title: RNA-Seq Analysis of Genes Differentially Expressed across temporal and spatial deposition of wall ingrowths in Arabidopsis Phloem Parenchyma Transfer Cells

city: Newcastle

first: Yuzhou

address: University Drive

institute: University of Newcastle

summary: Transfer cells (TCs) play important roles in facilitating enhanced rates of nutrient transport at key apoplasmic/symplasmic junctions along the nutrient acquisition and transport pathways in plants. TCs achieve this capacity by developing elaborate wall ingrowth networks which serve to increase plasma membrane surface area thus increasing the cell’s surface area-to-volume ratio to achieve increased flux of nutrients across the plasma membrane. Phloem parenchyma (PP) cells of Arabidopsis leaf veins trans-differentiate to become PP TCs which likely function in a two-step phloem loading mechanism by facilitating unloading of photoassimilates into the apoplasm for subsequent energy-dependent uptake into the sieve element/companion cell (SE/CC) complex. We are using PP TCs in Arabidopsis as a genetic model to identify transcription factors involved in coordinating deposition of the wall ingrowth network. Confocal imaging of pseudo-Schiff propidium iodide-stained tissue revealed different profiles of temporal development of wall ingrowth deposition across maturing cotyledons and juvenile leaves, and a basipetal gradient of deposition across mature adult leaves. RNA-Seq analysis was undertaken to identify differentially expressed genes common to these three different profiles of wall ingrowth deposition. This analysis identified 68 transcription factors up-regulated two-fold or more in at least two of the three experimental comparisons, with six of these transcription factors belonging to Clade III of the NAC-domain family. Phenotypic analysis of these NAC genes using insertional mutants revealed significant reductions in levels of wall ingrowth deposition, particularly in a double mutant of NAC056 and NAC018, as well as compromised sucrose-dependent root growth, indicating impaired capacity for phloem loading. Collectively, these results support the proposition that Clade III members of the NAC domain family in Arabidopsis play important roles in regulating wall ingrowth deposition in PP TCs.

overall_design: The sampling enabled three different temporal and spatial pair-wise comparisons for RNA-Seq analysis, namely: (i) cotyledons at Day 5 vs Day 10; (ii) Leaf 1 and Leaf 2 (first juvenile leaves) at Day 10 vs Day 16; and (iii) basal vs apical third (base vs tip) of Leaf 12 at Day 31. This analysis provided temporal and spatial comparisons of tissues with absent vs abundant wall ingrowth deposition in phloem parenchyma transfer cells.

first: Jiexi

last: Hou

first: Fen

last: Yu

first: Suong

last: Nguyen

first: David

last: McCurdy


title: Gene expression profiles of migrating cell types Drosophila embryogenesis

status: Public on Dec 11 2017

city: Pasadena

first: Young-Kyung

last: Bae

state: CA

address: 1200 E California Blvd

country: USA

institute: Caltech

type: Expression profiling by high throughput sequencing

summary: Cell migration is an instrumental process that ensures cells are properly positioned to support the specification of distinct tissue types during development. To provide insight, we used fluorescence activated cell sorting (FACS) to isolate two migrating cell types from the Drosophila embryo: caudal visceral mesoderm (CVM) cells, precursors of longitudinal muscles of the gut, and hemocytes (HCs), the Drosophila equivalent of blood cells. ~350 genes were identified from each of the sorted samples using RNA-seq, and in situ hybridization was used to confirm expression within each cell type or, alternatively, within other interacting, co-sorted cell types. To start, the two gene expression profiling datasets were compared to identify cell migration regulators that are potentially generally-acting. 73 genes were present in both CVM cell and HC gene expression profiles, including the transcription factor zinc finger homeodomain-1 (zfh1). Comparisons with gene expression profiles of Drosophila border cells that migrate during oogenesis had a more limited overlap, with only the genes neyo (neo) and singed (sn) found to be expressed in border cells as well as CVM cells and HCs, respectively. Neo encodes a protein with Zona pellucida domain linked to cell polarity, while sn encodes an actin binding protein. Tissue specific RNAi expression coupled with live in vivo imaging was used to confirm cell-autonomous roles for zfh1 and neo in supporting CVM cell migration, whereas previous studies had demonstrated a role for Sn in supporting HC migration. In addition, comparisons were made to migrating cells from vertebrates. Seven genes were found expressed by chick neural crest cells, CVM cells, and HCs including extracellular matrix (ECM) proteins and proteases. In summary, we show that genes shared in common between CVM cells, HCs, and other migrating cell types can help identify regulators of cell migration. Our analyses show that neo in addition to zfh1 and sn studied previously impact cell migration. This study also suggests that modification of the extracellular milieu may be a fundamental requirement for cells that undergo cell streaming migratory behaviors.

overall_design: Examination of genes expressed in two migrating cell populations (CVM and hemocytes) during their active cell migration and the rest of cell types of corresponding stages

first: Angelike

last: Stathopoulos


title: Osteoprotection through the deletion of the transcription factor Rorβ in mice

status: Public on Dec 09 2017

city: Rochester

last: Monroe

address: 200 1st St SW

institute: Mayo Clinic

summary:
Purpose: To identify gene expression changes (using RNAsequencing) in MC3T3-E1 cells where Rorβ has been deleted using CRISPR/Cas9 (and a control cell line)
Method: MC3T3-Control and MC3T3-Rorβ-CRISPR(KO) cells were osteoblast differentiated for 2 days, and RNA was harvested (n=3 for each cell line)
Results: We identified genes and pathways (using IPA) that were significantly altered in the Rorβ-CRISPR(KO) cell line, compared with the Control cell line
Conclusions: Many pathways were changed, namely the Wnt pathway which is important to the biology of Rorβ and to osteoblast differentiation in general

overall_design: Control and Rorβ-CRISPR(KO) cells (n=3) were osteoblast differentiated for 2 days and RNA was harvested and submitted for high-throughput RNA sequencing

first: Joshua

last: Farr


title: Genome-wilde identification of decapping substrates in the yeast Saccharomyces cervisiae

city: Worcester

first: Feng

last: He

state: MA

address: 368 Plantation Street

department: Microbiology and Physiological Systems

institute: University of Massachusetts Medical School

summary: To assess the roles of the Dcp2 C-terminal domain and the decapping activators Pat1, Lsm1, and Dhh1 in mRNA decapping, we used RNA-Seq to analyze the expression profiles of yeast cells harboring a truncation of the Dcp2 C-terminal domain, mutations that render Dcp2 catalytically inactive, or deletions of the PAT1, LSM1, and DHH1 genes. Consistent with our recent model for decapping regulation, we found that: i) the Dcp2 C-terminal domain is an effector of both negative and positive regulation and that loss of these control functions causes significant deregulation of mRNA decapping; ii) rather than being global activators of decapping, Pat1, Lsm1, and Dhh1 directly target specific subsets of yeast mRNAs and loss of the functions of each of these factors has substantial indirect consequences for genome-wide mRNA expression; and iii) transcripts targeted by Pat1, Lsm1, and Dhh1 exhibit only partial overlap and, as expected, are targeted to decapping-dependent decay.

overall_design: Genome-wide expression profiles of the wild-type strain and each of the mutant strains were generated by RNA-Seq, in triplicate, using Illumina HiSeq4000. The transcripts differentially expressed in different mutant cells were identified by comparisons to the transcripts expressed in wild-type cells.

first: Alper

last: Celik


title: ETV2 cooperates with SCL for timely gene activation during hemogenic endothelium specification [RNA-Seq]

status: Public on Dec 12 2017

city: Los Angeles

first: Dan

last: Duan

address: 615 Charles E. Young Dr, Los Angeles, 90095

institute: UCLA

summary: By RNA sequencing, we report here some hemato-vascular genes could be induced and some mesodermal/ cardiac genes could be repressed by SCL with delay in ES cell derived day 4.75 endothelial cells in the absence of ETV2

overall_design: Examination of gene expression in day 4.75 and day 7 EB (embryoid body) Tie2+CD31+CD41- endothelial cells derived from WT, SclKO, Etv2KOiSCL and Etv2KOiETV2 ES cells

first: Tonis

last: Org

first: Valerie

last: Kouskoff

first: Georges

last: Lacaud

first: Hanna

middle: K

last: Mikkola


title: Beta-adrenergically stimulated RNA expression in Syk deficient brown adipocytes

city: Cambridge

first: Marko

last: Knoll

address: 9 Cambridge Center

institute: Whitehead Institute

summary: Cre recombinase activity was induced in differentiating brown adipocytes from CreERT2 Sykflox/flox mice in vitro, which resulted in a partial loss of Syk protein in mature brown adipocytes. Such cells were viable, morphologically normal and displayed largely normal gene expression as indicated by mRNA sequencing and qPCR analysis, suggesting that Syk is not required for survival and gene expression of terminally differentiated brown adipocytes. mRNA sequencing of Syk depleted brown adipocytes treated with 0.1 microM isoproterenol for 6 h showed that 2460 genes were not induced or suppressed upon stimulation. Gene set enrichment analysis revealed a great enrichment for genes essential for mitochondrial respiration and biogenesis, for genes associated with and required for adipogenesis, as well as for genes responsive to various stimuli in adipocytes among genes highly ranked by reduced fold changes in response to isoproterenol in the Syk deficient brown adipocytes.

overall_design: Poly A+ RNA sequencing (TrueSeqStrandedPolyA) was performed on RNA samples from in vitro tamoxifen treated day 8 brown adipocytes derived from UBC-CreERT2 Sykflox/flox and Sykflox/flox mice 6 h following stimulation with 0.1 μM isoproterenol in serum free medium and from unstimulated controls using a Illumina HiSeq genome sequencer.

first: Heide

middle: C

last: Patterson

first: Harvey

middle: F

last: Lodish


title: Neurog3-Cre p300/CBP mouse islets RNA-seq

city: Toronto

first: Chi Kin

last: Wong

address: 600 University Avenue

country: Canada

institute: LTRI

summary: We have performed RNA-seq on mouse islets lacking all p300 (p300 KO), all CBP (CBP-null), and one copy of CBP and all p300 (triallelic). The data revealed that p300 and CBP regulate some distinct but largely overlapping genes in islets. This was further confirmed by GO term and transcription factor target analyses, which suggested that these coactivators regulate genes that function similarly and converge to Hnf1a pathway.

overall_design: Six WT, three p300IsletKO, three CBPIsletKO and three CBPHet; p300KO samples were sequenced in two batches at UBC Biomedical Research Centre Sequencing Core. Each library was sequenced to a depth of at least 20 million paired end reads on a NextSeq 500 (Illumina, CA, USA).

first: William

last: Gibson


title: Cytosine modifications exhibit circadian oscillations that are involved in epigenetic diversity and aging [Bisulfite-Seq]

first: Art

last: Petronis

state: Ontario

address: 250 College St

department: Campbell Family Mental Health Research Institute

institute: Centre for Addiction and Mental Health

type: Methylation profiling by high throughput sequencing

summary: Circadian rhythmicity governs a remarkable array of fundamental biological functions and is mediated by cyclical transcriptomic and proteomic activities. Epigenetic factors are also involved in this circadian machinery; however, despite extensive efforts, detection and characterization of circadian cytosine modifications at the nucleotide level have remained elusive. In this study, we report that a large proportion of epigenetically variable cytosines show a circadian pattern in their modification status in mice. Importantly, the cytosines with circadian epigenetic oscillations significantly overlapped with the cytosines exhibiting age-related changes in their modification status. Our findings suggest that evolutionary advantageous processes like circadian rhythmicity can also contribute to an organism’s deterioration.

