title: Genomic Analysis Reveals Pleiotropic Alleles at EDN3 and BMP7 Involved in Chicken Comb Color and Egg Production

city: Beijing

first: Xuemei

last: Deng

state: N/A = Not Applicable

address: No.2, Yuan Ming Yuan West Road, Haidian District

department: Department of animal breeding and genetics

institute: China Agricultural University

summary: Dongxiang blue-shelled chicken, an indigenous chicken breed in China, has segregated significantly for the dermal hyperpigmentation phenotype. Two lines of the chicken have been divergently selected with respect to comb color for over 20 generations. The recent selection has also resulted in a significant difference in egg production. The red comb line (RCL) chicken produces significantly higher number of eggs than that by the dark comb line (DCL) chicken. The objective of this study was to explore potential mechanisms involved in the relationship between comb color and egg production among chickens. We performed genome-wide association study to identify candidate genes associated with chicken comb color using SNP array data, and we conducted selective sweep analysis to identify putative regions of selection harboring pleiotropic genes affecting both comb color and egg production.

overall_design: Aﬀymetrix Axiom 600 K Chicken Genotyping Array were performed according to the manufacturer's directions on DNA extracted from brachial veins of chickens.  A total of 178 female chickens were  used in the study.

first: Xianggui

last: Dong


title: Amplicon of Single-Cell Genotyping of Transcriptomes

status: Public on Jun 01 2019

city: New York

first: Kyu-Tae

last: Kim

state: New York

address: 101 Avenue of the Americas

country: USA

institute: New York Genome Center

summary: Somatic cancer driver mutations may result in distinctly diverging phenotypic outputs. Thus, a common driver lesion may result in cancer subtypes with distinct clinical presentations and outcomes. The diverging phenotypic outputs of mutations result from the superimposition of the mutations with distinct progenitor cell populations that have differing lineage potential. However, our ability to test this hypothesis has been challenged by currently available tools. For example, flow cytometry is limited in its inability to resolve lineage commitment of early progenitors. Single-cell RNA sequencing (scRNA-seq) may provide higher resolution mapping of the early progenitor populations as long as high throughput technology is available to sequence thousands of single cells. Nevertheless, high throughput scRNA-seq is limited in its inability to jointly and robustly detect the mutational status and the transcriptional profile from the same cell.  To overcome these limitations, we propose the use of scRNA-seq combined with targeted mutation sequencing from transcrptional read-outs.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We apply this method to study myeloid neopasms, in which the comlex process of hematopoiesis is corrupted by mutated stem and progenitor cells.

first: Anna

middle: S

last: Nam

first: Ronan

last: Chaligne

first: Peter

last: Smibert

first: Dan

middle: A

last: Landau


title: Single-Cell Genotyping of Transcriptomes

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Nascent transcriptome of Xenopus laevis embryos at mid-blastula transition (MBT) stages

status: Public on May 31 2019

city: Philadelphia

first: Matthew

last: Good

state: PA

address: 421 Curie Blvd

department: Cell and Developmental Biology

institute: University of Pennsylvania

summary: To validate that EU-RNA imaging provides a direct readout of wide-spread zygotic transcription, we sought to identify the nascent transcriptome using RNA-seq. We micoinjected 5-ethynyl uridine (EU) into 1-cell Xenopus embryos, isolated total RNA from embryos at mid-blastula transition (MBT), biotinylated EU-RNA and purified it to generate cDNA libraries for sequencing. Total RNA from normal embyros were used as control. We found over 25,000 nascent genes in this EU-RNA dataset at mid-ZGA. The nascent transcriptome dataset captures nearly 90% of the transcripts present in the whole-embryo dataset and with similar or better read-depth, indicating that our EU-RNA imaging is truly representative of wide-spread zygotic transcription. Furthermore, of the known zygotic genes that are most highly induced at MBT, we detected all of them and at much higher levels than in the whole-embryo dataset. These results show that our labeling captures the nascent zygotic transcriptome. We found ~ 4-fold higher sensitivity for nascent transcripts in the EU-RNA dataset compared to the whole embryo dataset, and as excepted we did not detect thousands of maternal-only transcripts in the nascent dataset. Together, these results suggest that EU-labeling provides a visual readout of bona fide nascent zygotic transcripts.

overall_design: Duplicates for nascent EU-RNA from EU-injected embryos and total RNA from normal embryos, respectively

first: Hui

last: Chen

middle: C


title: RNA-seq of Single-Cell Genotyping of Transcriptomes


title: Interferon Regulatory Factor 8 (IRF8) Deficiency Promotes Osteoclast Transcriptional Program

city: Baltimore

first: Vivek

last: Thumbigere Math

state: MD

address: 650 W Baltimore Street

department: Periodontics

institute: Universityof Maryland

summary: Irf8 functions as negative regulator of osteoclastogenesis. Genetic deletion of Irf8 in mice results in osteoporosis, a low bone mass state caused by increased osteoclast activity. However, the effects of Irf8 ablation on genome wide regulation of osteoclast-specific genes is unknown. We performed RNA-seq analysis of Irf8-/- and Irf8+/+ bone marrow macrophages (BMMs) prior to (day 0) and after RANKL treatment (day 4 and day 8). Additionally, we have identified a novel IRF8 mutation in humans, that is associated with increased osteoclast activity and susceptibility to Multiple Idiopathic Cervical Root Resorption (MICRR). To gain insights into the functional consequences of human IRF8 mutation (hIRF8G388S) on osteoclastogenesis, we performed RNA-seq analysis of Irf8-/-   BMMs transduced with hIRF8WT, hIRF8G388S, and a larger deletion construct hIRF8379-389, followed by RANKL treatment. Comparative studies in Irf8-/- and hIRF8G388S cells show that IRF8 deficiency promotes significant enhancement of osteoclast-specific transcripts.

overall_design: RNA-seq analysis of transcriptional changes in BMMs stimulated with MCSF (day 0) and MCSF plus RANKL (day 4 and day 8). Both male and female mice and cells obtained from both genders were analyzed in this study.

last: Thumbigere-Math

first: Mahesh

last: Bachu

first: Stephen

last: Brooks


title: DOT1L inhibition reveals a distinct subset of enhancers dependent on H3K79 methylation (ChIP-seq)

status: Public on May 30 2019

city: Oxford

first: Thomas

last: Milne

address: John Radcliffe Hospital, Headington

department: MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Enhancer elements are a key regulatory feature of many important genes. Several general features including the presence of specific histone modifications are used to demarcate potentially active enhancers. Here we reveal that putative enhancers marked with H3 lysine 79 (K79) di or trimethylation (me2/3) (which we name H3K79me2/3 enhancer elements or KEEs) can be found in multiple cell types. Mixed lineage leukemia gene (MLL) rearrangements (MLL-r) such as MLL-AF4 are a major cause of incurable acute lymphoblastic leukemias (ALL). Using the DOT1L inhibitor EPZ-5676 in MLL-AF4 leukemia cells, we show that H3K79me2/3 is required for maintaining chromatin accessibility, histone acetylation and transcription factor binding specifically at KEEs but not non-KEE enhancers. We go on to show that H3K79me2/3 is essential for maintaining enhancer-promoter interactions at a subset of KEEs. Together, these data implicate H3K79me2/3 as having a functional role at a subset of active enhancers in MLL-AF4 leukemia cells.

overall_design: ChIP-seq

first: Laura

last: Godfrey

first: Nicholas

middle: T

last: Crump

first: I-Jun

last: Lau


title: In vivo gene signature of human skin with CO2 laser treatment

status: Public on May 28 2019

first: Luis

middle: Andres

last: Garza

address: 1550 Orleans St. Suite 204 CRBII Koch

department: Dermatology

institute: Johns Hopkins School of Medicine

summary:
How developmental programs reactivate in regeneration is a fundamental question in biology. We addressed this question through the study of Wound Induced Hair follicle Neogenesis (WIHN), an adult organogenesis model where stem cells regenerate entirely new hair follicles de novo following deep wounding. The exact mechanism is uncertain. Here we show that self-noncoding dsRNA activates the anti-viral receptor TLR3 to induce intrinsic retinoic acid (RA) synthesis in a gradient that predicts new hair follicle formation after wounding in mice. Additionally, in humans, rejuvenation lasers induce gene expression signatures for dsRNA and RA, with measurable increases in intrinsic RA synthesis. These results demonstrate a novel stimulus for retinoic acid synthesis by non-coding dsRNA, relevant to their broad functions in development and immunity.
The goal of this study is to investigate whole genome analysis in human skin with CO2 laser treatment, which leads to enhanced skin rejuvenation. Under Hopkins IRB (IRB00028768), 17 Caucasian women Fitzpatrick types I-III with average age of 55 and moderate to severe baseline photoaging were enrolled. Laser treatments and biopsy schedule were as listed, with treatments occurring both to the arm, and arm biopsies used for gene expression data listed.

overall_design: Analysis was performed on 32 skin samples from 16 individuals, of which 16 were control biological replicates and 16 were matched laser-treated biological replicates.


title: DOT1L inhibition reveals a distinct subset of enhancers dependent on H3K79 methylation (Capture-C)

overall_design: Next generation Capture-C


title: DOT1L inhibition reveals a distinct subset of enhancers dependent on H3K79 methylation (ATAC-seq)

overall_design: ATAC-seq


title: Single-cell analysis of cardiogenesis reveals basis for organ level developmental defects

status: Public on May 27 2019

city: San Francisco

first: Deepak

last: Srivastava

state: California

address: 1650 Owens Street

department: Cardiovascular Disease

institute: J. David Gladstone Institutes

summary: We employed single-cell RNA sequencing to interrogate early cardiac progenitor cells as they become specified during normal and Hand2-deficient cardiogenesis, to understand how dysregulation of specific cellular sub-populations can have catastrophic consequences.

overall_design: Examination of single cell transcriptomes from cardiac progenitors captured at E7.75, E8.25 and E9.25 from Wild type (WT) and Hand2-null mouse embryos.  At least 2 biological replicate embryos were analyzed per time point, per condition.

first: Tarja

middle: Y

last: de Soysa

first: Casey

last: Gifford


title: RNA sequencing in human GBM stem cells with Myc knockdown and PARP inhibitor treatment

city: Minneapolis

first: Jianfang

last: Ning

state: Minnesota

address: 530 Masonic Cancer Research Building, 425 East River Parkway

department: Neurosurgery

institute: University of Minnesota

summary: This experiment is to examine the effect of PARP inhibitor and Myc shRNA knockdown on transcriptome profiles in MYC-amplified human GBM stem cells MGG4.

