title: Aspartate Residues Far From the Active Site Drive O-GlcNAc Transferase Substrate Selection

status: Public on Jul 24 2019

city: Boston

first: Suzanne

last: Walker

state: MA

address: 4 Blackfan Circle

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: Abstract: O-GlcNAc is an abundant post-translational modification found on nuclear and cytoplasmic proteins in all metazoans. This modification regulates a wide variety of cellular processes, and elevated O-GlcNAc levels have been implicated in cancer progression. A single essential enzyme, O-GlcNAc transferase (OGT), is responsible for all nucleocytoplasmic O-GlcNAcylation. Understanding how this enzyme chooses its substrates is critical for understanding, and potentially manipulating, its functions. Here we use protein microarray technology and proteome-wide glycosylation profiling to show that conserved aspartate residues in the tetratricopeptide repeat (TPR) lumen of OGT drive substrate selection. Changing these residues to alanines alters substrate selectivity and unexpectedly increases rates of protein glycosylation. Our findings support a model where sites of glycosylation for many OGT substrates are determined by TPR domain contacts to substrate side chains five to fifteen residues C-terminal to the glycosite. In addition to guiding design of inhibitors that target OGT's TPR domain, this information will inform efforts to engineer substrates to explore biological functions.

overall_design: In this study, Invitrogen's Human ProtoArray protein microarray was used as a platform for high-throughput enzyme activity profiling. Multiple batches of microarrays were used over the course of the study, thus the platform represents a composite of the proteins on all microarray batches. 3 microarrays each were treated with wild-type OGT, the mutant dubbed D2A, or treated with reagents without enzyme. Enzyme microarrays were normalized 2 different ways; both modes of normalization are represented here.

first: Cassandra

last: Joiner

first: Zebulon

last: Levine

first: Chanat

last: Aonbangkhen

first: Christina

last: Woo


title: Dynamic Lineage Priming by ERK is Driven by Transcription Factor-Independent Enhancer Regulation

status: Public on Aug 08 2019

city: Copenhagen

first: Josh

middle: M

last: Brickman

address: 3B Blegdamsvej

department: reNEW

country: Denmark

institute: Copenhagen University

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Transcriptional responses of human synovial fibroblasts to TNF and IL-17A over time (RNA-seq Data 1)

status: Public on Jun 01 2019

city: Charlestown

first: Kamil

last: Slowikowski

state: Massachusetts

address: Mailstop CNY 149-8, 149 13th Street

country: USA

institute: Massachusetts General Brigham

summary: The combination of TNF and IL-17A has synergistic effects on the transcription of genes encoding chemokines and cytokines.

overall_design:
Human fibroblasts derived from individual with rheumatoid arthritis or osteoarthritis were stimulated with TNF or TNF and IL-17A and gene expression was assayed with RNA-seq.

RNA-seq Data 1 (n=175): 7 synovial fibroblast cell lines from patient tissues, 9 time points (0, 2, 4, 6, 8, 10, 12, 18, and 24 hours), 3 stimulations (TNF (1 ng/mL); TNF (1 ng/mL) and IL-17A (1 ng/mL); TNF (1 ng/mL) and IL-17A (10 ng/mL)).

---------------------------------------------------------------
Authors state "We don't have the required patient consents to deposit the raw sequencing reads."
Thus, this dataset is incomplete.

first: Hung

middle: N

last: Nguyen

first: Erika

middle: H

last: Noss

first: Daimon

middle: P

last: Simmons

first: Fumitaka

last: Mizoguchi

first: Gerald

middle: F

last: Watts

first: Michael

last: Gurish

middle: B

last: Brenner

first: Soumya

last: Raychaudhuri


title: Bone Marrow Stroma Cells: Vehicle Control vs. Substance P Treated

status: Public on May 18 2019

city: Newark

first: Pranela

last: Rameshwar

state: NJ

address: 185 South Orange Avenue

department: Medicine

institute: Rutgers NJ Medical School

summary: Gene expression profiling by cDNA microarray of bone marrow stromal cells from three healthy donors treated as follows: vehicle control; or stimulated with 10 nM substance P. Hematopoiesis is tightly regulated by the bone marrow (BM) niche. The niche is robust, allowing for the return of hematopoietic homeostasis after insults such as infection. Hematopoiesis is partly regulated by soluble factors such as neuropeptides, substance P (SP) and neurokinin A (NK-A), which mediate hematopoietic stimulation and inhibition, respectively. The hematopoietic effects of SP and NK-A are mostly mediated via BM stroma. Array analyses with 2400 genes indicated distinct changes in SP-stimulated BM stroma.

overall_design: Bone marrow stromal cells were harvested from three healthy donors. Two-condition experiment comparing gene expression of control bone marrow stromal cells vs. substance P treated bone marrow stromal cells for each donor. Biological replicates: 3 vehicle treated, 3 SP treated.

first: Gergues

last: Marina

first: Rameshwar

last: Pranela


title: Spatiotemporal single-cell analysis of gene expression in the mouse suprachiasmatic nucleus

status: Public on Jun 19 2019

city: Shanghai

first: shaoang

last: wen

state: Shanghai

address: NO.320 Yueyang Road Shanghai, China

country: China

institute: institute of neuroscience

summary: We apply geographical position sequencing (Geo-seq), a method that combines laser capture microdissection (LCM) and single-cell RNA-seq technology, to investigate the heterogeneous nature of suprachiasmatic nucleus (SCN) in adult mouse. The 3D quantitative data enables spatial gene expression pattern visualization . The dataset identified genes that are coexpressed in a specific region, mark domains of similar global pattern of expression, and can be used for mapping the position of single cells dissociated from adult SCN.

overall_design: In laser capture microdissection (LCM), hexagon grids with 40-μm maximal radius was used and the transcriptome of each hexagon was obtained using single-cell RNA-seq technology.

first: Meng

last: Zhao


title: Screening regulated pathway and genes expression in polyI:C treated cerulein-induced AP mice models

status: Public on May 15 2019

city: Wenzhou

first: Chaohao

last: Huang

state: Zhejiang

address: Nanbaixiang Town, Ouhai District, Wenzhou City, Zhejiang Province, China 325000, China,

department: Department of Surgery

institute: First affiliated hospital of Wenzhou Medical University

summary: Pancreas tissue derived from mice with intraperitoneal injection of saline, cerulein or polyI:C plus cerulein, total RNA was extracted and deep sequenced to compare the gene expression  profiles among control, acute pancreatitis and intervention of polyI:C on acute pancreatitis.

overall_design: Duplicated 2 control samples, 2 acute pancreatitis samples and 2 polyI:C-treated acute pancreatitis samples were sequneced and compared

first: Feng

last: Ma

first: Mengtao

last: Zhou


title: Resistant and susceptible cacao varieties exhibit defense gene polymorphism and different responses to Phytophthora megakarya inoculation

city: University Park

first: Mark

last: Guiltinan

state: Pennsylvania

address: 422 Life Sciences Bldg.

department: Plant Molecular Biology

institute: Penn State University

summary: Four month old grafted cacao plants (scions SCA6 and NA32) were spray inoculated with Phytophthora megakarya zoospores or distilled water. Leaf tissue was collected along a time course to measure transcriptomic response.

overall_design: Biological replicates were two leaves, collected from different plants, pooled together for RNA extraction. Collection was performed at five time points (0, 6, 24, 48, 72 hai). Four biological replicates were collected per genotype and treatment at each time point, except for the 48 hour time point, in which only Phyopthora treated samples were collected. Leaves were placed in RNA later and shipped to Penn State for RNA extraction. RNA was extracted using Invitrogen plant RNA reagent. Sample quality was checked using a nanodrop and bioanalyzer. Samples were sequenced using an Illumina Hiseq 2500.

first: Desire

last: Pokou

first: Andrew

last: Fister

first: Siela

last: Maximova


title: Transcriptional response of human synovial fibroblasts to TNF and IL-17A over time (Microarray Data 1)

first: Kamil

last: Slowikowski

overall_design:
Human fibroblasts derived from an individual with rheumatoid arthritis were stimulated with TNF, IL-17A, or TNF and IL-17A and gene expression was assayed with microarrays.

Microarray Data 1 (n = 60): 9 time points, 2 technical replicates, 5 different stimulations (Untreated, Media, IL-17A (1 ng/mL), TNF (1 ng/mL), TNF and IL-17A).

GeneChip™ Human Gene 1.0 ST Array ("affy_hugene_1_0_st_v1" on Bioconductor).

first: Hung

last: Nguyen

first: Erika

last: Noss

first: Daimon

last: Simmons

last: Mizoguchi


title: Transcriptomes of human trophoblast cell lines

status: Public on May 25 2019

city: CINCINNATI

first: Xuzhe

last: Zhang

state: Ohio

address: 3333 Burnet Avenue

department: Human Genetics

institute: Cincinnati Children's Hospital Medical Center

summary: We report the transcriptomes of human choriocarcinoma cell lines JEG3 and BeWo in order to provide information about genes expressed by human trophoblasts.

overall_design: Examination of transcriptomes in two cell lines, two samples in each cell line.

first: Mihaela

last: Pavlicev


title: Acetate promotes T cell effector function during glucose restriction

status: Public on May 14 2019

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University


title: Acetate promotes T cell effector function during glucose restriction [RNA-seq]

summary: Competition for nutrients like glucose can metabolically restrict T cells and contribute to their hyporesponsiveness during cancer. Metabolic adaptation to the surrounding microenvironment is therefore key for maintaining appropriate cell function. For instance, cancer cells use acetate as a substrate alternative to glucose to fuel metabolism and growth. Here we show that acetate rescued effector function in glucose-restricted CD8+ T cells. Mechanistically, acetate promoted histone acetylation and chromatin accessibility, and enhanced IFN-γ gene transcription and cytokine production in an acetyl-CoA synthetase (ACSS)-dependent manner. Ex vivo acetate treatment increased IFN-γ production by exhausted T cells, while reducing ACSS expression in T cells impaired IFN-γ production by tumor-infiltrating lymphocytes and tumor clearance. Thus, hyporesponsive T cells can be epigenetically remodeled and reactivated by acetate, suggesting that pathways regulating the use of substrates alternative to glucose could be therapeutically targeted to promote T cell function during cancer.

overall_design: RNA-seq was performed on acute (24h) or prolonged (120h) glucose restriction (1mM) CD8+ T cells exposed or not to 5mM Acetate, then restimulated for 4h with PMA/Ionomycin.

first: Jing

last: Qiu

first: Matteo

last: Villa

first: David

middle: E

last: Sanin

first: Michael

middle: D

last: Buck

last: O’Sullivan

first: Reagan

last: Ching

first: Mai

last: Matsushita

first: Katarzyna

last: Grzes

first: Frances

last: Winkler

first: Chhih-Hao

last: Chang

first: Jonathan

last: Curtis

first: Ryan

middle: L

last: Kyle

first: Nikki

last: van Teijlingen Bakker

first: Mauro

last: Corrado

first: Fabian

last: Hässler

first: Francesca

last: Alfei

first: Joy

last: Edwards-Hicks

first: Leonard

last: Maggi Jr

first: Dietmar

last: Zehn

first: Takeshi

last: Egawa

first: Bertram

last: Bengsch

first: Ramon

middle: I

last: Klein Geltink

first: Thomas

last: Jenuwein

first: Edward

middle: J

last: Pearce


title: F1 hybridization effects on mouse oocytes

status: Public on May 08 2019

city: East Lansing

first: Uros

last: Midic

state: MI

address: 474 S. Shaw Lane

department: Animal Sciences

institute: Michigan State University

summary: This dataset consists of germinal vesicle (GV) and metaphase II (MII) oocytes from B6, D2, and B6xD2 F1 mice. Oocytes from a single mother were pooled as one biological replicate to become one sample. The goal of the study was to explore the genetic effects on oocyte quality, and more specifically, to determine a viable explanation for the hybrid vigor phenotype displayed in F1 mice. This study is the first to combine oocytes of different stages and different genotypes (two parental inbred strains and F1 hybrid) into a single analysis capable of identifying molecular characteristics that distinguish F1 hybrids.

