title: Transcriptomic comparison of two barley genotypes differing in arsenic tolerance exposed to arsenate and phosphate treatments

city: Hangzhou

first: Gerald

last: Zvobgo

state: Zhejiang

address: Yuhang

department: Crop Science

institute: Zhejiang University

summary: RNA-sequencing was conducted on the two barley genotypes differing in As tolerance. A total of 2,942 differentially expressed genes (DEGs) were inclusively expressed in both genotypes under As (100µM) and As (100 µM) + P (50 µM).

overall_design: Comparison of two barley genotypes under arsenic and phosphorus treatments using RNA-seq technique.

first: Tichaona

last: Sagonda

first: Jonas

last: Lwalaba Wa Lwalabaa

first: Guoping

last: Zhang

first: James

last: Mapodzeke

first: Imran

middle: H

last: Shamsi

first: Guang

last: Chen

first: Noor

last: Muhammad


title: Expression of miRNAs in dorsal rat hippocampus: Effect of subchronic and chronic restraint stress

status: Public on Jul 13 2018

city: Independencia

first: Wladimir

middle: Antonio

last: Corrales

address: Olivos 1007

department: Biochemistry and Molecular Biology

country: Chile

institute: Universidad de Chile

summary: Studies conducted in rodents subjected to chronic stress and some observations in humans after psychosocial stress, have allowed to establish a link between stress and the susceptibility to many complex diseases, including mood disorders. The studies in rodents have revealed that chronic exposure to stress negatively affects synaptic plasticity by triggering changes in the production of trophic factors, subunit levels of glutamate ionotropic receptors, neuron morphology and neurogenesis in adult hippocampus. These modifications may account for the impairment in learning and memory processes observed in chronically stressed animals. It is plausible then, that stress modifies the interplay between signal transduction cascades and gene expression regulation in the hippocampus, therefore leading to altered neuroplasticity and functioning of neural circuits.     Considering that miRNAs play an important role in post-transcriptional-regulation of gene expression and participate in several hippocampus-dependent functions; we evaluated the consequences of chronic stress in the expression of miRNAs in dorsal (anterior) portion of the hippocampus, which participates in memory formation in rodents. Here, we show that male rats exposed to daily restraint stress (2.5 h/day) during 7 and 14 days display a differential profile of miRNA levels in dorsal hippocampus and remarkably, we found that some of these miRNAs belong to the miR-379-410 cluster. We confirmed a rise in miR-92a and miR-485 levels after 14 days of stress by qPCR, an effect that was not mimicked by chronic administration of corticosterone (14 days). Our in silico study identified the top-ten biological functions influenced by miR-92a, nine of which were shared with miR-485: Nervous system development, Tissue development, Behavior, Embryonic development, Organ development, Organismal development, Organismal survival, Tissue morphology, and Organ morphology. Furthermore, our in silico study provided a landscape of potential miRNA-92a and miR-485 targets, along with relevant canonical pathways related to axonal guidance signaling and cAMP signaling, which may influence the functioning of several neuroplastic substrates in dorsal hippocampus. Additionally, the combined effect of miR-92a and miR-485 on transcription factors, along with histone-modifying enzymes, may have a functional relevance by producing changes in gene regulatory networks that modify the neuroplastic capacity of the adult dorsal hippocampus under stress.

overall_design: Adult male rats were exposed to daily restraint stress (2.5 h/day) during 7 and 14 days. Animals were decapitated 24 h after the last stress exposure and hippocampi were dissected. Then RNA was extracted by using RNeasy minikit. miRNA expression was conducted using Affymetrix GeneChip 3.0 following the hibridization protocol.

first: Mauricio

last: Muñoz

first: Alexandra

last: García-Pérez

first: Xiaojiang

last: Xu

first: Macarena

last: Tejos

first: Elena

last: Vidal

first: Tomás

last: Moyano

first: Rodrigo

last: Gutiérrez

first: Felipe

last: Aguayo

first: Gonzalo

last: García-Rojo

first: Aniba

last: Pacheco

first: Esteban

last: Aliaga

first: Paulina

last: Rojas

first: John

last: Cidlowski

first: Jenny

last: Fiedler


title: Maternal gene expression data from dMLL3/4-depleted Drosophila embryos

status: Public on Jul 12 2018

city: Oeiras

first: Jorg

middle: D

last: Becker

address: Rua da Quinta Grande No 6

country: Portugal

institute: Instituto Gulbenkian de Ciencia

summary: Analysis of Drosophila melanogaster early embryos (pre-zygotic genome activation) following the germ line-specific depletion of the dMLL3/4 histone methyltransferase (also known as Trr). These results provide insight into the molecular mechanisms responsible for the assembly of the zygotic genome at fertilization.

overall_design: Drosophila embryos at a pre-zygotic genome (ZGA) activation stage were selected for RNA extraction and hybridization on Affymetrix microarrays. For this, early embryos (less than 1 hour post-laying) were dechorionated with a 50% commercial bleach solution and manually selected for the lack of morphological hallmarks of a post-ZGA state (selection for the absence of pole cells and cortical nuclei). The selected embryos were morphologically homogenous across the two experimental groups (Control RNAi and dMLL3/4 RNAi). Each group consisted of two temporally distinct biological replicates.

first: Pedro

last: Prudêncio

first: Leonardo

last: Guilgur

first: João

last: Sobral

first: Jörg

first: Rui

last: Martinho

first: Paulo

last: Navarro-Costa


title: CD153 expression by CD4 T cells is required for control of pulmonary Mycobacterium tuberculosis infection

status: Public on Jul 10 2018

city: Bethesda

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

country: USA

institute: National Institute of Allergy and Infectious Diseases

summary: Mycobacterium tuberculosis infection (Mtb) is the leading cause of death due to a single infectious agent and among the top ten causes of all human death worldwide1. CD4 T cells are essential for resistance to Mtb infection, and for decades it has been thought that IFN production is the primary mechanism of CD4 T cell-mediated protection2,3. However, IFN responses do not correlate with host protection, and several reports have demonstrated that additional anti-tuberculous CD4 T cell effector functions remain unaccounted for4-8. Here we show that the TNF superfamily molecule CD153 (TNFSF8) is required for IFN-independent control of pulmonary Mtb infection by CD4 T cells. In Mtb infected mice, CD153 expression is highest on Ag-specific Th1 cells in the lung tissue parenchyma, but its induction does not require Th1 polarization. CD153 deficient mice develop high pulmonary but not splenic bacterial loads and succumb early to Mtb infection. Reconstitution of T cell-deficient hosts with either CD153-/- or IFN-/- CD4 T cells fails to rescue mice from early mortality, but reconstitution with a mixture of CD153-/- and IFN-/- CD4 T cells provides similar protection as WT T cells. In Mtb infected non-human primates, CD153 expression is much higher on Ag-specific CD4 T cells in the airways compared to the blood, and the frequency of Mtb-specific CD153-expressing CD4 T cells inversely correlates with bacterial loads in granulomas. In Mtb infected humans, CD153 defines a subset of highly polyfunctional Mtb-specific CD4 T cells that are much more abundant in individuals with controlled latent Mtb infection compared to those with active TB. In all three species, Mtb-specific CD8 T cells did not upregulate CD153 following peptide stimulation. Thus, we have identified expression of CD153 by CD4 T cells as a major immune mechanism of host protection against pulmonary Mtb infection.

overall_design: Gene expression of IV+ and IV- cells in the lung of MTb infected mice, The cells were gated on live CD4+Foxp3-CD44hi and sorted into four populations: KLRG1-ivCD45dim, KLRG1-ivCD45+, KLRG1+ivCD45dim, and KLRG1+ivCD45+.   RNA from 15 to 25 mice were pooled for each replicate trial.

first: Michelle

middle: A

last: Sallin

first: Keith

last: Kauffman

first: Elsa

last: Du Bryn

first: Catherine

last: Riou

first: Taylor

middle: W

last: Foreman

first: Shunsuke

last: Sakai

first: Stella

last: Hoft

first: Paul

middle: J

last: Gardina

first: Alan

last: Sher

first: Rashida

last: Moore

first: Temeri

last: Wilder-Kofie

first: Ian

middle: N

first: Alessandro

last: Sette

first: Cecilia

middle: L

last: Arlehamn

first: Robert

last: Wilkinson

first: Daniel

last: Barber


title: Expression of Adhesive Pili and the Collagen-Binding Adhesin Ace Is Activated by ArgR Family Transcription Factors in Enterococcus faecalis.

city: Minneapolis

first: Gary

middle: M

last: Dunny

state: MN

address: 689 23rd Avenue S.E.

department: Department of Microbiology and Immunology

institute: University of Minnesota

type: Expression profiling by high throughput sequencing

summary: In E. faecalis OG1RF, disruption of the ahrC gene encoding a predicted ArgR family transcription factor results in a severe defect in biofilm formation in vitro, as well as significant attenuation of virulence in multiple experimental infection models. Using RNA-seq, we observed ahrC-dependent changes in expression of over 20 genes. AhrC-repressed genes included predicted determinants of arginine catabolism and several other metabolic genes and predicted transporters, while AhrC-activated genes included determinants involved in production of surface protein adhesins. Most notably, the structural and regulatory genes of the ebp locus encoding adhesive pili were positively regulated, as well as the ace gene, encoding a collagen binding adhesin. Using lacZ transcription reporter fusions, we determined that ahrC and a second argR transcription factor gene, argR2, both function to activate expression of ebpR, which directly activates transcription of the pilus structural genes. Our data suggest that in wild-type E. faecalis, the low levels of EbpR limit expression of pili, and that biofilm biomass is also limited by the amount of pili expressed by the bacteria. Expression of ace is similarly activated by AhrC and ArgR2, but ace expression is not dependent on EbpR. Our results demonstrate the existence of novel regulatory cascades controlled by a pair of ArgR family transcription factors that may function as a heteromeric protein complex.

overall_design: Used RNA-seq to identify the ahrC regulon of E. faecalis OG1RF under both biofilm and planktonic growth conditions in M9-YE using the CDC biofilm reactor (CBR). We compared the transcriptomes of wild-type OG1RF and an isogenic derivative with in-frame deletion mutant of ahrC (D983).  Also carried out RNA-seq analysis of wild-type OG1RF and the ΔahrC (D983) derivative in liquid cultures grown in BHI medium. For each strain and experiment, RNA libraries from two biological replicates were sequenced.

first: G

first: D

last: Manias


title: Predicting microRNA targeting efficacy in Drosophila

city: South San Francisco

first: Vikram

last: Agarwal

state: CA

address: 1130 Veterans Blvd

institute: Calico Life Sciences

summary: A series of transfections was performed in Drosophila S2 cells to explore: 1) the types of target sites that Drosophila microRNAs recognize, 2) the relative functional efficacy of these sites in mediating repression, and 3) the determinants that allow some sites to have greater potency than others. 3p-seq was also performed to help reannotate and quantify the landscape of 3' UTRs in Drosophila S2 cells.

overall_design: Nine mRNA profiles were generated, with Drosophila S2 cells transfected with one of 6 microRNAs (miR-1, miR-4, miR-92a, miR-124, miR-263a, and miR-997). These samples were compared to 3 biological replicates of a mock transfection condition. 3p-seq data for S2 cells was also generated to help reannotate and quantify 3' UTR isoforms.

