title: Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling [ChIP-seq]

summary: We used an approach combining PacBio data and published Illumina reads to de novo assemble D. busckii contigs. We generated Hi-C data from D. busckii embryos to order these contigs into chromosome-length scaffolds. For D. virilis we generated Hi-C data to order and orient the published Dvir_caf1 scaffolds into chromosome-length assemblies. Furthermore, we compared Hi-C matrices from these two new assemblies with D. melanogaster with respect to synteny blocks and dosage compensation as a chromosome-wide gene-regulatory mechanism.

sample_organism:
Drosophila virilis
Drosophila busckii

platform_organism:
Drosophila virilis
Drosophila busckii

overall_design: We are submitting sex-seperated H4K16ac ChIP-seq datasets from D. busckii and D. virilis that were processed on our D. busckii and D. virilis genome assemblies that we are also providing here. For the H4K16ac ChIP-seq samples (2 replicates each) we provide histone 3 (H3) ChIP-seq samples (1 replicate for D. busckii, 2 replicates for D. virilis) as well as input samples (1 replicate for D. busckii, 2 replicates for D. virilis) as controls.  We provide bigWig files of mapped reads of individual replicates as well as bigWig files of log2fold ratio input-normalized merged replicates. Processing of these samples was done on our D. busckii and D. virilis assemblies which we provide as fastq files. Raw data for generating both assemblies is deposited in SRA (SRR7029387-SRR7029398).

first: Gina

last: Renschler

first: Gautier

last: Richard

last: Valsecchi

first: Sarah

last: Toscano

first: Laura

last: Arrigoni

first: Fidel

last: Ramirez


title: Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling [HiC]

status: Public on Oct 14 2019

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

type:
Other
Third-party reanalysis

sample_organism:
Drosophila melanogaster
Drosophila virilis
Drosophila busckii

overall_design:
This series includes data for Hi-C for D. melanogaster, D. busckii, and D. virilis and genome assembly for D. busckii and D. virilis. Genome assembly data are available at the foot of this record.

Previously published whole genome sequencing data were used in the assembly of the D. busckii contigs.  Re-analyzed data includes PRJNA274996 (SRR1795010, SRR1794619, SRR1794616, SRR1794617, SRR1794614) and PRJNA196337 (SRR826809).

first: Claudia

middle: I


title: Developmental competence and antigen switch frequency can be uncoupled in Trypanosoma brucei II

status: Public on Oct 10 2019

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

country: United Kingdom

institute: Centre for Immunity, Infection and Evolution

type: Expression profiling by high throughput sequencing

summary: Antigen switch frequency and developmental capacity are independently selected traits

overall_design: RNA samples were taken in triplicate at two points - at the beginning and end of in vitro selection for loss of pleomorphism using a  GFPESproAnTat1.1ES NEK RNAi cell line

first: Kirsty

last: McWilliam

first: Monica

last: Mugnier

first: Liam

last: Morrison

first: Keith

middle: R

last: Matthews


title: Maltotriose consumption by hybrid Saccharomyces pastorianus is heterotic and results from regulatory cross-talk between parental sub-genomes

status: Public on Oct 08 2019

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

summary: S. pastorianus strains are hybrids of S. cerevisiae and S. eubayanus that have been domesticated for several centuries in lager-beer brewing environments. As sequences and structures of S. pastorianus genomes are being resolved, molecular mechanisms and evolutionary origin of several industrially relevant phenotypes remain unknown. This study investigates how maltotriose metabolism, a key feature in brewing, may have arisen in early S. eubayanus x S. cerevisiae hybrids. To address this question, we generated a near-complete genome assembly of Himalayan S. eubayanus strains of the Holarctic subclade. This group of strains have been proposed to be the origin of the S. eubayanus subgenome of current S. pastorianus strains. The Himalayan S. eubayanus genomes harbored several copies of an SeAGT1  -oligoglucoside transporter gene with high sequence identity to genes encountered in S. pastorianus. Although Himalayan S. eubayanus strains are unable to grown on maltose and maltotriose, their maltose-hydrolase and SeMALT1 and SeAGT1 maltose-transporter genes complemented the corresponding null mutants of S. cerevisiae. Expression, in a Himalayan S. eubayanus strain, of a functional S. cerevisiae maltose-metabolism regulator gene (MALx3) enabled growth on oligoglucosides. The hypothesis that the maltotriose-positive phenotype in S. pastorianus is a result of heterosis was experimentally tested by constructing a S. cerevisiae x S. eubayanus laboratory hybrid with a complement of maltose-metabolism genes that resembles that of current S. pastorianus strains. The ability of this hybrid to consume maltotriose in brewer's wort demonstrated regulatory cross talk between sub-genomes and thereby validated this hypothesis. These results provide experimental evidence of the evolutionary origin of an essential phenotype of lager-brewing strains and valuable knowledge for industrial exploitation of laboratory-made S. pastorianus-like hybrids.

sample_organism: Saccharomyces cerevisiae x Saccharomyces eubayanus

overall_design: Compare expression of maltose metabolism genes in S. eubayanus and S. cerevisiae x S. eubayanus strains  on various carbon sources

first: Marcel

last: van den Broek


title: PSEN1ΔE9, APPswe and APOE4 confer disparate phenotypes in human iPSC-derived microglia

city: Kuopio

first: Tarja

last: Malm

address: Neulaniementie 2

department: A.I. Virtanen Institute for Molecular Sciences

country: Finland

institute: University of Eastern Finland

summary: Here we elucidate the effect of Alzheimer’s disease (AD)-predisposing genetic backgrounds, APOE4, PSEN1ΔE9 and APPswe, on functionality of human microglia. We present a physiologically relevant high-yield protocol for producing human microglia-like cells (iMGLs) from induced pluripotent stem cells.  Differentiation is directed with small molecules through primitive erythromyeloid progenitors to recreate microglial ontogeny from yolk sac. The iMGLs express microglial signature genes and respond to ADP with intracellular Ca2+ release distinguishing them from macrophages. Using 16 iPSC lines from healthy donors, AD patients and isogenic controls, we reveal that the APOE4 genotype has a profound impact on several aspects of microglial functionality whereas PSEN1ΔE9 and APPswe mutations trigger minor alterations. The APOE4 genotype impairs phagocytosis, migration and metabolic activity of iMGLs but exacerbates their cytokine secretion. This indicates that APOE4 iMGLs are fundamentally unable to mount normal microglial functionality in AD.

overall_design: Human iPSC-derived microglia-like cells were collected and analyzed for gene expression using RNA-seq.

first: Henna

last: Konttinen


title: Genome-wide differential gene expression analysis in light or heavy polysomal RNAs of MYCN-amplified neuroblastoma cells after lncNB1 knockdown with siRNAs.

city: Kensington

first: Pei

last: Liu

address: C25 Lowy Cancer Research Centre

country: Australia

institute: CCIA

summary: lncNB1 stabilizes N-Myc protein expression through increasing E2F1 translation.

overall_design: We performed Affymetrix Clariom S_array in polysome associated RNA from BE(2)-C cells after transfection with Control siRNA, lncNB1 siRNA-1 or lncNB1 siRNA-2 for 48 hours.

first: Tao

middle: Y

first: Hui

last: Peng

first: Jinyan

last: Li


title: To identify transcripts that are differentially expressed in the MYCN amplified vs MYCN non-amplified cell lines using Next Generation Sequencing

summary:
The aims of this study are to compare transcripts that are differentially expressed in the MYCN amplified compare to the MYCN non-amplified neuroblastoma cell lines, in particular, long non-coding RNAs.
Methods: Ribosomal depleted RNAs from six human neuroblastoma cell lines were subjected to deep sequencing, using Illumina Hiseq.
Results: We identified 459 transcripts are differentially expressed betweeen the MYCN amplified and the MYCN non-amplified cell lines.
Conclusions: We have identified a novel long noncoding RNA lncNB1 that is highly expressed in the MYCN amplified compared to the MYCN non-amplified cell lines.

overall_design: mRNA profiles from 4 MYCN amplified and two MYCN non-amplified human neuroblastomas cell lines were generated by deep sequencing using Illumina Hiseq.

first: Jesper

last: Maag


title: Developmental competence and antigen switch frequency can be uncoupled in Trypanosoma brucei I

overall_design: Analysis of VSG expression diversity in triplicate samples of GFPESproAnTat1.1ES HYP2, NEK and DYRK RNAi cells  ± doxycycline pre- and post MACs enrichment for VSG AnTat1.1 negative cells


title: Genome wide differential gene expression analysis of MYCN-amplified neuroblastoma cells after lncNB1 knockdown with siRNAs

summary:
We identified that knocking lncNB1 reduces N-Myc protein stability, therefore, we performed affymetrix micoarray studies to investigate whether it was a direct or indirect effect.
lncNB1 stabilizes N-Myc protein expression through activating DEPDC1B gene transcription.

overall_design: We performed Affymetrix gene_array and Clariom_S_array in BE(2)-C cells after transfection with Control siRNA, lncNB1 siRNA-1 or lncNB1 siRNA-2 for 40 hours.

first: Pei-Yan

first: Chelsea

last: Mayoh

first: Nicholas

last: Ho

first: Bing


title: Heat Shock Factor 1 (HSF1) acquires transcriptional competence under 17b-estradiol in ERa-positive breast cancer cells

status: Public on Oct 05 2019

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

country: Norway

institute: University of Bergen

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Clonal selection confers distinct evolutionary trajectories in BRAF-driven cancers

status: Public on Oct 06 2019

city: Clevleand

first: Mohamed

middle: E.

last: Abazeed

state: OH

department: Radiation Oncology/Translational Hematology Oncology Research

country: USA

institute: Cleveland Clinic

summary: Analysis of BRAF variant gene expression activity after constitutive variant expression in immortalized lung ephithelial cells. The hypothesis tested in the present study was that the level of BRAF activity will vary based on the identity of the variant expressed. Results provide important information on the variation and continous quality of BRAF activity across diverse variants that were tested.

overall_design: Total mRNA obtained from BEAS2B cells transfected with BRAF variants

first: Abazeed

last: Mohamed

middle: E


title: Expression of metabolic hormone signalling genes in the brain of a triprolyl-human amylin transgenic mouse model of type 2 diabetes

city: Auckland

first: Tina

last: Nie

address: 3 Symonds St

department: School of Biological Sciences

country: New Zealand

institute: The University of Auckland

summary:
There is a need for greater understanding of the molecular mechanism underlying the development of insulin resistance in type 2 diabetes, and new models in which to study this. The hormone amylin is postulated to be involved in the development of this disease, as human amylin (hA) forms amyloid in the pancreases of diabetic patients, and wild-type hA oligomers have been shown to be cytotoxic to β-cells. By contrast, rodent amylin is non-amyloidogenic, so mice expressing wild-type hA have been developed. However, amylin-evoked β-cell loss in these models limits the secretion of amylin and insulin. We have developed transgenic mice that overexpress [25, 28, 29triprolyl]human amylin, a non-amyloidogenic variant of amylin, designated the Line 44 (L44) model. These mice develop obesity and hyperglycaemia. We examined the expression of 43 genes involved in amylin, insulin and leptin signalling in the brain of this model, at different disease stages, using the NanoString nCounter (NanoString Technologies, Seattle, WA, USA).
After onset of diabetes, mice remained hyperglycaemic for a period of time but blood glucose levels eventually returned to normoglycaemia. The incidence of diabetes (defined as having blood glucose measurements > 11 mM over 3 consecutive weeks) was gene-dose dependent; 81% of homozygous mice and 59% of hemizygous mice developed diabetes over 400 days. A proportion of nontransgenic mice (33%) also developed diabetes. As these were bred from hemizygous pairs this may be the result of epigenetic or environmental factors.