overall_design: The animals were singly housed with ad libitum access to food, water, and a 17 cm diameter running wheel mounted in the cage. The animals were entrained to a 24-hr light-dark cycle maintained at 12 hr light and 12 hr dark (LD 12:12), where Zeitgeber time 0 (ZT0) refers to light onset. Mice were euthanized for tissue collection at 9, 15, or 25 months of age by cervical dislocation. Harvested tissues were snap frozen in liquid nitrogen and stored in -80 °C prior to downstream processing. The sequencing experiment was performed in technical triplicates using padlock bisulfite/oxybisulfite sequencing (22306810).

first: Gabriel

last: Oh

first: Sasha

last: Ebrahimi

first: Matt

last: Carlucci

first: Aiping

last: Zhang

first: Akhil

last: Nair

first: Daniel

middle: E

last: Groot

first: Viviane

last: Labrie

first: Peixin

last: Jia

first: Edward

middle: S

first: Richie

middle: H

last: Jeremian

first: Miki

last: Susic

first: Tenjin

last: Shrestha

first: Martin

middle: R

last: Ralph

first: Juozas

last: Gordevicius

first: Karolis

last: Koncevicius


title: Identification of molecular pathways and candidate genes associated with cocks' comb size trait by genome-wide transcriptome analysis

status: Public on Dec 08 2017

city: Yangzhou

first: Yifan

last: Liu

address: No.58 Cangjie road

country: China

institute: Institute of Poultry Science, Chinese Academy of Agricultural Science

summary: In this study, RNA sequencing (RNA-seq) was employed to compare the whole transcriptomic differences between six Partridge Shank chickens that are divergent in comb sizes and divided into two groups. A total of 563 differentially expressed genes (DEGs) were found in the two groups. Among these DGEs, 277 were up-regulated and 286 were down-regulated in the big comb group. According to the animal QTL database, eight DEGs including BMP2 and CHADL matched the QTLs associated with the chicken comb traits. Functional annotation analysis revealed that the DEGs were involved in cell communication and calcium signaling. Protein-protein interaction network analysis showed that STK32A, PI3KR1, EDN1, HSPA5 and HSPA8 might have great impact on comb growth. Moreover, potential alternative splicing (AS) events and single nucleotide polymorphisms (SNP) were also identified.

overall_design: Examine gene expression level and identified DGEs related to comb size

first: Liu

last: Yifan


title: Integrated analysis of miRNA and mRNA expression profiles in 2-, 6- and 12-month-old Small Tail Han Sheep testes to explore the regulation in testis development

status: Public on Dec 10 2017

city: Changchun

first: Man

last: Bai

address: Xincheng Street

department: College of animal science and technology

institute: Jilin Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: The semen of Small Tail Han Sheep has characteristics of high yield, high density, and good motility. To reveal the key miRNAs, mRNAs and miR-Targets regulatory mechanisms in Small Tail Han Sheep testes development, integrated analysis of miRNA and mRNA expression profiles in 2-, 6-, and 12-month-old testes were investigated by RNA-seq technology and bioinformatics methods. As the results shown: 630, 102, and 322 differentially expressed (DE) mRNAs; 5, 1 and 4 DE known miRNAs; 132, 105 and 24 DE novel miRNAs were identified in 2- vs 6-month-old, 6- vs 12-month-old, and 2- vs 12-month-old testes, respectively. GO and pathway analysis showed: in 2- vs 6-month-old testes, DE mRNAs were mainly involved in sexual maturation process and the DE mRNAs were mainly involved in multiple metabolism and biosynthesis pathways; in 6- vs 12-month-old testes, DE mRNAs were mainly involved in metabolism and translation processes, and the most significant pathway that DE mRNAs involved in was ribosome pathway; in 2- vs 12-month-old testes, DE mRNAs were mainly involved in metabolism and physiological processes, and DE mRNAs were mainly involved in multiple metabolism and biosynthesis pathways. Subsequently, 76, 11 and 1 DE miR-Targets were identified in 2- vs 6-month-old, 2- vs 12-month-old, and 6- vs 12-month-old testes, respectively. 3 miR-Target regulatory networks were constructed based on these miR-Targets, which helped to elucidate the regulatory metabolism in Small Tail sheep testes development. Finally, 6 miRNAs and 7 mRNAs were selected to validate the RNA-seq data by RT-PCR.

overall_design: Investigation of mRNA and miRNA expression profiles in 2-, 6-, and 12-month-old Small Tail Han Sheep testes.

first: Huaizhi

last: Jiang


title: RNA-seq study comparing gene expression of wild-type and B. abortus ∆baaR deletion strain

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

summary: Comparison of the transcriptome profiles of wild-type Brucella abortus and a strain deleted for bab2_0215 (baaR), an IclR-family transcriptional regulator

overall_design: 3 samples for each strain (WT and ∆baaR) were analyzed

first: Julien

last: Herrou

middle: M

last: Czyż


title: Early ETI and PTI responses in Arabidopsis thaliana camta3-D (sr1-4d) mutant

city: Cologne

first: Barbara

last: Kracher

address: Carl-von-Linné-Weg 10

department: Plant-Microbe Interactions

country: Germany

institute: Max Planck Institute for Plant Breeding Research

summary: Innate immune responses of plant cells confer the first line of defence against pathogens. Signals generated by activated receptors are integrated inside the cell and converge on transcriptional programmes in the nucleus. In Arabidopsis, the CAMTA family of transcription factors plays a pivotal function in immunity. CAMTA binding motifs are highly enriched in the genes quickly induced during ETI and PTI. Using RNA-seq, we investigated the role of CAMTA TFs during the early ETI and PTI transcriptional responses.

overall_design: We compared the expression changes between an Arabidopsis mutant line carrying the camta3-D (sr1-4d) dominant negative mutation and Col-0 wild-type plants following treatment with the PAMP flg22 (100 nM), and the avirulent bacterial strains Pst DC3000 AvrRpm1 (OD600=0.001) and Pst DC3000 AvrRps4 (OD600=0.001). The expression changes were analysed at one time point after each treatment (1 hour for flg22 and 4 hours for Pst DC3000 AvrRpm1 and Pst DC3000 AvrRps4 treatments).

first: Takaki

last: Maekawa

first: Florence

last: Jacob

first: Paul

last: Schulze-Lefert


title: Time course RNA-seq analysis of expression changes upon MLACC expression in Arabidopsis using a dexamethasone-inducible system which mirrors NLR activation

summary: Innate immune responses of plant cells confer the first line of defence against pathogens. Signals generated by activated receptors are integrated inside the cell and converge on transcriptional programmes in the nucleus. The barley NLR intracellular receptor MLA is fully functionnal in Arabidopsis and the MLA N-terminal coiled-coil domain (MLACC) is sufficient for initiating the MLA-dependent immune signalling. Using RNA-seq, we analyzed the early MLACC-mediated transcriptional changes over time in a dexamethasone-inducible and pathogen-independent system.

overall_design: We used transgenic Arabidopsis plants expressing MLACC-mYFP under a dexamethasone-inducible promoter (DEXp), a genetic background in which an immune-like response can be turned on rapidly and synchronously in leaf cells after dexamethasone treatment. We used transgenic lines in WT and in the phytohormone-depleted and partially immunocompromised pen2 pad4 sag101 dde2 ein2 sid2 (ppsdes) sextuple mutant backgrounds to assess the contribution of the three main defense phytohormones (jasmonate, ethylene, salycilic acid) in the MLACC-mediated immune signalling. In order to substract defense-unrelated artifacts due to the dexamethasone treatment, we used plants expressing the mYFP under the dexamethasone-inducible promoter in WT background and non-transgenic sextuple mutant plants in parallel as negative control. Samples were collected at 0, 2, 4, 6, and 8 hours after dexamethasone infiltration into leaves. For each condition, three biological replicates were obtained.


title: c-Myc down-regulation is required for pre-acinar to acinar maturation in the pancreas (RNA-Seq)

city: Madrid

first: Enrique

last: Carrillo de Santa Pau

address: C/ Melchor Fernández Almagro, 3

department: Cancer Cell Biology Programme

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

summary: Multipotent pancreatic progenitors (MPC) are defined as Ptf1a+, Mychigh, Cpa+ cells. During the transition from MPC to unipotent acinar progenitors, c-Myc is down-regulated whereas Ptf1a is up-regulated, leading to the deployment of the acinar program. Here, we show that c-Myc and Ptf1a interact directly and c-Myc binds to, and represses, the transcriptional activity of the PTF1 complex in vitro and in vivo. Using Ela1-Myc mice, in which c-Myc is overexpressed in acinar cells starting at E14.5, we find that acinar cells fail to undergo normal maturation at P1 and this is followed by a massive subsequent repression of the acinar programme. Lineage tracing with Ptf1aCreERT2;Rosa26YFP and Ela1-Myc;Ptf1aCreERT2;Rosa26YFP mice receiving TMX at E15.5 and analyzed at E18.5 revealed that c-Myc overexpression is associated with activation of a hepatic programme but not with pancreatic lineage misspecification At 8 weeks, the silencing of the acinar program is associated with increased expression of the PRC2 complex in a c-Myc dependent manner. Genome wide studies show that Ptf1a and c-Myc display partially overlapping chromatin occupancy patterns and DNA binding competition. We conclude that c-Myc down-regulation during development is crucial for the maturation of pre-acinar to acinar cells. c-Myc overexpression may contribute to pancreatic carcinogenesis by restraining cell differentiation and rendering cells susceptible to transformation.

overall_design: Pancreas mRNA profiles of 8-week old wild type (WT) and ELA1-MYC mice were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Victor

middle: J

last: Sánchez-Arévalo Lobo

first: Francisco

middle: X

last: Real


title: c-Myc down-regulation is required for pre-acinar to acinar maturation in the pancreas (ChIP-Seq)

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Examination of Ptf1a and c-myc in Ela1-Myc mice


title: Next-Generation sequencing of the hippocampus transcriptome in aged and cognitive impaired rats

city: Phoenix

first: Matthew

last: Huentelman

state: AZ

address: 445 N 5th St

department: Neurogenomics

institute: TGen

summary: The current study employed next generation RNA sequencing using two different platforms (Illumina and Ion Proton) to examine gene expression differences related to brain aging, cognitive decline, and hippocampus subregions (CA1, CA3, DG). Young and aged rats were trained on a spatial episodic memory task. The results describe regional differences in gene expression and point to regional differences in vulnerability to aging. Aging was associated with increased expression of immune response related genes, particularly in the dentate gyrus. For the memory task, impaired performance of aged animals was linked to the regulation of Ca2+ and synaptic function in region CA1. Finally, we provided a transcriptomic characterization of the three subregions regardless of age or cognitive status, highlighting and confirming a correspondence between cytoarchitectural boundaries and molecular profiling.