first: Alexander

middle: O

last: Subtelny

first: Pratapan

last: Thiru

first: Igor

last: Ulitsky

first: David

middle: P

last: Bartel


title: Expression profiling of selenium deficiency in mouse colon and splenic leukocytes

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

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

overall_design: Refer to individual Series


title: Targeting the HBZ Viral Oncoprotein Transcriptional Network in Adult T-cell leukemia/lymphoma

first: Louis

last: Staudt

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

summary: Adult T-cell Leukemia/Lymphoma (ATLL) is a frequently incurable disease associated with the human lymphotropic virus type I (HTLV-I). The transcription factor HBZ is the only virally encoded gene that is expressed in all ATLL cases, but it is unclear why it may be essential in ATLL and how it might be targeted therapeutically. Here we performed RNA interference screening of ATLL lines and discovered that their proliferation depends on the transcription factors BATF3 and IRF4, which regulate the identity of normal immune cells. These factors, which are highly expressed in ATLL, cooperatively bind and transactivate genes that distinguish ATLL from other T cell malignancies, including BATF3 itself. HBZ binds to an ATLL-specific BATF3 super-enhancer and thereby regulates the expression of BATF3 and its downstream targets, including the oncogene MYC. The BET protein inhibitor JQ1 collapsed the transcriptional network directed by HBZ and BATF3, and was consequently toxic for ATLL lines and patient samples in vitro, and blocked growth of ATLL xenografts. Our study demonstrates that the HTLV-I virus exploits a regulatory module that can potentially be attacked therapeutically with BET protein inhibitors.

overall_design: For shRNA gene expression profiling, KK1 and ST1 cells were infected with either Ctrl, IRF4, BAFT3_A2, or BAFT3_bp360 shRNAs. Following puromycin selection, shRNA expression was induced for 1 day and 2 days in KK1 cells (n=6), and for 1 day and 2 days in ST1 cells (n=6). For JQ1 gene expression profiling, KK1 (n=4) and ST1 (n=4) cells were treated with either DMSO or JQ1 for 12 hours, 24 hours, 36 hours and 48 hours. For sgRNA gene expression profiling, KK1 and ST1 cells were infected with Ctrl, HBZ_1 or HBZ_2 sgRNAs. KK1 was tranduced by sgHBZ_1 for 7, 8 and 9 days (n=3). KK1 was transduced by sgHBZ_2 for 7 day (n=1). ST1 was tranduced by sgHBZ_1 for 7 and 8 days (n=2). SS1 was transduced by sgHBZ_2 for 7 and 8 days (n=2).


title: Systematic assessment of next-generation sequencing for quantitative small RNA profiling: A-to-I editing pools

status: Public on Jul 09 2018

city: Ann Arbor

first: Muneesh

last: Tewari

state: MI

address: 109 Zina Pitcher Pl

institute: University of Michigan

type: Non-coding RNA profiling by high throughput sequencing

summary: Small RNA-seq is increasingly being used for profiling of small RNAs. Quantitative characteristics of long RNA-seq have been extensively described, but small RNA-seq involves fundamentally different methods for library preparation, with distinct protocols and technical variations that have not been fully and systematically studied. Using common sets of reference samples, we evaluated the accuracy, reproducibility and bias of small RNA-seq library preparation for five distinct protocols and across nine different laboratories. As part of this larger study, we assessed reproducibility and accuracy of relative expression measurements using two pools of synthetic small RNA sequences, where subsets of the sRNAs vary in relative amount between pools A and B. The pools each contain 334 small RNAs, varying by 15 different ratios between pools A and B (10:1, 8:1, 5:1, 4:1, 3:1, 2:1, 1.5:1, 1:1, 1:1.5, 1:2, 1:3, 1:4 1:5, 1:8, 1:10). We find that although the sequencing bias varies extensively between protocols, the relative abundance measured between samples A and B is largely reproducible and accurate across labs and protocols. These results suggest that measurements of differential expression should be comparable across institutions and library preparation technologies.

overall_design: Six synthetic RNA pools were generated to assess the performance of three small RNA library preparation protocols: TruSeq, NEBNext and an in-house 4N_B protocol. The pools each contained a common set of 277 synthetic miRNA oligos in equimolar amounts, and oligos for 10 miRNAs with known miRNA Adenosine-to-Inosine (A-to-I) editing events. The six pools contained the edited (I) and unedited (A) variants of the oligos, keeping the total concentration of the miRNA the same (edited + unedited variant), but varying the percent edited oligo. The resulting six pools represented six different editing levels: 0%, 0.1%, 1%, 5%, 50% and 100% editing. Three labs sequenced each of the six pools in triplicate, using all three of the library preparation protocols.


title: Metabolic signaling directs the reciprocal lineage decisions of αβ and γδ T cells

status: Public on Jul 06 2018

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

summary:
The interaction between extrinsic factors and intrinsic signal strength governs thymocyte development, but mechanisms linking them remain elusive. We report that mTORC1 couples microenvironmental cues with metabolic programs in orchestrating reciprocal development of two fundamentally distinct lineages, αβ and γδ T cells. Loss of mTORC1 impairs αβ but promotes γδ T cell development, and disrupts metabolic remodeling of oxidative and glycolytic metabolism. Mechanistically, reactive oxygen species (ROS) controlled by mTORC1 serves as a key metabolic signal, and perturbation of redox homeostasis impinges upon fate decisions. Furthermore, singlecell RNA sequencing and genetic dissection reveal that mTORC1 links developmental signals from T cell receptors and NOTCH to coordinate metabolic activity and signal strength. Our results establish mTORC1-driven metabolic signaling as a fundamental mechanism underlying thymocyte lineage choices.
We used microarrays to compare the global transcription profiles of WT and Raptor-null cell populations in DN3a developing thymocytes, immaturesingle-positive (ISP) T-cells, and γδ T-cells

overall_design: In total 19 samples were analyzed: DN3a thymocytes (WT, n = 3; Rptor-/-, n = 3); ISP T-cells (WT, n = 4; Rptor-/-, n = 3); γδ T-cells (WT, n = 3; Rptor-/-, n = 3);

first: Kai

last: Yang

last: Bastardo Blanco

first: Hongbo

last: Chi


title: sRNA sequencing of liver from lean rats and ZDF rats treated with vehicle or colesevelam

city: Nashville

first: Leslie

middle: Roteta

last: Sedgeman

address: 2220 Pierce Avenue

institute: Vanderbilt University

summary: Colesevelam is a bile acid sequestrant approved to treat both hyperlipidemia and type 2 diabetes, but the mechanism for its glucose lowering effects is not fully understood. The aim of this study was to investigate the role of hepatic microRNA’s as regulators of metabolic disease and to investigate the link between the cholesterol and glucose lowering effects of colesevelam. To quantify the impact of colesevelam treatment in rodent models of diabetes, metabolic studies were performed in Zucker Diabetic Fatty (ZDF) rats and db/db mice. Colesevelam treatments significantly decreased plasma glucose levels and increased glycolysis in the absence of changes to insulin levels in ZDF rats and db/db mice. High-throughput sequencing and real-time PCR were used to quantify hepatic miRNA and mRNA changes, and the cholesterol-sensitive miR-96/182/183 cluster was found to be significantly increased in livers from ZDF rats treated with colesevelam compared to vehicle controls.  In summary, these results support that colesevelam likely improves glycemic control through hepatic miR-96/182/183, a mechanism that directly links cholesterol and glucose metabolism.

overall_design: Examination of miRNA changes in livers of ZDF rats treated with vehicle or colesevelam

first: Kasey

last: Vickers


title: DNA methylation reprogramming after spinal nerve injury [RRBS]

status: Public on Jul 05 2018

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

type: Methylation profiling by high throughput sequencing

summary: Purpose: Nerve injury-induced hyperactivity of primary sensory neurons in the dorsal root ganglion (DRG) contributes critically to chronic pain development, but its underlying mechanisms remain incompletely understood. Chronic neuropathic pain has a clear epigenetic component, however, most studies so far have focused on histone modifications. We determined changes of DNA methylation in the rat DRG, spinal cord, and prefrontal cortex after spinal nerve ligation (SNL).

overall_design: We used a rat model of neuropathic pain induced by spinal nerve ligation (SNL). We analyzed DNA methylation in dorsal root ganglia (DRG) by the RRBS method (Reduced Representation Bisulfite Sequencing).

first: Judit

last: Garriga

first: Geoffroy

last: Laumet

first: Shao-Rui

last: Chen

first: Yuhao

last: Zhang

first: Jozef

last: Madzo

first: Jean-Pierre

last: Issa

first: Hui-Lin

last: Pan


title: The Transcription Factor ZFfx Regulates Peripheral T Cell Self-renewal and Proliferation

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

summary: Peripheral T lymphocytes share many functional properties with hematopoietic stem cells (HSCs), including long-term maintenance, quiescence, and latent proliferative potential. In addition, peripheral T cells retain the capacity for further differentiation into a variety of subsets, much like HSCs. While the similarities between T cells and HSC has long been hypothesized, the potential common genetic regulation of HSCs and T cells has not been widely explored. We have studied the T cell-intrinsic role of Zfx, a transcription factor specifically required for HSC maintenance. We report that T cell-specific deletion of Zfx caused age-dependent depletion of naÃ¯ve peripheral T cells. Zfx-deficient T cells failed to undergo homeostatic proliferation in a lymphopenic environment, and showed impaired antigen-specific expansion and memory response. In addition, the invariant natural killer T cell (iNKT) cell compartment was severely reduced. Transcriptome analysis identified target genes of Zfx in T cells which are shared with HSCs. Zfx-deficient T cells also revealed activation of the stress response, elevated expression of cell cycle inhibitor Cdkn1a/p21 and reduced telomerase activity. These studies identify Zfx as an important regulator of peripheral T cell maintenance and expansion, and highlight the common molecular basis of HSC and T cell homeostasis.

overall_design: NaÃ¯ve CD4+CD62L+ splenocytes were sorted from spleens of control or Zfx T cell conditional knockout mice, aged 6-8 weeks.  Cell stimulation involved adding the CD4+CD62L+ T cells to plate-bound aCD3 (3mg/mL) and aCD28 (2mg/mL); these cells were collected after 12 hours.

first: Matthew

last: Smith-Raska

first: Teresita

last: Arenzana

first: Louise

last: D'Cruz

first: Aristotelis

last: Tsirigos

first: Ananda

last: Goldrath

first: Boris

last: Reizis


title: Expression data from human jejunum before and one month after Roux en Y Gastric Bypass (RYGB)

city: Jerusalem

first: Danny

last: Ben-Zvi

state: Israel

address: Ein Kerem

country: Israel

institute: Hebrew University of Jerusalem

summary:
RYGB reconfigures the intenstine such that food enters the jejunum after passing only a small gastric pouch. This new anatomy places the jejunum as the first part of the intestine that interacts with the food, with little to no gastric digestion, causing dramatic changes in jejunal morphology. Baseline is defined as the biopsy during RYGB. Patients are obese.
We used microarrays to study the global programme of gene expression before and 1 month after RYGB, with biopsies  taken from the same location the stomach-jejunum anastomosis.