overall_design: Experimental L44 mice were bred from hemizygous x hemizygous pairs. We analysed both the hemizygous and homoygous genotypes, with age-matched nontransgenic mice as controls (littermates if possible). Blood glucose and body weight were measured weekly from weaning. At predetermined time points mice were euthanised and brain samples taken. These time points were T1: 100 days (before the onset of diabetes), T2: diabetes oneset (3 blood glucose measurements > 11 mM) and T3: 400 days (post-diabetic). The brain was split into 4 regions: the hindbrain (including the cerebellum), left cortex, right cortex and midbrain (the remaining part of the brain, including the forebrain). RNA was extracted from each sample and analysed using the Nanostring nCounter platform to examine the expression of genes involved in the signalling pathways of amylin, insulin and leptin. Due to their large number, samples were pooled together for analysis. Two samples were pooled only if they were of the same genotype and collection time. The same quantity of RNA from each sample was mixed, thus results represent the mean of the two samples. E.g. sample T1 HB HEM 1/2 consists of RNA extracted from the hindbrain of mouse HEM 1 and HEM 2 at T1.

first: Shaoping

last: Zhang

first: Greeshma

last: Vazhoor Amarsingh

first: Hong

first: Mark

middle: J

last: McCann

first: Garth

last: Cooper


title: Gene Expression by granuloma macrophages from resistant and susceptible mice after 4h of phagocytosis of metacyclical Leishmania major

status: Public on Oct 04 2019

city: Münster

first: Niels-Arne

last: Münck

address: Roentgenstraße 21

department: Insitute of Immunology

institute: University of Münster

summary: The goal of this experiment was to identify genes which are differentially regulated between Leishmania major- infected  granuloma macrophages from mice resistant (C57 Bl/6) and susceptible (BALB/c) to experimental leishmaniasis

overall_design: There are four groups of triplicates: uninfected control samples of murine granuloma macrophages of C57BL/6 (resistant) and BALB/c (susceptible) origin and samples of granuloma macrophages infected with a 5x MOI of metacyclical Leishmania major.

first: Jan

middle: M

last: Ehrchen


title: Heat Shock Factor 1 (HSF1) acquires transcriptional competence under 17b-estradiol in ERa-positive breast cancer cells [ChIP-seq]

summary: Heat Shock Transcription Factor 1 (HSF1) is a well-known regulator of gene expression during acute environmental stress that enables the cells to survive. Its high level in estrogen receptor-positive breast cancer patients correlated with a worse prognosis. Here, we demonstrated that 17β-estradiol (E2) as well as bisphenol A (BPA) and propyl pyrazole triol (PPT, ERα agonist) led to HSF1 phosphorylation on S326 in ERα positive mammary breast cancer cells, but not in ERα-negative ones. We showed that ERK1/2 signaling was involved in this process and down-regulation of ERα expression abrogated it. E2activated HSF1 was transcriptionally potent. Chip-Seq and RNA-Seq analyses revealed that it could modulate the expression of several genes known to be essential for breast cancer cells growth and/or ERα action, i.e. HSPB8, LHX4, PRKCE, WWC1, and GREB1. Our findings indicate that a positive feedback loop between ERα and HSF1 signaling may exist which support the growth of estrogen-dependent tumors.

overall_design: We sequenced DNA immunoprecipitated from wild type MCF7 cells using rabbit polyclonal anti-HSF1 antibodies. Cells were untreated (control), subjected to hyperthermia or stimulated using estrogen (17beta-estradiol) for indicated time. Six ChIP replicates were collected and pooled per each sequenced sample. Input samples were included as negative control (no DNA enrichment was observed in mock-IP samples).

first: Natalia

last: Vydra

first: Wieslawa

last: Widlak


title: RNA-Seq of blood in preterm infants with Bronchopulmonary dysplasia.

city: Adelaide

first: Feargal

last: Ryan

state: Adelaide

address: North Terrace

institute: SAHMRI

summary: RNA-Seq of peripheral blood at 36 weeks post-menstrual age, the time BPD was diagnosed. Using this we identified more than 400 genes that were significantly changed in BPD infants compared to controls.

overall_design: RNA-Seq of peripheral blood from 21 infants, 11 with BPD and 10 age matched controls.  Samples collected at birth and again at 36 weeks post menstrual age.

first: David

last: Lynn


title: An enhancer cluster controls gene activity and topology of the SCN5A-SCN10A locus in vivo (Hi-C)

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

institute: Amsterdam UMC

summary: High-resolution chromosome conformation capture-sequencing of RE6-9 heterozygous mutants. We investigated the three-dimensional organization of the Scn5a-Scn10a locus in whole hearts of RE6-9 heterozyous mutants and wildtype littermates. Viewpoint were set on enhancer 1 (enh1, located in the intronic region of Scn10a) and the Scn5a promoter (P1_2). The liver of FVB mice was used as controle tissue to determine the specificity of the Scn5a-Scn10a interaction domain in the heart.

overall_design: 4C sequencing on whole heart of 8 weeks old heterozygous RE6-9 mutants and wildtype littermates, and liver of 8 weeks old FVB mice.

first: Joyce

middle: C

last: Man


title: Heat Shock Factor 1 (HSF1) acquires transcriptional competence under 17b-estradiol in ERa-positive breast cancer cells [RNA-seq]

first: Tomasz

overall_design: We sequenced mRNA from wild type MCF7 cells. Cells were untreated (control), stimulated using estrogen (17beta-estradiol) for indicated time or subjected to hyperthermia with subsequent recovery. Three biological replicates were performer, pooled and sequenced.


title: An enhancer cluster controls gene activity and topology of the SCN5A-SCN10A locus in vivo


title: An enhancer cluster controls gene activity and topology of the SCN5A-SCN10A locus in vivo (RNA-Seq)

summary: Whole transcriptome analysis of RE6-9 heterozygous mutants

overall_design: RNA-seq on ventricular tissue of 2 week old mice

middle: K


title: FFPEcap-seq: a method for sequencing capped RNAs in formalin-fixed paraffin-embedded samples

city: Salt Lake CIty

first: Jason

last: Gertz

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

summary: The majority of clinical cancer specimens are preserved as formalin-fixed paraffin-embedded (FFPE) samples. In order for clinical molecular tests to have wide reaching impact, they must be applicable to FFPE material. Accurate quantitative measurements of RNA derived from FFPE specimens is challenging due to low yields and high amounts of degradation. Here we present FFPEcap-seq, a method specifically designed for sequencing capped 5’ ends of RNA derived from FFPE samples. FFPEcap-seq combines enzymatic enrichment of 5’ capped RNAs with template switching to create sequencing libraries. We find that FFPEcap-seq can faithfully capture mRNA expression levels in FFPE specimens while also detecting enhancer RNAs that arise from distal regulatory regions. FFPEcap-seq is a fast and straightforward method for making high quality 5’ end RNA-seq libraries from FFPE-derived RNA.

overall_design: Ishikawa cells

first: Jeffery

last: Vahrenkamp


title: Differentiation of Induced Pluripotent Stem Cells towards Mesenchymal Stromal Cells is Hampered by Culture in 3D Hydrogels [RNA-Seq]

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

summary: Directed differentiation of induced pluripotent stem cells (iPSCs) towards specific lineages remains a major challenge in regenerative medicine, while there is a growing perception that this process can be influenced by the three-dimensional environment. In this study, we investigated whether iPSCs can differentiate towards mesenchymal stromal cells (MSCs) when embedded into fibrin hydrogels to enable a one-step differentiation procedure within a scaffold. Differentiation of iPSCs on tissue culture plastic or on top of fibrin hydrogels resulted in a typical MSC-like phenotype. In contrast, iPSCs embedded into fibrin gel gave rise to much smaller cells with heterogeneous growth patterns, absence of fibronectin, faint expression of CD73 and CD105, and reduced differentiation potential towards osteogenic and adipogenic lineage. Transcriptomic analysis demonstrated that characteristic genes for MSCs and extracellular matrix were upregulated on flat substrates, whereas genes of neural development were upregulated in 3D culture. Furthermore, the 3D culture had major effects on DNA methylation profiles, particularly within genes for neuronal and cardiovascular development, while there was no evidence for epigenetic maturation towards MSCs. Taken together, iPSCs could be differentiated towards MSCs on tissue culture plastic or on a flat fibrin hydrogel. In contrast, the differentiation process was heterogeneous and not directed towards MSCs when iPSCs were embedded into the hydrogel.

overall_design: Three different iPSC lines (donors 1-3) were differentiated toward MSCs either on tissue culture plastic, on fibrin gel, or within fibrin gel to compare the impact of different 2D and 3D culture conditions on gene expression with the Illumina HiSeq 2500

first: Roman

last: Goetzke

first: Hans

last: Keijdener

first: Julia

last: Franzen

first: Alina

last: Ostrowska

first: Selina

last: Nüchtern

first: Petra

last: Mela


title: Differentiation of Induced Pluripotent Stem Cells towards Mesenchymal Stromal Cells is Hampered by Culture in 3D Hydrogels [DNA methylation array]

type: Methylation profiling by genome tiling array

overall_design: Three different iPSC lines (donors 1-3) were differentiated toward MSCs either on fibrin gel or within fibrin gel to compare impact of 2D and 3D culture with a soft substrate on DNA methylation profiles with Illumina Infinium MethylationEPIC BeadChip


title: Differentiation of Induced Pluripotent Stem Cells towards Mesenchymal Stromal Cells is Hampered by Culture in 3D Hydrogels


title: eIF4A supports an oncogenic translation program in pancreatic ductal adenocarcinoma

status: Public on Oct 03 2019

city: Stockholm

first: Christian

last: Oertlin

address: Tomtebodavägen 23A

country: Sweden

institute: Karolinska Institutet

summary: Pancreatic ductal adenocarcinoma (PDA) is a lethal malignancy with limited treatment options. Although metabolic reprogramming is a hallmark of many cancers, including PDA, previous attempts to target metabolic changes therapeutically have been stymied by drug toxicity and tumour cell plasticity. Here, we show that PDA cells engage an eIF4F-dependent translation program that supports redox and central carbon metabolism. Inhibition of the eIF4F subunit, eIF4A, using the synthetic rocaglate CR-1-31-B (CR-31) reduced the viability of PDA organoids relative to their normal counterparts. In vivo, CR-31 suppresses tumour growth and extends survival of genetically-engineered murine models of PDA. Surprisingly, inhibition of eIF4A also induces glutamine reductive carboxylation. As a consequence, combined targeting of eIF4A and glutaminase activity more effectively inhibits PDA cell growth both in vitro and in vivo. Overall, our work demonstrates the importance of eIF4A in translational control of pancreatic tumour metabolism and as a therapeutic target against PDA.

overall_design: RNA sequencing of polysome-associated mRNA and total mRNA of treated and untreated normal mouse organoids, as well as treated and untreated pancreatic ductal adenocarcinoma mouse organoids. Each condition and RNA source combination was replicated 3 times, leading to a total of 24 samples.

first: Karina

last: Chan

first: Francis

last: Robert

first: Dana

last: Kapeller-Libermann

first: Daina

last: Avizonis

last: Park

first: Christina

last: Schoepfer

first: Brandon

last: Da Silva

first: Melissa

last: Yao

first: Faith

last: Gorton

first: Craig

last: Thomas

first: Lauren

last: Brown

first: John

middle: A

last: Porco Jr.