overall_design: Gene expression profiles for germinal vesicle (GV) and metaphase II (MII) oocytes from B6, D2, and B6xD2 F1 mice were compared.

first: Ashley

last: Severance

first: Keith

last: Latham


title: Acetate promotes T cell effector function during glucose restriction [ChIP-seq]

first: Immunometabolism

last: Department

overall_design: ChIP-seq was performed on acute (24h) or prolonged (120h) glucose restriction (1mM) CD8+ T cells exposed or not to 5mM Acetate.

first: Jing

last: Qiu

first: Matteo

last: Villa

first: David

last: Sanin

first: Michael

last: Buck

last: O’Sullivan

first: Reagan

last: Ching

first: Mai

last: Matsushita

first: Katarzyna

last: Grzes

first: Frances

last: Winkler

first: Chhih-Hao

last: Chang

first: Jonathan

last: Curtis

first: Erika


title: ZMYM2 inhibits Nanog-mediated reprogramming

status: Public on Apr 26 2019

city: Cambridge

first: Moyra

last: Lawrence

address: Tennis Court Road

department: Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

summary: RNASeq data from WT, Zmym2 knockout- and Zmym2 overexpressing- E14tg2a mouse embryonic stem cells

overall_design: RNASeq of ESCs in medium containing Serum and Leukaemia Inhibitory Factor (LIF)

first: Jose

last: Silva


city: Kyoto

first: Wooseok

last: Seo

address: Yoshida-Konoe-cho, Sakyo-ku

country: Japan

institute: Kyoto University Graduate School of Medicine

summary: Constitutive CD8 expression drives innate CD8+ T cell differentiation via induction of iNKT2 subset.

overall_design: Analysis of RNA from Cd8ab transgenic mice by RNA-seq.

first: Satoshi

last: Kojo

first: Michiko

last: Ohno-Oishi

first: Hisashi

last: Wada

first: Sebastian

last: Nieke

first: Sawako

last: Muroi

first: Ichiro

last: Taniuchi


title: RNA proximity sequencing reveals properties of spatial transcriptome organization in the nucleus

status: Public on May 03 2019

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

institute: MRC Laboratory of Molecular Biology

summary: Spatial transcriptomics aims to understand how the ensemble of RNA molecules in tissues and cells is organized in 3D space. Here we introduce Proximity RNA-seq, which identifies co-localization preferences for pairs or groups of chromatin-associated, nuclear-retained and nascent RNAs in cell nuclei. Proximity RNA-seq is based on massive-throughput RNA barcoding of sub-nuclear particles in water-in-oil emulsion droplets, followed by sequencing.

overall_design: 4 Proximity RNA-Seq datasets (Pools 2, 5, 7 & 8), 2 Hi-C datasets

first: Jörg

last: Morf

middle: W

first: Irene

last: Farabella

last: Cairns

first: Mayra

last: Furlan-Magaril

first: Luis

last: Jiménez-García

first: Xin

last: Liu

first: Frank

last: Craig

first: Simon

last: Walker

first: Anne

last: Segonds-Pichon

last: Andrews

first: Marc

middle: A

last: Marti-Renom

first: Peter

last: Fraser


title: Interleukin-8 modifies the expression profile of microRNA in rat primary skeletal muscle cells

status: Public on Apr 25 2019

city: Warszawa

first: Alicja

last: Majewska

address: Nowoursynowska 159

department: Department of Physiology Sciences

country: Poland

institute: Warsaw University of Life Sciences-SGGW Faculty of Veterinary Medicine

summary:
In the present study we examined the expression profile of microRNA in rat primary skeletal muscle cells (RSkMC) treated with IL-8, a chemokine and an angiogenic factor, which is released in visceral adipose tissue, but also found in contracting skeletal muscles. The miRNA microarray analysis revealed increased expression of 5 miRNA species,  which were not yet described in skeletal muscle, in RSkMC exposed to IL-8 (1 ng/ml) for 11 days of differentiation. In order to verify the microarray data, qRT-PCR analysis was performed to quantify miRNA expression. We confirmed the increased expression of miR-154-3p (fold change =1.91), miR-541-5p (fold change =1.36), miR-376c-3p (fold change =1.84), and miR-338-3p (fold change =1.6), whereas let-7a-1-3p did not show a significant change in expression, in comparison to control group.
Using Target Scan database we found potential targets for all miRNAs with expression modified by IL-8 and focused our further interest on genes and pathways involved in skeletal muscle hypertrophy, that is: myocilin, PKB/Akt and FoxO3.

overall_design: We compared the miRNA expression profiles of RSkMC exposed to IL-8 (1 ng/ml) for 11 days of differentiation to control group (untreated samples). Three microarrays were done for each experimental condition.

first: Marta

last: Milewska

first: Tomasz

last: Domoradzki

first: Maciej

last: Błaszczyk

first: Małgorzata

last: Gajewska

first: Magdalena

last: Hulanicka

first: Anna

last: Ciecierska

first: Katarzyna

last: Grzelkowska-Kowalczyk


title: Selective Inhibition of the Second Bromodomain of BET Family Maintains Anti-Tumor Efficacy and Improves Tolerability

status: Public on Apr 24 2019

city: North Chicago

last: Lu

state: IL

address: 1 North Waukegan Rd

department: Oncology Discovery

institute: Abbvie


title: Combinatorial discriminant analysis applied to RNAseq data reveals a set of 10 transcripts as signatures of infection of cattle with Mycobacterium avium subsp. Paratuberculosis (MAP).

status: Public on Apr 23 2019

city: Bologna

first: Daniel

last: Remondini

address: Viale Berti Pichat 6/2

department: Physics and Astronomy - DIFA

country: Italy

institute: Bologna University

summary: RNAseq experimental data of cattle positive to MAP infection are compared to negative uninfected controls, with the purpose to find a small set of differentially expressed genes able to discriminate between infected animals in a preclinical phase. A signature of 10 transcripts that differentiate between potentially infected, but clinically healthy, animals belonging to paratuberculosis positive herds and negative unexposed animals has been identified and crossvalidated.

overall_design: Total RNA was extracted from whole blood of 4-5 years old dairy cattles between the 170-190 days in milk belonging to infected and healthy herds. Animals from the infected herd categorized as positive or potentially exposed to the disease.

first: Giulietta

last: Minozzi


title: Synergy between variant PRC1 complexes defines Polycomb-mediated gene repression (RNA-Seq)

city: Oxford

first: Nadezda

last: Fursova

address: South Parks Rd

department: Department of Biochemistry

institute: University of Oxford

summary: The Polycomb system modifies chromatin and plays an essential role in repressing gene expression to control normal mammalian development. However, the components and mechanisms that define how Polycomb protein complexes achieve this remain enigmatic. Here we use combinatorial genetic perturbation coupled with quantitative genomics to discover the central determinants of Polycomb-mediated gene repression in mouse embryonic stem cells. In contrast to prevailing views, we demonstrate that canonical Polycomb repressive complex 1 (PRC1), which mediates higher order chromatin structures, contributes little to gene repression. Instead, we uncover an unexpectedly high degree of synergy between variant PRC1 complexes which is fundamental to gene repression. We further demonstrate that variant PRC1 complexes are responsible for distinct pools of H2A monoubiquitylation that are associated with repression of Polycomb target genes and silencing during X-chromosome inactivation. Together, these discoveries reveal a new variant PRC1-dependent logic for Polycomb-mediated gene repression.

sample_organism:
Drosophila melanogaster
Mus musculus

platform_organism:
Drosophila melanogaster
Mus musculus

overall_design: Mouse embryonic stem cells in which distinct PCGF-containing PRC1 complexes can be conditionally removed individually or in different combinations ( Pcgf4-/-; Pcgf2fl/fl, Pcgf1fl/fl, Pcgf3/5fl/fl, Pcgf1/3/5fl/fl, Pcgf1/3/5/2fl/fl, Pcgf1/3/5/6fl/fl and Ring1a-/-; Ring1bfl/fl) were profiled for gene expression using spike-in calibrated nuclear RNA-seq.

first: Neil

last: Blackledge

first: Robert

last: Klose


title: Differential expression of human tRNA genes drives the abundance of tRNA-derived fragments

status: Public on Apr 17 2019

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

type: Non-coding RNA profiling by high throughput sequencing

summary: The human genome encodes hundreds of tRNA genes but their individual contribution to the tRNA pool is not fully understood. Deep sequencing of tRNA transcripts (tRNA-Seq) can estimate tRNA abundance at single gene resolution, but tRNA structures and post-transcriptional modifications impair these analyses. Here we present a bioinformatics strategy to investigate differential tRNA gene expression and use it to compare tRNA-Seq datasets from cultured human cells and human brain. We find that sequencing caveats affect quantitation of only a subset of human tRNA genes. Unexpectedly, we detect several cases where the differences in tRNA expression among samples do not involve variations at the level of isoacceptor tRNA sets (tRNAs charged with the same amino acid but using different anticodons); but rather among tRNA genes within the same isodecoder set (tRNAs having the same anticodon sequence). Because isodecoder tRNAs are functionally equal in terms of genetic translation, their differential expression may be related to non-canonical tRNA functions. We show that several instances of differential tRNA gene expression result in changes in the abundance of tRNA-derived fragments (tRFs) but not of mature tRNAs. Examples of differentially expressed tRFs include: PIWI-associated RNAs, tRFs present in tissue samples but not in cells cultured in vitro, and somatic tissue-specific tRFs. Our data support that differential expression of tRNA genes regulate non-canonical tRNA functions performed by tRFs.

overall_design: Examination of the levels of Inosine 34 on tRNAs upon a CRISPR/Cas9-mediated knockdown of ADAT2, a subunit of the human heterodimeric adenosine deaminase acting on tRNA. 2x control cells and 2x ADAT2 KD cells.

first: Adrian

middle: G

last: Torres

last: Reina

first: Camille

last: Stephan-Otto Attolini

first: Lluís

last: Ribas de Pouplana


title: Systematic comparison of single-cell and single-nucleus transcriptomes during cardiomyocyte differentiation

status: Public on Apr 02 2019

city: Chicago

first: Alan

last: Selewa

address: 5454 S Shore Dr, Apt 503

institute: University of Chicago

summary:
Purpose:To systematically assess the differences between high-throughput single-cell and single-nuclei RNA-seq approaches, we compared Drop-seq and DroNc-seq, two microfluidic-based 3’ RNA capture technologies that profile total cellular and nuclear RNA, respectively, during a time course experiment of human induced pluripotent stem cells (iPSCs) differentiating into cardiomyocytes
Conclusions: Clustering of time-series transcriptomes from Drop-seq and DroNc-seq revealed six distinct cell types, five of which were found in both techniques. Furthermore, single-cell trajectories reconstructed from both techniques reproduced expected differentiation dynamics.