overall_design: Male Fisher 344 rats of two ages, young (5-6 months, total n = 10; n = 5 AZ, n = 5 FL) and aged (17-22 months, total n = 24; n = 11 AZ, n = 13 FL) were obtained from National Institute on Aging's colonies (Taconic, FL; Charles River, AZ). Animals were maintained on a 12:12 hour light/dark schedule, and provided ad libitum access to food and water prior to the set shifting task. The Morris Water Maze test was conducted, and behavioural data were acquired with either Noldus EthoVision computer tracking software (Noldus Information Technology, (Leesburg, VA) in FL or AnyMaze (Wood Dale, IL) in AZ) and included path-length and time in the goal and opposite quadrants. Two weeks following water maze testing, rats were anesthetized with isoflurane (Piramal Healthcare), decapitated and the brain was rapidly removed. The hippocampus was isolated, a 1-2 mm slice was removed from the dorsal hippocampus, and the CA1, CA3 and dentate gyrus (DG) regions were dissected [1, 8]. The collected tissue was immediately frozen in liquid nitrogen and stored in -80ºC until processed.

first: L

last: Ianov

first: M

last: De Both

last: Chawla

first: A

last: Rani

last: Kennedy

first: I

last: Piras

first: J

last: Day

last: Siniard

last: Kumar

middle: D

last: Sweatt

first: T

last: Foster

first: C

middle: A

last: Barnes


title: PRK1/PKN1 controls migration and metastasis of androgen-independent prostate cancer cells

city: Freiburg

first: Judith

last: Müller

address: Breisacherstr. 66

department: Uniklinik Urologie/ZKF

institute: University Freiburg

summary: The aim of this study is to describe expression changes related to the metastatic behavior of PCa cells after siRNA-mediated knockdown of PRK1.

overall_design: siRNA-mediated knockdown of PRK1 in androgen-independent prostate cancer cell line PC3-M_luc2

first: Cordula

last: Jilg

first: Dominica

last: Willmann

first: Roland

last: Schüle


title: c-Myc down-regulation is required for pre-acinar to acinar maturation in the pancreas

last: Carrillo de Santa Pau

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

overall_design: Refer to individual Series


title: Astrocyte-enriched pan-brain aging transcriptome

city: Freiburg im Breisgau

first: Galina

last: Erikson

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Normal brain aging is marked by a cognitive decline, spurred by changes in cellular metabolism and homeostatic dysregulation, as well as modifications in synapses and neuronal connectivity. Astrocytes are well positioned as an effector of these changes, although how properties of astrocytes change with age remains unclear. Here, we address this question by profiling astrocytic gene expression from multiple brain regions of adult (4 month-old) and aged (2 years-old) mice. We isolated mRNA from transgenic mice where ribosomes within astrocytes were genetically tagged (GFAP-cre x RPL22-HA, astrocyte ribotag). We then used RNA sequencing to identify and quantify the astrocyte-enriched mRNA, analyzing 4 different brain regions: visual cortex, somatomotor cortex, hypothalamus, and cerebellum. Overall, we find that astrocyte expression of inflammatory and immune response factors increase with age, as well as changes in genes associated with metabolism, cholesterol synthesis, and synaptogenesis. Going forward, these data contribute to an understanding of astrocyte diversity and provide insight into the role of astrocytes in normal aging.

overall_design: Profile of aging and adult astrocyte-enriched mRNA from 4 different brain regions from GFAP-Ribotag mice (ribosomal pulldown), with 3 biological replicates and 1 input (non-pulldown) sample per time point and region

last: Boisvert

first: Nicola

last: Allen


title: Hippocampal subfield transcriptomic profiles: Regional vulnerability to age and cognitive impairment

city: Gainesville

first: Thomas

state: Florida

address: 1149 Newell Drive Bldg 59

department: Neuroscience

institute: University of Florida-McKnight Brain Institute

summary: The current study employed next-generation RNA sequencing to examine gene expression related to brain aging and cognitive decline. Young and aged rats were trained on a spatial episodic memory task. Hippocampal regions CA1, CA3 and the dentate gyrus (DG) were isolated. Poly-A mRNA was examined using two different platforms, Illumina and Ion Proton. The Illumina platform was used to generate lists of genes that were differentially expressed across regions, ages, and in association with cognitive function. The gene lists were then retested using the Ion Proton platform. The results describe regional differences in gene expression and point to regional differences in vulnerability to aging. Aging was associated with increased expression of immune response related genes, particularly in the dentate gyrus. Finally, for the memory task used, impaired performance of aged animals was linked to the regulation of Ca2+ and synaptic function in region CA1.

overall_design:
The study contains a total of 10 young (5-6 months) and 24 aged (17-22 months) Fischer 344 male rats which were used to investigate expression patterns associated with aging and behavior. Prior to gene analysis, the animals were characterized on an episodic memory task across two academic institutions to test the reliability of the task (University of Florida: 5 young rats and 13 aged rats; University of Arizona: 5 young rats and 11 aged rats). Following total RNA isolation for the CA1, CA3 and DG regions, next-generation sequencing (NGS) libraries were prepared for two platforms, Illumina and Ion Proton. For both platforms, poly-A selection of mRNA was performed followed by library preparation protocols for each NGS system. In addition, whole transcriptome sequencing in Illumina was also performed using the ribominus method to investigate differential expression of additional RNA species across the hippocampus.

This Series includes only the samples examined using the Ion Proton platform.

first: Lara

last: Ianov

first: Matt

last: De Both

first: Monica

last: Chawla

first: Asha

last: Rani

first: Andrew

first: Ignazio

first: Jeremy

first: Ashley

first: Ashok

first: Carol

last: Huentelman


title: The Psychiatric Risk Gene Transcription Factor 4 (TCF4) Regulates Neurodevelopmental Pathways Associated With Schizophrenia, Autism, and Intellectual Disability

city: Cardiff

first: Matthew

middle: James

last: Hill

address: Maindy Road

country: United Kingdom

institute: Cardiff University

summary: Common genetic variants in and around the gene encoding transcription factor 4 (TCF4) are associated with an increased risk of schizophrenia whereas rare variants have been found in patients with intellectual disability (ID), developmental disorders and autism spectrum disorder (ASD). Haploinsufficiency of TCF4 also causes Pitt Hopkins syndrome (PTHS); a condition characterized by developmental delay, ID and autonomic dysfunction. To understand the role of TCF4 in these disorders, we have used chromatin immunoprecipitation and next generation sequencing (ChIP-seq) to identify the genomic binding sites for TCF4. In this study we identify 10,604 binding sites assigned to 5,437 genes. De novo motif enrichment found that approximately 77% of the TCF4 binding sites contained at least one E-box (5’-CAtcTG). Furthermore, the majority of TCF4 binding sites overlapped with H3K27ac histone mark for active enhancers. Enrichment analysis on the set of TCF4 targets identified numerous, highly significant functional clusters for pathways including nervous system development, ion transport and signal transduction and co-expression modules for genes associated with synaptic function and brain development. Importantly, we found that genes harboring de novo mutations in schizophrenia (P < 5.3 x 10-7), ASD (P < 2.5 x 10-4) and ID (P < 7.6 x 10-3) were also enriched among TCF4 targets. These data demonstrate that TCF4 binding sites are found in a large number of neuronal genes that include genetic risk factors for common neurodevelopmental disorders.

overall_design: 2 TCF4 ChIP samples and 2 IgG negative controls

first: Marc

middle: P

last: Forrest

first: David

last: Kavanagh

first: Katherine

last: Tansey

first: Adrian

last: Waite

first: Derek

last: Blake


title: Novel transplantation modalities for generating transcriptionally dependable new microglia from hematopoietic stem and progenitor cells

city: Milan

first: Jose

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

country: Italy

institute: OSR - San Raffaele Scientific Institute

summary: Recent pre-clinical and clinical evidences indicate that hematopoietic stem and progenitor cells (HSPCs) and/or their progeny can serve as vehicles for therapeutic molecule delivery across the blood brain barrier by contributing to the turnover of myeloid cell populations in the brain. However, the differentiation and functional characteristics of the cells reconstituted after transplantation are still to be determined, and in particular whether bona fide microglia could be reconstituted by the donor cell progeny post-transplant to be assessed. We here firstly demonstrate that HSPC transplantation can generate transcriptionally-dependable new microglia through a stepwise process reminiscent of physiological post-natal microglia maturation. Hematopoietic cells able to generate new microglia upon transplantation into myeloablated recipients are retained within human and murine long-term hematopoietic stem cells (HSCs). Similar transcriptionally dependable new microglia cells can also be generated by intra-cerebral ventricular delivery of HSPCs. Importantly, this novel route is associated to a clinically relevant faster and more widespread microglia replacement compared to systemic HSPC injection. Overall, this work supports the relevance and feasibility of employing HSPCs for renewing brain myeloid and microglia cells with new populations endowed with the ability to exert therapeutic effects in the central nervous system, and identifies novel modalities, such as transplantation of enriched stem cell fractions and direct brain delivery of HSPCs, for increasing the actual contribution of the transplanted cells to microgliosis and their therapeutic activity.

overall_design: mRNA profiles of µ and TAµ myeloid brain populations were obtained in triplicate mice of Adult control, P10 control and  Adult BU-treated mice after GFP Lin-transplantation (both µ and TAµ populations)

first: Alessia

last: Capotondo

first: Rita

last: Milazzo

first: Alessandra

last: Biffi


title: ChIP-seq analysis of H3K4me3 and H3K27ac localization in breast cancer cells treated with a novel KDM5 inhibitor, , 5-aza-2' Deoxycytidine, or both

city: Baltimore

first: Benjamin

last: Leadem

state: MD

address: 1650 Orleans St. Suite 541

institute: Johns Hopkins University

summary: Recently, the H3K4 demethylase, KDM5B, was shown to be amplified and overexpressed in luminal breast cancer, suggesting it might constitute a potential cancer therapy target.  Here, we characterize, in breast cancer cells, the molecular effects of a recently developed small-molecule inhibitor of the KDM5 family of proteins, either alone, or in combination with the DNA demethylating agent 5-aza-2’ deoxycytidine (DAC).  Alone, the KDM5 inhibitor (KDM5i) increased expression of a small number of genes, but when combined with DAC, the drug enhanced the effects of the latter for increasing expression of hundreds of DAC responsive genes.  ChIP-seq studies revealed that KDM5i resulted in the broadening of existing, and creation of thousands of new H3K4me3 domains.  When compared to DAC alone, increased promoter and gene body H3K4me3 occupancy at DAC responsive genes was observed in cells treated with the drug combination.  Importantly, treatment with either DAC or DAC+KDM5i induced a dramatic increase in H3K27ac at enhancers with an associated significant increase in target gene expression, suggesting a previously unappreciated effect of DAC on transcriptional regulation.  Finally, we found that KDM5i could synergize with DAC to reduce the viability of luminal breast cancer cells in in-vitro assays.   Our study provides the first look into the molecular effects of novel KDM5i compounds and suggests that combining these with DAC may represent an exciting new approach to epigenetic therapy.

