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

first: Aaron

last: Newman

overall_design: To evaluate the performance of CIBERSORTx, we profiled the following primary human samples:   (i) A scRNA-Seq dataset derived from peripheral blood mononuclear cells (PBMCs) obtained from a patient with non-small cell lung cancer (NSCLC) using droplet-based 10x Chromium v2 assay, and consisting of six major leukocyte subsets (B cells, CD4 T cells, CD8 T cells, NKT cells, NK cells, and monocytes). (ii) A bulk RNA-Seq dataset of whole-blood samples from 12 healthy adult donors. (iii) 302 Microarray GEPs of sorted populations from follicular lymphoma (FL) lymph nodes. (v) RNA-Seq GEPs from 26 bulk NSCLC tumors. (vi) 26x4 RNA-Seq GEPs of epithelial (EpCAM+), hematopoietic (CD45+), endothelial (CD31+), and stromal (CD10+) subpopulations, each of which FACS-purified from primary NSCLC tumor biopsies obtained from 26 subjects with newly diagnosed cancer.

first: Chloe

middle: B

last: Steen

first: Chih-Long

last: Liu

first: Andrew

last: Gentles

first: Aadel

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: Yeast sirutin family members maintain trannscription homeostasis to ensure genome stability

status: Public on May 04 2019

city: Worcester

first: Jessica

middle: Lauren

last: Feldman

state: MA

address: 373 Plantation St

country: USA

institute: UMass Medical School

type: Expression profiling by high throughput sequencing

summary: Loss of Hst3 and Hst4 leads to increased nascent transcription which increases the prevelance of R-loops and contributes to DNA damage phenotype of the mutant

overall_design: NET-seq, RNA-seq, DRIP-seq, Break-seq

middle: L

first: Craig

last: Peterson


title: Pioneering function of Isl1 in the epigenetic control of cardiomyocyte cell fate [Isl1_E8_75_RNA_seq]

status: Public on May 02 2019

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

country: Germany

institute: Medical Faculty Mannheim/University of Heidelberg

summary: Generation of widely differing and specialized cell types from a single totipotent zygote involves large-scale transcriptional changes and chromatin reorganization. Pioneer transcription factors play key roles in programming the epigenome and facilitating recruitment of additional regulatory factors during successive cell lineage specification and differentiation steps. Here we show that Isl1 acts as a pioneer factor driving cardiomyocyte lineage commitment by shaping the chromatin landscape of cardiac progenitor cells. Using an Isl1 hypomorphic mouse line which shows congenital heart defects, genome-wide profiling of Isl1 binding together with RNA- and ATAC-sequencing of cardiac progenitor cells and their derivatives, we uncover a regulatory network downstream of Isl1 that orchestrates cardiogenesis. Mechanistically, we show that Isl1 binds to compacted chromatin and woks in concert with the Brg1-Baf60c-based SWI/SNF complex to promote permissive cardiac lineage-specific alterations in the chromatin landscape not only of genes with critical functions in cardiac progenitor cells, but also of cardiomyocyte structural genes that are highly expressed when Isl1 itself is no longer present. Thus, the Isl1/Brg1-Baf60c complex plays a crucial role in orchestrating proper cardiogenesis and in establishing epigenetic memory of cardiomyocyte fate commitment.

overall_design: To gain insight into the molecular mechanisms underlying Isl1 function in cardiogenesis we performed RNA-Seq from Isl1-KO embryos at E8.5 to E9.

first: Julio

last: Cordero

first: Rui

last: Gao


title: Global transcriptional profiling unveils the interferon network in blood and tissues across different diseases [RNA-seq_Lung_6_module_generation]

status: Public on May 08 2019

city: London

first: Akul

last: Singhania

address: 1 Midland Road

country: United Kingdom

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 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.

first: Christine

middle: M

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

middle: J

last: Branchett

first: Laura

last: Conejero

first: Jing-Wen

last: Lin

first: Sophia

last: Davidson

first: Mark

middle: S

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

middle: R

last: Humphreys

last: Dodd

first: Peter

last: Openshaw

first: Katrin

middle: D

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: Microarray analysis of gene expression regulation by FTO in melanoma cells

status: Public on May 06 2019

city: Chicago

first: Yu-Ying

last: He

state: IL

address: 5841 S Maryland Ave, AMB N011

department: Medicine

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 microarray analysis to determine the potential demethylation and gene targets across the whole transcriptome for FTO, and identified more than 100 genes.

overall_design: Microarray analysis of control and FTO-knockdown Mel624 melanoma cells in duplicate.

first: Seungwon

last: Yang


title: FOXP2 regulates differential transcriptional programs in human subplate

status: Public on May 07 2019

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Mammalian brains are highly conserved at both the neuroanatomical and gene expression levels. However, the subplate is a neocortical subregion distinguished by a markedly different developmental trajectory among primates compared to other mammals. Moreover, the molecular mechanisms driving these species differences in subplate development remain mostly unknown. Here, we show that human FOXP2, a transcription factor important for speech and language, regulates gene expression programs consistent with subplate neuron expression patterns. These transcriptional profiles have unique overlaps with in vivo data from human fetal brain. We also distinguish DNA-dependent and DNA-independent mechanisms for human FOXP2 to repress patterns of germinal zone expression and promote excitatory neuron gene expression patterns.

overall_design: We carried out two RNA-sequencing (RNA-seq) experiments and one ATAC-sequencing (ATAC-seq) experiment in proliferating (hNP) and differentiated (hDN) human neural progenitor cells. For the first RNA-seq, four independent replicates of control and FOXP2-WT over-expressing samples were sequenced in hNPs and hDNs. Three replicates were used in the analysis. For the second RNA-seq three independent replicates of control, FOXP2-WT over-expressing, and FOXP2-KE over-expressing samples were used. The ATAC-seq chromatin was collected in parallel with the second RNA-seq experiment. Four independent replicates of replicates of control, FOXP2-WT overexpressing, and FOXP2-KE overexpressing samples were used. ATAC-seq data and data from the second RNA-seq experiment are published here: DOI:https://doi.org/10.1016/j.celrep.2019.04.044.

first: Stephane

last: Hickey

first: Stefano

last: Berto


title: CRISPR knockout screen implicates three genes in lysosome function

status: Public on May 01 2019

city: Ann Arbor

first: Jacob

last: Kitzman

state: MI

address: 4811 Med Sci II, 1241 E Catherine St

department: Department of Human Genetics

institute: University of Michigan

summary: Defective biosynthesis of the phospholipid PI(3,5)P2 underlies neurological disorders characterized by cytoplasmic accumulation of large acidic vacuoles. To identify novel genetic causes of lysosomal vacuolization, we developed an assay for enlargement of the lysosome compartment that is amenable to cell sorting and pooled screens. After calibration on cells lacking FIG4,  a known PI(3,5)P2 biosynthetic factor, we carried out a genome-wide knockout screen that captured fifteen genes, including VAC14 which is known to cause endosomal vacuolization. We selected three genes not previously associated with lysosome dysfunction for validation: C10orf35, LRRC8A, and MARCH7.  We isolated two clonal knockout cell lines for each gene and confirmed loss of protein expression. The knockout lines contained enlarged acidic vesicles with surface labeling of the endolysosomal marker LAMP2. This assay will be useful for characterizing variants of unknown significance in patients with neuromuscular or lysosomal storage disorders.  This genome-wide strategy for identification of genes with lysosomal function can also be adapted for drug screens to identify small molecules that correct vacuolization.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: We performed a CRSIPR screen to identify genes that, when mutated, result in accumulation of enlarged vacuoles.

middle: O


title: Pioneering function of Isl1 in the epigenetic control of cardiomyocyte cell fate [Isl1_Hypo_E10_5_RNA_seq]

first: Gergana

last: Dobreva

overall_design: We performed RNA-Seq profiling of 4 embryos at E10.5 Right ventricle Outflow tracts (OFT/RV) of Isl1 hypomorphic and control embryos.

first: Julio

last: Cordero

first: Rui

last: Gao


title: Juvenility and Vegetative Phase Transition in Tropical/Subtropical Tree Crops.

city: St. Lucia

first: Muhammad

middle: Umair

last: Ahsan

state: QLD

address: 306 Carmody Rd., The University of Queensland (UQ)

country: Australia

institute: The University of Queensland

type: Non-coding RNA profiling by high throughput sequencing

summary: In plants, juvenile to adult phase transition is regulated by the sequential activity of two microRNAs: miR156 and miR172. A decline in miR156 and increase in miR172 abundance is associated with phase transition. There is very limited information on phase transition in economically important horticultural tree crops, which have a significantly long vegetative phase affecting fruit bearing. Here we profiled various molecular cues known to be involved in phase transition and flowering, including the microRNAs miR156 and miR172, in three horticultural tree crops avocado (Persea americana), mango (Mangifera indica) and macadamia (Macadamia integrifolia). We observed that miR156 expression decreases as these trees age and can potentially be used as a juvenility marker. Consistent with findings in annual plants, we also observed conserved regulation of the miR156-SPL3/4/5 regulatory module in these genetically distant tree crops, suggesting that this pathway may play a highly conserved role in vegetative identity. Meanwhile, the abundance of miR172 and its target AP2-like genes, as well as the accumulation level of SPL9 transcripts, were not related with plant age in these crops except in avocado where miR172 expression increased steadily. Finally, we demonstrate that various floral genes, including AP1 and SOC1 were upregulated in the reproductive phase and can be used as potential markers for the reproductive phase transition. Overall, this study provides an insight into the molecular associations of juvenility and phase transition in horticultural trees where crop breeding and improvement is encumbered by long juvenile phases.

sample_organism:
Persea americana
Mangifera indica
Macadamia integrifolia

overall_design: Examination of 1 month (juvenile) old and 10 year old (mature/already flowering) avocado, macadamia and mango (1 month and 5 year old) trees,

middle: U

first: Alexander

last: Pocock

first: Milos

last: Tanurdzic

first: Stephen

last: Fletcher


title: Prospective analyses of white adipose tissue gene expression in relation to long-term body weight changes

city: Huddinge

first: Ingrid

last: Dahlman

address: Hälsovägen

country: Sweden

institute: Karolinska Institutet

summary:
The aim of this study was to investigate transcriptome signatures in human subcutaneous white adipose tissue (sWAT) before and after long-term weight changes and assess their predictive value for body weight change.
Long-term body weight change in adult women associates with altered sWAT transcriptome. Expression of genes associated with inflammation, insulin response, adipogenesis and lipogenesis are linked to weight loss. However, other pathways such as protein homeostasis not only associate with but also predict future weight gain suggesting that intrinsic factors in sWAT impact tissue expansion.

overall_design: A total of 56 women were followed longitudinally and subdivided into weight-stable (n=25), weight-gaining (n=14) and weight-losing (n=17) groups between baseline and follow-up (13±1 years). The subdivision is based on a cut-off for weight change between baseline and follow-up of ≥7%. Follow-up sWAT sample was missing for one weight-stable woman. The fasting sWAT transcriptome was analyzed by gene microarray at baseline and follow-up. Key genes associated with weight changes were validated using quantitative real-time PCR.