overall_design: Biopsies were taken during RYGB surgery and at a dedicated biopsy 1 month after surgery, from the same location. Samples were flash frozen and then RNA was extracted

first: Nicholas

last: Stylopoulos


title: Swarmer Cell Development of the Bacterium Proteus mirabilis Requires the Conserved Enterobacterial Common Antigen Biosynthesis Gene rffG

status: Public on Jul 04 2018

city: Cambridge

first: Murray

last: Tipping

state: MA

address: 16 Divinity Ave

department: MCB

institute: Harvard University

summary: Individual cells of the bacterium Proteus mirabilis can elongate up to 40- fold on surfaces before engaging in a cooperative surface-based motility termed swarming. How cells regulate this dramatic morphological remodeling remains an open question. In this paper, we move forward the understanding of this regulation by demonstrating that P. mirabilis requires the gene rffG for swarmer cell elongation and subsequent swarm motility.

overall_design: Examination of transcriptome of ∆rffG mutant compared to wildtype

first: Karine

last: Gibbs


title: GRHL2-dependent enhancer switching maintains a pluripotent stem cell transcriptional subnetwork after exit from naïve pluripotency [Illumina MouseRef-8 v2.0 expression]

city: Stanford

first: Amy

address: 279 Campus Drive West

institute: Stanford University

summary: During early development, pluripotent cells of the epiblast show extensive rewiring of enhancers with little associated change in gene expression. The mechanisms underlying and purpose of this rewiring are largely unknown. Here we identified a transcription factor, GRHL2, that is both necessary and sufficient to activate latent enhancers during the transition from naïve embryonic stem cells (ESC) to primed epiblast cells (EpiC). GRHL2 is necessary to maintain expression of its targets in EpiCs. However, these genes are already expressed at equivalent levels in ESCs, suggesting these genes switch enhancer usage during the transition. Identification of alternative enhancers driving these genes in ESCs uncovered an enrichment for the ESC-specific KLF transcription factors. While many KLF targets remain expressed in EpiCs, GRHL2 only regulates a specific subset promoting an epithelial program. These data suggest a model where a large naïve-specific transcriptional network is partitioned into smaller networks to uncouple their regulation in EpiCs, providing more flexibility in gene regulation during lineage specification.

overall_design: Total RNA was isolated from wildtype and GRHL2 knockout epiblast cells

first: Robert

last: Blelloch


title: Compounds released by the biocontrol yeast Hanseniaspora opuntiae protect plants against Corynespora cassiicola and Botrytis cinerea

city: Cuernavaca

first: Damien

last: Formey

state: Morelos

address: Avenida de la Universidad

department: Center for Genomic Science

country: Mexico

institute: UNAM

summary: Plant diseases induced by fungi are one of the most important limiting factors during pre- and post-harvest food production. For decades, synthetic chemical fungicides have been used to control these diseases, however, increase on worldwide regulatory policies and the demand to reduced their application, have led to search new ecofriendly alternatives such as the biostimulants. Commercial application of yeast as biocontrol, have shown low efficacy compared to synthetic fungicides, mostly due to the limited knowledge of the molecular mechanisms of yeast-induced responses. Interestingly, to date, only two genome-wide transciptomic analysis have been used to characterize the mode of action of biocontrols using the plant model Arabidopsis thaliana, missing, in our point of view, all its molecular and genomic potential. Here we described that compounds released by the biocontrol yeast Hanseniaspora opuntiae (HoFs) can protect Glycine max and Arabidopsis thaliana plants against the broad host-range necrotroph fungi Corynespora cassiicola and Botrytis cinerea, respectively. We show that HoFs have a long-lasting, dose-dependent local and systemic effect against Botrytis cinerea. Additionally, we performed a genome-wide transcriptomic analysis to identified HoFs-induced differentially expressed genes in Arabidopsis thaliana. Importantly, our work provides a novel and valuable information that can help the researchers to improve HoFs efficacy in order to become an ecofriendly alternative to synthetic fungicides

overall_design: RNAseq from HOF-treated Arabidopsis thaliana leaves

first: Mariana

last: Ferreira Saab

first: Martha

last: Torres

first: Wendy

last: Aragón

first: Emir

last: Alejandro Padilla

first: Alexandre

last: Tromas

first: Christian

last: Sohlenkamp

first: Kátia

middle: R

last: Freitas Schwan-Estrada

first: Mario

last: Serrano


title: Expression data of T follicular helper (Tfh) and memory CD4 T cells from non malignant tonsils (TONS).

city: Rennes

first: Patricia

last: Amé-Thomas

address: 2 Avenue du Pr Léon Bernard

department: Faculté de Médecine

country: France

institute: INSERM UMR1236

summary: GEP on Affymetrix Genechip HTA 2.0 microarrays was performed on ex vivo cell-sorted Tfh and memory CD4 T cells from TONS

overall_design: GEP was performed on 3 Tfh cell sampes and 3 memory CD4+ T cell samples from non malignant TONS


title: Chromatin remodeling factor BRG1 regulates stemness and chemosensitivity of glioma initiating cells

status: Public on Jul 03 2018

first: Meiyun

last: Fan

address: 19 S. Manassas Street

institute: University of Tennessee

summary: Glioblastoma multiforme (GBM) is a highly aggressive and malignant brain tumor that is refractory to existing therapeutic regimens due in part to the presence of stem-like cells, termed Glioma-Initiating Cells (GICs). The complex interactions between different signaling pathways and epigenetic regulation of key genes may be critical in the maintaining GICs in their stem-like state.  Although several signaling pathways have been identified as being dysregulated in GBM, the prognosis of GBM patients remains miserable despite improvements in targeted therapies.  In this report we identified that the BRG1 catalytic subunit of the SWI/SNF chromatin remodeling complex plays a fundamental role in the maintaining GICs in their stem-like state.  In addition, we identified a novel mechanism by which BRG1 maintains glucose levels critical for GICs. BRG1 downregulates the expression of TXNIP, a negative regulator of glycolysis.  BRG1 knockdown led to STAT3 upregulation, which in turn led to TXNIP activation.  We further identified that TXNIP is a STAT3-regulated gene. Moreover, BRG1 suppressed the expression of interferon-stimulated genes, which regulate tumorigenesis. We also demonstrate that BRG1 plays a critical role in the drug resistance of GICs and in GIC-induced tumorigenesis.  By genetic and pharmacological means, we found that inhibition of BRG1 can sensitize GICs to chemotherapeutic drugs, temozolomide and Carmustine. Our studies suggest that BRG1 may be a novel therapeutic target in GBM. The identification of the critical role that BRG1 plays GIC stemness and chemosensitivity in GICs will inform the development of better targeted therapies in GBM and possibly other cancers.

overall_design: pLKO.1 plasmids containing gene-specific or scrambled shRNA (control) were used to knockdown (KD) BRG1 in the GBMX16 patient-derived xenoline. Total RNA from GBMX16 and the GBMX16 BRG1 KD cells was extracted using the QIAshredder and RNeasy mini kits (Qiagen Inc., Frederick, MD).  Nanostring arrays were conducted against the Immunology panels on the nCounter Analysis system (NanoString, Seattle, WA), and the data was analyzed with nSolver software using a 2-fold cutoff value.

first: Debolina

last: Ganguly

first: Bhaskar

last: Kahali

first: Michelle

last: Sims

first: Chun

last: Cai

first: Lawrence

last: Pfeffer


title: Pathogenic tau-induced piRNA depletion promotes neuronal death through transposable element dysregulation in neurodegenerative tauopathies

city: San Antonio

first: Habil

last: Zare

state: TX

address: 7703 Floyd Curl Drive

department: Department of Cell Systems & Anatomy

institute: University of Texas Health Science Center in San Antonio

summary: Transposable elements, known colloquially as “jumping genes,” constitute approximately 45% of the human genome. Cells utilize epigenetic defenses to limit transposable element jumping, including formation of silencing heterochromatin and generation of piwi-interacting RNAs (piRNAs), small RNAs that facilitate clearance of transposable element transcripts. Here we identify transposable element activation as a key mediator of neuronal death in tauopathies, a group of neurodegenerative disorders, including Alzheimer’s disease, that are pathologically characterized by deposits of tau protein in the brain. Mechanistically, we find that heterochromatin decondensation and reduction of piwi/piRNAs drive transposable element activation in tauopathy. Using genetic and pharmacological approaches in a Drosophila melanogaster model of tauopathy, we provide evidence for a causal relationship between pathogenic tau-induced heterochromatin decondensation, piwi/piRNA depletion, active transposable element obilization, and neurodegeneration. We further report a significant increase in transcripts of the endogenous retrovirus class of transposable elements in human Alzheimer’s disease and progressive supranuclear palsy, suggesting that transposable element dysregulation is conserved in human tauopathy. Taken together, our data identify heterochromatin decondensation, piwi/piRNA depletion and consequent transposable element activation as a novel, pharmacologically targetable, mechanistic driver of neurodegeneration in tauopathy.

overall_design: For standard RNA-seq, three independent biological replicates of tau transgenic Drosophila samples were sequenced. Each sample consists of 500 ng of total RNA from six pooled heads (18 heads total). For small RNA-seq, four independent biological replicates were sequenced. The number of control samples is equal to the number of tau transgenic samples. The reads that are available in GSE115606 were extracted using sortmerna where FlyBase release 6.12 was used as the reference for transposable elements and piRNABank was used as the reference for piRNAs.

first: Bess

last: Frost

first: Wenyan

last: Sun

first: Hanie

last: Samimi


title: RELMa induced differential gene expression in CD11c+ cells

city: Riverside

first: Meera

middle: Goh

last: Nair

address: 301 School of Medicine Research Building, 900 University Avenue,

department: Division of Biomedical Sciences

institute: University of California Riverside

summary: Mouse lung CD11c+ cell gene expression changes following recombinant RELMa treatment

overall_design: RELMa-/- mice were infected with 500 L3 of Nippostrongylus brasiliensis worms and sacrificed at day 10 post infection. Lungs were collected, dissociated and sorted for CD11c+ cells. Cells were plated overnight at 37 deg C in 10% serum media. Cells were serum starved in 1% serum media for 2 hour and treated with 500ng/ml recombinant RELMa or PBS control. Cells were lysed with lysis buffer and an volume equivalent to 1000 cells per microliter was frozen at -80 deg C for NanoString analysis. Five microliter of each sample (~5000 cells) was applied to NanoString.


title: Transcriptome analysis of the effect of the hsl2 mutation in root tips

city: Zürich

first: Andreas

last: Kopf

address: Auguste-Piccard-Hof 1

department: Biology

country: Switzerland

institute: ETH Zürich

summary: Investigation of HSL2 effect in root cap sloughing

overall_design: Comparison of transcriptome of wild type (Col-0) and hsl2 mutant to elucidate effect on root cap sloughing

first: Jonfinn

last: Blix Knutsen

first: Reidunn

middle: B

last: Aalen


title: Transcriptome analysis of top3A-2 complementation lines in Arabidopsis thaliana

city: Karlsruhe

first: Annika

last: Dorn

address: Fritz-Haber-Weg 4

department: Botanical Institute II

country: Germany

institute: Karlsruhe Institute of Technology

summary: Transcriptome analysis of Attop3A-2 mutant lines in comparison to wild type plants and Attop3A-2::TOP3α-N-Term complementation lines in comparison to wild type plants

overall_design: Total RNA from two-week-old plantlets was extracted using the RNeasy Plant Mini Kit. Three biological replicates were performed. Library preparation and sequencing was performed by Eurofins Genomics. Sequencing was executed on an Illumina HiSeq with a sequencing mode of 1x100 bp reads.

first: Holger

last: Puchta

first: Alexander

last: Knoll


title: Gene expression analyses in otefin mutant Drosophila ovaries

city: Iowa City

first: Alexey

last: Soshnev

state: Iowa

address: 3159C MERF 375 Newton Rd

department: Biochemistry

institute: University of Iowa

summary: LEM Domain proteins are key components of the nuclear lamina. Mutations in LEM-D proteins cause dystrophic diseases associated with compromised adult stem cells, yet it remains unclear how LEM-D proteins support stem cell function. Studies described here use the homologue of the LEM-D protein emerin in Drosophila, Otefin (Ote) as a model to understand LEM-D protein function in adult stem cells. Loss of Ote causes female sterility due to a complex germline stem cell (GSC) phenotype that includes both an early block in germline differentiation followed by GSC death. In vivo cell cycle analysis revealed that ote mutant GSCs display a lengthened S phase.We find that loss of the DNA Damage Response (DDR) Chk2 is able to not only rescue the lengthened S phase, but also GSC death and the block in germline differentiation. Activation of detrimental checkpoint in absence of Ote is conserved in both male and female GSCs and surprisingly occurs independent of detectable canonical DDR triggers, including transposon de-repression and DNA damage. Two defects were found to occur upstream of Chk2 activation: nuclear lamina morphological defects and altered heterochromatin organization. Together, our data identify the primary cause for a compromised adult stem cell population in the absence of a LEM-D protein.

overall_design: Loss of otefin protein results in significant morphological defects in Drosophila ovary, with near complete loss of germline cells, making direct comparison of transcriptional profiles in Ote- and Ote+ ovaries challenging. We found that heterozygous loss of Chk2 suppresses early defect in germline differentiation in otefin mutants, thereby allowing generation of ote- egg chambers morphologically indistinguishable from wild type. Therefore, to identify transcriptional effects of ote loss, we generated two recombinant chromosomes carrying otefin mutant Pk allele in combination with one of the two independently generated Chk2 null alleles P6 (Pk-P6) or P30 (Pk-P30). The flies carrying the resulting double mutant chromosome over balancer CyO, containing wild type copies of both Chk2 and ote, were labeled as heterozygous (HET); the flies carrying double mutant chromosome over another otefin mutant allele G are otefin null and were labeled as such (NULL). The experiment compared gene expression in young virgin female ovaries dissected from  HET and NULL flies; four biological replicates were analyzed for each group.

first: Lacy

last: Barton

first: Pamela

middle: K

last: Geyer


title: Polymerase pausing induced by sequence-specific RNA binding protein drives heterochromatin assembly (NET-Seq)

city: San Francisco

first: Hiten

last: Madhani

department: Department of Biochemistry and Biophysics

institute: University of California, San Francisco

summary: In S. pombe, transcripts derived from the pericentromeric dg and dh repeats promote heterochromatin formation via RNAi as well as an RNAi-independent mechanism involving the RNAPII-associated RNA-binding protein Seb1 and RNA processing activities. We show that Seb1 promotes long-lived RNAPII pauses at pericentromeric repeat regions and their presence correlates with the heterochromatin-triggering activities of the corresponding dg and dh DNA fragments. Globally increasing RNAPII stalling by other means induces the formation of novel large ectopic heterochromatin domains. Such ectopic heterochromatin occurs even in cells lacking RNAi. These results uncover Seb1-mediated polymerase stalling as a signal necessary for heterochromatin nucleation.

overall_design: NET-Seq was conducted on 3 samples in replicate in S. pombe.

first: Jahan-Yar

last: Parsa

first: Selim

last: Boudoukha

first: Jordan

last: Burke

first: Christina

last: Homer


title: Polymerase pausing induced by sequence-specific RNA binding protein drives heterochromatin assembly (RNA-Seq)

overall_design: RNA-seq was conducted on 4 samples in replicate in S. pombe.


title: Epigenetic reprogramming in hepatic carcinogenesis

status: Public on Jul 02 2018

city: Hong Kong

first: Alfred Sze-Lok

last: Cheng

address: Rm 405A, Lo Kwee-Seong Integrated Biomedical Sciences Building, Area 39, CUHK

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Genomic sequencing of hepatocellular carcinoma (HCC) uncovers a paucity of actionable mutations, underscoring the necessity to exploit epigenetic vulnerabilities for therapeutics. In HCC, EZH2-mediated H3K27me3 represents a major oncogenic chromatin modification, but how it modulates the therapeutic vulnerability of signaling pathways remains unknown. Here, we identified that EZH2 maintains H3K27 methylome through epigenetic silencing of specific gene sets. ChIP-seq revealed enrichment of EZH2/H3K27me3 at silenced loci in HBx-transgenic (TG) mouse-derived HCCs, including tumor suppressors whose down-regulation significantly correlated with EZH2 overexpression and poor survival of HCC patients. Defining the aberrant chromatin landscape of HCC sheds light into the mechanistic basis of effective EZH2-targeted inhibition.

overall_design: The normal liver (NL) tissue from 3 month-old wild-type (WT) C57BL/6 mouse, and the non-tumor (NT) and tumor (T) tissues from 18 month-old HBx-TG mice were collected for ChIP-seq analyses using antibodies targeting EZH2 and H3K27me3. The genome-wide enrichment of EZH2 and H3K27me3 in T tissue was compared against those in NL and NT tissues, respectively, as to identify the epigenentically silenced gene sets unique to HCCs.

first: Ying-Ying

last: Lee

first: Myth

middle: T

last: Mok

first: Feng

last: Wu

first: Alfred

middle: S


title: LPS, Telmisartan and GW9662 treatment of microglial BV2 cells

city: BETHESDA

first: abdel

middle: G

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

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

overall_design: Refer to individual Series


summary: LPS and Telmisartan co-treatment of microglial BV2 cells.

overall_design: BV2 cells were treated with DMSO only, Telmisartan only, LPS only or Telmisartan and LPS.

first: Abdel

first: Juan

last: Saavedra


title: Polymerase pausing induced by sequence-specific RNA binding protein drives heterochromatin assembly (ChIP-Seq)

overall_design: ChIP-Seq was conducted on 70 samples of various strain backgrounds to visualize heterochromatin assembly and RNApolII denisites across the S. pombe genome.

middle: D


title: RNA-Seq of FACS-sorted cardiomyocytes

status: Public on Jul 01 2018

first: Roland

address: 555 Mission Bay Blvd South MC3122

department: CVRI

institute: UCSF

summary: The goal of this experiment was to evaluate the expression profile of cardiomyocytes freshly isolated from zebrafish embryos. Here we report mRNA abundance measurements for zebrafish cardiomyocytes at 20 hours post fertilization (hpf). We found that cardiomyocytes isolated from zebrafish embyros are enriched for orthologues of genes abundant in mammalian iPS-derived cardiomyocytes and other in vitro models of cardiomyocytes. It was also enriched with genes required for cardiac development in zebrafish and mammalian models.  Using a rapid-throughput CRISPR-Cas9 based G0 screening pipeline, we tested 50 abundant transcription factors derived from this profile, rediscoved transcription factors known to be required for cardiac development, and found a novel role for zbtb16a in cardiac development.

overall_design: Abundance measurements of cardiomyocytes purified from 20 hpf zebrafish embryos

first: Shaun

last: Coughlin


title: Expression data for two primary and two recurrent MTB;TAN-derived tumor cell lines

city: West Lafayette

first: Nathaniel

middle: Wesley

last: Mabe

state: Indiana

address: 201 S. University St.

department: Medicinal Chemistry and Molecular Pharmacology

institute: Purdue University

summary: Baseline gene expression for two primary and two recurrent tumor cell lines derived from MTB;TAN transgenic mice. Microarrays were performed in biological duplicate to determine differential gene expression between primary and recurrent tumor cell cohorts.

overall_design: 8 total samples total comprised of two parental primary and two parental recurrent tumor cell lines, each in biological duplicate. Samples were analyzed in R by simplaffy and limma packages for differential gene expression analysis between primary and recurrent cohorts.

first: James

middle: V

last: Alvarez

middle: W


title: Differential expression patterns of microRNAs in a mouse model after whole body radiation

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

summary: Rapid and reliable methods for conducting biological dosimetry are a necessity in the event of a large-scale nuclear event. Timely and accurate methods are thus critical in order to correctly evaluate and identify radiation dose exposure and triage appropriately. Alterations in microRNAs (miRNAs), small non-coding RNAs of 19-22 nucleotides, have been reported in cells/tumors subjected to radiation exposure, implying that miRNAs play an important role in cellular stress response to radiation. To examine the possibility of using microRNA as stable blood based biomarkers for radiation response, we have used microRNA microarray analysis. Differential microRNA expression pattern was evaluated (>1.5 fold and  p value <0.05) at 6, 24, 48 h and 7day time points in whole blood from mice exposed to 2, 4, 8, 12 and 15Gy  irradiation. More differentially expressed microRNAs (up and down) were seen after higher dose of radiation and later time points. Among the significantly upregulated microRNAs, miR-193b-3p and mir-92a-3p were consistently upregulated for all doses at earlier time points. We observed significant downregulation of several members of the miR-17 family (miR-17-5p, miR-20a-5p, miR-93-5p and miR-106b-5p) in response to radiation from 2 Gy onwards at 24 h, 48 h and at higher doses for the 7 d time-point. Whereas miR-34a, which regulates G1/S cell cycle checkpoint activation in response to radiation induced DNA damage, showed consistent upregulation for both low and high doses at later time points up to one week after exposure. Significant down regulation of miR-150-5p, miR-101, miR-140, miR-29b, miR-193b and miR-30 family of microRNAs were seen for low and high doses of radiation for all time points up to 7day. Low dose radiation (2Gy) exposure also resulted in down regulation of a group of microRNAs after one week; whereas these microRNAs showed upregulation after high dose exposure (8, 12 and 15Gy) up to one week. This dose and time dependent differential microRNA expression pattern might be useful in evaluating radiation response during and after therapeutic radiation treatment in patients. Ultimately, a combined approach of identifying biomarkers by assessing functional miRNA, target mRNAs and the resulting proteins to assess radiation exposure after mass-casualty incidents could provide a valuable tool in developing and implementing effective and timely medical countermeasures.

overall_design: 81 samples of mouse whole blood in 3 biological replicates taken 6h, 24h, 48h, or 7d after irradiation dose 0, 1, 2, 4, 8, 12, or 15Gy.  The experiment was run in two batches (A for low doses, B for higher doses).

first: Molykutty

middle: J

last: Aryankalayil

first: Sunita

last: Chopra

first: Joel

last: Levin

first: Iris

last: Eke

first: Adeola

last: Makinde

first: Uma

last: Shankavaram

first: Claire

last: Vanpouille-Box

first: Sandra

last: Demaria

first: C

middle: N

last: Coleman


title: Conservation of intracellular pathogenic strategy among distantly related Cryptococcal species

status: Public on Jun 30 2018

city: Baltimore

first: Anne

middle: E.

last: Jedlicka

address: 615 N. Wolfe street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins University, School of Public Health

summary:
We compared the interaction between Cryptococcus gattii species complex strain R265 and Cryptococcus neoformans species complex strain H99, molecular type VNI, with murine macrophages to ascertain similarities and differences in their intracellular pathogenic strategy. Parameters analyzed include non-lytic exocytosis using time-lapse microscopy, phagolysosomal pH by dual fluorescent microscopy, intracellular capsular growth, phagolysosomal membrane permeabilization by flow cytometry, and the macrophage transcriptional response by gene expression microarray analysis.
Using microarrays, we compared the transcriptional response of Bone Marrow-derived macrophages (BMDM) infected with  C. gattii species complex strain R265 or C. neoformans species complex strain H99, relative to uninfected BMDM collected from the same time intervals, 2hr and 24 hr post-infection. For analysis following normalization and summarization steps, a 2-way Analysis of Variance (ANOVA) with linear contrasts for treatment (infection/strain) and time (2 h or 24 h) vs. Control (uninfected) was performed with outputs of P value, Fold Change, and Mean Ratio. A linear contrast of uninfected controls (24 h uninfected vs 2 h uninfected) was also performed to generate a ‘time only’ gene list. Cutoff criteria for filtering gene lists was significant P values (p<0.01) with fold changes greater that 2 or less than –2. Ten genes from the filtered gene lists were selected for validation by qPCR, with four housekeeping genes for normalization and comparison.

overall_design: Control (uninfected)  and C. gattii- or C. neoformans-infected BMDM were harvested at 2hr and 24hr time points and processed in triplicate for each condition.

first: Joudeh

last: Freij

first: Man

last: Fu

first: Carlos

middle: M

last: De Leon Rodriguez

first: Amanda

last: Dziedzic

middle: E

first: Quigly

last: Dragotakes

first: Diego

middle: C

last: Rossi

first: Eric

middle: H

last: Jung

first: Carolina

last: Coelho

first: Arturo

last: Casadevall


title: Sex-specific gene-by-vitamin D interactions regulate susceptibility to CNS autoimmunity

city: 89 Beaumont ave

first: Dimitry

last: Krementsov

state: VT

address: 312C Rowell bldg, 106 Carrigan drive

department: BHSC

institute: University of Vermont

summary: Vitamin D3 (VitD) insufficiency is postulated to represent a major modifiable risk factor for multiple sclerosis (MS). While low VitD levels strongly correlate with higher MS risk in white populations, this is not the case for other ethnic groups, suggesting the existence of a genetic component. Moreover, VitD supplementation studies in MS so far have not shown a consistent benefit. We sought to determine whether direct manipulation of VitD levels modulates central nervous system (CNS) autoimmune disease in a sex-by-genotype-dependent manner. To this end, we used a dietary model of VitD modulation, together with the autoimmune animal model of MS, experimental autoimmune encephalomyelitis (EAE). To assess the impact of genotype-by-VitD interactions on EAE susceptibility, we utilized a chromosome substitution (consomic) mouse model that incorporates the genetic diversity of wild-derived PWD/PhJ mice. High VitD was protective in EAE in female, but not male C57BL/6J (B6) mice, and had no effect in EAE-resistant PWD/PhJ (PWD) mice. EAE protection was accompanied by sex- and genotype-specific suppression of proinflammatory transcriptional programs in effector CD4 T effector cells, but not CD4 Treg cells. Decreased expression of proinflammatory genes was observed with high VitD in female CD4 T cells, specifically implicating a key role of MHC class II genes, interferon gamma, and Th1 cell-mediated neuroinflammation. In consomic strains, effects of VitD on EAE were also sex- and genotype-dependent, whereby high VitD: 1) was protective, 2) had no effect, and, 3) unexpectedly had disease-exacerbating effects. Systemic levels of 25(OH)D differed across consomic strains, with higher levels associated with EAE protection only in females. Analysis of expression of key known VitD metabolism genes between B6 and PWD mice revealed that their expression is genetically determined and sex-specific, and implicated Cyp27b1 and Vdr as candidate genes responsible for differential EAE responses to VitD modulation. Taken together, our results support the observation that the association between VitD status and MS susceptibility is genotype-dependent, and suggest that the outcome of VitD status in MS is determined by gene-by-sex interactions.

overall_design: 2 cell types (CD4 T cells and CD4 T reg cells); 2 strains (B6 and PWD); 2 sexes; 2 diets (VitD high and VitD low); 4 biological replicates (mice) per condition.

first: Cory

last: Teuscher


title: Cell fate decisions of human iPSC-derived bipotential hepatoblasts depend on cell density

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

institute: Universitätsklinikum Düsseldorf

summary: During embryonic development bipotential hepatoblasts differentiate into hepatocytes and cholangiocytes- the two main cell types within the liver. Cell fate decision depends on elaborate interactions between distinct signalling pathways, namely Notch, WNT, TGFβ, and Hedgehog. Several in vitro protocols have been established to differentiate human pluripotent stem cells into either hepatocyte or cholangiocyte like cells (HLC/CLC) to enable disease modelling or drug screening. During HLC differentiation we observed the occurrence of epithelial cells with a phenotype divergent from the typical hepatic polygonal shape- we refer to these as endoderm derived epithelial cells (EDECs). These cells do not express the mature hepatocyte marker ALB or the progenitor marker AFP. However they express the cholangiocyte markers SOX9, OPN, CFTR as well as HNF4α, CK18 and CK19. Interestingly, they express both E Cadherin and Vimentin, two markers that are mutually exclusive, except for cancer cells. EDECs grow spontaneously under low density cell culture conditions and their occurrence was unaffected by interfering with the above mentioned signalling pathways.

overall_design: The transcriptomes of EDECs (treated with and without 100 nM y-secretase inhibitor I) derived from human ESC line H1 were compared to hepatocyte-like cells (HLCs) derived from the same precursors and to the pluripotent precursor ESCs by microarray analysis (PrimeView Human Gene Expression Array, Affymetrix, Thermo Fisher Scientific).

first: Nina

last: Graffmann


first: abdel

last: Elkahloun

summary: LPS, Telmisartan and GW9662 co-treatment of microglial BV2 cells.

overall_design: BV2 cells were treated with Telmisartan and LPS or Telmisartan+GW9662 and LPS.

first: Abdel

first: Juan

last: Saavedra


title: sox32 Alleles Generated from Four-guide Cas9 RNP Targeting in G0 Zebrafish Embryos

first: Roland

last: Wu

summary: We report long-read sequencing results from the sox32 allele targeted with a multi-guide Cas9 RNP strategy.  Embryos were cell-injected with Cas9 RNP programmed with 4 guides simultaneously targeting different portions of the sox32 gene. Genomic DNA was extracted from each embryo and the sox32 coding sequence and intron were amplified and sequenced. Six individual embryos were evaluated.  We found that the majority of sequences were unique and most involved mutations confined to the target sites rather than larger lesions spanning two or more target sites. We also found that alleles accumulated mutations over several DNA replication cycles, which may in part explain the diversity of alleles that were generated. This study is the first to use high-throughput sequencing to evaluate of an allele of this size mutated by a multi-guide Cas9 RNP strategy and provides insights into the dynamics of CRISPR-Cas9 RNP gene editing in vivo.

overall_design: Amplicon sequencing of 6 biological replicates using PacBio Sequencing

first: Shaun

middle: R

last: Coughlin


title: Effect of visible light on human skin fibroblasts

city: LYON

first: Jerome

last: Lamartine

address: 7 passage du Vercors

institute: Université Lyon I

summary: Artificial visible light is everywhere in our modern life. Our mode of social communication confronts us with screens of all kinds and their use is on the rise. People are therefore increasingly exposed to artificial visible light of which effects on skin are still largely poorly known. The purpose of this study was to model the artificial visible light emitted by electronic devices and subsequently assess the effect of such a light in normal human fibroblasts.

overall_design: 8 samples were analyzed correspondoing to 2 conditions (4 biological replicates by condition): Illuminated and non-illuminated cells

last: LAMARTINE

first: Nicolas

last: BECHETOILLE


title: Targeting the cMET pathway augments radiation response without adverse effect on hearing in NF2 schwannoma models

status: Public on Jun 26 2018

city: beijing

first: zhao

last: fu

address: No. 6 Tiantan Xili Dongcheng District

country: China

institute: Beijing Neurosurgical Institute

summary:
Neurofibromatosis type II (NF2) is a disease that needs new solutions. Vestibular schwannoma (VS) growth cause progressive hearing loss, and the standard treatment including surgery and radiotherapy, can further damage the nerve. There is an urgent need to identify an adjunct therapy that, by enhancing the efficacy of radiation, can help lower the radiation dose and preserve hearing.  The mechanisms underlying deafness in NF2 are still unclear. One of the major limitations in studying tumor-induced hearing loss is the lack of mouse models that allows hearing test. Here we developed a cerebellopontine angle (CPA) schwannomas model that faithfully recapitulates the tumor-induced hearing loss. Using this model we discovered that cMET blockade by crizotinib (CRZ) enhanced schwannoma radiosensitivity by enhancing DNA damage, and CRZ treatment combined with low-dose radiation was as effective as high-dose radiation. CRZ treatment had no adverse effect on hearing; however, it did not affect tumor-induced hearing loss, presumably because cMET blockade did not change tumor HGF levels. cMET gene knockdown study independently confirmed the role of cMET pathway in mediating the effect of CRZ.  Furthermore, we evaluated the translational potential of cMET blockade in human schwannomas. We found that human NF2-associated and sporadic VSs showed significantly elevated HGF expression and cMET activation compared to normal nerves, which correlated with tumor growth and cyst formation. Using organoid brain slice culture, cMET blockade inhibited the growth of patient-derived schwannomas. Our findings provide the rationale and necessary data for the clinical translation of combined cMET blockade with radiation therapy in NF2 patients.
We found that human NF2-associated and sporadic VSs showed significantly elevated HGF expression and cMET activation compared to normal nerves, which correlated with tumor growth and cyst formation.

overall_design: Affymetrix GeneChip Human Genome HTA_2_0 Array was used to test global gene expression in  seventeen human NF2-associated VSs, ten human sporadic VSs and four normal control vestibular nerves to identify aberrant expression of the HGF and cMET in VSs.

first: Fu

last: Zhao

first: Lei

last: Xu

first: Yingchao

first: Pinan

last: Liu

last: Zhang

first: Jie

last: Chen

first: Lukas

last: Landegger

first: Limeng

first: Yanling

first: Jing

first: Takeshi

last: Fujita

first: Anat

last: Stemmer-Rachamimov

first: Gino

last: Ferraro

first: Hao

first: Alona

last: Muzikansky

first: Scott

last: Plotkin

first: Konstantina

last: Stankovic

first: Rakesh

last: Jain


title: Short-term low-dose mTORC1 inhibition in aged rats counter-regulates age-related gene changes and blocks age-related kidney pathology

city: Cambridge

first: Jun

last: Shi

address: 181 Massachusetts Avenue

institute: Novartis Institutes for Biomedical Research

summary: Rapalogs, inhibitors of mTORC1 (mammalian target of rapamycin complex 1), increase life span and delay age-related phenotypes in many species. However, the molecular mechanisms have not been fully elucidated. We determined gene expression changes comparing 6- and 24-month-old rats in the kidney, liver, and skeletal muscle, and asked which of these changes were counter-regulated by a clinically-translatable (short-term and low-concentration) treatment, with a rapalog (RAD001). Surprisingly, RAD001 had a more pronounced effect on the kidney under this regimen in comparison to the liver or skeletal muscle. Histologic evaluation of kidneys revealed that the severity of chronic progressive nephropathy lesions was lower in kidneys from 24-month-old rats treated with RAD001 compared with vehicle. In addition to other gene expression changes, c-Myc, which has been shown to regulate aging, was induced by aging in the kidney and counter-regulated by RAD001. RAD001 caused a decrease in c-Myc protein, which could be rescued by a proteasome inhibitor. These findings point to settings for use of mTORC1 inhibitors to treat age-related disorders, and highlight c-Myc regulation as one of the potential mechanisms by which mTORC1 inhibition is perturbing age-related phenotypes.

overall_design: Transcriptional profiling was performed in kidney, liver and gastrocnemius muscles from three experimental groups of male Sprague Dawley rats. Rats aged 4.5 month (m) and 22.5 m were treated with vehicle and rats aged 22.5 m were treated with RAD001 for 6 weeks, with a read-out at 6 and 24 months.

first: Tea

last: Shavlakadze

first: Jiang

last: Zhu

first: Sharon

last: Wang

first: Weihua

last: Zhou

first: Bret

last: Morin

first: Marc

middle: A

last: Egerman

first: Lin

last: Fan

first: Yanqun

first: Oleg

last: Iartchouk

first: Angelika

last: Meyer

first: Reginald

last: Valdez

first: Joan

middle: B

last: Mannick

first: David

last: Glass

first: Klickstein

last: Lloyd


title: Comparative miRNA expression profiles in individuals with chronic or aggressive periodontitis

city: Belo Horizonte

first: Sérgio

last: Amaral

state: Mg

address: Av. Antonio Carlos

country: Brazil

institute: Universidade Federal de Minas Gerais

summary:
The present study aimed to compare the miRNA expression profile in individuals with chronic (CP) and aggressive (AP) periodontitis.
Eighteen non-smokers individuals (CP = 9 and AP = 9) without any history of systemic diseases or previous periodontal therapy were selected at the Clinics of Periodontology from the Federal University of Minas Gerais. Gingival tissue samples were collected during the initial periodontal therapy. miRNAs were isolated and expression patterns of 754 miRNAs were assessed with a quantitative miRNA PCR array. miRNAs expression profiles were compared between CP and AP groups.
No differences were observed in the miRNAs expression profiles between CP and AP groups (p>0.05). According to miRNA microarray analyses, the most expressed miRNAs in both groups were hsa-miR-1274b, hsa-let-7b, hsa-miR-24, hsa-miR-19b, hsa-miR-720, hsa-miR-126, hsa-miR-17 and hsa-miR-21.
Findings suggested that there were no differences in miRNAs expression profiles between chronic and aggressive forms of periodontitis. The overexperssion of especific miRNAs could provide insights on the pathogenesis of both forms of the disease.

overall_design: The present investigation was an observational cross sectional study and STROBE guidelines were followed when appropriate. Participants were selected at the Clinics of Periodontology from the School of Dentistry, Federal University of Minas Gerais. During the period of data collection, from July/2015 to March/2016, ~230 individuals sought periodontal care in the unit of the study and were determined to be eligible

last: Antonucci Amaral

first: Thaís

last: Santos Fontes Pereira

first: João

last: Artur Ricieri Brito

first: Sheila

last: Cavalca Cortelli

first: José

last: Roberto Cortelli

first: Ricardo

last: Santigo Gomez

first: Fernando

last: Oliveira Costa

first: Luís

last: Otávio Miranda Cota


title: Differential regulation of cerebral metabolic genes after hyperglycemic and normoglycemic cardiac arrest

status: Public on Jun 22 2018

city: Uppsala

first: Rickard

last: Lindblom

address: House 50, 4th floor, Uppsala University Hospital

department: Cardiothoracic Surgery and Anesthesiology

country: Sweden

institute: Uppsala University Hospital

summary:
Severe cerebral ischemia caused by events such as ischemic stroke or cardiac arrest is a relatively common and life-threating condition. Those who survive frequently suffer from significant cerebral dysfunction, often with poor outcome. To date the treatment options are limited. Concomitant hyperglycemia is frequently perceived both in focal and global transient ischemia, augmenting the ischemic brain injury as revealed by experimental and clinical studies.
The aim with the current study was to improve the understanding of the pathogenesis behind how concomitant hyperglycemia can augment the cerebral injury seen after cerebral ischemia. To that end we performed a global transcriptome analysis of brains from hyperglycemic and normoglycemic pigs after transient global ischemia.

overall_design: Pigs were openly randomized to high or normal glucose levels, as regulated by glucose and insulin infusions with target levels of 8.5–10 mM and 4–5.5 mM, respectively. The animals were subjected to cardiac arrest of 5 min followed by 8 min of cardiopulmonary resuscitation and direct-current shock to restore spontaneous circulation. Global expression profiling of the cortex using microarrays was performed in both groups.

middle: P

first: Maria

last: Molnar

first: Charlotte

last: Israelsson

first: Belinda

last: Fridman

first: Lars

last: Wiklund

first: Fredrik

last: Lennmyr


title: Expression data of CXCR5+ICOS+ (DP) and CXCR5-ICOS- (DN) CD8+T cells from classical Hodgkin Lymphoma (cHL) lymph nodes

status: Public on Jun 21 2018

city: Rennes

first: Patricia

last: Amé-Thomas

address: 2 Avenue du Pr Léon Bernard

institute: INSERM UMR1236

summary: GEP on Affymetrix Genechip HTA 2.0 microarrays was performed on ex vivo cell-sorted DP and DN CD8+ T cells from cHD lymph nodes

overall_design: GEP was performed on 3 DP and 3 DN CD8+ T cell samples from cHD lymph nodes


title: RNA-seq for RpoN

first: Xin

last: Deng

address: To Yuen Building

department: Biomedical Sciences

institute: City University of Hong Kong

summary: Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen of humans, most notably those with cystic fibrosis or whose immune systems are compromised. As a global regulator, RpoN has been characterized to control a group of virulence-related factors and quorum sensing (QS) genes in P. aeruginosa, but its detailed molecular regulatory mechanism is largely elusive. To further gain insights into the direct targets of RpoN in vivo, this study focused on identifying the potential targets of RpoN directly regulating QS system and T6SS. We performed a chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-seq) assay that identified 1, 068 binding sites of RpoN, including mostly metabolic genes, a group of genes in QS (lasI, rhlI and pqsR) and type VI secretion system (T6SS) (hcpA and hcpB). The direct regulation of these genes by RpoN has been biochemically and genetically verified. Results revealed that, on one hand, the deletion of rpoN resulted in reduced production of pyocyanin, motility and proteolytic activity. On the other hand, the production of rhamnolipids and biofilm formation was higher in the RpoN mutant than in the wild-type. In sum, the results indicated that RpoN had direct and profound effects on QS and T6SS, which provides new cues to better understand the detailed regulatory networks of virulence.

overall_design: RNA-seq for RpoN


title: Whole genome expression array of malaria infected human hosts

status: Public on Jun 23 2018

city: Kolkata

first: Bijurica

last: Chakraborty

state: West  Bengal

address: 35, Ballygunge Circular Road

country: India

institute: University of Calcutta

summary: We hypothesize that human malarial infection will result in a global transcriptomic alteration which will depend upon the strain of invading Plasmodium pathogen.

overall_design: Total RNA obtained from PBMC fraction of P. falciparum, P. vivax and post malaria fever remission patient samples.

first: Sanghamitra

last: Sengupta


title: Microarray analysis in acute myeloid leukemia (AML)-derived THP-1 cells expressing or not SAMHD1

status: Public on Jun 18 2018

city: Columbus

first: Serena

last: Bonifati

state: Ohio

address: 1900 Coffey Road

department: Veterinary Biosciences

institute: Ohio State University College of Veterinary Medicine

summary: Gene expression analysis in THP-1 cells with SAMHD1 knockout (KO) compared to THP-1 control cells expressing endogenous SAMHD1 reveals that the expression of more than 1000 genes is significantly affected by SAMHD1.

overall_design: AML-derived THP-1 cells expressing SAMHD1 (control cells) or with SAMHD1 KO (generated through CRISPR-Cas9 technology) were used to acquire the gene expression profile in the presence or absence of SAMHD1. Three biological replicates for each cell lines were used for the analysis.

first: Lianbo

last: Yu

first: Li

last: Wu


title: Identifying downstream targets of microRNA-181a in chondrosarcoma cells.

status: Public on Jun 19 2018

city: Providence

first: Richard

last: Terek

state: RI

address: 1 Hoppin St

institute: Rhode Island Hospital

summary: microRNAs are small (22-24 nucleotide), non-coding RNA transcripts that play a role in RNA silencing and post transcriptional regulation of gene expression. They have been implicated to have profound roles in many cancers. The role of microRNAs in chondrosarcoma progression is not well understood. Our lab has identified miR-181a to be up-regulated in chondrosarcoma. miR-181a modulates CXCR4 signaling by targeting RGS-16, leading to increased levels of VEGF and MMP-1, major factors in tumor invasion. In an effort to identify other targets of miR-181a apart from RGS-16, we carried out a gene array to compare gene expression between untreated/control CS-1(chondrosarcoma cell line) cells and CS-1 cells transduced with a lenti virus expression construct with anti-miR-181a sequence.

overall_design: We performed global gene expression profiling using  Affymetrix GeneChip® Human Transcriptome Array 2.0 on 3 sample groups: 1. CS-1 (chondrosarcoma cell line) cells 2. CS-1 cells transduced with a lentiviral expression construct containing a control sequence. 3. CS-1 cells transduced with a lentiviral expression construct containing the anti-miR-181a sequence. Each sample group had 3 replicates. The data generated from the array(.CEL files ) was processed by Affymetrix® Expression Console™ Software to generate .CHP files.

first: R

first: X

last: Sun

first: A

last: Alladin


title: Expression data from Drd2+ cells of mouse mPFC

status: Public on Jun 16 2018

city: Toronto

first: Martin

last: Beaulieu

state: Ontario

address: 1 king's college circle room 4336

department: Pharmacology and Toxicology

country: Canada

institute: University of Toronto

summary:
The heterogeneity of cortical dopamine D2 receptor expressing cells is not well characterized
We performed microarrays to study expression of all the transcriprts specifically from Drd2+ neurons of mouse mPFC. For this we immunoprecipitated ribosomes from mPFC of D2Cre::RiboTag mouse, where ribosomal subunit Rpl22 is tagged with HA epitope specifically in Drd2+ neurons

overall_design: Mouse mPFC was dissected rapidly on ice and ribosomes were precipitated using anti-HA antibodies. Subsequently RNA was isolated from immunoprecipitated ribosomes using RNA isolation columns.

first: Jivan

last: Khlghatyan

first: Clementine

last: Quintana

first: Jean-Martin


title: Transcriptome analyses of Atlantic salmon muscle genes induced by DNA vaccine against salmon alphavirus subtype 3 (SAV3)

status: Public on Jun 13 2018

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

summary: Vaccination of pre-smolt salmon with a plasmid encoding the structural polypeptide of salmonid alphavirus subtype 3 (SAV3) gives protection against infection and development of pancreas disease (PD) mediated with production of antibodies against the virus. The present study analysed transcript responses in the muscle to vaccination with this plasmid (pSAV), pcDNA3.3 was used as a control. pSAV and pcDNA3.3 had similar abilities to up-regulate typical type I IFN stimulated genes. In contrast, pSAV caused higher up-regulation of IFNγ and several IFNγ inducible genes. Compared to pcDNA3.3, pSAV also gave larger increase in transcripts of marker genes for B-cells, T-cells and antigen presenting cells (APCs), which suggests attraction of these cells and that their role in the adaptive immune response elicited by pSAV.