overall_design: There are totally 4 samples. GBM cell MGG4 expressing scramble shRNA or shRNA targeting Myc were grown in doxycycline (Dox, 1 mg/ml) for 6 days, treated with olaparib (Ola, 10 microM) or DMSO for 24h, and harvested for RNA extraction, followed by RNA sequencing

first: Jian-Fang

first: Monica

last: Stanciu

first: Melissa

middle: R

last: Humphrey

first: Joshua

last: Gorham

first: Hiroko

last: Wakimoto

first: Reiko

last: Nishihara

first: Jacqueline

last: Lees

first: Lee

last: Zou

first: Robert

middle: L

last: Martuza

first: Hiroaki

first: Samuel

middle: D

last: Rabkin


title: Robust elimination of genome-damaged cells safeguards against brain somatic aneuploidy following Knl1 deletion

status: Public on May 25 2019

city: Ann Arbor

first: Kenneth

last: Kwan

state: MI

address: 109 Zina Pitcher Pl

department: MBNI & Human Genetics

institute: University of Michigan

summary: The brain is a genomic mosaic shaped by cellular responses to genome damage. Here, we manipulate somatic genome stability by conditional Knl1 deletion from embryonic mouse brain. KNL1 mutations cause microcephaly and KNL1 mediates the spindle assembly checkpoint, a safeguard against chromosome missegregation and aneuploidy. We find that following Knl1 deletion, segregation errors in mitotic neural progenitor cells give rise to DNA damage on the missegregated chromosomes. This triggers rapid p53 activation and robust apoptotic and microglial phagocytic responses that extensively eliminate cells with somatic genome damage, thus causing microcephaly. By leaving only karyotypically normal progenitors to continue dividing, these mechanisms provide a second safeguard against brain somatic aneuploidy. Without Knl1 or p53-dependent safeguards, genome-damaged cells are not cleared, alleviating microcephaly, but paradoxically leading to total pre-weaning lethality. Thus, mitotic genome damage activates robust responses to eliminate somatic mutant cells, which if left unpurged, can impact brain and organismal fitness.

overall_design: We sequenced a total of 16 samples of rRNA-depleted RNA from E15.5 mouse cerebral cortex. A total of 15 mice were used and 16 UMI RNA-seq libraries were generated. 7 samples were controls (wild type or heterozygote), 5 samples were hGFAP-Cre Knl1 (Casc5) conditional KO, and 4 samples were hGFAP-Cre Knl1/Trp53 double conditional KO.

first: Lei

last: Shi

first: Adel

last: Qalieh

first: Mandy

last: Lam


title: DOT1L inhibition reveals a distinct class of enhancers dependent upon H3K79 methylation

first: Thomas

last: Milne


title: Distinct modes of mitochondrial metabolism uncouple T cell differentiation and function

status: Public on Jun 03 2019

city: New Haven

first: Jun

last: Zhao

state: CT

address: 300 George Street

department: Pathology/Immunology

institute: Yale University

summary: RNA-sequencing results for cells expressing sgRNA targetting Slc25a1, Slc25a11, or an empty vector control.  WT control cells compared to Sdhc cKO.

overall_design: 12 samples.

first: Richard

last: Flavell

first: Joseph

last: Craft


title: Satb1 integrates DNA sequence, shape, motif density and torsional stress to selectively bind a subset of putative targets in nucleosome-dense regions of the genome

city: Stanford

first: Jan

last: Liphardt

address: 443 Via Ortega, Shriram Center 020

department: Bioengineering

institute: Stanford university

summary: Satb1 (Special AT-rich sequence binding protein 1) coordinates chromatin architecture and regulates a diverse set of cellular and developmental processes. It is not yet clear how Satb1 selects it targets throughout the genome and which cellular parameters modulate its binding landscape. We have used single molecule live cell imaging and deep sequencing to quantify the arrangement of SatB1 molecules in the living nucleus and relate those spatial patterns to specific genomic features. We found that Satb1 preferentially binds to nucleosome dense regions and can access consensus motifs embedded in nucleosomes, features that epitomize 'pioneer' factors. Super-resolution live cell microscopy paired with deep sequencing showed that Satb1 binds iteratively to a set of closely clustered binding sites in the nucleus, and that binding is highly cooperative in regions with high motif density. Further, we observed that Satb1 uses DNA shape information from motif-flanking regions to narrow its binding spectrum. Satb1/DNA interactions were mechanosensitive. Increasing negative torsional stress enhanced binding and Satb1 stabilized base unpairing regions (BURs) against melting by molecular machines such as topoisomerases. Indeed, the ability of a small number of 'master' regulators to control diverse biological programs suggests that these regulators must use a multiparameter, combinatorial logic to select the cell-type and temporally appropriate chromatin state

overall_design: Analysis of the interaction of Satb1 and Chromatin by coupling various genomics tools and high resolution imaging

first: Quanming


title: Transcriptomic analysis of Streptococcus pyogenescolonizing the vaginal mucosa identifies hupY, an MtsR-regulated adhesin involved in heme utilization

city: Chicago

first: Yan

last: Li

state: IL

address: 900 East 57th St.

department: Center for Research Informatics

institute: The University of Chicago

summary: Streptococcus pyogenes (Group A Strep, GAS) is a serious human pathogen with the ability to colonize mucosal surfaces such as the nasopharynx and vaginal tract, often leading to infections such as pharyngitis and vulvovaginitis. We present genome-wide RNASeq data showing the transcriptomic changes GAS undergoes during vaginal colonization. These data reveal that the regulon controlled by MtsR, a master metal regulator, is activated during vaginal colonization. This regulon includes two genes highly expressed during vaginal colonization, hupYZ. Here we show that HupY binds heme in vitro, affects intracellular concentrations of iron, and is essential for proper growth of GAS using hemoglobin or serum as the sole iron source. HupY is also important for murine vaginal colonization of both GAS and the related vaginal colonizer and pathogen, Streptococcus agalactiae (Group B Strep, GBS). These data provide essential information on the link between metal regulation and mucosal colonization in both GAS and GBS.

overall_design: RNASeq data from WT GAS samples taken from liquid culture or the murine vaginal tract

first: Laura

last: Cook

first: Nilanjana

last: Chatterjee

first: Jorge

last: Andrade

first: Michael

last: Federle

first: Zehava

last: Eichenbaum


title: Iron-dependent H3K9me demethylation during B cell activation and proliferation

status: Public on May 24 2019

city: Shanghai

first: Yuhang

last: Jiang

address: 320 Yueyang Road

department: Institute of Health Sciences

country: China

institute: Shanghai Institutes for Biological Sciences, CAS

summary: To explore whether iron is required for BCR-induced H3K9 demethylation during B cell activation, we performed ChIP-seq to check the H3K9me2 modification in control (iron-normal) and iron-deficient B cells

overall_design: Examination of H3K9me2 in control B cells,control B cells with anti-IgM stimulation, iron-deficient B cells with anti-IgM stimulation

first: Xiaoren

last: Zhang


title: CD248 knockdown in in vitro differentiated adipocytes exposed to hypoxia

status: Public on May 23 2019

city: Stockholm

first: Paul

last: Petrus

address: Hälsovägen 7

country: Sweden

institute: Karolinska intitute

summary:
Human adipose tissue derived stem cells were differentiated to adipocytes in vitro. At the end of differentiation, cells were treated with siRNA targeting CD248 followed by exposure to 1% oxygen levels.
Microarray analysis were performed to identify differentially regulated genes.

overall_design: The experiment provides information regarding the genes differentially expressed by CD248 knock down and how the response to hypoxia is influenced by reduced CD248 levels. Cells were lysed for RNA at the end of differentiation.

first: Mikael

last: Rydén


title: Hcr1/eIF3j is a 60S ribosomal subunit recycling accessory factor in vivo

city: Bethesda

first: Nicholas

last: Guydosh

address: 8 Center Dr, Bldg 8, 220

department: NIDDK

institute: National Institutes of Health

summary: Hcr1/eIF3j is a sub-stoichiometric subunit of eukaryotic initiation factor 3 (eIF3) that can dissociate the post-termination 40S ribosomal subunit from mRNA in vitro. We examined this ribosome recycling role in vivo by ribosome profiling and reporter assays and found that loss of Hcr1 led to reinitiation of translation in 3’UTRs, consistent with a defect in recycling. However, the defect appeared to be in recycling of the 60S subunit, rather than the 40S subunit, because reinitiation did not require an AUG codon and was suppressed by overexpression of the 60S dissociation factor Rli1/ABCE1. Consistent with a 60S recycling role, overexpression of Hcr1 could not compensate for loss of 40S recycling factors Tma64/eIF2D and Tma20/MCT-1. Intriguingly, loss of Hcr1 triggered higher expression of RLI1 via an apparent feedback loop. These findings suggest Hcr1/eIF3j is recruited to ribosomes at stop codons and may coordinate the transition to a new round of translation.

overall_design: 25 biological samples are included in the study for ribosome footprinting and mRNA-Seq. These include wild-type and combination knockouts of Hcr1 and mutations of other eIF3 subunits and known ribosome recycling factors.

first: David

middle: J

last: Young


title: A single-nucleus RNA-sequencing pipeline to decipher the molecular anatomy and pathophysiology of human kidneys

city: La Jolla

first: Kun

address: 9500 Gilman Drive

institute: UCSD

summary: Defining cellular and molecular identities within the kidney is necessary to understand its organization and function in health and disease. Here we demonstrate a reproducible method with minimal artifacts for single-nucleus Droplet-based RNA sequencing (snDrop-Seq) that we use to resolve thirty distinct cell populations in human adult kidney. We define molecular transition states along more than ten nephron segments spanning two major kidney regions. We further delineate cell type-specific expression of genes associated with chronic kidney disease, diabetes and hypertension, providing insight into possible targeted therapies. This includes expression of a hypertension-associated mechano-sensory ion channel in mesangial cells, and identification of proximal tubule cell populations defined by pathogenic expression signatures. Our fully optimized, quality-controlled transcriptomic profiling pipeline constitutes a tool for the generation of healthy and diseased molecular atlases applicable to clinical samples.

overall_design:
Single-nucleus (sn)Drop-seq was used to generate RNA expression estimates across two kidney regions (cortex and medulla), 15 different individuals, 7 different tissue processing methods, and from tissues acquired from two different institutions (Washington University and University of Michigan through KPMP consortium).
From the resulting ~18,000 sequenced nuclei passing QC filtering (>400 <5000 non-MT genes detected, >50 post-QC nuclei per library, >30 nuclei per cluster), we identified 30 different cell populations (see supplementary file UCSD-WU_Single_Nuclei_Cluster_Annotations.csv).

first: Blue

middle: B

last: Lake

first: Song

last: Chen

first: Masato

last: Hoshi

first: Nongluk

last: Plongthongkum

first: Sanjay

last: Jain


title: In vitro gene signature of cultured adult keratinocytes stimulated by all trans retinoic acid (atRA) and/or Poly I:C

status: Public on May 22 2019

first: Luis

last: Garza

summary:
How developmental programs reactivate in regeneration is a fundamental question in biology. We addressed this question through the study of Wound Induced Hair follicle Neogenesis (WIHN), an adult organogenesis model where stem cells regenerate entirely new hair follicles de novo following deep wounding. The exact mechanism is uncertain. Here we show that self-noncoding dsRNA activates the anti-viral receptor TLR3 to induce intrinsic retinoic acid (RA) synthesis in a gradient that predicts new hair follicle formation after wounding in mice. Additionally, in humans, rejuvenation lasers induce gene expression signatures for dsRNA and RA, with measurable increases in intrinsic RA synthesis. These results demonstrate a novel stimulus for retinoic acid synthesis by non-coding dsRNA, relevant to their broad functions in development and immunity.
Hand keratinocytes were treated with atRA (0.1 uM) and/or Poly I:C (0.1 ug/ml). RNA was extracted and sent for microarray analysis

overall_design: Keratinocytes were isolated from one source of human hand (dorsal palm). Cells were cultured in KGM-GOLD (Keratincoytes growth media from Lonza) supplemented with ROCK inhibitor (10 uM; Y-27632) and treated with atRA (0.1 uM) for 2 days and Poly I:C (0.1 ug/ml) for 3 days. Total RNAs were extracted from the three treatments plus one control and sent for microarray analysis

first: Ruosi


title: In vivo gene signature of TLR3KO mice stimulated by ethanol (EtOH) or all trans retinoic acid (atRA) treatment

summary:
How developmental programs reactivate in regeneration is a fundamental question in biology. We addressed this question through the study of Wound Induced Hair follicle Neogenesis (WIHN), an adult organogenesis model where stem cells regenerate entirely new hair follicles de novo following deep wounding. The exact mechanism is uncertain. Here we show that self-noncoding dsRNA activates the anti-viral receptor TLR3 to induce intrinsic retinoic acid (RA) synthesis in a gradient that predicts new hair follicle formation after wounding in mice. Additionally, in humans, rejuvenation lasers induce gene expression signatures for dsRNA and RA, with measurable increases in intrinsic RA synthesis. These results demonstrate a novel stimulus for retinoic acid synthesis by non-coding dsRNA, relevant to their broad functions in development and immunity.
The goal of this experiment is to investigate the profile of gene expression rescued by atRA in TLR3KO mice.