title: Pioneering function of Isl1 in the epigenetic control of cardiomyocyte cell fate [E8.75_Embryo_ATAC-seq]

summary: Generation of widely differing and specialized cell types from a single totipotent zygote involves large-scale transcriptional changes and chromatin reorganization. Pioneer transcription factors play key roles in programming the epigenome and facilitating recruitment of additional regulatory factors during successive cell lineage specification and differentiation steps. Here we show that Isl1 acts as a pioneer factor driving cardiomyocyte lineage commitment by shaping the chromatin landscape of cardiac progenitor cells. Using an Isl1 hypomorphic mouse line which shows congenital heart defects, genome-wide profiling of Isl1 binding together with RNA- and ATAC-sequencing of cardiac progenitor cells and their derivatives, we uncover a regulatory network downstream of Isl1 that orchestrates cardiogenesis. Mechanistically, we show that Isl1 binds to compacted chromatin and woks in concert with the Brg1-Baf60c-based SWI/SNF complex to promote permissive cardiac lineage-specific alterations in the chromatin landscape not only of genes with critical functions in cardiac progenitor cells, but also of cardiomyocyte structural genes that are highly expressed when Isl1 itself is no longer present. Thus, the Isl1/Brg1-Baf60c complex plays a crucial role in orchestrating proper cardiogenesis and in establishing epigenetic memory of cardiomyocyte fate commitment

overall_design: Genome wide ATAC-sequencing profiles in cardiac progenitors derived from control and Isl1 knockdown.


title: scRNA sequencing of 2 leukemia patients in remission after T cell therapy

city: Seattle

first: Kelly

last: Paulson

state: WA

address: 1100 Fairview Ave N

institute: University of Washington/Fred Hutch Cancer Research Center

summary: peripheral blood samples of two leukemia patients in remission were profiled by single cell RNA sequencing approximately 1 year after receiving WT1 specific transgenic T cell therapy, at a time when patients were in clinical remission

overall_design: single cell RNA sequencing of peripheral blood mononuclear cells

first: Aude

last: Chapuis

first: Phil

last: Greenberg

first: Valentin

last: Voillet

first: Raphael

last: Gottardo


title: Pioneering function of Isl1 in the epigenetic control of cardiomyocyte cell fate [Isl1_RNA_seq]

overall_design: Nkx2.5GFP reporter ES cell line stably transfected with Isl1Sh constructs were generated. Isl1Knockdown ES cell lines were differentiated into cardiovascular progenitors. Genomewide RNA-seq profiles were generated.


title: Quantitative proteomic and single-nucleus transcriptomics map of the sinus node elucidates the foundation of cardiac pacemaking

city: Copenhagen

first: Tune

middle: Hannes

last: Pers

address: Blegdamsvej 3B

department: Novo Nordisk Foundation Center for Basic Metabolic Research

country: Denmark

institute: University of Copenhagen

summary: The sinus node is a collection of highly specialised cells constituting the heart’s pacemaker. It is keenly debated whether the so-called membrane or alternatively Ca2+ clocks provide the molecular substrate of pacemaking. By high-resolution mass spectrometry, we quantified >7,000 proteins from sinus node and neighbouring atrial muscle. The abundances of 575 proteins differed between the two tissues, including particular differences in metabolic profiles and extracellular matrix composition. Most notably, the data reveal significant differences between the tissues in the ion channels responsible for the membrane clock, but not in Ca2+ clock proteins, suggesting that the membrane clock underpins pacemaking. By performing single-nucleus RNA sequencing of sinus node biopsies, we attributed protein abundances to specific cell types. Consistent with these results, incorporation of the ion channel expression differences into a biophysically-detailed atrial action potential model resulted in pacemaking and a sinus node-like action potential. Combining our quantitative proteomics data with computational modeling, we estimate ion channel copy numbers for sinus node myocytes. Our findings provide detailed insights into the unique molecular make-up of the pacemaker of the heart.

overall_design: Single-nucleus transcriptomics using the 10X Genomics Chromium system.

first: Maren

last: Schrölkamp

first: Kristoffer

last: Egerod

first: Jonatan

last: Thompson

middle: H

first: Alicia

last: Lundby


title: Gene expression data from normal mouse choroid plexus, choroid plexus papilloma and choroid plexus carcinoma

city: La Jolla

first: Jun

last: Wang

state: CA

address: 2880 Torrey Pines Scenic Drive

institute: Sanford Burnham Prebys Medical Discovery Institute

summary:
Atoh1-Cre; Myc/Myc mice developed choroid plexus papilloma and Atoh1-Cre; Myc/Myc; p53fl/fl mice developed choroid plexus carcinoma.
By studying the gene expression profiles of normal choroid plexus, choroid plexus papilloma and choroid plexus carcinoma in mice, we aim to gain a better understanding of the biology of choroid plexus tumors

overall_design: 5 replicates each of normal choroid plexus, choroid plexus papilloma and choroid plexus carcinoma were collected from different mice. Total RNAs were extracted from the collected tissue and microarray analysis was performed to obtain the gene expression profiles of all samples.

first: Robert

last: Wechsler-Reya


title: Unfolding the inactive X chromosome

status: Public on May 03 2019

city: Boston

first: Chen-Yu

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

summary: The inactive X chromosome (Xi) is folded in a stepwise process into a compartment-less structure. Here we investigate if the Xi can be unfolded in post-XCI cells. We began with ablating structural maintenance of chromosomes hinge domain containing 1 (Smchd1) in female mouse embryonic fibroblasts (MEFs), a cell type in which XCI is completed. We then performed in situ Hi-C on one Smchd1+/+ (wild-type, WT) and one Smchd1-/- (knockout, KO) MEF clone to probe the role of SMCHD1 in maintaining the higher-order structure of the Xi. To determine if the change in chromosome structure is accompanied by altered gene expression, we performed RNA-seq on two WT and two independently generated Smchd1-/- clones treated with either DMSO or 5-aza-2'-deoxycytidine (Aza), a DNA demethylating agent. In addition, we performed H3K27me3 and H2AK119ub ChIP-seq and Xist Capture Hybridization Analysis of RNA Targets with deep sequencing (CHART-seq) on one WT and one Smchd1-/- MEF clone to determine if there is an alteration in the epigenetic state of the Smchd1-/- Xi. Finally, we examined the role of Xist, Polycomb repressive complex 1 (PRC1), and Heterogeneous Nuclear Ribonucleoprotein K (HNRNPK) in regulating the Xi structure in post-XCI cells. To do so we performed in situ Hi-C on WT and Smchd1-/- MEFs depleted with either PRC1 or HNRNPK, as well as on fibroblasts in which Xist is deleted on the Xi (XidelXist).

overall_design: RNA-seq, H3K27me3 ChIP-seq, H2AK119ub ChIP-seq, Xist CHART-seq, and in situ Hi-C on WT and Smchd1-/- female MEFs. In situ Hi-C on Xi?Xist fibroblasts. In situ Hi-C on WT and Smchd1-/- female MEFs treated with scramble siRNAs or siRNAs against Ring1A and Ring1B (PRC1 KD) or HNRNPK (HNRNPK KD).

first: Jeannie

middle: T

last: Lee


title: Mouse Gsr-null liver transcriptome

city: Bozeman

first: Edward

last: Schmidt

state: MT

address: 109 Lewis Hall

department: Microbiology & Immunology

institute: Montana State University

summary: Genetic disruption of Gsr in mouse elicits only subtle changes in the liver transcriptome. Transcriptome analysis of Gsr-null livers was performed to further our understanding of pathways that may compensate for loss of Gsr, one of the two NADPH-dependent cytosolic disulfide reductases.

overall_design: Livers were harvested from male wild-type or Gsr-null 15-20 week old mice (n = 5, WT; n = 6, Gsr-null) between 2:00 p.m. and 4:00 p.m. Liver RNA was purified and processed for microarray analysis.

middle: E

first: Justin

last: Prigge


title: Pioneering function of Isl1 in the epigenetic control of cardiomyocyte cell fate [ISL1_Embryo_Chip_seq]

first: Gergana

last: Dobreva

overall_design: Genome wide Isl1 binding in E8.25-E9.0 anterior part of embryos by ChIP-sequencing

first: Julio

last: Cordero

first: Rui

last: Gao


title: Pioneering function of Isl1 in the epigenetic control of cardiomyocyte cell fate [ISL1_CPC_ChIP_seq]

overall_design: genome wide Isl1 Profiles in D5 cardiac progenitors derived from Nkx2.5gfp Es cell line.


title: Trancriptome profiling of bitransgenic sSHIP X C(3)1 Tag mammary cancer cells

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

summary: Study of sSHIP promoter expression as potential marker of mammary cancer stem cells isolation from transgenic mice Tg11,5kb-GFP X C(3)1 Tag

overall_design: Comparisons of genes expressed in Lin-CD49f+GFP+ cells versus Lin-CD49f+GFP- cells

first: R

last: Bourette

first: L

last: Tian


title: Paternally-acting canonical RNA-directed DNA methylation pathway genes sensitizes Arabidopsis endosperm to paternal dosage [RNA-Seq]

city: Cambridge

first: satyaki

middle: P

last: Rajavasireddy

state: Massachusetts

address: 455 Main Street

institute: Whitehead Institute for Biomedical Research

summary: Seed development is sensitive to parental dosage, with excess maternal or paternal  genomes creating reciprocal phenotypes. Paternal genomic excess results in extensive  endosperm proliferation without cellularization and eventual seed abortion. We  previously showed that loss of the RNA POL IV gene nrpd1 in tetraploid fathers  represses seed abortion in paternal excess crosses. Here we show genetically that  RNA-directed DNA methylation (RdDM) pathway activity in the paternal parent is  sufficient to determine the viability of paternal excess seeds. The status of the RdDM  pathway in paternal excess endosperm does not impact seed viability. Comparison of  endosperm transcriptomes, DNA methylation, and small RNAs from balanced and  paternal excess endosperm demonstrates that paternal excess seed abortion is unlikely  to be dependent on either transposable element or imprinted gene mis-regulation. We  suggest instead that loss of paternal RdDM modulates expression at a small subset of  genes and desensitizes endosperm to paternal excess. Finally, using allele-specific  transcription data, we present evidence of a transcriptional buffering system that up37  regulates maternal alleles and represses paternal alleles in response to excess paternal  genomic dosage. These findings prompt reconsideration of models for dosage  sensitivity in endosperm.

overall_design:
Examination of parent-of-origin specific and total gene expression in wild type and nrpd1 endosperm 6 days after pollination - 10 samples.
Balanced (Replicate1) GSM2858422
Balanced (Replicate2) GSM2858423
Balanced (Replicate3) GSM2858424
Balanced (Replicate4) GSM2482916
Balanced (Replicate5) GSM2482917

first: Mary

last: Gehring

first: Satyaki

last: PRV


title: Examination of ATF1 transcription factor binding peaks in colorectal cancer HCT116 cells

city: Wuhan

first: Tian

last: Jianbo

state: HuBei

address: Hangkong Road13, School of Public Health, Tongji Medical College, HUST

department: Key Laboratory for Environment and Health (Ministry of Education),

country: China

institute: Huazhong University of Science and Technology

summary: ATF1 encodes a sequence-specific activating TF containing a bZIP DNA binding domain, which is overexpressed in CRC tumor tissues compared with their paired normal tissues in two independent cohorts and that ATF1 amplification also frequently occurs across multiple cancer types. Moreover, ATF1 is more highly expressed in advanced stages of CRC. Mechanistically, ATF1 overexpression could provoke cell proliferation and xenograft growth in vitro and in vivo by affecting cell apoptosis, However, the exact mechanism and downstream transcriptional programs by which ATF1 provokes tumor activity are not well understood. We performed ChIP-seq in HCT116cells to investigate the regulatory mechamisms of ATF1.

overall_design: HCT116 cells treated with 3xFlag-ATF1 and then performed a falg-ATF1_ChIP-Seq.

first: Jianbo


title: Drosophila Trf4-1 involvement in mRNA and primary miRNA transcription

first: xi

last: zhou

state: Hubei

address: Luojia Hill

department: State Key Laboratory of Virology, College of Life Sciences

institute: Wuhan University

summary: Drosophila Trf4-1 is a polyadenylation polymerase or terminal nucleotidyl transferase (PAP/TENT) that has been reported to add poly(A) tails to snRNAs in nucleus or mRNAs in cytoplasm. Here, we found that the loss of Trf4-1 resulted in the reduction of mRNAs and primary miRNAs (pri-miRNAs) in both Drosophila S2 cells and adult flies. Interestingly, the role of Trf4-1 in transcription is independent of its PAP/TENT activity. Moreover, using the chromatin immunoprecipitation assay, we uncovered that the loss of Trf4-1 led to abnormal RNA polymerase II accumulation and reduced H3K4me3 binding in promoter regions.

overall_design: Small RNA profile of RNAi based knock-down cells

first: Yongxiang

last: Liu

first: Ming

first: Xin

first: Jia

last: Quan

first: Yuan

last: Fang

first: Yujie

first: Yang

last: Qiu

last: Yu

first: Xi

last: Zhou


title: RNA-Seq Analysis of Periocular Neural Crest and Embryonic Corneal Transcriptomes

city: Houston

first: Peter

middle: Y

last: Lwigale

state: Texas

address: 6100 Main street

department: BioSciences

institute: Rice University

summary:
Purpose: The goal of this study was to evaluate changes in the transcriptome profile during periocular neural crest differentiation into corneal endothelium and keratocytes.
Methods: RNA profiles of chick embryonic day (E3) periocular neural crest, E5 corneal endothelium, and E7 corneal endothelium plus keratocytes were generated in triplicate by deep sequencing using Illumina HS4000. Bowtie2 and HISAT were used to map clean reads to reference gene and genome, respectively. An average mapping ratio of 76.26% to the reference gene and 93.10% to the genome were generated with Galgal5 reference assembly.Transcripts were normalized and presented as Fragments Per Kilobase Million (FPKM). Differentially expressed genes between pNCvsEn and pNCvsKEn were examined. Expression of some candidate genes was validated by in situ hybridization.
Results: 790 transcripts were enriched between pNC and En, and 865 transcripts were enriched between pNC and KEn. Enriched transcripts correspond with KEGG pathways involved in cell proliferation, synthesis of extracellular matrix, focal adhesion, metabolism, and cancer. The RNA-Seq data serves as platform for further analyses of the molecular networks involved in NCC differentiation into corneal cells, and provides insights into genes involved in corneal dysgenesis and adult diseases.

first: Lian

last: Bi


title: Expression data from hypothalamic samples of WT mice fed normal diet vs high fat diet

city: Concord

first: Eirini

last: Vagena

address: 2331 Saint George Dr

institute: UCSF

summary:
The consumption of a 60% high fat diet leads to increased body weight and the development of the metabolic syndrome. We analyzed hypothalamic samples of WT mice as it has been previously shown that the hypothalamus plays a crucial role in the regulation of energy homeostasis.
We used microarrays to detail the global programme of gene expression affected by the consumption of a high fat diet specifically in the hypothalamus of WT mice.

overall_design: Young adult WT mice fed either normal chow or a high fat diet were sacrificed and hypothalamic samples were isolated. RNA extraction and hybridization on Affymetrix microarrays was performed. We sought to compare the effects of the consumption of a high fat diet versus normal chow on the hypothalamus. We decided to compare either a short exposure to high fat diet (4 wks) or long exposure (8 wks) to mice fed a normal chow.

first: George

last: Baillie


title: The tissue factor-thrombin axis drives pancreatic ductal adenocarcinoma through tumor cell-derived PAR-1

city: West Lafayette

first: Stephen

last: Konieczny

state: Indiana

address: 1203 W. State Street

department: Biological Sciences

institute: Purdue University

summary: RNA-Seq analysis reporting the transcriptional changes induced by treatment of mouse pancreatic ductal adenocarcinoma cell lines with thrombin for 24h

overall_design: Total mRNA profiles from C57Bl/6 mouse derived KPC [KRas-G12D; TRP53-R172H; Elas-CreER] pancreatic cancer cells or CRISPR/Cas9 generated KPC-Par1-KO cell lines 24h post treatment with either 1 U/mL thrombin or vehicle

first: Yi

last: Yang

first: Amanda

last: Stang

first: Brett

last: Monia

first: Alexey

last: Revenko

first: Joseph

last: Palumbo

first: Patrick

middle: G

last: Schweickert

first: Nadia

last: Atallah

first: Matthew

last: Flick


title: 10x Genonics Drop-seq single-cell RNA-seq of neonatal (P1.5) testis cells from mice treated with DMSO or Retinoic Acid.

city: San Antonio

first: Brian

middle: P.

last: Hermann

address: 1 UTSA Circle

department: Department of Biology

institute: University of Texas at San Antonio

summary: To reveal distinct transcriptomes associated with response of neonatal prospermatogonia to retinoic acid (RA), unselected testis cells from animals treated with RA or DMSO were used for 10x Genomics analysis 12 hours after treatment at P1.

overall_design: Unselected testis cells isolated from animals 12hr after treatment with DMSO or RA at midnight of P1 were used for this study. Two replicate experiments were performed using testes pooled from separate litters. Data are from a total of 34,153 cells.

first: Anukriti

last: Singh

first: Lorena

last: Roa-de-la-Cruz

first: Ellen

middle: K

last: Velte

first: Christopher

middle: B

last: Geyer


title: Paternally-acting canonical RNA-directed DNA methylation pathway genes sensitizes Arabidopsis endosperm to paternal dosage

first: satyaki

last: Rajavasireddy

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Investigation into whether the RD2 element in serotype M28 isolates of group A Streptococcus influences global gene expression

city: Reno

first: Paul

last: Sumby

state: NV

address: 1554 N. Virginia St.

institute: University of Nevada

summary: We used RNA-Seq to compare a parental M28 isolate with an isogenic mutant in which the RD2 element had been deleted.

overall_design: Parental M28 isolate MGAS6180 and an RD2 deletion mutant derivative (M28ΔRD2) were compared following growth in THY broth to the exponential phase of growth (an O.D.600 of 0.5).

first: Poulomee

last: Sarkar


title: Paternally-acting canonical RNA-directed DNA methylation pathway genes sensitizes Arabidopsis endosperm to paternal dosage [Bisulfite-seq]

overall_design: Sequencing of two replicates of bisulfite treated DNA from Balanced endosperm (Ler x Col), Lethal paternal excess endosperm (Ler x 4N Col), and Viable paternal excess endosperm (Ler x 4N nrpd1)

first: Mary

last: Gehring

first: Satyaki

last: PRV


title: Paternally-acting canonical RNA-directed DNA methylation pathway genes sensitizes Arabidopsis endosperm to paternal dosage [miRNA-Seq]

overall_design:
Sequencing of two replicates of small RNA from Lethal paternal excess endosperm (Ler x 4N Col) and two replicates of small RNA from Viable paternal excess endosperm (Ler x 4N nrpd1)
balanced_1 GSM2482928
balanced_2 GSM2482929
balanced_3 GSM2482930


title: Gene expression in p75NTR knockout mouse liver

city: Helsinki

first: Juho

last: Väänänen

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

summary: Comparison of gene expression patterns in liver of wildtype and p75NTR knockout mice

overall_design: Liver tissues from adult wildtype and homozygous p75NTR KO mice were processed for RNA sequencing analyses

first: Dan

last: Lindholm

last: Duc Pham

first: Maciej

last: Lalowski


title: Chromosomal deletion and chromatin remodeling Drive ABT-199 Resistance in B-cell Lymphomas

first: Jun

last: Qi

address: 450 Brookline Avenue

department: Cancer Biology

institute: Dana-Farber


title: Elevated Nrf2 response in TrxR1/Gsr-null livers

first: Edward

last: Schmidt

summary:
Liver-specific depletion of both of the cytosolic NADPH-dependent disulfide reductases, TrxR1 and Gsr, was shown to result in increased activation of Nrf2 as compared to elimination of either of these enzymes alone.
Activation of transcription factor Nrf2 and its downstream cytoprotective target genes by oxidative and electrophilic insults can protect cells from potentially carcinogenic damage. However, many cancers have an activated Nrf2 response, which can protect cancer cells from oxidative stress radiation. Gene expression profiles in TrxR1/Gsr-null livers provide a basis for understanding the complex responses to chronically elevated oxidative stress and damage.

overall_design: Livers were harvested from female wild-type and TrxR1/Gsr-null 4-week-old mice (n = 4, each genotype) between 10:00 a.m. and 11:30 a.m. Liver RNA was purified and processed for microarray analysis.

first: Justin

last: Prigge


title: Mouse Gsr-null and TrxR1/Gsr-null liver transcriptomes


title: Chromosomal deletion and chromatin remodeling Drive ABT-199 Resistance in B-cell Lymphomas [ChIP-seq]

summary: Drug-tolerant “persister” cells underlie the emergence of drug-resistant clones and allow residual tumors to survive therapy; thus, represent an attractive therapeutic target to mitigate relapse.  With the promising outcome, yet some resistance cases surfaced after the approval of venetoclax (ABT-199), we defined a novel invasive drug resistance mechanism induced by Bcl2 inhibitor via examining the evolution of drug tolerant persister clones generated with ABT-199 treatment. The ABT-199 drug-tolerant persister cells showed genetic alteration by losing the copy number at 18q21 paralleled with BCL2, PMAIP1 and TCF4 gene downregulation.  The persister status are generated through major enhancer-remodeling mediated transcriptional activation of the super enhancer, which offered unique opportunity for overcoming the drug resistance.  The insight of major determinant for ABT-199 persistence evolution identified the molecular vulnerability in Bcl2 inhibitor resistant lymphoma cells through CDK7 pathway inhibition. The combined CDK7 and BCL2 inhibition was found to be more effective against ABT-199 persistence ex vivo and in vivo rather than the parental line, and CDK7 inhibition eliminated the persister phenotype by blocking dynamic active enhancer formation to further prevent the evolution of drug resistance.  Together, these studies unified genetic alteration and non-mutational adaptive response as a drug resistance mechanism, more importantly, demonstrated a rationale for transcriptional inhibition-based combination strategies to prevent and overcome drug resistance in B-cell malignancies.