overall_design: Drop-seq and DroNc-seq each on 2 hiPSC cell lines differentiating into cardiomyocytes across 5 time points. DroNc-seq on post-mortem primary heart tissue.


title: A lineage commitment checkpoint in early ILC development

status: Public on Apr 22 2019

city: Bethesda

first: Margaret

middle: C

last: Cam

state: MD

institute: NIH

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

overall_design: Refer to individual Series


title: Gene expression profiling of aneuploid IMR90 cells induced by Rb, DNMT1 and MAD2 depletion

status: Public on Mar 31 2019

city: Palermo

first: Salvatore

last: Feo

address: Viale delle Scienze, Edificio 16

department: Dept. of Biological, Chemical and Pharmaceutical Sciences and Technologies

institute: University of Palermo

summary: Segregation errors of chromosomes into daughter cells lead to aneuploidy that is considered a major feature of solid tumors. How diploid cells face chromosome mal-segregation and the mechanisms driving aneuploidy tolerance in tumor cells are not yet completely defined. Thus, an important goal in cancer genetics is to identify gene networks leading to aneuploidy as well involved in its tolerance. To this aim we induced aneuploidy in IMR90 human primary cells and analyzed their gene expression profiles by DNA microarrays.   Bioinformatics analysis revealed the presence of shared differentially expressed genes, up or down regulated in IMR90 cells after depletion of pRb, DNMT1 and MAD2 all inducing aneuploidy. Normalized data were also analyzed with the Gene Set Enrichment Analysis (GSEA) software to detect deregulated gene-sets associated with the aneuploidy phenotype. GSEA analysis suggested the existence of shared gene-sets/pathways characterizing aneuploidy cells that might be exploited for novel therapeutic approaches in cancer

overall_design: To search for a molecular signature shared by different IMR-90 aneuploid cell populations generated by depletion of DNMT1, MAD2 and pRb we performed transcriptome analysis to compare expression profiles between IMR-90 cells transfected with siRNA to DNMT1, MAD2 and pRb genes and those transfected with a negative control.

first: Serena

last: Bivona


title: Aging-exacerbated demyelinating injury is associated with microglia-derived reactive oxygen species: alleviation by indapamide

status: Public on Mar 29 2019

city: Calgary

first: V. Wee

last: Yong

state: AB

address: 3330 Hospital Dr. NW

country: Canada

institute: University of Calgary

summary: We sequenced the transcriptome of young (6-8 week) and middle-aged (8-10 month old) C57BL/6 female mice that were naïve or had injured ventrolateral spinal cord white matter. We found several differentially expressed genes, many suggesting an altered immune response to injury with advancing age.

overall_design: Naïve or injured (72 hours after the local injection of lysolecithin) ventrolateral white matter of the spinal cord was isolated using laser capture microdissection. RNA was then extracted using RNeasy MiniKit (Qiagen) as per manufacturer’s instruction and sequenced using the Illumina NextSeq500. Tissue was pooled from 5 animals per condition and 3 replicates were sequenced for the analysis.

first: Nathan

last: Michaels

first: Kennedy

last: Lemmon

first: Jason

middle: R

last: Plemel

first: Samuel

middle: K

last: Jensen

first: Dennis

last: Brown

first: Manoj

last: Mishra

first: Khalil

middle: S

last: Rawji

first: Marcus

last: Koch

first: V


title: Combined Inhibition of Epigenetic Readers and Transcription Initiation Targets the EWS-ETS Transcriptional Program in Ewing Sarcoma

city: Berlin

first: Guenther

middle: HS

last: Richter

address: Augustenburger Platz 1

department: Department of Pediatrics, Division of Oncology and Hematology

country: Germany

institute: Charité - Universitätsmedizin Berlin

summary: Background: Previously, we used inhibitors blocking BET bromodomain binding proteins (BRDs) in Ewing sarcoma (EwS) and observed that long term treatment resulted in the development of resistance. Here, we analyze the possible interaction of BRD4 with cyclin-dependent kinase (CDK) 9. Methods: Co-immunoprecipitation experiments (CoIP) to characterize BRD4 interaction and functional consequences of inhibiting transcriptional elongation were assessed using drugs targeting of BRD4 or CDK9, either alone or in combination. Results: CoIP revealed an interaction of BRD4 with EWS-FLI1 and CDK9 in EwS. Treatment of EwS cells with CDKI-73, a specific CDK9 inhibitor (CDK9i), induced a rapid downregulation of EWS-FLI1 expression and block of contact-dependent growth. CDKI-73 induced apoptosis in EwS, as depicted by cleavage of Caspase 7 (CASP7), PARP and increased CASP3 activity, similar to JQ1. Microarray analysis following CDKI-73 treatment uncovered a transcriptional program that was only partially comparable to BRD inhibition. Strikingly, combined treatment of EwS with BRD- and CDK9-inhibitors re-sensitized cells, and was overall more effective than individual drugs not only in vitro but also in a preclinical mouse model in vivo. Conclusion: Treatment with BRD inhibitors in combination with CDK9i offers a new treatment option that significantly blocks the pathognomonic EWS-ETS transcriptional program and malignant phenotype of EwS.

overall_design: Ewing sarcoma cell lines A673, SKNMC or TC-71 cells were treated with 2 µM CDK9 inhibitor I-73 or solvent control for 8 hrs at 37 °C, 5% CO2

first: Oxana

last: Schmidt

first: Tim

last: Hensel

first: Günther

middle: H


title: Acetate promotes T cell effector function during glucose restriction [ATAC-seq]

first: Immunometabolism

last: Department

overall_design: ATAC-seq was performed on acute (24h) or prolonged (120h) glucose restriction (1mM) CD8+ T cells exposed or not to 5mM Acetate.

first: Jing

last: Qiu

first: Matteo

last: Villa

first: David

last: Sanin

first: Michael

last: Buck

last: O’Sullivan

first: Reagan

last: Ching

first: Mai

last: Matsushita

first: Katarzyna

middle: M

last: Grzes

first: Frances

last: Winkler

first: Chhih-Hao

last: Chang

first: Jonathan

last: Curtis

first: Ryan

last: Kyle

first: Nikki

last: van Teijlingen Bakker

first: Mauro

last: Corrado

first: Fabian

last: Hässler

first: Francesca

last: Alfei

first: Joy

last: Edwards-Hicks

first: Leonard

last: Maggi Jr.

first: Dietmar

last: Zehn

first: Takeshi

last: Egawa

first: Bertram

last: Bengsch

first: Ramon

last: Klein Geltink

first: Thomas

last: Jenuwein

first: Edward

last: Pearce

first: Erika


title: Testosterone-Dependent Porcine miR-26a-5p and let-7g-5p Act as Signaling Mediators to Regulate Sperm Apoptosis via Targeting PTEN and PMAIP1

status: Public on Mar 19 2019

city: Yaan

first: jideng

last: Ma

address: Xinkang road

institute: Sichuan Agricultural University(SICAU),

summary: We found that differentially expressed (DE) miRNAs were mainly enriched in pathways involved in cell apoptosis, including mTOR and p53 signaling pathways. Furthermore, gain- and loss-of-function analyses and dual luciferase assays demonstrated that endogenous miR-26a-5p and let-7g-5p have potential anti-apoptotic and pro-survival functions in sperm cells through targeting PTEN and PMAIP1 genes. Further comparisons revealed high similarities in miRNA profiles between seminal plasma exosomes and sperm cells, both in HC and CT groups. Our study revealed that miRNAs in sperm cells and seminal plasma exosomes have important functions in male reproduction, suggesting they could be used as potential treatment targets or novel diagnostic markers for male infertility.

overall_design: We used small RNA sequencing to detect miRNA transcriptomes of sperm from pigs with prepubertal hemicastration (HC) and compared them with control libraries (CT) (3 vs. 3). The relationship between sperm cells and corresponding seminal plasma exosomes  with respect to miRNAome was also detected.

first: Jideng

first: Yu

last: Fan


status: Public on Mar 26 2019

city: Santiago

first: Rodrigo

last: Pulgar

state: Metropolitana

address: El Líbano 5524, Macul

department: INTA

country: Chile

institute: University of Chile

summary: The transcriptional profile of intracellular P. salmonis was determined using a whole-genome microarray. Our microarray contained 5,309 different probes targeting 2,850. In our experimental design, the gene expression profile obtained from intracellular P. salmonis was compared with the transcriptome of control bacteria grown in culture medium. RNA from P. salmonis and SHK-1 cells were extracted simultaneously to avoid changes in transcriptomic profile after the bacterial purification process and eukaryotic RNA was depleted using the MicrobEnrich Kit.

overall_design: Two-condition experiment. For each condition studied, three independent biological replicates were analyzed for each condition (intracellular P. salmonis/P. salmonis grown in culture medium). Statistical analysis (adjusted p value<0.05) combined with a 2-fold variation cut-off indicated that 966 genes were differentially expressed at 12 days post-infection. Of these, 497 genes demonstrated increased expression while 469 genes were down-regulated.

first: Verónica

last: Cambiazo


title: The P-class pentatricopeptide repeat protein binds to the 5’ untranslated and translated regions of chloroplast psbI-ycf12 transcript and is involved in mRNA stability

city: Nagoya

first: Chieko

last: Sugita

state: Aichi

address: Chikusa-ku Furo-cho

department: Center for Gene Research

institute: Nagoya University

summary: Chloroplast gene expression is controlled by numerous nuclear-encoded RNA-binding proteins. Among them, pentatricopeptide repeat (PPR) proteins are known to be a key player in posttranscriptional regulation in chloroplasts. However, the functions of many PPR proteins remain unknown. In this study, we characterized the function of a chloroplast-localized P-class PPR protein PpPPR_21 in Physcomitrella patens. Knockout (KO) mutants of PpPPR_21 exhibited a reduced growth of the protonemata and lower photosynthetic activity. Immuno-blot analysis and blue-native gel analysis showed a remarkable reduction of the photosystem II (PSII) reaction center protein and poorly formation of the PSII super-complexes in the KO mutants. To access whether PpPPR_21 is involved in the chloroplast gene expression, chloroplast genome-wide microarray analysis and northern blot hybridization were performed. These analyses indicated that the psbI-ycf12 transcript encoding the low molecular weight subunits of PSII, did not accumulate in the KO mutants while other psb transcripts accumulated at similar levels of WT and the KO mutants. A complemented PpPPR_21 KO moss transformed with the cognate full-length PpPPR_21 cDNA rescued the psbI transcript accumulation level. RNA binding experiments showed that the recombinant PpPPR_21 bound efficiently to the 5’-untraslated and translated region of the psbI mRNA. The present study suggests that PpPPR_21 may be essential for accumulation of a stable psbI-ycf12 mRNA.

overall_design: To characterize the function of a chloroplast-localized P-class PPR protein PpPPR_21 in Physcomitrella patens, gene expression of organellar genome of 4 day old protonema cells of PpPPR_21 KO mutants and wild type  were measured.

