title: Uterine glands impact uterine receptivity, luminal fluid homeostasis and blastocyst implantation

status: Public on Nov 22 2016

city: Columbia

first: Thomas

last: Spencer

address: 920 East Campus Drive

department: Animal Sciences

institute: University of Missouri

summary: Uterine glands are essential for pregnancy in mice and likely humans, because they secrete or transport bioactive substances that regulate uterine receptivity for blastocyst implantation. In mice, the uterus becomes receptive to blastocyst implantation on day 4, but is refractory by day 5. Here, blastocysts could be recovered from progesterone-induced uterine gland (PUGKO) but not wildtype (WT) mice on day 5 post-mating. Anti-adhesive Muc1 protein and microvilli were present on the luminal epithelium of PUGKO but not WT uteri. A number of known uterine receptivity genes and gland-specific genes were altered in the PUGKO uterus. Next, the uterus and uterine luminal fluid (ULF) were obtained from WT and PUGKO mice on day 3, 4 and 5. Transcriptome analysis revealed that 580 genes were decreased in the PUGKO uterus, however ULF secrotome analysis revealed that many proteins and several amino acids were increased in the PUGKO ULF. Of note, many proteins encoded by many gland-specific genes were not identified in the ULF of WT mice. These results support the ideas that uterine glands secrete factors that regulate ULF homeostasis and interact with other cell types in the uterus to influence uterine receptivity and blastocyst implantation for the establishment of pregnancy.

overall_design: Endometrium from wild-type and PUKGO mice were subjected to RNA sequencing from days 3, 4, and 5 of pseudopregnancy (n=4 per day per group)

first: Andrew

last: Kelleher

first: Gregory

last: Burns

first: Susanta

last: Behura

first: Guoyao

last: Wu


title: Gene expression changes in yeast cells deleted for Nat4 and cells grown in calorie-restriction

city: Nicosia

first: Antonis

last: Kirmizis

address: 1 University Avenue, PO BOX 20537

department: Department  of Biological Sciences

country: Cyprus

institute: University of Cyprus

type: Expression profiling by high throughput sequencing

summary: We report here mRNA-seq data of wild-type and Nat4-deletion mutant yeast cells. We also report mRNA-seq data of wild-type yeast cells grown under non-calorie restriction (NCR) and calorie restriction (CR) conditions.

overall_design: Comparison of differential gene-expression changes detected in Nat4-deletion mutant and cells grown in calorie restriction

first: Diego

last: Molina-Serrano

first: Vassia

last: Schiza

first: Jan

last: Oppelt


title: Exon Junction Complex (EJC) proteins bind nascent transcripts independently of pre-mRNA splicing in Drosophila melanogaster

city: Birmingham

first: Saverio

last: Brogna

address: Edgbaston

country: United Kingdom

institute: University Birmingham

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ChIP-seq Y14

overall_design: Y14 ChIP-seq in S2 cells


title: RNA-seq of hippocampus from wild type and CTCF cko animals

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

country: Israel

institute: Weizmann Institute of Science

summary: CTCF is an organizer of higher-order chromatin structure, and regulates gene expression.  Genetic studies have implicated mutations in CTCF in intellectual disabilities.  However, there is no knowledge of the role of CTCF-mediated chromatin structure in learning and memory.  We show that depletion of CTCF in postmitotic neurons, or depletion in the hippocampus of adult mice through viral-mediated knockout, induces deficits in learning and memory. These deficits in learning and memory at the beginning of adulthood are correlated with impaired long term potentiation and reduced spine density, with no changes in basal synaptic transmission and dendritic morphogenesis and arborization. Cognitive disabilities are associated with downregulation of cadherin and learning-related genes. In addition, CTCF knockdown attenuates fear conditioning-induced hippocampal gene expression of key learning genes and loss of long-range interactions at the BDNF and Arc loci. This study identifies CTCF-dependent gene expression regulation and DNA structure as regulators of learning and memory.

overall_design: 3 biological replicates of wild type and 3 biological replicates of CTCF cko mice

first: Elliott

last: Evan

first: Dev

middle: S

last: Sams


title: DNA methylome study of Norway spruce

city: Fuzhou

first: Haifeng

last: Wang

state: Fujian

address: Shangxia dian

country: China

institute: Fujian Agriculture and Forestry University

type: Methylation profiling by high throughput sequencing

summary: Bisulfite treatment libraries were made to characterize DNA methylation of Norway spruce

overall_design: Genome-wide methylome was done by Illumina TruSeq preparation kits followed by high-throughput sequencing with Illumina HiSeq 2500

first: Steve

last: Jacobsen


title: ChIP-seq of CTCF from mouse hippocampus

overall_design: 2 biological replicates of mice and one input sample


title: The effect of Foxc1 deficiency on undifferentiated and differentiated human primary keratinocytes

city: Denver

first: Lianghua

last: Bin

state: Colorado

address: 1400 Jackson street

department: Department of Pediatrics

country: USA

institute: National Jewish Health

summary: In this study, we used a RNA-sequencing (RNA-seq) approach to analyze the whole transcriptomes of human primary Keratinocytes (KC) at undifferentiated stage and differentiated stage with and without FOXC1 knockdown. Each treatment condition have 2 or 3 replicates. 10 million reads were collected. A total of 8202 genes were designated as present (RPKM>5 in at least one sample).   635 genes were differentially expressed (FDR<0.01, P<0.000774201).  FOXC1 knock-down significantly impaired keratinocytes differentiation process.

overall_design: Proliferating foreskin normal human keratinocytes were seeded in 24 well-dishes and transfected with scrambled siRNA and FOXC1 siRNA duplexes. The following day, half of the wells were differentiated in vitro by increasing Ca2+ concentration in culture media from 0.06mM to 1.3 mM for 5 days. The other half wells of cells were cultured in 0.06mM CaCl2.  Both undifferentiated and differentiated cells were harvested for total RNA extraction.  RNA sequencing libraries were made using Illumina RNA sequencing library construction protocol.  RNA libraries were sequenced by 100bp reads on Illumina Hi-seq 2000.

first: L

first: M

last: Edwards


title: ATAC-seq analysis of chromatin accessibility and nucleosome positioning in Drosophila melanogaster precellular blastoderm embryos

city: Evanston

first: Shelby

middle: A

last: Blythe

state: IL

address: Northwestern University, Hogan Hall, 2205 Tech Drive

department: Molecular Biosciences

institute: Northwestern University

summary:
Purpose: The goal of this study was to measure how chromatin accessibility and nucleosome positioning changes as embryos undergo the midblastula transition (MBT).

Methods: Single or paired embryos were collected at three minute intervals over the three cell cycles leading up to the MBT (nuclear cycles 11, 12, and 13). Embryos were subjected to ATAC-seq library preparation following established protocols. Thirteen total timepoints were collected. At least three biological replicates were collected per timepoint. Samples were subjected to paired end sequencing on an Illumina HiSeq 2500. Wild type (diploid) embryos were compared with haploid (sesame) embryos to determine whether changes in chromatin accessibility are governed by measurement of the nucleo-cytoplasmic ratio, a well known biological timer that controls the onset of the MBT.

Results: Chromatin accessibility changes dynamically during the period leading up to the MBT. Initially, genomic enhancer elements are accessible, but during NC12 and NC13, large scale chromatin remodeling results in a gain of accessibility for promoter elements and insulators. A substantial fraction of the dynamic chromatin accessibility is temporally regulated by the mechanism that measures the embryonic nuclear-cytoplasmic ratio, as determined by comparison between haploid and diploid embryos. A substantial fraction of open chromatin regions remain 'accessible' during mitotic metaphase.

overall_design:
Embryos were collected in a three minute time course spanning three cell cycles and prepared for ATAC seq analysis. Triplicate biological replicates were collected per timepoint. Samples were subjected to paired end sequencing (2x 67bp) on an Illumina HiSeq 2500.

Please note that replicates were pooled for generating processed files, and each processed data file is linked to the first replicate sample (of the corresponding samples) (*_rep1).

first: Eric

middle: F

last: Wieschaus


title: Tet proteins influence the balance between neuroectoderm and cardiac mesoderm fate choice by inhibiting Wnt signaling

status: Public on Nov 21 2016

city: La Jolla

first: ANJANA

last: RAO

state: CA

address: 9420 Athena Circle

institute: La Jolla Institute for Allergy and Immunology

summary: To determine the global distribution of Tet3 DNA binding sites, we performed ChIP-seq in neural precursor cells (NPCs). We report that Tet3-binding sites clustered close to transcription start sites (TSS), with a low frequency of binding at distal regions relative to the TSS. DNA motif analysis identified a CpG-rich sequence as the highest-ranked motif among Tet3-binding sites. GO analysis of Tet3 target genes showed enrichment for genes related to mesoderm development and neural differentiation. IPA analysis showed that Tet3 target genes were also strongly enriched for components of the Wnt signaling pathway.

overall_design: To determine the global distribution of Tet3 DNA binding sites, we performed ChIP-seq experiments using Tet3 antibodies in neural precursor cells (NPCs).

first: Xiang

last: Li

first: Anjana

last: Rao


title: RNA-sequencing transcriptome profiling of normal human keratinocytes differentiation

summary: In this study, we used a RNA-sequencing (RNA-seq) approach to analyze the whole transcriptomes of human primary Keratinocytes (KC) at different differentiation stages.    An average of 72.56 million reads were collected for each sample: 87.68% of the sequences could mapped to the human genome, and 66.70% of sequence mapped to known human genes.  A total of 17,446 ± 220 genes were expressed during the course of differentiation.  1024 transcription factors (TF) and genes encoding TF binding proteins were detected during the course of differentiation were expressed during the course of KC differentiation.

overall_design: Foreskin normal human keratinocytes were differentiated in vitro by increasing Ca2+ concentration in culture media from 0.06mM to 1.3 mM.  Undifferentiated cells and cells under differentiation for 24 hrs, 48hrs, 72 hours, 96 hours and 120 hours were harvested for total RNA extraction.  RNA sequencing libraries were made using eukaryotic long non-coding RNA sequencing library construction protocol.  RNA libraries were deep sequenced by 100bp paired-reads on Illumina His-seq 2000.


title: Tet-dependent transcriptional programs during mESC differentiation

summary: Tet-family dioxygenases catalyze conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) in DNA. Here, we show that Tet3 deficiency impairs neural differentiation of mouse ESCs, resulting in skewing towards cardiac mesoderm; conversely, ectopic expression of Tet3 enhances neural differentiation and limits cardiac mesoderm specification. To determine the effects of Tet3 gain and loss on global gene expression profiles during mESC differentiation, we performed whole transcriptome RNA-sequencing (RNA-seq) analysis of (i) WT and Tet3 KO mESCs differentiating into neuroectoderm under SFEB culture (days 6 and 10); and (ii) Control and Tet3-overexpressing mESCs in non-permissive neural differentiation conditions containing FBS (days 4 and 7). Genome-wide analyses showed that Tet3 mediates cell-fate decision by inhibiting Wnt signaling.

overall_design: Total RNA obtained from ES cells under the following conditions: (i) WT and Tet3 KO mESCs differentiating into neuroectoderm under SFEB culture (days 6 and 10); and (ii) Control and Tet3-overexpressing mESCs in non-permissive neural differentiation conditions containing FBS (days 4 and 7). Multiplexed libraries were constructed using SOLiD Total RNA-seq kit. Libraries were sequenced on the SOLiD 5500 platforms according to the manufacturer's instructions.


title: Profiling of epithelial and stromal cells in early proximal colon preneoplasia with matched normals.