first: Mikhail

last: Doubrovin

first: Michael

last: Pollak

first: Ola

last: Larsson

first: Jerry

last: Pelletier

first: Iok

last: Chio


title: Enriched environmental conditions modify the gut microbiome composition and fecal markers of inflammation in Parkinson’s disease

status: Public on Oct 01 2019

city: Tübingen

first: Jakob

last: Admard

address: Calwerstr. 7

department: Institut für Medizinische Genetik und Angewandte Genomik

institute: Universitätsklinikum Tübingen

summary: We used a transgenic mouse model overexpressing the complete human SNCA genes modeling familial and sporadic forms of Parkinson’s disease to study whether environmental conditions such as standard versus enriched environment changes the gut microbiome and influences disease progression.

overall_design: Experimental setup consists of control and transgenic mice kept under standard environment and enriched environment conditions, with replicates in each genotype and condition.

first: Yogesh

last: Singh

first: Mohamed

last: El Hadidi

last: Matthes

first: Zinah

last: Wassouf

first: Julia

last: Schulze-Hentrich

first: Ursula

last: Kohlhofer

first: Leticia

last: Quintanilla-Martinez de Fend

first: Daniel

last: Huson

first: Olaf

last: Riess

first: Nicolas

last: Casadei


title: Epigenetic pattern after EZH1,2 inhibition in lymohoma cells

city: Minato-ku

first: Makoto

last: Yamagishi

state: Tokyo

address: 4-6-1, Shirokanedai

country: Japan

institute: The University of Tokyo

type: Genome binding/occupancy profiling by genome tiling array

summary: Although global H3K27me3 reprogramming is a hallmark of cancer, no effective therapeutic strategy for H3K27me3-high malignancies harboring EZH2WT/WT has yet been established. We explored epigenome and transcriptome in EZH2WT/WT aggressive lymphomas, and found that mutual interference and compensatory function of co-expressed EZH1 and EZH2 rearrange their own genome-wide distribution, thereby establishing restricted chromatin and gene expression signatures. Direct comparison of leading compounds introduced potency and a mechanism-of-action of the EZH1/2 dual-inhibitor (valemetostat). The synthetic lethality was observed in all lymphoma models and primary adult T-cell leukemia–lymphoma (ATL) cells. Opposing actions of EZH1/2-polycomb and SWI/SNF complexes are required for facultative heterochromatin formation. Inactivation of chromatin-associated genes (ARID1A, SMARCA4/BRG1, SMARCB1/SNF5, KDM6A/UTX, BAP1, KMT2D/MLL2) and oncovirus infection (HTLV-1, EBV) trigger EZH1/2 perturbation and H3K27me3 deposition. Our study provides the mechanism-based rationale for chemical dual-targeting of EZH1/2 in cancer epigenome.

overall_design: We explored epigenome (EZH1/2 occupancies and histone modifications) in aggressive lymphoma samples and cell lines treated with EZH1/2 inhibitors by using ChIP-on-chip platform

last: Hori

first: Dai

last: Fujikawa


title: Expression analysis after EZH1,2 inhibition in lymohoma cells

status: Public on Oct 02 2019

summary: To define gene expression alteration by EZH1/2 ihibition, we performed gene expression profiling in lymphoma cells after treatment of inhibitors or shRNAs

overall_design: Total RNA samples from lymphoma cells were subjected to Cy-3 labeling followed by human whole genome gene expression microarray analyses.


title: Extensive Transcriptional and Translational Regulation Occur During the Maturation of Malaria Parasite Sporozoites

city: University Park

first: Scott

last: Lindner

state: Pennsylvania

address: W224 Millennium Science Complex

department: Biochemistry and Molecular Biology

institute: Penn State University

summary: These data were used to assess gene expression and dynamics between oocyst sporozoites and salivary gland sporozoites for both Plasmodium falciparum and Plasmodium yoelii.

sample_organism:
Plasmodium falciparum 3D7
Plasmodium yoelii yoelii 17XNL

overall_design: Sporozoites (Plasmodium falciparum, Plasmodium yoelii) from either the oocyst or salivary gland of Anopheles stephensi mosquitoes were purified twice by an Accudenz discontinuous density gradient and their RNA was extracted using a Qiagen Rneasy Kit with added DNaseI module. All experiments were done in biological triplicate.

first: Kristian

last: Swearingen

first: Melanie

last: Shears

middle: P

last: Walker

first: Erin

middle: N

last: Vrana

first: Kevin

last: Hart

first: Allen

last: Minns

first: Photini

last: Sinnis

first: Robert

middle: L

last: Moritz

first: Stefan

middle: H

last: Kappe


title: ADP-ribosylation Levels Correlate with Gene Expression Patterns and Clinical Outcomes in Ovarian Cancers

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: Inhibitors of nuclear poly(ADP-ribose) polymerase (PARP) enzymes (e.g., PARP-1) have improved clinical outcomes in ovarian cancer, especially in patients with BRCA1/2 gene mutations or additional homologous recombination (HR) DNA repair pathway deficiencies.  These defects serve as biomarkers for response to PARP inhibitors (PARPi).  We sought to identify an additional biomarker that could predict responses to both conventional chemotherapy and PARPi in ovarian cancers.  We focused on cellular ADP-ribosylation (ADPRylation), which is catalyzed by PARP enzymes and detected by detection reagents we developed previously.  We determined molecular phenotypes of 34 high-grade serous ovarian cancers and associated them with clinical outcomes.

overall_design: We used our recombinant antibody-like ADP-ribose detection reagents to characterize the levels and patterns of ADP-ribosylation in a cohort of ovarian cancer tumor tissue samples and relate the results to molecular, cellular, and clinical outcomes.

first: Lesley

last: Conrad

first: Ken

last: Lin

first: Tulip

last: Nandu

first: Bryan

last: Gibson

first: Ali

last: Gazdar

first: Jayanthi

last: Lea

first: W


title: The mithralog EC-7072 is highly cytotoxic to chronic lymphocytic leukemia cells by targeting the B-cell receptor signaling pathway

city: Oviedo

first: Seila

last: Lorenzo-Herrero

state: Asturias

address: Julian Claveria

department: Functional Biology

country: Spain

institute: University of Oviedo

summary: EC-7072, an analogue of Mithramycin A, exerts a direct cytotoxic effect on primary leukemic cells from patients with chronic lymphocytic leukemia (CLL) in vitro. To elucidate the underlying mechanisms mediating this effect, RNA sequencing was carried out employing total RNA from primary leukemic cells exposed to EC-7072. Data analysis revealed a dramatic impact of the compound on the transcriptional profile of CLL cells, unraveling a modulation of key mediators associated to homeostasis and survival of CLL cells, including B-cell receptor signaling. Likewise, EC-7072 activated the expression of a pro-apoptotic network, while downregulating the expression of essential anti-apoptotic proteins such as BCL2.

overall_design: mRNA profiles of leukemic cells from 8 patients with chronic lymphocytic leukemia exposed to EC-7072

first: Christian

last: Sordo-Bahamonde

first: Francisco

last: Morís

first: Segundo

last: González

first: Alejandro

last: López-Soto


title: Exploration  of the degS mutant effects the growth of Vibrio cholerae and its global regulatory function  by RNA sequencing

status: Public on Sep 29 2019

city: 遵义市

first: 健

last: 黄

state: 贵州省

address: 汇川区大连路149号遵义医学院附属医院

country: China

institute: 遵义医学院附属医院

summary: we aimed to characterize the molecular functions and further investigate the regulatory network of degS in V. cholerae.

overall_design: To uncover the  underlying molecular basis and further investigate the regulatory network of degS in V. cholerae,  we used high-throughput RNA sequencing (RNA-Seq) technology to analyze the differential  transcriptomic profile between the wild type and degS mutant strains.

first: Jian

last: Huang


title: Genome-wide histone modification and accessibility maps of mESCs, in the pluripotent state and after induced differentiation

status: Public on Sep 30 2019

city: Berlin

first: Laura

middle: V

last: Glaser

address: Ihnestraße 63-73

department: Computational Molecular Biology

institute: Max Planck Institute for Molecular Genetics

summary: Gene expression networks are tightly regulated by transcription factors (TF) and their targeted regulatory genomic elements (enhancers), which are known to correlate with specific histone modifications and chromatin accessibility. The identification of enhancers on a genome wide level is an important prerequisite for many functional studies, however the prediction of enhancer elements, especially with in response to changing conditions, remains challenging.  Here we report the generation of a genome-wide mESC enhancer prediction map, comparing the pluripotent state and induced differentiation, by the integration of data on transcription, chromatin accessibility and multiple histone modifications.

overall_design: mESCs, in the pluripotent state or after induced differentiation, were assessed for genome-wide changes in (i) gene expression by RNA-seq for poly-adenylated transcripts using biological triplicates, (ii) chromatin accessibility by ATAC-seq, and (iii) enrichment of eight specific chromatin marks by ChIP-seq.

first: Alisa

last: Fuchs

first: Ho-Ryun

last: Chung

first: Sebastiaan

last: Meijsing


title: Whole brain transcriptomic analysis of Tbr1-K228E mutant mice

city: Daejeon

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

country: South Korea

institute: IBS/KAIST

summary: Mutations of Tbr1, a high-confidence ASD (autism spectrum disorder)-risk gene encoding the transcription regulator TBR1, in mice have been shown to induce diverse ASD-related molecular, synaptic, neuronal, and behavioral dysfunctions. However, it remains unclear whether Tbr1 mutations derived from autistic individuals cause similar dysfunctions in mice remains unclear. Here we generated and characterized mice carrying the TBR1-K228E de novo mutation identified in human ASD and identified various ASD-related phenotypes. In heterozygous mice carrying this mutation (Tbr1+/K228E mice), the levels of the TBR1-K228E protein, which cannot bind to target DNA, were strongly increased. RNA-Seq analysis of the Tbr1+/K228E embryonic brain indicated significant changes in the expression of genes associated with neurons, astrocytes, ribosomes, neuronal synapses, and ASD risk. The Tbr1+/K228E neocortex displayed abnormal distribution of parvalbumin-positive interneurons, with the density lower in superficial layers but higher in deep layers. This was associated with increased inhibitory synaptic transmission in layer 6 pyramidal neurons, which was resistant to compensation by network activity. Behaviorally, Tbr1+/K228E mice showed decreased social interaction, increased self-grooming, and modestly increased anxiety-like behaviors. These results suggest that the human heterozygous TBR1-K228E mutation induces ASD-related protein, transcriptomic, neuronal, synaptic, and behavioral dysfunctions in mice.

overall_design: Whole brain transcriptome of E16.5 wild-type and Tbr1-K228E mutant mice.

first: Chaehyun

last: Yook

first: Soo

first: Hyojin

last: Kang


title: Nucleotide resolution mapping of Spo11-linked DNA breaks in the yeast genome

status: Public on Sep 28 2019

city: Brighton

first: William

last: Gittens

state: I am not in the U.S. or Canada

address: Science Park Road

department: Genome Damage and Stability Centre

institute: University of Sussex

summary: DNA topoisomerases are required to resolve DNA topological stress. Despite this essential role, abortive topoisomerase activity generates aberrant protein-linked DNA breaks, jeopardising genome stability. Here, to understand the genomic distribution and mechanisms underpinning topoisomerase-induced DNA breaks, we map Top2 DNA cleavage with strand-specific nucleotide resolution across the S. cerevisiae and human genomes - and use the meiotic Spo11 protein to validate the broad applicability of this method to explore the role of diverse topoisomerase family members. Our data characterises Mre11-dependent repair in yeast, and defines two strikingly different fractions of Top2 activity in humans: tightly localised CTCF-proximal, and broadly distributed transcription-proximal, the latter correlated with gene length and expression. Moreover, single nucleotide accuracy enables us to reveal the influence primary DNA sequence has upon Top2 cleavage - distinguishing canonical DNA double-strand breaks (DSBs) from a major population of DNA single-strand breaks (SSBs) induced by etoposide (VP16) in vivo.