overall_design: Study of H3K27ac and Pol2 localization in Mantle cell lymphoma cell line and Mantle cell lymphoma, double hit lymphoma, and B-cell lymphoblastic lymphoma/leukemia

middle: M

last: Park


title: Genome-wide Identification of DEAD-box RNA Helicase Targets Reveals Roles for RNA Secondary Structure Remodeling in mRNA Processing (Structure-seq)

first: Elizabeth

middle: J

last: Tran

state: IN

address: 175 S. University Street

department: Biochemistry

summary: Accurate gene expression requires the coordination of RNA processing with assembly of messenger RNA-protein (mRNP) complex. RNA helicases are a class of enzymes that unwind RNA duplexes in vitro and have been are proposed to remodel RNA structure in vivo. Herein, we provide evidence that the DEAD-box protein Dbp2 remodels RNA structure to facilitate efficient pre-mRNA processing in S. cerevisiae. First, we find that Dbp2 associates with the 3’ ends and 3’ splice-sites of mRNAs genome-wide.  Using structure-seq to map RNA secondary structure, we find altered secondary structures in dbp2∆ cells that overlap polyadenylation elements and correlate with inefficient termination. We also identify a role for Dbp2 in pre-mRNA splicing and show that both splicing and termination require Dbp2 helicase activity.  This reveals that DEAD-box RNA helicases unwind structure in vivo and that structural alteration of pre-mRNA is essential for proper gene expression.

overall_design: Structure-seq libraries for the wild type and dbp2∆cells. For each strain, there are DMS-treated and untreated samples, with the untreated ones serving as a control. There are 3 biological replicates for the wild type and 2 for dbp2∆ in both DMS-treated and untreated condition.

first: Yu-Hsuan

last: Lai

first: Krishna

last: Choudhary

first: Shraon

last: Aviran


title: Genome-wide Identification of DEAD-box RNA Helicase Targets Reveals Roles for RNA Secondary Structure Remodeling in mRNA Processing


title: DNA methylation from a Type I restriction modification system influences gene expression and virulence in Streptococcus pyogenes [PacBio]

status: Public on Apr 30 2019

city: Ann Arbor

first: Taylor

last: Nye

address: 1105 N University Ave

department: MCDB

institute: University of Michigan

summary: We used Pacific Biosciences Single Molecule Real-Time sequencing platform to identify modified motifs in an RM deficient strain of Streptococcus pyogenes

overall_design: Examination of modified motifs in an RM system deficient strain of Streptococcus pyogenes

first: Lyle

middle: A

last: Simmons

first: Michael

last: Watson Jr


title: Genome-wide Identification of DEAD-box RNA Helicase Targets Reveals Roles for RNA Secondary Structure Remodeling in mRNA Processing (iCLIP-seq)

overall_design: Individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) of Dbp2 and Set1 in Saccharomyces cerevisiae. 3 biological replicates for both Dbp2- and Set1-iCLIP. Set1-iCLIP serves as a negative control in this study.


title: comparative RNA-seq analysis of murine lung infected with A.fumigatus

city: Terre Haute

first: Steven

last: Templeton

address: 620 Chestnut St. HH135

institute: Indiana University School of Medicine - Terre Haute

summary: We report the application of RNA-seq analysis for high-throughput profiling of murine lungs infected with Aspergillus fumigatus. We compared the lung transcription of wildtype murine lungs and lungs from mice deficient in metabolic cytokine adiponectin.

overall_design: Examination of 2 different mice strain and comparison of lung transcripts in response to Aspergillus fumigatus infection.

first: Nansalmaa

last: Amarsaikhan


title: DNA methylation from a Type I restriction modification system influences gene expression and virulence in Streptococcus pyogenes


title: Transcriptomic characterization of Malus domestica response to Fe and P deficiency

city: Udine

first: Fabio

last: Marroni

address: Via delle Scienze 208

country: Italy

institute: Università di Udine

summary: Transcriptomic characterization of Malus domestica response to iron and phosphorus deficiency.

overall_design: RNA of roots of control plants, roots of Fe-deprived plants and roots of P-deprived plants were sequenced in triplicate on an Illumina HiSeq2000 Sequencer (9 samples in total).

first: Laura

last: Zanin

first: Nicola

last: Tomasi

first: Roberto

last: Pinton

first: Michele

last: Morgante


title: Field pathogenomics of Fusarium head blight reveals pathogen transcriptome differences due to host resistance

city: Urbana

first: Santiago

middle: Xavier

last: Mideros

state: Illinois

address: AW-101 Turner Hall / 1102 S. Goodwin Av.

department: Crop Sciences

institute: University of Illinois at Urbana Champaign

summary: Fusarium head blight (FHB), caused by Fusarium graminearum, is a detrimental disease that affects small grains such as wheat around the world. Management of FHB is difficult, and improved methods of surveillance as well as a better understanding of pathogen aggressiveness are needed for improved control. F. graminearum disease severity varies depending on the resistance of the host genotype. In this study, we used the field pathogenomics method to investigate gene expression and population structure of isolates collected from wheat lines of varying resistance levels (susceptible, intermediate, and resistant) as well as an axenic control. Differential gene expression was found among isolates collected from different host genotypes. Candidate gene sets were identified for both F. graminearum infection of specific host genotypes and general infection to wheat. Population structure of isolates from different resistance level sources was the same, with all isolates belonging to the NA1 population.

overall_design: SRA Study: SRP159931, Bioproject: PRJNA486288. Naturally infected head spikelet samples were collected from 3 wheat varieties (resistant, intermediate and susceptible to Fusarium head blight) from 4 different locations in central Illinios, plus an axenic control from a pure culture of F. graminearum. 13 samples total

first: Leigh

last: Fall

first: Melissa

last: Salazar

first: Jenny

last: Drnevich

first: Jessica

middle: R

last: Holmes

first: Meng-Chun

last: Tseng

first: Frederic

middle: L

last: Kolb

middle: X


title: Chromosomal deletion and chromatin remodeling Drive ABT-199 Resistance in B-cell Lymphomas [RNA-seq]

first: Jun

last: Qi

overall_design: All samples were prepared in biological triplicates. 1x106 Cells were treated for 6 hours with either 50/250nm THZ1 or DMSO at equal concentration as vehicle control. Total RNA was isolated using the Rneasy Plus Mini (Qiagen Cat# 74134) and ERCC spike in controls (Life Technologies, Cat 4456740) were added after total RNA extraction (1ul to 5000ng RNA). Library prep was conducted using TruSeq Stranded mRNA Library Prep Kit (Illumina Cat #RS-122-2101/2) according to manufacture instruction. RNA sequencing was done on HiSeq 2500v4 high output (50-bp, single-end reads).

first: Paul

last: Park


title: miR-450a acts as a tumor suppressor in ovarian cancer by readjusting energy metabolism

city: Bethesda

first: Markus

last: Hafner

state: MD

address: 50 South Drive

department: NIAMS

institute: NIH

summary: Dysregulation of miRNA expression is associated with multiple diseases, including cancers where they can have oncogenic or tumor suppressive function. Here we investigated the potential tumor suppressive function of miR-450a, one of the most significantly downregulated miRNAs in ovarian cancer. RNAseq analysis revealed multipe genes involved in the epithelial-to-mesenchymal transition (EMT) were suppressed by miR-450a overexpression ovarian cancer cell line A2780. Consistently, miR-450a overexpression reduced tumor migration, invasion and increased anoikis in A2780 and SKOV-3 cell lines and reduced tumor growth in ovarian xenographic model. Combining AGO-PAR-CLIP and RNAseq analysis, we identified a panel of potential miR-450a targets of which many, including TIMMDC1, MT-ND2, ACO2 and ATP5B, regulate energetic metabolism. miR-450a expression indeed decreased mitochondrial membrane potential but increased glucose uptake and viability after glutamine withdrawal, characteristics of less invasive ovarian cancer cell lines, which are also less dependent on glutamine. In summary, we propose in this work that miR-450a acts as a tumor suppressor in ovarian cancer cells by modulating targets associated with glutaminolysis, which would lead to a decrease in the production of lipids, amino acids and nucleic acids, and also inhibition of signaling pathways associated with EMT

overall_design: RNA-Seq from 3 different biological samples from SKOV3 and A2780 cell lines after miR-450a overexpression; small RNA-Seq from 3 different biological from A2780 cell line after miR-450a or miR-450b overexpression; AGO 4SU-PAR-CLIP from 2 to 4 biological samples from A2780 cells lines after miR-450a overexpression.

first: Bruna

last: Muys

first: Josane

middle: F

last: de Sousa

last: Plaça

first: Luíza

last: de Araújo

first: Aishe

last: Sarshad

first: Dimitrios

last: Anastasakis

first: Xiantao

last: Wang

first: Xiao

last: Li

first: Greice

last: de Molfetta

first: Anelisa

last: Ramão

first: Ashish

last: Lal

first: Daniel

middle: O

last: Vidal

first: Wilson

last: Silva Jr


title: Microarray data for Bhlhe40-sufficient and -deficient resident macrophages

city: St. Louis

first: Brian

middle: T

last: Edelson

state: MO

address: 425 S. Euclid Ave.

department: Pathology and Immunology

institute: Washington University in St. Louis

summary:
Most tissue-resident macrophage populations develop during embryogenesis, self-renew in the steady state, and can expand during type 2 immunity. Whether shared mechanisms regulate macrophage proliferation in homeostasis and disease is unclear. We found that the transcription factor Bhlhe40 was cell-intrinsically required in large peritoneal macrophages (LPMs) for self-renewal and maintenance, but was not required in other resident macrophages. Bhlhe40 was selectively necessary in LPMs for proliferation, but not polarization, in response to IL-4. During a helminth infection,
Bhlhe40 was required for normal LPM cell cycling. Bhlhe40 repressed the expression of Maf and Mafb and directly promoted expression of cell cycle-related transcripts to enable proliferation of LPMs. Genomic sites bound by Bhlhe40 in LPMs included some co-bound by the macrophage lineage-determining factor PU.1 and others uniquely bound by Bhlhe40, including Maf and cell cycle-related loci. Our findings demonstrate a tissue-specific control mechanism regulating resident macrophage proliferation in homeostasis and type 2 immunity.

overall_design: Bhlhe40+/+=Bhlhe40WT, Bhlhe40-/-=Bhlhe40KO, LysM-Cre+ Bhlhe40fl/fl=Bhlhe40LysM. AMs, 2 Bhlhe40+/+ and 2 Bhlhe40-/- samples sorted from naïve mice. Naïve LPMs, 3 Bhlhe40+/+ and 3 Bhlhe40-/- samples sorted from naïve mice. IL-4c-stimulated LPMs, 2 Bhlhe40+/+, 2 Bhlhe40-/-, and 2 LysM-Cre+ Bhlhe40fl/fl  samples sorted from IL-4c-treated mice

first: Nicholas

middle: N

last: Jarjour


title: Genome-wide analysis of pSTAT3 (Tyr705) in diffuse large B-cell lymphoma

city: Madison

first: Lixin

last: Rui

state: WI

address: 1111 Highland ave, Room 4053

institute: Wisconsin Ins for Medical Res

summary:
Diffuse large B cell lymphoma (DLBCL), the most common non-Hodgkin lymphoma, includes two main molecular subtypes: activated B cell-like (ABC) DLBCL and germinal center B cell-like (GCB) DLBCL. ABC DLBCL is more aggressive, with the activated JAK1-STAT3 pathway that promotes cell survival. In order to study the underlying pathogenic mechanism, we performed a ChIP-seq experiment by phospho-STAT3(Tyr705) antibody in ABC DLBCL cell lines, and identified 3,456 STAT3 target genes genome-wide. In parallel, ChIP-seq experiment was performed with STAT3 antibody in α-IgM stimulated naïve B cells for verification of these targets of STAT3 protein.
TMD8 was treated by eithor DMSO or AZD1480 (JAK inhibitor) for 4hrs, ChIP-seq experiments were performed by pSTAT3(Tyr705) antibody (#9145S, Cell signaling). Naïve B cells were collected from peripheral blood mononuclear cells by Naive B Cell Isolation kit (miltenyi biotec; 130-091-150), and treated by 10ug/ml α-IgM (southernbiotech; #2020-01) for 24hrs. ChIP-seq experiments were performed by STAT3 antibody (SC-482X, Santa Cruz).