status: Public on Nov 23 2016

city: Farmington

first: Allen

last: Mo

state: CT

address: 263 Farmington Avenue

department: Center for Molecular Medicine

institute: UConn Health

summary: Progression of nonmalignant colonic cells harboring somatic mutations depends upon interactions with surrounding stroma; however, details of this interaction are poorly understood. We performed targeted transcriptional profiling of laser-captured epithelial and stromal cells from ACF, the earliest detectable human colonic pre-neoplastic lesion. Within ACF epithelium carrying non-overlapping mutations in KRAS, BRAF, or APC, we observed broad NF-kB-related inflammatory changes and specific differences associated with each mutation, including BRAFV600E-mediated senescence. Additionally, we identified ACF-associated stromal changes indicative of immune cell infiltration and fibroblast activation. Our results provide new insight into intercellular signaling changes that control the earliest stages of CRC development.

overall_design: Epithelial and stromal targetted mRNA profiles of biopsied proximal colon ACF and normal samples. Each ACF had a detected mutation for either KRAS, BRAF, or APC via DNA-MS. Epithelial and stromal cells were individually isolated using laser capture microdissection. mRNA profiles were evaluated using two Ampliseq RNA panels (off the shelf Apoptotic panel, and custom Senescence panel of 20 genes)

first: Daniel

middle: W

last: Rosenberg


title: Tet-dependent transcriptional programs during early embryogenesis

summary: To determine the transcriptional effects of lack of Tet proteins during early embryogenesis, we performed single-embryo RNA-sequencing of control and TKO embryos (E6.75; 4 embryos from each group). Genome-wide analyses showed that Tet deficiency promotes the expression of mesoderm-related genes during early embryogenesis in vivo.

overall_design: Control and Tet1/2/3 TKO embryos were collected at E6.75. Single embryos were lysed and converted into double stranded cDNA using SMARTer ultra-low RNA kit for Illumina sequencing (Clontech). 1 ng of cDNA for each sample was used for preparing libraries using Nextera XT DNA sample preparation kit (IIlumina). Libraries were sequenced on Illumina HiSeq 2500 platforms according to the manufacturer's instructions.


title: Arabidopsis microRNA expression regulation in a wide range of abiotic stress responses

city: Poznań

first: Zofia

last: Szweykowska-Kulińska

address: Umultowska 89

department: Department of Gene Expression

country: Poland

institute: Adam Mickiewicz University

type: Non-coding RNA profiling by high throughput sequencing

summary: Arabidopsis microRNA expression regulation was studied in a wide array of abiotic stresses such as drought, heat, salinity, copper excess/deficiency, cadmium excess and sulphur deficiency. A home-built RT-qPCR mirEX platform for the amplification of 289 Arabidopsis microRNA transcripts was used to study their response to abiotic stresses. Small RNA sequencing and Northern hybridization were performed to study the expression of mature microRNAs. In the case of common climate change related stresses such as drought, heat and salinity we observed broad induction of the level of primary miRNAs that was not observed at the level of microRNAs.. In the case of local soil pollution stresses, that are represented by heavy metal contaminations or deprivation of a specific micro- or macroelement, the transcriptional response of pri-miRNAs was quite limited but also not predictive to the level of the mature microRNA. This points to an essential role of posttranscriptional regulation of microRNAs expression. We found that the level of several microRNAs can be differentially regulated in early and late response to stress. New Arabidopsis microRNAs responsive to abiotic stresses were discovered. Three microRNAs: miR319a/b, miR319b.2, and miR400 have been found to be responsive in several abiotic stresses and thus can be regarded as a general stress-responsive microRNA species. Additionally, a new target for miR319b.2 – TBL10 has been experimentally confirmed. However, its level under different abiotic stresses is unchanged in comparison to control conditions. In the promoter  region of the TBL10 gene we found the presence of many stress-responsive  elements. We suggest that transcriptional induction resulting in the increase of transcript levels is downregulated by the increase of the miR319b.2 ultimately resulting  in a stable level of TBL10 mRNA. Our experiments show the existence of a complex regulatory network involved in the microRNA level control that is necessary to fine-tune plant response to environmental cues.

overall_design: Arabidopsis thaliana abiotic stress responses miRNAs: 30%SWC drought, 20%SWC drought, 0.5h heat (37˚C), 6h heat (37˚C), 24h NaCl [250mM] excess, 24h copper deficiency, 24h copper [10μM] excess, 24h cadmium [10μM] excess, 24h sulfur deficiency

first: Maria

last: Barciszewska-Pacak

first: Kaja

last: Milanowska

first: Katarzyna

last: Knop

first: Dawid

last: Bielewicz

first: Przemyslaw

last: Nuc

first: Patrycja

last: Plewka

first: Andrzej

last: Pacak

first: Franck

last: Vazquez

first: Artur

last: Jarmolowski

first: Wojciech

last: Karlowski

last: Szweykowska-Kulinska


title: Gene expression profile analysis of CD8+ T cells isolated from splenic red and white pulp upon LCMV infection

city: Atlanta

first: Mehul

middle: Shamal

last: Suthar

state: GA

address: 954 Gatewood Road, Office 2022

institute: Emory University

summary: We performed RNAseq analysis on CD8+ T cells isolated from splenic white and red pulp upon lymphocytic choriomeningitis virus-Arm infection to understand how cell function and fate are determined. Analyses of transcriptional profiles revealed that decisions for gene expression patterns to become a memory cell were established during the early contraction phase by 11 days post infection (dpi) and their expression remained constant throughout the T cell development. This study may have important implication for development of efficacious vaccines.

overall_design:
C57BL/6 mice that received P14 T cells were infected with LCMV Arm. At 0, 7, 11, 15, 33 days post infection, P14 T cells were sorted from splenic white and red pulp for RNAseq analysis

The sample titles contain sample information according to the following scheme:
First digit(s) = refers to unique sample ID (#1-50; 41 and 42 were removed due to poor quality)
Second digit(s) = refers to the timepoint (0, 7, 11, 15, 33 days)
C or T = designation refers to circulating (C; red pulp) or tissue (T; white pulp)
Third digit(s) = refers to biological replicate (#1-5)

first: Young-Jin

last: Seo

first: Prithiviraj

last: Jothikumar

first: Cheng

last: Zhu

first: Arash

last: Grakoui


title: Tet proteins influence the balance between neuroectodermal and mesodermal fate choice by inhibiting Wnt signaling

first: ANJANA

last: RAO

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

overall_design: Refer to individual Series


title: Effects of combined heat shock and glucose-deprivation on wild type and os2 mutant cells of Neurospora crassa.

city: Saint Paul

first: Nora

last: Plesofsky

state: MN

address: 1479 Gortner Avenue

department: Plant Biology

institute: University of Minnesota

summary: Whereas the combined stresses kill wild type cells, the os2 signaling mutant survives them.

overall_design: RNA was extracted from wild type and os2 mutant cells subjected to 30 degree control conditions, 45 degree heat shock, or heat shock combined with 2-deoxyglucose

first: Robert

last: Brambl


title: Genome-wide occupancy of EBF1-wt & EBF1-H240A

city: Freiburg

first: Senthilkumar

last: Ramamoorthy

address: Stübeweg 51

department: Cellular & Molecular Immunology

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: To study the function of EBF1-H240 residue, genome-wide EBF1 ChIP was performed in A-MuLV transformed pro-B  (Ebf1fl/fl;RERTCre) cells transduced with Ebf1wt and Ebf1H240A expressing vectors.

overall_design: A-MuLV transformed Ebf1fl/fl RERTCre pro-B cells were treated with 2μM 4-hydroxy-tamoxifen (4-OHT) 24h after transduction.  GFP+ cells were sorted two days after transduction and maintained in a 2μM 4-hydroxy-tamoxifen containing medium for 5 days and the replacement was validated. The cells were expanded further and used for ChIP analysis.

first: Cheng-Yuan

last: Yang


title: TET proteins regulate lineage specification and TCR-mediated expansion of iNKT cells (SMART-Seq)

city: Espoo

first: Sini

last: Rautio

address: Konemiehentie 2

country: Finland

institute: Aalto University

summary: TET proteins oxidize 5-methylcytosine to 5-hydroxymethylcytosine and further oxidation products in DNA. Here we report that simultaneous deletion of Tet2 and Tet3 in mouse double-positive thymocytes resulted in dysregulated development and proliferation of invariant natural killer T (iNKT) cells. Tet2-Tet3-double-deficient (DKO) iNKT cells displayed pronounced skewing towards the NKT17 lineage, with increased DNA methylation and impaired expression of genes encoding the key lineage-specifying factors T-bet and ThPOK. Transfer of purified Tet2-Tet3 DKO iNKT cells into immunocompetent recipient mice resulted in uncontrolled expansion dependent on the nonclassical MHC protein CD1d, which presents lipid antigens to iNKT cells. Our data indicate that TET proteins regulate iNKT cell fate by ensuring proper development and maturation and suppressing aberrant T cell antigen receptor (TCR)-mediated proliferation.

overall_design:
Gene expression in wild type iNKT cells, Tet3 KO and Tet2/3 DKO iNKT cells,
wildtype and Tet2/3 DKO tetramer+TCRb+CD24-NK1.1- cells
wildtype and Tet2/3 DKO stage 0 cells
wildtype and Tet2/3 DKO NKT1 cells

first: Ageliki

last: Tsagaratou

first: Anjana

last: Rao


title: Interaction of CNOT3 with EBF1 regulates gene-specific transcription and mRNA stability in B lymphopoiesis

summary: EBF1 interacts with CNOT3 and histidine 240 of EBF1 is a critical residue for this interaction. We studied H240 dependent EBF1 occupancy and gene expression regulation by genome-wide ChIP and microarray analysis. We also performed RNASeq analysis in pro-B cells to study the role of Cnot3 in early B cells development. This SuperSeries is composed of the SubSeries listed below.

first: Rudolf

last: Grosschedl


title: CTCF ChIP-seq of WT and RNA-seq of WT and CTCF cko mouse

first: Gilgi

last: Friedlander


title: Gene expression profile of Cnot3(+/+) & Cnot3 (∆/∆) pro-B cells

summary: To study the role Cnot3 in early B cells development, RNASeq analysis of pro-B cells (B220+ and CD43+) was performed in tamoxifen treated Cnot3(fl/fl) RERTCre and Cnot3+/+;RERTCre mice.

overall_design: Two individual replicates of Cnot3(fl/fl) RERTCre and Cnot3(+/+) RERTCre mice were tamoxifen treated periodically. Ten days after the initial treatment, B220+CD43+ pro-B cells were sorted from the bone marrow and RNASeq analysis was performed.


title: Control of Hoxd gene transcription in the mammary bud by hijacking a pre-existing regulatory landscape

city: Geneva

first: Leonardo

last: Beccari

address: 30 Quai Ernest Ansermet

department: Genetics and Evolution

country: Switzerland

institute: University of Geneva

summary: In this work we have analyzed the transcriptomic profiles of E13.5 mouse embryonic mammary buds. We show that Hoxd8 and Hoxd9, two gene members of the HoxD cluster, are transcribed during mammary bud development. Yet, unlike in other developmental contexts, their co-expression does not rely upon the same regulatory mechanism. Hoxd8 is regulated by the combined activity of closely located sequences and the most distant telomeric gene desert. On the other hand, Hoxd9 is controlled by an enhancer sequence also located within the telomeric gene desert, but which has no impact on Hoxd8 transcription, thus constituting an exception to the global regulations systematically observed at this locus. The latter DNA region is also involved in Hoxd gene regulation in other contexts and strongly interacts with Hoxd9 in all tissues analyzed so far as well as in other vertebrate species, indicating that its regulatory activity was already operational before the appearance of mammary glands. Within this DNA region and neighboring the CS39 limb enhancer, we further identified a short sequence conserved in therian mammals and capable of enhancer activity in the mammary buds. We propose that Hoxd gene regulation in embryonic mammary buds evolved by hijacking a preexisting regulatory landscape, which was already at work before the emergence of mammals in structures such like the limbs or the intestinal tract.