overall_design: Two TLR3KO mice at telogen stage were wounded on back skin with 1.2 cm2 size. Next day (wound day 1-WD1), 30 ul of EtOH or 0.1 ug/30 ul of atRA was locally treated onto wounded skin of one TLR3KO mouse.


title: Chromatin rewiring mediates programmed evolvability via aneuploidy

first: Suzanne

middle: M

last: Noble

state: CA

address: 513 Parnassus Ave., Box 0414

institute: UCSF

summary: Eukaryotes have evolved elaborate mechanisms to ensure that chromosomes segregate with high fidelity during mitosis and meiosis, and yet specific aneuploidies can be adaptive during environmental stress.  Here, we identify a chromatin-based system for inducible aneuploidy in a human pathogen. Candida albicans utilizes chromosome missegregation to acquire resistance to antifungal drugs and for ploidy reduction after mating.  We discovered that the ancestor of C. albicans and two related pathogens evolved a variant of histone H2A that lacks the conserved phosphorylation site for Bub1 kinase, a key regulator of chromosome segregation. Using engineered strains, we show that expression of this variant controls the rates of aneuploidy and antibiotic resistance in this species.  Moreover, whole genome chromatin precipitation analysis reveals that CENP-A/Cse4, the histone H3 that specifies centromeres, is depleted from tetraploid mating products and virtually eliminated from cells exposed to aneuploidy-promoting cues.  Thus, changes in chromatin regulation can confer the capacity for rapid evolution in eukaryotes.

overall_design: ChIP-seq in diploid and tetraploid C. albicans to understand the role of histone variants in chromosome loss.

first: Hiten

last: Madhani

first: Jahan-Yar

last: Parsa

first: Jordan

last: Burke


title: Noncoding dsRNA induces retinoic acid synthesis to stimulate hair follicle regeneration via TLR3

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

How developmental programs reactivate in regeneration is a fundamental question in biology. We addressed this question through the study of Wound Induced Hair follicle Neogenesis (WIHN), an adult organogenesis model where stem cells regenerate de novo hair follicles following deep wounding. The exact mechanism is uncertain. Here we show that self-noncoding dsRNA activates the anti-viral receptor toll like receptor 3 (TLR3) to induce intrinsic retinoic acid (RA) synthesis in a pattern that predicts new hair follicle formation after wounding in mice. Additionally, in humans, rejuvenation lasers induce gene expression signatures for dsRNA and RA, with measurable increases in intrinsic RA synthesis. These results demonstrate a potent stimulus for RA synthesis by non-coding dsRNA, relevant to their broad functions in development and immunity.

overall_design: Refer to individual Series


title: Genome-wide strategies reveal downstream target genes of Npas4l associated with cardiovascular development in zebrafish [RNA-Seq 2]

status: Public on May 21 2019

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

summary: The development of a vascular network is essential to nourish tissues and sustain organ function throughout life.  Endothelial cells (ECs) are the building blocks of blood vessels, yet our understanding of EC specification in vertebrates remains incomplete.  cloche/npas4l mutants have broadly been used as an avascular model in zebrafish, but little is known about the molecular mechanism of action of Npas4l.  Here, to identify the direct and indirect target genes of this transcription factor, we combined complementary genome-wide approaches, including transcriptome analyses and chromatin immunoprecipitation (ChIP).  The cross-analysis of these datasets indicate that Npas4l functions as a master regulator by directly inducing a wave of transcription factor genes crucial for hematoendothelial specification in vertebrates, including etv2, tal1, and lmo2.  We identified additional target genes acting downstream of npas4l and investigated the function of a subset of them using CRISPR/Cas9 technology.  Phenotypic characterization of tspan18b mutants reveals a novel role for tspan18b in developmental angiogenesis, confirming the reliability of the datasets generated.  Collectively, these data represent a useful resource for future studies aimed to investigate novel genes with a potential role in vascular development and EC fate determination in vertebrates.

overall_design: RNA-seq examination of Tg(hsp70l:loxP-STOP-loxP-npas4l-GGGGGLSRS-P2A-mCherry)bns298 zebrafish embryos at 6-somite stage, in duplicates.

first: Michele

last: Marass

first: Arica

last: Beisaw

first: Claudia

last: Gerri

first: Francesca

last: Luzzani

first: Nana

last: Fukuda

first: Stefan

last: Günther

first: Sven

last: Reischauer

first: Didier

last: Stainier


title: Genome-wide strategies reveal downstream target genes of Npas4l associated with cardiovascular development in zebrafish [ATAC-Seq]

overall_design: ATAC-seq examination of wild type and npas4lbns297/bns297 zebrafish embryos.


title: Oncogenic biogenesis of pri-miR-17~92

status: Public on May 20 2019

city: Montreal

first: Ariel

middle: Octavio

last: Donayo

state: Quebec

address: 3655 Promenade Sir William Osler Room 707

department: Goodman Cancer Research Centre

country: Canada

institute: McGill University

type: Non-coding RNA profiling by high throughput sequencing

summary: The microRNAs encoded by the miR-17~92 polycistron are commonly overexpressed in cancer and orchestrate a wide range of oncogenic functions. Here, we identify a novel mechanism for miR-17~92 oncogenic function through the disruption of endogenous miRNA processing. We show that upon oncogenic overexpression of the miR-17~92 primary transcript (pri-miR-17~92), the Microprocessor complex remains associated with partially processed intermediates that aberrantly accumulate. These intermediates reflect a series of hierarchical and conserved steps in the early processing of the pri-miR-17~92 transcript. Encumbrance of the Microprocessor by miR-17~92 intermediates leads to the broad, but selective, downregulation of co-expressed polycistronic miRNAs, including miRNAs derived from tumour suppressive miR-34b/c, and from the Dlk1-Dio3 polycistrons. We propose that the newly identified steps of polycistronic miR-17~92 biogenesis contribute to the oncogenic re-wiring of gene regulation networks. Our results reveal new functional paradigms for polycistronic miRNAs in cancer.

overall_design: SRA Study: SRP117775 / SRA Bioproject: PRJNA407603 / miRNA-seq on isogenic B-cells with 3 levels of miR-17~92 (flox, deleted, overexpressed), and similarly on MEF (in triplicates). Also on MEF deleted miR-17~92 with overexpressed miR-290~295 or empty plasmid control (in triplicates)

middle: O

first: Radia

last: Johnson

first: Hsin-Wei

last: Tseng

first: Said

last: Izreig

first: Alexandra

last: Gariepy

first: Vinay

middle: K

last: Mayya

first: Edlyn

last: Wu

first: Roshni

last: Alam

first: Carine

last: Lussier

first: Russell

middle: G

last: Jones

first: Thomas

middle: F

last: Duchaine


title: Genome-wide strategies reveal downstream target genes of Npas4l associated with cardiovascular development in zebrafish

first: Carsten

last: Kuenne

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


title: Small extracellular vesicles are key regulators of non-cell autonomous intercellular communication in senescence via the interferon protein, IFITM3

city: London

first: Robert

last: Lowe

address: 4 Newark Street

department: Blizard Institute

institute: QMUL

summary: Senescence is a cellular phenotype present in health and disease, characterized by a stable cell cycle arrest and an inflammatory response, denominated senescence-associated secretory phenotype (SASP). The SASP is important in influencing the behaviour of neighbouring cells and altering the microenvironment; yet, this role has been mainly attributed to soluble factors. Here, we show that both the soluble factors in addition to small extracellular vesicles (sEV) are capable of transmitting paracrine senescence to nearby cells. Analysis of individual cells internalizing sEV, using a Cre-reporter system, show a positive correlation between sEV uptake and senescence activation. Interestingly, we find an increase in the number of multivesicular bodies during senescence in vivo. sEV protein characterization by mass spectrometry (MS) followed by a functional siRNA screen identify the Interferon Induced Transmembrane Protein 3 (IFITM3) as partially responsible for transmitting senescence to normal cells. Altogether, we found that sEV contribute to paracrine senescence.

overall_design: SASP related mRNA transcripts in HFFF2 treated with sEV from iRAS cells in comparison with HFFF2 treated with sEV from iC cells


title: Genome-wide strategies reveal downstream target genes of Npas4l associated with vascular development in zebrafish [ChIP-Seq]

overall_design: ChIP-seq examination of Npas4l-HA of zebrafish embryos compared to input.

first: Michele

last: Marass

first: Arica

last: Beisaw

first: Claudia

last: Gerri

first: Francesca

last: Luzzani

first: Nana

last: Fukuda


city: Heidelberg

first: Karsten

last: Rippe

state: Germany

address: Im Neuenheimer Feld 267-BQ24

department: Division of Chromatin Networks

institute: DKFZ

type: Methylation profiling by high throughput sequencing

summary:
In chronic lymphocytic leukemia (CLL) a diverse set of genetic mutations is embedded in a deregulated epigenetic landscape that drives cancerogenesis. To elucidate the role of aberrant chromatin features, we mapped DNA methylation, 7 histone modifications, nucleosome positions, chromatin accessibility, binding of EBF1 and CTCF as well as the transcriptome of B cells from CLL patients and healthy donors. A globally increased histone deacetylase activity was detected and half of the genome comprised transcriptionally downregulated partially DNA methylated domains demarcated by CTCF. CLL samples displayed a H3K4me3 redistribution and nucleosome gain at promoters as well as changes of enhancer activity and enhancer linkage to target genes. A DNA binding motif analysis identified transcription factors that gained or lost binding in CLL at sites with aberrant chromatin features. These findings were integrated into a gene regulatory enhancer containing network enriched for B cell receptor signaling pathway components. Our study predicts novel molecular links to targets of CLL therapies and provides a valuable resource for further studies on the epigenetic contribution to the disease.