overall_design: This data set contains maps of Spo11-linked DNA breaks in the S. cerevisiae genome, generated by CC-seq of meiotic SK1 cells.

first: Matthew

last: Neale


title: Genome-wide maps of histone H3 variant CENP-A/Cnp1 in the meiotic haploid progeny of wip1∆/+, mhf1∆/+ and mhf2∆/+ and genome-wide maps of histone H3 variant CENP-A/Cnp1 in mhf2+ (or mhf2∆) carrying the inactivated Centromere 1 or Centromere 2.

city: Hangzhou

first: Min

last: Lu

state: Zhejiang

address: Yuhangtang road 866

institute: Zhejiang University, Life Sciences Institute

summary: We report the high-throughput profiling of histone variant CNEP-A/Cnp1 in fission yeast Schizosaccharomyces pombe. By obtaining 1-10 ng immunoprecipitated DNA, we generated genome-wide CENP-A/Cnp1 maps of the wild type meiotic haploid progeny of heterozygous deletion diploid wip1∆/+, mhf1∆/+ and mhf2∆/+ and CENP-A/Cnp1 maps of mhf2+ carrying the inactivated Centromere 1 or Centromere 2. We find that CENP-A/Cnp1 spreading into the pericentromeric regions in wild type meiotic progeny of heterozygous deletion diploid wip1∆/+, mhf1∆/+ and mhf2∆/+.

overall_design: 4 wild type meiotic haploid progeny of heterozygous deletion diploid wip1∆/+, mhf1∆/+ and mhf2∆/+ were examined by anti-CENP-A/Cnp1 ChIP-seq. And biological replicates of mhf2+ carrying the inactivated Centromere 1 or Centromere 2 were examined by anti-CENP-A/Cnp1 ChIP-seq.

first: Xiangwei

last: He


title: Genome-wide maps of chromatin state (centromeric histone H3 variant CENP-A/Cnp1) in the meiotic progeny from the genetic crossing of mhf2∆ (cen1_inactive) × clr4∆ (cen1_active).

summary: We report the high-throughput profiling of histone variant CNEP-A/Cnp1 in fission yeast Schizosaccharomyces pombe. By obtaining 1-10 ng immunoprecipitated DNA, we generated genome-wide CENP-A/Cnp1 maps of  the meiotic progeny from the genetic crossing of mhf2∆ (cen1_inactive) × clr4∆ (cen1_active) in fission yeast. We find that heterochromatin is not required for the induction of centromere inactivation.

overall_design: 4 meiotic progeny (4 viable spores from 1 intact tetrad) from the genetic crossing of mhf2∆ (cen1_inactive) × clr4∆ (cen1_active) were examined by anti-CENP-A/Cnp1 ChIP-seq.


title: Genome-wide maps of chromatin state (H3K9me2 or CENP-A/Cnp1) in wt strains carrying the inactivated Centromere 1 or 2 or Cnp1 spreading with ura4 inserted into the right side of the repetitive sequences of Chromosome 1 (designated as otr1R::ura4)

summary: We report the high-throughput profiling of histone modification (H3K9me2) or histone variant CNEP-A/Cnp1 in fission yeast Schizosaccharomyces pombe. By obtaining 1-10 ng immunoprecipitated DNA, we generated genome-wide H3K9me2 or CENP-A/Cnp1 maps of wild type strains carrying the inactivated Centromere 1 or Centromere 2 or Cnp1 spreading in fission yeast with a reporter gene ura4 cassette inserted into the right side of the repetitive sequences of Chromosome 1 . We find that neocemtromeres are formed preferably at pericentromeric regions ubiquitously and asymmetrically in all three centromeres of these indicated strains.

overall_design: 3 wild type strains carrying the inactivated Centromere 2; 7 wild type strains carrying the inactivated Centromere 1 and 5 wild type strains carrying the Cnp1 spreading were examined by anti-CENP-A/Cnp1 ChIP-seq. 2 wild type strains carrying the inactivated Centromere 2 and 1 wild type strain carrying the Cnp1 spreading were examined by anti-H3K9me2 ChIP-seq.


title: Genome-wide maps of chromatin state (heterochromatin H3K9me2 or centromeric histone H3 variant CENP-A/Cnp1) in both mhf2∆ and mhf2+ carrying the inactivated Centromere 1 or Centromere 2.

summary: We report the high-throughput profiling of histone modification (H3K9me2) or histone variant CNEP-A/Cnp1 in fission yeast Schizosaccharomyces pombe. By obtaining 1-10 ng immunoprecipitated DNA, we generated genome-wide H3K9me2 or CENP-A/Cnp1 maps of both mhf2∆ and mhf2+ carrying the inactivated Centromere 1 or Centromere 2 in fission yeast. We find that neocemtromeres are formed preferably at pericentromeric regions in single depletion of CENP-T-W-X-S.

overall_design: 4 mhf2∆ and mhf2+ carrying the inactivated Centromere 1 or Centromere 2 were examined by anti-CENP-A/Cnp1 ChIP-seq. 2 mhf2+ carrying the inactivated Centromere 1 or Centromere 2  were examined by anti-H3K9me2 ChIP-seq.


title: Genome-wide maps of chromatin state (heterochromatin H3K9me2 or centromeric histone H3 variant CENP-A/Cnp1) in the meiotic progeny from the crossings of mhf2+ (cen1_inactive) × mhf2+ (cen1_active) and mhf2∆ (cen1_inactive) × mhf2+ (cen1_active)

summary: We report the high-throughput profiling of histone modification (H3K9me2) or histone variant CNEP-A/Cnp1 in fission yeast Schizosaccharomyces pombe. By obtaining 1-10 ng immunoprecipitated DNA, we generated genome-wide H3K9me2 or CENP-A/Cnp1 maps of  the meiotic progeny from the genetic crossings of mhf2+(cen1_inactive) × mhf2+ (cen1_active) and mhf2∆ (cen1_inactive) × mhf2+ (cen1_active) in fission yeast. We find that the endogenous Centromere 1 in mhf2+ is converted to the inactivated Centromere 1 by mhf2∆ through genetic crossing.

overall_design: 8 meiotic progeny (8 viable spores from 2 intact tetrads) from the genetic crossing of mhf2+ (cen1_inactive) × mhf2+ (cen1_active); 14 meiotic progeny (4 viable spores from 1 intact tetrad and 10 viable spores from 2 incomplete tetrads) from the genetic crossing of mhf2∆ (cen1_inactive) × mhf2+ (cen1_active) were examined by anti-H3K9me2 ChIP-seq.  4 meiotic progeny (4 viable spores from 1 intact tetrad) from the genetic crossing of mhf2∆ (cen1_inactive) × mhf2+ (cen1_active) were examined by anti-CENP-A/Cnp1 ChIP-seq.


title: Glioblastoma-Associated Microglia Reprogramming Is Mediated by Functional Transfer of Extracellular miR-21

city: Charlestown

first: Erik

last: Abels

state: Massachusetts

address: 149 13th Street

department: Neurology

institute: Massachusetts General Hospital

summary:
Method: Analysis of the transcriptomal changes of EV-GFP uptake by microglia after implantation of glioma cells into miR-21 null mouse brain.
Result: miR-21 is transferred from glioma to microglia through EV, resulting in downregulation of miR-21 target mRNAs

overall_design: mRNA expression of microglia isolated from control and tumor-bearing miR-21 null brains analyzed by RNAseq, using Illumina Nextseq.

first: Sybren

last: Maas

first: Lisa

last: Nieland

first: Zhiyun

last: Wei

first: Pike

middle: S

last: Cheah

first: Eric

last: Tai

first: Christy-Joy

last: Kolsteeg

first: Sophie

last: Dusoswa

first: David

middle: T

last: Ting

first: Suzanne

last: Hickman

first: Joe

last: El Khoury

first: Anna

last: Krichevsky

first: Marike

middle: D

last: Broekman

first: Xandra

middle: O

last: Breakefield


title: Nucleotide resolution mapping of Top2-linked DNA breaks in the yeast genome

first: William

last: Gittens

summary: DNA topoisomerases are required to resolve DNA topological stress. Despite this essential role, abortive topoisomerase activity generates aberrant protein-linked DNA breaks, jeopardising genome stability. Here, to understand the genomic distribution and mechanisms underpinning topoisomerase-induced DNA breaks, we map Top2 DNA cleavage with strand-specific nucleotide resolution across the S. cerevisiae and human genomes—and use the meiotic Spo11 protein to validate the broad applicability of this method to explore the role of diverse topoisomerase family members. Our data characterises Mre11-dependent repair in yeast and defines two strikingly different fractions of Top2 activity in humans: tightly localised CTCF-proximal, and broadly distributed transcription-proximal, the latter correlated with gene length and expression. Moreover, single nucleotide accuracy reveals the influence primary DNA sequence has upon Top2 cleavage—distinguishing sites likely to form canonical DNA double-strand breaks (DSBs) from those predisposed to form strand-biased DNA single-strand breaks (SSBs) induced by etoposide (VP16) in vivo. This data set contains maps of Top2 CCs in the S. cerevisiae genome, generated by CC-seq of BY4741 cells -/+ etoposide (VP16).

first: Matthew

last: Neale


title: eQTL analysis of 5 DAP maize kernel

city: Beijing

first: Junling

last: Pang

address: No.12 Zhongguancun South St.,Haidian District

institute: Chinese Academy of Agricultural Sciences

summary: Kernel development is accompanied by complex gene networks. Expression quantitative trait loci (eQTL) analysis is an efficient way to detect the regulatory elements of genes, especially the trans-eQTLs help to construct the regulatory networks of genes and contribute to a better understanding of the intrinsic mechanisms of biological processes. Till now, the 15 DAP (day after pollination) eQTL has been elucidated in maize kernel, but little is known about the early stage. Here, we conduct eQTL analysis for 5 DAP maize kernel using 318 maize inbred lines. The results will provide insights into the genetic basis of early kernel development.

overall_design: The raw data have been submitted to SRA database, with the SRA Study accession (SRP119998) and BioProject accession  (PRJNA413629).


title: Nucleotide resolution mapping of Top2-linked DNA breaks in the human genome

summary: DNA topoisomerases are required to resolve DNA topological stress. Despite this essential role, abortive topoisomerase activity generates aberrant protein-linked DNA breaks, jeopardising genome stability. Here, to understand the genomic distribution and mechanisms underpinning topoisomerase-induced DNA breaks, we map Top2 DNA cleavage with strand-specific nucleotide resolution across the S. cerevisiae and human genomes—and use the meiotic Spo11 protein to validate the broad applicability of this method to explore the role of diverse topoisomerase family members. Our data characterises Mre11-dependent repair in yeast and defines two strikingly different fractions of Top2 activity in humans: tightly localised CTCF-proximal, and broadly distributed transcription-proximal, the latter correlated with gene length and expression. Moreover, single nucleotide accuracy reveals the influence primary DNA sequence has upon Top2 cleavage—distinguishing sites likely to form canonical DNA double-strand breaks (DSBs) from those predisposed to form strand-biased DNA single-strand breaks (SSBs) induced by etoposide (VP16) in vivo.

overall_design: This data set contains maps of Top2 CCs in the Human genome, generated by CC-seq of RPE-1 cells -/+ etoposide (VP16).