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design: Fish was recieved intramuscular injection of plasmids or PBS. Muscle samples were collected one week after treatment.

first: Børre

last: Robertsen

first: Mehrdad

last: Sobhkhez


title: Comparison of the Transcriptome Profile of four Tissue Specific MSCs: Significance and Therapeutic Implications

status: Public on Jun 15 2018

city: amman

first: DANA

last: HATTAB

address: queen rania street

country: Jordan

institute: CELL THERAPY CENTER

summary:
Performing global gene expression profiling for different types of (Mesenchymal stem cells) MSCs can provide important information that might help in understanding the biology and ontogeny of MSCs. Additionally, it might help in the understanding of the propensity and capacity of MSCs from a particular source to differentiate toward a particular lineage or adopt a certain fate.
We used microarrays to detail the global  gene expression profiling for different types of MSCs including bone marrow (BM), Adipose Tissue (AT), Umbilical cord (UC)  and placenta(PL). The MSCs transcriptome profile was additionally compared to the transcriptome profile of dermal fibroblasts.

overall_design: All MSCs (BM, AT, UC and PL) and fibrpblats were cultured and processed under similar conditions. Platelet lysate was used instead of fetal bovine serum (FBS), as a serum supplement. Affymetrix® Microarray and Human Transcriptome Analysis 2 (HTA 2) chips were used for transcriptome profiling.

first: Dana

last: Alhattab

first: Fatima

last: Jamali

first: Abdalla

last: Awidi


status: Public on Jun 05 2018

city: Geneva

first: Hicham

last: CHAHTANE

address: 30, Quai Ernest-Ansermet

department: Department of Plant Biology

institute: University of Geneva

summary:
Effect of GA on PAC and PAO1 treated Arabidopsis seeds.

Seeds were treated during 20h with paclobutrazol (PAC) or with lyophilized extracts of Pseudomonas aeruginosa liquid culture medium (PAO1).
Experiments were also performed with exogenous application of gibberellic acid.

overall_design:
RNA-seq of wildtype and della mutant seeds treated with MOCK, PAC, PAC + GA, PAO1 extract or PAO1 extract + GA

contributor: Genomics Platform of the Institute of Genetics and Genomics (iGE3), University of Geneva

last: Chahtane

first: Luis

last: Lopez-Molina


title: Genomic analysis for hematopoietic stem and progenitors cells (HSPC) generated in vitro according to ex vivo expansion protocols and their comparison with HSPC obtained fresh

city: Mexico

first: Hector

last: Mayani

state: Mexico City

address: Cuahutemoc 330

institute: Oncology Research Unit

summary: Expansion for hematopoietic cells from umbilical cord blood is a strategy for use this cell source in clinic transplants, however, it is important to know about the genomic changes that can occur in expanded cells. In order to detect global expression profiles changes in hematopoietic stem and progenitors cells generated in vitro, we analyzed hematopoietics populations obtained by FACS in fresh from umbilical cord blood. HSC (fHSC) was defined as CD34+ CD38- CD71- CD45RA- Lin- and were cocultured with stromal cell line OP-9 plus FL, SCF, IL3, IL6, TPO, GMCSF and G-CSF by 7 days, after time we repurified HSC population by FACS using same immunophenotype (ivHSC). In other hand, fresh erythroid progenitors cells (fEPC) were identified as CD34+CD38+CD71+CD45RA- Lin- and fresh myeloid progenitors cells (fMPC) were identified as CD34+CD38+CD71-CD45RA+Lin-. In vitro progenitors cells (ivEPC and ivMPC) were obtained by culturing fHSC in Stemspan serum-free media plus SCF, TPO, IL6, FL and IL3 by 10 days, after time cells were repurified by FACS using same immunophenotype for fresh progenitors. In vitro generated cells were compared with their corresponding fresh population cells.

overall_design: Global expressions patterns were compared between generated in vitro populations of Hematopoietic Stem Cells (HSC) and Myeloid Progenitor Cells (MPC), and Erythroid Progenitors Cells (EPC) with HSC, MPC and EPC populations obtained freshly from Umbilical Cord Blood from healthy donors. Each group has at least two or up to four different samples. Populations were purified by FACS and processed in order to obtain those different populations.

first: Roberto

last: Dircio

first: Julieta

last: Corral

first: Ileana

last: Mondragon

first: Fredy

last: Beltran

first: Alberto

last: Cedro

first: Patricia

last: Flores

first: Alfredo

last: Hidalgo

first: Lourdes

last: Arriaga


title: Overexpression of chicken IRF7 increased viral replication and programmed cell death to the avian influenza virus infection through TGF-beta/FoxO signaling axis in DF-1

status: Public on Jun 01 2018

city: Davis

first: Huaijun

last: Zhou

state: CA

address: Meyer 3307, One shields Ave.

institute: UC Davis

summary: To elucidate the functional role of chicken IRF7 against avian influenza virus (AIV) infection, we generated inducible IRF7 overexpression DF-1 cell lines that could fine control the IRF7 expression level and performed in vitro infection using low pathogenic AIVs (LPAIVs) followed by RNA-seq.

overall_design: Transcriptiome analysis of either low pathgenic influenza virus (H6N2) or mock infected chicken IRF7 overexpression DF-1 cell lines and  respective control cell line

first: Tae-Hyun

last: Kim


title: Transcriptional profile of Mycobacterium tuberculosis in an in vitro model of intraocular tuberculosis

city: Chandigarh

first: Indu

last: Verma

address: Research Block-A, Sector-12

institute: PGIMER

summary: We studied M. tuberculosis transcriptome by whole genome microarray for the identification of key pathogenic determinants that are involved in the pathogenesis of intraocular tuberculosis.

overall_design: Retinal pigment epithelial (ARPE-19) monolayer cells were infected with M. tuberculosis H37Rv (MOI of 10:1). On 3-day post infection (dpi) intracellular M. tuberculosis RNA was isolated and compared to the control M. tuberculosis RNA isolated from inoculum used during infection. Three independent experiments were performed.  Altogether, 2 control and 6 experimental samples were analyzed on 8 X 15K format microarray slides.

first: Sudhanshu

last: Abhishek


title: RNA-seq Analysis of the stem of Wild Type and HDT1 Transcriptomes

status: Public on May 31 2018

first: zhang

middle: yong

last: zhuo

address: Beijing Forestry University

institute: Beijing Forestry University

summary: RNA-seq was performed to examine the differential expressed transcriptomes in hdt1 plants during stem development compare to wild type plants.

overall_design: To examine the differential expressed transcriptomes in hdt1 plants during stem development, the stem from hdt1 mutants and wild type plants at 35-days after flowering were collected for RNA-seq analysis. No replicates include in each samples.

first: Yongzhuo

last: Zhang


title: ChIP-on-chip Rad52 in early S phase (time 60min)

city: Bordeaux

first: Pei-Yun Jenny

last: Wu

address: 1 Rue Camille Saint Saens

institute: Institute of Biochemistry and Cellular Genetics

summary: ChIP-on-chip of Rad52 at time 60' after cdc25-22 release in the following strains: cdc25-22, cdc25-22 rad3∆

overall_design: Each ChIP was compared to its reciprocally labeled input sample. Triplicates for every strain.

first: Blanca

last: Gómez-Escoda

first: Pei-Yun


title: Detection of a genomic duplication by copy number analysis

summary: Comparative genomic hybridization of strains PN1 (no duplication) and PN1400 (duplication in Chromosome 3)

overall_design: Genomic DNA of strains PN1 and PN1400 were reciprocially labeled for competitive hybridization. For each experiment, genomic DNA of each strain was labelled in duplicate with two different dyes for a dye-swap average.

last: Gomez-Escoda


title: Alterations in sperm DNA Methylation, Non-Coding RNA expression, and histone retention mediate Vinclozolin induced epigenetic transgenerational inheritance of disease

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

summary: Environmental factors have been shown to induce the epigenetic transgenerational inheritance of disease through the germline. This study was designed to investigate vinclozolin induced concurrent alterations of a number of different epigenetic processes including DNA methylation and histone retention in sperm. Gestating female rats were exposed transiently to vinclozolin during fetal gonadal development and then F1, F2 and F3 generation sperm were analyzed.

overall_design: The experimental design involved a daily transient exposure of gestating female F0 generation rats during embryonic day E8-E14 to 100 mg/kg per day of vinclozolin in dimethylsulfoxide (DMSO) using intraperitoneal injection. A control generation lineage involved the exposure during day 8-14 of gestation to vehicle DMSO (dimethylsulfoxide) alone. Six different gestating females from different litters for each control and vinclozolin lineage were used. The F1 generation offspring were obtained and aged to 90 day postnatal age and selected males and females bred within the control or vinclozolin lineage. The F2 generation offspring were obtained and aged to 90 days and selected males and females from different litters bred to generate the F3 generation. No sibling or cousin breeding were used to avoid any inbreeding artifacts. All the males were sacrificed at 120 days of age for epididymal sperm collection. The differential DNA methylation regions (DMRs) between the control versus vinclozolin lineages were determined using methylated DNA immunoprecipitation (MeDIP) followed by DNA sequencing (MeDIP-Seq) and bioinformatics analysis. The differential histone retention regions (DHRs) for the F1, F2 and F3 generation for the control versus vinclozolin lineage sperm were analyzed. The procedure involved assessment of differential histone retention sites (DHRs) through a comparison of the control versus vinclozolin lineage sperm using the edgeR analysis similar to that used for the DNA methylation analysis.

first: Millissia

last: Ben Maamar

first: Ingrid

last: Sadler-Riggleman

first: Daniel

last: Beck

first: Margaux

last: McBirney

first: Eric

last: Nilsson

first: Rachel

last: Klukovich

first: Yeming

last: Xie

first: Chong

last: Tang

first: Wei

last: Yan


title: ChIP-on-chip of RPA (Ssb1) in cdc25-22 and  cdc25-22 rad3∆ in Schizosaccharomyces pombe

summary: ChIP-on-chip of RPA at time 60' (early S phase) in synchronized cells after cdc25-22 release

overall_design: Each ChIP was compared to its reciprocially labeled input sample. Triplicates for every strain.


title: Cell Type-specific Analysis of Transcriptome Changes in the Porcine Endometrium on Day 12 of Pregnancy

city: Lindau

first: Stefan

middle: Michael

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

institute: University of Zurich

summary: the aim of this present study was to characterize the complex transcriptome changes in different endometrial cell types during the preimplantation period for improving our understanding of localization of endometrial gene expression regulation in context of recognition of pregnancy. To do this analysis in a transcriptome-wide manner, RNA-seq was performed for samples derived from luminal epithelium (LE), glandular epithelium (GE), and stroma (S) isolated by the use of LCM

overall_design: three types of endometrial cells, luminal epithelial (LE), glandular epithelial (GE), and stromal cells (S) were isolated by laser capture microdissection from endometria of Day 12 pregnant and cyclic control gilts (each group n=4), respectively, and then subjected to RNA-sequencing (RNA-Seq). The obtained datasets were compared to a RNA-Seq dataset from complete endometrial tissue samples collected in the same experiment.