Mallm JP, Iskar M, Ishaque N, Klett LC, Kugler SJ, Muino JM, Teif VB, Poos AM, Großmann S, Erdel F, Tavernari D, Koser SD, Schumacher S, Brors B, König R, Remondini D, Vingron M, Stilgenbauer S, Lichter P, Zapatka M, Mertens D & Rippe K (2019) Linking aberrant chromatin features in chronic lymphocytic leukemia to deregulated transcription factor networks. Mol Syst Biol 15, e8339. doi: 10.15252/msb.20188339

overall_design: We analyzed a carefully selected cohort of clinically and genetically fully characterized primary leukemia cells in bulk samples and at the single cell level for genome-wide DNA-methylation, nucleosome position, DNA-accessibility by ATAC-seq, the 7 most relevant histone modifications plus CTCF and EBF1 by ChIPseq as well as the transcriptome. Raw sequencing data for all the samples are available at the European Genome-phenome Archive (http://www.ebi.ac.uk/ega/), under the accession number EGAS00001002518.

first: Jan-Philipp

last: Mallm

first: Murat

last: Iskar

first: Naveed

last: Ishaque

first: Lara

last: Klett

first: Sabrina

last: Kugler

first: Jose

last: Muino

first: Vladimir

last: Teif

last: Poos

first: Sebastian

last: Großmann

first: Fabian

last: Erdel

first: Daniele

last: Tavernari

first: Sandra

last: Koser

last: Schumacher

first: Benedikt

last: Brors

first: Rainer

last: König

first: Daniel

last: Remondini

first: Martin

last: Vingron

first: Stephan

last: Stilgenbauer

first: Peter

last: Lichter

first: Marc

last: Zapatka

last: Mertens


title: Genome-wide strategies reveal downstream target genes of Npas4l associated with cardiovascular development in zebrafish [RNA-Seq 1]

first: Carsten

last: Kuenne

overall_design: RNA-seq examination of wild type and npas4l bns297/bns297 zebrafish embryos at 6-somite stage, in duplicates.

first: Michele

last: Marass

first: Arica

last: Beisaw

first: Claudia

last: Gerri

first: Francesca

last: Luzzani

first: Nana

last: Fukuda

first: Stefan

last: Günther

first: Sven

last: Reischauer

first: Didier

last: Stainier


title: Suppressor mutations in ribosomal proteins and FliY restore Bacillus subtilis swarming motility in the absence of EF-P [Ribosome Profiling]

city: Bloomington

middle: B.

last: Kearns

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University

summary: Translation elongation factor P (EF-P) alleviates ribosome pausing at a subset of motifs encoding consecutive proline residues and is required for growth in many organisms. Here we show that Bacillus subtilis EF-P also alleviated ribosome pausing at sequences encoding tandem prolines, and ribosomes paused within several essential genes without a corresponding growth defect in an efp mutant. The B. subtilis efp mutant is instead impaired for flagellar biosynthesis which results in the abrogation of a form of motility called swarming. We isolate swarming suppressors of efp and identify mutations in 8 genes that suppressed the efp mutant swarming defect, many of which encode conserved ribosomal proteins or ribosome-associated factors. One mutation abolished a translational pause site within the flagellar C-ring component FliY to increase flagellar number and restore swarming motility in the absence of EF-P. Our data support a model wherein EF-P-alleviation of ribosome pausing may be particularly important for macromolecular assemblies like the flagellum that require precise protein stoichiometries.

overall_design: 4 Bacillus subtilis strains with 3 biological replicates each were analyzed. DK1042 is the wild type and parent strain.

first: Katherine

last: Hummels


title: Suppressor mutations in ribosomal proteins and FliY restore Bacillus subtilis swarming motility in the absence of EF-P [RNA sequencing]


title: Suppressor mutations in ribosomal proteins and FliY restore Bacillus subtilis swarming motility in the absence of EF-P.


title: The landscape of transcription initiation across latent and lytic KSHV genomes

city: Nashville

first: Jeff

last: Rathmell

state: TN

address: 1211 Medical Center Drive

department: PMI

institute: Vanderbilt University Medical Center

summary: Precise promoter annotation is required for understanding the mechanistic basis of transcription initiation. Here we use RAMPAGE to profile genome wide KSHV transcription initiation events, which will provide basis for further virus transcripts expression studies.

overall_design: We performed RAMPAGE in iSLK.219 and TREx-BCBL1-RTA cell lines, samples were taken at latency and dox induced lytic activation for 12h, 24h, 48h, 72h and 96h.

first: Xiang

last: Ye

first: Yang

last: Zhao

first: John

last: Karijolich


title: Retention of paternal epigenetic memory in the developing teleost germline [RNA-Seq]

status: Public on May 19 2019

city: Sydney

first: Ksenia

last: Skvortsova

state: NSW

address: 384 Victoria St, Darlinghurst

department: Genomics and Epigenetics

country: Australia

institute: Garvan Institute

summary: Two waves of DNA methylation reprogramming occur during mammalian embryogenesis; during preimplantation development and during primordial germ cell (PGC) formation. However, it is currently unclear how evolutionarily conserved these processes are. Here we characterize the DNA methylomes of zebrafish PGCs at four developmental stages and unravel retention of paternal epigenetic memory, in stark contrast with the findings in mammals. Gene expression profiling of zebrafish PGCs at same developmental stages revealed that the embryonic germline is defined by a small number of markers that display strong developmental stage-specificity and that are uncoupled from DNA methylation-mediated regulation.

overall_design: Using low-input RNA-seq we have profiled transcriptomes of zebrafish primordial germ cells (PGCs) and age-matched somatic cells at 4 (blastula), 7 (gastrula), 24 (pharyngula prim-5) and 36 (pharyngula prim-25) hours post-fertilization

first: Ozren

last: Bogdanovic


title: Expression changes in mouse oligodendrocytes after deletion of the Ep400 chromatin remodeler

status: Public on May 17 2019

city: Erlangen

first: Michael

last: Wegner

state: Bavaria

address: Fahrstr. 17

department: Institut of Biochemistry

summary: To address the role of INO80/SWR-type remodeling complexes, we deleted Ep400 at defined times of mouse oligodendrocyte development. Whereas oligodendrocyte precursors are specified and develop normally without Ep400, terminal differentiation is dramatically impaired resulting in hypomyelination. RNA-Seq studies were performed on cultured and FACS sorted control and Ep400-deficient mouse oligodendrocytes  to analyze changes in gene expression. These revealed that genes associated with the myelination program and with response to DNA damage are altered in Ep400-deficient oligodendrocytes.

overall_design: OPC mRNA profiles of 6-day old control (ctrl) and Ep400 cko mice were generated using the Illumina HiSeq 2500 platform.

first: Olga

last: Elsesser

first: Franziska

last: Fröb


title: Whole-transcriptome RNA-seq analysis of zebrafish epidemal MLCs

city: HK

first: Zilong

last: WEN

address: Academic Bld., HKUST, Clearwater Bay, Kowloon

department: Division of Life Science

country: Hong Kong

institute: Hong Kong University of Science and Technology

summary: In order to have a comprehensive comparison of  locally restricted mpeg1+ cells (MLCs) and cLCs, we isolated  locally restricted mpeg1+ cells and cLCs from heat-shock labeled zebrafish epidermis and performed whole-transcriptome RNA-sequencing. As the controls, keratinocytes, T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T-SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile.

overall_design: Different cell types form zebrafish epidemis, including locally restricted mpeg1+ cells, cLCs, keratinocytes, T cells and neutrophils were isolated by manually picking. Each cell types contain 3-4 replicated from 3-4 indipendent experiments. cDNA libraries were generated using Smart-seq2 protocol, library construction and whole-transcriptome RNA-sequencing were proformed by Novogene.

first: Xi

last: Lin

first: Qiuxia

last: Zhou

first: Jin

last: Xu


title: Retention of paternal epigenetic memory in the developing teleost germline


title: Genotype variation in rice (Oryza sativa L.) tolerance to Fe toxicity might be linked to root cell wall lignification

status: Public on May 16 2019

city: Porto Alegre

first: Janette

middle: Palma

last: Fett

state: Rio Grande do Sul

address: Avenida Bento Gonçalves 9500

department: Centro de Biotecnologia

country: Brazil

institute: Universidade Federal do Rio Grande do Sul

summary:
Iron (Fe) is an essential element to plants, but can be harmful if accumulated to toxic concentrations. Fe toxicity can be a major nutritional disorder in rice (Oryza sativa) when cultivated under waterlogged conditions, as a result of excessive Fe solubilization of in the soil.
However, little is known about the basis of Fe toxicity and tolerance at both physiological and molecular level. Here we aim at understand the genotypic differences in two rice cultivars with contrasting phenotypes under Fe toxicity.

overall_design: To identify mechanisms and potential candidate genes for Fe tolerance in rice, we comparatively analyzed the effects of Fe excess on two cultivars with distinct tolerance to Fe toxicity, EPAGRI 108 (tolerant) and BR-IRGA 409 (susceptible), on gene expression. We collected root samples from the two cultivars under control conditions and after three days of Fe excess.

middle: P

first: Ricardo

last: Stein

first: Felipe

last: Ricachenevsky


title: Accessible chromatin profiles of B cell subsets from healthy and SLE subjects

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: SLE is characterized by the production of autoantibodies that arise from the B cell lineage.  Therefore, we sought to assess the epigenetic and transcriptome profiles of distinct B cell subsets known to be expanded in SLE from healthy and SLE subjects.  These data define the differentiation heirarchy of B cell subsets and the epigenetic and transcriptional consequences of SLE on human B cells.

overall_design: Five distinct B cell subsets were FACS isolated from a cohort of SLE and HC subjects.  For a subset of subjects, circulating Antibody Secreting Cells (ASC) were also isolated for comparisons.  Cells were FACS sorted and accessible chromatin profiles determined by ATAC-seq.

first: C

first: J

last: Boss


title: Spontaneous mutations in FgSAD1 suppress the growth defect of the Fgprp4 mutant by affecting tri-snRNP stability and its docking in Fusarium graminearum

status: Public on May 15 2019

city: Xianyang

first: Xiaoping

last: Li

state: Shaanxi

address: Yangling,

department: College of Plant protection

institute: Northwest A&F University,

summary: Purpose: For detecting splicing defects in wild type PH-1 and sector S139 and transformant D10. Our results showed that S139 and D10 had similar intron retention levels (un-spliced introns). The intron retention levels in S139 were significantly higher than those in PH-1 (P<0.001,t-test). For the 15,211 introns in the 6,995 genes expressed across two strains, approximately 25% of them had an over 2-fold intron retention rate in comparison with the intron retention rate in PH-1, indicating splicing defects in S139 and D10.

overall_design: The vegetative hyphae of the PH-1, S139, and D10 were harvested from 16h liquid YEPD cultures. Total RNAs was extracted using RNeasy Mini Kit (QIAGEN, US) following the manufacturer’s instructions. Library construction and sequencing with an Illumina Hiseq 2000 sequencer were performed at Shanghai Biotechnology Corporation (Shanghai, China). At least 25 Mb high-quality reads were obtained for each sample. The resulting RNA-seq reads were mapped onto the reference genome of F. graminearum strain PH-1 with the Tophat2 program (ccb.jhu.edu/software/tophat/index.shtml). The intron retention rate was defined as the number of reads that aligned to the predicted intron divided by the number of reads aligned to the corresponding transcript.

first: Qiaojun

last: Jin


title: Differential expression data between E15.5 outflow tracts of Gata4 G295S mutant embryos and littermate controls

city: Columbus

first: Vidu

last: Garg

state: OH

address: 700 Children's Drive WB4239

department: Cardiovascular Research

institute: Research Institute at Nationwide Children's Hospital

summary: E15.5 embryos were micro-disscted from Gata4 G295S mutant mice and littermate controls, RNA was isolated using Norgen total RNA isolation, and libraries were generated with the RNA TruSeq Stranded Total RNA kit. 50 base pair paired end reads were obtained on an illumina high seq 2500. Fastq files were aligned to the mouse genome using STAR aligner. QC was performed using RNASeQC and RSeQC. BAM files were processed using cufflinks pipeline.

overall_design: The project aims to assess the differential gene expression at E15.5 between the outflow tracts of Gata4 G295S mutant embryos and wildtype littermate controls.

first: Stephanie

last: LaHaye


title: Antifibrotic effect of metformin in the lung

status: Public on May 14 2019

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

summary: This experiment includes treatment of human pulmonary fibroblasts obtained from IPF patients with metformin. Since, we would like to investigate the transcriptome profile of these samples following metformin treatment. There will be two groups consist of four samples each. First group treated with metformin for 72 hours, while the second group treated with vehicle.

overall_design: 2 groups with 4 (vehicle control) and 3 (metformin treated) biological replicates

first: Saverio

last: Bellusci

first: Elie

last: El Agha


title: TCF-1 regulation of CD8+ T cell chromatin accessibility

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

institute: Monash University

summary: CD8+ T cell differentiation traditionally results in the emergence of two subsets, Tc1 cells that produce interferon (IFN)-gamma and memory cells that mediate immune protection against pathogen infections. More recently, it has emerged that other specialized CD8+ T cell populations develop in immune responses and are critical to orchestrate complete immune protection. These subsets include tissue-resident memory (Trm) T cells, follicular cytotoxic T cells and two CD8+ T cell subsets that produce interleukin (IL)-17, namely, mucosal-associated invariant T (MAIT) cells and Tc17 cells. Here we investigated the role of TCF-1 in CD8+ T cell differentiation by using Assay for Transposase-Accessible Chromatin sequencing (ATAC-Seq) to determine the chromatin accessibility landscape of CD8+ T cells and how this is controlled by TCF-1. Loss of TCF-1 was associated with global changes in the chromatin architecture in CD8+ T cells leading to increased accessibility of Rorc and Tc17 effector genes IL-17a and IL-17f in Tc17 cells. In contrast, we observed reduced accessibility of Tbx21, Eomes and Irf4 loci in Tc17 cells, genes normally required for the induction of Tc1 and memory CD8+ T cells

overall_design: ATAC-Seq data were generated from mouse spleen and lymph node CD8+T cells to investigate how TCF-1 controls the chromatin accessibility landscape.

first: Lisa

last: Mielke

first: Yang

last: Liao

first: Gabrielle

last: Belz


title: DEDD regulates cell cycle related genes

city: South Bend

first: Siyuan

last: Zhang

address: 1234 N Notre Dame Ave

department: Biological Sciences

institute: University of Notre Dame

summary: In DEDD knocked-down triple-negative breast cancer, cell cycle related gene expressions have been altered

overall_design: We transfected a TNBC cell line MDA-MB-468 with anti-DEDD shRNA to study DEDD dependent transcriptome changes

first: Yingjia

last: Ni

first: Q

last: Wang


title: Gene expression analysis of IL-17 producing T cells from human spleen

summary: IL-17 is a key cytokine important for defense against infection and plays a critical role in inflammatory diseases. To understand the diversity and identify a core gene signature among IL-17-producing T cell populations we isolated CD4+ and CD8+ IL-17 producing T cells for RNA sequencing.

overall_design: RNASeq data were generated from human spleen cells to investigate the different gene signatures between IL-17-producing T cell populations.

first: Vanessa

last: Bryant


title: DNA methylation profiles profiles of B cell subsets from healthy and SLE subjects

first: Chris

last: Scharer

overall_design: Five distinct B cell subsets were FACS isolated from a cohort of SLE and HC subjects.  For a subset of subjects, circulating Antibody Secreting Cells (ASC) were also isolated for comparisons.  Cells were FACS sorted into lysis buffer, DNA purified and DNA methylation profile assayed by Reduced Representation Bisulfite Sequencing (RRBS).

first: C


title: Genome-wide profile of RBPJ, H3K4me1, H3K4me3 and H3 in mouse brain pericytes

status: Public on May 12 2019

first: Marek

last: Bartkuhn

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

summary:
Background: Pericytes are capillary-associated mural cells especially prominent in the central nervous system where they regulate vascular permeability and blood-brain barrier integrity. Despite their relevance for neurovascular unit homeostasis and their involvement in the pathobiology of neurodegenerative diseases, signalling mechanisms responsible for functional specialization and intercellular communication remain elusive.
Objectives: The main goal of this study is to understand the relevance of Rbpj (the common downstream mediator of Notch signalling, an important mediator of cell-to-cell communication) in brain pericytes. In particular, the ChIP-Seq results aimed at the identification of genes bound to RBPJ in cultured mouse brain pericytes.

overall_design: Mouse pericytes (RD1) were analyzed by ChIP-Seq using an RBPJ-specific antibody to identify the genomic sites bound RBPJ. Subsequently, ChIP-Seq versus H3K4me1 and H3K4me3 were used to discriminate between proximal and distal RBPJ binding sites, respectively. Two replicates of each sample are included.

first: Benedetto

last: Giaimo

first: Rodrigo

last: Diéguez-Hurtado

first: Ralf

middle: H

last: Adams


title: Thyroid hormone receptor alpha is required for thyroid hormone-dependent neural cell proliferation during tadpole metamorphosis

status: Public on May 13 2019

city: Ann Arbor

first: Robert

last: Denver

state: Michigan

address: 1105 North University Ave

department: MCDB

institute: University of Michigan

summary: Using tadpoles mutant for thyroid hormone receptor alpha (thra), we show that TRa is required for thyroid hormone (T3) induction of cell proliferation in the brain. RNA-sequencing showed that the TRa is required for 95% of the gene regulation responses to T3.

overall_design: Wild type and thra mutant tadpoles were treated with vehicle (DMSO) or T3 (5 nM) added to the aquarium water for 16 hr before sacrifice and tissue harvest. The region of the brain containing the preoptic area/hypothalamus/thalamus was microdissected, RNA isolated and RNA sequencing conducted.

first: Luan

last: Wen


title: Fate plasticity and reprogramming in genetically distinct populations of Danio leucophores

city: Seattle

first: Victor

last: Lewis

state: Washington

address: 1959 NE Pacific St., UW-HSB H502

institute: University of Washington

summary: Understanding genetic and cellular bases of adult form remains a fundamental goal at the intersection of developmental and evolutionary biology. The skin pigment cells of vertebrates, derived from embryonic neural crest, are a useful system for elucidating mechanisms of fate specification, pattern formation, and how particular phenotypes impact organismal behavior and ecology. In a survey of Danio fishes, including zebrafish Danio rerio, we identified two populations of white pigment cells—leucophores—one of which arises by transdifferentiation of adult melanophores and another that develops from a yellow/orange xanthophore-like progenitor. Single-cell transcriptomic, mutational, chemical and ultrastructural analyses of zebrafish leucophores revealed cell-type specific chemical compositions, organelle configurations and genetic requirements. At the organismal level, we identified distinct physiological responses of leucophores during environmental background matching and we show that leucophore complement influences behavior. Together, our studies revealed new, independently arisen pigment cell types and mechanisms of fate acquisition in zebrafish, and illustrate how concerted analyses across hierarchical levels can provide insights into phenotypes and their evolution.

overall_design: Single-cell RNA-seq experiments were performed on the 10X Genomics platform using zebrafish fin pigment cells FACs sorted for mCherry. For additional details see associated publication

first: David

last: Parichy


title: Analyses of IL-17-producing CD8 T cells

first: Wei

last: Shi

state: Victoria

address: Wellington Rd

summary: Transcriptional profiling of conventional and novel CD8 T cell subsets using RNA sequencing

overall_design: Naïve, effector, memory and Tc17 CD8 T cells were isolated from naïve B7 and Tcf7-deficient mice for analyses by RNAseq. Tc17 cells have been recently identified but have not yet been mapped. This experiment aimed to determine the unique and shared freatures of Tc17 cells compared with other CD8 T cell populations in various tissues.

middle: T

first: Lisa

middle: C


title: Next-generation Sequencing Facilitates Quantitative Analysis of Wild Type and EED cKO mice Hippocampus Dentate Gyrus Transcriptomes

status: Public on May 11 2019

city: beijing

first: Peipei

last: liu

address: No. 25-1 West Beisihuan Rd, Haidian District, Beijing

department: State Key Laboratory of Stem cells and Reproductive Biology

institute: institute of zoology,Chinese academy of sciences

summary:
Purpose:Quantification differentially expressed genes and find target genes. The goals of this study are to compare Wild Type and EED cKO hippocampus dentate gyrus transcriptome profiling (RNA-seq) to quantitative reverse transcription polymerase chain reaction (qRT–PCR)  differentially expressed genes and find target genes
Methods: Hippocampus dentate gyrus mRNA profiles of 14-day-old wild-type (WT) and Embryonic Ectoderm Development conditional knockout (EED cKO) mice were generated by deep sequencing, in two biological replicates,using BGISEQ-500 platform.All RNA-Seq data were aligned to mouse genome version mm10 using HISAT.We use cluster software and Euclidean distance matrix for the hierarchical clustering analysis of the expressed gene and sample program at the same time, the clustering results can be viewed with javaTreeview. qRT–PCR validation was performed using  SYBR Green assays.
Results:Only transcripts that showed more than 2-fold differential expression compared to control were subjected to relevance network analysis. 1047 candidate genes that were differentially expressed with biological functional groups as compared between WT and EED cKO mice .
Conclusions: Our study represents the first detailed analysis of Wild Type and EED cKO mice hippocampus dentate gyrus transcriptomes, with two biologic replicates, generated by RNA-seq technology.

overall_design: Hippocampus dentate gyrus mRNA profiles of 14-day-old  WT and EED cKO mice were generated by deep sequencing, in two biological replicates, using BGISEQ-500 platform.

first: Pei-Pei

last: Liu

first: Chang-Mei


title: High frequency of pathogenic germline variants in genes associated with homologous recombination repair in patients with advanced solid cancers

city: København Ø

first: Mathias

middle: Husted

last: Torp

address: Blegdamsvej 9

department: Genomic Medicine

country: Denmark

institute: Rigshospitalet

summary: We identified pathogenic and likely pathogenic variants in 17.8% of the patients within a wide range of cancer types. In particular, mesothelioma, ovarian cancer, cervical cancer, urothelial cancer, and cancer of unknown primary origin displayed high frequencies of pathogenic variants. In total, 22 BRCA1 and BRCA2 germline variant were identified in 12 different cancer types, of which 10 (45%) variants were not previously identified in these patients. Pathogenic germline variants were predominantly found in DNA repair pathways; approximately half of the variants were within genes involved in homologous recombination repair. Loss of heterozygosity and somatic second hits were identified in several of these genes, supporting possible causality for cancer development. A potential treatment target based on pathogenic germline variant could be suggested in 25 patients (4%).