title: Human lung and lung draining lymph node T cell sequencing

status: Public on Sep 27 2019

city: Chicago

first: Carole

last: Ober

state: IL

address: 920 E 58TH ST

department: Human Genetics

institute: The University of Chicago

summary: We report the transcriptional profiles of human lung and lung draining lymph node T cell subsets that were sorted from paired samples. Naïve, central memory, effector memory and tissue resident memory CD4 and CD8 T cell subsets were sorted by FACS. Samples then underwent RNA sequencing to compare the similarities and differences between these T cell subsets and across tissues.

overall_design: Comparison of gene expression of T cell subsets from 11 donors

first: Nathan

last: Schoettler


title: Transcriptomic analysis of two models of zebrafish beta-catenin-driven HCC

city: San Francisco

first: Kimberley

middle: Jane

last: Evason

state: CA

address: 513 Parnassus Ave, Room M545

department: Pathology

institute: University of California, San Francisco

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

overall_design: Refer to individual Series


title: Bulk transcriptomic analysis of two models of zebrafish beta-catenin-driven HCC

summary: Up to 41% of hepatocellular carcinomas (HCCs) result from activating mutations in the CTNNB1 gene encoding β-catenin. β-catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC-associated CTNNB1 mutations stabilize the β-catenin protein, leading to nuclear and/or cytoplasmic localization of β-catenin and downstream activation of Wnt target genes. In patient HCC samples, β-catenin nuclear and cytoplasmic localization are typically patchy, even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in β-catenin activation are not well understood. To define mechanisms of β-catenin-driven HCC initiation, we generated a Cre-lox system that enabled switching on activated β-catenin in 1) a small number of hepatocytes in early development; or 2) the majority of hepatocytes in later development or adulthood. We discovered that switching on activated β-catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/β-catenin signaling heterogeneity later in hepatocarcinogenesis, we performed RNA-seq analysis of zebrafish β-catenin-driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre-lox HCC model revealed that “Cancer” and “Liver Tumor” categories were significantly altered, indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single-cell level, 2.9% to 15.2% of hepatocytes from zebrafish β-catenin-driven HCC expressed two or more of the Wnt target genes axin2, mtor, glula, myca, and wif1, indicating focal activation of Wnt signaling in established tumors. Thus, heterogeneous β-catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis.

overall_design: Examination of HCC and nonHCC liver samples from two different models of zebrafish, compared to wildtype/nonHCC siblings.

first: Sharanya

last: Kalasekar

first: Srishti

last: Kotiyal

first: Christopher

last: Conley

first: Cindy

last: Phan

first: Annika

last: Young


title: Regional Epigenetic Variation in Asexual Snail Populations among Urban and Rural Lakes

city: Pullman

first: Michael

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

type: Methylation profiling by high throughput sequencing

summary: Epigenetic variation has the potential to control environmentally dependent development and contribute to phenotypic responses to local environments. Environmental epigenetic studies of sexual organisms confirm the responsiveness of epigenetic variation, which should be even more important when genetic variation is lacking. A previous study of an asexual snail, Potamopyrgus antipodarum, demonstrated that different populations derived from a single clonal lineage differed in both shell phenotype and methylation signature when comparing lake versus river populations. Here, we examine methylation variation among lakes that differ in environmental disturbance and pollution histories.  The differential DNA methylation regions (DMRs) identified among the different lake comparisons suggested a higher number of DMRs and variation between rural Lake 1 and one urban Lake 2 and between the two urban Lakes 2 and 3, but limited variation between the rural Lake 1 and urban Lake 3. DMR genomic characteristics and gene associations were investigated. Observations suggest there is no effect of geographic distance or any consistent pattern of DMRs between urban and rural lakes. Environmental factors may influence epigenetic response.

overall_design: Snails were collected from a rural Lake 1 (Lake Lytle), and two urban lakes, Lake 2 (Capitol Lake) and Lake 3 (Lake Washington) on the Northwest Pacific coast. DNA methylation was assessed for each sample population using MeDIP-seq.

first: Jennifer

last: Thorson

first: Mark

last: Smithson

first: Ingrid

last: Sadler-Riggleman

first: Daniel

last: Beck

last: Dybdahl


title: Single-cell transcriptomic analysis of two models of zebrafish beta-catenin-driven HCC

overall_design: Examination of three 6mpf liver samples from three different transgenic lines with/without 4-hydroxytamoxifen (TAM) treatment.


title: Centromere repositioning in Schizosaccharomyces pombe

first: Min

last: Lu


title: Genome-wide maps of chromatin state (centromeric histone H3 variant CENP-A/Cnp1) in clr4∆ and the transformants from the deletion of clr4 in mhf2∆ (cen2_inactive) or mhf2+ (cen1_inactive).

summary: We report the high-throughput profiling of histone variant CNEP-A/Cnp1 in fission yeast Schizosaccharomyces pombe. By obtaining 1-10 ng immunoprecipitated DNA, we generated genome-wide CENP-A/Cnp1 maps of  clr4∆ and the transformants from the deletion of clr4 in mhf2∆ (cen2_inactive) or mhf2+ (cen1_inactive) in fission yeast. We find that heterochromatin is not required for the induction of centromere inactivation in mhf2∆ and the maintenance of neocentromere in mhf2+.

overall_design: Only one biological replicate of these strains were examined by anti-CENP-A/Cnp1 ChIP-seq.

first: Xiangwei

last: He


title: Genome-wide maps of chromatin state centromeric histone H3 variant CENP-A/Cnp1 in the meiotic progeny from the genetic crossings of mhf2+ (cen1_inactive) × mhf2+ (cen1_active) and mhf2∆ (cen1_inactive) × mhf2+ (cen1_active).

summary: We report the high-throughput profiling of histone variant CNEP-A/Cnp1 in fission yeast Schizosaccharomyces pombe. By obtaining 1-10 ng immunoprecipitated DNA, we generated genome-wide CENP-A/Cnp1 maps of  the meiotic progeny from the genetic crossings of mhf2+(cen1_inactive) × mhf2+ (cen1_active) and mhf2∆ (cen1_inactive) × mhf2+ (cen1_active) in fission yeast. We find that endogenous Centromere 1 in mhf2+ is converted to the inactivated Centromere 1 by mhf2∆ through genetic crossing. We also find that Cnp1 spreading into the pericentromeric regions occurs in the wild-type progeny of these two genetic crossings.

overall_design: 8 meiotic progeny (8 viable spores from 2 intact tetrads) from the genetic crossing of mhf2+ (cen1_inactive) × mhf2+ (cen1_active); 14 meiotic progeny (4 viable spores from 1 intact tetrad and 10 meiotic progeny spores from random spores) from the genetic crossing of mhf2∆ (cen1_inactive) × mhf2+ (cen1_active) were examined by anti-CENP-A/Cnp1 ChIP-seq.


title: m6A-RNA mapping, SND1-RNA binding profile mapping and SND1-depletion in KSHV-infected B-lymphocytes

status: Public on Oct 15 2019

city: leeds

first: Agne

last: Antanaviciute

address: University of Leeds, St. James’s University Hospital

institute: University of Leeds

summary: We have mapped m6A sites and endogenous SND1 binding sites in the viral and cellular transcriptome using TREx BCBL1-Rta cells. In addition, we have depleted SND1 in TREx BCBL1-Rta cells and BCBL1 cells and analyzed their RNA expression profile both during latency and lytic replication.

overall_design: Identification of m6A sites in TREx BCBL1-Rta cells at 0h, 8 and 20 h post-lytic reactivation. SND1 transcriptome-wide binding profile in TREx BCBL1-Rta cells at 0h, 8 and 20 h post-lytic reactivation. RNA expression profile in scramble and SND1-depleted cells in both latent and reactivated TREx BCBL1-Rta cells for 24 h. Same RNA expression profile in shRNA scramble and shRNA SND1-depleted BCBL1 cells.

first: Belinda

last: Baquero-Perez

first: Ian

last: Carr

first: Adrian

last: Whitehouse


title: Genome-wide maps of chromatin state (heterochromatin H3K9me2 or centromeric histone H3 variant CENP-A/Cnp1) in heterozygous deletion diploid mhf2∆/+ and the meiotic haploid progeny of heterozygous deletion diploid wip1∆/+, mhf1∆/+ and mhf2∆/+.

summary: We report the high-throughput profiling of histone modification (H3K9me2) or histone variant CNEP-A/Cnp1 in fission yeast Schizosaccharomyces pombe. By obtaining 1-10 ng immunoprecipitated DNA, we generated genome-wide H3K9me2 or CENP-A/Cnp1 maps of heterozygous deletion diploid mhf2∆/+ and the meiotic haploid progeny of heterozygous deletion diploid wip1∆/+, mhf1∆/+ and mhf2∆/+ in fission yeast. We find that centromere inactivation and neocentromere formation occur independently and postzygotically in single depletion of CENP-T-W-X-S.

overall_design: 1 heterozygous deletion diploid mhf2∆/+ and 7 meiotic haploid progeny wip1+, mhf1+ and mhf2+ (wild type alleles) were examined by anti-H3k9me2 ChIP-seq. 10 meiotic haploid progeny wip1∆, mhf1∆ and mhf2∆ were examined by anti-CENP-A/Cnp1 ChIP-seq.


title: Cytosolic phospholipase A2 alpha regulates TLR signaling and migration in metastatic 4T1 cells

status: Public on Sep 26 2019

city: Trondheim

first: Hanna Maja

last: Tunset

state: Trondelag

address: Olav Kyrres gate 9

department: Dept of Circulation and Medical Imaging

institute: NTNU

summary:
We aimed at characterizing the response to reduced cPLA2α activity in metastatic versus non-metastatic cells.
We employed an isogenic murine cell line pair displaying metastatic (4T1) and non-metastatic (67NR) phenotype to investigate the role of cPLA2α on migration. Further, we elucidate the effect of reduced cPLA2α activity on global gene expression in the metastatic cell line
We found that cPLA2α inhibition may inhibit metastasis through an anti-migratory effect, possibly involving Toll-like receptor signaling and type I interferons

overall_design: Subconfluent cells were treated with 15 uM  cPLA2α inhibitor treated or vehicle (DMSO)  for 24 h before RNA isolation.

first: Hanna


title: AhR activation by TCDD (2,3,7,8-Tetrachlorodibenzo-p-dioxin) attenuates Pertussis toxin-induced inflammatory responses by differential regulation of Tregs and Th17 cells through specific targeting by microRNA

city: Columbia

first: Philip

middle: Brandon

last: Busbee

state: SC

address: 6439 Garners Ferry Road

department: Pathology, Microbiology, and Immunology

institute: University of South Carolina School of Medicine

summary: We used microRNA microarrays to identify dysregulated microRNAs in CD4+ T cells isolated from splenocytes of C57BL/6 mice exposed to pertussis toxin (PTX) and treated with TCDD.

overall_design: CD4+ T cells were sorted from splenocytes of mice exposed to PTX and treated with vehicle or TCDD.

first: Zinah

middle: Z

last: Al-Ghezi

first: Mitzi

last: Nagarkatti

first: Prakash


title: The lung-enriched p53 mutants V157F and R158L/P regulate a novel transcriptome in lung cancer