overall_design: MCF-7 cells were treated with either a mock treatment, KDM5 inhibitor (CPI-455), DAC, or both.  Cells were treated with either DAC or treament mock for 3 days, followed by 3 days of KDM5i or treatment mock.  Cells were fixed and chromatin was isolated immediately following this treatment.  H3K4me3 and H3K27ac localization was determined by ChIP-seq

first: Leadem

last: Benjamin

first: Baylin

last: Stephen


title: Transcriptome analysis of the biosynthesis of anthocyanins in Begonia semperflorens under low-temperature and high-light conditions

city: Zhengzhou

first: Wang

middle: jia

last: wan

state: Henan

address: Wenhua Road

department: academy of forestry

institute: Henan Agricultural University

summary: Anthocyanins are considered as a stress indicator due to their involvement in the response to many stresses including high light (HL) and low temperature (LT). With the development of transcriptomics, it is necessary to find the different and common points in the mechanisms of LT-induced and HL-induced anthocyanin biosynthesis . In the present study, we determined the transcriptomes of Begonia semperflorens leaves under three different conditions (CK, HL and LT). To validate the DEGs, we selected four core genes involved in anthocyanin biosynthesis to perform RT-qPCR, and then determined anthocyanin content. In total, 94,880 unigenes with a mean length of 635 bp were assembled. The N50 values of the transcripts and unigenes were 2,286 bp and 1,064 bp, respectively. The functional annotations of the unigenes were analysed against five protein databases. DEGs related to anthocyanin biosynthesis, transportation and regulation were identified. We also analysis the enrichment pathway, and discuss the difference in mechanisms of anthocyanin induced under low-emperature and high-light conditions. This study is the first to examine broad-scale gene expression in B. semperflorens. By identifying DEGs regulated by both LT and HL conditions, we found that anthocyanin accumulation was employed as a common strategy by Begonia seedlings in resisting LT and HL stress. By identifying DEGs regulated differently by LT and HL conditions, we found that Begonia seedlings also had some different strategies for resisting LT and HL stresses: anthocyanins were biosynthesized under HL condition, while lignin, proanthocyanidins and anthocyanins under LT condition.

overall_design: The four parallel samples of each treatment were then mixed together as each treatment sample. A leaf sample of at least 0.3 g was prepared from each sample, immediately frozen in liquid nitrogen and then stored at -80°C for RNA extraction.

first: Kai

last: Zhang

first: Jia

middle: W

last: Wang


title: Genes uniquely expressed in human growth plate chondrocytes uncover a distinct regulatory network

first: Daniel

last: Cohn

address: 615 Charles E Young Dr. South

department: Molecular, Cell, and Developmental Biology

institute: University of California, Los Angeles

summary: In this study we explore the gene set that is selectively expressed in chondrocytes and therefore determines the unique properties and functions of cartilage tissue. Through identification of cartilage-selective transcription factors, lncRNAs, enhancers and protein-coding genes, we address the determinants of cartilage-selective gene expression, including interactions among the regulatory molecules and selectively active promoters, which define the pattern of gene expression and ultimately chondrocyte biology. Among 34 previously undescribed cartilage selective lncRNAs, one particular lncRNA was found to be co-expressed with and reciprocally regulated by SOX9, the master transcriptional regulator of chondrogenesis, revealing a new aspect of the regulation of the gene for this critical determinant of chondrocyte function. Finally, we relate cartilage-selective gene expression to the human and mouse skeletal disorders that result from mutations in many of the selectively regulated genes, providing clinical context to the basic biological discoveries.

overall_design: Identification of cartilage-selective genes in human fetal cartilage by RNA-seq


title: Bladder-cancer-associated mutations in RXRA activate peroxisome proliferator-activated receptors to drive urothelial proliferation

status: Public on Dec 07 2017

city: St. Louis

first: Vivek

middle: K

last: Arora

state: MO

address: 660 S Euclid Ave

institute: Washington University School of Medicine

summary: RXRA regulates transcription as part of a heterodimer with 14 other nuclear receptors, including the peroxisome proliferator-activated receptors (PPARs).   Analysis from the TCGA raised the possibility that hyperactive PPAR signaling, either due to PPAR gamma gene amplification or RXRA hot-spot mutation (S427F/Y) drives 20-25% of bladder cancers.  Here we characterize mutant RXRA, demonstrating it induces enhancer/promoter activity in the context of RXRA/PPAR heterodimers.  Structure-function studies indicate the RXRA substitution allosterically regulates the PPAR AF2 domain via an aromatic interaction with the terminal tyrosine found in PPARs.  In urothelium, we find PPAR agonism is sufficient to drive growth factor independent growth, but only after deletion of the tumor suppressors Kdm6a and Trp53.  Similarly, mutant RXRA stimulates growth factor independent growth, in a manner reversible by PPAR inhibition.  These studies reveal a pro-tumorigenic interaction between loss of tumor suppressors and PPAR activation and implicate PPARs as targetable drivers of bladder cancer.

overall_design: Two independent bladder cancer cell lines, JMSU-1 and 575A, were transfected with retrovirus to generate stable cell lines expressing either human wild-type RXRA (RXRAwt) or a mutant form of RXRA, RXRA S427F (RXRAS427F).  RNA-seq was performed in biological triplicate on RXRAwt-expressing cells treated with vehicle or the PPARG agonist pioglitazone (pio), and RXRAS427F-expressing cells treated with vehicle.  Fragments were sequenced on an Illumina HiSeq-2500 or HiSeq-3000.  Transcriptomes in the wild-type and S427F conditions were compared to establish a causal role of the RXRA hot-spot mutation S427F in the hyper-activation of PPAR singling.

first: Angela

last: Halstead

first: Andrew

last: Schriefer


title: Chromatin Open/Close Logic in Cellular Reprogramming [RNA-Seq]

city: Guangzhou

first: dongwei

last: Li

state: Guangdong province

address: 190 Kai Yuan Avenue, Science Park

department: South China Institute for Stem Cell Biology and Regenerative Medicine

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

summary: The reprogramming of fibroblasts into pluripotent stem cells by Oct4, Sox2, Myc and Klf4 represents a unique system to understand the logic of cell fate decisions. The reprogramming process can be divided into initial, middle and maturation phases that are coupled to the ordered execution of multiple biological processes, of which one of the earliest is a mesenchymal to epithelial transition (MET). Yet, despite these critical insights, less is known about how the reprogramming factors alter the chromatin state to convert somatic cells back to pluripotent cells. Here we report the global chromatin accessibility dynamics as cells reprogram from a somatic to a pluripotent state as assessed by assay for transposase-accessible chromatin with sequencing (ATAC-seq). We show that chromatin changes during reprogramming are defined by a fast initial wave of chromatin changes from accessible/open to inaccessible/closed (OC), which is followed by a slower opening up of chromatin from closed to open (CO), and ends with a climactic wave of CO. The initial OC wave includes loci enriched with motifs for AP-1, TEAD, RUNX and ETS-family transcription factors. Consistently, over-expression of one of the AP-1-family members c-Jun, c-Fos and Fra1blocked reprogramming. c-Jun inhibits reprogramming by preventing OSK-driven OC and skewing the overall OC-CO dynamics.  Paradoxically, we show that Sox2 and to a less extent Oct4 and Klf4 are CO-, not OC-, mediators , suggesting that they must first activate potent OC factors to remodel chromatin. Indeed, we show that Sap30, a component of the Sin3 complex8, functions as such an OC factor. Together, our results reveal the chromatin accessibility logic during reprogramming and identify Sap30 as one of the first responders that help silence somatic genes.

overall_design: chromatin accessible profile of reprogramming cell were generated by ATAC-seq, in two replicates, using illumina nextseq 500

first: Dongwei


title: Xist-mediate chromatin inaccessibility requires B repeat

city: Oxford

first: Guifeng

last: Wei

address: South Parks Road

department: Department of Biochemistry

institute: University of Oxford

summary: The noncoding Xist RNA could mediate chromosome inaccessiblity, especially for the pre-open chromatin regions (enhancer, promoter, CTCF). However, Xist lacking the B-repeats loss the ability of closing the chromatin accessibility. ATAC-seq is consistent with the observation by ATAC-see. XR-PID denotes the Xist RNA polycomb interacting domain, including the entire B-repeats and part of C repeats.

overall_design: ATAC-seq for Dox-induced Xist and XistDelXR-PID cells, which contains Xist transgenes in male autosomes.

first: G

last: Pintacuda

first: N

last: Brockdorff


title: CLCN2 Chloride Channel Mutations in Familial Hyperaldosteronism Type II

city: Seoul

first: Jungmin

last: Choi

address: 73, Goryeodae-ro, Seongbuk-gu

country: South Korea

institute: Korea University College of Medicine

summary: Primary aldosteronism (PA), a common cause of severe hypertension, features constitutive production of the adrenal steroid aldosterone. We analyzed a multiplex family with familial hyperaldosteronism type II (FH-II) and 80 additional probands with unsolved early-onset PA. Eight probands had novel heterozygous variants in CLCN2, including two de novo mutations and four independent occurrences of the identical p.Arg172Gln mutation; all relatives with early-onset PA carried the CLCN2 variant found in probands. CLCN2 encodes a voltage-gated chloride channel expressed in adrenal glomerulosa that opens at hyperpolarized membrane potentials. In this data set, we examined RNA expression in H295R cells transfected with empty vector, WT and p.Arg172Gln CLCN2. Expression of CLCN2 led to increased expression of CYP11B2 and its upstream regulator NR4A2.

overall_design: RNA-seq of 2 independently transfected replicates each of empty vector, WT and p.Arg172Gln CLCN2.

first: Ute

middle: I

last: Scholl

first: Julia

last: Schewe

first: Richard

last: Lifton


title: In Vivo Target Gene Activation via CRISPR/Cas9-Mediated Trans-Epigenetic Modulation [RNA-seq]

city: La Jolla

first: Hsin-Kai

last: Liao

address: 10010 N. Torrey Pines Rd.

institute: Salk Institute

summary: Here we show the mRNA sequencing in mouse liver (1) by induction of dgIL-10 (2) by induction of dgKlotho.

overall_design: Gene expression of (1) dgMock vs dgIL-10, (2) dgMock vs dgKlotho

first: Juan

middle: C

last: Izpisua Belmonte

first: Fumiyuki

last: Hatanaka

first: Toshikazu

last: Araoka

first: Pradeep

last: Reddy

first: Min-Zu

last: Wu

first: Yinghui

last: Sui

first: Takayoshi

last: Yamauchi

first: Masahiro

last: Sakurai

first: David

last: O'Keefe

first: Estrella

last: Nuñez

first: Pedro

last: Guillen

first: Josep

last: Campistol

first: Cheng-Jang

first: Li-Fan

last: Lu

first: Concepcion

last: Rodriguez Esteban


title: Arabidopsis epiRILs, epiHybrids and Colombia wild type

city: Amsterdam

first: Maike

last: Stam

address: Science Park 904

department: Swammerdam Institute for Life Sciences

country: Netherlands

institute: University of Amsterdam


title: Genome re-sequencing of Arabidopsis epiRILs and epiHybrids

summary:
Despite the importance and wide exploitation of heterosis in commercial crop breeding, the molecular mechanisms behind this phenomenon are not completely understood.
In this study we aimed to understand and quantify the contribution of DNA methylation variation to heterosis in various traits of Arabidopsis. Therefore we created epigenetic hybrid lines from ddm1-derived epiRILs.
We performed whole genome sequencing on four epiHybrids and their parental lines (epiRILs & Col-wt) in duplicates to examine structural variants in hybrids genome wide and with a focus on previously mapped QTL regions.

overall_design: WGS is performed in four epiRIL lines and four epiHybrid lines (epiRILs 92, 150, 193, 232 and epiHybrids 92H, 150H, 193H, 232H and Col-wt)

first: Kathrin

last: Lauss

first: René

last: Wardenaar

first: Frank

last: Johannes


title: Genome wide study of microglia in Specific-pathogen-free (SPF) and Germ-free (GF) mice at different stages in males and females.