overall_design: investigation of expression features related to Class 4 and 5 germline mutations in cancer patients

first: Ida

middle: V

last: Tuxen

first: Birgitte

last: Bertelsen

first: Christina

middle: W

last: Yde

first: Migle

last: Survilaite

first: Savvas

last: Kinalis

first: Olga

last: Oestrup

first: Kristoffer

last: Rohrberg

first: Iben

last: Spangaard

first: Eric

last: Santoni-Rugiu

first: Karin

last: Wadt

first: Morten

last: Mau-Sorensen

first: Ulrik

last: Lassen

first: Finn

last: Nielsen


title: Gene expression profiling of brain cortex pericytes from control and Rbpj-knockout mice at P7 and P10

city: Münster

first: Rodrigo

last: Diéguez-Hurtado

address: Röntgenstraße 20

department: Department of Tissue Morphogenesis

institute: Max Planck Institute for Molecular Biomedicine/University of Münster

summary:
Background: Pericytes are capillary-associated mural cells especially prominent in the central nervous system where they regulate vascular permeability and blood-brain barrier integrity. Despite their relevance for neurovascular unit homeostasis and their involvement in the pathobiology of neurodegenerative diseases, signalling mechanisms responsible for functional specialization and intercellular communication remain elusive.
Objectives: The main goal of this study is to understand the relevance of Rbpj (the common downstream mediator of Notch signalling, an important mediator of cell-to-cell communication) in brain pericytes and to identify molecular signatures associated to Rbpj deletion.
Methods: We used mouse genetic experiments to knockout Rbpj specifically in pericytes using a mural cell-specific Cre-driver (PdgfrbCreERT2). Inclusion of the Rpl22-HA (RiboTag) construct allowed Cre-mediated HA-labeling of ribosomal proteins and consequent isolation of actively translating mRNA from pericytes. PdgfrbCreERT2 transgenic mice were used to drive recombination of Rpl22-HA (RiboTag) allele and/or Rbpj-lox conditional knockout. Tamoxifen administration from postnatal day 1 (P1) to P3 allowed efficient recombination in pericytes. Brain cortices were collected at P7 or P10 and HA-tagged polyribosomes were immunoprecipitated using anti-HA coated beads. Total RNA was extracted and sequencing libraries prepared.
Results: Pericyte-specific Rbpj deletion induces severe changes in the neurovascular unit characterized by defects in vascular morphogenesis, brain hemorrhaging, altered extracellular matrix composition and strong inflammatory responses. Analysis of pericytes translatome of Rbpj-KO mice compared to controls revealed profound changes in pericyte identity, increased expression of vascular smooth muscle cell markers and increased signaling through TGFbeta, among other alterations in mural cell behavior.

overall_design: Brain cortices from 3 mice per group were collected and homogenized. RNA associated to HA-tagged polyribosomes (RiboTag) was purified and used for sequencing library preparation. Mice at postnatal day (P) 7 and P10 were used from the following groups:  Control (PdgfrbCreERT2 +/T; Rpl22-HA p/p) vs. Rbpj-KO (PdgfrbCreERT2 +/T; Rpl22-HA p/p; Rbpj-lox p/p).

first: Katsuhiro

last: Kato

first: Ralf

last: Adams


title: Microbiota-dependent IL-33 restricts the virulence of binary toxin expressing epidemic Clostridium difficile via ILC2s.

status: Public on May 09 2019

city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

institute: Signature Science, LLC

summary: Hypervirulent epidemic strains of Clostridium difficile (C. difficile), referred to as NAPI/027, express an additional virulence factor, binary toxin (CDT), and are associated with more severe disease.  Emerging evidence indicates gut immunity to C. difficile is a delicate balance between protection and pathology.  To identify potential therapeutic host immune targets, we conducted a transcriptome analysis of host genes altered by NAPI/027 infection and identified interleukin-33 (IL-33) as a candidate immune target.  Using a murine model, we show that both endogenous IL-33 and exogenous IL-33 treatment protect from the enhanced mortality, weight-loss and tissue pathology which is characteristic of hypervirulent C. difficile.  IL-33 mediated protection was elicited through type-2 innate lymphoid cells (ILC2s) and adoptive transfer of purified ILC2s was sufficient to mitigate CDI- associated mortality and weight-loss. Furthermore, dysregulated IL-33 signaling via the soluble IL-33 decoy receptor (sST2) predicted disease severity and mortality in human patients.  Lastly, colonic IL-33 expression appears to be regulated by the microbiota as antibiotic- depletion of IL-33 was rescued with mouse fecal microbiota transplant (FMT) and a human fecal spore preparation (HSP). Thus, IL-33 signaling is a novel therapeutic pathway for severe CDI which can potentially be targeted with rationally designed microbial therapies.

overall_design: Microarray expression profiling in Clostridium difficile toxin infected mice

first: Alyse

middle: L

last: Frisbee

middle: D

first: William

middle: A

last: Petri


title: Transcriptome profile of Dictyostelium discoideum slugs in clonal and chimeric development

city: Bath

first: Atahualpa

last: Castillo Morales

address: Claverton Down

department: Biology and Biochemistry

institute: University of Bath

summary: Social interactions are typically characterised by conflict and competition. This antagonism can play a critical role in evolutionary processes, such as promoting diversity through maintenance of alternative strategies or driving accelerated evolution through arms-race like escalation. However, despite our sophisticated understanding of how conflict shapes social traits, we still have limited knowledge of how it impacts molecular evolution across the underlying ‘social genes’. To address this problem, we analysed the genome wide impact of social interactions in a microbe. To understand broad-scale processes shaping molecular evolution at social genes we have used four different, but complementary, approaches to identify sets of social genes. For ease, we have named these sets ‘sociality’, ‘chimerism’, ‘antagonism’ and ‘cheater’ genes. Chimerism genes are defined as those up-regulated in chimeric aggregations in comparison to clonal aggregations. This is based on the logic that chimeric development will be characterised by conflict, and hence these genes will show the signatures of conflict driven evolution. Using genome sequences from 67 Dictyostelium discoideum strains, we find that social genes often exhibit enhanced polymorphism and accelerated evolution. However, these patterns are not consistent with the expectation of conflict driven processes, but instead reflect relatively relaxed purifying selection. This pattern reflects the fact that social interactions are conditional, and therefore selection on genes expressed in social interactions is diluted by generations of inactivity. This results in the ‘Red King’ process, wherein dilution of selection by inactivity enhances the role of drift, resulting in increased polymorphism and accelerated evolution.

overall_design: Two conditions (clonal development of three strains: NC34.2, NC58.1 and NC87.1 vs chimeric development of 50%:50% pairwise mixtures : NC34.2+NC58.1, NC34.2+NC87.1 and  NC87.1+NC58.1). Aggregates isolated at 14hrs, when slugs had formed. Two biological replicates for sample in each condition.

first: A

last: Castillo-Morales

first: J

last: de Oliveira

first: B

last: Stewart

first: N

last: Gruenheit

last: Howie

first: S

middle: E

last: Battom

first: R

last: de Brito

first: L

last: Hurst

last: Urrutia

first: C

middle: R

last: Thompson

middle: B

last: Wolf


title: Effect of Ro 08-2750 treatment on gene expression of human leukemia cell lines MOLM13 and K562

city: New York City

first: Michael

last: Kharas

state: NY

address: 1275 York Avenue

department: Molecular Pharmacology

institute: Memorial Sloan Kettering Cancer Center

summary: RNA-sequencing on human leukemia cell lines MOLM13 (AML, MLL-AF9+) and K562 (CML-BC, BCR-ABL+) after Ro 08-2750 treatment (20 uM, 4hours)

overall_design: Cells were cultured at 0.5M/mL and treated with the small-molecule Ro 08-2750 for 4hours at 20 uM

first: Gerard

last: Minuesa

first: Maria

last: Passarelli

first: Lauren

last: Fairchild

first: Christina

last: Leslie

middle: G


title: Identification of HIV Transmitting CD11c+ Human Epidermal Dendritic Cells

status: Public on May 08 2019

city: Westmead

middle: Dinny

last: Graham

address: 176 Hawkesbury Rd

department: Westmead Institute for Medical Research

institute: University of Sydney

summary: Langerhans cells (LC) represent one of the first lines of contact between the immune system and sexually transmitted pathogens, and in the human epidermis LCs have been thought to represent the only mononuclear phagocyte (MNP) population. Here we show an additional epidermal MNP subset that can be distinguished from LCs phenotypically as CD11chi, CD1c+ MR+ (epidermal CD11c+ DCs). These cells are transcriptionally similar to dermal cDC2 but express higher levels of costimulatory markers and are more efficient at T cell stimulation. Importantly, compared to LC, epidermal CD11c+ DCs are i) enriched in the epithelium of anogenital tissues where they preferentially interact with HIV, ii) express the higher levels of the HIV entry receptor CCR5, iii)  support the higher levels of HIV uptake and replication and iv) are more efficient at transferring virus to CD4 T cells. Importantly these findings were observed using both a lab-adapted and transmitted/founder strain of HIV. We also describe a cell population that can be discerned from LCs by their lower surface expression of CD45, HLA-DR and CD33 (epidermal CD33low cells). These are transcriptionally similar to LCs but do not appear to function as APCs as do not secrete cytokines, express negligible amounts of costimulatory molecules and are very weak inducers of T cell proliferation. They also do not act as HIV target cells. Our findings reveal a new subset of epidermal DCs in skin and anogenital tissues with a potential key role in sexual transmission of HIV.

overall_design: Sorted cell populations from four donors were captured directly into lysis buffer and polyA RNA transcripts were reverse transcribed, amplified and sequenced using the Smart-seq 2 protocol described by Picelli et al (Nature Methods. 2013;10(11):1096-8).  Each sample was sequenced across 4 HiSeq lanes and the data for each lane is represented as an independent sample (GSM).

first: Andrew

middle: N

last: Harman

first: Kirstie

middle: M

last: Bertram

first: Patrick

last: Ellis


title: Role of ACLY in gene regulation during adipocyte differentiation

city: Philadelphia

first: Kathryn

last: Wellen

state: PA

address: 421 Curie Blvd, BRB 653

department: Cancer Biology

institute: University of Pennsylvania

summary: RNA-sequencing from Aclyf/f and Acly-/- preadipocytes generated from Aclyf/f mice and induced to differentiate to adipocytes.

overall_design: Examination of gene expression during adipocyte differentiation, with Acly intact or deleted


title: A distal super enhancer mediates estrogen-dependent mouse uterine–specific gene transcription of Insulin-like growth factor 1 (Igf1)

city: Research Triangle Park

first: Sylvia

last: Hewitt

state: NC

address: 111 Alexander Dr

department: RDBL

institute: NIEHS

summary: Insulin-like growth factor 1 (IGF1) is primarily synthesized in and secreted from the liver; however, estrogen (E2), through E2 receptor α (ERα), increases uterine Igf1 mRNA levels. Previous ChIP-Seq analyses of the murine uterus have revealed a potential enhancer region distal from the Igf1 transcription start site (TSS) with multiple E2-dependent ERα-binding regions. Here, we show E2-dependent super enhancer–associated characteristics and suggest contact between the distal enhancer and the Igf1 TSS. We hypothesized that this distal super-enhancer region controls E2-responsive induction of uterine Igf1 transcripts. We deleted 430 bp, encompassing one of the ERα-binding sites, thereby disrupting interactions of the enhancer with gene-regulatory factors. As a result, E2-mediated induction of mouse uterine Igf1 mRNA is completely eliminated, whereas hepatic Igf1 expression remains unaffected. This highlights the central role of a distal enhancer in the assembly of the factors necessary for E2-dependent interaction with the Igf1 TSS and induction of uterus-specific Igf1 transcription. Of note, loss of the enhancer did not affect fertility or uterine growth responses. Deletion of uterine Igf1 in a PgrCre;Igf1f/f model decreased female fertility, but did not impact the E2-induced uterine growth response. Moreover, E2-dependent activation of uterine IGF1 signaling was not impaired by disrupting the distal enhancer or by deleting the coding transcript. This indicated a role for systemic IGF1, suggested that other growth mediators drive uterine response to E2, and that uterine-derived IGF1 is essential for reproductive success. Our findings elucidate the role of a super enhancer in Igf1 regulation and uterine growth.