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Lung cancer is the leading cause of cancer-related deaths in the US, and alterations in the tumor suppressor gene TP53 are the most frequent somatic mutation among all histologic subtypes of lung cancer. Mutations in TP53 frequently result in a protein that exhibits not only loss of tumor suppressor capability but also gain of oncogenic function (GOF). The canonical p53 hotspot mutants R175H and R273H, for example, confer upon tumors a metastatic phenotype in murine models of mutant p53. To our knowledge, GOF phenotypes of the less often studied V157, R158, and A159 mutants – which occur with higher frequency in lung cancer compared with other solid tumors – have not been defined. In this study, we aimed to define whether the lung mutants are simply equivalent to full loss of the p53 locus, or whether they additionally acquire the ability to drive new downstream effector pathways. Using a publicly available human lung cancer dataset, we characterized patients with V157, R158, and A159 p53 mutations. Additionally, we show here that cell lines with mutant p53-V157F, p53-R158L, and p53-R158P exhibit a loss of expression of canonical wildtype p53 target genes. Furthermore, these lung-enriched p53 mutants regulate genes not previously linked to p53 function including PLAU. Paradoxically, mutant p53 represses genes associated with increased cell viability, migration, and invasion. These findings collectively represent the first demonstration that lung-enriched p53 mutations at V157 and R158 regulate a novel transcriptome in human lung cancer cells and may confer de novo function.

overall_design: RNA-seq in p53 mutant NCI-H2087 (V157F), NCI-H441 (R158L), and NCI-H2110 (R158P) cells

first: Steven

middle: B

last: McMahon

first: Julie

last: Barta


title: Gene expression during embryonic wound healing of Xenopus laevis after inhibition of production of NO.

city: Vestec by Prague

first: Radek

last: Šindelka

address: Průmyslová 595

country: Czech Republic

institute: Institute of Biotechnology, Czech Academy of Science, v.v.i.

summary: We analyzed the gene expression profile during the first 90 minutes of embryonic wound healing and compared it with embryos with a chronic problem with the production of nitric oxide (NO) (embryos originating from oocytes that were injected with morpholinos against nos1 and nos3) and embryos with an acute problem with the production of NO (embryos incubated in a solution containing TRIM).

overall_design: Embryos at stages 24-26 were injured using forceps (at middle ventral side) and five pieces of the wounded tissue were collected from each replicate.

first: Pavel

last: Abaffy

first: Silvie

last: Tomankova

first: Ravindra

last: Naraine

last: Sindelka


title: Gene expression during embryonic wound healing of Xenopus laevis.

summary: We analyzed the gene expression profile during the first 90 minutes of embryonic wound healing.

overall_design: Embryos at stages 24-26 were injured using forceps (at middle ventral side) and five pieces of wounded tissue were collected from each replicate.


title: Methylome sequencing of Burkholderia pseudomallei D286, H10, PMC2000, R15 and 982

status: Public on Sep 25 2019

city: Kajang

first: Hirzahida

last: Mohd Padil

state: Selangor

address: Bangi

country: Malaysia

institute: Universiti Kebangsaan Malaysia

summary: We report the methylome sequencing and annotation of Burkholderia pseudomallei D286 based on high-throughput profiling using PacBio SMRT technology

overall_design:
SMRT, PacBio sequencing
Submitter states that efforts to obtain raw data files were unsuccessful

first: Nor

last: Mat-Akhir

first: Kar

middle: W

last: Hong

first: Kok

middle: G

last: Chan

first: Mohd

middle: F

last: Mohd-Raih

first: Sheila

last: Nathan


title: Transcriptome profiles in the catkins of two Castanea mollissima cultivars for dissecting the mechanisms of Shorter Catkins Mutation.

first: weitao

last: Mao

state: Beijing

department: Innovation group

institute: BEIJING ACADEMY OF FORESTRY AND POMOLOGY SCIENCES

summary: Chinese Chestnut (Castanea mollissima BL.) has high nutritional and ecological value, so it is widely planted.However, the number of male flowers far exceeds the number of female flowers is an important factor limiting the yield of Chinese chestnut.A naturally occurring mutation in male catkin has been found on a Chinese chestnut tree in the mountains of Beijing, China.This mutant is shorter than the normal catkin.Studies have shown that this mutation can significantly reduce the number of male flowers, promote the differentiation of female flowers, and improve the yield of Chinese chestnut.In this research, we provided the RNA sequencing data of two groups of mutants and normal catkin.The comparative analyses of catkins transcriptomes presented here provides a valuable resource for discovery of genes and networks involved in the regulate the sex of the flower.

overall_design: RNA sequencing of two groups of mutants and normal catkins.

first: Guanglong

last: Hu

first: Weitao


title: Chromatin Loop Extrusion Plays a Fundamental Mechanistic Role in Antibody Class Switching [CSR-HTGTS-Seq]

city: Boston

first: Frederick

last: Alt

state: MA

address: 1 Blackfan Circle

department: PCMM

institute: Boston Children's Hospital

type: Genome variation profiling by high throughput sequencing

summary: In a B lymphocyte immunoglobulin heavy chain locus (IgH), a developmentally assembled V(D)J exon encoding an antibody variable region lies upstream of exons encoding a  constant region (C), allowing generation of IgH chain transcripts and IgM-class antibodies1.  Mouse IgH class switch recombination (CSR) replaces Cwith one of 6 sets of constant region exons (CHs) that lie 100-200kb downstream1.  Each CH is flanked upstream by a promoter, non-coding I-exon, and long repetitive switch (S) region1,2.  Cytokines/activators induce specific I-promoter transcription and activation-induced cytidine deaminase (AID)2,3.  AID is transcriptionally-targeted to initiate DNA breaks in S and activated downstream acceptor S regions, which are joined in deletional orientation to complete CSR4,5.  3’IgH regulatory region (3’IgHRR) enhancers control upstream I promoters and, thereby, CSR via linear competition involving I promoter/3’IgHRR interactions6-11.  Here, we report that synapsis of regulatory elements, S regions and DSBs for CSR is achieved by chromatin loop extrusion.  In naive B cells, 3’IgHRR enhancers and adjacent 3’IgH CTCF-binding elements (CBEs) interact via loop extrusion with the upstream Igh intronic enhancer (iE)/S locale to generate dynamic 200kb 3’Igh basal loop.  In CSR-activated B cells, induced transcription from I-promoters within this basal loop generates dynamic sub-loops that directionally align S and target S regions near the 3’IgHRR for CSR.  In CH12F3 B lymphoma cells, inactivation of the constitutively active I-promoter abrogates looping and CSR to S, while activating transcription, looping, and CSR to upstream S regions.  CBEs inserted upstream of I in convergent orientation with 3’IgH CBEs generate sub-loops that activate inversional S CSR.  In I-promoter-deleted CH12F3 cells, this ectopic CBE-based sub-loop inactivates upstream S region CSR, while transcriptionally activating non-S region sequences adjacent to the inserted CBEs for S synapsis and CSR.  Together, our findings implicate chromatin loop extrusion in the “unprecedented mechanism”5 by which Igh organization in cis promotes orientation-specific CSR DSB joining.

overall_design: We performed CSR-HTGTS-Seq, 3C-HTGTS, GRO-Seq and ChIP-Seq in mature splenic B cells with different stimulation and different mutants of CH12F3 cells to study roles of cohesin-mediated chromatin loop extrusion in IgH class switch recombination.

first: Xuefei

last: Zhang


title: Chromatin Loop Extrusion Plays a Fundamental Mechanistic Role in Antibody Class Switching [GRO-Seq]

summary: In a B lymphocyte immunoglobulin heavy chain locus (IgH), a developmentally assembled V(D)J exon encoding an antibody variable region lies upstream of exons encoding a m constant region (Cm), allowing generation of mIgH chain transcripts and IgM-class antibodies1.  Mouse IgH class switch recombination (CSR) replaces Cmwith one of 6 sets of constant region exons (CHs) that lie 100-200kb downstream1.  Each CH is flanked upstream by a promoter, non-coding I-exon, and long repetitive switch (S) region1,2.  Cytokines/activators induce specific I-promoter transcription and activation-induced cytidine deaminase (AID)2,3.  AID is transcriptionally-targeted to initiate DNA breaks in Sm and activated downstream acceptor S regions, which are joined in deletional orientation to complete CSR4,5.  3’IgH regulatory region (3’IgHRR) enhancers control upstream I promoters and, thereby, CSR via linear competition involving I promoter/3’IgHRR interactions6-11.  Here, we report that synapsis of regulatory elements, S regions and DSBs for CSR is achieved by chromatin loop extrusion.  In naive B cells, 3’IgHRR enhancers and adjacent 3’IgH CTCF-binding elements (CBEs) interact via loop extrusion with the upstream Igh intronic enhancer (iEm)/Sm locale to generate dynamic 200kb 3’Igh basal loop.  In CSR-activated B cells, induced transcription from I-promoters within this basal loop generates dynamic sub-loops that directionally align Sm and target S regions near the 3’IgHRR for CSR.  In CH12F3 B lymphoma cells, inactivation of the constitutively active Ia-promoter abrogates looping and CSR to Sa, while activating transcription, looping, and CSR to upstream S regions.  CBEs inserted upstream of Ia in convergent orientation with 3’IgH CBEs generate sub-loops that activate inversional Sa CSR.  In I-promoter-deleted CH12F3 cells, this ectopic CBE-based sub-loop inactivates upstream S region CSR, while transcriptionally activating non-S region sequences adjacent to the inserted CBEs for S synapsis and CSR.  Together, our findings implicate chromatin loop extrusion in the “unprecedented mechanism”5 by which Igh organization in cis promotes orientation-specific CSR DSB joining.


title: Sustained reprioritization of metabolic pathways is associated with persistence and biofilm formation in non-typeable Haemophilus influenzae

status: Public on Sep 24 2019

city: Columbus

first: Alistair

last: Harrison

state: OH

address: 700 Children's Drive

department: Center for Microbial Pathogenesis

institute: The Research Institute at Nationwide Children's Hospital

summary: We used an in vitro evolved strain of nontypeable Haemophilus influenzae (NTHI)  to examine the metabolic contributions to persistence RNASeq analysis identified 55 transcripts that significantly changed in amount within in vitro biofilms formed by RM33, as compared to the parental strain. Expression of genes encoding all enzymes within the tryptophan and glycogen pathways was significantly increased in biofilms formed by RM33 and the parental strains.  In addition, increases were observed in metabolite transport, adhesin production and DNA metabolism, while we observed pyruvate ato have  a pivotal role  in the metabolic pathways associated with persistence.

overall_design: Gene expression was quantified in triplicate samples of 86-028NP (the parent) and RM33 (the persister strain) that were growing in in vitro biofilms.

first: Rachael

last: Hardison

first: Rachel

middle: M

last: Wallace

first: James

last: Fitch

first: Derek

middle: R

last: Heimlich

first: Megan

last: O'Bryan

first: Robert

middle: P

last: Sebra

first: Laura

last: Dubois

first: Lisa

last: St. John-Williams

first: Peter

last: White

first: M. Arthur

last: Mosely

first: J. Will

last: Thompson

first: Sheryl

last: Justice

first: Kevin

last: Mason


title: Chromatin Loop Extrusion Plays a Fundamental Mechanistic Role in Antibody Class Switching

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

overall_design: Refer to individual Series


title: TET3 regulates cellular identity and DNA methylation in neural progenitor cells

status: Public on Sep 23 2019

city: London

first: Miguel

last: Branco

address: 4 Newark Street

institute: Blizard Institute

summary: TET enzymes oxidize 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC), a process thought to be intermediary in an active DNA demethylation mechanism. Notably, 5hmC is highly abundant in the brain and in neuronal cells. Here we show that Tet3 is highly upregulated during neuronal differentiation and necessary to maintain silencing of pluripotency-associated genes in neural precursor cells (NPCs). Indeed, Tet3 knockdown (KD) in NPCs led to a significant increase in Oct4 and Nanog gene expression, with OCT4-positive cells appearing as cellular aggregates. Moreover, Tet3 KD led to a genome-scale loss of DNA methylation and hypermethylation of a small number of CpGs that are notably located at neurogenesis-related genes and at imprinting control regions (ICRs) of three imprinted genes (Peg10, Zrsr1 and Mcts2). Our results suggest that TET3 plays a pivotal role in maintaining neural stem cell identity and DNA methylation levels in neural precursor cells, and point to a non-catalytic role for TET3 in neural differentiation.

overall_design: Mouse embryonic stem cells containing inducible shRNAs for Tet3 or a non-targetting control were differentiated to neural precursor cells. Knockdown was induced with doxyxycline for 5 days. Genomic DNA was extracted to generate oxRRBS libraries.

first: Mafalda

last: Santiago

first: Claudia

last: Antunes

first: Marta

last: Guedes

first: Michelina

last: Iacovino

first: Michael

last: Kyba

first: Wolf

last: Reik

first: Nuno

last: Sousa

first: Luisa

last: Pinto

first: C

last: Marques


title: Single-cell Transcriptomic Atlas of the Human Retina Identifies Cell Types Associated with Age-Related Macular Degeneration [Seq-Well]

city: New Haven

first: Brian

last: Hafler

state: Connecticut

address: 300 George Street

institute: Yale School of Medicine

summary: Here we perform massively parallel single-cell RNA sequencing (scRNA-seq) of human retinas using two independent platforms, and report the single-cell transcriptomic atlas of the human retina. Using a multi-resolution network-based analysis, we identify all major retinal cell types, and their corresponding gene expression signatures.

overall_design: Refer to individual series

first: M

last: Menon

first: S

last: Mohammadi

first: J

last: Davila-Velderrain

first: B

middle: A

last: Goods

first: T

last: Cadwell

first: Y

last: Xing

first: Rachamimov

last: Stemmer

first: A

middle: K

last: Shalek

middle: C

last: Love

first: K

last: Kellis


title: Distinct Roles of BET Family Members in ERα Enhancer Function and Gene Regulation in Breast Cancer Cells [RNA-seq]

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: Estrogen (E2)-dependent gene regulation mediated by estrogen receptor alpha (ERα) plays a mitogenic role in ER-positive breast cancer cells.  Although clinical applications of selective estrogen receptor modulators (SERMs), which directly interact with ERα to alter ERα activity, have been effective as a first line of treatment for breast cancer patients, a large subset of the patients will develop resistance after prolonged use of SERMs.  Thus, there is a great need to develop alternative therapeutic strategies for SERM-resistant breast cancers.  Here, we describe the potential use of the bromodomain family member protein (BRD) selective bromodomain inhibitor, JQ1, to alter E2-dependent gene expression program and inhibit E2-dependent growth of breast cancer cells.  We show that each family member has partially redundant roles as ERα coregulators that are required for ERα-mediated gene transcription.  Furthermore, we demonstrate the function of BRD3 as a molecular sensor of total BRD activity by the compensatory control of its protein levels.  In addition, BRD3 colocalizes with a subset of ERα binding sites (ERBSs) that are enriched for active enhancer features and associated with highly E2-induced genes.  Collectively, we illustrate a critical role of the BET family members in ERα dependent gene expression.

overall_design:
RNA-seq datasets were generated using MCF-7 cells treated with 100 nM E2 for 3 hours in the presence of 500 nM JQ1 to determine JQ-1-affected E2 responsive gene expression.

Please note that each processed data was generated from both replicates (i.e *rep1 and *rep2 samples) and linked to the corresponding *rep1 sample records.

first: Shino

last: Murakami

first: Rui

last: Li

first: Anusha

last: Nagari

first: Minho

last: Chae

first: Cristel

middle: V

last: Camacho

first: Lee


title: Single-cell Transcriptomic Atlas of the Human Retina Identifies Cell Types Associated with Age-Related Macular Degeneration [Microfluidics]

status: Public on Sep 21 2019

first: Brian

last: Hafler

overall_design: Three replicates of macula and peripheral retinas.

middle: D

middle: S

last: Rachamimov


title: Chromatin Loop Extrusion Plays a Fundamental Mechanistic Role in Antibody Class Switching [ChIP-Seq]

first: Frederick

last: Alt

first: Xuefei

last: Zhang


title: Single-cell Transcriptomic Atlas of the Human Retina Identifies Cell Types Associated with Age-Related Macular Degeneration


title: The impact of pro-inflammatory cytokines on the β-cell regulatory landscape provides insights into the genetics of type 1 diabtes [H3K27ac ChIP-seq]

status: Public on Sep 20 2019

city: Badalona

first: Mireia

last: Ramos-Rodríguez

state: Please Selec

address: Carretera de Can Ruti, camí de les escoles s/n

institute: Germans Trias i Pujol University Hospital and Research Institute

summary: Early stages of type 1 diabetes (T1D) are characterized by local autoimmune inflammation and progressive loss of insulin-producing pancreatic β cells. We show here that exposure to pro-inflammatory cytokines unmasks a striking plasticity of the β-cell regulatory landscape. We expand the repertoire of human islet regulatory elements by mapping stimulus-responsive enhancers linked to changes in the β-cell transcriptome, proteome and 3D chromatin structure. Our data indicates that the β cell response to cytokines is mediated by the induction of novel regulatory regions as well as the activation of primed regulatory elements pre-bound by islet-specific transcription factors. We found that T1D-associated loci are enriched of the newly mapped cis-regulatory regions and identify T1D-associated variants disrupting cytokine-responsive enhancer activity in human β cells. Our study illustrates how β cells respond to a pro-inflammatory environment and implicate a role for stimulus-response islet enhancers in T1D.

overall_design: ChIP-seq of H3K27ac performed in control and cytokine-treated EndoC-βH1 cells and human pancreatic islets from non-diabetic cadaveric donors.

first: Lorenzo

last: Pasquali


title: HIV infection and use of illicit substances promote secretion of semen exosomes that reprogram monocyte morphology

city: Stony Brook

first: Hussein

last: Kaddour

state: NY

address: 100 Nicolls Road

department: Pharmacological Sciences

institute: Stony Brook University

summary:
HIV transmission involves the adhesion to and migration of infected cells, including monocytes across biological barriers comprising extracellular matrix components. Recently, semen exosomes (SE) from HIV uninfected (HIV-) and HIV infected (HIV+) subjects were shown to contain molecules that were adhesive to Jurkat T cells. Since monocyte trafficking across various biological barriers are intensified by HIV and/or illicit substances, such as cocaine, we sought to understand how SE from HIV infected subjects’ comorbid with illicit drug abuse influence monocyte gene expression and behavior. Therefore, a model of U937 monocyte adhesion on collagen-coated surface in the presence and absence of SE from various clinical (HIV-Drug-, HIV-Drug+, HIV+Drug-, and HIV+Drug+) groups was developed. Using this system, we demonstrate by Microarray analysis that SE from different clinical groups reprogramed gene expression profile of monocytes cultured atop collagen.
In line with altered gene expression is increased adhesion of monocytes to collagen following treatment with SE from all clinical groups compared to vehicle. Interestingly, SE from HIV+ subjects’ comorbid with drug abuse potentiated monocyte adhesion to collagen. Mechanistically, SE-Drug and SE-HIV altered monocyte shape, induced actin cytoskeleton reorganization, formation of membrane ruffles and lamellipodia-like structures, as well as focal-adhesion contacts. The cytoskeletal reorganization induced by SE-Drug is associated with impairment of cell motility, while SE-HIV increased cell chemotaxis toward HIV secretome. The observation of SE-Drug and SE-HIV mediated alteration of monocyte transcriptome and cellular behavior reported herein is key to understanding the contribution of exosomes to long-term neuro, vascular, and mucosal perturbations associated with psychostimulants (methamphetamine, cocaine, opioids, and alcohol) comorbidity with HIV infection.

overall_design: Three Biological replicates of U937 cells were treated with vehicle PBS (P) or with semen exosomes from one of the four different clinical groups (A: HIV-Drug-, B: HIV-Drug+, C: HIV+Drug-, and D: HIV+Drug+)

first: Yuan

last: Lyu

first: Steven

last: Kopcho

first: Tyler

last: Panzner

first: Nadia

last: Shouman

first: chioma

last: Okeoma


title: Chromatin Loop Extrusion Plays a Fundamental Mechanistic Role in Antibody Class Switching [3C-HTGTS]


title: Unexpected cross-talk between the pathogen defense mechanisms of apoptosis, necroptosis, and pyroptosis.

city: South San Francisco

first: Rohit

last: Reja

address: 1 DNA Way

institute: Genentech


title: The impact of pro-inflammatory cytokines on the β-cell regulatory landscape provides insights into the genetics of type 1 diabtes [UMI-4C]

overall_design: UMI-4C assays performed in control and pro-inflammatory cytokine-treated human pancreatic islets from non-diabetic cadaveric donors.


title: Regulation of CHD2 expression by a long noncoding RNA is essential for mammalian development

city: Rehovot

first: Igor

last: Ulitsky

address: Hertzl St.

country: Israel

institute: Weizmann Institute of Science

summary: Long noncoding RNAs (lncRNAs) are enriched in regions flanking transcription- and chromatin-associated genes, but the functional importance of such co-location events is largely unclear. Chromodomain helicase DNA binding protein 2 (Chd2) is chromatin remodeller with various reported functions in cell differentiation and DNA damage response. Heterozygous mutations in human CHD2 have been implicated in epilepsy, neurodevelopmental delay, and intellectual disability. Here we show that Chaser, a highly conserved long noncoding RNA transcribed from a region in close proximity to the transcription start site of Chd2 and on the same strand, acts in concert with the CHD2 protein to maintain proper Chd2 expression levels. Loss of Chaser in mice leads to substantially increased levels of Chd2 mRNA and protein in the embryo and in adult tissues, early postnatal lethality in homozygous animals, and severe growth retardation in heterozygotes. Mechanistically, over-production of Chd2 induced by loss of Chaser leads to increased transcriptional interference by inhibiting promoters found downstream of highly expressed genes. We further show that Chaser production represses Chd2 expression  solely in cis, and the phenotypic consequences of Chaser loss are rescued when Chd2 is perturbed as well. Targeting Chaser is thus a potentially viable strategy for increasing CHD2 levels in haploinsufficient individuals.

overall_design: RNA-seq of mEFs from different genetic background with RNA-seq, RIP-seq of CHD2 in Neuro2a cells, Pol2 on mEFs and mESCs

first: Aviv

last: Rom


title: Genome-wide examination of ETS1 genomic occupation from pluripotent to cardiac hESC

city: Suzhou

first: Hang

last: Ruan

state: Jiangsu

address: 199 Ren'ai Road

department: IBMS

institute: Soochow University

summary: Examination of genomic occupation of ETS1 on Day 0, 2, 5, 9 and 14 hESC-derived cardiomyocyte via ChIP-seq.

overall_design: To further unbiasedly evaluate the regulatory potential of ETS1 on hESC-derived cardiomyocyte, we assessed their genomic occupation on Day 0, 2, 5, 9 and 14 via ChIP-seq.

first: Hanshi

last: Xu

first: Li

last: Wang

first: Leng

last: Han


title: Engineering orthogonal signaling pathways reveals the sparse distribtion of protein protein interactions in sequence space [RNA-seq]

city: Cambridge

first: Conor

middle: James

last: McClune

address: 31 Ames St

department: Biology

institute: Massachusetts Institute of Technology

summary: To test the global insulation of selected PhoQ*-PhoP* variants, we used RNA-Seq to examine gene expression in strains carrying one of six different PhoQ-PhoP variant pairs. In each case, cells were grown in medium with either excess or limiting extracellular Mg2+ to repress or stimulate PhoQ, respectively, before harvesting RNA. Each system produced a similar induction of known PhoP-dependent genes. To assess whether a variant PhoQ cross-phosphorylated other response regulators, we took advantage of the fact that, when active, most response regulators autoregulate and promote expression of themselves and their cognate histidine kinase2. Notably, none of the six strains tested showed significant induction of other two-component systems relative to a wild-type control. Similar results are seen for the chimeric pathway AQ4-PhoP4, which was induced with its ligand: trans-zeatin.