first: Tetsuo

last: Ebihara

first: Takuya

last: Matsuda

first: Mizuho

last: Ichinose

first: Hiroshi

last: Yamamoto

first: Toshiharu

last: Shikanai

first: Mamoru


title: H3.3 K27M depletion increases differentiation and extends latency of diffuse intrinsic pontine glioma growth in vivo

status: Public on Mar 18 2019

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

summary: Xenografts from human pediatric brainstem gliomas bearing K27M in H3F3A were transduced with non silencing or H3F3A shRNA to assess the impact of the K27M on tumor growth, gene expression and epigenetics

overall_design: RNA-seq and ChIP-seq for H3K27me3 and H3K4me3 for knock-down or control tumors from three different human xenografts. Multiple tumors tested for each xenograft line.


title: Transcriptomic analysis of intervertebral discs isolated from wild type and Adgrg6-deficient mice

status: Public on Mar 17 2019

city: San Francisco

first: Nadav

last: Ahituv

state: CA

address: 1550 4th Street

institute: UCSF

summary:
Purpose: Degenerative changes of the intervertebral disc are a leading cause of back pain and disability worldwide. However, precise mechanisms driving the initiation and progression of pathology have remained elusive. We find that adhesion G-protein coupled receptor Adgrg6 plays a critical role in maintaining postnatal intervertebral disc homeostasis. The goal of this study is to uncover early molecular changes in Adgrg6-defeicnet intervertebral discs prior to overt histopathology.
Methods: Intervertebral disc mRNA profiles of 20-day-old wild type and Col2Cre; Adgrg6f/f mutant mice were generated by deep sequencing in triplicates. Cutadapt and perl scripts were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC. We used HISAT2 to map reads to the genome of Mus Musculus (GRCm38.88). The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from biological samples were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare. After the ﬁnal transcriptome was generated, StringTie and Ballgown was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM. The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package Ballgown.
Results: We found 884 differential expressed genes with statistical significance (p value < 0.05, and with a more stringent cut-off adjusted p value <0.05 and fold-change >2, we observed 42 differential expressed genes. Enriched pathways and biological processes using gene ontology (GO) terms included extracellular matrix, positive regulation of fibroblast proliferation, extracellular matrix structural constituent conferring tensile strength, regulation of tyrosine phosphorylation of STAT protein, and ion transport. We also find significantly increased expression of fibrotic collagens, induced expression of some Suppressor of Cytokine Signaling (SOCS) genes, and dysregulated expression of some components associated with ion transport system. Several of the significantly upregulated genes are associated with biomarkers or risk of lumbar disc degeneration and osteoarthritis in humans or animal models.
Conclusions: Our study provides detailed analysis of intervertebral disc transcriptomes from both wild type and Adgrg6-deficient mice, with three biological replicates, prior to overt histopathology. Our transcriptomic analysis demonstrated a robust dysregulation of several important pathways and components of the intervertebral disc homeostasis, including induction of fibrotic gene expression, alteration of ion transport component, as well as changes in some chondrogenic and catabolic factors, prior to the onset of histopathology and disc degeneration. These data strongly suggest that ADGRG6 signaling is a critical factor for the maintenance of healthy gene expression profiles in the IVD.

first: Zhaoyang

last: Liu

first: Jingjing

last: Zhao

first: Nadja

last: Makki

first: Ryan

last: Gray


title: Transcriptome profile of HCV-specific CD8 cells from acute, resolved and chronic patients

status: Public on Mar 01 2019

city: PARMA

first: Barbara

last: Montanini

state: PR

address: Parco Area delle Scienze 23/A

department: Life Sciences

institute: University of Parma

summary:
HCV-specific CD8 cells are deeply exhausted in chronic hepatitis C and their function can only be partially corrected by modulation of up-regulated inhibitory pathways, suggesting a more complex molecular interplay. With the aim of identifying more suitable molecular targets to correct T cell dysfunction, we compared the transcriptome profile of HCV-specific CD8 cells of acute and chronic patients with the reference profile of HCV- and Flu-specific CD8 cells from patients able to resolve HBV infection spontaneously and from healthy subjects. First, the gene-expression profile of HCV-specific CD8 T cells from patients with chronically-evolving acute infection, that correspond to early but not established T exhausted cells, is consistent with a substantial functional impairment at the energetic and metabolic levels that leads to the accumulation of reactive oxygen species that contributes to the activation of stress sensor signaling pathways. A specific inhibition of the hyperactivated signaling downstream effectors elicits a functional metabolic T cell reconstitution in the majority of the tested patients early during HCV infection. Second, a predominant feature of late exhausted HCV specific T cells is a global downregulation of gene expression that affects multiple core processes, ranging from proteasome-dependent protein turnover to DNA repair, transcription, metabolism and cell cycle, that is presumably a consequence of precocious and dysregulated activity of histone methyltransferases (e.g. G9a and EZH2 HMTs). Third, a functional inhibition of HMTs leads to a T cell function reconstitution both as anti-viral cytokine production and as proliferative capacity and to a metabolic restoration specifically for late exhausted CD8 T cells with a strongly preferential effect on HCV-specific T cells.
Virus-specific CD8+ T cells were isolated and sorted from early acute self-limited (5 patients), early chronic (8 patients), late resolved (4 patients), late chronic (7 patients) and from five healthy donors. RNA from sorted CD8+ T cells was processed, amplified, labeled, and hybridized to Agilent microarrays.

overall_design: Valeria,Barili

first: Paola

last: Fisicaro

first: Simone

last: Ottonello

first: Carlo

last: Ferrari


title: H3.3 K27M depletion increases differentiation and extends latency of diffuse intrinsic pontine glioma growth in vivo [RNA-Seq]

summary: xenografts from human pediatric brainstem gliomas bearing K27M in H3F3A were transduced with non silencing or H3F3A shRNA to assess the impact of the K27M on tumor growth, gene expression and epigenetics

first: Andre

last: Silveira

first: Lawryn

last: Kasper

first: Suzanne

last: Baker


title: H3.3 K27M depletion increases differentiation and extends latency of diffuse intrinsic pontine glioma growth in vivo [ChIP-Seq]


title: NCBP2 modulates neurodevelopmental defects of the 3q29 deletion in Drosophila and Xenopus laevis models

status: Public on Mar 12 2019

city: State College

first: Santhosh

last: Girirajan

state: PA

address: 205A Life Sciences Building

department: Biochemistry and Molecular Biology

institute: Pennsylvania State University

summary: The 1.6 Mbp deletion on chromosome 3q29 is associated with a range of neurodevelopmental disorders, including schizophrenia, autism, microcephaly, and intellectual disability. Despite its importance towards neurodevelopment, the role of individual genes, genetic interactions, and disrupted biological mechanisms underlying the deletion have not been thoroughly characterized. Here, we used quantitative methods to assay Drosophila melanogaster and Xenopus laevis models with tissue-specific individual and pairwise knockdown of 14 homologs of genes within the 3q29 region. We identified developmental, cellular, and neuronal phenotypes for multiple homologs of 3q29 genes, potentially due to altered apoptosis and cell cycle mechanisms during development. Using the fly eye, we screened for 314 pairwise knockdowns of homologs of 3q29 genes and identified 44 interactions between pairs of homologs and 34 interactions with other neurodevelopmental genes. Interestingly, NCBP2 homologs in Drosophila (Cbp20) and X. laevis (ncbp2) enhanced the phenotypes of homologs of the other 3q29 genes, leading to significant increases in apoptosis that disrupted cellular organization and brain morphology. These cellular and neuronal defects were rescued with overexpression of the apoptosis inhibitors Diap1 and xiap in both models, suggesting that apoptosis is one of several potential biological mechanisms disrupted by the deletion. NCBP2 was also highly connected to other 3q29 genes in a human brain-specific interaction network, providing support for the relevance of our results towards the human deletion. Overall, our study suggests that NCBP2-mediated genetic interactions within the 3q29 region disrupt apoptosis and cell cycle mechanisms during development.

overall_design: mRNA-sequencing of Drosophila neuron-specific RNAi knockdown (whole head) for four individual 3q29 homologs (DLG1, NCBP2, FBXO45, and PAK2), two pairwise knockdowns of 3q29 homologs (NCBP2/DLG1 and NCBP2/FBXO45), and two VDRC wild-type controls (GD and KK backgrounds). Sequencing was performed using Illumina HiSeq 2000 on three biological replicates per sample, with two-three technical replicates per biological replicate.

first: Mayanglambam

last: Singh

first: Matthew

last: Jensen


title: Gene expression in B16.SIY tumor cells deficient in IFN-g signaling

first: Jason

middle: B

last: Williams

state: Illinois

address: 929 E. 57th St GCIS W423H

department: Pathology

summary: We performed RNASeq on purified tumor cells from wild-type, IFNgR2-, and Jak1-mutant tumors on day 7 after tumor engraftment. To investigate whether IFN-g-insensitive tumor cells showed decreased expression of a negative immune regulatory factor, RNASeq was performed on purified tumor cells from WT, IFNgR2-, and Jak1-mutant tumors on day 7 after tumor engraftment.  Compared to wild-type, we found 375 and 305 differentially expressed genes in IFNgR2- and Jak1-mutant tumor cells respectively. 228 of these genes were shared between IFNgR2- and Jak1-mutant tumor cells. Overlapping downregulated genes included those involved in antigen presentation, immune functions, extracellular matrix, ubiquitination, and GTPase activity.RNA sequencing and alignment to gene features were performed by the University of Chicago Genomics Core facility using the Illumina HiSeq platform. Raw read counts were processed by TMM normalization followed by log2 transformation. Genes expressed in fewer than three samples were removed from further analysis. Limma voom was used to identify differentially expressed genes between each mutant cohort and the wild-type cohort with a cutoff fold change > 2 and adjusted p-value < 0.05.

overall_design: Wild-type, IFNgR2-, and Jak1-mutant tumor cells were inoculated into C57BL/6 mice and tumors were extracted 7 days later. Tumors were enzymatically digested for 30 min at 37oC with rotation. Tumor suspension was Ficolled and buffer layer was washed twice with PBS. Cells were stained with CD45, CD3, Thy1, CD19 antibodies and a live-dead permeability dye to gate out hematopoietic cells and dead cells. Tumor cells were cell sorted based on dsRed and BFP expression into RLT buffer and quickly frozen.  RNA was extracted using the RNEasy micro kit (QIAGEN) and submitted for single-end RNA sequencing.

first: Thomas

middle: F

last: Gajewski


title: Separation of breast cancer and organ microenvironment transcriptomes in metastases

city: Richmond

first: Wright Center for Clinical and Translational Research

last: Bioinformatics Core

state: VA

address: 203 E Cary St

institute: Virginia Commonwealth University

summary: The seed-and-soil hypothesis was described over a century ago to describe why cancer cells (seeds) grow in certain organs (soil). Since then, the genetic properties that define the cancer cells have been heavily investigated, however, the genetic mediators within the organ microenvironment that mediate successful metastatic growth are less understood. In these studies, a set of human breast cancer patient-derived xenograft (PDX) metastasis models were utilized. Mammary tumors and metastases to the liver, lung, and brain were RNA-sequenced with the goal of identifying complementary cancer and organ-specific genetic properties that mediate metastatic growth. During metastatic growth of PDXs, the genetic changes that occurred in the liver and lung microenvironment were more consistent and higher in magnitude than the cancer cell transcriptomes . Integration of the liver microenvironment gene signature into genetic data from liver metastasis autopsy samples or fine-needle aspirates revealed the contribution of the microenvironment to the metastatic transcriptome. These insights identify cancer and organ-specific genetic drivers  of metastasis.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

first: Mohammad

last: Alzubi

first: Tia

last: Turner

first: Amy

last: Olex

first: Sahib

last: Sohal

first: Nick

middle: P

last: Tobin

first: Jonas

last: Bergh

last: Hatschek

first: Joel

last: Parker

first: Carol

last: Sartorius

first: Charles

last: Perou

first: Mikhail

last: Dozmorov

first: J

last: Harrell


title: Identification of Zeb1 as a single marker for prostate stem cells in the basal cell compartment

city: Shanghai

first: Xue

last: Wang

state: Shanghai China

address: Huashan Rd. 1940, build 3.  Shanghai,

institute: SJTU CHINA

summary: The prostate basal cell compartment is postulated to contain stem/progenitors due to its resistance to castration, capability to differentiation into basal, luminal and neuroendocrine cell lineages of prostate epithelium, and susceptibility to oncogenic transformation. However, the heterogeneity and the interrelationship among different cell subpopulations within prostate basal cells remain largely unknow. Here we find that the core epithelial-to-mesenchymal transition (EMT) inducer Zeb is exclusively expressed in a prostate basal cell subpopulation. The Zeb1+ basal cells are resistant against androgen deprivation, possess greater efficiency to produce prostate spheroids in vitro, undergo self-renewal, and can generate functional prostate with all three cell lineages in vivo at the single cell level. Utilizing unbiased single cell transcriptomic analysis of over 9000 mouse prostate basal cells, we find that Zeb1+ basal cell subset shares gene expression profile with both epithelial and mesenchymal cells and stands out uniquely among all the cell clusters. Pseudotemporal reconstruction revealed three cell lineage trajectories through which the Zeb1+ basal cell subset gives rise to differentiated basal cells, and androgen dependent or independent intermediate cells. at the starting point in the developmental trajectories of cell clusters in prostate basal epithelium. In addition, Zeb1 positive basal cells can be detected in human prostate samples. Our data demonstrate that these Zeb1+ cells are bona fide PSCs in the basal cell compartment. Identification of the prostate stem cell (PSC) and its differentiation path is crucial to advance our understanding of prostate development and tumorigenesis.

overall_design: Exploration of transcriptional differences and interations among different subpopulations within prostate basal cells

first: Helen

last: Zhu


title: Nuclear GFP ChIP-seq from bone marrow-derived dendritic cells of GFP-cGAS knock-In mice

status: Public on Feb 27 2019

city: Paris

first: Nicolas

last: Manel

address: 12 rue Lhomond

department: INSERM U932

country: France

institute: Institut Curie

summary: Cytosolic DNA activates cyclic GMP-AMP (cGAMP) synthase (cGAS), an innate immune sensor pivotal in anti-microbial defense, senescence, auto-immunity and cancer. cGAS is considered a sequence-independent DNA sensor with limited access to nuclear DNA because of compartmentalization. However, the nuclear envelope is a dynamic barrier and cGAS is present in the nucleus. Here, we identify determinants of nuclear cGAS localization and activation. We show that nuclear-localized cGAS synthesizes cGAMP and induces innate immune activation of dendritic cells, but cGAMP levels are 200-fold lower than following transfection with exogenous DNA. Using cGAS ChIP-seq and a GFP-cGAS knock-in mouse, we find nuclear cGAS enrichment on centromeric satellite DNA, confirmed by imaging, and to a lesser extent with LINE elements. The non-enzymatic N-terminal domain of cGAS determines nucleo-cytoplasmic localization, enrichment on centromeres and activation of nuclear-localized cGAS. These results reveal a preferential functional association of nuclear cGAS with centromeres.

overall_design: Sample 1 is one mouse and sample 2 is a pool of two mice

first: Matteo

last: Gentili

first: Xavier

last: Lahaye

first: Francesca

last: Nadalin

first: Guilherme

last: Nader

first: Emilia

last: Puig Lombardi

first: Solene

last: Herve

first: Nilushi

last: De Silva

first: Derek

last: Rookhuizen

first: Elina

last: Zueva

first: Christel

last: Goudot

first: Mathieu

last: Maurin

first: Aurore

last: Bochnakian

first: Sebastian

last: Amigorena

first: Matthieu

last: Piel

first: Daniele

last: Fachinetti

first: Arturo

last: Londono-Vallejo


title: The N-terminal domain of cGAS determines preferential association with centromeric DNA and innate immune activation in the nucleus

first: Nicolas

last: Manel


title: Chromatin mapping and single-cell immune profiling defines the temporal dynamics of ibrutinib drug response in chronic lymphocytic leukemia

status: Public on Feb 22 2019

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary:
Chronic lymphocytic leukemia (CLL) is a genetically, epigenetically, and clinically heterogeneous disease. Despite this heterogeneity, the Bruton tyrosine kinase (BTK) inhibitor ibrutinib provides effective treatment for the vast majority of CLL patients. To define the underlining regulatory program, we analyzed high-resolution time courses of ibrutinib treatment in closely monitored patients, combining cellular phenotyping (flow cytometry), single-cell transcriptome profiling (scRNA-seq), and chromatin mapping (ATAC-seq). We identified a consistent regulatory program shared across all patients, which was further validated by an independent CLL cohort. In CLL cells, this program starts with a sharp decrease of NF-κB binding, followed by reduced regulatory activity of lineage-defining transcription factors (including PAX5 and IRF4) and erosion of CLL cell identity, finally leading to the acquisition of a quiescence-like gene signature which was shared across several immune cell types.  Nevertheless, we observed patient-to-patient variation in the speed of its execution, which we exploited to predict patient-specific dynamics in the response to ibrutinib based on pre-treatment samples. In aggregate, our study describes the cellular, molecular, and regulatory effects of therapeutic B cell receptor inhibition in CLL at high temporal resolution, and it establishes a broadly applicable method for epigenome/transcriptome-based treatment monitoring.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
176 ATAC-seq samples of primary immune cell types from chronic lymphocytic leukemia patients and normal donors
12 scRNA-seq samples of peripheral blood mononuclear cells from chronic lymphocytic leukemia patients

Refer to individual Series for more details.


title: Nuclear GFP ChIP-seq from human Monocyte Derived Dendritic Cells transduced with GFP-NLS-cGAS or GFP-NLS

overall_design: Three independent donors were analyzed. Donor 1 was transduced only with GFP-NLS-cGAS. Donor 2 and 3 were transduced with GFP-NLS-cGAS and GFP-NLS.

first: Matteo

last: Gentili

first: Xavier

last: Lahaye


title: Chromatin mapping and single-cell immune profiling defines the temporal dynamics of ibrutinib drug response in chronic lymphocytic leukemia [ATAC-seq]

summary: Chronic lymphocytic leukemia (CLL) is a genetically, epigenetically, and clinically heterogeneous disease. Despite this heterogeneity, the Bruton tyrosine kinase (BTK) inhibitor ibrutinib provides effective treatment for the vast majority of CLL patients. To define the underlining regulatory program, we analyzed high-resolution time courses of ibrutinib treatment in closely monitored patients, combining cellular phenotyping (flow cytometry), single-cell transcriptome profiling (scRNA-seq), and chromatin mapping (ATAC-seq). We identified a consistent regulatory program shared across all patients, which was further validated by an independent CLL cohort. In CLL cells, this program starts with a sharp decrease of NF-κB binding, followed by reduced regulatory activity of lineage-defining transcription factors (including PAX5 and IRF4) and erosion of CLL cell identity, finally leading to the acquisition of a quiescence-like gene signature which was shared across several immune cell types.  Nevertheless, we observed patient-to-patient variation in the speed of its execution, which we exploited to predict patient-specific dynamics in the response to ibrutinib based on pre-treatment samples. In aggregate, our study describes the cellular, molecular, and regulatory effects of therapeutic B cell receptor inhibition in CLL at high temporal resolution, and it establishes a broadly applicable method for epigenome/transcriptome-based treatment monitoring.

overall_design: 176 ATAC-seq samples of primary immune cell types from chronic lymphocytic leukemia patients and normal donors

first: André

last: Rendeiro

first: Thomas

last: Krausgruber

first: Nikolaus

last: Fortelny

first: Fangwen

last: Zhao

last: Penz

first: Matthias

last: Farlik

first: Linda

last: Schuster

first: Amelie

last: Kuchler

first: Szabolcs

last: Tasnády

first: Marienn

last: Réti

first: Mátrai

last: Zoltán

first: Donat

last: Alpar

first: Csaba

last: Bödör

first: Christian

last: Schmidl


title: Chromatin mapping and single-cell immune profiling defines the temporal dynamics of ibrutinib drug response in chronic lymphocytic leukemia [scRNA-seq]

last: Bock

overall_design: 12 scRNA-seq samples of peripheral blood mononuclear cells from chronic lymphocytic leukemia patients


title: The dynamic m(6)A methylation landscape of human tissues

status: Public on Feb 19 2019

city: Guangzhou

first: Shan

last: Xiao

address: Southern Shatai Road

department: Developmental Biology

institute: Southern Medical University

summary: The diversity of tissues arises from complex processes, linking to human development and disease. One such process is N(6)-methyladenosine (m(6)A), which is widespread and has been implicated in many critical biological processes. However, the dynamic distribution, function, and regulation of m(6)A across diverse human tissues remain largely unresolved. Here we report 21 whole-transcriptome m(6)A methylomes across eight major fetal tissues using m(6)A-sequencing. Our data reveal a large fraction of novel m(6)As related to tissue-specific processes as well as a large number of novel long intergenic non-coding RNA (lincRNA) m(6)As, which display a unique consensus motif and distribution pattern distinct from sites on mRNA.

overall_design: Examination of m(6)A modifications in eight fetal tissues.

first: Weishi

last: Wang

first: Laixin

last: Xia

first: Qitao

last: Huang

first: Mei

last: Zhong


title: Epigenomic signatures in liver and blood of Wilson disease patients include hypermethylation of liver-specific enhancers

status: Public on Feb 14 2019

city: Davis

first: Charles

middle: E

last: Mordaunt

address: 3318 Tupper Hall, One Shields Ave

department: Medical Microbiology and Immunology

institute: University of California, Davis

type: Methylation profiling by high throughput sequencing

summary: Wilson disease (WD) is an autosomal recessive disease caused by mutations in ATP7B encoding a copper transporter. Consequent copper accumulation results in a variable WD clinical phenotype involving hepatic, neurologic, and psychiatric symptoms, without clear genotype-phenotype correlations. The goal of this study was to analyze alterations in DNA methylation at the whole-genome level in liver and blood from patients with WD to investigate epigenomic alterations associated with WD diagnosis and phenotype. We used whole-genome bisulfite sequencing (WGBS) to examine distinct cohorts of WD subjects to determine whether DNA methylation could differentiate patients from healthy subjects and subjects with other liver diseases and distinguish between different WD phenotypes. WGBS analyses in liver identified 969 hypermethylated and 871 hypomethylated differentially methylated regions (DMRs) specifically identifying patients with WD, including 18 regions with genome-wide significance. WD-specific liver DMRs were associated with genes enriched for functions in folate and lipid metabolism and acute inflammatory response and could differentiate early from advanced fibrosis in WD patients. Functional annotation revealed that WD-hypermethylated liver DMRs were enriched in liver-specific enhancers, flanking active liver promoters, and binding sites of liver developmental transcription factors, including Hepatocyte Nuclear Factor 4 alpha (HNF4A), Retinoid X Receptor alpha (RXRA), Forkhead Box A1 (FOXA1), and FOXA2. DMRs associated with WD progression were also identified, including 15 with genome-wide significance. However, WD DMRs in liver were not related to large-scale changes in proportions of liver cell types. DMRs detected in blood differentiated WD patients from healthy and disease control subjects, and distinguished between patients with hepatic and neurologic WD manifestations. WD phenotype DMRs corresponded to genes enriched for functions in mental deterioration, abnormal B cell physiology, and as members of the polycomb repressive complex 1 (PRC1). 44 DMRs associated with WD phenotype tested in a small validation cohort had a predictive value of 0.9. We identified a disease-mechanism relevant epigenomic signature of WD that reveals new insights into potential biomarkers and treatments for this complex monogenic disease.

overall_design: Investigation of DNA methylation with whole-genome bisulfite sequencing (WGBS) in liver and blood samples from Wilson disease (WD), Non-alcoholic fatty liver disease (NAFLD), primary sclerosing cholangitis (PSC), and healthy control (HC) subjects. Liver biopsies: 10 WD, 5 NAFLD, 6 HC subjects. Whole blood: 40 WD, 10 NAFLD, 10 PSC, 12 HC subjects.

first: Janine

last: LaSalle

first: Valentina

last: Medici


title: Genome-wide maps of chromatin state and gene expression in control and TPA-stimulated pre-B leukemic 697 line

status: Public on Feb 06 2019

city: Taipei

first: Wei-Yi

last: Chen

address: No. 155, Sec 2, Linong St.

department: Institute of Biochemistry and Molecular Biology

country: Taiwan

institute: National Yang Ming Chiao Tung University

summary: Linker histone H1 has been correlated with transcriptional inhibition, but the mechanistic basis of the inhibition and its reversal during gene activation has remained enigmatic. We report that H1-compacted chromatin, reconstituted in vitro, blocks transcription by abrogating core histone modifications by p300 but not activator and p300 binding. Transcription from H1-bound chromatin is elicited by H1 chaperone NAP1, which is recruited in a gene-specific manner through direct interactions with activator-bound p300 that facilitate core histone acetylation (by p300) and concomitant eviction of H1 and H2A/H2B. An analysis in B cells confirms the strong dependency on NAP1-mediated H1 eviction for induction of the silent CD40 gene and further demonstrates that H1 eviction, seeded by activator-p300-NAP1 interactions, is propagated over a CTCF-demarcated region through a distinct mechanism that also involves NAP1. Our results confirm direct transcriptional inhibition by H1 and establish a gene-specific H1 eviction mechanism through an activator-p300-NAP1-H1 pathway.

overall_design: Genome-wide binding/occupancy profiling of Histone H1 and CTCF by ChIP-seq and gene expression profiling by RNA-seq in 697 cells treated without or with TPA (12-O-tetradecanoylphorbol-13-acetate)

first: Miho

last: Shimada

first: Robert

last: Roeder


title: DNA:cytoplasm ratio defines an upper limit to cell size

status: Public on Feb 07 2019

city: Cambridge

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

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

sample_organism:
Saccharomyces cerevisiae
Candida albicans
Saccharomyces cerevisiae W303

overall_design: Refer to individual Series


title: Selective Inhibition of the Second Bromodomain of BET Family Maintains Anti-Tumor Efficacy and Improves Tolerability (LNCaP RNA-seq)

status: Public on Feb 04 2019

city: North Chicago

first: Xin

last: Lu

address: 1 North Waukegan Rd

institute: Abbvie

summary: Here we report the discovery of ABBV-744, a first in class, highly potent and selective inhibitor of BET family BD2 domains with drug like properties.  RNA-seq analysis revealed that ABBV-744 elicited potent inhibition of AR-dependent transcription without causing broad transcription alterations associated with exposure to pan BET inhibitors.

overall_design: mRNA profiles of LNCaP cells treated with ABBV-075, ABBV-744, or Enzalutmide in the presence or absence of DHT were generated by deep sequencing, in duplicate, using Illumina HiSeq3000.

first: Emily

last: Faivre

first: Paul

last: Hessler


title: Transcriptome analysis of tubulointerstitial tissues of patients with focal segmental glomerulosclerosis

status: Public on Jan 29 2019

city: Nanjing

first: Hao

last: Bao

state: Jiangsu

address: 305 East Zhong Shan Road

department: National Clinical Research Center of Kidney Diseases, Jinling Hospital

institute: Nanjing university

summary:
Transcriptome comparison of tubulointerstitial tissues from kidneys with focal segmental glomerulosclerosis (FSGS) and tubulointerstitial tissues from the unaffected portion of surgical nephrectomies.
High-density Affymetrix Human Transcriptome Arrays (HTA) 2.0 were used for the gene expression analysis.

overall_design: Focal segmental glomerulosclerosis (FSGS) is a common podocytopathy. Renal tubulointerstitial tissues from focal segmental glomerulosclerosis patients and controls were manually isolated under a stereomicroscope using 2 dissection needle holders in RNAlater at 4°C.Affymetrix HTA 2.0 microarray was used to perform a global analysis of the gene expression pattern in the tissues.

first: Zhihong

last: Liu


title: RNA-sequencing of NALT from mouse after intranasal immunization with B. abortus rMDH loaded chitosan nanoparticles (CNs)

city: Seoul

first: Soojin

last: Shim

address: Kwan-ak ro

country: South Korea

institute: Seoul National University

summary: Brucellosis is a serious zoonotic disease caused by the genus Brucella, a group of Gram-negative and facultative intracellular bacteria. At present, although live attenuated vaccine such as Rev.1, S19 and RB51 have been widely used for bovine brucellosis, these vaccines have some drawbacks, and safe and effective alternatives have been demanded. Previously, our group showed that several Brucella proteins malate dehydrogenase (rMDH) are effective in eliciting IgG responses in murine model following intraperitoneal injection. The Brucella infections are usually transmitted through mucosal membrane via oral or aerosol exposure. Therefore, induction of mucosal immunity is promising contribute in development of vaccine. In the study, rMDH was loaded with chitosan nanoparticles (CNs) which is mucoadhesive, biocompatible, nontoxic, and immune-enhancing adjuvant to induce both systemic and mucosal immunity. Then, in order to evaluate immunogenicity of the antigen in BALB/C mouse, total RNA from nasal-associated lymphoid tissues at 1 h, 6 h, 12 h after intranasal immunization was analyzed using RNA-seq.

overall_design:
mRNA profiles of NALT from mice at 1 hour, 6 hours, and 12 hours after immunization with CNs - rMDH.
PBS *h = NALT from mice at *hours after immunization with PBS as control 1
CNs *h = NALT from mice at *hours after immunization with chitosan nanoparticles (CNs) only as control 2
TF *h = NALT from mice at *hours after immunization with rTrigger Factor (recombinant protein vector) loaded CNs as control 3
MDH *h =NALT from mice at *hours after immunization with rMDH loaded CNs as test group.

first: HanSang

last: Yoo


title: Differential expression of mRNAs in IFN-gamma treated HTR-8/SVneo versus untreated control by next generation sequencing

city: New Delhi

first: Satish

middle: Kumar

last: Gupta

address: Aruna Asaf Ali Marg

country: India

institute: NAtional Institute of Immunology

summary: The goal of this study is to compare genes expressed by IFN-gamma treated HTR-8/SVneo cells to genes expressed in untreated control HTR-8/SVneo cells to identify genes which play a role during IFN-gamma-mediated HTR-8/SVneo cells invasion

overall_design: cDNA libraries were made from total RNA of untreated control and 24 h IFN-gamma treated samples by TruSeq RNA Library Prep Kit v2. Deep sequencing of cDNA libraries were performed with the help of Illumina Genome Analyzer IIx. Raw sequence data was imported into the CLC Genomics Workbench 6.5.1. software. The sequence reads were trimmed for adapter sequences and low quality base. The trimmed raw sequences were subjected to mRNA-sequence analysis, by mapping them to Human Genome GRCH37.p.13  .

first: Sonam

last: Verma


title: IL-27 and TCR stimulation promote T cell expression of multiple inhibitory receptors

status: Public on Jan 17 2019

first: Devan

last: Moodley

address: 50 Hampshire St, 8th floor

institute: Surface Oncology

summary: Inhibitory receptors (IR) are a diverse group of cell surface molecules that modulate T cell activation, but there are gaps in our knowledge of the cell extrinsic factors that regulate their expression. The present study found that in vivo overexpression of IL-27 led to increased T cell expression of PD-L1, LAG-3, TIGIT, and TIM-3. In vitro, TCR stimulation alone promoted expression of multiple IRs, while IL-27 alone induced expression of PD-L1. However, the combination of intermediate TCR stimulation and IL-27 resulted in synergistic induction of LAG-3, CTLA-4, and TIGIT. In vivo, infection with Toxoplasma gondii resulted in parasitespecific effector T cells that expressed high levels of IR and at local sites of infection where IL-27 production was highest, IL-27 was required for maximal effector cell expression of PD-L1, LAG-3, CTLA-4 and TIGIT. Together, these results affirm the critical role of TCR signals in the induction of IR expression, but find that during infection, IL-27 provides a signal that promotes T cell expression of inhibitory receptors.

overall_design: Six-week-old female Balb/c mice were injected with 20 μg of either empty vector or linked human IL-27 minicircle DNA (System Biosciences, Palo Alto, CA) in 2 ml 0.9% normal saline via the tail vein over the course of 5 seconds (3 replicates each). Spleens were collected from mice five days after minicircle injection. Total RNA was extracted from splenocytes after mechanical dissociation and ACK lysis, with the RNeasy® Mini Kit (Qiagen, Cat. No: 74104). Gene expression profiling on was performed on Affymetrix GeneChip™ Mouse Gene 2.0 ST Arrays (Applied Biosystems, Cat. No: 902118).

first: Jonathan

last: DeLong

first: Aisling

last: O’Hara Hall

first: Matt

last: Rausch

first: Devapregasan

first: Joseph

last: Perry

first: Jeongho

last: Park

first: Anthony

middle: T

last: Phan

first: Daniel

last: Beiting

first: Merle

last: Elloso

first: Ross

last: Kedl

last: Hill

first: Christopher

last: Hunter


title: Transcriptome analysis of regeneration in Xenopus laevis twin embryos

status: Public on Feb 01 2019

city: Los Angeles

first: Edward

last: De Robertis

address: 615 Charles E. Young Drive South

department: Biological chemistry

institute: HHMI/UCLA

summary: Animal embryos have the remarkable property of self-organization. Over 125 years ago Hans Driesch separated the two blastomeres of sea urchin embryos and obtained twins, in what was the foundational experiment of experimental embryology. Since then, embryonic twinning has been obtained experimentally in many animals by diverse methods. In a recent study, we developed bisection methods that generate identical twins reliably from Xenopus blastula embryos. In the present study we investigated the transcriptome of regenerating half-embryos after sagittal and dorsal-ventral (D-V) bisections. Individual embryos were operated at midblastula with an eyelash hair and cultured until early gastrula (stage 10.5) or late gastrula (Stage 12) and analyzed the transcriptome of each half-embryo by RNAseq. Because many genes are activated by wound healing, stringent analyses were used to identify genes upregulated in identical twins but not in either dorsal or ventral fragments. At early gastrula cell division-related genes such as histones were identified, whereas at late gastrula pluripotency genes (such as sox2) and germ layer determining genes (such as eomesodermin, ripply2 and activing receptor ACVRI) and a number of secretory pathway components (serpinH1, fucoleptin and sialyl transferase). These findings are consistent with a model in which cell division is required to heal damage, while maintaining pluripotency to permit formation of the organizer with a displacement of 900 from its original site. In addition, the extensive transcriptomic data presented here (30 RNA-seq libraries of individual whole or regenerating half-embryos) provides a useful resource for data mining gene expression during early vertebrate development.

overall_design: A genome-wide study of genes that regulate regeneration of twin embryos in Xenopus laevis

first: Yuki

last: Moriyama

first: Eric

last: Sosa

first: Yi

last: Ding


title: Mitochondrial Membrane Potential Regulates Nuclear Gene Expression in Macrophages Exposed to PGE2 (RNA-seq)

status: Public on Jan 16 2019

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

summary: Metabolic engagement is intrinsic to immune cell function. Prostaglandin E2 (PGE2) has been shown to modulate macrophage activation, yet how PGE2 might affect metabolism is unclear. Here we show that PGE2 causes mitochondrial membrane potential (Δψm) to dissipate in interleukin-4 activated macrophages (M(IL-4)). Effects on Δψm are a consequence of PGE2-initiated transcriptional regulation of genes in the malate-aspartate shuttle (MAS), particularly GOT1. Reduced Δψm causes alterations in the expression of 126 voltage regulated genes (VRGs) including Resistin like molecule-α (RELMα), a key marker of M(IL-4), and genes that regulate cell cycle. The transcription factor ETS variant 1 (ETV1) plays a role in the regulation of 38% of the VRGs. These results reveal ETV1 as a Δψm-sensitive transcription factor, and Δψm as a mediator of mitochondrial-directed nuclear gene expression.

overall_design: RNA-seq was performed on bone marrow derived macrophages (triplicate) exposed to IL-4 alone or in combination with PGE2 or Valinomycin plus no stimulation controls. In addition, RNA-seq was performed on bone marrow derived macrophages stimulated in the same way as before, however the transcription factor ETV1 was knocked down.

first: David

last: Sanin

first: Mai

last: Matsushita

first: Ramon

middle: I

last: Klein Geltink

first: Katarzyna

last: Grzes

first: Nikki

last: van Teijlingen Bakker

first: Mauro

last: Corrado

first: Agnieszka

last: Kabat

first: Michael

middle: D

last: Buck

first: Jing

last: Qiu

first: Simon

middle: J

last: Lawless

first: Alanna

last: Cameron

first: Matteo

last: Villa

first: Francesc

last: Baixauli

first: Annette

last: Patterson

first: Fabian

last: Hässler

last: Curtis

first: Christina

last: O’Neill

last: O’Sullivan

first: Duojiao

last: Wu

first: Gerhard

last: Mittler

first: Stanley

last: Huang

first: Erika

middle: L

last: Pearce


title: Mitochondrial Membrane Potential Regulates Nuclear Gene Expression in Macrophages Exposed to PGE2

first: Immunometabolism

last: Department


title: Expression changes in the prefrontal cortex after neurotransmission blocking of nucleus accumbens pathways

status: Public on Jan 03 2019

city: Fujisawa-city

first: Shuhei

last: Yao

state: Kanagawa

institute: Takeda pharmaceutical company LTD.

summary: GSEA using both edgeR and voom statistics revealed that the ES of two types of corticothalamic neurons, CTX.Glt25d2-positive layer 5b and CTX.Ntsr1-positive layer 6 neurons, were downregulated by both NAc D1- and D2-RNB. In contrast, the ES of CTX.S100a10 corticostriatal neurons were upregulated and downregulated by NAc D1- and D2-RNB, respectively. These data show that cortical neurons are asymmetrically regulated by subcortical pathways in the mPFC-NAc-VP/SNr-MD/VD-mPFC circuit.

overall_design: mPFC mRNA profiles of the NAc D1- or D2-RNB mice

first: Takatoshi

last: Hikida

first: Tom

last: Macpherson

first: Makiko

last: Morita

first: Ayumi

last: Fukakusa

first: Haruhide

last: Kimura

first: Keisuke

last: Hirai

first: Tatsuya

last: Ando

first: Hiroyoshi

last: Toyoshiba

first: Akira

last: Sawa


title: Expression data of colon adenocarcinoma and normal colon

status: Public on Dec 31 2018

city: Singapore

first: bin

last: zhang

address: 14 Medical Drive, #12-01

department: Cancer Science Institute of Singapore

country: Singapore

institute: National University of Singapore

summary: To identiy the differentially expressed gene between in colon adenocarcinoma and normal colon, we performed microarray to quantify the gene expressions.

overall_design: RNA was extracted from 10 normal colon and 10 colon adenorcarcinoma samples and then hybrided to microarray.

first: Zhi

last: Kwok


title: RRBS investigation of matched side-population trophoblast, cytotrophoblast and extravillous trophoblast populations from 4 human placentae

status: Public on Dec 25 2018

city: Auckland

first: Teena

last: Gamage

state: Scotland

country: New Zealand

institute: Grafton

summary: To better understand how DNA methylation influences placentation, DNA from  first trimester primary trophoblast populations (side-population trophoblasts, cytotrophoblasts and extravillous trophoblasts) isolated using FACS underwent reduced representation bisulfite sequencing and were compared to publicly available data of blastocyst-derived and somatic cell populations.

overall_design: Comparisons were made between three matched trophoblast populations (side-population trophoblasts, cytotrophoblasts, extravillous trophoblasts)  from four first trimester human placentae isolated using FACS. DNA from each of the three trophoblast populationswas extracted using a Qiagen DNA Mini Kit (Qiagen, Germany). DNA quantity was assessed using a Qubit® dsDNA HS Kit (Molecular Probes, USA) or Qubit® dsDNA BR Kit (Molecular Probes, USA). RRBS was undertaken on 500ng of DNA per sample as previously described (Chatterjee et al., 2012a) using the MspI  restriction enzyme in the RRBS library preparation  with one size selection step (150-325bp). Libraries were amplified with 15–18 cycles. RRBS libraries underwent single-ended (100bp) sequencing using an Illumina HiSeq2000 (Chatterjee et al., 2012b). The reads were aligned to human GRCh37 reference genome assembly using  Bismark aligner (Krueger and Andrews, 2011). The resulting bam files were sorted and Bismark methylation extractor (Krueger and Andrews, 2011) was used to determine DNA methylation status and to yield CpG report files. Publicly avaliable data of blastocyst-derived and somatic cell populations were obtained from SRA for comparison.   Analysis of these report files was performed using R package “methylKit” (Akalin et al., 2012).

first: William

last: Schierding

first: Peter

last: Tsai

first: Jackie

last: Ludgate

first: Lawrence

middle: W

last: Chamley

first: Robert

last: Weeks

first: Erin

middle: C

last: Macaulay

first: Joanna

last: James


title: Physically Isolated OptiPrep (TM) Fractions for exRNA Analysis

status: Public on Dec 15 2018

city: San Diego

first: Louise

last: Laurent

address: 9500 Gilman Drive

country: USA

institute: UC San Diego

summary: An integrative analysis of human biofluid data in the exRNA Atlas revealed the existence of distinct extracellular RNA cargo types. In order to detect differences in density between cargo types, cushioned density gradient ultracentrifugation (C-DGUC) of serum and plasma was performed using OptiPrem (TM) density gradient.

overall_design:
250 ml whole blood was collected from five adult female and five adult male consenting donors supervised by Dr. Louise C. Laurent at the University of California, San Diego, Department of Obstetrics, Gynecology, and Reproductive Sciences and Sanford Consortium for Regenerative Medicine. These samples were utilized to generate the serum and plasma OptiPrep (TM) fractions (1-3, 4-7, 9-12) and whole biofluid. Plasma and serum were fractionated using cushioned density gradient ultracentrifugation (C-DGUC) via OptiPrep (TM) density gradient. RNA was then isolated and sequenced, and western blot and mass spectrometry analyses were performed. 78 of 80 samples were used in the exRNA data analysis (2 samples were not used due to low read count)
RNA-Seq raw data is to be made available through dbGaP (controlled access) due to patient privacy concerns.

first: Srimeenakshi

last: Srinivasan

first: Isidore

last: Rigoutsos


title: Mitochondrial Membrane Potential Regulates Nuclear Gene Expression in Macrophages Exposed to PGE2 (ATAC-seq)

first: Immunometabolism

last: Department

overall_design: ATAC-seq was performed on bone marrow derived macrophages (triplicate) exposed to IL-4 alone or in combination with PGE2 or Valinomycin plus no stimulation controls.

first: David

last: Sanin

first: Mai

last: Matsushita

first: Ramon

last: Geltink

first: Katarzyna

last: Grzes

first: Nikki

middle: v

last: Bakker

first: Mauro

last: Corrado

first: Agnieszka

last: Kabat

first: Michael

last: Buck

first: Jing

last: Qiu

first: Simon

last: Lawless

first: Alanna

last: Cameron

first: Matteo

last: Villa

first: Francesc

last: Baixauli

first: Annette

last: Patterson

first: Fabian

last: Hässler

first: Jonathan

last: Curtis

first: Christina

last: O’Neill

last: O’Sullivan

first: Duojiao

last: Wu

first: Gerhard

last: Mittler

first: Stanley

last: Huang

first: Erika

last: Pearce

first: Edward


title: Assessment of RNA Isolation Kit Biases Toward Preferential Detection of exRNA Cargo Types

first: Louise

last: Laurent

summary: An integrative analysis of human biofluid data in the exRNA Atlas revealed the existence of distinct extracellular RNA cargo types. To determine whether different RNA isolation kits biased detection of certain exRNA cargo types, an integrative analysis was performed using pooled plasma and serum samples, where 10 different RNA isolation kits were applied.

overall_design:
Data from a total of 108 plasma and 74 serum samples (taken from pooled healthy controls) were analyzed for the study. 10 different RNA isolation kits were used throughout the study. Donors of analyzed samples varied in sex - 95 female, 87 male. RNA isolation experiments were done in triplicate for each lab.
RNA-Seq raw data is to be made available through dbGaP (controlled access) due to patient privacy concerns.

first: Srimeenakshi

last: Srinivasan

first: Clara

first: Kirsty

last: Danielson

first: Justyna

last: Filant

first: Courtney

last: Moeller

first: Parham

last: Nejad

first: Anu

last: Paul

first: Ravi

last: Shah

first: Bridget

last: Simonson

first: Xuan

last: Zhang

first: Leonora

last: Balaj

first: Saumya

last: Das

first: Roopali

last: Gandhi

first: Tushar

last: Patel

first: Anil

middle: K

last: Sood

first: Isidore

last: Rigoutsos


title: Transcriptional responses of Candida glabrata biofilm cells to fluconazole

status: Public on Jan 01 2019

city: Braga

first: Rosana

last: Alves

address: Campus de Gualtar

department: Biology

country: Portugal

institute: Universidade do Minho

summary: In this study we performed a whole-transcriptome analysis of C. glabrata biofilm cells exposed to different environmental conditions and constraints in order to identify the molecular pathways involved in fluconazole resistance and understand how acidic pH niches, associated with the presence of acetic acid, are able to modulate these responses.

overall_design: 12 samples in total (4 different growth conditions in triplicate - RPMI pH7; RPMI pH7 + Fluconazole; RPMI pH5 + acetic acid and RPMI pH5 + acetic acid + fluconazole)

first: Sandra

last: Paiva


title: Expression differences in wild type and 35S::CLE41 Arabidopsis stems

status: Public on Dec 01 2018

city: Durham

first: Peter

last: Etchells

address: South Road

department: Biosciences

country: United Kingdom

institute: Durham University

summary: Arabidopsis CLE41 regulates vascular organisation, cell division and xylem differentiation. 35S::CLE41 lines are characterised by an increase in the number of undifferentiated cells in vascular bundles and by radial patterning defects. To identify further genetic components involved in controlling vascular development, we compared the transcriptomes of one 35S::CLE41 line with that of wild type counterparts using microarray analysis.  Inflorescence stem tissue was compared in 5 weeks old plants 1 cm above the rosette leaves where vascular bundles of 35S::CLE41 plants contained an average of 100.7 ± 9.1 undifferentiated cells compared to 59.5 ± 5.5 in wild type counterparts. Genes with a putative role in vascular development demonstrate changes in gene expression between the two genotypes tested.

overall_design: 6 samples; 3x wild type replicates, 3x 35S::CLE41 replicates

first: J


title: Response of Phaeocystis antarctica under changing iron conditions

city: Bremerhaven

first: Sara

last: Beszteri

address: Am Handelshafen 12

institute: Alfred Wegener Institute

summary: The study aims at deciphering the response of Phaeocystis antarctica under iron limitation and iron supplementation at a transcriptomic level.

overall_design:
Phaeocystis antarctica strain #25, isolated from Ross Sea, was acclimated under iron limitation. From that stock culture, 4 replicates were inoculated under iron limitation for 48h 16:8 light:dark. After 48h, Ferric chloride was added to the 4 replicates. Samples were taken at 0h (before iron supplementation), and at 14h, 24h and 72h (after iron supplementation), in all 4 replicates except 14h (3 samples). BioProject accession: PRJNA395466, SRA Study accession: SRP113407

Please note that the processed data identifiers belong to TSA project GFUQ00000000 (status: processing).  The lookup table of the gene IDs and TSA IDs is available at the foot of this record.

first: Mariam

middle: R

last: Rizkallah

first: Stephan

last: Frickenhaus

first: Lars

last: Harms

first: Vladimir

last: Benes

first: Ahmed

last: Moustafa

first: Steffi

last: Gaebler-Schwarz


title: Early lineage commitment defines alveolar epithelial ontogeny in the lung

status: Public on Feb 08 2019

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary: During the step-wise specification and differentiation of tissue specific multipotent progenitor cells, lineage-specific transcriptional networks are either activated or repressed to orchestrate progenitor cell commitment. The gas exchange niche in the lung contains two major epithelial cell types, alveolar type 1 (AT1) and type 2 (AT2) cells, and the timing of lineage commitment of these cells is critical for correct formation of this niche and postnatal survival. To define the ontogeny of alveolar cell fate in the lung, we used lineage tracing studies combined with spatially specific mRNA transcript and protein expression combined with single cell RNA-seq analysis. These studies reveal that commitment to alveolar epithelial cell fate occurs far earlier than previously appreciated, concomitant with the proximal-distal specification of epithelial progenitors and branching morphogenesis. Using a novel dual lineage tracing system, we show that a small population of alveolar cells express markers of both AT1 and AT2 cells, whose fate is ultimately restricted to a single lineage. However, these bi-transcriptional cells generate only a minor portion of the mature alveolar epithelium. These data reveal a new paradigm of organ formation where early lineage commitment occurs during the nascent stages of development coincident with broad tissue patterning processes including axial patterning of the endoderm and branching morphogenesis.

overall_design: Lungs were harvested from a e15.5 and e17.5 Nkx2-1-GFP embryos and all were combined from a single litter.  Dead cells were negatively selected using DAPI and positively selected by expression of GFP.  Cells were loaded on to a GemCode instrument (10X Genomics) to produce single-cell bar-coded droplets using 10X Single Cell 3’ v2 chemistry. Libraries generated were sequenced across at least one lane on the Illumina HiSeq2500 instrument with the HiSeq Rapid SBS kit.

first: David

last: Frank

first: Rajan

last: Jain

first: Edward

last: Morrisey


title: Quantitative Analysis of Wild Type and Lztr1 +/- Transcriptomes in MEFs (murine embryonic fibroblasts)

status: Public on Nov 29 2018

city: Leuven

first: Peihua

last: Zhao

address: Herestraat 49

country: Belgium

institute: KU Leuven

summary: The goals of this study are to compare  MEFs transcriptome profiling (RNA-seq) from Lztr1 +/+ and +/- mice. MEFs were isolated from E12,5 embryos,

overall_design: mRNA profiles of wild type (WT) and Lztr1 +/- MEFs were generated by deep sequencing, in triplicate, using Illumina HiSeq2500.

first: Silvia

last: Pandolfi

first: Anna

last: Sablina


title: Genome-wide lung transcriptional profiling of mouse models for pneumonia given human adipose-derived mesenchymal stem cells treatment or Prekallikrein

status: Public on Oct 31 2018

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

summary:
Adult mesenchymal stem cells exert immunomodulatory effects that might improve the host response during sepsis. Knowledge on the effect of adipocyte-derived mesenchymal stem cells (ASCs) in sepsis is limited.  Klebsiella (K.) pneumoniae is a common cause of gram-negative pneumonia and sepsis. The aim of this study was to determine the effect of human ASCs on the host response during pneumosepsis in mice. For this mice were infected with K. pneumoniae via the airways to induce a gradually evolving infection in the lung cumulating in pneumosepsis. One or 6 hours (h) after infection, mice were infused intravenously with ASCs or vehicle, and euthanized after 16h or 48h respectively. The effects of freshly cultured and cryopreserved ASCs were compared, the latter formulation being more clinically relevant. Intravenously administered ASCs were visualized in lung tissue by immunostaining at 1 and 3h, but not at 15h after infusion. While early after infection ASCs did not or only modestly influence bacterial loads, they reduced bacterial burdens in lungs and distant organs at 48h.  ASCs reduced the lung levels of pro-inflammatory cytokines and attenuated lung pathology, but did not influence distant organ injury. ASCs strongly modified the lung transcriptome in both uninfected mice and mice with pneumosepsis, especially affecting. Cryopreserved and cultured ASCs induced largely similar effects. These data indicate that human ASCs induce profound immune modulatory effects in the lungs, resulting in reduced bacterial burdens and lung inflammation during pneumosepsis caused by a common human pathogen, suggesting that ASCs may be an adjunctive therapeutic in this condition.
Experimental groups were defined as follows: (1) plac_cryo, placebo treated and K.pneumoniae infected control mice for cryopreserved MSCs; (2) plac_cult, placebo treated and K.pneumoniae infected control mice for cultured MSCs; (3) cryo, K.pneumoniae infected mice treated with cryopreserved MSCs; (4) cult, K.pneumoniae infected mice treated with cultured MSCs; (5) n_cult, non-infected control mice for cultured MSCs; (6) n_cryo, non-infected control mice for cryopreserved MSCs; (7) n, normal mouse lung baseline.
In a separate experiment, mice were treated with a selective prekallikrein (PKK) directed antisense oligonucleotide (ASO) or a scrambled control ASO for 3 weeks prior to infection. Host response readouts were determined at 12 or 36 hours postinfection, including genome-wide messenger RNA profiling of lungs, or mice were followed for survival
Pre-processing and quality control of the scans were performed by using the oligo method (version 1.44) and probes were annotated using the platform design info for Affymetrix Clariom_S_Mouse_HT available through Bioconductor. Array data were background corrected by Robust Multi-array Average (RMA) and quantiles-normalized. Microarray quality control was performed by means of the array quality metrics method (version 3.36.0). The occurrence of non-experimental chip effects was evaluated by the surrogate variable analysis method (version 3.28.0) and corrected using the combat method.

overall_design: Pneumonia was induced by intranasal inoculation with 10^4 colony forming units (CFU) K. pneumoniae serotype 2 (ATCC 43816, Rockville, MD). In all human-derived mesenchymal stem cell experiments mice were intravenously (i.v.) infused with 1 x 10^6 adipose derived stem cells (ASCs) at 1 or 6 hours after infection. In a separate experiment, mice were treated with a selective prekallikrein (PKK) directed antisense oligonucleotide (ASO) or a scrambled control ASO for 3 weeks prior to infection.  We performed genome-wide scans of pulmonary gene expression in uninfected and infected mice treated with ASCs. For this analysis we selected the 16 hour time point to avoid confounding effects by differences in bacterial burden observed at later time points. RNA was isolated from lung homogenate using the Nucleospin RNA isolation kit (Macherey-Nagel, Düren, Germany) as described by the manufacturer. RNA samples with integrity number (RIN) > 6 (Agilent Bioanalyzer) were included for microarrays.

first: Tom

last: van der Poll


title: Whole genome copy number profiles of FFPE samples from patients with metasatic colorectal cancer (mCRC)

status: Public on Nov 21 2018

city: Osaka-Sayama

first: Yoshihiko

last: Fujita

address: 377-2 Ohno-Higashi

country: Japan

institute: Kinki university School of Medicine

type: Genome variation profiling by genome tiling array

summary: Metastatic colorectal cancer (mCRC) is associated with multiple somatic copy number alterations (SCNAs). We analyzed SCNAs to estimate overall survival (OS) and progression free suvival (PFS) for mCRC patients treated with bevacizumab in combination with oxaliplatin or irinotecan.

overall_design: Genomic DNAs were purified from 154 FFPE samples for mCRC patients treated with bevacizumab plus irinotecan (FOLFIRI) or oxaliplatin (FOLFOX) and the response was analyzed by array CGH profiling.

first: Y

first: K

last: Nishio


title: Whole transcriptome profile of citrulline-specific B cells from patients with rheumatoid arthritis

status: Public on Nov 16 2018

city: Houston

first: Navin

last: Varadarajan

state: Texas

address: 4726 Calhoun Rd

department: Chemical and Biomolecular Engineering

institute: University of Houston

summary: Although the contribution of B-cell derived autoreactive antibodies to rheumatoid arthritis (RA) has been studied extensively, the autoantibody-independent roles of B cells in the progression of the disease is not well-defined. By utilizing whole transcriptome profiling of human citrulline-specific B cells, we identified diverse inflammatory pathways, cytokines and transcriptional programs that define the biological role of B cells in RA and identify targets for drug intervention. Significantly, we identified the restricted expression of IL15Rα on citrulline-specific B cells and also demonstrated that B cells can express the epidermal growth factor amphiregulin (AREG) under inflammatory conditions. Mechanistically, we demonstrate that AREG has a direct impact on the cellular effectors of RA; it increases the proliferation and invasiveness of RA fibroblast-like synoviocytes (FLS) and synergizes with ACPA to enhance differentiation of osteoclasts. Overall, we present the first comprehensive transcriptome profile of autoreactive B-cell in an autoimmune disease, which can serve as a foundational dataset for studying the multi-faceted roles of B cells in autoimmune diseases

overall_design: Whole transcriptome profile of CCP-specific B cells (RA-CCPPOS) with that of CCP-negative B cells (RA-CCPNEG) from the same donor and hemagglutinin-specific (HAPOS) B cells from healthy individuals elicited upon vaccination with seasonal influenza virus

first: Ankit

last: Mahendra