first: Shuqin

last: Zeng

first: Jochen

last: Bick

first: Susanne

last: Ulbrich


title: SET-9 and SET-26 are H3K4me3 readers and play critical roles in germline development and longevity

city: Ithaca

first: Siu

middle: Sylvia

last: Lee

state: NY

address: 520 Campus road

institute: Cornell University

summary: SET-9 and SET-26 are highly homologous paralogs that share redundant function in germline development, but SET-26 alone plays a key role in longevity and heat stress response. SET-26 is broadly expressed, but SET-9 is only detectable in the germline, which likely account for their different biological roles. SET-9 and SET-26 bind to H3K4me3 in vitro and in vivo, and their loss results in broadening of H3K4me3 domains. SET-9 and SET-26 also regulate the RNA expression of a subset of their target genes, irrespective of their H3K4me3 status. We propose that SET-9 and SET-26 function to organize local chromatin environment and to regulate the expression of specific target genes, and these activities together contribute to their critical roles in germline development, stress response, and longevity. SET-9 and SET-26 are highly homologous to human MLL5, a factor implicated in leukemia and glioblastoma, and our findings help to provide new insights into MLL5.

overall_design: H3K4me3 ChIP-seq  in N2,  F1 and F3 set-9 set-26, and glp-1, glp-1;set-26; RNA-seq for N2, F1 set-9 set-26, glp-1, glp-1;set-26, glp-1;daf-16 ,glp-1;set-26;daf-16

first: Wang

last: Wenke


title: Real-time quantitative PCR analysis of colon tissues of DSS-induced colitis mice.

status: Public on May 30 2018

city: Chongqin

first: Xiaodong

address: 30, gaotanyan Street, shapingba District

institute: Army medical university

summary: Inflammatory bowel disease (IBD) is a multifactorial disease involving defective immune responses against invasive microbiota. A Rab32-dependent pathway that eliminates intracellular bacteria in dendritic cells (DCs) was recently reported. In this study, we examined whether Rab32 in DCs participates in the pathogenesis of IBD

overall_design: WT and Rab32 dendritic cell specific knock out mice were administrated with 2.5% DSS for 9 days to induce colitis. On day 9, colon tissues were harvest for qPCR analysis. 3 mice in each group.

first: Qinshan

last: Ni

first: Daxue

last: Zhou


title: Simultaneous control of non-coding RNA on the G2/M phase of the cell cycle in hepatocellular carcinoma [miRNA]

city: Nanning

first: Guangqiang

last: Ye

address: NO.22 Shuangyong Road

institute: The First Affiliated Hospital of Guangxi Medical University

summary:
The differential ncRNA and mRNA expression profile was compared between hepatocellular carcinoma and paracancerous normal tissues by microarray
We use microarray to detail the gene expression of hepatocellular carcinoma and paracancerous normal tissues and Identify differentially expressed genes

overall_design:
The tissues from hepatocellular carcinoma and paracancerous were selected RNA extraction and hybriduzation on Affymetrix miRNA arrays. We sought to Investigate the interaction of non-coding RNAs  in hepatocellular carcinoma

The para-cancerous tissue comes from the same patient as the tumor sample. For example, sample id Ca2 is the tumor sample, Ca2p is the the para-cancerous tissue and Ca2 and Ca2p come from the same patient 2.

first: Guoliang

last: Zhao


title: Simultaneous control of non-coding RNA on the G2/M phase of the cell cycle in hepatocellular carcinoma [lncRNA and mRNA]

type:
Expression profiling by array
Non-coding RNA profiling by array

overall_design:
The tissues from hepatocellular carcinoma and paracancerous were selected RNA extraction and hybriduzation on lncRNA+mRNA arrays. We sought to Investigate the interaction of  RNAs  in hepatocellular carcinoma. Cancer and paracancerous normal tissues were taken from the same patient.

Please note that these arrays are dual channel but were processed in a single-channel analysis. Raw data files are listed in the description field and are available in a tar archive at the foot of this record.


title: ChIP-on-chip Rad52 in unperturbed S phase (no HU treatment)

first: Pei-Yun Jenny

last: Wu

summary: ChIP-on-chip of Rad52 at time 90' after cdc25-22 release in the following strains: cdc25-22, cdc25-22 rad3∆, cdc25-22 rif1∆ and cdc25-22 rif1∆rad3∆

overall_design: Each ChIP was compared to its reciprocially labeled input sample. Duplicates for every strain.

first: Blanca

last: Gomez-Escoda

first: Pei-Yun


title: Post-slippage cells increase expression of factors associated with SASP.

status: Public on May 17 2018

city: Singapore

first: Crasta

last: Karen

state: Singapore

address: 59 Nanyang Drive

department: Lee Kong Chian School of Medicine

country: Singapore

institute: Nanyang Technological University

summary:
Human transcriptome analysis of U2OS cells treated with nocodazole or DMSO (Control).
The gene expression profiling will reveal senescence-associated genes induced upon nocodazole treatment. Our preliminary data show that antimitotic drugs treatment promote post-slippage senescence.

overall_design: We analyzed RNA samples extracted from treated cells using the Affymetrix Human Transcriptome 2.0 Arrays. Array data was processed by Partak genomic suite software. Two biological replicates were performed.

first: Karen

last: Crasta

first: Bing

last: Cheng

first: Alex

last: Wong


title: Simultaneous control of non-coding RNA on the G2/M phase of the cell cycle in hepatocellular carcinoma

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Multiscale analysis of a regenerative therapy for treatment of volumetric muscle loss injury

status: Public on May 23 2018

city: Lexington

first: Darrell

middle: Orlyn

last: Ricke

state: MA

address: 244 Wood Street

department: Group 48 Bioengineering Systems & Technology

institute: MIT Lincoln Laboratory

summary: Skeletal muscle possesses a remarkable capacity to regenerate when injured, but when confronted with major traumatic injury resulting in volumetric muscle loss (VML), the regenerative process consistently fails. The loss of muscle tissue and function from VML injury has prompted development of a suite of therapeutic approaches but these strategies have proceeded without a comprehensive understanding of the molecular landscape that drives the injury response. Herein, we administered a VML injury in an established rodent model and monitored the evolution of the healing phenomenology over multiple time points using muscle function testing, histology, and expression profiling by RNA sequencing. The injury response was then compared to a regenerative medicine treatment using orthotopic transplantation of autologous minced muscle grafts (~1 mm3 tissue fragments). A chronic inflammatory and fibrotic response was observed at all time points following VML. These results suggest that the pathological response to VML injury during the acute stage of the healing response overwhelms endogenous and therapeutic regenerative processes. Overall, the data presented delineate key molecular characteristics of the pathobiological response to VML injury that are critical effectors of effective regenerative treatment paradigms.

overall_design: RNA-Seq time couse of muscle volumetric muscle loss injury healing with controls

middle: O

first: Carlos

last: Aguilar


title: Deregulated MicroRNAs in Cancer-Associated Fibroblasts from Front Tumor Tissues of Lung Adenocarcinoma as Potential Predictors of Tumor Promotion

status: Public on Apr 28 2018

city: Tlalpan

first: Claudia

last: Rangel Escareño

address: Periferico Sur 4809

department: Computational Genomics

institute: INMEGEN

summary: Cancer-associated fibroblasts (CAFs) promote tumor progression through several mechanisms. MicroRNAs (miRNAs) play a key role in CAFs tumor-promoting properties, however, their role in CAFs from different topological areas in lung cancer progression remains unclear. This study aimed to characterize the miRNA expression profile of fibroblasts isolated from matched tumor front (F-CAFs), inner tumor (In-CAFs), and normal adjacent tissue (NFs) in lung adenocarcinoma, using microarray analysis and RT-qPCR. Proliferation and invasion assays of A549 lung cancer cells were performed in the presence of conditioned medium from F-CAFs, In-CAFs and NFs. Pathway enrichment analysis and miRNA-target networks were performed to identify tumorigenesis-related miRNAs. Both F-CAFs and In-CAFs enhanced the proliferation and invasion of A549 cells compared to NFs; however, F-CAFs showed a significantly stronger effect than In-CAFs. qPCR demonstrated three downregulated miRNAs in F-CAFs versus NFs (miR-145-3p, miR-299-3 p, miR-505-3p) and two in F-CAFs versus In-CAFs (miR-410-3p, miR-485-5p). Deregulated miRNAs showed significant association to “pathways in cancer”, “Wnt signaling pathway”, and “TGF-beta signaling pathway”, targeting tumor-promoting growth factors as IGF1 and VEGFA. Our findings suggest that deregulated miRNAs in F-CAFs, which showed the strongest effect on the invasive and proliferative capacity of A546 cancer cells, present potential predictive association with tumor-promoting properties.

overall_design: Tissue samples from the tumor front (F-CAF, 4 samples), matched inner tumor tissue (In-CAF, 4 samples), and matched  adjacent normal (NF, 4 samples) lung tissue from each patient with primary NSCLC subtype adenocarcinoma  (tumor stage 2) were obtained by surgical resection at the Instituto Nacional de Enfermedades Respiratorias; RNA extraction and hybridization on miRNA 4.0 Affymetrix microarray were performed.

first: Maria

last: Negrete-Garcia

first: Sandra

middle: L

last: Ramírez-Rodriguez

last: Rangel-Escareño

first: Said

last: Muñoz-Montero

first: Javier

last: Kelly-García

last: Vázquez-Manríquez

first: Patricio

last: Santillán

first: Martha

last: Montaño Ramírez

first: Gustavo

last: Ramírez-Martínez

first: Alejandra

last: Ramírez-Venegas

last: Ortiz-Quintero


title: c-Myc/BMI1 axis is essential for SETDB1-mediated breast tumorigenesis

status: Public on May 01 2018

first: Phillip

last: Koeffler

address: 14 Medical Drive

institute: Cancer Science Institute

summary: Copy number gain/amplification of SETDB1 has been found in several human cancers, but the detailed oncogenic mechanism(s) of SETDB1 contributing to breast cancer remains largely unexplored. In this project, we analyzed the transcriptome of human breast cancer cell lines (MDA-MB-231 and MDA-MB-453) upon silencing of SETDB1 to explore the potential mechanism(s) underlying SETDB1 promoted breast cancer. In MDA-MB-231 cells, SETDB1 was silenced by shRNA-1. In MDA-MB-453 cells, SETDB1 was reduced by shRNA-3.

overall_design: Differences in gene expression was analyzed in breast cancer cell lines followed by shRNA mediated knock down of SETDB1

first: Jin-Fen

last: Xiao

first: H


title: Spontaneous Tfh cells in lupus mice vs B6/J

city: Gainesville

first: Laurence

last: Morel

state: FL

address: 1395 Center Drive, D6-6

department: Pathology and Immunology

institute: University of Florida

summary: Autoimmune T follicular helper (Tfh) cells have different properties from B6/J nonautoimmune tfh cells.  To compare differences in Tfh cells due to ongoing SLE disease, spontaneous splenic Tfh (CD4+CXCR5+PD-1+) were cell sorted from a pre-enriched population of negatively isolated total CD4 cells by autoMACS. New zealand derived triple congenic lupus strain was compared with B6/J. RNA was immediately extracted with no culturing or treatment of cells.

overall_design: 5 pooled samples of Tfh cells from Triple Congenic Mice and 3 pooled samples from B6/J mice.

first: Seung-Chul

last: Choi

first: Anton

last: Titov

first: Ceclia

last: Lopez

first: Henry

middle: V

last: Baker