overall_design: ERa or Histone 3 modifications ChIP seq of pre-pubertal (21 days old) or ovariectomized adult uterine tissue treated for one hour with saline vehicle (V) or estradiol (E2); ERa  ChIP seq of ovariectomized adult uterine tissue treated for 6, 8 or 12 hours with  estradiol (E2); SMC1a ChIP seq or HiC of ovariectomized adult uterine tissue treated for one hour with saline vehicle (V) or estradiol (E2) or progesterone (P4); RNA seq of ovariectomized adult uterine tissue treated for two hours with saline vehicle (S) or for two, six or  24 hours with estradiol (E2)

first: Sydney

last: Lierz

first: Marleney

last: Garcia

first: Katherine

middle: J

last: Hamilton

first: Artiom

last: Gruzdev

first: Sara

last: Grimm

first: John

middle: P

last: Lydon

first: Francesco

last: DeMayo

first: Kenneth

middle: S

last: Korach


title: Global transcriptional profiling unveils the interferon network in blood and tissues across different diseases [RNA-seq_Test_HDM_model_BAL_Blood]

city: London

first: Akul

last: Singhania

address: 1 Midland Road

institute: The Francis Crick Institute

summary: We have performed modular analyses to decipher the global transcriptional response and capture a breadth of distinct immune responses in the lungs and blood of mice infected or challenged with a broad spectrum of infectious pathogens, including parasites (Toxoplasma gondii), bacteria (Burkholderia pseudomallei), viruses (Influenza A virus and Respiratory Syncytial virus (RSV)) and fungi (Candida albicans), or allergens (House dust mite (HDM), systemic and intra-nasal challenge). In a distinct set of infectious diseases, we tested the blood modular transcriptional signatures in mice infected with Plasmodium chabaudi chabaudi (malaria), murine cytomegalovirus (MCMV), Listeria monocytogenes and chronic Burkholderia pseudomallei. We also investigated the transcriptional profiles of sorted CD4 T cells (total CD4+, CD4+ CD44 high and CD4+ CD44 low) from lung and blood samples from mice challenged with HDM allergen. Moreover, we used mice deficient in either Ifnar or Ifngr, or both, to reveal the individual roles of each pathway in controlling disease in mice infected with Toxoplasma gondii.

overall_design: RNA-seq analysis of bronchoalveolar lavage (BAL) and blood samples obtained from mice challenged intra-nasally with House dust mite (HDM) allergy.

first: Christine

first: Leona

last: Gabryšová

first: Lúcia

last: Moreira-Teixeira

first: Evangelos

last: Stavropoulos

first: Jonathan

last: Pitt

first: Probir

last: Chakravarty

first: Annika

last: Warnatsch

first: William

last: Branchett

first: Laura

last: Conejero

first: Jing-Wen

last: Lin

first: Sophia

last: Davidson

first: Mark

last: Wilson

first: Gregory

last: Bancroft

first: Jean

last: Langhorne

first: Eva

last: Frickel

first: Abdul

last: Sesay

first: Simon

last: Priestnall

first: Eleanor

last: Herbert

first: Marianna

last: Ioannou

first: Qian

last: Wang

first: Ian

last: Humphreys

last: Dodd

first: Peter

last: Openshaw

first: Katrin

last: Mayer-Barber

first: Dragana

last: Jankovic

first: Alan

last: Sher

first: Clare

last: Lloyd

first: Nicole

last: Baldwin

first: Damien

last: Chaussabel

first: Venizelos

last: Papayannopoulos

first: Andreas

last: Wack

first: Jacques

middle: F

last: Banchereau

first: Virginia

last: Pascual

first: Anne

last: O’Garra


title: Global transcriptional profiling unveils the interferon network in blood and tissues across different diseases [RNA-seq_HDM_sorted_CD4_Tcells]

first: Akul

last: Singhania

overall_design: RNA-seq analysis of sorted CD4 T cells (total CD4+, CD4+CD44high and CD4+CD44low) from lung and blood samples obtained from mice challenged systemically with House dust mite (HDM) allergy.

first: Christine

last: Graham

first: Leona

last: Gabryšová

first: Lúcia

last: Moreira-Teixeira

first: Evangelos

last: Stavropoulos

first: Jonathan

last: Pitt

first: Probir

last: Chakravarty

first: Annika

last: Warnatsch

first: William

last: Branchett

first: Laura

last: Conejero

first: Jing-Wen

last: Lin

first: Sophia

last: Davidson

first: Mark

last: Wilson

first: Gregory

last: Bancroft

first: Jean

last: Langhorne

first: Eva

last: Frickel

first: Abdul

last: Sesay

first: Simon

last: Priestnall

last: Herbert


title: Aging Human Hematopoietic Stem Cells Manifest Profound Epigenetic Reprogramming of Enhancers That May Predispose to Leukemia

city: Cincinnati

first: Nathan

last: Salomonis

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

summary: Aging is associated with functional decline of hematopoietic stem cells (HSC) as well as an increased risk of myeloid malignancies. We performed an integrative characterization of epigenomic and transcriptomic changes, including single-cell RNA-seq, during normal human aging. Lineage-CD34+CD38- cells (HSC-enriched, HSCe) undergo age-associated epigenetic reprogramming consisting of redistribution of DNA methylation and reductions in H3K27ac, H3K4me1 and H3K4me3. This reprogramming of aged HSCe globally targets developmental and cancer pathways which are comparably altered in AML of all ages; encompassing loss of 4,656 active enhancers, 3,091 bivalent promoters, and deregulation of several epigenetic modifiers and key hematopoietic transcription factors, such as KLF6, BCL6 and RUNX3. Notably, in vitro downregulation of KLF6 results in impaired differentiation, increased colony forming potential and changes in expression that recapitulate aging and leukemia signatures. Thus, age-associated epigenetic reprogramming may form a predisposing condition for the development of age-related AML.

overall_design: We profiled the human HSCe (Lineage-, CD34+, CD38-) transcriptome with aging at the single cell level. Single-cell RNAseq was performed on FACS isolated human bone marrow derived HSCe from 5 young (24-37 yo) and 4 aged donor (64-71 yo). Donors had no known hematological malignancy.

first: Emmalee

last: Adelman

first: Andre

last: Olsson

first: Tingting

last: Qin

first: R

middle: C

last: Lindsley

first: Rafael

last: Bejar

first: H

last: Grimes

first: Maria

last: Figueroa


title: Global transcriptional profiling unveils the interferon network in blood and tissues across different diseases [RNA-seq_Toxoplasma_WT_IFNR_KO_4tissues]

first: Akul

last: Singhania

overall_design: RNA-seq analysis of lung, blood, liver and spleen samples obtained from wild type mice and interferon (IFN) receptor knockout mice (ifnar-/-, ifngr-/- and double ifnar-/- x ifngr-/-) infected with Toxoplasma gondii.

first: Christine

last: Graham

first: Leona

last: Gabryšová

first: Lúcia

last: Moreira-Teixeira

first: Evangelos

last: Stavropoulos

first: Jonathan

last: Pitt

first: Probir

last: Chakravarty

first: Annika

last: Warnatsch

first: William

last: Branchett

first: Laura

last: Conejero

last: Lin

first: Eleanor

first: Marianna

last: Ioannou

first: Qian

last: Wang

first: Ian

last: Humphreys

last: Dodd

first: Peter

last: Openshaw

first: Katrin

last: Mayer-Barber

first: Dragana

last: Jankovic

first: Alan

last: Sher

first: Clare

last: Lloyd

first: Nicole

last: Baldwin

first: Damien

last: Chaussabel

first: Venizelos

last: Papayannopoulos

first: Andreas

last: Wack

first: Jacques

last: Banchereau

first: Virginia

last: Pascual

first: Anne

last: O’Garra


title: Global transcriptional profiling unveils the interferon network in blood and tissues across different diseases [RNA-seq_blood4_module_testing]

first: Akul

last: Singhania

overall_design: RNA-seq analysis of blood samples obtained from mice infected with Plasmodium chabaudi chabaudi, murine cytomegalovirus (MCMV), Listeria monocytogenes and chronic Burkholderia pseudomallei.

first: Christine

last: Graham

first: Leona

last: Gabryšová

first: Lúcia

last: Moreira-Teixeira

first: Evangelos

last: Stavropoulos

first: Jonathan

last: Pitt

first: Probir

last: Chakravarty

first: Annika

last: Warnatsch

first: William

last: Branchett

first: Laura

last: Conejero

first: Jing-Wen

last: Lin

first: Sophia

last: Davidson

first: Mark

last: Wilson

first: Gregory

last: Bancroft

first: Jean

last: Langhorne

first: Eva

last: Frickel

first: Abdul

last: Sesay

first: Simon

last: Priestnall

last: Herbert


title: Synthetic modeling reveals HOXB genes are critical for the initiation and maintenance of human leukemia

status: Public on May 07 2019

city: Vancouver

first: Martin

last: Hirst

state: British Columbia

address: 2125 East Mall

department: Microbiology and Immunology

institute: University of British Columbia

summary: We report here an efficient, reproducible model of T-cell leukemia in which lentiviral transduction of normal human cord blood yields aggressive leukemia that appears indistinguishable from natural disease. We utilize this synthetic model to uncover a role for oncogene-induced HOXB activation which is operative in leukemia cells-of-origin and persists in established tumors where it defines a novel subset of patients distinct from other known genetic subtypes and with poor clinical outcome. We show further that anterior HOXB genes are specifically activated in human T-ALL by an epigenetic mechanism and confer growth advantage in both pre-leukemia cells and established clones.

overall_design:
We performed epigenetic profiling (H3K27me3, H3K27ac) using massively parallel sequencing-based assays on CD34+ human cord blood cells transduced with a combination of activated NOTCH1 (NOTCH1ΔE, encoded on a GFP-tagged lentiviral vector) and LMO2/TAL1/BMI1 (encoded on an mCherry-tagged lentiviral vector), and then cultured on OP9-DL1 feeders. Non-transduced cells sorted from the same cultures as transduced cells serve as negative controls.
*** Raw data provided at European Genome-phenome Archive (EGA) under accession EGAS00001003627. ***

first: Manabu

last: Kusakabe

first: Ann

last: Sun

first: Kateryna

last: Tyshchenko

first: Rachel

last: Wong

first: Aastha

last: Nanda

first: Claire

last: Shanna

first: Samuel

last: Gusscott

first: Elizabeth

last: Chavez

first: Alireza

last: Lorzadeh

first: Alice

last: Zhu

first: Ainsleigh

last: Hill

first: Stacy

last: Hung

first: Scott

last: Brown

first: Artem

last: Babaian

first: Xuehai

last: Wang

first: Robert

last: Holt

first: Christian

last: Steidl

first: Aly

last: Karsan

first: R

middle: K

last: Humphries

first: Connie

last: Eaves

first: Andrew

last: Weng


title: Global transcriptional profiling unveils the interferon network in blood and tissues across different diseases [microarray_lung_6]

first: Akul

last: Singhania

overall_design:
Microarray analysis of lung samples obtained from mice infected or challenged with Toxoplasma gondii, Influenza A virus, Respiratory Syncytial virus (RSV), acute Burkholderia pseudomallei, Candida albicans, and House dust mite (HDM) allergen.