overall_design: TMD8 cells were treated by eithor DMSO or AZD1480(JAK inhibitor) for 4hrs. Naïve B cells were collected from peripheral blood mononuclear cells by Naive B Cell Isolation kit (miltenyi biotec; 130-091-150), and treated by 10ug/ml α-IgM (southernbiotech; #2020-01) for 24hrs.

first: Li

last: Lu


title: CHD4 is essential for transcriptional repression and lineage progression in B lymphopoiesis [ATAC-seq]

city: Denver

first: James

last: Hagman

state: Colorado

address: 1400 Jackson St

department: Biomedical Research

institute: National Jewish Health

summary: Cell-lineage specification is a tightly regulated process that is dependent on appropriate expression of lineage- and developmental stage-specific transcriptional programs. Accessibility and inaccessibility of gene loci are controlled dynamically during cellular development. Here, we show that Chromodomain Helicase DNA-binding protein 4 (CHD4), a major ATPase/helicase subunit of Nucleosome Remodeling and Deacetylase Complexes (NuRD) in lymphocytes, is essential for specification of the early B cell lineage transcriptional program. In the absence of CHD4 in early B cell progenitors in vivo, B cell progenitors are arrested at an early pro-B-like stage of development, unresponsive to IL-7 receptor signaling and complete V(D)J rearrangements at Igh loci inefficiently. Importantly, CHD4-deficient B cells express a significant number of non-B cell lineage genes, including genes involved in the development of other hematopoietic lineages and neuronal cells. The absence of CHD4 increased chromatin accessibility at hundreds of these gene loci, suggesting that its ability to repress transcription by mobilizing nucleosomes and compacting chromatin is a barrier against inappropriate transcription. Together, our data demonstrate the importance of CHD4 in establishing and maintaining an appropriate transcriptome in early B lymphopoiesis via chromatin accessibility.

overall_design: ATAC-seq analysis of two independent samples each from wild type or Chd4 conditional knockout pro-B cells.

first: Tessa

last: Arends

first: Carissa

last: Dege

first: Alexandra

last: Bortnick

first: Thomas

last: Danhorn

first: Jennifer

last: Knapp

first: Haiqun

last: Jia

first: Laura

last: Harmacek

first: Courtney

last: Fleenor

first: Desiree

last: Straign

first: Kendra

last: Walton

first: Sonia

last: Leach

first: Ann

last: Feeney

first: Cornelis

last: Murre

middle: P

last: O'Connor


title: CHD4 is essential for transcriptional repression and lineage progression in B lymphopoiesis [RNA-seq]

overall_design: RNA-seq transcriptome analysis of three independent RNA samples each from wild type or Chd4 conditional knockout pro-B cells.

first: Brian


title: Resistin-like molecule α provides vitamin A-dependent antimicrobial protection of the skin

city: Pittsburgh

first: Zheng

last: Kuang

state: PA

address: 4400 Fifth Avenue

institute: Carnegie Mellon University

summary: The skin is the human body’s largest organ and is in contact with a diverse community of microorganisms  that includes both resident and pathogenic bacteria. Skin immune defenses include the production of  antimicrobial proteins that kill bacteria directly. However, we still have an incomplete understanding of  how skin antimicrobial proteins promote homeostasis with resident bacterial communities and limit  infection. Here, we show that resistin-like molecule α (RELMα) is an antibacterial protein that is produced  by keratinocytes and sebocytes in the mouse skin. RELMα expression was induced in mouse skin by  resident and pathogenic skin bacteria and was bactericidal for several bacterial species found on the skin,  including Streptococcus pyogenes. Mice lacking RELMα had altered resident skin bacterial communities  and were more susceptible to bacterial infection, indicating that RELMα controls bacterial colonization of  the skin. RELMα expression required dietary vitamin A and could be induced by therapeutic retinoids that  protected against bacterial infection in a RELMα-dependent manner. Resistin, another member of the  RELM family, was expressed in human skin, required retinoids for expression, and killed skin bacteria,  indicating a conserved function for RELM proteins in skin innate immunity. Our findings thus identify  members of the RELM family as antibacterial proteins that provide vitamin A-dependent antimicrobial  protection of the skin, and provide insight into why skin immunity requires adequate dietary vitamin A.

overall_design: Skin transcriptomes from 6 germ-free mice,  3 germ-free mice colonized with Staphylococcus aureus, 3 conventional mice on a control diet and 2 conventional mice on a vitamin A deprived diet were analyzed in this study

first: Tamia

last: Harris

first: Sureka

last: Gattu

first: Daniel

middle: C

last: Propheter

first: Shai

last: Bel

first: Kelly

last: Ruhn

first: Jay-Hyun

last: Jo

first: Christos

last: Zoubolis

first: Heidi

middle: H

last: Kong

first: Julia

last: Segre

first: Lora

middle: V

last: Hooper


title: Bhlhe40 mediates tissue-specific control of macrophage proliferation in homeostasis and type 2 immunity

last: Edelson

overall_design: Refer to individual Series


title: The biotroph Agrobacterium tumefaciens thrives in tumors by exploiting a wide spectrum of plant host metabolites

status: Public on Apr 29 2019

city: Gif-sur-Yvette

first: Almudena

last: González Mula

state: Ile-de France

address: 1 Avenue de la Terrasse

institute: CNRS

summary: Purpose:  The goals of this study is to compare the reponse of Agrobacterium tumefaciens C58 in the presence of GHB and GABA to delineated the key-genes associated to the response of these metabolites in A. tumefaciens C58.

overall_design: Agrobacterium tumefaciens C58 RNA profiles in the presence of GHB and GABA were generated by deep sequencing, in triplicate, using HiSeq technology.

last: Gonzalez-Mula


title: Transcriptome sequencing of WT and chloroquine resistance transporter (TgCRT) ortholog-deficient Toxoplasma parasites

city: Clemson

first: Zhicheng

last: Dou

state: South Carolina

address: 190 Collings Street

institute: Clemson University

summary:
Purpose: TgCRT spans the membrane of the digestive vacuole of Toxoplasma parasites. The deletion of TgCRT causes the swelling of the digestive vacuole, which could interfere with the physiology and function of the VAC. The goals of this study are to compare transcriptome profiling (RNA-Seq) of WT and TgCRT-deletion strains to understand what strategies Toxoplasma takes to regulate the size and morphology of the digestive vacuole to help parasite disseminate infection.
Methods: WT and TgCRT-deficient parasites were grown in human foreskin fibroblast cells for 2 days. The parasites were syringed, filter-purified, and resuspended in ice-cold PBS buffer. A trizol-based method was used to extract the total RNA from both strains. Total RNA was subjected to cDNA library construction using Illumina TruSeq RNA sample prep kit and Hi-Seq transcriptome sequencing.
Results: Approximately 20 million sequence reads per sample were mapped to the genome of Toxoplasma GT1 strain (release 34). The differential gene analysis identified 102 genes with a fold-change ≥1.5 and FDR <0.05.
Conclusions: Our study found that the ∆crt parasites reduce the transcript levels of several endolysosomal proteases, which could alleviate the proteolytic activities within the VAC to minimize the swelling. In addition, the RNA-Seq analysis also suggests that the parasites may activate their signaling pathways to manage the stress caused by the swelled VAC and increase other transporters to regulate the morphology of the digestive vacuole.

Grant title: Regulation of proteolytic activity within a digestive vacuole in Toxoplasma gondii, the most common pathogen causing infectious posterior uveitis in infants and children

Name of the funding source: Knights Templar Eye Foundation

Principal Investigator: Dr. Zhicheng Dou

overall_design: Total RNAs of WT and ∆crt parasites were converted to cDNA libraries that were subjected to Illumina HiSeq transcriptome sequencing. The assay was replicated in duplicate.


title: Human brain tissues from healthy controls and multiple sclerosis patients

city: Los Angeles

first: Yuichiro

last: Itoh

state: California

address: 635 Charles E. Young Drive South

department: Neurology

institute: UCLA

summary: Multiple sclerosis (MS) is characterized by cell proliferation, migration and damage in various cell types in different CNS regions and causes disabilities related to distinct neurological pathways, such as walking, vision and cognition. Here, region-specific transcriptomic approach was used to determine changes in gene expression in five different CNS regions (hippocampus, frontal cortex, internal capsule, corpus callosum, and parietal cortex) in MS.

overall_design: Five MS patients (average age = 57.6 years) and five age-matched healthy controls (average age = 56.2 years) fresh frozen autopsy samples were obtained from Human Brain and Spinal Fluid Research Center in Los Angeles.

first: Rhonda

last: Voskuhl


title: Gene expression in human adipose tissue derived stromal cells (ADSC) after exposure to hypoxia

status: Public on Apr 27 2019

city: Moscow

first: Natalia

last: Kalinina

address: 27-1, Lomonosovsky av

country: Russia

institute: Lomonosov Moscow State University

summary:
Analysis of mRNA expression in ADSCs exposed to severe hypoxia. Hypothesis tested that hypoxia stimulates the expression of angiogenesis and neurogenesis-related genes in cultured ADSC.