status: Public on Dec 06 2017

city: Singapore

first: jinmiao

last: chen

address: 8A Biomedical Grove, #04-06 Immunos

country: Singapore

institute: Singapore Immunology Network

summary: ATACseq was performed on microglia from male and female, SPF or GF mice to elucidate the chromatin accessibility implicated by microbiota and gender. Differential accessible regions (DARs) between the various groups gave some ideas on what different pathways or functions might be affected due to the different factors.

overall_design: Microglia from SPF and GF mice from embryonic and adult stages of both gender were sorted for sequencing. DARs were obtained to observe if any signicant genes were affected.

first: Donovan

last: Low

first: Florent

last: Ginhoux

first: Ronnie

last: Blecher

first: Ido

last: Amit


title: Structural and functional adaptation of Haloferax volcanii TFEα/β

city: London

first: Finn

last: Werner

address: Gower Street

department: Institute of Structural and Molecular Biology

institute: University College London

summary:
Purpose: The Haloferax volcanii ∆tfeB strain provided a unique opportunity to study a putative role of TFEβ in the regulation of gene expression.
Results: The deletion of the tfeB gene in H. volcanii results in the aberrant expression of approximately one third of all genes, consistent with its function as a basal transcription initiation factor. Interestingly, tfeB deletion particularly affects foreign genes including a prophage region.
Conclusions: Our results confirm the dual function of TFE as basal factor and regulator of transcription

overall_design: We isolated total RNA from Haloferax volcanii ∆tfeB H2644 and H2645 and the parental H53 strain during early exponential growth (O.D.650=0.2) and subjected it to next generation RNA sequencing (RNA-seq)

first: Thorsten

last: Allers


title: nhr1 RNAi

city: Kansas City

first: Alejandro

last: Sanchez Alvarado

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

summary: NHR-1 RNAI vs Unc afte 4, 6, 8 and 11 feedings

overall_design: 4 replicates of each of 4 nhr-1 timepoints with matching controls

first: Shasha

last: Zhang

first: Eric

last: Ross

last: Sánchez Alvarado


title: Bladder cancer associated mutations in RXRA activate peroxisome proliferator-activated receptors

first: Vivek

last: Arora

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

overall_design: Refer to individual Series


title: ChIP-seq Analysis of MCF7 Cells on Treatment with Estradiol with internal controls

city: York

first: Andrew

middle: Nicholas

last: Holding

address: Wentwork Way

department: Biology

institute: University of York

summary: A key challenge in quantitative ChIP-seq is the normalisation of data in the presence of genome-wide changes. Data-based methods often rely on assumptions that do not hold true. Misapplication of these methods to ChIP-seq data results in the suppression of the biological signal or erroneous measurement of differential occupancy. To develop methods that address this challenge, we generated two ChIP-seq datasets, measuring Estrogen Receptor-alpha (ER) binding and H4K12ac histone marks in MCF7 before and after 100 nm Estradiol treatment for 45 minutes and 2 hours respectively.

overall_design: 2 ER ChIP-seq experiments implementing internal normalisation strategies

first: Florian

last: Markowetz

middle: N


title: DNA methylome of potato

city: Fuzhou

first: Haifeng

last: Wang

state: Fujian

address: Shangxia dian

institute: Fujian Agriculture and Forestry University

summary: Bisulfite treatment libraries were made to characterize DNA methylaiton of potato

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


title: Additive Effects of Quorum Sensing Anti-activators on Pseudomonas aeruginosa Virulence Traits and Transcriptome

city: Seattle

first: Kyle

middle: Lowe

last: Asfahl

state: Washington

address: 1705 NE Pacific St

department: Microbiology

institute: University of Washington

summary: RNA-seq of the previously uncharacterized QslA and QteE regulons revealed overlapping, yet distinct groups of differentially expressed genes. Simultaneous inactivation of qteE and qslA had the largest effect on gene expression with 999 genes induced and 798 genes repressed in the double mutant vs. wild-type. We found that LasR and RhlR-activated QS genes formed a subset of the genes induced in the qteE, qslA, and double mutant. The activation of almost all of these QS genes was advanced from stationary phase to log phase in the qteE qslA double mutant.

overall_design: 5 strains x 2 growth phases x 3 replicates = 30 samples total

middle: L

first: Martin

last: Schuster


title: The histone code reader Spin1 controls skeletal muscle development

city: Freiburg

first: Holger

last: Greschik

address: Breisacher Strasse 66

department: ZKF

institute: University Medical Center Freiburg

summary: We report developmental defects in Spin1(Myf5-Cre) mice, in which Spin1 is ablated in skeletal muscle.

overall_design:
RNA sequencing of skeletal muscle of Spin1(Myf5-Cre) and control fetuses at E15.5 and E16.5 and of tibialis anterior of surviving Spin1(Myf5-Cre) and control mice at three weeks of age (P21).
ChIP sequencing using primary myoblast isolated from 10-day old mice and anti-SPIN1 antibody (custom SPIN1-5867) or anti-H3K4me antibody (Diagenode, C15410003).

first: Dominica

last: Willmann

first: Roland

last: Schüle


title: The contribution of the post-transcriptional regulator CsrA to RNA stability and translation and identification of binding partners

city: Gainesville

first: Anastasia

middle: Haley

last: Potts

state: FL

address: 1355 Museum Drive, Bldg. 981

department: Department of Microbiology and Cell Science

institute: University of Florida

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


summary: Analysis of RNA binding partners of the post-transcriptional regulator CsrA to translation during exponential growth in Escherichia coli

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

overall_design: 5 biological replicates CLIP-seq samples from 3xFLAG-CsrA and untagged control strains

middle: H

first: Tony

last: Romeo


title: Bladder Cancer Associated Mutations in RXRA activate Peroxisome Proliferator-Activated Receptors to Drive Urothelial Proliferation

first: Angela

middle: M

last: Halstead

last: Schriefer


title: Carrageenan catabolism is conferred by a complex regulon in marine heterotrophic bacteria

city: Jouy-en-Josas

first: Tatiana

last: Rochat

address: Domaine de Vilvert

country: France

institute: INRA

summary: Macroalgae contribute substantially to primary production in coastal ecosystems. Their biomass, mainly consisting of polysaccharides, is cycled into the environment by marine heterotrophic bacteria (MHB), using largely uncharacterized mechanisms. In Zobellia galactanivorans, we discovered and characterized the complete catabolic pathway for carrageenans, major cell wall polysaccharides of red macroalgae, providing a model system for carrageenan utilization by MHB. We further demonstrate that carrageenan catabolism relies on a multifaceted carrageenan-induced regulon, including a non-canonical polysaccharide utilization locus (PUL) and several distal genes. The genetic structure of the carrageenan utilization system is well conserved in marine Bacteroidetes, but modified in other MHB phyla. The core system is completed by additional functions which can be assumed by non-orthologous genes in different species. This complex genetic structure is due to multiple evolutionary events including gene duplications and horizontal gene transfers. These results allow for an extension on the definition of bacterial PUL-mediated polysaccharide digestion.

overall_design: The RNA-seq transcriptome analysis was performed using Zobellia galactanivorans DsijT strain cultivated in marine minimal medium with D-galactose (D-gal; reference condition), kappa-carrageenan (KC), iota-carrageenan (IC) or 3,6-anhydro-D-galactose (D-AnG), as unique carbon source. Expression values were calculated from three independent biological replicates (A, B and C). Total RNA were extracted, mRNA enriched using the Illumina Ribo-Zero rRNA Removal kit (Bacteria), then RNA-seq libraries were generated with the ScriptSeq V2 kit (Illumina). The sequencing was performed with a NextSeq 500 platform using a single-end 75 bases run.

first: Gurvan

last: Michel


title: Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins

city: Paris

first: Axel

last: Cournac

address: 25 rue Dr. Roux

institute: Institut Pasteur

summary: As in Eukaryotes, bacterial genomes are not randomly folded. Bacterial genetic information is generally carried on a circular chromosome with a single origin of replication from which two replication forks proceed bidirectionaly towards the opposite terminus region. Here we investigate the higher-order architecture of the Escherichia coli genome, showing its partition into two structuraly distinct entities by a complex and intertwined network of contacts: the replication terminus (ter) region and the rest of the chromosome. Outside ter, the condensin MukBEF and the ubiquitous nucleoid-associated protein (NAP) HU promote DNA contacts in the megabase range. Within ter, the MatP protein prevents MukBEF activity and contacts are restricted to ~280 kb creating a domain with distinct structural properties. We also show how other NAPs contribute to nucleoid organization, such as H-NS that restricts short-range interactions. Combined, these results reveal the contributions of major, evolutionary conserved proteins in a bacterial chromosome organization.

overall_design: Chromosome conformation capture of E. coli wt cells and several deletion mutants (fis. hns. matP. mukB. hupAB. mukBmatP) in different growth conditions

first: Virginia

last: Lioy

first: Martial

last: Marbouty

first: Stephane

last: Duigou

first: Julien

last: Mozziconacci

first: Olivier

last: Espeli

first: Frederic

last: Boccard

first: Romain

last: Koszul


title: Dissecting cell-type composition and activity-dependent transcriptional state in mammalian brains by massively parallel single-nucleus RNA-Seq

city: Philadelphia

first: Hao

last: Wu

state: PA

address: 415 Curie Boulevard

department: Genetics

institute: University of Pennsylvania

summary: Massively parallel single-cell RNA sequencing can precisely resolve cellular diversity in a high-throughput manner at low cost, but unbiased isolation of intact single cells from complex tissues, such as adult mammalian brains, is challenging. Here, we integrate sucrose-gradient assisted nuclei purification with droplet microfluidics to develop a highly scalable single-nucleus RNA-Seq approach (sNucDrop-Seq), which is free of enzymatic dissociation and nuclei sorting. By profiling ~18,000 nuclei isolated from cortical tissues of adult mice, we demonstrate that sNucDrop-Seq not only accurately reveals neuronal and non-neuronal subtype composition with high sensitivity, but also enables in-depth analysis of transient transcriptional states driven by neuronal activity, at single-cell resolution, in vivo.

overall_design: Single-nucleus RNA sequencing analysis of adult mouse cerebral cortex

first: Peng

last: Hu

first: Emily

last: Fabyanic

first: Deborah

last: Kwon

first: Sheng

last: Tang

first: Zhaolan

last: Zhou


title: RNA-seq of chicken small yellow follicles with different FSHR expression level

city: Tai'an

first: Wang

last: Yiya

state: Shandong

address: Daizong Street no.61

institute: Shandong Agricultural University

summary: The aim of study was to identify the differentially expressed genes in SYF by using Illumina RNA deep sequencing, one SYF has the highest expression level of FSHR, the other has the lowest expression level of FSHR. We sampled six follicles from three chickens.In order to discover the key genes that regulate the process of follicle selection. From RNA-seq results, we got 26.63G reads,when mapping the reads to chicken genome, 75.13%-78.40% reads were successfully mapped, and more than 98% reads were unique.and we found 1382 new genes,functional annotation of the new gene was also performed.