Please note that [1] the sample description field lists the corresponding raw data file. [2] the negative numbers in the non-normalized data matrices suggest background subtraction may have occurred. However, the provided raw data is only available raw data from which all processed data was generated.

first: Christine

last: Graham

first: Leona

last: Gabryšová

first: Lúcia

last: Moreira-Teixeira

first: Evangelos

last: Stavropoulos

first: Jonathan

last: Pitt

first: Probir

last: Chakravarty

first: Annika

last: Warnatsch

first: William

last: Branchett

first: Laura

last: Conejero

first: Jing-Wen

last: Lin

first: Sophia

last: Davidson

first: Mark

last: Wilson

first: Gregory

last: Bancroft

first: Jean

last: Langhorne

first: Eva

last: Frickel

first: Abdul

last: Sesay

first: Simon

last: Priestnall

first: Eleanor

last: Herbert

first: Marianna

last: Ioannou

first: Qian

first: Ian

last: Humphreys

last: Dodd

first: Peter

last: Openshaw

first: Katrin

last: Mayer-Barber

first: Dragana

last: Jankovic

first: Alan

last: Sher

first: Clare

last: Lloyd

first: Nicole

last: Baldwin

first: Damien

last: Chaussabel

first: Venizelos

last: Papayannopoulos

first: Andreas

last: Wack

first: Jacques

last: Banchereau

first: Virginia

last: Pascual

first: Anne

last: O’Garra


title: An ErbB2/c-Src axis drives mammary tumorigenesis through metabolically directed translational regulation of Polycomb Repressor Complex 2 [ChIP-Seq]

status: Public on May 06 2019

city: Montreal

first: Harvey

middle: Wilmore

last: Smith

state: Quebec

address: Life Sciences Complex, Room 602, 1160 Pine Avenue West

department: Goodman Cancer Research Centre

institute: McGill University

summary: Perturbations in histone modifications alter transcription and promote carcinogenesis. Breast cancers frequently overexpress the histone methyltransferase EZH2, the catalytic subunit of Polycomb Repressor Complex 2 (PRC2). However, the mechanisms driving EZH2 overexpression are obscure and elucidating the role of PRC2 in breast cancer, which is highly heterogeneous, is challenging given its context-dependent oncogenic and tumor suppressive functions. Here, using genetically engineered mouse, PDX and cell line models, we show that the tyrosine kinase c-Src links energy sufficiency with PRC2 subunit overexpression via control of mRNA translation. In breast cancers initiated by the oncogene ErbB2, c-Src stimulates mitochondrial ATP production to suppress energy stress and permit sustained activation of the mammalian/mechanistic target of rapamycin complex 1 (mTORC1), which increases the translation of mRNAs encoding the PRC2 subunits Ezh2 and Suz12. We show that Ezh2 overexpression and activity are pivotal in ErbB2-mediated mammary tumorigenesis. These results reveal the hitherto unknown c-Src/mTORC1/PRC2 axis, which is essential for ErbB2-driven carcinogenesis.

overall_design: ChIP Seq of H3K27me3 in c-Src-deficient ErbB2+ murine mammary tumor cell lines and control, wild-type ErbB2+ mammary tumor cell lines. 2 biological replicates per genotype were sequenced.

first: William

last: Muller

middle: W


title: Global transcriptional profiling unveils the interferon network in blood and tissues across different diseases [RNA-seq_blood6_module_generation]

first: Akul

last: Singhania

overall_design: RNA-seq analysis of blood samples obtained from mice infected or challenged with Toxoplasma gondii, Influenza A virus, Respiratory Syncytial virus (RSV), acute Burkholderia pseudomallei, Candida albicans, and House dust mite (HDM) allergen.

first: Christine

last: Graham

first: Leona

last: Gabryšová

first: Lúcia

last: Moreira-Teixeira

first: Evangelos

last: Stavropoulos

first: Jonathan

last: Pitt

first: Probir

last: Chakravarty

first: Annika

last: Warnatsch

last: Branchett

first: Laura

last: Conejero

first: Jing-Wen

last: Lin

first: Sophia

last: Davidson

first: Mark

last: Wilson

first: Gregory

last: Bancroft

first: Jean

last: Langhorne

first: Eva

last: Frickel

first: Abdul

last: Sesay

first: Simon

middle: L

last: Priestnall

first: Eleanor

last: Herbert

first: Marianna

last: Ioannou

last: Wang

middle: D


title: High-throughput tissue dissection and cell purification with digital cytometry [scRNA-Seq]

city: Stanford

first: Aaron

last: Newman

state: California

address: 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine, Department of Biomedical Data Science

institute: Stanford University

summary: Tissue composition is a major determinant of phenotypic variation and a key factor influencing disease outcomes. Although scRNA-Seq has emerged as a powerful technique for characterizing cellular heterogeneity, it is currently impractical for large sample cohorts and cannot be applied to fixed specimens collected as part of routine clinical care. To overcome these challenges, we extended Cell type Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORT) into a new platform for in silico cytometry. Our approach enables the simultaneous inference of cell type abundance and cell type-specific gene expression profiles (GEPs) from bulk tissue transcriptomes. The utility of this integrated framework, called CIBERSORTx, is demonstrated in multiple tumor types, including melanoma, where single cell reference profiles are used to dissect primary clinical specimens, revealing cell type-specific signatures of driver mutations and immunotherapy response. We anticipate that digital cytometry will augment single cell profiling efforts, enabling cost-effective, high throughput tissue characterization without the need for antibodies, disaggregation, or viable cells.

overall_design:
Single cell libraries were prepared from cryopreserved NSCLC PBMC single cell suspensions using Chromium with v2 chemistry (10x Genomics), and were sequenced on a NextSeq 500 (Illumina).
Raw data are not available for this Series due to patient privacy concerns.

first: Chloe

last: Steen

first: Chih-Long

last: Liu

first: Andrew

last: Gentles

first: Aadel

middle: A

last: Chaudhuri

first: Florian

last: Scherer

first: Michael

last: Khodadoust

first: Mohammad

last: Shahrokh Esfahani

first: Bogdan

last: Luca

first: David

last: Steiner

first: Maximilian

last: Diehn

first: Ash

last: Alizadeh


title: An ErbB2/c-Src axis drives mammary tumorigenesis through metabolically directed translational regulation of Polycomb Repressor Complex 2

first: Harvey

last: Smith

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

overall_design: Refer to individual Series


title: Ethylene-mediated improvement in sucrose accumulation in ripening sugarcane involves increased sink strength

city: Nanning

first: Dong-Liang

last: Huang

email: hdl666@163.com, Huangdl@gxaas.net

address: 174 Daxue Road

institute: Sugarcane Research Institure of Guangxi Academy of Agricultural Sciences

summary: Transcripts libraries were prepared from three sugarcane genotypes with high-sugar (HS), medium-sugar (MS) or low-sugar (LS) content that were treated with ethylene or H2O. The libraries  were sequenced with the Illumina paired-end HiSeq platform.Transcriptomic analyses have identified about 160,000 unigenes of which 86000 annotated genes were classified into functional groups associated with carbohydrate metabolism, signaling, localization, transport, hydrolysis, growth, catalytic activity, membrane and storage, suggesting the structural and functional specification, including sucrose accumulation, occurring in maturing internodes. About 25,000 genes were differentially expressed between all genotypes and treatments combined. Genotype had a dominant effect on differential gene expression than ethylene treatment. Sucrose and starch metabolism genes were more responsive to ethylene treatment in low-sugar genotype. Ethylene caused differential gene expression of many stress-related transcription factors, carbohydrate metabolism, hormone metabolism and epigenetic modification. Ethylene-induced expression of ethylene-responsive transcription factors, cytosolic acid- and cell wall-bound invertases, and ATPase was more pronounced in low- than in high-sugar genotype, suggesting an ethylene-stimulated sink activity and consequent increased sucrose accumulation in low-sugar genotype.

overall_design: Two biological replicates each with two technical replicates for each treatment from 3 genotypes were sequenced. The fastq files of the three technical replicates were merged togeher. After quality assessment and data clearance, more than 3 billion (G) reads from each sample were retained as high-quality reads and they were used for subsequent analysis.

first: Zhong-Liang

last: Chen

first: Cui-Xian

last: Qin

first: Ming-Hua

last: Long

first: Prakash

last: Lakshmanan


title: An ErbB2/c-Src axis drives mammary tumorigenesis through metabolically directed translational regulation of Polycomb Repressor Complex 2 [RNA-Seq]

status: Public on May 03 2019

overall_design: Steady state mRNA levels were determined by RNA-Seq in two independent murine wild-type ErbB2+ breast cancer cell lines and two independent ErbB2+ breast cancer cell lines with conditional deletion of c-Src, each in biological duplicate.

first: William

last: Muller


title: m6A IP sequencing analysis of m6A mRNA methylation regulation by FTO in melanoma cells

city: Chicago

first: zhike

last: lu

state: IL

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

summary: N6-methyladenosine (m6A) RNA methylation is the most abundant internal chemical modifications in eukaryotic messenger RNA (mRNA) as well as long non-coding RNA (lncRNA). Recently, m6A RNA methylation research was revived by the discovery of the fat mass- and obesity-associated protein (FTO) as the first RNA demethylase, implicating that m6A RNA methylation is a reversible and dynamic modification and may have critical biological functions. Emerging evidence has shown that m6A modifications in mRNAs and lncRNAs play crucial roles in regulating RNA fate and function in biological processes in the past several years. As the first identified RNA demethylase that regulates the demethylation of target mRNAs, FTO has been reported to play an oncogenic role in leukemia and glioblastoma stem cells. To identify the target genes of FTO in melanoma cells,  we used m6A IP seq coupled with RNA seq to determine the potential demethylation and gene targets across the whole transcriptome for FTO, and identified more than 1,000 genes.

overall_design: m6A IP seq of control and FTO-knockdown melanoma cells in duplicate

first: Zhike

last: Lu

first: Jiangbo

last: Wei

first: Seungwon

last: Yang


title: Global transcriptional profiling unveils the interferon network in blood and tissues across different diseases

first: Akul

last: Singhania


title: Global transcriptional profiling unveils the interferon network in blood and tissues across different diseases [Microarray_Blood_6]

overall_design:
Microarray analysis of blood samples obtained from mice infected or challenged with Toxoplasma gondii, Influenza A virus, Respiratory Syncytial virus (RSV), acute Burkholderia pseudomallei, Candida albicans, and House dust mite (HDM) allergen.

Please note that [1] the sample description field lists the corresponding raw data file. [2] the negative numbers in the non-normalized data matrices suggest background subtraction may have occurred. However, the provided raw data is only available raw data from which all processed data was generated.

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