These data provide important information allowing to explain the role of ADSC in the stimulation of tissue regeneration

overall_design: Total RNA was extracted from ADSCs cultured in serum-free medium in either normoxic or hypoxic conditions

first: Tatiana

last: Lopatina


title: α7 nicotinic acetylcholine receptor signaling modulates fetal sheep brain astrocytes transcriptome in response to endotoxin stress: comparison to microglial transcriptome and implications for autism spectrum disorder

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: Neuroinflammation in utero may result in lifelong neurological disabilities. Astrocytes play a pivotal role, but the mechanisms are poorly understood. No early postnatal treatment strategies exist to enhance neuroprotective potential of astrocytes. We hypothesized that agonism on α7 nicotinic acetylcholine receptor (α7nAChR) in fetal astrocytes will augment their neuroprotective transcriptome profile, while the antagonistic stimulation of α7nAChR will achieve the opposite. Using an in vivo - in vitro model of developmental programming of neuroinflammation induced by lipopolysaccharide (LPS), we validated this hypothesis in primary fetal sheep astrocytes cultures re-exposed to LPS in presence of a selective α7nAChR agonist or antagonist. Our RNAseq findings show that a pro-inflammatory astrocyte phenotype acquired in vitro by LPS stimulation is reversed with α7nAChR agonistic stimulation. Conversely, antagonistic α7nAChR stimulation potentiates the pro-inflammatory astrocytic phenotype. Furthermore, we conduct a secondary transcriptome analysis against the identical α7nAChR experiments in fetal sheep primary microglia cultures and against the Simons Simplex Collection for autism spectrum disorder and discuss the implications.

overall_design: Samples from four sheep were used. From each animal we cultured astrocytes, and treated with lipopolysaccharide (LPS), LPS plus AR-R17779 hydrochloride (Tocris Bioscience Cat# 3964), a selective α7nAChR agonist, or LPS plus 100 nM α-Bungarotoxin (Tocris Bioscience Cat# 2133), a selective α7nAChR antagonist, or vehicle (control). There were four replicates for each treatment, except AR-R17779 hydrochloride, for which there were only three.

first: M

last: Cao

first: H

last: Liu

first: J

middle: W

last: Weaver

last: Cortes

first: L

middle: D

last: Durosier

first: P

last: Burns

first: G

last: Fecteau

first: A

last: Desrochers

last: Schulkin

last: Antonelli

first: R

last: Bernier

last: Dorschner

first: T

middle: K

last: Bammler

middle: G

last: Frasch


title: Loss of Lin28a Attenuates Cardiac Hypertrophy Induced by Pressure Overload

city: Chapel Hill

first: Jiandong

state: NC

address: 111 Mason Farm Road

department: Department of Pathology and Laboratory Medicine

institute: UNC at Chapel Hill

summary: Pathological cardiac hypertrophy is a major risk factor for the development of heart failure and sudden cardiac death, yet the molecular mechanism of cardiac hypertrophy is not fully understood. Recently, we found that the expression of Lin28a, a RNA-binding protein, was significantly upregulated during the early stages of cardiac hypertrophy. Interestingly, cardiac specific conditional deletion of Lin28a blunted pressure overload-induced cardiac hypertrophic responses. Given that Lin28a can bind to diverse mRNA to regulate their abundance and/or translation, we conducted RNA-seq to profile the cardiac transcriptome alteration without Lin28a under pressure overload.  It showed that metabolic pathways, including glycolysis and biosynthetic pathway, were remarkedly affected. Thus, our study identifies Lin28a as a crucial regulator of cardiac hypertrophy via its role in metabolic programming.

overall_design: Cardiac mRNA profiles of  cardiac specific Lin28 knockout mice and their control littermates subjected to pressure overload at Day 5 were generated by deep sequencing, in duplicate, using Illumina HiSeq 2500 (50bp x2).

first: Hong

last: Ma

first: Shuo

last: Yu

first: Ziqing

first: Li

last: Qian


title: Transcriptome profiles of three Muscat table grape cultivars at three developmental stage

city: beijing

first: LEI

last: SUN

institute: BEIJING ACADEMY OF FORESTRY AND POMOLOGY SCIENCES

summary: Vitis vinifera is widely grown worldwide for making wine and for use as table grapes. Of the existing cultivars, some have a floral and fruity flavour, referred to as a Muscat flavour. It is well-documented that this flavour originates from a series of terpene compounds, but the mechanism of terpene content differences among the Muscat-type cultivars remains unclear. Transcript and terpene metabolite profiles were integrated to elucidate the molecular mechanism of this phenomenon. In this research, three genotypes with different aromatic strengths were investigated by RNA sequencing. A total of 27 fruit samples from three biological replicates were sequenced on Illumina HiSeq 2000 at three stages, corresponding to the veraison; berries had intermediate Brix value and were harvest-ripe. After quality assessment and data clearance, a total of 254.18 Gb of data with more than 97% Q20 bases were obtained, approximately 9.41 Gb data were generated per sample. These results will provide a valuable dataset for the discovery of the mechanism of terpene biosynthesis.

overall_design: RNA sequence of 3 table grape cultvars at 3 developmental stages

first: Lei

last: Sun

first: Baoqing

last: Zhu


title: DNA methylation from a Type I restriction modification system influences gene expression and virulence in Streptococcus pyogenes [RNA-seq]

first: Taylor

last: Nye

summary: We used Illumina NGS to measure mRNA levels and perform subsequent differential expression analysis between wild type and RM system deficient strains of Streptococcus pyogenes

overall_design: Examination of mRNA levels across wild type and an RM system deficient strain of Streptococcus pyogenes

middle: M

first: Lyle

middle: A

last: Simmons

first: Michael

middle: E

last: Watson Jr


title: Unravelling the mechanisms of PFOS toxicity by combining morphological and transcriptomic analyses in zebrafish embryos

status: Public on Apr 28 2019

city: Barcelona

first: Rubén

middle: Francisco

last: Martínez López

state: Cataluña

address: Carrer Jordi Girona, 18-26

department: Environmental Toxicology

country: Spain

institute: IDAEA-CSIC

summary:
Purpose: the goal of this project is to study the effects of the PFOS (perfluorooctanesulfonate) in the transcriptome profiling (RNA-seq) of exposed zebrafish larvae.
Methods: Total RNA was isolated from the samples using AllPrep DNA/RNA Mini Kit (Qiagen, CA, USA) as described by the manufacturer. Three high quality sample per condition were chosen to the mRNA enrichment using KAPA Stranded mRNA-Seq Kit Illumina® Platforms (Kapa Biosystems). Transcriptomic profiles were generated by deep sequencing using Illumina TruSeq SBS Kit v3-HS (pair-ended; 2x76bp) on a HiSeq2000 sequencing system. Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.13.48) and followed by generation of FASTQ sequence files by CASAVA.
Statistical analysis: RNA-seq reads were aligned to the D. rerio reference genome (GRCz10) using STAR version 2.5.1b . Genes annotated in GRCz10.84 were quantified using RSEM version 1.2.28 with default parameters. Differential expression analysis between all PFOS conditions was performed with the DESeq2 (v.1.10.1) R package with the Likelihood ratio test option. ANOVA-PLS was performed on the normalized data using the lmdme package in R (v. 1.0.136, R Core Team).
Results: We generated on average 39 million paired-end reads for each sample and identified aproximatelly 24500 transcripts. 1434 differentially expressed genes (DEGs) were detected which could be divided in 2 clusters including 767 and 667 genes, respectively. Affected metabolic pathways were analyzed from the DEGs: lipid transport and metabolism, protein ubiquination, antigen processing, immune system, apoptosis, trans-membrane, cell matrix, Zn-ion binding, cytokines and JAK-STAT signaling pathways', among others, were down or upregulated.
Conclusions: Our results suggest a complex, multiple endocrine disruption-like toxic effects at a concentrations well bellow the 1 mg/L, considered as the LOAEC/NOAEC for many of the macroscopic effects traditionally linked to PFOS toxicity in zebrafish embryos. While our results confirm the known effect of PFOS in lipid metabolism, we found a clear decrease on expression of many genes related to natural immunity and defense against infections. We propose that this transcriptional pattern may be a marker for the immunotoxic effects of PFOS and other related substances in fish and other vertebrates, including humans. We concluded that our analysis allowed us the identification of underlying molecular mechanisms occurring simultaneously at the exposed animals. While this approach is very useful to analyze the effects of compounds, like PFOS, able to interact with different cellular targets, we believe that it can be also applied to the characterization of the different toxic components present in complex natural mixtures.

overall_design: Whole embryo (5 dpf; wild type zebrafish) mRNA profiles of 4 groups (control, 0.03, 0.3 and 1 ppm of PFOS) were generated by deep sequencing, in triplicate, using Illumina TruSeq SBS Kit v3-HS (pair-ended) on a HiSeq2000 sequencing system.

last: Martínez

first: Laia

last: Navarro-Martín

first: Chiara

last: Luccarelli

first: Anna

last: Esteve-Codina

first: Demetrio

last: Raldúa

first: Carlos

last: Barata

first: Romà

last: Tauler

first: Benjamin

last: Piña


title: Genome-wide Identification of DEAD-box RNA Helicase Targets Reveals Roles for RNA Secondary Structure Remodeling in mRNA Processing (RNA Pol II ChIP-seq)

city: West Lafayette

first: Elizabeth

middle: J

last: Tran

address: 175 S. University Street

institute: Purdue University

summary: Proper formation of messenger RNA-protein complexes (mRNPs) is critical for accurate gene expression and requires temporal regulation of mRNA structures. RNA helicases are major players that control mRNP/mRNA structures throughout the life of mRNAs. Our group has shown that the DEAD-box RNA helicase Dbp2 in S. cerevisiae is a bona fide RNA helicase in vitro that is required for proper transcription termination and assembly of RNA-binding proteins onto poly(A)+ RNA in vivo. Here, we utilized multiple genome-wide approaches to identify the mRNAs and processing steps targeted by the enzymatic activity of Dbp2. We found that Dbp2 promotes efficient termination of mRNA transcription through remodeling of RNA structures at the 3’ end of mRNAs. This finding elucidates how an RNA helicase regulates gene expression by modulating RNA structures at a genome-wide scale. In addition, Dbp2 facilitates efficient splicing, for which the helicase activity of Dbp2 is required. This reveals a previously uncharacterized role of RNA helicases besides known splicing factors. Overall, our work shows that Dbp2 plays a critical role in pre-mRNA processing and how RNA structure remodeling impacts gene expression.

overall_design: RNA Pol II ChIP-seq libraries for the wild type and dbp2∆cells expressing 3XFLAG tagged Rpb3. For each strain, there are input and IP samples. There are 3 biological replicates for the wild type and 3 for dbp2∆.

first: Yu-Hsuan

last: Lai


title: Identification of genes regulated by the antitermination factor NasT during denitrification in Bradyrhizobium diazoefficiens.

status: Public on Apr 26 2019

city: Sendai

first: Cristina

last: Sanchez

address: 2-1-1 Katahira, Aoba-ku

department: Graduate School of Life Sciences

country: Japan

institute: Tohoku University

summary:
Purpose: Identification of genes regulated by NasT during denitrifying growth in B. diazoefficiens.
Methods: Two biological replications were processed for each strain (wild-type USDA 110 and ΔnasT mutant). Sequencing was performed in an Illumina HiSeq 2000 Sequencing System in paired-end mode running 100x2 cycles (performed by Hokkaido System Science Co., Ltd.). Mapping of reads to the reference genome, read counting, normalization to RPKM (reads per kilobase per million mapped reads), and calculations of expression values were performed with default values with the CLC Genomic Workbench software 9.5.3. From the total reads that were generated, ~85% were trimmed, and from those, ~42% could be mapped onto the B. diazoefficiens genome. Genes with fewer than 10 reads per 1 million mRNA reads were omitted from the following analysis. A gene with a fold change ≥2 or ≤‒2 and a q value (estimate of false discovery rate) ≤0.05 was considered up- or down- regulated, respectively. The results were validated by qRT–PCR.
Conclusion: A total of 77 genes were differentially expressed in the ∆nasT mutant compared to those of the wild-type strain, with 38 genes decreased and 37 genes increased in the ∆nasT mutant. Most of these genes were related to nitrogen metabolism.

overall_design: RNA-seq transcription profiling of two replicates of B. diazoefficiens wild type and ∆nasT mutant grown anaerobically in the presence of nitrate at 10 mM.