overall_design: RNA-seq of six small yellow follicles come from three chickens

first: Yiya

last: Wang

first: Yunliang

last: Jiang


title: The contribution of the post-transcriptional regulator CsrA to translation

first: Anastasia

last: Potts

summary: Analysis of the contribution of the post-transcriptional regulator CsrA to translation during exponential growth in Escherichia coli

overall_design: 5 biological replicates of ribosome protected fragments and paired RNA samples from wild type and csrA::kan mutant strains were analyzed

first: Tony

last: Romeo


title: The vertebrate protein Dead end maintains primordial germ cell fate by inhibiting somatic differentiation

city: Muenster

first: Theresa

last: Gross-Thebing

department: Institute of Cell Biology

institute: University Clinic Muenster

summary: Maintaining cell fate relies on robust mechanisms that prevent the differentiation of specified cells into other cell types. This is especially critical during embryogenesis, when extensive cell proliferation, patterning and migration events take place. Here we show that vertebrate primordial germ cells (PGCs) are protected from reprogramming into other cell types by the RNA-binding protein Dead end (Dnd). PGCs knocked down for Dnd lose their characteristic morphology and adopt that of various somatic cell types. Concomitantly, they gain a gene expression profile reflecting differentiation into cells of different germ layers, in a process that we could direct by expression of specific cell-fate determinants. Importantly, we visualized these events within live zebrafish embryos, which provide temporal information regarding cell reprogramming. Our results shed light on the mechanisms controlling germ cell fate maintenance and are relevant for the formation of teratoma, a tumor class composed of cells from more than one germ layer.

overall_design: Transcriptome profiling of 13hpf sorted germ cells of zebrafish embryos injected with either control or dead end Morpholino

first: Katsiaryna

last: Tarbashevich

first: Erez

last: Raz

first: Jochen

last: Seggewiss

first: Christian

last: Ruckert


title: Genome-wide gene expression profile from Arabidopsis epiRILs, epiHybrids and Colombia wild type

first: Maike

last: Stam

summary:
Despite the importance and wide exploitation of heterosis in commercial crop breeding, the molecular mechanisms behind this phenomenon are not completely understood.
In this study we aimed to understand and quantify the contribution of DNA methylation variation to heterosis in various traits of Arabidopsis. Therefore we created epigenetic hybrid lines from ddm1-derived epiRILs.
We performed RNA sequencing on four epiHybrids and their parental lines (epiRILs & Col-wt) in duplicates/triplicates to understand gene expression changes in hybrids genome wide and with a focus on previously mapped QTL regions.

overall_design: RNA-seq was performed in four epiRIL lines, four epiHybrid lines and Colombia wild type (epiRILs 92, 150, 193, 232 and epiHybrids 92H, 150H, 193H, 232H and Col-wt)

first: Kathrin

last: Lauss

first: Rurika

last: Oka

first: Frank

last: Johannes


title: Covalent inhibitor of the Rho family inhibits the migration of breast cancer cells

city: Shanghai

first: Cheng

last: Luo

state: Shanghai

address: No. 555 Zuchongzhi Road

institute: Shanghai Institute of Materia Medica

summary: Small GTPase proteins usually serve as molecular switches in various biological process, such as the proliferation, survival, and migration of cells. Mutations or aberrant activations of small GTPase proteins, such as Ras, are frequently observed in various kinds of cancers. Drug discovery efforts that target the Ras family proteins are making breakthroughs, while the discovery of efficient inhibitors that target the Rho family proteins is still stagnant. Protein members from the Rho family, such as RhoA and Cdc42, are key regulators of the migration and invasion of cancer cells. Thus inhibitors of the Rho family proteins are promising to become drug candidates that target cancer metastasis, which is a principal cause of cancer recurrence and chemotherapy failure. Here we show the discovery and characterization of a novel covalent inhibitor named DC-RC-063 that targets the Rho family proteins, using a combined approach of computations and experiments. Revealed by solved crystal structures, compound DC-RC-063 inhibited the activation of RhoA, by disrupting protein-protein interactions, in an allosteric manner. As compound DC-RC-063 inhibited the migration and invasion of breast cancer MDA-MB-231 cells, our findings proved that the Rho family proteins are targetable for covalent inhibitors via an allosteric mechanism. The novel binding site revealed by this inhibitor can be exploited for further development of anti-cancer drugs that target cancer metastasis.

overall_design: RNA-Seq in breast cancer MDA-MB-231 cells in the presence or absence of Rho family covalent inhibitor

first: Zhongya

last: Sun

first: Hao

last: Zhang

first: Liping

last: Liao


title: hMTR4 plays a central role in creating balanced nuclear RNA pools for degradation and export V

first: Hong

last: Cheng

address: 320 YueYang Road

department: Shanghai Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences

summary: To examine whether the competition between hMTR4 with AlyREF is important for the specific exosome recruitment,we sequenced the RNAs associating with hMTR4 in control and AlyREF overexpression cells.

overall_design: hMTR4 associated  RNAs isolated from control or AlyREF overexpression HeLa cells were generated by deep sequencing, using Illumina HiSeq X Ten.

first: Xudong

last: Wu

first: Jungang

last: Gu


title: Prep1 prevents premature adipogenesis of mesenchymal progenitors

city: Milan

first: Marco

middle: J.

last: Morelli

address: via Adamello 16

department: Center for Genomic Science of IIT@SEMM

institute: Istituto Italiano di Tecnologia


title: Prep1 prevents premature adipogenesis of mesenchymal progenitors [RNA-seq]

summary: Transcriptional regulators are crucial in adipocyte differentiation. We now show that the homeodomain-containing transcription factor Prep1 is a repressor of adipogenic differentiation since its down-regulation (DR) in both ex vivo bone marrow-derived mesenchymal stromal cells (MSC) and in vitro 3T3-L1 pre-adipocytes significantly increases their adipogenic differentiation ability. Prep1 acts at a stage preceding the activation of the differentiation machinery because its DR makes cells more prone to adipogenic differentiation even in the absence of the adipogenic inducers. Prep1 DR expands the DNA binding landscape of C/EBP(CAAT enhancer binding protein ) without affecting its expression or activation. The data indicate that Prep1 normally acts by restricting DNA binding of transcription factors to adipogenic enhancers, in particular C/EBP.

overall_design: mRNA profiles of 3T3-L1 cells with Prep1 down-regulated levels of expression 2 days before (-2 days) and 1 day after (1 day) of induction of adipogenic differentiation were generated by deep sequencing, in duplicates

first: Dmitry

last: Penkov


title: Breast cancer cells treated with a novel KDM5 inhibitor, 5-aza-2' Deoxycytidine, or both.

city: Baltimore

first: Benjamin

last: Leadem

address: 1650 Orleans St. Suite 541

institute: Johns Hopkins University


title: First insights into the pleiotropic role of vrf (yedF), a newly characterized gene of Salmonella Typhimurium

city: Barcelona

first: Dietmar

last: Fernandez Orth

state: Barcelona

address: C/Doctor Aiguader 88 Primera Planta, 08003, Isglobal CREAL

institute: IsGlobal

summary:
Salmonella possesses virulence determinants that allow replication under extreme conditions and invasion of host cells, causing disease. Here, we examined four putative genes, predicted to encode membrane proteins (ydiY, ybdJ, STM1441 and ynaJ) and a putative transcriptional factor (yedF). These genes were identified in a previous, study of a S. Typhimurium clinical isolate and its multidrug-resistant counterpart. For STM1441 and yedF a reduced ability to interact with HeLa cells was observed in the knock-out mutants, but an increase in this ability was absent when these genes were overexpressed, except for yedF which phenotype was rescued when yedF was restored.

In the absence of yedF, decreased expression was seen for: i) virulence-related genes involved in motility, chemotaxis, attachment and survival inside the host cell; ii) global regulators of the invasion process (hilA, hilC and hilD); and iii) factors involved in LPS biosynthesis. In contrast, an increased expression was observed for anaerobic metabolism genes. We propose yedF is involved in the regulation of Salmonella pathogenesis and contributes to the activation of the virulence machinery. Moreover, we propose that, when oxygen is available, yedF contributes sustained repression of the anaerobic pathway. Therefore, we recommend this gene be named vrf, for virulence-related factor.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: A transcriptomic comparison between the SL1344 strain and ∆yedF, using the RNA-Seq technique (3 replicates of each strain)

last: Fernández-Orth

first: Clara

last: Ballesté-Delpierre


title: hMTR4 plays a central role in creating balanced nuclear RNA pools for degradation and export VI

summary: To examine whether the competition between hMTR4 with ALYREF is important for the specific exosome recruitment, we performed stranded RNA-seq using rRNA-depleted nuclear RNAs isolated from ALYREF and control overexpression cells.

overall_design: rRNA-depleted RNAs isolated from control, ALYREF overexpression HeLa cells were generated by deep sequencing, using Illumina HiSeq X Ten.


title: Transcriptomal changes during differentiation of human iPS cells to PGC-like cells

city: Charlestown

first: Toshihiro

last: Shioda

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

summary: Pluripotent stem cell-derived human primordial germ cell (PGC)-like cells (hPGCLCs) may provide important opportunities to study human PGCs. We produced CD38+ hPGCLCs with a high efficiency [~43% of FACS-sorted embryoid body (EB) cells] from primed-pluripotency induced pluripotent stem cells (iPSCs) via 72-hour reprogramming towards ERK-independent naïve pluripotency. RNA-seq confirmed transcriptomal consistency of our hPGCLCs with hPGCLCs previously produced using various other methods. Immunohistochemical studies identified hPGCLCs exclusively at the outermost surface layer of EBs mostly as scattered cells, and live cell imaging revealed actively migrating hPGCLCs forming cellular protrusions. Both CD38+ hPGCLCs and CD38- EB cells significantly expressed PRDM1 and TFAP2C, but PRDM1 mRNA of CD38- cells lacked the 3’-untranslated region with let-7 and other miRNA binding sites known to regulate PRDM1 mRNA stability. Genes expressed specifically in hPGCLCs included early-PGC markers KIT, NANOS3, and SOX17, and cell migration genes, and their promoter sequences were enriched with TFAP2C binding motif. Whereas all hPGCLCs strongly expressed the CXCR4 chemotaxis receptor, its ligand CXCL12/SDF1 was not significantly expressed in the whole EBs. Exposure of hPGCLCs to CXCL12/SDF1 induced cell migration and anti-apoptosis genes; in contrast, genes involved in nuclear division were suppressed. Our study demonstrates a transcriptomal consistency of hPGCLCs produced using varying methods as well as distinct roles and/or regulation of PRDM1 and TFAP2C expression in development of human and mouse PGCs. Relevance of hPGCLCs to early-stage human embryonic PGCs randomly migrating in the midline region of human embryos before initiating directional chemotaxis under CXCR4-CXCL12/SDF1 signaling has also been suggested.

overall_design: Human iPS cells with primed pluripotency were converted to naïve pluripotency for 72 hours and then subjected to embryoid body formation, from which CD38-positive PGC-like cells and CD38-negative cells were isolated by FACS. Total RNA was extracted from FACS-enriched cells and subjected to RNA-seq.

first: Shino

last: Mitsunaga

first: Keiko


title: The contribution of the post-transcriptional regulator CsrA to RNA stability

first: Anastasia

last: Potts

summary: Analysis of the contribution of the post-transcriptional regulator CsrA to RNA stability during exponential growth in Escherichia coli

overall_design: 2 replicate time courses with 5 time points from wild type and csrA::kan mutant strains were analyzed

first: Tony

last: Romeo


title: The fitness landscape of tumor suppression in lung adenocarcinoma in vivo

city: Menlo Park

first: Christopher

middle: Dennis

last: McFarland

state: CA

address: 2647 Alpine RD

department: Cancer Systems Biology

institute: Stanford University

summary: Survey of genetic interaction among 31 tumor genotypes using Tuba-seq approach

overall_design: Ultra-deep sequencing of DNA barcode amplicon

middle: D


title: Rheostatic Chromatin Control of Promiscuous Transcription by Aire and Brg1 [ATAC-Seq]

city: Stanford

first: Andrew

middle: S.