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

overall_design: We performed RNAseq on strains containing variants of PhoQP with re-engineered, functional interfaces in order to measure potential interference with other two-component signaling pathways. RNA was harvested from each strain after 30 min induction with low MgSO4 or 30 min repression with high MgSO4. An identical experiment was conducted on the chimeric AQ4-PhoP4 pathway, with induction by trans-zeatin in place of low MgS04.

first: Christopher

last: Voigt

first: Michael

middle: T

last: Laub


title: NODULE INCEPTION recruits the lateral root developmental program for symbiotic nodule organogenesis

city: Cologne

first: Tak

last: Lee

address: Carl-von-Linne weg 10

institute: Max Planck Institute for Plant Breeding Research

summary: In order to better understand the commonalities and differences in lateral root and nodule development, we compared their organogenesis and correlated this with changes in gene expression. To initiate lateral roots in Medicago truncatula we turned 2-day-old seedlings 135°, before returning them to their original axis of growth, while for nodule initiation we applied droplets of Sinorhizobium meliloti on the susceptibility zone of the root.

overall_design: Medicago truncatula mRNA samples from root tissues after 12-72 hours of lateral root initiation. segment of root tissues in 0-168 hours after applying Sinorhizobium meliloti in wild type (jemalong cultivar Jester) was compared with mock treatments. Samples of root segment from cre-1,nin-1 mutants was collected after 12,24 hours after applying Sinorhizobium meliloti and 24 hours for lbd16-1, and lbd16/lbd11 mutants which were also compared with mock treated samples. The mRNA samples from overexpression of LBD11,LBD16 was collected from hairy root transformations of Medicago truncatula

first: Katharina

last: Schiessl

first: Jodi

last: Lilley


title: Single-Cell reconstruction of differentiation trajectory reveals essential dynamics in human cardiac lineage commitment

summary: Transcriptomic profiling of hESC-dreived cardiomyocyte on Day 0, 2, 5, 9, 14 and 60 hESC-derived cardiomyocyte via Single cell RNA-seq.

overall_design: To gain insight into the onset of cardiac lineage commitment, we performed single-cell RNA-sequencing (scRNA-seq) on over 7,500  cells captured across 6 key time points (Day 0, 2, 5, 9, 14 and 60) during in vitro cardiac differentiation of human ESCs, using a newly developed single-cell platform, ICELL8 (Takara). Here, we applied a widely used cardiomyocyte differentiation protocol3  that was reported to produce a population of more than 90% cardiac troponin T (TNNT2)-positive cardiomyocytes.


title: Single cell RNA-seq of intestine from E18.5 Mlkl -/- and Casp8 C362A/C362A Mlkl -/- embryos

summary: Caspase-8 is a protease with both pro-death and pro-survival functions: it is required  for apoptosis induced by death receptors such as TNFR1 (tumour necrosis factor   receptor 1), and it has a critical role in suppressing necroptosis mediated by the   kinase RIPK3 (receptor interacting protein kinase 3) and the pseudokinase MLKL  (mixed lineage kinase-like). Mice lacking caspase-8 display MLKL-dependent   embryonic lethality, as do mice expressing catalytically inactive caspase-8 mutant   C362A. However, Casp8C362A/C362A Mlkl-/- mice die in the perinatal period, whereas   Casp8-/- Mlkl-/- mice are viable, indicating that inactive caspase-8 also has a pro-death   scaffolding function. Here we show that caspase-8 C362A triggers ASC speck   formation and caspase-1-dependent pyroptosis in MLKL-deficient intestinal epithelial   cells (IECs) around embryonic day 18. Pyroptosis contributed to the perinatal lethal   phenotype because a number of Casp8 C362A/C362A Mlkl-/- Casp1-/- mice survived beyond   weaning. Transfection studies suggested inactive caspase-8 adopts a distinct   conformation to wild-type caspase-8, enabling it to engage the caspase-1 adaptor ASC.   Wild-type caspase-8 was found in the Triton X-100 soluble fraction, whereas wild-type   caspase-8 inhibited with the pan-caspase inhibitor emricasan, or inactive caspase-8   mutant C362A, were detected in the insoluble fraction. Moreover, inhibited or   inactive caspase-8 shifted ASC into the insoluble fraction. Perinatal lethality was   recapitulated when expression of caspase-8 C362A was restricted to IECs, but   intriguingly, only in the absence of MLKL. Hence, unanticipated plasticity in death   pathways is revealed such that IECs can undergo caspase-1-dependent death when   caspase-8-dependent apoptosis and MLKL-dependent necroptosis are inhibited.

overall_design: Whole intestines from E18.5 embryos (One E18.5 Mlkl -/- and one Casp8 C362A/C362A Mlkl -/- ) were dissociated into single cells and sequenced.

first: Kim

last: Newton


title: Engineering orthogonal signaling pathways reveals the sparse distribtion of protein protein interactions in sequence space [degenerate_library_sort_seq]

summary:
The specificity of the kinase-regulator interaction is driven by a limited set of interfacial residues in each protein that strongly. To identify combinations of these interface residues that are functional and potentially insulated from existing two-component signaling pathways in E. coli, we constructed a dual library of mutants in which the key, coevolving interface residues of a canonical two-component system, PhoQ and PhoP, were randomized. We used NNS codons to randomize six residues in PhoQ and five residues in PhoP, all of which lie at the interface formed by the two proteins in complex and that are critical to determining partner specificity in all two-component signaling pathways.
To identify functional combinations of residues, we first grew the library of PhoQ-PhoP variants overnight in medium with low Mg2+, which activates PhoQ. Because cells must phosphorylate PhoP to grow when extracellular Mg2+ is limiting, this step enriches for functional PhoQ-PhoP variants. Variants that survived selection in limiting Mg2+ were then subjected to Sort-Seq, using fluorescence-activated cell sorting (FACS) and deep sequencing to quantify the signal responsiveness of variants in the library. To gauge the phosphorylation of PhoP in vivo, we used a fluorescent transcriptional reporter, PmgrB-yfp. In the presence of low extracellular Mg2+, functional PhoQ promotes the phosphorylation of PhoP and the production of YFP, whereas in the presence of high concentrations of Mg2+, PhoQ drives the dephosphorylation of PhoP, limiting the accumulation of YFP). The library was grown in each condition for 6 hours before sorting and sequencing.
To identify variants that are signal responsive and drive YFP production specifically in low Mg2+, we sorted cells from each condition into 8 separate bins and deep sequenced the randomized regions of variants collected in each bin. We then calculated the frequency of each variant in each bin to yield the distributions of individual variants in low and high Mg2+, which were fit to Gaussians. From these fits, we assessed the mean level of YFP in each condition and the fold-induction, or signal responsiveness, of each variant detected in the library.

The 11 codons / amino acids listed in this dataset refer to codons 12, 14, 15, 18, and 19 in PhoP and codons 284, 288, 289, 292, 302, and 303 in PhoQ, in that order.

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

overall_design: Compatability of PhoQ and PhoP variants were analyzed by deep sequenceing bins sorted by fluorescence under different Mg2+ conditions


title: Expression data from NASH-induced mouse liver treated with isorhamnetin

status: Public on Sep 19 2019

city: Tsukuba

first: Munkhzul

last: Ganbold

state: Ibaraki Prefecture

address: 1 Chome-1-1 Tennodai

institute: AIST-University of Tsukuba Open Innovation Laboratory for Food and Medicinal Resource Engineering (FoodMed-OIL)

summary:
Gene expression profiling reveals a potential role of isorhamnetin in the mitigation of NASH features including steatosis, liver injury, and fibrosis
Microarray gene expression profiling was conducted for technical replicates of healthy liver as control (CTL), NASH-induced (NASH), NASH-induced treated with isorhamnetin for 14 days (50 mg/kg of body weight) (NASH+ISO) liver tissues to identify its effect in the regulation of pathways involved in pathologic features of NASH.

overall_design: Total RNA was extracted from liver tissue stocked at -80°C using Isogen (Nippon Gene Co. Ltd., Toyama, Japan). The integrity and the dosage of RNA was quantified using NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA). RNA samples were prepared for gene expression profiling analysis with GeneChip® 3' Expression Arrays using 3' IVT PLUS Reagent Kit (Affymetrix Inc., Santa Clara, CA, USA). One hundred ng of total RNA from each sample was used to generate amplified and biotinylated complementary RNA (cRNA) from poly (A) RNA in a total RNA sample according to the user manual. IVT Incubation time was 16 hour. GeneAtlas® Hybridization, Wash and Stain Kit was used for hybridizing 3' IVT Array Strips according to the user manual. Mouse genome array strip (MG-430 PM) was hybridized for 16 hours in a 45°C incubator, washed and stained and finally imaging was done with the GeneAtlas Fluidics and Imaging Station.


title: CASP8 C362A KI MLKL KO e16.5 intestine RNAseq

summary: Caspase-8 is a protease with both pro-death and pro-survival functions: it is required for apoptosis induced by death receptors such as TNFR1 (tumor necrosis factor receptor 1) 1, and it has a critical role in suppressing necroptosis mediated by the kinase RIPK3 (receptor interacting protein kinase 3) and the pseudokinase MLKL (mixed lineage kinase-like) 2-4.  Mice lacking caspase-8 display MLKL-dependent embryonic lethality 4, as do mice expressing catalytically inactive caspase-8 mutant C362A.  However, Casp8C362A/C362A Mlkl-/- mice die in the perinatal period, whereas Casp8-/- Mlkl-/- mice are viable 4, indicating that inactive caspase-8 also has a pro-death scaffolding function.  Here we show that inactive caspase-8 activates pyroptosis in MLKL-deficient intestinal epithelial cells around embryonic day 18, triggering the formation of ASC specks.  Accordingly, intestinal atrophy and perinatal lethality in Casp8C362A/C362A Mlkl-/- mice was prevented by loss of caspase-1.  In transfection studies, inactive caspase-8 mutants C362A or C362S were found in both the triton X-100 insoluble and soluble fractions, whereas wild-type caspase-8 existed only in the soluble fraction.  Moreover, inactive caspase-8 shifted co-transfected ASC into the insoluble fraction, whereas wild-type caspase-8 did not.  Thus, a defense mechanism is revealed that would allow intestinal epithelial cell death in the face of pathogens expressing virulence factors to inhibit caspase-8-dependent apoptosis and necroptosis.

overall_design: RNA was extracted from e16.5 mouse intestine for the following genotypes - Casp8 wildtype MLKL knockout (Casp8 WT MLKL KO), Casp8 MLKL double knockout (Casp8 KO MLKL KO), and Casp8 C362A knockin MLKL knockout (Casp8 KI MLKL KO).


title: The impact of pro-inflammatory cytokines on the β-cell regulatory landscape provides insights into the genetics of type 1 diabtes [ATAC-seq]

first: Mireia

last: Ramos-Rodríguez

overall_design: ATAC-seq performed in control and cytokine-treated EndoC-βH1 cells (3 replicates) and human pancreatic islet preparations (3 replicates) from non-diabetic cadaveric donors.

first: Lorenzo

last: Pasquali


title: Tox4 Modulates Cell Fate Reprogramming to iPS Cells and Direct Reprogramming

city: Leuven

first: Vincent

last: Pasque

address: Herestraat 49 bus 804

department: Development and Regeneration

country: Belgium

institute: KU Leuven

overall_design: Refer to individual Series