last: Sánchez

first: Arthur

middle: F

last: Siqueira

first: Hisayuki

last: Mitsui

first: Kiwamu

last: Minamisawa


title: Chromatin immunoprecipitation sequencing (ChIP-Seq) for Bhlhe40 from naïve and IL-4c-stimulated large peritoneal macrophages (LPMs)

first: Brian

middle: T

last: Edelson

overall_design:
LPMs were sorted from pooled naïve and pooled IL-4c-treated C57BL/6 mice. Chromatin was crosslinked and immunoprecipitation (Novus Biologicals, anti-Dec1, catalog NB100-1800, Lot C1) was performed for Bhlhe40-bound genomic regions, which were sequenced along with input DNA controls from the same samples.
DNA from 1 naïve LPM ChIP and 1 IL-4c-stimulated ChIP were sequenced, as well as input DNA. Cells were pooled from multiple mice for each immunoprecipitation.

first: Nicholas

last: Jarjour

first: Irina

last: Shchukina


title: Local inhibition of PRC2 activity by histone H3.3K27M drives replication defects through misregulation of the JNK pathway [RNA-seq]

city: Geneva

first: Florian

last: Steiner

address: 30, Quai Ernest-Ansermet

department: Department of Molecular and Cellular Biology

country: Switzerland

institute: University of Geneva

summary: Substitution of lysine 27 with methionine in histone H3.3 is a recently discovered driver mutation of pediatric high-grade gliomas. Tumor cells carrying the mutation show a dramatic decrease in H3K27me3 levels due to physical inhibition of PRC2 methyltransferase activity. Here we use a C. elegans model to quantify the antagonistic effects of the H3.3K27M oncohistone on H3K27 trimethylation genome wide. We demonstrate that PRC2 is locally both simulated by H3K27me3 and inhibited by the oncohistone in a concentration-dependent manner.

overall_design: Examination of mRNA levels in gonads of wild type and H3.3K27M-carrying worms.

first: Kamila

last: Delaney


title: m7G methylation by METTL1 regulates let-7 microRNAs [m7G-RIP-Seq Caco2]

city: Genova

first: Luca

last: Pandolfini

state: Genova

address: Via Enrico Melen 83, Building B

department: Center for Human Technologies

institute: Istituto Italiano di Tecnologia - I

summary: Methylation of N7-methylguanosine (m7G) is found at mRNA caps and at defined internal positions within abundant tRNAs and rRNAs. However, its detection within low abundance mRNAs and microRNAs (miRNAs) has been hampered by lack of sensitive detection strategies. Here, we adapt a chemical reactivity assay to detect internal m7G in RNA from eukaryotic cells. Using this approach, alongside a confirmational RNA immunoprecipitation assay, we identify m7G within miRNAs inhibiting cell migration, and show that METTL1 mediates this m7G methylation. Using Let-7 as an example we demonstrate that METTL1 activity is necessary for correct processing, is required for Let-7 dependent gene regulation and consequently has a negative effect on cell migration. These results identify m7G modification as a new pathway for the regulation of miRNAs.

overall_design: Identification of miRNAs harboring m7G modification. Total RNA from a human lung cancer cell line (A549 cells) was decapped, 5' end dephosphorylated, and treated with NaBH4 and low pH to generate abasic sites at positions harbouring m7G. These sites were exposed to a biotin-coupled aldehyde reactive probe (N-(aminooxyacetyl)-n'-(D-biotinoyl) hydrazine; ARP) that covalently binds to the abasic RNA sites. Modified RNAs were then pulled-down using streptavidin-beads, small RNA libraries were prepared and RNAs were identified by NGS. To confirm the validity of this approach and to provide an independent verification of m7G-methylated miRNAs, we performed a RIP-Seq experiment employing an antibody that recognizes m7G in RNA.

first: Isaia

last: Barbieri


title: m7G methylation by METTL1 regulates let-7 microRNAs [BoRed-Seq & m7G-RIP-Seq A549]


title: m7G methylation by METTL1 regulates let-7 microRNAs [Expression Microarray KD A549]

overall_design: Microarray global gene expression analysis to identify transcripts affected by depletion of METTL1 in human A549 cells


title: Requirements for multivalent Yb body assembly in transposon silencing in Drosophila

city: Tokyo

first: Shigeki

last: Hirakata

address: 2-11-16 Yayoi, Bunkyo-ku

department: Department of Biological Sciences

institute: The University of Tokyo

summary: Female sterile (1) Yb (Yb) is a primary component of Yb bodies, perinuclear foci known as the site of PIWI-interacting RNA (piRNA) biogenesis in Drosophila ovarian somatic cells. Yb consists of Helicase C-terminal (Hel-C), RNA helicase and extended Tudor (eTud) domains. We previously showed that the RNA helicase domain is necessary for Yb−RNA interaction, Yb body formation and piRNA biogenesis. Here, we investigated the functions of the two other domains and found that Hel-C and eTud are necessary for Yb to self-associate and to interact with RNAs and other Yb body components, respectively. Both domains were essential for Yb body formation and transposon silencing. Without eTud, piRNA production was completely impaired. Loss of Hel-C severely reduced the levels of transposon-targeting piRNAs, although genic piRNAs unrelated to transposon silencing were still produced. Similar phenotypes were observed when mutations in flamenco, the primary source of transposon-targeting piRNAs, led to the expression of attenuated RNAs. Yb bodies are liquid-like multivalent condensates whose assembly depends on Yb self-association and widespread Yb−flamenco RNA binding.

overall_design: Four piRNA-seq libraries: piRNA libraries were prepared from RNA associated with Flag-Piwi immunoprecipitates (with size selection at 23-30 nt).

first: Mikiko

last: Siomi


title: m7G methylation by METTL1 regulates let-7 microRNAs

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

overall_design: Refer to individual Series


title: BET protein proteolysis targeting chimera (PROTAC) exerts potent lethal activity against Mantle Cell Lymphoma cells

city: Houston

first: Kapil

last: Bhalla

state: TX

address: 1515 Holcombe Blvd

department: Leukemia

institute: MD Anderson Cancer Center

summary: Bromodomain extraterminal protein (BETP) inhibitors transcriptionally repress oncoproteins and NFkB target genes, which undermines the growth and survival of MCL cells. However, BETi treatment causes accumulation of BETPs, associated with reversible binding and incomplete inhibition of BRD4, which potentially compromises the activity of BETi in MCL cells. Unlike BETi, BET-PROTACs (proteolysis-targeting chimera) ARV-825 and ARV-771 (Arvinas, Inc.) recruit and utilize an E3-ubiquitin ligase to effectively degrade BETPs in MCL cells. BET-PROTACs induce more apoptosis than BETi of MCL cells, including those resistant to ibrutinib. BET-PROTAC treatment induced more perturbations in the mRNA and protein expressions than BETi, with depletion of c-Myc, CDK4, cyclin D1, and the NFkB transcriptional targets Bcl-xL, XIAP and BTK, while inducing the level of HEXIM1, NOXA and CDKN1A/p21. Treatment with ARV-771, which possesses superior pharmacological properties compared to ARV-825, inhibited the in vivo growth and induced greater survival improvement than the BETi OTX015 of immune-depleted mice engrafted with MCL cells. Co-treatment of ARV-771 with ibrutinib or the BCL2-antagonist venetoclax or CDK4/6 inhibitor palbociclib synergistically induced apoptosis of MCL cells. These studies highlight promising and superior pre-clinical activity of BET-PROTAC than BETi, requiring further in vivo evaluation of BET-PROTAC as a therapy for ibrutinib-sensitive or resistant MCL.

overall_design: Twelve samples in biologic triplicates

middle: N


title: Innate Lymphoid Cells-Containing Fraction of Murine Lamina Propria Cells Produces Interleukin-17 upon Incubation with Giardia lamblia

status: Public on Apr 25 2019

city: Seoul

first: Juri

last: Kim

address: 50-1, Yonsei-ro, Seodaemun-gu

department: Environmental Medical Biology

country: South Korea

institute: Yonsei University

summary: Innate lymphoid cells (ILCs) are key players during an immune response at the mucosal surfaces, such as lung, skin, and gastrointestinal tract. Giardia lamblia is an extracellular protozoan pathogen that inhabits the human small intestine. In this study, an ILC-containing fraction (ICF) were prepared from the lamina propria of murine small intestine and incubated with G. lamblia trophozoites in the presence of transwell membranes. Transcriptional changes in Giardia-exposed ICFs were examined by RNA-seq analysis, resulting in identification of activation of several immune pathways.

overall_design: mRNA expression profiles of the mouse ILC-containing fraction (ICF) only cells or G. labmlia incubated ICF cells by Illumina Hi-seq 4000.

first: Soon-Jung

last: Park

first: Hye-Yeon

last: Lee

first: Eun-Ah


title: RNA sequencing on primary murine chondrocytes expressing mutant Idh1

city: Durham

first: Hongyuan

last: Zhang

address: 450 Research Drive

department: Orthopaedic Surgery / Cell Biology

institute: Duke University

summary: We report expression of a mutant Idh1 in murine chondrocytes caused a global change in the gene expression profile.

overall_design: mRNA profile of primary sternal chondrocytes from Col2a1Cre;Idh1 fl/fl mice and two control groups - Col2a1Cre and Idh1 fl/fl mice.

first: Benjamin

last: Alman


title: Single-cell RNA-seq analysis of human tonsil CD14+ cells

city: Paris

first: Paul

last: Gueguen

address: 26 rue D'Ulm

department: Inserm U932

institute: Institut Curie

summary: We performed single-cell RNA-seq on CD14+ cells isolated from the tonsils of one healthy donor. We used the 10x chromium technology.

overall_design: Tonsil phagocytes were prepared by centrifugation on a Ficoll gradient. Dendritic cells and macrophages were enriched by negative selection using magnetic beads. Cell populations were further isolated by cell sorting. Cellular suspensions (3500 cells) were loaded on a 10X Chromium instrument (10X Genomics) according to manufacturer’s protocol.

first: Elodie

last: Segura

first: Mélanie

last: Durand

first: Mylène

last: Bohec


title: Single-cell RNA-seq analysis of human tonsil CD4 T cells

summary: We performed single-cell RNA-seq on CD4 T cells isolated from the tonsils of one healthy donor. We used the 10x chromium technology.

overall_design: Tonsil CD4 T cells were enriched by negative selection using magnetic beads. Cell populations (CXCR5+PD-1low T cells, CXCR5+PD-1int T cells and CXCR5+PD-1high T cells ) were further isolated by cell sorting. Cellular suspensions (3500 cells) were loaded on a 10X Chromium instrument (10X Genomics) according to manufacturer’s protocol.


title: IL-12 abrogates calcineurin-dependent immune evasion during leukemia progression

city: Atlanta

first: Christopher

last: Porter

state: GA

address: 1760 Haygood Drive

department: Pediatrics

institute: Emory University

summary: Exploitation of the immune system has emerged as an important therapeutic strategy for acute lymphoblastic leukemia (ALL). However, the mechanisms of immune evasion during leukemia progression remain poorly understood. We sought to understand the role of calcineurin in ALL and observed that knocking-down calcineurin B (CnB) in leukemia cells dramatically prolonged survival in immune-competent but not immune-deficient recipients. Furthermore, immune-competent recipients were protected from challenge with leukemia if they were first immunized with CnB-deficient leukemia, suggesting robust adaptive immunity. In the bone marrow, recipients of CnB-deficient leukemia had expansion of T cell populations as compared to controls. Gene expression analyses of leukemia cells extracted from bone marrow identified Cn-dependent significant changes in the expression of immuno-regulatory genes. We confirmed increased secretion of IL-12 from CnB-deficient leukemia cells, sufficient to induce T cell activation ex vivo, an effect that was abolished when IL-12 was neutralized. Strikingly, recombinant IL-12 prolonged survival of mice challenged with highly aggressive B-ALL. Moreover, gene expression analyses from children with ALL demonstrate prolonged survival in those with higher expression of either IL-12A or IL-12B. These data suggest that leukemia cells are dependent upon calcineurin for immune evasion by restricting the regulation of pro-inflammatory genes, particularly IL-12.

