for this functional aspect of Baf53a.

overall_design: Comaprison between Baf53a-expressing or Baf53b-expressing Baf53a-deficient ES cells.

first: Bo

last: Zhu

first: Atsushi

last: Ueda

first: Xiaohong

last: Song

first: Takashi

last: Yokota

first: Tadayuki

last: Akagi


title: Polycomb Repressive Complex 2 methylates Elongin A to regulate transcripiton [BrU-RNA-seq]

city: Boston

first: Behfar

last: Ardehali

address: Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, CPZN7250

department: Molecular Biology

institute: MGH, Harvard Medical School

summary: Polycomb repressive complex 2 (PRC2-EZH2) methylates histone H3 at lysine 27 (H3K27) and is required to maintain gene repression during development. Misregulation of PRC2 is linked to a range of neoplastic malignancies, which is believed to involve methylation of H3K27. However, the full spectrum of non-histone substrates of PRC2 that might also contribute to PRC2 function is not known.  We characterized the target recognition specificity of PRC2 and used the resultant data to screen for novel potential targets. The RNA polymerase II (Pol II) transcription factor, Elongin A (EloA), is methylated by PRC2 in vivo. Mutation of the methylated EloA residue decreased repression of many, but not all, PRC2 target genes as measured by both steady state and nascent RNA levels. We propose that PRC2 regulates transcription of a subset of target genes in part via methylation of EloA.

overall_design:
We examined the nascent transcripiton profile of mES cells by adding 5-Bromouridine (BrU) to the media for 10 min. Following RNA isolation,  BrU-labelled nascent RNA species were affinity purified using BrdU antibody and sequenced after library preparation.

Please note that each .bw file was generated from two replicate samples together and linked to the corresponding *rep1 sample records.

first: M

middle: B

first: Anthony

last: Anselmo


title: Kdm2b regulates somatic reprogramming through variant PRC1 complex dependent function

status: Public on Nov 18 2017


title: YY1 is a structural regulator of enhancer-promoter loops [scRNA-seq]

first: Richard

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: There is considerable evidence that chromosome structure plays important roles in gene control, but we have limited understanding of the proteins that contribute to structural interactions between gene promoters and their enhancer elements. Large DNA loops that encompass genes and their regulatory elements depend on CTCF-CTCF interactions, but most enhancer-promoter interactions do not depend on this structural protein.  Here we show that the transcription factor Yin Yang 1 (YY1) contributes to enhancer-promoter structural interactions in a manner analogous to DNA interactions mediated by CTCF.  YY1 binds to active enhancers and promoter-proximal elements in all cells examined.  YY1 forms dimers that can facilitate DNA interactions. Deletion of YY1 binding sites or depletion of YY1 can disrupt enhancer-promoter looping and normal gene expression.  We propose that YY1-mediated enhancer-promoter interactions are a general feature of mammalian gene control.

overall_design: Single-cell RNA-seq in mouse embryonic stem cells with and without YY1 protein

first: Abraham

last: Weintraub

first: Charles

last: Li

first: Alicia

last: Zamudio

first: Alla

last: Sigova

first: Nancy

last: Hannett

first: Daniel

last: Day

first: Brian

last: Abraham

first: Malkiel

last: Cohen

first: Behnam

last: Nabet

first: Dennis

middle: L

last: Buckley

middle: E

last: Guo

first: Denes

last: Hnisz

first: Rudolf

last: Jaenisch

first: James

last: Bradner

first: Nathanael

last: Gray


title: Enhancer-binding of Brd4 controls cell differentiation

status: Public on Nov 17 2017

city: Bethesda

first: Kai

last: Ge

state: MD

address: 50 South Dr Rm 4154

department: NIDDK

institute: NIH

summary: The epigenomic reader Brd4 is an important drug target for cancers. However, its role in cell differentiation and animal development remains largely unclear. Using two conditional knockout mouse strains and derived cells, we demonstrate that Brd4 controls cell identity gene induction and is essential for adipogenesis and myogenesis. Brd4 co-localizes with lineage-determining transcription factors (LDTFs) on active enhancers during differentiation. LDTFs coordinate with H3K4 mono-methyltransferases MLL3/MLL4 (KMT2C/KMT2D) and H3K27 acetyltransferases CBP/p300 to recruit Brd4 to enhancers activated during differentiation. Brd4 deletion prevents the enrichment of Mediator and RNA polymerase II transcription machinery, but not that of LDTFs, MLL3/MLL4-mediated H3K4me1, and CBP/p300-mediated H3K27ac, on enhancers. Consequently, Brd4 deletion prevents enhancer RNA production, cell identity gene induction and cell differentiation. Interestingly, Brd4 is dispensable for maintaining cell identity genes in differentiated cells. These findings identify Brd4 as an enhancer epigenomic reader that links active enhancers with cell identity gene induction in differentiation.

overall_design: Expression profiling by RNA-seq, and profiling of Brd4 by ChIP-seq during adipogenesis of brown preadipocytes in culture (D0, D2, D7) and in C2C12 myocytes

first: Ji-Eun

last: Lee

first: Young-Kwon

last: Park

first: Sarah

first: Younghoon

last: Jang

first: Nicholas

last: Waring

first: Binbin

last: Lai

first: Weiqun

last: Peng


title: Dissection and Function of Autoimmunity-associated TNFAIP3 (A20) Gene Enhancers in Humanized Mouse Models [ChIP-seq]

city: New York

first: Lionel

middle: B.

last: Ivashkiv

state: NY

address: 535 East 70th Street

institute: Hospital for Special Surgery

summary: Enhancers affect gene expression and disease. Little is known about enhancers that regulate human disease-associated genes in their native chromosomal context in primary cells relevant for pathogenesis. We used a BAC transgenic approach combined with CRISPR- and recombineering-mediated genome editing to dissect enhancers that regulate human TNFAIP3/A20, which is tightly linked with autoimmune diseases, in vivo and in primary immune cells. >20 enhancers in the A20 superenhancer were redundant; A20 expression was regulated by a topologically associating subdomain (sub-TAD) that harbors 5 enhancers. Deletion of this sub- TAD enhanced inflammatory responses and autoantibody production, establishing its functional importance in vivo. We identified cell- and activation-specific enhancers within this sub-TAD, including a key role for an enhancer harboring a proposed causal SLE-associated SNV. These findings map genomic regions that regulate human A20 expression to prevent inflammatory pathology and autoimmunity, and provide a platform for causally linking enhancers and SNVs with disease phenotypes.

overall_design: Analysis of epigenomic changes in human macrophages stimulated with LPS

first: Kyuho

last: Kang


title: DNA methylation signatures of injection illicit drug use (IDU) and hepatitis C (HCV) predict HIV pathophysiologic frailty

city: New Haven

first: Ke

last: Xu

address: 300 George St.

department: department of psychiatry

institute: Yale University

type: Methylation profiling by genome tiling array

overall_design: Refer to individual Series


title: Polycomb Repressive Complex 2 methylates Elongin A to regulate transcripiton [RNA-seq]

first: Behfar

last: Ardehali

overall_design:
We examined the transcripitonal profile of EEDnull, EloAnull, EloA mutant, and parental mouse embryonic stem cells by RNAseq.

Please note that the .bw processed data file was generated from the *mESC replicate samples together and linked to the corresponding *rep1 sample records.

first: M

first: Anthony

last: Anselmo


title: Differential gene expression in the intestine of sea cucumber (Apostichopus japonicus) under low and high salinity conditions

city: Qingdao

first: Lina

last: Sun

address: Nanhai Road 7

institute: Institute of Oceanology, Chinese Academy of Sciences

summary: Sea cucumber, Apostichopus japonicus is a very important species for aquaculture, and its behavior and physiology can respond to the initial change in salinity. It is important to understand the molecular responses of A. japonicus when exposed to ambient changes in salinity In this study, RNA-seq provided a general overview of the gene expression profiles of the intestine of A. japonicus exposed to high salinity (SD40), normal salinity (SD30) and low salinity (SD20) environment.

overall_design: Sea cucumbers were acclimated in tanks containing aerated sand-filtered seawater (salinity 30%, pH 8.0) at 15 ± 0.5°C for one week before use and were fed once each day at 8:00 am during this period. The animals were then assigned randomly to three groups (20 individuals in each group). One group of sea cucumbers was maintained as the control group with normal salinity (SD30) of around 30, whereas the other two groups were kept in sea water where the salinity was gradually increased and decreased to high salinity (SD40) of around 40 and low salinity (SD20) of around 20 at a rate of 2.5 per 6 h.

first: Libin

last: Zhang


title: YY1 is a structural regulator of enhancer-promoter loops [ChIA-PET]

first: Richard

last: Young

overall_design: ChIA-PET (Chromosome interaction analysis by paired-end tags) in mouse embryonic stem cells targeting CTCF- or YY1-associated interactions

first: Abraham

last: Weintraub

first: Charles

middle: H

last: Li

first: Alicia

last: Zamudio

first: Alla

last: Sigova

first: Nancy

last: Hannett

first: Daniel

last: Day

first: Brian

middle: J

last: Abraham

first: Malkiel

last: Cohen

first: Behnam

last: Nabet

first: Dennis

last: Buckley

first: Yang

last: Guo

first: Denes

last: Hnisz

first: Rudolf

last: Jaenisch

first: James

first: Nathanael


title: DNA methylation signatures of injection illicit drug use (IDU) and hepatitis C (HCV) predict HIV pathophysiologic frailty I

first: Ke

last: Xu

state: CT

address: 300 George St., Suite 901

department: Department of Psychiatry

summary: Genome wide DNA methylation profiling of IDU+/HCV+ and IDV-/HCV- individuals for DNA samples extracted from peripheral blood. The Illumina Infinium Human DNA methylation 450 Beadchip was used to obtain DNA methylation profiles across approximately 480,000 CpGs. Samples included 216 IDU+/HCV+ and 170 IDU-/HCV- individuals. The goal was to identify genome-wide differentially methylated CpG sites between IDU+/HCV+ and IDU-/HCV- samples.

overall_design: Bisulfite converted DNA from the 386 DNA samples were hybridized to the Illumina Infinium 450K Human Methylation Beadchip. The samples were extracted from whole blood. The subjects including 216 IDU+/HCV+ and 170 IDU-/HCV- were recruited from the Veteran Aging Cohort Study. All subjects were inform consented and the study protocol was approved by Connecticut Veteran Affair Healthcare System IRB and Yale Human Research Protection Program at Yale University.

first: Xinyu

first: Amy

last: Justice


title: YY1 is a structural regulator of enhancer-promoter loops

first: Richard

middle: A


title: YY1 is a structural regulator of enhancer-promoter loops [HiChIP]

overall_design:
HiChIP against H3K27ac-marked nucleosomes in mouse embryonic stem cells
HiChIP against YY1 in Jurkat, HCT-116, and K562 cells

first: Abraham

first: Charles

first: Alicia

last: Bradner

last: Gray


title: YY1 is a structural regulator of enhancer-promoter loops [RNA-Seq]

last: Young

overall_design: Single-end 40 bp Poly-A RNA-seq in mouse embryonic stem cells before and after YY1 depletion

last: Weintraub

first: Alla

first: Nancy

first: Daniel


title: Polycomb Repressive Complex 2 methylates Elongin A to regulate transcription

first: Behfar

last: Ardehali


title: YY1 is a structural regulator of enhancer-promoter loops [ChIP-Seq]

overall_design: ChIP-Seq for YY1 in mouse embryonic stem cells

last: Li

last: Zamudio

last: Sigova

first: Brian

first: Malkiel

first: Behnam

first: Dennis


title: Alterations in DNA replication timing identify TP63 as a novel marker of progeroid diseases [Chip]

city: Tallahassee

first: David

last: Gilbert

state: FL

address: 319 Stadium Drive

department: Biology

institute: Florida State University

summary: Progeroid syndromes are rare genetic disorders that phenotypically resemble natural aging. Despite identification of causal mutations, mechanisms that generate their clinical manifestations remain elusive. Here, we identified a DNA replication timing (RT) signature that distinguishes progeroid syndromes from normal aging and identifies TP63 gene as a new disease marker. Abnormal TP63 RT appears early during differentiation of progeroid iPSCs and is associated with altered gene variant expression. Our findings demonstrate the utility of RT signatures to identify novel biomarkers not detected by other methods, reveal abnormal TP63 RT as an early event in progeroid disease progression and offer TP63 gene regulation as a potential therapeutic target.

overall_design: Genome-wide replication timing profiles were constructed from HGPS patients, normal individuals of different ages and cells entering cellular senescence.

first: JuanCarlos

last: Rivera-Mulia


title: Knockdown of NUP62 of human head and neck squamous cell carcinoma cell line UMSCC1

first: Shin-ichi

last: Horike

summary: p63, especially its dominant isoform ∆Np63⍺, plays essential roles in squamous cell carcinomas (SCCs); yet the mechanisms controlling its nuclear transport remain unknown. Nucleoporins (NUPs) are a family of proteins building nuclear pore complex (NPC) and mediating nuclear transport across the nuclear envelope. Recent evidence suggests a cell-type-specific function for certain NUPs; however, the significance of NUPs in SCC biology remains unknown. In this study, we report that nucleoporin 62 (NUP62) is highly expressed in stratified squamous epithelia, which is further elevated in SCCs. Depletion of NUP62 inhibited the proliferation ability and augmented differentiation characteristics of SCC cells. This loss of dedifferentiation status was associated with defects in ∆Np63⍺ nuclear transport. We further found that differentiation inducible Rho kinase reduced an interaction between NUP62 and ∆Np63a by phosphorylation of phenylalanine-glycine regions of NUP62, resulting in attenuated ∆Np63⍺ nuclear import. Our results characterize NUP62 as a key gatekeeper for ∆Np63⍺ and uncover its significant function to control ∆Np63⍺ nuclear transport in SCC.

overall_design: Comparison between negative control cells and NUP62 knocked down cells. There are two biological replicates for each conditions.

first: Masaharu

last: Hazawa

first: De-Chen

last: Lin

first: Akiko

last: Kobayashi

first: Yan-Yi

last: Jiang

first: Liang

first: Firli

last: Rahmah Primula Dewi

first: Mahmoud

last: Shaaban Mohamed

first: H

last: Hartono

first: Mitsutoshi

last: Nakada

first: H.

middle: P

last: Koeffler

last: Wong


title: H3S10ph broadly marks early-replicating domains in interphase ESCs and shows reciprocal antagonism with H3K9me2

city: Montreal

first: Carol

last: Chen

state: QC

address: 1001 Decarie Boulevard, Rm E01.4380

department: Human Genetics

country: Canada

institute: Research Institute of McGill University Hospital Centre

summary: Pervasive phosphorylation of histone H3 at serine 10 (H3S10ph) by Aurora B/C plays an important role in mitosis; however, this mark has also been observed at specific genic promoters and enhancers in interphase, implicating mitosis-independent functions. Using the FUCCI cell cycle reporter, we found that 30% of the genome is persistently marked with H3S10ph in interphase mouse embryonic stem cells (ESCs). H3S10ph demarcates broad gene-rich euchromatic regions in G1 and shows remarkable correlation with domains of early DNA replication timing (RT). Consistent with mitosis-independent H3S10 kinase activity, this pattern was preserved in ESCs treated with hesperidin, a potent inhibitor of Aurora B/C. Disruption of H3S10ph by expression of non-phosphorylatable H3.3S10A results in ectopic spreading of H3K9me2 into adjacent H3S10ph-enriched euchromatic regions, mimicking the phenotype observed in Drosophila JIL-1 kinase mutants. Conversely, H3S10ph domains expand in interphase Glp-/- ESCs, revealing that H3S10ph expansion is restricted by H3K9me2. Strikingly, spreading of H3S10ph at RT transition regions (TTRs) is accompanied by aberrant strand-biased transcription initiation of genes and repetitive elements co-oriented with the replication fork, indicating that H3K9me2 plays a critical role in establishing repressive chromatin on the leading strand. Finally, we show that H3S10ph is also present in interphase murine embryonic fibroblasts (MEFs), but is restricted to intragenic regions of actively transcribing genes. Our study provides a detailed map of interphase H3S10ph in ESCs and MEFs, uncovering a previously unappreciated crosstalk between the opposing marks H3S10ph and H3K9me2, and a role for the latter in ensuring appropriate transcription at TTRs in ESCs.

overall_design: H3S10ph ChIP & Inputs in asynchnous and FUCCI-sorted ESCs H3S10ph ChIP & Inputs in DMSO and Hesperadin-treated ESCs YFP & H3K9me2 ChIP in H3.3-YFP, 2 H3.3S10A-YFP overexpressing ESC clonal lines H3K9me2 & H3S10ph in Glp-/- and corresponding WT ESCs H3K36me3, H3K4me3, RNA-seq in G9a-/-, Glp-/- and corresponding WT ESCs H3S10ph ChIP & Inputs in DMSO and Hesperadin-treated WT and G9a-/- MEFs.

first: Preeti

last: Goyal

first: Mohammad

last: Karimi

first: Marie

last: Abildgaard

first: Hiroshi

last: Kimura

first: Matthew

last: Lorincz


title: Alterations in DNA replication timing identify TP63 as a novel marker of progeroid diseases

first: David

last: Gilbert


title: Characterization of neuroendocrine tumors in heterozygous mutant MENX rats: a novel model of invasive medullary thyroid carcinoma [thyroid]

status: Public on Nov 15 2017

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

summary:
CDKN1B (p27) was formally established as a tumor suppressor gene (tsg) following the identification of inactivating germline mutations in rats (MENX syndrome) and patients (MEN4 syndrome) developing multiple neuroendocrine tumors (NETs). MENX-affected rats are homozygous for the predisposing p27 mutation, suggesting a canonical tsg function. In contrast, mice heterozygous for a defective Cdkn1b allele are already predisposed to tumor formation (haploinsufficiency). We here report that heterozygous mutant rats (p27+/mut) develop the same NETs seen in the homozygous (p27mut/mut) animals but with slower progression. In the tumors of p27+/mut rats, the wild-type allele is neither lost nor silenced, implying that p27 is haploinsufficient for tumor suppression also in this model.
Transcriptome profiling of rat NETs having different p27 dosages revealed a tissue-specific, dose-dependent effect of p27 on gene expression. In p27+/mut rats, thyroid neoplasms progress to invasive and metastatic medullary thyroid carcinomas (MTCs) accompanied by increased calcitonin levels, as in humans. Comparison of expression signatures of late-stage versus early-stage MTCs from p27+/mut rats identified genes potentially involved in tumor aggressiveness. The expression of a subset of these genes was evaluated in human MTCs, and found associated with aggressive RET-M918T-positive tumors. Altogether, p27 haploinsufficiency in MENX rats uncovered a novel, representative model of invasive/metastatic MTC, exploitable for translational studies of this aggressive and often incurable cancer.

overall_design: We compared medullary thyroid carcinomas from heterozygous and homozygous p27Kip1/Cdkn1b mutant rats. Heterozygous animals were analyzed at the age of 9 and 18 months

first: Sara

last: Molatore

first: Andrea

last: Kügler

first: Martin

last: Irmler

first: Tobias

last: Wiedemann

first: Frauke

last: Neff

first: Annette

last: Feuchtinger

first: Elke

last: Pulz

first: Mercedes

last: Robledo

first: Federico

last: Roncaroli

first: Natalia

last: Pellegata


title: Genome wide mapping of ETV6 binding sites in pre-B leukemic cells

first: Daniel

last: Sinnett

state: Quebec

address: 3175 Cote-Sainte-Catherine

institute: CHU Sainte-Justine

summary:
Background: Genetic alterations in the transcriptional repressor ETV6 are associated with hematological malignancies. Notably, the t(12;21) translocation leading to an ETV6-AML1 fusion gene is the most common genetic alteration found in childhood acute lymphoblastic leukemia. Moreover, most of these patients also lack ETV6 expression, suggesting a tumor suppressor function.
Results: To gain insights on ETV6 DNA-binding specificity and genome wide transcriptional regulation capacities, we performed chromatin immunoprecipitation experiments coupled to deep sequencing in a t(12;21)-positive pre-B leukemic cell line. This strategy led to high quality ETV6-bound regions. ETV6 binding is mostly cell type-specific as only few regions are shared with other blood cell subtypes. Peaks localization and motif enrichment analyses revealed a unique binding profile that is associated with the presence of the ETV6-AML1 fusion product.
Conclusions: We described the first ETV6 binding map in the t(12;21) background. This study highlighted the complex and unique interplay between ETV6 and ETV6-AML1 and underscored the highly regulated mechanisms of ETV6 binding. ETV6 inactivation observed in this context could induce specific transcriptional changes promoting leukemic transformation.

overall_design: Genome wide ETV6 binding sites were identified through chromatin immunoprecipitation sequencing in ETV6-HA transduced Reh cells compared to ETV6 (negative IP control), each in triplicates

first: Benjamin

last: Neveu

first: Maxime

last: Caron

first: Karine

last: Lagacé

first: Chantal

last: Richer

last: Sinnet


title: Transcription Factor Activating Protein 4 is synthetically lethal and a master regulator of MYCN-amplified neuroblastoma

first: Gonzalo

last: Lopez

address: 1399 Park avenue

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

summary: Despite the identification of MYCN amplification as an adverse prognostic marker in neuroblastoma, MYCN inhibitors have yet to be developed. Here, by integrating evidence from a whole genome shRNA library screen and the computational inference of master regulator proteins, we identify Transcription Factor Activating Protein 4 (TFAP4) as a critical effector of MYCN amplification in neuroblastoma, providing a novel synthetic lethal target. We demonstrate that TFAP4 is a direct target of MYCN in neuroblastoma cells, and that its expression and activity strongly negatively correlate with neuroblastoma patient survival. Silencing TFAP4 selectively inhibits MYCN-amplified neuroblastoma cell growth both in vitro and in vivo, in xenograft mouse models. Mechanistically, silencing TFAP4 induces neuroblastoma differentiation, as evidenced by increased neurite outgrowth and up-regulation of neuronal markers. Taken together, our results demonstrate that TFAP4 is a master regulator of MYCN-amplified neuroblastoma and may represent a valuable novel therapeutic target.

overall_design:
Control and TFAP4 KD RNA-seq in two neuroblastoma cell lines

**Please note that raw data for the following 7 samples have been lost and thus are not included in the current records;
GSM2742417 - SKNDZ Control RNASeq [SD013]
GSM2742419 - SKNDZ TFAP4 KD RNASeq [SD008]
GSM2742420 - SKNDZ TFAP4 KD RNASeq [SD0014]
GSM2742422 - NGP Control RNASeq [SD011]
GSM2742423 - NGP Control RNASeq [SD017]
GSM2742425 - NGP TFAP4 KD RNASeq [SD012]
GSM2742426 - NGP TFAP4 KD RNASeq [SD018]


title: Lysophosphatidylcholine regulates sexual stage differentiation in the human malaria parasite Plasmodium falciparum

city: Tampa

first: Rays HY

last: Jiang

address: 3720 Spectrum Blvd, Suite 304

department: Department of Global Health

institute: University of South Florida

summary:
Purpose: The goal of this study was to identify genes associated with increased sexual differentiation in P. falciparum.
Method: RNAseq analysis of two different P. falciparum strains (NF54 and Pf2004/164tdTom) cultured under sexual differentiation-inducing (-SerM) and non-inducing (-SerM/LysoPC and -SerM/Serum) conditions
Results: We found a total of 342 genes significantly induced in response to LysoPC depletion, thereby determining changes associated with sexual differentiation and limiting Kenndedy pathway substrates.

overall_design: RNAseq profiles were generated from tightly synchonised P. falciparum cultures during the process of sexual commitment, in 2 different stains, using 3 different conditions. mRNA was collected from 3 consecutive time points each.

first: Nicolas

last: Brancucci

first: Joseph

last: Gerdt

first: ChengQi

last: Wang

first: Mariana

last: De Niz

first: Nisha

last: Philip

first: Swamy

middle: R

last: Adapa

first: Min

last: Zhang

first: Eva

last: Hitz

first: Igor

last: Niederwieser

first: Sylwia

middle: D

last: Boltryk

first: Marie-Claude

last: Laffitte

first: Martha

last: Clark

first: Christof

last: Grüring

first: Deepali

last: Ravel

first: Alexandra

last: Soares

first: Allison

last: Demas

first: Selina

last: Bopp

first: Belén

last: Rubio-Ruiz

first: Ana

last: Conejo-Garcia

first: Dyann

last: Wirth

first: Edyta

last: Gendaszewska-Darmach

first: Manoj

middle: T

last: Duraisingh

first: John

last: Adams

first: Till

last: Voss

first: Andrew

last: Waters

first: Rays

first: Jon

last: Clardy

first: Matthias

last: Marti


title: Colonic single-cell RNA-seq

city: Nashville

first: Ken

last: Lau

state: TN

address: 2215 Garland Ave. MRBIV10475

department: Cell and Developmental Biology

institute: Vanderbilt University

summary: WT untreated C57Bl6 mouse.

overall_design: 2 replicates (different cells) from same mouse in single sequencing run.

first: Alan

last: Simmons


title: RNA-seq of Wildtype Staphylococcus aureus USA300 NRS384

city: South San Francisco

first: Mark

last: McCreary

state: California

address: 1 DNA Way, MS 93

department: Bioinformatics

institute: Genentech

summary: Methicillin-resistant Staphylococcus aureus (MRSA) infections result in more than 200,000 hospitalizations and 10,000 deaths in the United States each year and remain an important medical challenge. To better understand the transcriptome of Staphylococcus aureus USA300 NRS384, a community-acquired MRSA strain, we have conducted an RNA-Seq experiment on WT samples.

overall_design: RNA-Seq analysis was performed on log phase WT Staphylococcus aureus USA300 NRS384 grown at 30 degrees C and grown at 37 degrees C. Each condition was performed in triplicate thereby yielding a total of 6 samples for RNA-Seq analysis.

first: Michael

last: Lopez

first: Irene

last: Tan

first: Donghong

last: Yang

first: Jing

last: Kang

first: Zora

last: Modrusan

first: Cary

last: Austin

first: Min

last: Xu

first: Eric

last: Brown


title: SMAD2/3 binding pattern in triple-negative breast cancer cell lines, Hs578T and BT549  [ChIP-seq]

city: Tokyo

first: Masato

last: Morikawa

address: 2-21-1 Kaga, Itabashi-ku

department: Advanced Comprehensive Research Organization

institute: Teikyo University

summary: SMAD2 and SMAD3 have diverse binding profiles in triple-negative breast cancer cell lines.

overall_design: SMAD2/3 ChIP-seq analyses were performed in 2 different TNBCs at 2 different time points after TGFβ treatment.

first: Mai

last: Kobayashi

first: Anders

last: Sundqvist

first: Daizo

last: Koinuma

first: Kohei

last: Miyazono

first: Peter

last: ten Dijke


title: Linoleic Acid Stimulation of WT Staphylococcus aureus USA300 NRS384

summary: Methicillin-resistant Staphylococcus aureus (MRSA) infections result in more than 200,000 hospitalizations and 10,000 deaths in the United States each year and remain an important medical challenge. A key factor of S. aureus pathogenesis is the production of virulence proteins that are secreted into the extracellular matrix damaging host tissues and forming abscesses that may serve as replicative niches for the bacteria. We recently discovered that host-derived cis-unsaturated fatty acids activate the transcription and translation of EsxA, a protein that plays a central role in abscess formation in clinically relevant MRSA strains. Additionally, we discovered that fatty acid stimulation of EsxA is dependent on fakA, a gene that encodes a protein responsible for the incorporation of exogenous fatty acids into the S. aureus phospholipid membrane. In order to gain a comprehensive understanding of host-fatty-acid-sensing in S. aureus, we performed RNA-Seq analysis on WT Staphylococcus aureus USA300 NRS384, a community-acquired MRSA strain, in the presence and absence of 10μM linoleic acid.

overall_design: RNA-Seq analysis was performed on WT Staphylococcus aureus USA300 NRS384 in the presence and absence of 10μM linoleic acid. Each condition was performed in triplicate thereby yielding a total of 6 samples for RNA-Seq analysis.


title: Role of Foxp1 in mouse embryonic neural stem cells (NSCs)

status: Public on Nov 14 2017

city: Utrecht

first: Paul

last: Coffer

address: Uppsalalaan 6

department: Regenerative Medicine Center

country: Netherlands

institute: UMC Utrecht

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

overall_design: Refer to individual Series


title: Streptococcus agalactiae stringent response RNA-seq

city: Baltimore

first: Suvarna

last: Nadendla

address: 670 W.Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland School of Medicine

summary: Transcriptome analysis of Streptococcus agalactiae (group B Streptococcus) grown under control conditions or coincubated with serine hydroxamate to induce the bacterial stringent response

overall_design: Two strains of S. agalactiae (10/84 and A909) were grown to mid-log phase either in control broth or coincubated with serine hydroxamate. Each strain-condition pair was  RNA was extracted and used for RNA-seq in order to identify differentially expressed genes.

first: Thomas

last: Hooven

first: Adam

last: Ratner

first: Hervé

last: Tettelin


title: DDM1/Lsh remodelers allow methylation of DNA wrapped in nucleosomes

city: Norwich

first: David

last: Lyons

state: Norfolk

address: Colney Lane

institute: John Innes Centre

summary: Eukaryotic DNA is wrapped around histone octamers to form nucleosomes, which are separated by linker DNA bound by histone H1. In many species, the DNA exhibits methylation of CG dinucleotides, which is epigenetically inherited via a semiconservative mechanism. How methyltransferases access DNA within nucleosomes remains mysterious. Here we show that methylation of nucleosomes requires DDM1/Lsh nucleosome remodelers in Arabidopsis thaliana and mouse. We also show that removal of histone H1, which partially restores methylation in ddm1 mutants, does so primarily in the linker DNA between nucleosomes. In h1ddm1 compound mutants, substantial portions of the genome exhibit dramatically periodic methylation that approaches wild-type levels in linker DNA but is virtually absent in nucleosomes. We also present evidence that de novo methylation supplements semiconservative maintenance of CG methylation across generations. Overall, our results demonstrate that nucleosomes and H1 are barriers to DNA methylation, which are overcome by DDM1/Lsh nucleosome remodelers.

overall_design: Bisulfite sequencing to determine single-base DNA methylation: 4 different genotypes from F4 generation, without replicates; MNase sequencing to identify nucleosome positions genomewide: single generation in leaf tissue for 4 different genotypes, 2 or 3 biological replicates; RNA-seq to define expression deciles in wild-type: single generation in leaf tissue for WT, 2 replicates.


title: The Epstein-Barr virus episome maneuvers between nuclear chromatin compartments during reactivation [DNA-seq]

status: Public on Nov 13 2017

first: JJ

last: Miranda

address: 3009 Broadway

institute: Barnard College, Columbia University

summary: Using chromatin conformation capture methods, we learned that the latent episome of the human Epstein-Barr virus (EBV) displays preferential chromosome association that correlates with gene density. The episome avoids gene-rich chromosomes and favors gene-poor chromosomes. Kaposi’s sarcoma-associated herpesvirus behaves similarly, but human papillomavirus does not, suggesting limited evolutionary conservation of this strategy. Moreover, the strongest contacts we detected between the human genome and EBV episome localized to OriP, the latent origin of replication. This genetic element, and the EBNA1 protein that binds there, are sufficient to reconstitute chromosome association preferences of the entire episome. Upon reactivation from latency, however, these preferences are lost. Detailed mapping of changes in interchromosomal contacts reveal that the episome moves away from repressive heterochromatin and toward activating euchromatin. Our work adds three-dimensional relocalization to the molecular events that occur during the genetic switch from EBV latency to reactivation. The involvement of only a myriad of interchromosomal contacts also argues for a possible role of this type of long-range association in gene regulation.

sample_organism:
Homo sapiens
human gammaherpesvirus 4

platform_organism:
Homo sapiens
human gammaherpesvirus 4

overall_design:
DNA-seq examination of viral DNA in latent LGNFR- and reactivated LGNFR+ Akata-ZTA cells pre-treated with acyclovir and induced with doxycycline.

Please note that the wig files are a slightly modified format in that they display a viral genome not available as a chromosome on the UCSC genome browser. The wig files are readable by the IGV browser (as described in the associated publication).

first: Stephanie

last: Moquin

first: J


title: Large-scale low-cost NGS library preparation using a robust Tn5 purification and tagmentation protocol [polyA]

city: Barcelona

first: Lars

last: Velten

address: C. Dr. Aiguader 88, P05

department: Bioinformatics and Genomics

country: Spain

institute: CRG

summary: In recent years, tagmentation-based library preparation using a hyperactive version of the Tn5 transposase gained more and more popularity. The limited hands-on time, robustness and high efficiency of the method are essential for the processing of next-generation sequencing libraries form little input material like single cells or the processing of hundreds of samples simultaneously. The hyperactive Tn5 is commercially available (Nextera XT DNA library preparation kit), however, high-throughput experiments with hundreds of samples are costly. Here, we present a highly reproducible Tn5 transposase purification strategy via an N-terminal His6-Sumo3 tag and the workflow for the tagmentation-based NGS library preparation. We demonstrate that NGS libraries processed with the in-house produced Tn5 are of the same quality like those processed with the Nextera XT DNA library preparation kit and that the purification of the transposase is reproducible across institutes. Producing the Tn5 transposase in-house allows for customized experimental design and reduces costs of large-scale experiments dramatically. We describe a novel single cell polyadenylation site mapping protocol that benefits from the fact that the in-house produced Tn5 can be loaded with any desired linker oligonucleotide for tagmentation.

overall_design: For samples labeled polyA, full-length cDNA was amplified from 15pg of HeLa RNA using a modified smart-seq2 protocol, which uses a 3' end specific adapter carrying a sample barcode of length 6nt as well as a unique molecular identifier of length 8nt. cDNA was  tagmented with a single adapter (loaded onto Tn5), technical replicates were performed on different cDNA samples. PCR was performed using batch-specific index primers complementary to the tagmentation adapter as well as a primer complementary to the 3' end specific adapter. Fragments were size selected to achieve a median library size of approximately 350-450 bp and sequenced asymetrically: The i7 index read was used for demultiplexing into sample batches, a first read of 14 cycles was used to assign the cell- and molecular identifier whereas a second read of 290 cycles was used to identify gene and polyadenylation site. Both tagmentation- and smartseq2 replicates are included.

first: Bianca

last: Hennig

first: Ines

last: Racke

first: Chelsea

last: Tu

first: Matthias

last: Thoms

first: Hüseyin

last: Besir

first: Kim

last: Remans

middle: M

last: Steinmetz


title: Network-based, cross-cohort discovery of transcriptional mechanisms presiding over maintenance of high-risk neuroblastoma subtype state

first: Gonzalo

last: Lopez

summary: Network-based analysis of neuroblastoma samples from two large cohorts identified master regulator proteins controlling the transcriptional state of three high-risk molecular subtypes. In particular, a TEAD4-MYCN positive feedback loop emerged as the core regulatory motif of a small protein module presiding over implementation and stability of the subtype associated with MYCN amplification. Specifically, MYCN transcriptionally activates TEAD4, which in turn activates MYCN both transcriptionally and post-translationally. The resulting MYCN-TEAD4 positive feedback loop plays a critical role in maintaining aberrant activity of a 10-protein regulatory module that causally regulates the transcriptional state of this subtype. Consistently, loss of TEAD4 activity induces core module activity collapse and abrogates neuroblastoma cell viability in vitro and in vivo, thus suggesting novel therapeutic strategies for this important childhood cancer.

overall_design: Study of the transcriptional control by TEAD4 and MYCN positive feedback loop using RNA-seq profiles of TEAD4, WWTR1 and MYCN shRNA knockdowns in neuroblastoma BE2 cells. ChIP-Seq analysis using TEAD4 antibody in BE2 cells.

first: Presha

last: Rajbhandari


title: Transcriptomic profiles of D29, StarStuff and L5

city: Pittsburgh

first: Rebekah

last: Dedrick

address: 4249 Fifth Ave

department: Biological Sciences

institute: University of Pittsburgh

summary: The gene expression profiles of mycobacteriophage D29 and StarStuff were analyzed 15min, 30min, 60min and 150min post-infection (MOI=3), as well as a StarStuff lysogen.  The gene expression profiles of 30min and 150min post-induction of an L5 thermo-inducible lysogen, as well as the L5 lysogen itself.

sample_organism:
Fromanvirus D29
Fromanvirus L5
Mycobacterium phage StarStuff

overall_design: Total RNA was isolated, depleted of rRNA and library prepped (Illumina TruSeq)

first: Graham

middle: F

last: Hatfull

first: Travis

last: Mavrich

first: Rebecca

last: Garlena


title: The Epstein-Barr virus episome maneuvers between nuclear chromatin compartments during reactivation [RNA-seq]

overall_design: RNA-seq examination of viral transcription in the Namalwa cell line that contains integrated EBV


title: Foxp1 binding profiling in mouse embryonic neural stem cells (NSCs)

first: Paul

last: Coffer

summary: By chromatin-immunoprecipitating (ChIP) Foxp1 in NSCs we identified genome-wide binding sites for Foxp1

overall_design: Foxp1 ChIP-sequencing of mouse embryonic neural stem cells derived from E14.5 CD-1 mice

first: L

last: Braccioli

first: S

last: Vervoort

first: P


title: YY1 is a structural regulator of enhancer-promoter loops [4C-Seq]

city: Cambridge

first: Richard

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: There is considerable evidence that chromosome structure plays important roles in gene control, but we have limited understanding of the proteins that contribute to structural interactions between gene promoters and their enhancer elements. Large DNA loops that encompass genes and their regulatory elements depend on CTCF-CTCF interactions, but most enhancer-promoter interactions do not depend on this structural protein.  Here we show that the transcription factor Yin Yang 1 (YY1) contributes to enhancer-promoter structural interactions in a manner analogous to DNA interactions mediated by CTCF.  YY1 binds to active enhancers and promoter-proximal elements in all cells examined.  YY1 forms dimers that can facilitate DNA interactions. Deletion of YY1 binding sites or depletion of YY1 can disrupt enhancer-promoter looping and normal gene expression.  We propose that YY1-mediated enhancer-promoter interactions are a general feature of mammalian gene control.

overall_design: 4C-Seq (Chromosome conformation capture) in mouse embryonic stem cells

first: Abraham

last: Weintraub

first: Charles

last: Li

first: Alicia

last: Zamudio

first: Alla

last: Sigova

first: Nancy

last: Hannett

first: Daniel

last: Day

first: Brian

last: Abraham

first: Malkiel

last: Cohen

first: Behnam

last: Nabet

first: Dennis

last: Buckley

first: Yang

last: Guo

first: Denes

last: Hnisz

first: Rudolf

last: Jaenisch

first: James

last: Bradner

first: Nathanael

last: Gray


title: MSK1 regulates luminal cell differentiation and metastatic dormancy in breast cancer

first: Aikaterini

last: Symeonidi

state: Barcelona

address: Baldiri i Reixac, 10

department: Oncology

institute: Institut for Research in Biomedicine (IRB-Barcelona)

summary: For many breast cancer (BCa) patients, symptomatic bone metastases appear after years or even decades of latency. How metastatic cells disseminate, and how micrometastatic lesions remain dormant and undetectable yet initiate colonization, are major questions in cancer research. Here we identify and functionally analyse a molecular mechanism involved in bone metastatic latency of estrogen receptor–positive (ER)+ BCa. We developed an in vivo loss-of-function, genome-wide shRNA screening to identify genes relevant for long-latent relapse in BCa. This screen revealed the kinase MSK1 as an important regulator of metastatic dormancy. Importantly, low MSK1 expression associates with early metastasis in ER+ BCa patients. Reduced MSK1 levels impaired cellular differentiation and increased the bone homing and growth capacity of metastatic cells. MSK1 modulates chromatin status at promoters to regulate the expression of luminal differentiation genes, including those for the GATA-3 and FOXA1 transcription factors, which prevent the progression of ER+ BCa towards metastasis. Our results identify the regulation of luminal cell differentiation by MSK1 via modulation of chromatin remodelling to be a key mechanism for controlling metastatic dormancy in BCa. We propose that MSK1 could be a useful marker for stratifying BCa patients as high- or low-risk for early relapse, allowing patients to receive appropriate treatments.

overall_design: 4 samples were analysed, 2 shControl samples for each of the phosphorylation sites (S10P and S28P) and 2 samples of the shMSK1 for each of the phosphorylation sites. In addition, for the shControl and shMSK1 Input-DNA was used.

first: Sylwia

last: Gawrzak

first: Lorenzo

last: Rinaldi

first: Enrique

last: Arenas

first: Fernando

last: Salvador

first: Federico

last: Rojo

first: Ivan

last: del Barco Barrantes

first: Juan-Miguel

last: Cejalvo

first: Marta

last: Palafox

first: Marc

last: Guiu

first: Antonio

last: Berenguer-Llergo

first: Camille

last: Stephan-Otto Attolini

first: Jelena

last: Urosevic

first: Anna

last: Bellmunt

first: Sara

last: Gregorio

first: Daniela

last: Kalafatovic

last: Arnal-Estapé

first: Barbara

last: Müllauer

first: Rianne

last: Groeneveld

first: Cristina

last: Serra

first: Javier

last: Cortes

first: Ana

last: Rovira

first: Montse

last: Muñoz

last: Lluch

first: Joaquin

last: Arribas

first: Violeta

first: Joan

last: Albanell

first: Aleix

last: Prat

first: Angel

last: Nebreda

first: Salvador

last: Aznar-Benitah

first: Roger

last: Gomis


title: The Epstein-Barr virus episome maneuvers between nuclear chromatin compartments during reactivation [ChIP-seq]

first: JJ

last: Miranda

overall_design: ChIP-seq identification of binding sites for two EBV proteins on the episomal viral genome

first: Stephanie

last: Moquin

first: J


title: Patient-derived organoid cultures model human primary liver cancer in vitro

first: Charles

middle: Richard

last: Bradshaw

address: Tennis Court Road

institute: Gurdon Institute

summary: The study of human liver cancer has been hampered by the lack of reliable models that faithfully recapitulate the physiopathology of the patient’s original tumour ex vivo. Here, we describe the first culture system to allow the establishment and long-term expansion of human primary liver cancer (PLC) organoids (called tumoroids) from the three most common PLC subtypes: Hepatocellular carcinoma (HCC), Cholangiocarcinoma (CC) and mixed HCC/CC tumours (CHC). We evaluated whether tumoroid lines maintain the expression profile and the genomic landscape of the original tumor they derived from by performing genome-wide (RNAseq/WES) analyses before and after culture. These analyses reveal that the cultures closely recapitulate the gene expression and the mutational landscape of the original tumor, allowing discrimination between different tumor subtypes (HCC, CHC, CC).

overall_design: We generated RNAseq and WES data from healthy donor and 7 tumoral human PLC tissues and their derived organoid cultures maintained in our defined medium.

first: Laura

last: Broutier

first: Meritxell

last: Huch


title: The Epstein-Barr virus episome maneuvers between nuclear chromatin compartments during reactivation [HiC-seq]

sample_organism:
Homo sapiens
human gammaherpesvirus 4
human papillomavirus 31
Human gammaherpesvirus 8
Human papillomavirus 16

overall_design: Hi-C examination of host-viral genome interactions during reactivation and latency


title: Epigenetical regulation in zebrafish heart regeneration

status: Public on Nov 12 2017

city: Shanghai

first: Jizhou

last: Yan

address: 999 Hucheng Ring Road,

institute: Shanghai Ocean University

summary: Hitological and ultrastrucural observations show that zebrafish can restore the strcuture od the damaged heart heart via cell conversion. Dynamic immunohistochemistry analyses indicate that H3K9M3 and H3K9Ac may invlove the processes of cytoplasmic remodeling and nuclear reorganization.We then employ ChIP-seq to identify the targets of the two histone marks.

overall_design: ChIP-seq was used to analyze chromatin-binding sites by two histone marks:H3K9M3 and H3K9Ac at 0dpa, 6dpa and 9dpa

first: Hui

last: Zhang

first: Huiping

last: Guo


title: Examining alterations in gene expression of PC3-wt (PSMA -ve) vs PC3-PSMA (PSMA +ve) cells

status: Public on Nov 11 2017

city: Boston

first: Charalambos

last: Kaittanis

address: 55 Fruit St, White 427

department: GCMI

institute: Massachusetts General Hospital

summary:
The biological role of PSMA, a biomarker expressed in prostate cancer and by the neovasculature of solid tumors, remains unknown. Although PSMA processes folates in our duodenum, and in the brain cleaves NAAG to control neuronal signaling, little is known about its role in cancer.
We used microarrays to detail the glonal perturbations in gene expression in the absence of PSMA, in order to identify disease-specific driving pathways that may lead to new therapies for cancer.

overall_design: PC3-wt (PSMA -ve) cells grown on Petri dishes and in complete media where compared with PC3 cells expressing PSMA

first: Haley

last: Hieronymus


title: Examining alterations in gene expression of prostate cancer cells in presence or absence of PSMA


title: SMAD2/3 are redirected to novel sites in MCF10A MII after prolonged TGFβ stimulation

first: Masato

last: Morikawa


title: The full transcription map of mouse papillomavirus type 1 (MmuPV1)

status: Public on Nov 10 2017

city: Frederick

first: Vladimir

last: Majerciak

address: 1050 Boyles Street

department: National Cancer Institute

institute: NIH

summary: The comprehensive analysis of MmuPV1 expression was performed using total RNA-seq of wart tissues obtained from infected FoxN1nu/nu mice.

overall_design: Athymic FoxN1nu/nu mice were experimentally infected with quasivirions containing MmuPV1 synthetic genome at three anatomical sites (ear, muzzle, and tail). The warts tissues formed at the infection sites were harvested together with uninfected control ears for total RNA extraction and RNA-seq using Illumina platform was performed on ribo-minus total RNA.

first: Zhi-Ming

last: Zheng


title: APOBEC3s induce mutations during the repair of CRISPR-Cas9-generated DNA breaks.

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

summary: APOBEC-AID family of cytidine deaminase prefers single-stranded nucleic acids for cytidine to uracil deamination. Single-stranded nucleic acids are commonly involved in the DNA repair system for breaks generated by CRISPR-Cas9. Here, we show in human cells that APOBEC3s can trigger the cytidine deamination of single-stranded oligodeoxynucleotides, which ultimately results in base substitution mutations in genomic DNA through the homology-directed repair (HDR) of Cas9-generated double-strand breaks . In addition, the APOBEC3-catalyzed deamination in genomic single-stranded DNA formed during the repair of Cas9 nickase-generated single-strand breaks can be further processed to yield mutations mainly involving insertions or deletions (indels). Mechanistically, both APOBEC3-mediated deamination and DNA repair proteins play important roles in the generation of these indels. Correspondingly, optimizing conditions for the repair of CRISPR-Cas9-generated DNA breaks, such as using double-stranded donors in HDR or temporarily suppressing endogenous APOBEC3s, can substantially repress these unwanted mutations in genomic DNA.

overall_design: Determination of base substituitons and insertions/deletions induced by APOBECs during the repair of CRISPR-Cas9-generated DNA breaks

first: Jia

last: Chen

first: Bin

last: Shen

first: Wei

last: Xue

first: Liqun

last: Lei

first: Bei


title: Human embryonic stem cells contribute to embryonic and extraembryonic lineages in mouse embryos through inhibition of apoptosis

city: Beijing

first: Qi

last: Zhou

address: Datun Road, Chaoyang District

institute: Institute of Zoology,CAS

summary: We generated hESCs with inducible expression of anti-apoptotic gene BCL2 and BCL2L1, and found that the BCL2- and BCL2L1-overexpression could inhibit apoptosis of hESCs without affecting their pluripotent state.

overall_design: mRNA profiles of human embryonic stem cells with inducible expression of anti-apoptotic gene BCL2 and BCL2L1 were generated by RNA sequencing using Illumina HiSeq 4000

first: Tianda

last: Li

first: Guihai

last: Feng


title: Large-scale low-cost NGS library preparation using a robust Tn5 purification and tagmentation protocol

first: Lars

last: Velten

overall_design: Refer to individual Series


title: Determinants of H3K4me pattern establishment

first: Luis

last: Soares

address: 240 Longwood Ave, Building C1-207

department: BCMP

institute: Harvard Medical School

summary: A hallmark of genes transcribed by RNA polymerase II (RNApII) is a "gradient" of histone H3 lysine 4 (H3K4) methylation. Various factors differentially bind to H3K4me3 near promoters, H3K4me2 just downstream, and H3K4me1 further downstream to modulate gene expression. Set1/COMPASS, the single S. cerevisiae H3K4 methyltransferase, binds transcribing RNApII, but COMPASS may also be allosterically regulated by specific subunits and histone H2B ubiquitylation. To ask whether differential H3K4 methylation is determined by regulated activity at specific gene locations or by the amount of time COMPASS spends near the nucleosome, ChIP-Seq analyses was performed in cells with altered transcription elongation rates or with Set1 fused to RNApII. Our results support a simple model where higher H3K4 methylations result from both increased duration and frequency of COMPASS proximity to the nucleosome.

overall_design: 99 Samples of H3K4me3, H3K4me2, H3K4me1, H3, RPB3, RPB4, Ser5 and Ser2 ChIP-Seq for S.cerevisiae in wild type and relevant mutant conditions.

first: Steve

last: Buratowski


title: Gene expression response of Salmonella enterica serovar Enteritidis phage type 8 to subinhibitory concentrations of trans-cinnamaldehyde and eugenol

status: Public on Nov 09 2017

city: Irvine

first: Michael

last: McClelland

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

summary: Transcriptional profiles of mid-exponentially growing Salmonella enterica sv Enteritidis PT8 cultures in response to exposure to trans-cinnamaldehyde (0.01%; 0.75mM) or eugenol (0.04%; 2.46mM)

sample_organism: Salmonella enterica subsp. enterica serovar Enteritidis

overall_design: Total RNA was harvested from three biological replicates of mid-exponentially growing Salmonella enterica sv Enteritidis PT8 cultures before or after 15min or 30 min exposure to plant-derived compounds trans-cinnamaldehyde (0.01%) or eugenol (0.04%) at subinhibitory concentrations.

first: Steffen

last: Porwollik

first: Anup

middle: K

last: Johny

first: Jonathan

middle: G

last: Frye


title: An RNAi screen reveals an essential role for HIPK4 in human skin epithelial differentiation from iPSCs

city: heidelberg

first: Lionel

last: Larribere

address: im neuenheimer Feld

institute: DKFZ

summary: Molecular mechanisms that are responsible for the development of human skin epithelial cells are not completely understood so far. As a consequence, the efficiency to establish a pure skin epithelial cell population from human induced pluripotent stem cells (hiPSC) remains poor. Using an approach including RNA interference and high-throughput imaging of early epithelial cells, we could identify candidate kinases which are involved in skin epithelial differentiation. Among them, we found HIPK4 to be an important inhibitor of this process. Indeed, its silencing increased the amount of generated skin epithelial precursors, increased the amount of generated keratinocytes and improved growth and differentiation of organotypic cultures, allowing for the formation of a denser basal layer and stratification with the expression of several keratins. Our data bring substantial input in the regulation of human skin epithelial differentiation and for improving differentiation protocols from pluripotent stem cells.

overall_design: Total RNA obtained from isolated hiPSCs, NHK, differentiated cells at day 5, day 10 and day 30 in control or siHIPK4 condition

last: Larribère

first: Jochen

last: Utikal