last: Koh

address: 279 Campus Drive B203

summary: Chromatin Accessibility Profiles of mTECs from Aire-/- and Brg1-/- mice and their littermate controls.

overall_design: DAPIneg, CD45neg, Epcam+, UEA+, Ly51lo, MHCIIhi and MHCIIlo mTECs were sorted from respective mice and ATAC-seq profiling was performed.

first: Erik

last: Miller

first: Jason

last: Buenrostro

first: David

last: Moskowitz

first: William

last: Greenleaf

first: Howard

last: Chang

first: Gerald

last: Crabtree


title: Molecular and Functional Resemblance of Terminally Differentiated Cells Derived from Isogenic Human iPSCs and Somatic Cell Nuclear Transfer Derived ESCs

first: Joseph

last: Wu

state: Carlifornia

address: Stanford University School of Medicine

institute: Stanford University School of Medicine

summary: Here we performed genome-wide RNA-seq and Reduced Representation Bisulfite Sequencing (RRBS-seq) in isogenic human induced pluripotent stem cells (iPSCs) and somatic cell nuclear transfer-derived embryonic stem cells (nt-ESCs), genetically matched in vitro fertilization-derived ESCs (IVF-ESCs), and their respective differentiated cells (cardiomyocytes and endothelial cells). We generated the transcriptome and DNA methylome map in human pluripotent stem cells and their differentiated cells with single-nucleotide resolution. We compared the genetic (genetic makeup) and epigenetic (reprogramming approach) influence on the gene expression and DNA methylation profiles and found that genetic composition is the major contributor of the transcriptional and epigenetic variances observed in the undifferentiated and differentiated cells originated from different reprogramming mechanisms.

overall_design: RNA-seq and RRBS-seq of 6 cell lines

first: Ming-Tao

last: Zhao

first: Ning-Yi

last: Shao

first: Michael

last: Snyder


title: Single cell RNA-seq of mouse lung vascular transcriptomes

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

summary: By analyzing about 1500 vascular single cell transcriptomes from adult mouse lung, we provide molecular definitions of the principal vascular (endothelial and mural cells), and vascular-associated cell classes.

overall_design: We used different transgenic mouse reporter lines with fluorescent expression in different populations of vascular cells, Cldn5(BAC)eGFP mice that strongly labels lung endothelial cells, mice positive for Pdgfrb(BAC)eGFP and NG2dsRed.  We chose to focus our efforts to adult mice 10 to 19 weeks old in order to primarily define fully differentiated and quiescent vascular cells and we chose a methodology based on fluorescence-activated cell sorting (FACS) into 384-well plates followed by the SmartSeq2 methodology for the generation and sequencing of full length polyadenylated cDNAs

last: Vanlandewijck

first: Liqun

first: Maarja

last: Mäe

first: Johanna

last: Andrae

first: Christer

last: Betsholtz


title: Genome-wide DNA methylation profiles from Arabidopsis epiRILs, epiHybrids and Colombia wild type

city: Amsterdam

first: Maike

last: Stam

address: Science Park 904

institute: University of Amsterdam

summary:
Despite the importance and wide exploitation of heterosis in commercial crop breeding, the molecular mechanisms behind this phenomenon are not completely understood.
In this study we aimed to understand and quantify the contribution of DNA methylation variation to heterosis in various traits of Arabidopsis. Therefore we created epigenetic hybrid lines from ddm1-derived epiRILs.
We performed whole genome bisulfite sequencing on four epiHybrids and their parental lines (epiRILs & Col-wt) in duplicates to understand methylome remodelling in hybrids genome wide and with a focus on previously mapped QTL regions.

overall_design: BS-seq was performed in four epiRIL lines, four epiHybrid lines and Colombia wild type (epiRILs 92, 150, 193, 232 and epiHybrids 92H, 150H, 193H, 232H and Col-wt)

first: Kathrin

last: Lauss

first: René

last: Wardenaar

first: Frank

last: Johannes


title: hMTR4 plays a central role in creating balanced nuclear RNA pools for degradation and export

first: Hong

last: Cheng

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

overall_design: Refer to individual Series


title: RNA-sequencing for peel roughing disorder of Satsuma mandarin fruit.

city: Changsha

first: Lu

last: Xiaopeng

address: 1 Nongda Rad.

institute: Hunan Agricultural University

summary: Roughing disorder (RD) is a significant quality barrier in citrus fruit, occurring more easily on easy-peeling mandarins. As RD is not yet well understood, this study aimed to examine the changes and synergic molecular processes involved. Peel with RD was induced by severely defruiting Satsuma mandarin trees. Morphology observations, RNA-sequencing and untargeted and targeted metabolic analyses were conducted.

overall_design: Examination of differences between CK and RD peels.

first: Xiaopeng

last: Lu

first: Jiang

last: Xiong

first: Shenxi

last: Xie


title: Impact of regulatory variation across human iPSCs and differentiated cells [RNA-seq]

status: Public on Dec 05 2017

city: Chicago

first: Nicholas

middle: E

last: Banovich

state: IL

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

summary:
Induced pluripotent stem cells (iPSCs) are an essential tool for studying cellular differentiation and cell types that are otherwise difficult to access. Here we investigate the use of iPSCs and iPSC-derived cells to study the impact of genetic variation across different cell types and as models for the genetics of complex disease. We established a panel of iPSCs from 58 well-studied Yoruba lymphoblastoid cell lines (LCLs); 14 of these lines were further differentiated into cardiomyocytes. We characterized regulatory variation across individuals and cell types by measuring RNA, chromatin accessibility and DNA methylation. Regulatory variation between individuals is lower in iPSCs than in the differentiated cell types, consistent with the intuition that developmental processes are generally canalized. While most cell-type- specific regulatory effects lie in chromatin that is open only in the affected cell-types, we find that 20% of cell-type specific effects are in shared open chromatin. Finally, we developed deep neural network models to predict open chromatin regions in these cell types from DNA sequence alone and were able to use the sequences of segregating haplotypes to predict the effects of common SNPs on tissue-specific chromatin accessibility. Our results provide a framework for using iPSC technology to study regulatory variation in cell types that are otherwise inaccessible.

Keywords: Expression profiling by high throughput sequencing

overall_design: Immortalized lymphoblastoid cell lines from 58 African individuals were reprogrammed into induced pluripotent stem cells

first: Yang

last: Li

first: Anil

last: Raj

first: Michelle

last: Ward

first: Po

middle: Y

last: Tung

first: Jonathan

last: Burnett

first: Marsha

last: Myrthil

first: Samantha

last: Thomas

first: Diego

last: Calderon

first: Peyton

last: Greenside

first: Anshul

last: Kundaje

last: Pritchard

first: Yoav

last: Gilad


title: ChIP-RX of GM15850 cells treated with synthetic transcription elongation factors

city: Madison

first: Aseem

last: Ansari

state: WI

address: 440 Henry Mall

department: Biochemistry and The Genome Center

institute: University of Wisconsin-Madison

summary: Switching a paused RNA polymerase II into productive elongation is tightly-regulated, especially at genes involved in human development and disease. To exert control on this rate-limiting step, we designed sequence-specific synthetic transcription elongation factors (Syn-TEFs). These molecules are composed of programmable DNA-binding ligands flexibly tethered to a small molecule that binds a component of the transcription elongation machinery. The resultant bifunctional molecules convert constituent modules from broad-spectrum inhibitors of transcription into a gene-specific stimulator of transcriptional elongation. Here, we present Syn-TEF1, a molecule that actively facilitates transcription across repressive GAA repeats that silence frataxin expression in Friedreich’s ataxia, a debilitating and ultimately lethal neurodegenerative disease with no effective therapy.

overall_design: The global effect on expression of synthetic transcription elongation factor (Syn-TEF1) and its constituent parts was examined in cells from a patient with FRDA (GM15850) and a healthy sibling control patient (GM15851). Spike-ins from mouse (mm9) were used for normalization.

first: Graham

middle: S

last: Erwin

first: Matthew

middle: P

last: Grieshop

first: Asfa

last: Ali

middle: A

last: Lawlor

middle: Z


title: Cystathionine-β-Synthase Promotes Colon Carcinogenesis

city: Galveston

first: Celia

last: Chao

state: TX

address: 301 University Boulevard

department: Surgery

institute: Univ TX Medical Branch

summary:
Purpose: The goal of this study is to investigate the role of CBS enzyme in colorectal carcinogenesis
Methods: RNA-Seq transcriptome analysis of CBS-overexpression in NCM356 cels compared to control vector cells

overall_design: RNA-seq transcriptome profiling of NCM356-CBS overexpressing cells vs. vector cells

first: Mark

middle: R

last: Hellmich

first: Steven

middle: G

last: Widen


title: Transcriptional Responses in Mouse Models of Invasive Pulmonary Aspergillosis

city: Blacksburg

first: Shiv

middle: D.

last: Kale

state: VA

address: 1015 Steger Hall, Life Science Circle

department: Biocomplexity Institute

institute: Virginia Tech

summary: Abstract From manuscript: Incidences of invasive pulmonary aspergillosis, an infection caused predominantly by Aspergillus fumigatus, have increased due to the growing number of immunocompromised individuals. While A. fumigatus is reliant upon deficiencies in the host to facilitate invasive disease, the distinct mechanisms that govern the host-pathogen interaction remain enigmatic, particularly in the context of distinct immune modulating therapies. To gain insights into these mechanisms, RNA-Seq technology was utilized to sequence RNA derived from lungs of 2 clinically relevant, but immunologically distinct murine models of IPA on days 2 and 3 post inoculation when infection is established and active disease present. Our findings identify notable differences in host gene expression between the chemotherapeutic and steroid models at the interface of immunity and metabolism. RT-qPCR verified model specific and nonspecific expression of 23 immune-associated genes. Deep sequencing facilitated identification of highly expressed fungal genes. We utilized sequence similarity and gene expression to categorize the A. fumigatus putative in vivo secretome. RT-qPCR suggests model specific gene expression for nine putative fungal secreted proteins. Our analysis identifies contrasting responses by the host and fungus from day 2 to 3 between the two models. These differences may help tailor the identification, development, and deployment of host- and/or fungal-targeted therapeutics.

sample_organism:
Mus musculus
Aspergillus fumigatus

platform_organism:
Mus musculus
Aspergillus fumigatus

overall_design: Three biological replicates were conducted for each model (chemotherapeutic and steroid) and time point (day 2 and day 3 post inncoulation) resulting in a total of 12 samples. One replicate for the chemotherapeutic model for day 2 failed during sequencing analysis, and therefore that model and time point only has 2 biological replicates. The successful 11 samples data are presented.