overall_design: 8 samples total; 4 each of murine BCR-ABL1+/Arf null leukemia with a nonsilencing shRNA or shRNA directed against calcineurin B

first: Jennifer

last: Rabe


title: Mycofactocin is associated with ethanol metabolism in Mycobacteria

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary: Mycobacterium tuberculosis (Mtb) assimilates cholesterol during chronic infection, and its in vitro growth in presence of cholesterol requires Mycofactocin (MFT) biosynthesis genes, although the basis of this requirement is unclear. MFT belongs to the class of ribosomally synthesized and post-translationally modified peptides conserved in many Actinobacteria, and its biological function and structure requires further confirmation. To identify the function of MFT, we characterized mft gene deletion mutants constructed in M. smegmatis, M. marinum and Mtb. We found that the growth deficit of mft deletion mutants in cholesterol – a phenotypic basis for gene essentiality prediction – is ethanol-dependent. Furthermore, functionality of MFT was strictly required for mycobacterial growth in ethanol, implicating its role in ethanol metabolism. Although ethanol is a poor growth substrate, it perturbed the cellular metabolism profoundly. Transcriptional analysis revealed that the disruption of MFT caused respiration dysfunction and associated redox imbalance, which is proposed as an underlying mechanism of growth retardation of MFT mutants in cholesterol. Finally, MSMEG_6242 was found to be indispensable for ethanol assimilation and is a candidate catalytic interactor with MFT. The function of MFT appears to resemble pyrroloquinoline quinone cofactor, similar to their biosynthetic steps. While our results serve as a salutary reminder that gene essentiality is dependent on a context in which it is probed, they also establish MFT as a redox cofactor, along with flavin or nicotinamide, to enable the function of its dependent enzymes in mycobacteria.

sample_organism:
Mycolicibacterium smegmatis
Mycobacterium tuberculosis H37Rv

platform_organism: Mycobacterium tuberculosis variant bovis

overall_design: Microarray experiments were performed as dual-color hybridizations on custom Agilent M.smegmatis 4x44K (Agilent-017184) and Agilent Mtb V3 (Agilent-035148) arrays. To compensate for dye-specific effects, a dye-reversal color-swap was applied.

first: Gopinath

last: Krishnamoorthy

first: Stefan

last: Kaufmann


title: Identification of the pharmacological effects of Chrysanthemum morifolium Ramat. leaves extracts on high-fat diet induced obese mice through lipid-, and glucose metabolism

status: Public on Apr 24 2019

city: Daegu

first: Ri

last: Ryu

address: 80 Daehak-ro

department: Food Science and Nutrition

institute: Kyungpook National University

summary: We investigated that ethanol extracts of Chrysanthemum morifolium Ramat. leaves improved metabolic disease on high-fat diet induced obese mice using metabolic profiling of lipid-, glucose, inflammation and RNA-seq transcriptomic profling.

overall_design: Total RNA of epididymal adipose tissue was obtained from normal diet, high-fat diet (HFD), chrysanthemum leaf ethanol extract (CLE) or luteolin added high-fat diet-fed mice and mRNA expression-associated with lipid metabolism, thermogenesis and inflammation were measured in epididymal adipose tissue.

first: Myung-Sook

last: Choi


title: LIF-responsive genes in tumor-associated myeloid cells from ascitic fluid of syngeneic ovarian cancer model

status: Public on Apr 23 2019

first: Joan

last: Seoane

address: Vall d'Hebron 119-129

institute: VHIO

summary:
LIF has an important role in immunosupression in different scenarios, such as embryo implantation in the uterus, autoimmune disease or organ transplantation. We decided to study the role of LIF on the immune response to cancer. We found that tumors expressing high levels of LIF promote an immune-tolerant microenvironment precluding the anti-tumor immune response.
To establish the effect of LIF on tumor-associated myeloid cells (TAMCs), we used a syngeneic ovarian tumor model (ID8 cell line). We treated animals bearing tumors with anti-LIF antibody and isolated myeloid (CD11b+) cells from the ascites. RNA was extracted from the CD11b+ cells and the transcriptomic analysis was performed.

overall_design: Tumor bearing C57BL6 mice were treated from the day 12 after inoculation with anti-LIF neutralizing antibody for 25 days (twice a week)and euthanized. The ascitic fluid was extracted and myeloid cells were isolated with CD11b magnetic beads. CD11b+ cells were lysed for RNA extraction and hybridized on Affymetrix microarrays. We sought to obtain a decrease in M2-like phenotype genes in response to the treatment.


title: Selective Class IIa HDAC inhibitor alters gene expression in NRVMs

city: Aurora

first: Timothy

last: McKinsey

state: CO

department: Division of Cardiology

institute: University of Colorado Anschutz Medical Campus

summary: Expression profiling of neonatl rat ventricular cardiomyocytes (NRVMs) upon the treatement of Class IIa HDAC inhibitor

overall_design: NRVMs were treated with 3 μM TMP195 or DMSO for 48 hours, two sets for each treatment

first: Friederike

last: Schrelter

first: Tianjing

last: Hu


title: m7G methylation by METTL1 regulates let-7 microRNAs [m7G-RIP-Seq KD A549]

first: Luca

last: Pandolfini

first: Isaia

last: Barbieri


title: Tolerance Induction in Diabetogenic BDC-2.5 T cells

first: Braxton

middle: L

last: Jamison

address: 12800 East 19th Avenue Mail Stop 8333

department: Department of Immunology and Microbiology

institute: University of Colorado School of Medicine

summary: CD4 T cells play a critical role in promoting the development of autoimmunity in Type 1 Diabetes (T1D). The diabetogenic CD4 T cell clone BDC-2.5, originally isolated from a non-obese diabetic (NOD) mouse, has been widely used to study the contribution of autoreactive CD4 T cells and relevant antigens to autoimmune diabetes. Recent work from our lab has shown that the antigen for BDC-2.5 T cells is a hybrid insulin peptide (2.5HIP) consisting of an insulin C-peptide fragment fused to a peptide from chromogranin A (ChgA), and that endogenous 2.5HIP-reactive T cells are major contributors to autoimmune pathology in NOD mice. The objective of this study was to determine if poly(lactide-co-glycolide) (PLG) nanoparticles (NPs) loaded with the 2.5HIP antigen (2.5HIP-PLG) can tolerize BDC-2.5 T cells. Infusion of 2.5HIP-PLG NPs was found to prevent diabetes in an adoptive transfer model by impairing the ability of BDC-2.5 T cells to produce pro-inflammatory cytokines through induction of anergy, leading to an increase in the ratio of Foxp3+ regulatory T cells to IFN-γ+ effector T cells. This work is the first to use a hybrid insulin peptide, or any neoepitope, to re-educate diabetogenic T cells and may have significant implications for the development of an antigen-specific therapy for T1D patients.

overall_design: Sequencing of FACS-sorted BDC-2.5 TCR-transgenic, CD4-positive, Foxp3-negative (GFP-negative) effector T cells (Teffs) was performed in order to determine the mechanisms of tolerance induction. Activated BDC-2.5 T cells were adoptively transferred into NOD.scid mice and Teffs were sorted from spleen/lymph nodes of 2.5HIP-PLG treated or untreated mice (pooled from 4 mice per group) 6 days after T cell transfer. RNA-Seq data are from 1 experiment without replicates. An up-regulation of anergy related genes in tolerized Teffs was found.

first: Tobias

last: Neef

first: Andrew

last: Goodspeed

first: Brenda

last: Bradley

first: Rocky

last: Baker

first: Stephen

last: Miller

first: Kathryn

last: Haskins


title: The extruded non-template strand determines the architecture of R-loops

city: Davis

first: Frederic

last: Chedin

state: CA

address: 1 Shields Avenue

department: MCB

institute: UC Davis

summary: We show that these R-loop objects impose specific physical constraints on the DNA, as revealed by the presence of stereotypical angles in the surrounding DNA. Biochemical probing and mutagenesis experiments revealed that the formation of R-loop objects at Airn is dictated by the extruded non-template strand, suggesting that R-loops possess intrinsic sequence-driven properties. Consistent with this, we show that R-loops formed at the fission yeast gene sum3 do not form detectable R-loop objects. Our results reveal that R-loops differ by their architectures and that the organization of the non-template strand is a fundamental characteristic of R-loops, which could explain that only a subset of R-loops is associated with replication-dependent DNA breaks.

overall_design: Characterization of R-loop at Airn using Atomic Force Microscopy (AFM) and Single Molecule R-loop Footprinting sequencing (SMRF-seq)

first: Yeraldinne

last: Carrasco-Salas

first: Amélie

last: Malapert

first: Shaheen

last: Sulthana

first: Bastien

last: Molcrette

first: Léa

last: Chazot-Franguiadakis

first: Pascal

last: Bernard

first: Frédéric

last: Chédin

first: Cendrine

last: Faivre-Moskalenko

first: Vincent

last: Vanoosthuyse


title: Respiratory chain inactivation links cartilage-mediated growth retardation to mitochondrial   diseases

city: Cologne

first: Bent

last: Brachvogel

address: Joseph-Stelzmann Street 52

institute: University of Cologne

summary: In childhood skeletal growth is driven by transient expansion of cartilage in the growth plate. Common belief is that energy production in this hypoxic tissue mainly relies on anaerobic glycolysis and not on mitochondrial respiratory chain (RC) activity. However, children with mitochondrial diseases causing RC dysfunction often present with short stature, which indicates that RC activity may be essential for cartilage-mediated skeletal growth. To elucidate the role of the mitochondrial RC in cartilage growth and pathology, we generated mice with impaired RC-function in cartilage. These mice develop normally until birth, but their later growth is retarded. A detailed molecular analysis revealed that metabolic signaling and extracellular matrix formation is disturbed and induces cell death at the cartilage-bone junction to cause a chondrodysplasia-like phenotype. Hence, the results demonstrate the overall importance of the metabolic switch from fetal glycolysis to postnatal RC activation in growth plate cartilage and explain why RC dysfunction can cause short stature in children with mitochondrial disease

overall_design: The RNA from femoral growth plates of 12 days old Cre and CreTW littermate mice or cultured chondrocytes was isolated by phenol-chloroform extraction and RNA integrity was confirmed by   microcapillary electrophoresis (2100 Bioanalyzer, Agilent). For microarray analysis, 100ng RNA of growth plate cartilage from four Cre and CreTW mice, respectively, were amplified, labeled and hybridized to a 8x60K whole genome mRNA microarray using the Agilent protocol. Microarrays were scanned (Agilent G2595C scanner), data extracted and analyzed by GeneSpring V14.9 software (Agilent). mRNAs were selected according to their differential expression, to their similar expression levels in all four microarrays of a given genotype and to their statistical significance.

first: Tatjana

last: Holzer


title: Local inhibition of PRC2 activity by histone H3.3K27M drives replication defects through misregulation of the JNK pathway

first: Florian

last: Steiner