overall_design: RNA-seq analysis  of e13.5 mammary buds and adjacent embryonic skin

first: Ruben

last: Schep

first: Anamaria

last: Necsulea

first: Denis

last: Duboule


title: Partially exhausted CD8+ T cells are associated with clinically beneficial response to Teplizumab in new onset type I diabetes (whole blood RNA-seq)

city: Seattle

first: Scott

last: Presnell

state: WA

address: 1201 Ninth Avenue

institute: Benaroya Research Institute

summary: Biologic agents active in other autoimmune settings have had variable effectiveness in newly diagnosed type 1 diabetes (T1D) where treatment across therapeutic targets is accompanied by transient stabilization of C-peptide levels in some patients, followed by progression at the same rate as in control groups. Why disparate treatments lead to similar clinical courses is currently unknown. Here, we use integrated systems biology and flow cytometry approaches to elucidate immunologic mechanisms associated with C-peptide stabilization in T1D subjects treated with the anti-CD3 monoclonal antibody, teplizumab. This work is part of the Immune Tolerance Network AbATE study (Autoimmunity-Blocking Antibody for Tolerance in Recently Diagnosed Type 1 Diabetes); data are also available through the ITN TrialShare portal: https://www.itntrialshare.org/project/Studies/ITN027AIDB/Study%20Data/begin.view?.

overall_design: We performed bulk RNA-seq on 190 whole blood samples from visit months 0 (R: 14, NR: 16: C: 15, total: 45), 6 (R: 16, NR: 17, C: 15, total: 48), 12 (R: 13, NR: 14, C: 16, total: 43), and 24 (R: 17, NR: 20, C: 17, total: 54).

first: S

last: Long

first: Jerill

last: Thorpe

first: Hannah

last: DeBerg

first: Vivian

last: Gersuk

first: James

last: Eddy

first: Kristina

middle: M

last: Harris

first: Mario

middle: R

last: Ehlers

first: Kevan

middle: C

last: Herold

first: Gerard

middle: T

last: Nepom

first: Peter

last: Linsley


title: Partially exhausted CD8+ T cells are associated with clinically beneficial response to Teplizumab in new onset type I diabetes (bulk RNA-seq of sorted CD8+ T-cells)

overall_design: We performed bulk RNA-seq on 63 sorted CD8+ T-cell samples from 3 responders at visit month 6 (N = 34, 15, 14); we sorted cells with and without EOMES-associated inhibitory receptors (TIGIT, KLRG1); prior to RNA extraction, cells were either unstimulated, stimulated with anti-CD3 and anti-CD28, or stimulated with additional PVR-Fc treatment.


title: ARID1A loss impairs enhancer-mediated gene regulation and drives colon cancer in mice [primary cells_ChIP-seq]

city: Boston

middle: J

last: Park

state: MA

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

summary: Genes encoding subunits of SWI/SNF chromatin remodeling complexes are collectively mutated in ~20% of all human cancers. Although ARID1A is the most frequent target of mutations, the mechanism by which its inactivation promotes tumorigenesis is unclear. Here, we demonstrate that Arid1a functions as a tumor suppressor in the mouse colon, but not the small intestine, and that invasive ARID1A-deficient adenocarcinomas resemble human colorectal cancer (CRC). These tumors lack deregulation of APC/beta-catenin, crucial gatekeepers in common forms of intestinal cancer. ARID1A normally targets SWI/SNF complexes to enhancers, where they function in coordination with transcription factors (TFs) to facilitate gene activation. ARID1B preserves SWI/SNF function in ARID1A-deficient cells, but defects in SWI/SNF targeting and control of enhancer activity cause extensive dysregulation of gene expression. These findings represent an advance in colon cancer modeling and implicate enhancer-mediated gene regulation as a principal tumor suppressor function of ARID1A.

overall_design: ChIP-seq for H3K27ac and H3K4me3 in Primary Colon Epithelial cells form WT and ARID1A-KO mice.

first: Radhika

last: Mathur

first: Burak

middle: H

last: Alver

first: Charles

last: Roberts


title: ARID1A loss impairs enhancer-mediated gene regulation and drives colon cancer in mice [HCT116_ChIP-seq]

overall_design: ChIP-seq of three histone modifications (H3K27ac, H3K4m3, H3K4me1) and two SWI/SNF complex subunits (SMARCA4 and SMARCC1) in HCT116 colorectal cancer line for ARID1A WT and KO cells.


title: ARID1A loss impairs enhancer-mediated gene regulation and drives colon cancer in mice [HCT116_RNA-seq]

overall_design: RNA-seq in HCT116 colorectal cancer line for ARID1A WT, and Homozygous and Heterozygous KO cells.


title: ARID1A loss impairs enhancer-mediated gene regulation and drives colon cancer in mice

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: EPOP Functionally Links Elongin and Polycomb in Pluripotent Stem Cells

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

summary: The cellular plasticity of pluripotent stem cells is thought to be sustained by genomic regions that display both active and repressive chromatin properties. These regions exhibit low levels of gene expression, yet the mechanisms controlling these levels remain unknown. Here, we describe Elongin BC as a binding factor at the promoters of bivalent sites. Biochemical and genome-wide analysis shows that Elongin BC is associated with Polycomb Repressive Complex 2 (PRC2) in pluripotent stem cells. Elongin BC is recruited to chromatin by the PRC2-associated factor EPOP (Elongin- and POlycomb-associated Protein, also termed C17orf96, esPRC2p48, E130012A19Rik), a protein expressed in the inner cell mass of the mouse blastocyst. Both EPOP and Elongin BC are required to maintain low levels of expression at PRC2 genomic targets. Our results indicate that keeping the balance between activating and repressive cues is a more general feature of chromatin in pluripotent stem cells than previously appreciated.

overall_design: List of ChIPseq samples (C17orf96, EloB, Suz12, H3K27me3, H3K4me3) and RNAseq samples (control, C17orf96, Suz12, EloB)

first: Malte

last: Beringer

first: Luciano

last: DiCroce


title: An excitatory ARC to PVH circuit that rapidly induces satiety and is regulated by α-MSH

first: John

middle: N

last: Campbell

state: Massachusetts

address: Center for Life Science, room 7-717

department: Medicine

institute: Beth Israel Deaconess Medical Center

summary: Neurons in the arcuate nucleus (ARC) sense the fed/fasted state and regulate hunger.  ARCAgRP neurons release GABA, NPY and the melanocortin-4 receptor (MC4R) antagonist, AgRP, and are activated by fasting1-4.  When stimulated, they rapidly and potently drive hunger5,6.  ARCPOMC neurons, in contrast, release the MC4R agonist, α-MSH, and are viewed as the counterpoint to ARCAgRP neurons.  They are regulated in an opposite fashion and their activity leads to decreased hunger2,4,7.  Together, ARCAgRP and ARCPOMC neurons constitute the ARC feeding center.  Against this, however, is the finding that ARCPOMC neurons, unlike ARCAgRP neurons, fail to affect food intake over the timescale of minutes to hours following opto- or chemogenetic stimulation5,8.  This suggests a rapidly acting component of the ARC satiety pathway is missing.  Here, we show that excitatory ARC neurons identified by expression of vesicular glutamate transporter 2 (VGLUT2) and the oxytocin receptor, unlike ARCPOMC neurons, rapidly cause satiety when chemo- or optogenetically manipulated.  These glutamatergic ARC projections synaptically converge with GABAergic ARCAgRP projections on MC4R-expressing neurons in the paraventricular hypothalamus (PVHMC4R neurons), which are known to mediate satiety9.  ARCPOMC neurons also send dense projections to the PVH.  Importantly, the α-MSH they release post-synaptically potentiates glutamatergic synaptic activity onto PVHMC4R neurons – including that emanating from ARCVglut2 neurons.  This suggests a means by which α-MSH can bring about satiety – via postsynaptic potentiation of this novel ARCVglut2 to PVHMC4R satiety circuit.  Thus, while fast (GABA and NPY) and slow (AgRP) ARC hunger signals are delivered together by ARCAgRP neurons10,11, the temporally analogous satiety signals from the ARC, glutamate and α-MSH, are delivered separately by two parallel, interacting projections (from ARCVGLUT2 and ARCPOMC neurons).  Discovery of this rapidly acting excitatory ARC → PVH satiety circuit, and its regulation by α-MSH, provides new insight into regulation of hunger/satiety.

overall_design: 23 samples representing single neurons dissociated from the arcuate hypothalamus of two young adult male vGLUT2-IRES-Cre mice

first: Henning

last: Fenselau

first: Anne

last: Verstegen

first: Joseph

last: Madara

first: Jie

last: Xu

first: Bhavik

middle: P

last: Shah

first: Jon

last: Resch

first: Zongfang

last: Yang

first: Yael

last: Mandelblat-Cerf

first: Yoav

last: Livneh

first: Bradford

middle: B

last: Lowell


title: ARID1A loss impairs enhancer-mediated gene regulation and drives colon cancer in mice [primary cells_RNA-seq]

first: Peter

last: Park

overall_design: RNA-seq in Primary Colon Epithelial cells form WT and ARID1A-KO mice.

first: Radhika

last: Mathur


title: SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation [cell line_ChIP-seq]

summary: SMARCB1 (SNF5/INI1/BAF47), a core subunit of the SWI/SNF (BAF) chromatin remodeling complex, is inactivated in nearly all pediatric rhabdoid tumors. These aggressive cancers are among the most genomically stable, suggesting an epigenetic mechanism by which SMARCB1 loss drives transformation. Here, we show that despite indistinguishable mutational landscapes, human RTs show distinct enhancer H3K27ac signatures, which reveal remnants of differentiation programs. We show that SMARCB1 is required for the integrity of SWI/SNF complexes and that its loss alters enhancer targeting     markedly impairing SWI/SNF binding to typical enhancers, particularly those required for differentiation, while maintaining SWI/SNF binding at super-enhancers. We show that these retained super-enhancers are essential for rhabdoid tumor survival, including some that are shared across all subtypes, such as SPRY1, and other lineage-specific super-enhancers like SOX2 in brain-derived RTs. Taken together, our findings reveal a novel chromatin-based epigenetic mechanism underlying the tumor suppressive activity of SMARCB1.

overall_design: ChIP-seq of three histone modifications (H3K27ac, H3K4m3, H3K4me1) and two SWI/SNF complex subunits (SMARCA4 and SMARCC1) in three Smarcb1 deficient rhabdoid tumor cell lines, before and after Smarcb1 re-expression.

first: Xiaofeng

last: Wang

first: Ryan

last: Lee

first: Burak

last: Alver

first: Charles

last: Roberts


title: SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation [primary tissue_RNA-seq]

overall_design: RNA-seq for three primary Rhabdoid tumor samples


title: SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation [primary tissue_ChIP-seq]

overall_design: ChIP-seq of three histone modifications: H3K27ac, H3K4m3, H3K4me1 in primary Rhabdoid tumor samples


title: Stress profile elicited by trehalose-6-phosphate accumulation in Mycobacterium tuberculosis

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

institute: University of Duesseldorf

summary: The otsB2 gene encoding trehalose-6-phosphate phosphatase is essential for in vitro growth of Mycobacterium tuberculosis and required to establish an acute infection in mice. Essentiality of otsB2 is due to direct or indirect toxic effects associated with the substrate trehalose-6-phosphate that accumulates when OtsB2 gene expression is impaired. In order to gain insight into the molecular basis of trehalose-6-phosphate mediated toxic effects, whole genome transcriptome profiling was done using RNA-seq. A conditional otsB2 mutant of Mycobacterium tuberculosis was generated by inserting an anhydrotetracycline-inducible promoter cassette upstream of the otsB2 start codon,and the transcriptome profile of a fully induced mutant resembling the wildtype phenotype was compared to that of a partially silenced mutant under conditions where 30% residual growth relative to the fully induced mutant was observed.

overall_design: Three biological replicates of each the fully induced (at 200 ng/ml anhydrotetracycline) and the partially silenced (at 30 ng/ml anhydrotetracycline) conditional Mycobacterium tuberculosis otsB2 mutant were analyzed

first: Rainer

last: Kalscheuer

first: Rene

last: Deenen


title: SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation

overall_design: Refer to individual Series


title: RNA-seq of E11.5 TrkC neurons of Runx3-P2+/- and Runx3-P2-/- mice

status: Public on Nov 20 2016

first: Ester

last: Feldmesser

state: Rehovot

address: POB 25

department: Life Science Core Facilities

institute: Weizmann Institute

summary: To gain insight into the role of Runx3 in TrkC neurons we performed RNA-seq on E11.5 TrkC neurons isolated from cervical ganglia of Runx3-P2+/- and Runx3-P2-/- mice

overall_design: Runx3-P2 mice express GFP in TrkC neurons enabling the FACS  isolation of TrkC neurons from E11.5 embryos, Heterozygote Runx3-P2+/-(n=pool of 4) and homozygote Runx3-P2-/- (n=pool of 4) TrkC/GFP neurons were isolated,

first: Yoram

last: Groner

first: Ditsa

last: Levanon

first: Varda

last: Negreanu


title: RNA sequencing of  Cyfip2N/- and Cyfip2N/N mice

first: Camron

last: Bryant

state: Massachusetts (MA)

address: 72 E. Concord St. R-604

department: Pharmacology and Experimental Therapeutics

institute: Boston University School of Medicine

summary: RNA-seq analysis of 8 Cyfip2N/- and 8 Cyfip2N/N mice. Cyfip2N/- are mice contain one copy of the B6NJ missense mutation and one copy of the nonsense mutation (binge-resistant; N/-), whereas Cyfip2N/N are mice that have two mutated B6NJ allele (binge-prone; N/N), at rs240617401, a marker denoting a missense SNP in Cyfip2.  Genotype identity is denoted as either J for binge-resistant; N/-, or N for binge-prone; N/N.

overall_design: A sample size of N=8 per genotype was employed (4 females, 4 males; 82-84 days old at the time of sacrifice). Striatum punches were harvested on Day 24 immediately following the 5-min behavioral test on the EPM, stored in RNAlater for 48 h, blotted dry with a kimwipe, and transferred to -80ºC. Total RNA was isolated and shipped to the University of Chicago Genomics Core Facility for cDNA library preparation using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit (50 bp single-end reads). Samples were sequenced using the Illumina HiSeq 4000 with 16 samples per lane over four lanes (technical quadruplicates). FASTQ files were quality checked via FASTQC and all samples exhibited Phred quality scores greater than 30 (i.e. less than 0.1% sequencing error). FASTQ files were used to align reads to the reference genome using TopHat (mm10; UCSC Genome Browser). Read counts per gene were quantified using the HTSeq Python package.

first: Stacey

last: Kirkpatrick

first: Jiayi

last: Wu


title: Allelic expression in tibial growth plates from 21 day old C57BL/6J x CAST/EiJ F1s

status: Public on Nov 19 2016

city: Charlottesville

last: Farber

state: VA

department: Center for Public Health Genomics

institute: University of Virginia

summary: We have identified candidate genes from the Feml2 QTL influencing femur length through allele specific expression analysis of growth plates in C57BL/6J x CAST/EiJ F1 hybrids. This work provides the foundation to identify novel genes affecting bone geometry.

overall_design: total RNA sequencing in 7 male C57BL/6JxCAST F1s

first: Juan

last: Medrano

first: Olivia

middle: L

last: Sabik


title: SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation [cell line_RNA-seq]

first: Peter

last: Park

overall_design: RNA-seq in six Smarcb1 deficient rhabdoid tumor cell lines, before and after Smarcb1 re-expression.

last: Wang


title: Reprogramming postnatal human epidermal keratinocytes toward functional neural crest fates

city: AMHERST

first: Stelios

last: Andreadis

state: NY

address: 908 Furnas Hall

department: Chemical & Biological Engineering

institute: University at Buffalo

summary: During development, neural crest cells are induced by signaling events at the neural plate border of all vertebrate embryos.  Initially arising within the central nervous system, NC cells subsequently undergo an epithelial to mesenchymal transition to migrate into the periphery, where they differentiate into diverse cell types. Here we provide evidence that postnatal human epidermal keratinocytes, in response to FGF2 and IGF1 signals, can be reprogrammed toward a neural crest fate.  Genome-wide transcriptome analyses show that keratinocyte-derived NC cells are similar to those derived from human embryonic stem cells.  Moreover, they give rise in vitro and in vivo to neural crest derivatives such as peripheral neurons, melanocytes, Schwann cells and mesenchymal cells (osteocytes, chondrocytes, adipocytes and smooth muscle). By demonstrating that human KRT14+ keratinocytes can form neural crest cells, even from clones of single cells, our results have important implications in stem cell biology and regenerative medicine.

overall_design: mRNA profiles of KC and KC derived NC (from 3 biological replicates) were generated by deep sequencing using Illumina HiSeq 2500 platform (pair-end (2x50 bp) rapid run mode).


title: Gene expression analysis on arsenic-induced malignant transformation

city: Baltimore

first: Akira

last: Oki

state: MD

address: 1550 Orleans street

institute: Johns hopkins university

summary:
Arsenic is environmental risk factor and has been linked to urothelial carcinoma incidence.  Arsenic exposure-induced malignant transformed cells was established from normal urothelial cells by chronic arsenic exposure for 10 months.
The purpose of the present study is to elucidate the relevant molecular alterationon on arsenic-induced malignant transformation.

overall_design: Total RNA was obtained from the passage-matched un-exposed cells, arsenic exposed cells, and BFTC 905 cells that was establsihed from arsenic exposed patient, as a series of process from normal to arsenic-induced cancer.

first: Mohammad

middle: O

last: Hoque

last: Ooki


title: Partially exhausted CD8+ T cells are associated with clinically beneficial response to Teplizumab in new onset type I diabetes

first: Scott

last: Presnell

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


title: RNA-sequencing analysis of a wildtype CHO cell line (CHO-K1), a mutant CHO cell line (pgsA745) that lacks xylosyltransferase (XylT) activity, and pgsA745 stably transfected with XylT1 (pgsA745-XylT1).

first: Nathan

last: Lewis

address: 9500 Gilman Drive

department: Pediatrics

institute: UCSD

summary: We report a a large deletion in the gene encoding for laminin subunit α2 (Lama2) in CHO pgsA745.

overall_design: RNA of three different cell lines was extracted and analyzed.

first: Xander

last: van Wijk

first: Björn

last: Hallström

first: Shangzhong

last: Li

first: Bjørn

middle: G

last: Voldborg

first: Bernhard

last: Palsson

middle: E

first: Jeffrey

middle: D

last: Esko


title: Genome-wide maps of chromatin state in human monocytes and monocyte-derived DCs

city: Shanghai

first: PIN

last: WANG

address: Xiangyin Road 800

institute: SMMU

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in human monocyte devried DCs. By obtaining about 15 million mapped reads for each sample from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of human monocytes and monocyte-derived DCs. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.

overall_design: Examination of 3 different histone modifications, H3K4me3/H3K27ac/H3K27me3, in 2 cell types,human monocytes and monocyte-derived DCs.

first: Pin

first: Xuetao

last: Cao


title: Cardiac Transcriptome Dynamics and MEF2 Function in Response to Chronic β-Adrenergic Blockade During Heart Failure

city: Toronto

first: John

last: McDermott

state: ON

address: 4700 Keele Street

country: Canada

institute: York University

summary: 1) Profiling RNA expression in mice with surgically induced pressure overload (Transverase aortic contriction aka TAC) and/or Atenolol (AT) treated mice. 2)Profiling RNA expression in MEF2A depleted cardiomyocytes.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: 1) Four groups of mice (Sham+Sol (Samples 4C,D,E), TAC+Sol (Samples 2C,D,E), Sham+AT (Samples 3A,B,D), TAC+AT(Samples 1B,E,F)) with three replicates. 2) Primary cardiomyocytes were transfected with scrambled control (scr) or siMEF2A in duplicate.

first: Stephanie

last: Wales

first: Sara

last: Hashemi


title: Robertsonian translocations modify genomic distribution of gH2AX and H3.3 in mouse germ cells

city: Montreal

first: Anna

middle: K

last: Naumova

state: QC

address: 1001 Decarie Blvd

department: Obstetrics and Gynecology

institute: McGill University

summary:
Purpose: determine if gH2AX and H3.3 are enriched at unsynapsed regions of chromosomes involved in translocations in mouse germ line (meiotic prophase I)

Methods: testes were isolated from 4-week or 6-week old heterozygous carriers of a single Robertsonian translocation RB(8;12) or 3 Robertsonian translocations RB(8;12), RB(1;3) and RB(9;14) and controls. ChIP assays were conducted as described in Smagulova 2011. Experiments done in triplicate.

Results: We find enrichment of gH2AX in the proximal gene-rich regions of translocation-associated chromosomes and reduced enrichment of gH2AX and H3.3 at sex chromosomes

overall_design: Testes gH2AX and H3.3 occupancy profiles were generated using  ChIP and next generation sequencing

first: Shawn

last: Fayer

first: Qi

last: Yu

first: Joongbaek

last: Kim

first: Sanny

last: Moussette

first: Rafael

last: Camerini-Otero


title: High throughput sequencing in synchronized yeast meiotic culture with pCUP1-IME1 pCUP1-IME4 strain

status: Public on Nov 18 2016

city: Stony Brook

first: Bruce

last: Futcher

address: STONY BROOK UNIVERSITY

department: Molecular Genetics & Microbiology

institute: Stony Brook University

summary: We used pCUP1-IME1 pCUP1-IME4 strain to generate synchronized yeast meiotic culture and measure the RNA expression through meiotic progression

overall_design: RNA expression in yeast meiosis timecourse

first: Yifeng

last: Xu


title: Synchronized yeast meiotic culture timecourse


title: The de novo DNA methyltransferase DNMT3C protects male fertility from transposon activity (small RNA-seq)

city: paris

first: teissandier

last: aurelie

address: 26 rue d'Ulm

country: France

institute: institut curie

summary: To allow the characterization of the populations of small RNAs in the testes of mutant animal, small-RNA fraction of total testis RNA was isolated and sequenced.

overall_design: Comparison of small RNA-seq populations from whole testis RNA of mutant Dnmt3C IAP/IAP and control Dnmt3C IAP/WT at 16.5 dpc. A parallel experiment done with Miwi2 KO/WT and KO/KO at the same developmental stages was conducted as a control.

first: Joan

last: Barau

first: Deborah

last: Bourc'his


title: Misregulation of an activity-dependent splicing network as a common mechanism underlying autism spectrum disorders

first: Manuel

last: Irimia

state: Barcelona

address: 88 Dr. Aiguader

department: MELIS

institute: Universitat Pompeu Fabra - Centre for Genomic Regulation

summary: A key challenge in understanding and ultimately treating autism is to identify common molecular mechanisms underlying this genetically heterogeneous disorder. Transcriptomic profiling of autistic brains has revealed correlated misregulation of the neuronal splicing regulator nSR100/SRRM4 and its target microexon splicing program in more than one-third of analyzed individuals. To investigate whether nSR100 misregulation is causally linked to autism, we generated mutant mice with reduced levels of this protein and its target splicing program. Remarkably, these mice display multiple hallmark features of autism, including altered social behaviors, synaptic density and signaling. Moreover, increased neuronal activity, which is often associated with autism, results in a rapid decrease in nSR100 and splicing of microexons that significantly overlap those misregulated in autistic brains. Collectively, our results provide evidence that misregulation of an nSR100-dependent splicing network controlled by changes in neuronal activity is causally linked to a substantial fraction of autism cases.

overall_design: Hippocampal neurons were harvested from E16.5 C57bl/6 mice and cultured in vitro for 10 days. Neurons were then treated with 55 mM KCl and RNA was harvested after 0.5 h or 3 h of KCl treatment. Untreated controls were also harvested. Biological dublicates were sequenced for each condition

first: Mathieu

last: Quesnel-Vallières

first: Zahra

last: Dargaei

first: Thomas

last: Gonatopoulos-Pournatzis

first: Joanna

last: Ip

first: Mingkun

last: Wu

first: Timothy

last: Sterne-Weiler

first: Shinichi

last: Nakagawa

first: Melanie

middle: A

last: Woodin

first: Benjamin

last: Blencowe

first: Sabine

last: Cordes


title: ChIP-Seq Samples for p63 in HNSCC Cells to Investigate How ACTL6A and p63 Activate Hippo-YAP in SCC

first: Kenneth

last: Ross

address: 450 Brookline Ave., Rm M640

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

summary: Loss-of-function mutations in SWI/SNF chromatin remodeling subunit genes are observed in many cancers, but an oncogenic role for SWI/SNF is not well established. Here we reveal that ACTL6A, encoding a SWI/SNF subunit linked to stem and progenitor cell function, is frequently co-amplified and highly expressed together with the p53 family member p63 in head and neck squamous cell carcinoma (HNSCC). ACTL6A and p63 physically interact and cooperatively control a transcriptional program that promotes proliferation and suppresses differentiation, in part through activation of the Hippo-YAP pathway via regulators including WWC1.  Consequently, loss of ACTL6A or p63 in tumor cells induces YAP phosphorylation and inactivation, associated with growth arrest and terminal differentiation, all phenocopied by WWC1 overexpression. In vivo, ectopic ACTLC6A/p63 expression promotes tumorigenesis, while ACTL6A expression and YAP activation are highly correlated in primary HNSCC and predict poor patient survival. Thus, ACTL6A and p63 collaborate as oncogenic drivers in HNSCC.

overall_design: ChIP-Seq experiment to examine binding of p63 in head and neck squamous cell carcinoma (HNSCC) cell line JHU-029

first: Srinivas

middle: V

last: Saladi

first: Leif

middle: W

last: Ellisen


title: Epigenome maps of time-resolved monocyte to macrophage differentiation and innate immune memory (ATAC-Seq)

city: Nijmegen

first: Hendrik

last: Stunnenberg

address: Geert Grooteplein 28

department: Molecular Biology

country: Netherlands

institute: Radboud University

summary: Innate immune memory is the phenomenon whereby innate immune cells such as monocytes or macrophages undergo functional reprogramming after exposure to microbial components such as LPS.  We apply an integrated epigenomic approach to characterize the molecular events involved in LPS-induced tolerance in a time dependent manner. ChIP-seq, RNA-seq, WGBS and ATAC-seq data were generated. This analysis identified epigenetic programs in tolerance and trained macrophages, and the potential transcription factors involved.

overall_design: Time-course in vitro culture of human monocytes. Two innate immune memory states can be induced in culture through an initial exposure of primary human monocytes to either LPS or BG for 24 hours, followed by removal of stimulus and differentiation to macrophages for an additional 5 days. Cells were collected at baseline (day 0), 1 hour, 4 hour, 24 hour and 6 days.

first: Boris

last: Novakovic

first: Ehsan

last: Habibi

first: Shuangyin

last: Wang

first: Henk


title: Epigenome maps of time-resolved monocyte to macrophage differentiation and innate immune memory (RNA-Seq)


title: The de novo DNA methyltransferase DNMT3C protects male fertility from transposon activity

first: teissandier

last: aurelie


title: Epigenome maps of time-resolved monocyte to macrophage differentiation and innate immune memory


title: The de novo DNA methyltransferase DNMT3C protects male fertility from transposon activity (Bisulfite-seq).

summary: To evaluate the impacts of the Dnmt3C IAP mutation in the methylome of germ cells, mutant and control whole genome bisulfite sequencing experiments were conducted starting from genomic DNA obtained from FACS-sorted germ cells.

overall_design: Comparison of whole genome methylome maps of germ cells of mutant Dnmt3C IAP/IAP and control Dnmt3C IAP/WT isolated from testis at 10 dpp.

first: Joan

last: Barau

first: Deborah

last: Bourc'his


title: Epigenome maps of time-resolved monocyte to macrophage differentiation and innate immune memory (ChIP-Seq)


title: RNA-Seq expression profiling of hepatocellular carcinoma and adjacent non-tumor liver tissues

city: New Orleans

first: Jinqiang

last: Zhang

address: 1430 Tulane Ave

department: Pathology

institute: Tulane University

summary: Three pairs of hepatocellular carcinoma and adjacent non-tumor tissues were from 3 male patients suffering from stage I or II HCC with hepatitis C virus background. RNA-Seq libraries were prepared from total RNA using polyA enrichment strategy. The libraries were sequenced on Illumina HiSeq2000 instruments.

overall_design: Examination of transcriptome differences between HCC and adjacent non-tumor tissue.

first: Chang

last: Han

first: Tong


title: The de novo DNA methyltransferase DNMT3C protects male fertility from transposon activity (RNA-Seq).

summary: To allow identification of differentially expressed genes and transposons in Dnmt3C IAP/IAP mutants, mutant and control RNA-Seq experiments were conducted starting from whole testis RNA.

overall_design: Comparison of RNA-seq results from whole testis RNA of mutant Dnmt3C IAP/IAP and control Dnmt3C IAP/WT at 16.5 dpc, 10 dpp, and 20 dpp.


title: HBEC-shp53-PCHD7

city: Dallas

first: Kathryn

last: O'Donnell

state: TX

address: 6000 Harry Hines Blvd, NA6.300

institute: UT Southwestern Medical Center

summary: We studied the effects of ectopic expression of Protocadherin 7 (PCDH7) on Human Bronchial Epithelial Cells (HBECs).

overall_design: Immortalised HBECs were established with overexpression of CDK4 and telomerase, and knocking down p53 in these cells was achieved using stable expression of shRNA specific for TP53 gene. PCDH7 or GFP were ectopically expressed in the resulted HBEC-shp53 cells using Lenti-virus. Stable infected cells were selected and harvested for RNA isolation in triplicates. RNA-seq was performed to study the effects of PCDH7 on the expressional profile of the HBEC-shp53 cells.

first: Xiaorong

last: Zhou


title: Allele specific deletion of enhancer clusters within mouse F1 embryonic stem cells

first: Jennifer

last: Mitchell

state: Ontario

address: 25 Harbord Street

department: Cell and Systems Biology

institute: University of Toronto

summary: We provide data from several targeted deletions of transcriptional enhancer clusters within mouse F1 embryonic stem (ES) cells.  We targeted these regions for deletion with CRISPR/Cas9 genome editing tools.  We demonstrate through heterozygous enhancer cluster deletion and  allele specific RNA-seq that enhancer clusters differ in their regulatory activity as the magnitude of the observed change in transcription upon enhancer cluster deletion varies greatly.

overall_design: Strand specific RNA-seq after heterozygous or homozygous enhancer cluster deletion in mouse F1 ES cells (M. musculus129 x M. castaneus)

first: Scott

last: Davidson

first: Sakthi

last: Moorthy


title: EPOP interacts with Elongin BC and USP7 to modulate the chromatin landscape

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

institute: Philipps University of Marburg

overall_design: Refer to individual Series


title: A polymorphic intronic enhancer at 19q12 drives CCNE1 expression in bladder cancer cells

city: Lebanon

first: Michael

last: Cole

state: NH

address: One Medical Center Dr

institute: Geisel School of Medicine at Dartmouth

summary: We performed chromatin immunoprecipitation against a marker of active regulatory elements in bladder cancer cell lines to highlight regulatory regions specific to the bladder cancer genome. We then compared our dataset to other publicly available datasets to identify any novel, bladder-specific regulatory regions that also overlap with bladder-associated inherited polymorphisms. We used this procedure to determine that there is an intronic enhancer within the CCNE1 gene that binds KLF5 and modulates CCNE1 expression.

overall_design: Examination of 1 histone modification (H3K27ac) in 3 different bladder cancer cell lines

first: Jillian

middle: M

last: Pattison


title: Dynamic Transcriptome in Limonium bicolor Leaf Development: Insights into Genes Controlling Salt Gland Differentiation

city: Jinan

first: Baoshan

state: Shandong

address: No.88 East Wenhua Road, Jinan 250014, Shandong, China

department: College of Life Sciences

institute: Shandong Normal University

summary: The salt glands in the epidermis of recretohalophytes play a pivotal role in salt tolerance by secreting excess salts from tissues. Irrespective of the importance of understanding the secretion process, nothing is known about the molecular mechanisms of salt gland development. Limonium bicolor possesses multi-cellular salt glands in the epidermis and provides a model to study salt gland development. We applied next-generation sequencing to profile early leaf development using five distinctly different developmental stages, which were quantified by successive collections of the first true leaf of L. bicolor with precise spatial and temporal resolution. Twenty-two percent of the genes were differentially expressed along the developmental gradient. Cluster analysis revealed specific expression patterns at one stage, and identified enriched functions specific for each developmental stage. Seventy-two genes were identified as highly involved in salt gland differentiation. Salt glands have high homology with trichomes, which was also confirmed by mutants with increased salt gland densities. A model is proposed to illustrate genes participating in salt gland differentiation. This unique dataset lays the foundation for identifying key genes involved in salt gland development and salt secretion, which is a requisite for understanding mechanisms that could make agriculture possible in saline areas worldwide.

overall_design: Five samples were analyzed as stage A, B, C, D and E. Each sample were sequenced in two different lines for biological replicates.

first: Fang

last: Yuan

first: Ming-Ju

last: Lv

first: Bingying

last: Leng

first: Guangyong

last: Zheng

first: Zhongtao

last: Feng

first: Pinghua

last: Li

first: Xinguang

last: Zhu


title: TSLP acts on neutrophils to drive complement-mediated killing of methicillin-resistant Staphylococcus aureus

city: West Lafayette

first: Majid

last: Kazemian

state: Indiana

address: 201 S. University Street Hansen Life Sciences Bldg, HANS, 225

department: Biochemistry and Computer Science

institute: Purdue University

summary: Staphylococcus aureus can cause serious skin, respiratory, and other life-threatening invasive infections in humans, and methicillin-resistant S. aureus (MRSA) strains have been acquiring increasing antibiotic resistance. While MRSA was once mainly considered a hospital-acquired infection, the emergence of new strains, some of which are pandemic, has resulted in community-acquired MRSA infections that often present as serious skin infections in otherwise healthy individuals. Accordingly, defining the mechanisms that govern the activation and regulation of the immune response to MRSA is clinically important and could lead to the discovery of much needed rational targets for therapeutic intervention.  Because the cytokine thymic stromal lymphopoetin (TSLP) is highly expressed by keratinocytes of the skin3, we investigated its role in host-defense against MRSA. Here we demonstrate that TSLP acts on neutrophils to increase their killing of MRSA. In particular, we show that both mouse and human neutrophils express functional TSLP receptors. Strikingly, TSLP enhances mouse neutrophil killing of MRSA in both an in vitro whole blood killing assay and an in vivo skin infection model. Similarly, TSLP acts directly on purified human blood neutrophils to reduce MRSA burden. Unexpectedly, we demonstrate that TSLP mediates these effects both in vivo and in vitro by engaging the complement C5 system. Thus, TSLP increases MRSA killing in a neutrophil- and complement-dependent manner, revealing a key connection between TSLP and the innate complement system, with potentially important therapeutic implications for control of MRSA infection.

overall_design: mRNA expression analysis. 16 samples are from 2 donors, 8 samples per donor, 2 time points (4hr and 16 hr), and 4 conditions (control, TSLP treated, Heat Killed MRSA treated, and TSLP+HKM treated) .

first: Erin

last: West

first: Rosanne

last: Spolski

first: Zu

middle: X

last: Yu

first: Claudia

last: Kemper

first: Warren

last: Leonard


title: Epigenetic Memory Underlies Cell Autonomous Heterogeneous Behavior of Hematopoietic Stem Cells

status: Public on Nov 17 2016

city: Boston

first: Peter

last: Kharchenko

address: 10 Shattuck St.

department: DBMI

institute: Harvard Medical School

summary: Stem cells determine homeostasis and repair of many tissues and are increasingly recognized as functionally heterogeneous. To define the extent of and molecular basis for heterogeneity we overlaid functional, transcriptional and epigenetic attributes of hematopoietic stem cells (HSCs) at a clonal level using endogenous fluorescent tagging.  Endogenous HSC had clone-specific functional attributes in vivo. The intra-clonal behaviors were highly stereotypic, conserved under the stress of transplantation, inflammation and genotoxic injury, and associated with distinctive transcriptional, DNA methylation and chromatin accessibility patterns. Further, HSC function corresponded to epigenetic configuration but not always to transcriptional state. Therefore, hematopoiesis under homeostatic and stress conditions represents the integrated action of highly heterogeneous clones of HSC with epigenetically scripted behaviors. This high degree of epigenetically driven cell autonomy among HSCs implies that refinement of the concepts of stem cell plasticity and of the stem cell niche are warranted.

overall_design: LKS SLAM cells associated with different clonal clusters were separated using flow cytometry, and examined using RNA-seq, WGBS, ATAC-seq.

first: Vionnie

first: David

middle: T

last: Scadden


title: EPOP interacts with Elongin BC and USP7 to modulate the chromatin landscape (USP7 KO)

first: Robert

last: Liefke

summary: Gene regulatory networks are pivotal for many biological processes. In mouse embryonic stem cells (mESCs) the transcriptional network can be divided into three functionally distinct modules: Polycomb, Core and Myc. The Polycomb module represses developmental genes, while the Myc module is associated with proliferative functions and its mis-regulation is linked to cancer development. Here, we show that in mESCs the Polycomb Repressive Complex 2 (PRC2) associated protein EPOP (a.k.a C17orf96, esPRC2p48, E130012A19Rik) co-localizes at chromatin with members of the Myc and Polycomb module. EPOP interacts with the transcription elongation factor Elongin BC and the H2B deubiquitinase USP7 to modulate transcriptional processes in mESCs similar to MYC. EPOP is commonly up-regulated in human cancer and we demonstrate that its loss impairs the proliferation of several human cancer cell lines. Our findings establish EPOP as a unique modulator of transcriptional processes, impacting both Polycomb and active gene transcription in mammalian cells.

overall_design: Genome-wide investigation of the role of EPOP, Elongin BC and USP7 in mESCs

first: Violetta

last: Karwacki-Neisius

first: Yang

last: Shi


title: Global accessibility of mitotic chromosomes

city: Berkeley

first: Sheila

middle: S

last: Teves

state: California

address: 475D Li Ka Shing Center

department: Molecular Cell Biology

institute: UC Berkeley

summary: To test if mitotic chromosomes have decreased accessibility, we utilized Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) analysis where the integration of sequencing-compatible adaptors by the Tn5 transposase is directly correlated with the accessibility of genomic regions

overall_design: We performed ATAC-seq in 50,000 asynchronous cells as well as 50,000 Nocodazole-synchronized mitotic cells in two biological replicates each.

last: Tjian


title: Cells to Investigate How ACTL6A and p63 Activate Hippo-YAP in SCC

first: Kenneth

last: Ross

state: MA

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


title: RNA-seq of SOX5 overexpressing primary human neuronal progenitors

city: Irvine

first: Vivek

last: Swarup

state: CALIFORNIA

address: 3400 Bio Sci 3

department: Neurobiology and Behavior

institute: University of California Irvine

summary: Purpose: The goal of this study was to assess gene expression changes in neurons overexpressing SOX5 using human primary neuronal culture system. Methods: 6 samples each from control GFP and SOX5 overexpressing neurons were used to isolate total RNA using miRNeasy kit, Qiagen.  We performed rRNA-depleted 69bp paired end stranded RNA-seq on neurons overexpressing either GFP or SOX5 tagged with GFP. Overexpression of SOX5 in neurons validated that a significant proportion of Attenuated cortical patterning (ACP) genes are regulated by SOX5, and that predicted SOX5 targets exhibit a net downregulation, consist with its repressive function. This supports the prediction that attenuated patterning of SOX5 between cortical regions contributes to direct alterations in SOX5 targets and likely to indirect alterations in SOX5 non-targets in the ACP set. delpleted 69 bp stranded RNA-seq in

overall_design: SOX5 was overexpressed in primary human neuronal cultures using a lentiviral system. Briefly full-length human SOX5 gene was cloned in pLVU/GFP vector (gift from Lars Ittner [Addgene plasmid #24177]) using the gateway recombination technique. Lentivirus was produced in HEK293T cells using a second generation packaging vector system (psPAX2, a gift from Didier Trono [Addgene plasmid #12260] and pCMV-VSV-G, a gift from Bob Weinberg [Addgene plasmid #8454]) as described by Stewart et al., 200331. Primary human neurons were infected at plating at a multiplicity of infection (MOI) of 10 with either the SOX5 overexpressing construct or a control pLVU-GFP backbone vector. 14 days after infection, RNA from the samples were isolated using miRNeasy micro kit (Qiagen, Carlsbad) and 50bp paired-end libraries were prepared using SMARter Stranded Total RNA sample prep kit (Clontech) with rRNA depletion. Libraries were then multiplexed and sequenced with HiSeq 2500 instrument (Illumina).

first: V

first: D

middle: H

last: Geschwind


title: Impact of regulatory variation across human iPSCs and differentiated cells

city: Chicago

first: Nicholas

last: Banovich

state: IL

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

middle: I

last: Li

first: Anil

last: Raj

first: Michelle

middle: C

last: Ward

first: Po

middle: Y

last: Tung

first: Jonathan

last: Burnett

first: Marsha

last: Myrthil

first: Samantha

last: Thomas

first: Diego

last: Calderon

first: Peyton

last: Greenside

first: Anshul

last: Kundaje

last: Pritchard

first: Yoav

last: Gilad


title: Distinct roles of transcription factors KLF4, Krox20 and PPARg in adipogenesis

city: Bethesda

first: Kai

last: Ge

address: 50 South Dr Rm 4154

department: NIDDK

institute: NIH

summary: Much of our knowledge on adipogenesis comes from cell culture models of preadipocyte differentiation. Adipogenesis is induced by treating confluent preadipocytes with the adipogenic cocktail, which activates transcription factors (TFs) glucocorticoid receptor (GR) and CREB within minutes and increases expression of TFs C/EBPb/d, KLF4 and Krox20 within hours. All of these TFs have been shown to be capable of promoting adipogenesis in culture when they are overexpressed. However, it has remained unclear whether endogenous KLF4 and Krox20 are required for adipogenesis in culture and in vivo. Using conditional knockout mice and derived white and brown preadipocytes, we show that endogenous KLF4 and Krox20 are dispensable for adipogenesis in culture and brown adipose tissue development in mice. In contrast, the master adipogenic TF PPARg is essential. These results challenge the existing model on transcriptional regulation in the early phase of adipogenesis and highlight the need of studying adipogenesis in vivo.

overall_design: Expression profiling by RNA-seq during adipogenesis (D0, 1h, 2h, 4h, D2, D7) in 3T3-L1 and brown preadipocytes in culture. Expression profiling by RNA-seq in brown adipose tissues of adult mice or embryos.

first: Young-Kwon

last: Park

first: Limin

last: Wang

first: Anne

middle: B

last: Giampietro

first: Binbin

last: Lai

first: Ji-Eun

last: Lee


title: Arnica montana stimulates extracellular matrix gene expression in human macrophages differentiated to wound-healing phenotype.

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

country: Italy

institute: University of Verona

summary: Arnica m. effects were associated with a purported anti-inflammatory and tissue healing actions after trauma, bruises, or tissue injuries, but its cellular and molecular mechanisms are largely unknown. Here Arnica m. dilutions were tested using an in vitro model of macrophages polarized towards a “wound-healing” phenotype. The monocyte-macrophage human THP-1 cell line was cultured and differentiated with phorbol-myristate acetate and Interleukin-4, then exposed for 24 h to Arnica m. centesimal (c) dilutions 2c, 3c, 5c,9c, 15c or Control. None of these treatments affected cell viability. A total of 20 genes were differentially expressed comparing cells treated with Arnica m. 2c with those treated with Control only. Of these, 7 genes were up-regulated and 13 were down-regulated. Functional gene enrichment analysis showed that the most significantly upregulated function concerned 4 genes with a conserved site of EGF-like region (p<0.001) and three genes of proteinaceous extracellular matrix, including heparin sulphate proteoglycan 2 (HSPG2), fibrillin 2 (FBN2), and fibronectin (FN1) (p <0.01). Protein assay in supernatants confirmed a statistically significant increase of fibronectin production in Arnica m. 2c treated cells (p<0.05). Pooled extracts of cells treated with increasing dilutions of Arnica m. (3c, 5c, 15c) showed up-regulation of the same group of genes although with lower effect size. The down-regulated transcripts derive from mitochondrial genes coding for some components of electron transport chain. These findings provide new insights into the action of Arnica m. in tissue healing and repair, identifying increased fibronectin production by macrophages as a major therapeutic target.

overall_design: Expression analysis of differentiated THP-1 cell line exposed at Arnica m. centesimal (c) dilution 2c, plus control non-exposed line both in 5 replicates.

first: Marta

last: Marzotto

first: Clara

last: Bonafini

first: Debora

last: Olioso

first: Laura

last: Bettinetti

first: Francesca

last: Di Leva

first: Elisabetta

last: Galbiati

first: Paolo

last: Bellavite


title: EPOP interacts with Elongin BC and USP7 to modulate the chromatin landscape (Elongin B KO)

first: Robert

last: Liefke

first: Violetta

last: Karwacki-Neisius

first: Yang

last: Shi


title: RNA-seq study reveals unique transcriptome expression in systemic lupus erythematosus patients with distinct autoantibody profile

city: Varanasi

first: Geeta

last: Rai

state: Uttar Pradesh

address: Institute of Science

department: Molecular and Human Genetics

country: India

institute: Banaras Hindu University

summary: Systemic lupus erythematosus patients exhibit remarkable heterogeneity in clinical manifestations and autoantibody repertoires. This complexity poses major barrier in diagnosis and effective treatment of SLE. To address this we studied the SLE patients in groups categorized on the basis of distinct sera autoantibodies. SLE patients were segregated into three group based on the presence of autoantibodies against i) dsDNA only ii) ENA (extractable nuclear antigens) only or iii) both.

overall_design: The mRNA profiles of each SLE patient sample and controls were generated by deep sequencing, using Illumina HiSeq 2000 platform.

first: Richa

first: Sudhir

last: Chauhan

first: Vikas

last: Singh

first: Madhukar


title: Arnica montana stimulates extracellular matrix gene expression in human macrophages differentiated to wound-healing phenotype. Tested on 5 concentrations.

overall_design: Expression analysis of differentiated THP-1 cell line exposed at Arnica m. centesimal (c) dilutions 2c, 3c, 5c,9c, 15c plus control non-exposed line


title: EPOP interacts with Elongin BC and USP7 to modulate the chromatin landscape (EPOP KO)

overall_design: Genome-wide investigation of the role of EPOP in mESCs and SH-SY5Y cells


title: Transcriptome profiling (RNA-seq) of CREBBP+/+ and CREBBP+/- clones of U2932 DLBCL cell line

status: Public on Nov 16 2016

city: Zürich

first: Hind

last: Hashwah

address: Winterthurerstrasse 190

department: Institute of Molecular Cancer Research

institute: University of Zürich

summary:
Purpose: Diffuse large B cell lymphomas (DLBCL) frequently harbor mutations in the histone acetyltransferase CREBBP, however their functional contribution to lymphomagenesis remains largely unknown. This study aims at elucidating and characterizing the molecular pathways affected by mutations in CREBBP.
Methods: U2932, a DLBCL cell line that has wild type expression of CREBBP was manipulated by CRISPR-Cas9 strategy to mutate one allele of CREBBP and examine the pathways affected. RNA was isolated using the NucleoSping RNA Kit (Macherey-Nagel) from five wild type (CREBBP+/+) and five heterozygous clones (CREBBP+/-). RNA quality was assessed by Bioanalyzer 2100 followed by library preparation using the TruSeq RNA Sample Prep Kit v4 (Illumina). Sequencing was subsequently performed on the Illumina HiSeq 2500 instrument. RNA-seq reads were quality-checked with fastqc, which computes various quality metrics for the raw reads. RNA-seq reads were mapped to the GRCh38 reference human genome using STAR and reads were counted according to Ensembl gene annotation using the featureCounts function in the Rsubread Bioconductor package. Statistical analysis of differential expression was conducted with the DESeq2 package.

overall_design: Trascriptomic profiles of CREBBP+/+ and CREBBP+/- clones were generated by deep sequencing.

first: Hubert

last: Rehrauer


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type, ebr1 and EIP1-OX  Transcriptomes

city: Shanghai

first: He

last: zuhua

state: Shanghai

address: 300 Fenglin Road

department: SIBS

institute: Institute of Plant Physiology and Ecology

summary: Crop breeding for board-spectrum disease resistance is the most profitable strategy to control diseases. However, knowledge on genes and mechanism of board-spectrum resistance is very limited. We fund a rice mutant ebr1 (enhanced blight and blast resistance 1) showed broad-spectrum resistance to both bacterial Xanthomonas oryzae pv. oryzae and fungal Magnaporthe oryzae associated with spontaneous programmed cell death (PCD), autoimmunity activation and stunting. EBR1 is located at the chromosome centromere and encodes a previously unknown RING-type protein with E3 ubiquitin ligase activity. Extensive yeast two-hybrid screening identified one EIP (EBR1-interacting) protein, EIP1, which belongs to the BAG (Bcl-2 associated athanogene) family that have been associated with stress responses and modulation of cell death.cross kingdoms. We showed that EIP1 is a specially target of EBR1 and is a key player activating PCD and immunity including the salicylic acid and jasmonate defense pathways in rice. Its function is suppressed EBR1-mediated degradation through ubiquitination. EIP1-RNAi could restore the PCD and disease resistance phenotypes of ebr1, while EIP1 overexpression caused strong PCD and enhanced resistance to rice pathogens likely ebr1. Together, our study reveals a unique E3 ligase-BAD protein module that orchestrates autoimmunity and trade-off between defense and growth in rice.

overall_design: The RNA profiles of two-months of WT line ZH11 and the ebr1 mutant plants  and  EIP1_OX line 7-2 were generated by deep sequence dependent on illumina Hiseq4000.

first: Quanyuan

last: You

first: Qun

last: Li

first: Zuhua

last: He


title: RNA-seq of Arabidopsis thaliana Col-0 siliques

city: Zurich

first: Antonin

last: Marchais

address: Universitatstrasse 2

department: Department of Biology

institute: ETHZ

summary: Paired-end Illumina RNA sequencing of Arabidopsis thaliana Col-0 siliques.

overall_design: mRNA profiles of Arabidopsis Col-0 WT siliques were generated by paired-end deep sequencing, in replicate using Illumina HiSeq 2000.

first: Pauline

last: Jullien

first: Nathan

last: Pumplin

first: Clement

last: Chevalier

first: Gregory

last: Schott

first: Caroline

last: Otto

first: Olivier

last: Voinnet


title: Next Generation Sequencing Facilitates Quantitative Analysis of  nf-ycQ in Arabidopsis thaliana seedlings Transcriptomes

city: Guangzhou

first: Yang

last: Tang

state: Guangdong Province

address: No.723 Xingke Road, Tianhe District

department: South China Botanical Garden

institute: Chinese Academy of Sciences

summary: We generated 18 Gb of high-quality sequencing data (~3 Gb per sample) and catalogued the expression profiles of 27,416 annotated Arabidopsis thaliana genes in each sample. The analysis showed differences of transcriptomes between wild-type Col and Nuclear Factor Y (NF-Y) C1,3,4,9 loss of function mutant nf-yc quadruple (nf-ycQ) seedlings treated with 2 days red light. We identified numerous differentially expressed genes that exhibited distinct expression patterns. These genes have known or potential roles in growth and development of Arabidopsis thaliana. Therefore, they are appealing candidates for further investigation of the gene expression and associated regulatory mechanisms related to NF-YCs in light signaling pathway.

overall_design: RNA-seq analysis profiles of wild-type Col and T-DNA knockout mutant of nf-ycQ seedlings treated with 2 days red light were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.

first: Xingliang

last: Hou


title: RNA-seq data of Paracoccus denitrificans grown under different N2O levels

city: Norwich

first: Hannah

last: Gaimster

address: Norwich Research Park

institute: UEA

summary: We report here the RNA seq results of sRNA enriched Paracoccus denitrificans grown under three different N2O levels (high N2O reffered to as CuL/ low N2O reffered to as CuH/ Low N2O aerobic reffered to as CuH O2)

overall_design: Three different copper regimes for 16 hours.  Total RNA was isolated and processed by vertis Biotechnologie AG to isolate the sRNA fraction. This was then converted to cDNA and sequenced.


title: Differential gene expression in the body wall of the sea cucumber (Apostichopus japonicus) under strong lighting and dark conditions

city: Qingdao

first: Lina

last: Sun

address: Nanhai Road 7

institute: Institute of Oceanology, Chinese Academy of Sciences

summary: RNA-seq provided a general overview of the gene expression profiles of the body walls of A. japonicus exposed to strong light (“light”), normal light (“control”) and fully dark (“dark”) environment.

overall_design: The animals were then divided randomly into three groups. One group of sea cucumbers was maintained as the control group with natural light (“control”) with the light intensity around 100 lux; the other two groups were exposed to strong (“hard”) light exposure (“light”) with the light intensity around 2,000 lux, and in a fully dark tank covered by a shade cloth (“dark”) for 2 hours.

first: Libin

last: Zhang


title: Resetting cancer stem cell regulatory nodes upon MYC inhibition

city: Milano

first: Federico

last: Zambelli

address: Via Giovanni Celoria 26

department: Department of Biosciences

institute: University of Milan

overall_design: Refer to individual Series


title: Different Enhancer Classes in Drosophila Bind Different Architectural Proteins and Mediate Unique Chromatin Interactions and 3D Architecture [ChIP-seq]

city: Atlanta

first: Victor

last: Corces

state: GA

address: 1510 Clifton Rd

department: Biology

institute: Emory University

summary: In this study, we further characterized the hkCP and dCP enhancers, which were identified by STARR-seq, and shown to have an intrinsic capacity to interact with a specific type of core promoter depending on the presence of a DRE motif [9]. hkCP enhancers are marked by H3K4me3, associated with TAD borders, and mediate large TSS-clustered interactions to promote robust transcription. Furthermore, they contain the architectural proteins CAP-H2, Chromator, DREF and Z4. In contrast, dCP enhancers are marked by H3K4me1, associated with chromatin loop anchors and are more commonly associated with single TSS-contacts. dCP enhancers are depleted of the hkCP-specific architectural proteins and show an enrichment for Fs(1)h-L and Rad21 instead. Thus, our data supports the model that the unique occupancy of architectural proteins in the distinct enhancer classes are key contributors to the types of interactions that enhancers can mediate genome-wide, ultimately affecting enhancer-promoter specificity.

overall_design: Analysis of the protein occupancy and chromatin interactions of the two distinct enhancer classes in Drosophila

first: Caelin

last: Cubenas-Potts

first: Michael

middle: J

last: Rowley

first: Xiaowen

last: Lyu

first: Ge

first: Elissa

last: Lei


title: Genome-wide chromatin binding of MYC, Omomyc, RNA polymerase II (Pol II), and Pol II Ser-2p in human glioblastoma cells and glioblastoma stem cells expressing or not Omomyc

summary: MYC deregulation is common in human cancer and has a role in sustaining the aggressive cancer stem cell populations. MYC mediates a broad transcriptional response controlling normal biological programs but its activity is not clearly understood. We address MYC function in cancer stem  cells through the inducible expression of Omomyc – a MYC derived polypeptide interfering with MYC activity – taking as model the most lethal brain tumor, glioblastoma. Omomyc bridles the key cancer stem-like cell features and affects tumor microenvironment, inhibiting angiogenesis. This occurs because Omomyc interferes with proper Myc localization and binds to DNA, with a preference for sites previously occupied by MYC. This is accompanied by (leads to) selective repression of master transcription factors for glioblastoma stem-like cell identity like POU3F2, SOX2, and OLIG2, upregulation of effectors of tumor suppression and differentiation such as PTEN, ID4, MIAT, and modulation of the expression of microRNAs that target molecules implicated in glioblastoma growth and invasion like EGFR and ZEB1. Data support a novel view of MYC as a network stabilizer that strengthens the regulatory nodes of the gene expression programs controlling cell phenotype and highlight Omomyc as model molecule for targeting cancer stem cells.

overall_design: We employed patient-derived glioblastoma stem cells BT168 and the human glioblastoma cell line U-87 MG, each harboring a Doxycycline-inducible FLAG-Omomyc construct (FO), to study through ChIP-seq the chromatin binding sites of MYC, Omomyc, RNA Pol II, and RNA Pol II phospho Ser-2, in the presence or absence of Omomyc. ChIP enriched and input genomic DNAs were sequenced by Illumina HiSeq 2000 platform. The study includes 21 samples.

first: Mauro

last: Savino

first: Sergio

last: Nasi

first: Giulio

last: Pavesi


title: Different Enhancer Classes in Drosophila Bind Different Architectural Proteins and Mediate Unique Chromatin Interactions and 3D Architecture

middle: G


title: Genome-wide mRNA expression in human glioblastoma cells and glioblastoma stem cells expressing or not Omomyc

summary: MYC deregulation is common in human cancer and has a role in sustaining the aggressive cancer stem cell populations. MYC mediates a broad transcriptional response controlling normal biological programs but its activity is not clearly understood. We address MYC function in cancer stem  cells through the inducible expression of Omomyc – a MYC derived polypeptide interfering with MYC activity – taking as model the most lethal brain tumour, glioblastoma. Omomyc bridles the key cancer stem-like cell features and affects tumour microenvironment, inhibiting angiogenesis. This occurs because Omomyc interferes with proper Myc localisation and binds to DNA, with a preference for sites previously occupied by MYC. This is accompanied by (leads to) selective repression of master transcription factors for glioblastoma stem-like cell identity like POU3F2, SOX2, and OLIG2, upregulation of effectors of tumour suppression and differentiation such as PTEN, ID4, MIAT, and modulation of the expression of microRNAs that target molecules implicated in glioblastoma growth and invasion like EGFR and ZEB1. Data support a novel view of MYC as a network stabiliser that strengthens the regulatory nodes of the gene expression programs controlling cell phenotype and highlight Omomyc as model molecule for targeting cancer stem cells.

overall_design: We employed patient-derived glioblastoma stem cells BT168 harboring a Doxycycline-inducible FLAG-Omomyc construct (FO), to study mRNA expression in the presence or absence of Omomyc. RNAs prepared from cells treated or not with DOX for up to 48 hours were sequenced by Illumina HiSeq 2000 and 2500 platforms. The study includes 29 samples.


title: Transcriptional Profiling of Cultured, Embryonic Epicardial Cells Identifies Novel Genes and Signaling Pathways Regulated by TGFβR3 in vitro

city: Nashville

first: Daniel

last: DeLaughter

state: TN

address: Preston Research Building Room 460

department: Cell and Developmental Biology

institute: Vanderbilt University Medical School

summary: The epicardium plays an important role in coronary vessel formation and Tgfbr3-/- mice exhibit failed coronary vessel development associated with decreased epicardial cell invasion. Immortalized Tgfbr3-/- epicardial cells display the same defects. Tgfbr3+/+ and Tgfbr3-/- cells incubated for 72 hours with VEH or ligands known to promote invasion via TGFβR3 (TGFβ1, TGFβ2, BMP2), for 72 hours were harvested for RNA-seq analysis. We selected for genes >2-fold differentially expressed between Tgfbr3+/+ and Tgfbr3-/- cells when incubated with VEH (604), TGFβ1 (515), TGFβ2 (553), or BMP2 (632). Gene Ontology (GO) analysis of these genes identified dysregulated biological processes consistent with the defects observed in Tgfbr3-/- cells, including those associated with the extracellular matrix interaction. GO and Gene Regulatory Network (GRN) analysis identified distinct expression profiles between TGFβ1-TGFβ2 and VEH-BMP2 incubated cells, consistent with the differential response of epicardial cells to these ligands in vitro. Despite the differences observed between Tgfbr3+/+ and Tgfbr3-/- cells after TGFβ and BMP ligand addition, GRNs constructed from these gene lists identified NF-ĸB as a key nodal point for all ligands examined. Tgfbr3-/- cells exhibited decreased expression of genes known to be activated by NF-ĸB signaling. NF-ĸB activity was stimulated in Tgfbr3+/+ epicardial cells after TGFβ2 or BMP2 incubation, while Tgfbr3-/- cells failed to activate NF-ĸB in response to these ligands. Tgfbr3+/+ epicardial cells incubated with an inhibitor of NF-ĸB signaling no longer invaded into a collagen gel in response to  TGFβ2 or BMP2.  These data suggest that NF-ĸB signaling is dysregulated in Tgfbr3-/- epicardial cells and that NF-ĸB signaling is required for epicardial cell invasion in vitro. Our approach successfully identified a signaling pathway important in epicardial cell behavior downstream of TGFβR3. Overall, the genes and signaling pathways identified through our analysis yield the first comprehensive list of candidate genes whose expression is dependent on TGFβR3 signaling.

overall_design: 2 immortalized epicardial cell lines (Tgfbr3+/+ and Tgfbr3-/-) were incubated with 4 different treatments (Vehicle, TGFB1, TGFB2, BMP2) for 3 days and subject to RNA-seq analysis in duplicate.

first: Cynthea

middle: R

last: Clark

first: Danos

last: Christodoulou

first: Christine

middle: E

last: Seidman

first: H

last: Baldwin

first: J

first: Joey

last: Barnett


title: Distinct Enhancer Classes in Drosophila Bind Different Architectural Proteins and Mediate Unique Chromatin Interactions and 3D Architecture [Hi-C]

last: Li


title: Exosomal short RNA sequencing experiments

city: Woodbury

first: Ashwin

last: Prakash

state: NY

address: 500 Sunnyside Blvd

institute: Cold Spring Harbor Labs

summary: The characterization of extracellular vesicular RNA (EV RNA) derived from nine cell types demonstrated the diversity of cell type specific RNA biotypes. A large proportion of these cell type specific RNAs are denoted by their processing into shorter versions of their full length structures as they function with the cells of origin.   specific portions of annotated pre-miRNA, tRNA, YRNA and other RNAs within EVs.  Our results also establish the cell state specific dynamicity in EV RNA distributions, qualifying one of the important aspects of communication. In addition, the study highlights both the temporal dynamics and spatial localization of intact EV RNA after transfer into a recipient cell, and their ability to elicit a wide range of transcriptional changes within them. We also demonstrated the cell type specificity in response from two different cell types, when exposed to the same EV RNA stimuli, underscoring the context dependent interpretation of the complex EV RNA message. In doing so, we shed light on a novel and under-appreciated medium of non-cell autonomous regulation of gene expression, through which cells in a complex multicellular organism may shape the transcriptional landscape of other cells and achieve synchronized functioning of involved cells in response to a certain micro-environment at the system level.

first: Sudipto

last: Chakrabortty

first: Thomas

last: Gingeras


title: Aryl Hydrocarbon Receptor deficiency influences B cell response

city: London

first: Brigitta

last: Stockinger

address: Ridgeway

institute: The Francis Crick Institute

summary: The aryl hydrocarbon receptor (AhR), a transcription factor known for mediating xenobiotic toxicity, is expressed in B cells, which are known targets for environmental pollutants. However, it is unclear what the physiological functions of AhR in B cells are. We show here that expression of Ahr in B cells is up-regulated upon B cell receptor (BCR) engagement and IL-4 treatment. Addition of a natural ligand of AhR, FICZ, induces AhR translocation to the nucleus and transcription of the AhR target gene Cyp1a1, showing that the AhR pathway is functional in B cells. AhR-deficient (Ahr-/-) B cells proliferate less than AhR-sufficient (Ahr+/+) cells following in vitro BCR stimulation and in vivo adoptive transfer models confirmed that Ahr-/- B cells are outcompeted by Ahr+/+ cells. Transcriptome comparison of AhR-deficient and sufficient B cells identified cyclin O (Ccno), a direct target of AhR, as a top candidate affected by AhR deficiency.

overall_design: Total RNA obtained from in vitro activated AhR sufficient and AhR deficient B cells

first: Matteo

last: Villa


title: A genetic interaction between RAP1 and telomerase reveals an unanticipated role for RAP1 in telomere protection

city: Madrid

first: Gonzalo

last: Gomez-Lopez

state: Madrid

address: Calle Melchor Fdez Almagro 3

department: Structural Biology

institute: CNIO

summary: RAP1 is one of the components of mammalian shelterin, the capping complex at chromosome ends or telomeres, although its role in telomere protection has remained elusive. RAP1 binds along chromosome arms, where it regulates gene expression and has been shown to function in metabolism control. Telomerase is the enzyme that elongates telomeres and its deficiency causes a premature aging in mice. We describe an unanticipated genetic interaction between RAP1 and telomerase. While RAP1 deficiency alone does not impact in mouse survival, mice lacking both RAP1 and telomerase show a progressive decreased survival with increasing mouse generation as compared to telomerase single mutants. Telomere shortening was more pronounced in Rap1-/- Terc-/- than in Terc-/- counterparts, leading to an earlier onset of DNA damage and its consequent DNA damage response as well as accelerated degenerative pathologies in the intestines. In its turn, telomerase deficiency abolishes RAP1-mediated obesity and liver pathologies. Mouse embryonic fibroblasts with shorten telomeres present less amount of telomere-bound RAP1 but in contrast show higher numbers of RAP1 bound extratelomeric sites genomewide. Absence of RAP1 leads to deregulation of several metabolic pathways, and these changes were more pronounce in cells with short telomeres suggesting that RAP1 release from telomere foci could constitute a coordinated genomic response to telomere shortening. Our findings also demonstrate that although RAP1 is not a key factor in telomere capping under normal conditios, under stress situation such as critical telomere shortening RAP1 exerts an important function for telomere protection and justify its evolutionary conservation as a shelterin component in mammalian cells.

overall_design: RNA-Seq and ChIP-Seq

first: Paula

last: Martínez

last: Gómez-López

first: David

last: Pisano

first: Juana

last: Flores

first: Maria

last: Blasco


title: RNA sequencing of mouse bone marrow cells from transgenic mice following short term induction of mutant U2AF1(S34F) or U2AF1(WT) expression concurrent with sudemycin D6 (or vehicle) treatment in vivo

status: Public on Nov 15 2016

first: Matt

last: Walter

address: 4940 parkview

department: oncology

institute: washington university in st.louis school of medicine

summary: Mutations in spliceosome genes occur in the bone marrow of approximately 50% of patients with myelodysplastic syndromes (MDS), with mutations in the splicing factor gene U2AF1 found in ~11% of MDS patients. We hypothesized that cells harboring a spliceosome gene mutation would have increased sensitivity to further perturbation of the spliceosome by splicing modulator drugs. To examine the effects of the splicing modulator drug sudemycin D6 on primary hematopoietic cells expressing mutant U2AF1(S34F), we treated transgenic mice expressing either mutant U2AF1(S34F) or U2AF1(wildtype, WT) concurrently with 5 days of sudemycin D6 treatment in vivo. We harvested bulk bone marrow cells 18 hours after the last day of treatment and performed strand-specific transcriptome sequencing to examine the cumulative pre-mRNA splicing changes associated with both mutant U2AF1 expression and sudemycin D6 treatment.

overall_design: RNA was extracted from U2AF1(S34F)- or U2AF1(WT)-expressing transgenic mouse bone marrow cells treated in vivo with sudemycin D6 for transcriptome analysis (transgene induction was for 7 days, with concurrent drug infusion for 5 days).  Ribosomal RNA was depleted prior to strand-specific RNA sequencing (TruSeq stranded library production, followed by 2 x 126 bp paired-end sequencing performed on the HiSeq2500 platform from Illumina).  Five samples were sequenced per genotype and treatment (n=5).  Reads were aligned to the mouse mm9 reference genome using TopHat (version 2.0.8), and we performed all subsequent analyses in R.

first: Cara

middle: L

last: Shirai

first: Brian

last: White

first: Matthew