first: Tariq

last: Ayubi

first: Dawoon

last: Chung

first: Nuria

last: Tubau-Juni

first: Andrew

last: Leber

first: Ha

middle: X

last: Dang

first: Saikumar

last: Karyala

first: Raquel

last: Hontecillas

first: Christopher

middle: B

last: Lawrence

first: Robert

last: Cramer

first: Josep

last: Bassaganya-Riera


title: Analyzing the Function of Exosome’s microRNA in Milk by Comparing the Expression of microRNA in Milk and Exosome

city: Hohhot

first: Zhihong

last: Liu

address: 306 Zhao Wu Da

institute: inner Mongolia agricultural university

summary: Milk contains fats, carbohydrates, proteins, RNAs and enzymes, but also mRNA and microRNAs(miRNA), which plays an important role in neonatal innate and adaptive immunity. The following study investigates whether or not miRNA of exosome in milk is a vital pathway for miRNA of milk absorbing. Briefly, 280 pre-miRNAs and 326 mature miRNA were found. 37 exosomal miRNAs were upregulated (twice fold) compared to miRNAs found outside the exosomes. Among these miRNAs, ssc-miR-193a-3p’s expression was up regulated 1467.35 times, while ssc-miR-423-5p、ssc-miR-551a、ssc-miR-138、ssc-miR-1 and ssc-miR-124a were highly concentrated and upregulated from 13.58 to 30.06 times. Moreover, all of these miRNAs play essential roles in cell’s development and basic physiology processes in immune system. Following the analysis of target gene prediction and related signaling pathways, 9262 target genes showed to be mainly concentrated on three signaling pathway: metabolic pathways、pathways in cancer, and Phosphatidylinositol 3-kinase /Protein Kinase B(PI3K/Akt) signaling pathways. In addition, more than 20 miRNAs showed to be highly concentrated on exosomes, such as MECP2、GYS1、 LRRC8A、BCL9L、PHRF1 and ELOVL1, all closely related to immunity and engendering of gene.  After performing in-depth research on miRNA’s localization, distribution and function related metabolism, we found that these exosome concentrated miRNA’s target genes were interrelated to development and basic cell functions, like metabolism and immunity. These results imply that miRNAs in breast milk can influence offspring via milk exosomes.

overall_design: Three Experimental swine milk. Small intestine of piglets at 31 days old was collected from Pig Breeding Farm in Chongqing Academy of Animal Science, China. Exosome were collected from the swine milk. Three individuals were randomly selected for biological replicates.

first: Yuchun

last: Xie


title: Differential gene expression analysis for California yellowtail (Seriola dorsalis) to investigate slow- and fast-growing larvae over different growth stages

city: Ames

middle: J

last: Severin

email: severin@iastate.edu, csiva@iastate.edu

state: IA

address: 2200 Osborn Drive

department: Office of Biotechnology

institute: Iowa State University

summary: In this study, we describe the generation of whole larval transcriptomes for the California yellowtail (S. dorsalis) at three developmental stages: two, seven, and seventeen days post hatching (dph) using RNA-Seq on the Illumina HiSeq 2500 sequencing platform. Transcriptional profiles and differential gene expression were also investigated for slow- and fast-growing larvae over these same stages.

overall_design: Yellowtail larvae were sampled opportunistically at 2, 7, and 17 dph with three replicates for each time point; the replicates within each time point were sampled from separate spawning events.

first: John

last: Hyde

first: Catherine

last: Purcell


title: Prep1 prevents premature adipogenesis of mesenchymal progenitors [ChIP-seq]

first: Marco

last: Morelli

summary: Transcriptional regulators are crucial in adipocyte differentiation. We now show that the homeodomain-containing transcription factor Prep1 is a repressor of adipogenic differentiation since its down-regulation (DR) in both ex vivo bone marrow-derived mesenchymal stromal cells (MSC) and in vitro 3T3-L1 pre-adipocytes significantly increases their adipogenic differentiation ability. Prep1 acts at a stage preceding the activation of the differentiation machinery because its DR makes cells more prone to adipogenic differentiation even in the absence of the adipogenic inducers. Prep1 DR expands the DNA binding landscape of C/EBPß(CAAT enhancer binding protein ß) without affecting its expression or activation. The data indicate that Prep1 normally acts by restricting DNA binding of transcription factors to adipogenic enhancers, in particular C/EBPß.

overall_design: ChIP-seq performed using Cebpß Ab

first: Dmitry

last: Penkov


title: Synthetic transcription elongation factors

first: Aseem

last: Ansari


title: Genome-wide analysis of Gtf3c1, RNAP3 occupancy and H3K4me1, H3K27ac chromatin modifications in primary mouse cortical neurons

city: London

first: Luca

last: Crepaldi

address: Gower Street

department: MRC Laboratory for Molecular Cell Biology

institute: University College London

summary: SINEs are a highly abundant class of retrotransposons that were initially considered a non-functional “junk” DNA due to their non coding, repetitive nature. SINEs frequently possess an internal RNAPIII promoter, which recruits the RNAPIII transcriptional machinery, including the general nuclear complex TFIIIC. We recently discovered that in response to neuronal depolarisation, SINEs may represent a novel class of neuronal enhancers and reasoned that RNAPIII and TFIIIC binding may provide a means of identifying enhancer SINEs genome-wide. To this end, we first performed ChIPseq analysis on resting and depolarised mouse cortical neurons, using an antibody that targets the DNA binding subunit of TFIIIC (Gtf3c1), RNA Polymerase III and the enhancer markers H3K4me1 and H3K27ac .

overall_design: ChIPseq analysis of Gtf3c1, RNAP3, H3K4me1 and H3K27ac in primary mouse cortical neurons either untreated or depolarized with 50 mM KCl for 45 min. Total chromatin input was used as a control. For each experimental condition, 3 biological replicates were used.

first: Antonella

last: Riccio

first: Cristina

last: Policarpi


title: RNA-seq of GM15850 and GM15851 cells treated with synthetic transcription elongation factors.

overall_design: The global effect on expression of synthetic transcription elongation factor (Syn-TEF1) and its constituent parts was examined in cells from a patient with FRDA (GM15850) and a healthy sibling control patient (GM15851).

first: Graham

last: Erwin

first: Matthew

last: Grieshop

first: Asfa

last: Ali


title: A lineage of myelolymphoblastic innate cells unmasked by inactivation of mTOR complex 1

city: Washington

first: Yang

state: DC

address: 111 Michigan Ave NW

department: Center for Cancer and Immunology Research

institute: Childrens' National Medical Center

summary: Blockades in hematopoiesis deprive the host of vital blood cells and frequently cause leukemia.  Here we show that inactivation of mTORC1 in hematopoietic stem cells by deletion of Raptor unmasked a cell type, hereby called myelolymphoblastic innate cell (MLIC) based on unique gene expression signature, cell surface markers, morphology and functions. The MLICs are CD11b(+)Gr-1(-)B7-H1(high)F4/80(low) and have morphology of lymphoblasts with active Ig loci but no gene rearrangement. Within weeks of Raptor deletion, the MLICs account for nearly 50% of bone marrow cells and are found throughout both the lymphoid and non-lymphoid organs. Nevertheless, the MLICs are not malignant as they undergo very limited proliferation in vivo. Importantly, the MLICs broadly express pattern-recognition receptors and produce large amounts of inflammatory cytokines in response to all TLR ligands tested, rendering the host highly susceptible to pathogen-associated molecular patterns. Our data suggest that hematopoietic cell-intrinsic mTORC1 prevents development of self-destructive innate immune attack by suppressing generation of MLICs.

overall_design: Raptor F/F mice were crossed with Mx1-Cre mice for more than 2 generations to get Raptor F/F (Ctrl) and Raptor F/F, Mx1-Cre (cKO) mice. Sex-matched 6-8 weeks old Ctrl mice and cKO mice were treated with polyinosinic: polycytidylic acid (pIpC) every other day for consecutive 7 times by intra-peritoneal (i.p.) injection to induce Cre expression and Raptor deletion in mouse hematopoietic system. Raptor mice were sacrificed 2-3 weeks after the last injection of pIpC. Whole BM cells from Raptor Ctrl mice (n=3) and FACS-sorted CD11b(+)Gr-1(-) BM MLICs from Raptor cKO mice (n=3) were used for RNA isolation and subsequent cDNA libraries construction. mRNA profiles of Ctrl-WBM and cKO-MLIC were examined by RNA-sequencing, in triplicate, using Illumina HiSeq 2000.

first: Fei

last: Tang

first: Peng

last: Zhang

first: Ya

last: Cui

first: Liguo

first: Taijiao

last: Jiang

first: Pan

last: Zheng


title: Supplementation with estradiol cypionate at the onset of a synchronized proestrus alters the uterine gene expression of suckled anestrous beef cows

city: Pirassununga

first: Mario

last: Binelli

state: SP

address: Rua Duque de Caxias Norte, 255

department: department of animal reproduction

country: Brazil

institute: University of Sao Paulo (USP)

summary:
Purpouse: The aim was evaluated the impact of estradiol cypionate (ECP) supplementation at the onset of a proestrus [i.e. at progesterone (P4) device removal of the synchronization of ovulation protocol] on the global endometrial gene expression of suckled anestrous beef cows
Methods: A total of 12 suckled cows presenting absence of corpus luteum detected by ultrasound received 2 mg of estradiol benzoate im and an intravaginal P4 device. Eight days later, P4 devices were removed, and the cows received 500 mg of sodium cloprostenol IM. Cows were blocked according to body condition score and the diameter of largest follicle (LF) at P4 device removal and were randomly assigned to receive an im treatment with 1mg of ECP (ECP, n=6) or not (CON, n=6) at the P4 device removal. All cows received 10μg of buserelin acetate 48 h after the P4 device removal and were timed artificially inseminated immediately after. Cows presenting a new corpus luteum formed 6 d after the GnRH treatment had an endometrial fragment collected by transcervical biopsy
Results: The integrated analysis was performed using DAVID database. A total of 135 transcripts were differentially expressed between ECP and CON groups, of which 73 genes were up regulated by ECP suplmentation and 62 genes in the CON cows.  Two pathways were overrepresented by the ECP-induced transcripts: pathways in cancer (n=5 genes) and small cell lung cancer (n=3 genes). On the other hand, ECP-inhibited transcripts indicated the enrichment of three pathways: Parkinson’s disease (n=3 genes), oxidative phosphorylation (n=3 genes) and Alzheimer’s disease (n=3 genes). More specifically, ECP-induced transcripts associated with pathways in cancer [gene symbol (fold change); respectively] were LAMC3 (1.55), PTCH1 (1.51), PTCH2 (1.52), PIK3R3 (1.22) and PIAS1 (1.18), whereas ECP-inhibited transcripts associated with oxidative phosphorylation were ATP5F1 (1.18), ATP5J (1.24) and NDUFB3 (1.37).
Conclusion: The ECP supplementation at onset of the synchronized proestrous slightly alters the uterine transcriptome.

overall_design: endometrial mRNA profiles of endocrine manipulated cows were generated by deep sequencing using Illumina HiScanSQ platform

first: Manoel

last: Francisco de Sá Filho

first: Fernando

last: Mesquita

first: Sonia

last: Andrade

first: Gustavo

last: Gasparin

first: Angela

last: Gonella

first: Luiz

last: Lehmann Coutinho


title: Gene Expression Profiling of human and mouse melanoma cell lines after shRNA-mediated knockdown of JMJD2C or LSD1

status: Public on Dec 04 2017

city: Berlin

first: Maja

last: Milanovic

address: Augustenburgerplatz 1

department: Hematology and Oncology

institute: Charite University Medicine, Berlin

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus