title: CSB ablation induced apoptosis is mediated by Increased Endoplasmic Reticulum Stress Response: a gene expression study

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

country: Italy

institute: European Brain Research Institute

summary: The DNA repair protein, Cockayne syndrome group B (CSB), has been recently identified as a promising anticancer target. Suppression, by antisense technology, of this protein causes devastating effects on tumor cells viability, through a massive induction of apoptosis, while being non-toxic to non-transformed cells. To gain insights into the mechanisms underlying the pro-apoptotic effects observed after CSB ablation, global gene expression patterns were determined, to identify genes that were significantly differentially regulated as a function of CSB expression. The one-color Agilent microarray platform was used. The study revealed that response to endoplasmic reticulum stress and response to unfolded proteins were ranked top amongst the cellular processes affected by CSB suppression.

overall_design: A total of n=16 samples were processed: 4 experimental groups, 2 time points (6 and 12 h after transfection) and 2 biological replicates for each experimental point(time+group). The 4  experimental groups (one test and three controls) are: cells incubated with antisense oligonucleotides specifically inducing CSB mRNA degradation (ASO), mock treated cells (CTRL), transfection reagents alone (OLF) and cells treated with sense oligonucleotides (SO).

first: Manuela

last: Caputo

first: Alessio

last: Balzerano

first: Mara

last: D’Onofrio

first: Rossella

last: Brandi

first: Silvia

last: Bongiorni

first: Stefano

last: Brancorsini

first: Mattia

last: Frontini

first: Luca

last: Proietti De Santis


title: RNA expression profile of liver-specific IGF2BP2/IMP2/p62 transgenic mice compared to wild-type mice

status: Public on May 31 2019

city: Saarbrucken

first: Sonja

middle: M.

last: Kessler

address: Campus C2 3

country: Germany

institute: Saarland University

summary: Livers of p62/IMP2-2 transgenic mice with C57Bl6J/DBA2 background as described in Tybl et al., J Hepatol, 2011

overall_design: Untreated livers of animals with an age of 5 weeks were used.

first: Cristina

last: Cadenas

first: Agapios

last: Sachinidis

first: Jan

middle: G

last: Hengstler

first: Alexandra

middle: K

last: Kiemer

middle: M


title: Cardiac Stretch-Induced Transcriptomic Changes are Axis-Dependent

status: Public on Jun 01 2019

city: La Jolla

first: Andrew

last: McCulloch

state: CA

address: 9500 Gilman Dr

department: Bioengineering

country: USA

institute: University of California, San Diego

type: Expression profiling by high throughput sequencing

summary: The goal of this study was to examine the effect of the major axis of biaxial mechanical stretch on cardiac myocyte gene expression and to identify the signaling pathways and transcription factors regulating these changes. Neonatal cardiac myocytes were cultured on a micropatterned substrate, and the primary stretch axis was applied either parallel or transverse to the myofibril direction. RNA sequencing was conducted to study whole genomic expression changes after acute cardiac myocyte stretch. The results showed a more robust gene response to longitudinal than to transverse stretch. After 30 minutes of stretch, 53 and 168 genes were considered differentially expressed (DE) from transverse and longitudinal stretch, respectively. After 4 hours, the number of DE genes increased to 795 in longitudinal stretch while it decreased to 35 in transverse stretch. Gene ontology term (GO) analysis indicated enrichment of TF activity and protein kinase activity by both stretch axes; whereas longitudinal but not transverse stretch caused expression of genes involved in sarcomere organization and cytoskeletal protein binding.

overall_design: Two stretch durations (30 minutes and 4 hours), and both axes of stretch (transverse and longitudinal) were studied for a total of 4 different stretch conditions. A fifth condition of non-stretched cells was used as a control. Three stretchers for each condition served as biological replicates.

first: Kyle

middle: S

last: Buchholz

first: Alexander

middle: C

last: Zambon

middle: D

first: Jeffrey

middle: H

last: Omens


title: Chemical disarming of isoniazid resistance in Mycobacterium tuberculosis

city: St. Louis

first: Gregory

middle: A

last: Harrison

state: MO

address: 660 South Euclid Avenue

department: Molecular Microbiology

institute: Washington University School of Medicine

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

overall_design: Refer to individual Series


title: Analysis of Nod factor receptor proteins in Rice

city: Cuernavaca

first: Luis

middle: Fernando

last: Lozano

state: Morelos

address: Av. Universidad 2001

country: Mexico

institute: Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México

summary: in this work, initially we ectopically expressed the legume Nod factor receptor genes (NFRP genes – MtNFP, MtLYK3 and LjLNP) in rice and assessed their impact on NF perception and consequently-triggered biological processes in roots. RNA-seq transcriptomic analysis revealed that the ectopic expression of the legume NFRPs in roots suppressed diverse genes associated with plant pathogen interaction and other defense response pathways including the ones involved in secondary metabolism. Overall, results the study indicate that (1) rice (control) plants have inherent ability to perceive NFs, and the perception of NFs resulted in suppression of a significant number of genes involved in innate immune response in roots; (2) Ectopic expression of NFRPs primed root hairs to respond to NFs; and (3) Expression of NFRPs made rice roots hypersensitive to NFs, as they triggered massive up-regulation of diverse defense response and secondary metabolism genes.

overall_design: RNA-seq was performed with RNA samples isolated from the root samples of RMh and PhL plants subjected to with and without NF treatment,  such as (A) RMh untreated, (B) RMh treated with NFs, (C) PhL untreated and (D) PhL treated with NFs, and DEGs were compared: C vs A, B vs A and D vs C

first: Alma

last: Altuzar-Molina

first: Marlene

last: Ortiz-Berrocal

first: Mario

last: Ramirez

first: Lourdes

last: Martinez

last: Velazquez

first: Swatismita

last: Dhar-Ray

first: Sonia

last: Silvente

first: Nestor

last: Mariano

first: Svetlana

last: Shishkova

first: Georgina

last: Hernandez

first: Reddy

middle: P

last: Maheswara


title: RNA-sequencing of hypoxic Mycobacterium tuberculosis treated with C10

summary: We sought to identify which genes were dysregulated in hypoxic Mycobacterium tuberculosis upon treatment with C10. We cultured Mycobacterium tuberculosis in an air-tight vessel for 2 weeks in the presence of either DMSO or 50 μM C10, and used RNA-sequencing to compare transcriptional profiles.

overall_design: Three condition experiment: bacteria were cultured in hypoxic conditions in the presence of DMSO or 50 μM C10. Aerobically growing M. tuberculosis in 7H9 medium was included as a control. Each group was performed with three biological replicates.

first: Christina

middle: L

last: Stallings


title: Expression data from S.cerevisiae treated with tunicamycin

city: London

first: Patrick

last: Lajoie

state: Ontario

address: 1151 Richmond street

department: Anatomy and Cell Biology

country: Canada

institute: University of Western Ontario

summary:
S.cerevisiae cells carrying a wild-type TOR1 allele or hyperactive TOR1L2134M allele were treated with the ER stressor, tunicamycin, and differential gene expression was examined between WT TOR1 and hyperactive TOR1LM
We used microarrays to examine differential gene expression in cells expressing hyperactive TOR1LM following ER stress . We identified changes in expression of cell wall genes.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Two independent culutres of S.cerevisiae carrying WT TOR1 or TOR1LM were treated with 2.5 μg/mL tunicamcyin for 2 hrs before RNA extraction and hybridization on Affymetrix microarrays

first: David

middle: E

last: Carter

first: Khadija

last: Ahmed


title: GADD45 promotes locus specific DNA demethylation and 2C cycling in embryonic stem cells

city: Mainz

first: Emil

last: Karaulanov

address: Ackermannweg 4

institute: Institute of Molecular Biology

type: Methylation profiling by high throughput sequencing

summary:
Mouse embryonic stem cell cultures contain a rare cell population of "2C-like" cells resembling 2-cell embryos, the key stage of zygotic genome activation (ZGA). Little is known about positive regulators of the 2C-like state and 2-cell stage embryos. We found that GADD45 (growth arrest and DNA damage 45) proteins, regulators of TET mediated DNA demethylation, promote both states.

This SuperSeries is composed of the SubSeries listed below.


title: Gene expression changes in GADD45 deficient 2-cell mouse embryos

summary: To study the role of GADD45 proteins in early mouse development, RNA-seq expression profiling was performed with Gadd45a/Gadd45b double knockout (DKO) and wild-type (WT) mouse embryos at 2-cell stage (2C).

overall_design: Gadd45a and Gadd45b knock-out mice (Gupta et al. 2005; Hollander et al. 1999) were interbred to obtain double heterozygous mice, which were further crossed to generate Gadd45a/Gadd45b double mutants (DKO). For RNA-sequencing, 2-cell stage embryos were collected from 3-4 week old wild-type and DKO super-ovulated and naturally fertilized females 20 h after the appearance of the vaginal plug. Between 23 and 35 embryos derived from the same litter were pooled into one biological sample (n=4 per genotype).

first: Katrin

last: Schüle

first: Manuel

last: Leichsenring

first: Tommaso

last: Andreani

first: Viviana

last: Vastolo

first: Medhavi

last: Mallick

first: Michael

last: Musheev

first: Christof

last: Niehrs


title: RNA-sequencing of Mycobacterium tuberculosis treated with C10

first: Gregory

last: Harrison

summary: We sought to identify pathways dysregulated in Mycobacterium tuberculosis upon treatment with the compound C10. We treated M. tuberculosis with DMSO, 5 μM C10, or 25 μM C10 for 48 hours in Sauton's medium and used RNA-sequencing to compare transcriptional profiles.

overall_design: Three condition experiment: bacteria were treated with DMSO (control), 5 μM C10, or 25 μM C10, performed with three biological replicates per treatment.


title: Methylome profiling of GADD45 deficient mouse embryonic stem cells

summary: In order to study the physiological impact of GADD45 proteins on DNA methylation, we compared the methylation levels of Gadd45a,b,g triple knockout (TKO) and wild-type (Control) mouse embryonic stem cells (mESC) via whole genome bisulfite sequencing (WGBS).

overall_design: Gadd45a,b,g triple knockout (TKO) mouse embryonic stem cells (mESC) were generated using the CRISPR/Cas9 system. Control clones were generated using the same system but without specific gRNA. Genomic DNA was extracted from two Gadd45 TKO and two Control mESC clones and subjected to whole-genome bisulfite sequencing (WGBS).


title: Epigenetic regulation of tumor-associated myeloid cell activity by CBP/EP300 bromodomain

city: South San Francisco

first: Suchit

last: Jhunjhunwala

address: 1 DNA Way, MS-444A

institute: Genentech

type: Genome binding/occupancy profiling by high throughput sequencing


title: SMARTer single cell total RNA sequencing [FACS sorted cells]

city: Ghent

first: Celine

last: Everaert

address: De Pintelaan 185

country: Belgium

institute: University Ghent

summary: Before sorting, cells were washed twice in 1X PBS buffer (DPBS without calcium chloride and magnesium chloride; Sigma Aldrich, D8537) and labelled with 7-AAD (BD Pharmingen, 51-68981E) for live/dead differentiation and FITC-conjugated antibody [anti-CD47 (BD Pharmingen, 556045) for A375 and anti-CD81 (BD Pharmingen, 551108) for Jurkat].

overall_design: single cell total RNA-seq data was generated for FACS sorted A375 and Jurkat cells

first: Karen

last: Verboom

first: Nathalie

last: Bolduc

first: Ken

last: Livak

first: Nurten

last: Yigit

first: Dries

last: Rombaut

first: Jasper

last: Anckaert

first: Simon

last: Lee

first: Morten

middle: T

last: Venø

first: Jørgen

last: Kjems

first: Frank

last: Speleman

first: Pieter

last: Mestdagh

first: Jo

last: Vandesompele


title: Transcriptomic analysis of Candida albicans and Candida glabrata co-culture biofilms

city: College Station

first: Katy

last: Kao

state: Texas

address: 3122 TAMU Room 200

department: Chemical Engineering

institute: Texas A&M University

summary: Candida spp. are commensal opportunistic fungal pathogens that often colonize and infect mucosal surfaces of the human body. Candida, along with other microbes in the microbiota, generally grow as biofilms in a polymicrobial environment. Due to the nature of cellular growth in a biofilm (such as production of a protective extracellular matrix) and the recalcitrance of biofilms, infections involving biofilms are very difficult to treat with antibiotics and perpetuate the cycle of infection. The two most commonly isolated Candida spp. from Candida infections are Candida albicans and Candida glabrata, and the presence of both of these species results in increased patient inflammation and overall biofilm formation. This work aims to investigate the interspecies interactions between C. albicans (Ca) and C. glabrata (Cg) in co-culture through transcriptome analysis over the course of biofilm growth. We report that during co-culture, lipid biosynthesis and transporter genes were significantly modulated in both Ca and Cg. Differentially expressed genes in Ca during co-culture growth included putative transporter genes (C2_02180W_A and C1_09210C_B; up-regulated), amino acid biosynthesis (ARO7; up-regulated most in Ca:Cg 1:3), and lipid-related genes (LIP3 and IPT1; down-regulated). Differentially expressed genes in Cg in co-culture included putative transmembrane transporters (CAGL0H03399g and CAGL0K04609g; up-regulated), an oxidative stress response gene (CAGL0E04114g; down-regulated most in Ca:Cg 1:3), genes involved in the TCA cycle (LYS12 and CAGL0J06402g; down-regulated), and several genes involved in cell wall/membrane biosynthesis (SEC53, GAS2, VIG9; down-regulated). Additionally, confocal microscopy was utilized for membrane lipid analysis between monoculture and co-culture biofilms. Through filipin-stained lipid analysis, we found that there was a significant increase in cell membrane lipid content in Ca:Cg 1:3 biofilms compared to Ca and Ca:Cg 3:1 biofilms. These results suggest substantial modifications of both cell wall, cell membrane, and transporters in both Ca and Cg during the time course of co-culture growth, which allows for increased biofilm formation and virulence in Candida co-culture biofilms.

sample_organism:
Candida albicans
Nakaseomyces glabratus

platform_organism:
Candida albicans
Nakaseomyces glabratus

overall_design: total of 30 samples: 5 biofilm conditions of C. albicans (Ca), C. glabrata (Cg), and 3 ratios of the two species in Ca:Cg 3:1, 1:1, and 1:3. We also collected samples at 3 time points (6h, 12h, 24h) and had two biological replicates

first: Michelle

last: Olson

first: Arul

last: Jayaraman

first: Ulisses

last: Braga-Neto

first: Mahdi

last: Imani


title: Expression data from iPSC-derived mimetic Vγ9Vδ2 T cells and mimetic NK cells

city: Singapore

first: Jieming

last: Zeng

address: 31 Biopolis Way, The Nanos, #06-01

country: Singapore

institute: Institute of Bioengineering and Nanotechnology

summary:
We designed and demonstrated a synthetic strategy to derive mimetic Vγ9Vδ2 T cells endowed with NKRs  from iPSCs.
We used microarrays to compare mRNA expression profiles of such iPSC-derived mimetic Vγ9Vδ2 T cells with other peripheral blood lymphocytes.

overall_design: We reprogrammed γδ T cell into iPSCs (γδ T-iPSCs) and then used an “NK cell-promoting” protocol to differentiate γδ T-iPSCs and to induce expression of natural killer receptors (NKRs). RNA was extracted from such produce iPSC-derived mimetic Vγ9Vδ2 T cells and hybridized on microarray.

first: Shin

middle: Y

last: Tang

first: Shu

last: Wang


title: Role of GADD45 proteins in embryonic stem cells and their derivatives

first: Emil

last: Karaulanov

summary: We generated Gadd45a,b,g triple-knockout mouse embryonic stem cells and performed RNA-seq expression profiling under six different conditions of cell culture and in vitro differentiation.

overall_design: Gadd45a,b,g  triple knockout (TKO) mouse embryonic stem cells (mESC) were generated by CRISPR/Cas9. RNA-Seq was performed to compare the transcriptome in three independent Gadd45 TKO versus three independent control mESC lines under different conditions: (i) Serum cultured mESC, (ii) Vitamin C treated mESC, (iii) 2i treated mESC, (iv) mESC differentiated as embryoid bodies (EB), (v) mESC differentiated as a serum-free monolayer, and (vi) EB stimulated with retinoic acid (RA).

first: Katrin

last: Schüle

first: Manuel

last: Leichsenring

first: Tommaso

last: Andreani

first: Viviana

last: Vastolo

first: Medhavi

last: Mallick

first: Michael

last: Musheev

first: Christof

last: Niehrs


title: Epigenetic regulation of tumor-associated myeloid cell activity by CBP/EP300 bromodomain [ChIP-seq]

first: Suchit

last: Jhunjhunwala

summary: ChIP-seq for H3K27Ac mark in MDSCs isloated from MDA-MB-231.X1.1 xenograft

overall_design: 3 Samples analyzed.

first: Denise

last: De Almeida Nagata

first: Jane

last: Grogan


title: Genome-wide association study on Tuberculosis in the Chinese Population

city: Beijing

first: Yong-Biao

last: Zhang

state: Select a State or Province

address: Beichen west road 1#

country: China

institute: Beijing Institute of Genomics

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: We perform the first two-stage GWAS on TB in the Chinese population. We examined 900,015 genetic variants in 1,008 TB patients using the HumanOmniZhongHua-8 v1.1 BeadChip.

overall_design: To investigate the loci associated withTuberculosis, we performed GWAS on patients from China .

first: A-Dong

last: Shen


title: Identification of G-protein-coupled receptors associated with differentiation and development of porcine subcutaneous preadipocytes.

city: Tsukuba

first: Masaaki

last: Taniguchi

state: Ibaraki

address: 2 Ikenodai

department: Division of Animal Breeding and Reproduction Research

country: Japan

institute: Institute of Livestock and Grassland Science National Agriculture Food Research Organization

summary: G-protein-coupled receptors (GPCRs) are membrane proteins that enable cells to sense molecular signals and to respond in a broad range of biological processes according to the circumstances of cells. Recent studies elucidated that short-medium chain fatty acids can stimulate GPCRs to activate signaling pathways for adipocyte differentiation. As for differentiation of Porcine Subcutaneous Pre-Adipocyte (PSPA), it has been demonstrated that octanoate supplementation in differentiation medium is essential for growth arrest which triggers differentiation initiation of PSPA followed by lipid synthesis and accumulation to develop into fully matured adipocyte. Previously we detected 10 candidate GPCR genes considered to affect adipocyte differentiation of PSPA. Transfection of small interfering RNA (siRNA) for the candidate genes indicated that knockdown of three genes (A, B and C) obviously decreased the differentiation of PSPA. Therefore we investigated gene expression profiles of PSPA transfected with siRNA for each of three GPCR genes using a porcine custom microarray. Our result indicated that larger numbers of down-regulated genes were detected more than up-regulated genes by the siRNA transfection. Gene ontology analysis elucidated that genes up-regulated by knockdown of Gene A, B and C were categorized in biological processes of skeletal system development, mitosis, and cell adhesion, respectively. Interestingly, knockdown of all three genes commonly down-regulated genes categorized in PPAR signaling pathway and immune response. Differentiation of PSPA might be attributable to the alteration of gene expression profiles regulated by GPCRs identified in this study.

overall_design: Four samples were analyzed with triplicates. Adipocytes transfected with 3 target siRNAs and 1 negative control siRNA were labeled by Cy3 while preadipocytes with no transfection were labeled by Cy5.

first: Hirohide

last: Uenishi

first: Ikuyo

last: Nakajima

first: Yuki

last: Nakamura

first: Aisaku

last: Arakawa

first: Satoshi

last: Mikawa


title: Epigenetic regulation of tumor-associated myeloid cell activity by CBP/EP300 bromodomain [RNA-seq]

summary: CBP bromodomain inhibitor effects on mouse MDSCs sorted out of MDA-MB-231.X1.1 xenograft

overall_design: Two cell types, gMDSC and mMDSC, from mice treated with with CBP inhibitor or vehicle. 5 replicate samples of each cell type were used.


title: Study to evaluate the effect of the type of tissue on gene expression measurements

status: Public on May 30 2019

city: Houston

first: Bruno

middle: Valentin

last: Sinn

state: TX

address: 2130 W Holcombe Blvd

department: Translational Molecular Pathology

institute: University of Texas - MD Anderson Cancer Center

summary: To evaluate the effect of tissue type (cytology vs. surgical tissue) on gene expression measurements. Information was used to select probesets with a high spatial reproducibility for the development of gene signatures.

overall_design: 88 breast cancer samples were obtained at the time of surgery prior to any systemic treatment. In addition to a solid tissue sample, a scrape (=cytology) sample was taken by scraping with a scalpel over the cut-surface of the tumor. Samples were stored in RNAlater and profiled on Affymetrix U133A microarrays.

middle: V

first: William

middle: F

last: Symmans


title: Study to evaluate the effect of technical repetition on gene expression measurements

summary: To evaluate the effect of technical repetition on gene expression measurements, we repeated the laboratory protocol at 6 different steps. Information was used to select probesets with a high technical reproducibility for the development of gene signatures.

overall_design: 20 breast cancer samples were profiled on Affymetrix U133A microarrays. The samples were chopped in pieces, mixed and 80% were used to repeat the laboratory protocol at five different levels: RNA extraction, cDNA synthesis, cRNA synthesis and re-scan of the same chip. The remaining 20% of the sample mix were used to repeat all steps, resulting in a total of six technical replicates.


title: Expression Profiles of Circular RNAs in colon biopsies from Crohn’s Disease Patients by Microarray Analysis

city: Nanjing

first: Xiaojun

last: LI

state: China

address: 305 East  Zhongshan Road，Xuanwu Distriction

department: Institute of Clinical Laboratory Science,

institute: Jinling Hospital, Nanjing University School of Medicine

summary: To investigate the expression profiles of circRNAs in colon tissues of the patients with Crohn’s Disease(CD) , ulcerative colitis (UC) and healthy controls (HC), we used circRNA microArray analysis form Arraystar to examine the expression of circRNAs in colon tissues of CD,UC and HC.

overall_design: 12 pinch tissues of colonic biopsies from 4 CD patients, 4 UC patients and 4 healthy controls were conducted with Human circRNA Array v2.0 microarray (8×15K, Arraystar) to acquire expression profiles.

first: Yu-an

last: Hu

first: Yan

last: Zhu

last: Li


title: Study to compare SET ER/PR index values from Affymetrix U133A microarrays to values from targeted RNASeq and to validate technical reproducibility on U133A microarrays

summary:
63 samples were profiled in replicates on Affymetrix microarrays and using a custom RNASeq panel. The samples were randomly split in a training and validation cohort. SET ER/PR was calculated and a linear model was trained and validated to reproduce values obtained by microarray using RNASeq.
In addition, the microarray replicates were used to validate the technical reproducibility of SET ER/PR.

overall_design: 63 tissue samples were taken of breast cancer patients without any prior systemic treatment. The samples were stored in RNA later for processing on both Affymetrix U133A microarrays and using a custom RNASeq panel.


title: Integrated analyses of histone methylation and RNA expression in beta cells sorted from mice with multiparity-induced diabetes identified effector genes of pancreatic beta cell dedifferentiation and dysfunction.

city: New York

first: Taiyi

middle: Diana

last: Kuo

state: NY

address: 1150 St Nicholas Ave., Ste. 237

department: Medicine

institute: Columbia University

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

overall_design: Refer to individual Series


title: Study to evaluate the effect of intratumoral heterogeneity on gene expression measurements

summary: To evaluate the effect of intratumorally heterogeneity on gene expression measurements, we profiled and compared samples from different macroscopic tumor areas. Information was used to select probe sets with a high spatial reproducibility for the development of gene signatures.

overall_design: Samples were taken from three macroscopic tumor areas from 51 surgical breast cancer specimens prior to any systemic treatment. Samples were profiled on Affymetrix U133A microarrays to evaluate the reproducibility of each probeset.


title: Study for evaluating the effect of different microarray platforms on gene expression measurements

summary: 88 breast cancer samples were profiled on Affymetrix U133A and Plus2 microarrays.

overall_design: 88 tissue samples were taken from surgical specimens of patients without any prior systemic treatment. The samples were then chopped in pieces, mixed, split up in two equal parts and stored in RNA later for processing on both Affymetrix U133A and Plus2.0 microarrays.


title: Breast cancer and normal breast tissue samples to estimate the effect of contamination of breast cancer samples with normal breast tissue

summary:
PURPOSE: To estimate the effect of contamination with normal breast tissue for the development of gene signatures robust to pre-analytical conditions.
METHODS: We evaluated the effect of contamination with normal breast tissue on gene signatures by comparing microarray profiles of breast cancer samples contaminated with increasing amounts of normal breast tissue.

overall_design: A set of 10 breast cancer samples were mixed with increasing amounts of 10 individual normal breast tissue samples. Samples were contaminated with 0, 10, 25, 50, 75, 80, 85, 90, 95 and 100 % of normal breast tissue, respectively.


title: Lysosomal dysfunction in Down syndrome is APP-dependent and mediated by APP-βCTF (C99)

city: Orangeburg

first: Sandipkumar

last: Darji

address: 140 Old Orangeburg Rd, Bldg 39

department: Center for Dementia Research

institute: Nathan Kline Institute for Psychiatric Research

summary: Lysosomal failure underlies pathogenesis of numerous congenital neurodegenerative disorders and is an early and progressive feature of Alzheimer’s disease (AD) pathogenesis. Here, we report that lysosomal dysfunction in Down Syndrome (Trisomy 21) requires the extra gene copy of amyloid precursor protein (APP) and is mediated by the beta cleaved carboxy terminal fragment of APP (APP-βCTF, C99).  In primary fibroblasts from individuals with Down Syndrome (DS), lysosomal degradation of autophagic and endocytic substrates is selectively impaired causing them to accumulate in enlarged autolysosomes/lysosomes.  Direct measurements of lysosomal pH uncovered a significant elevation (0.6 units) associated with slowed LC3 turnover and the inactivation of cathepsin D (CTSD) and other lysosomal hydrolases known to be unstable or less active when lysosomal pH is persistently elevated.  RNA sequencing analysis excluded a transcriptional contribution to hydrolase declines.  Normalizing lysosome pH by delivering acidic nanoparticles to lysosomes ameliorated lysosomal deficits, implicating pH elevation as their primary basis.  Cortical neurons cultured from the Ts2 mouse model of DS exhibited lysosomal deficits similar to those in DS cells.  Lowering APP expression with siRNA or BACE1 inhibition reversed cathepsin deficits in both fibroblasts and neurons.  Deleting one BACE1 allele from adult Ts2 mice had similar rescue effects in vivo.  The modest elevation of endogenous APP-βCTF needed to disrupt lysosomal function in DS is relevant to sporadic AD where APP-βCTF, but not APP, is also elevated.  Our results extend evidence that impaired lysosomal acidification drives progressive lysosomal failure in multiple forms of AD.

overall_design: (1) mRNA-Seq profiling of six Trisomic and six Disomic human fibroblasts samples (3 replicates from 2 individuals in each group) from 5 months (3 replicates) and 2 years (3 replicates) old unrelated inviduals treated with either siRNA against human APP (siAPP) or a negative control DsiRNA (siNC). (2) A separate Differential Gene Expression (DGE) analysis was also carried out to compare transcriptomic profile of human Disomic and Trisomic fibroblasts using Disomic samples treated with siNC (3 replicates each of 5 months and 2 years individuals; Total = 6) in conjunction with age matched untreated human Disomic fibroblasts samples already deposited by Letourneau et al. (GSM1338333, GSM1338336) and Sullivan et al. (GSM2105075, GSM2105077); and Trisomic samples treated with siNC (3 replicates each of 5 months and 2 years individuals; Total = 6) in conjunction with age matched untreated human Trisomic fibroblasts samples from Letourneau et al. (GSM1338325, GSM1338326, GSM1338327) and Sullivan et al. (GSM2105044, GSM2105047). The final count of samples for the Disomic and Trisomic group is 11 and 10 respectively.

first: Ying

last: Jiang

first: Yutaka

last: Sato

first: Eunju

last: Im

first: Martin

last: Berg

first: Matteo

last: Bordi

first: Asok

last: Kumar

first: Panaiyur

last: Mohan

first: Urmi

last: Bandyopadhyay

first: Antonio

last: Diaz

first: Ana

last: Cuervo

first: Ralph

last: Nixon


title: Identification of EOMES-expressing spermatogonial stem cells and their regulation by PLZF

city: Farmington

first: William

last: Flynn

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

summary: Long-term maintenance of spermatogenesis in mammals is supported by GDNF, an essential growth factor required for spermatogonial stem cell (SSC) self-renewal. Exploiting a transgenic GDNF overexpression model, which expands and normalizes the pool of undifferentiated spermatogonia between Plzf +/+ and Plzf lu/lu mice, we used RNAseq to identify a rare subpopulation of cells that express EOMES, a T-box transcription factor. Lineage tracing, conditional ablation, and busulfan challenge show that these are long-term SSCs that contribute to steady state spermatogenesis as well as regeneration following chemical injury. EOMES+ SSCs have a lower proliferation index than EOMES− GFRA1+ spermatogonia in wild-type but not in Plzf lu/lu mice. This comparison demonstrates that PLZF regulates their proliferative activity and suggests that EOMES+ SSCs are lost through proliferative exhaustion in Plzf lu/lu mice. Single cell RNA sequencing of EOMES+ cells from Plzf +/+ and Plzf lu/lu mice support a hierarchical model of a slow-cycling long-term SSC population supporting more rapid-cycling short-term SSCs.

overall_design: 384-well plate-based 3'-end scRNA-seq was performed on two groups, Plzf +/+ and Plzf lu/lu, of cells across 4 plates.  Plzf +/+ cells were spread across 2 plates and Plzf lu/lu cells were spread over 1 plate.  The 4th plate contains both Plzf lu/lu (up to well C15) and Plzf +/+ (well C15 onward). Each sample in this record represents one plate.

first: Manju

last: Sharma

first: Anuj

last: Srivastava

first: Heather

last: Fairfield

first: David

last: Bergstrom

first: Robert

last: Braun


title: SET ER/PR - A robust 18-gene Predictor for Sensitivity to Endocrine Therapy for Metastatic Breast Cancer

first: Bruno

last: Sinn

summary:
There is clinical need to predict sensitivity of metastatic hormone receptor-positive and HER2-negative (HR+/HER2-) breast cancer to endocrine therapy, and targeted RNA sequencing (RNAseq) offers diagnostic potential to measure both transcriptional activity and functional mutation.
We developed the SET ER/PR index to measure gene expression microarray probe sets that were correlated with hormone receptors (ESR1 and PGR) and robust to pre-analytical and analytical influences. We tested SET ER/PR index in biopsies of metastastic HR+/HER2- breast cancer against the treatment outcomes in 140 patients. Then we customized the SETER/PR assay to measure 18 informative, 10 reference transcripts, and sequence the ligand binding domain (LBD) of ESR1 using droplet-based targeted RNAseq, and tested that in residual RNA from 53 patients.   Higher SET ER/PR index in metastatic samples predicted longer progression-free (PFS) and overall survival (OS) when patients received endocrine therapy as next treatment, even after adjustment for clinical-pathologic risk factors (PFS: HR 0.534, 95% CI 0.299 to 0.955, p = 0.035; OS: HR 0.315, 95% CI 0.157 to 0.631, p = 0.001). Mutated ESR1 LBD was detected in 8/53 (15%) of metastases, involving 1% to 98% of ESR1 transcripts (all had high SETER/PR index).
A signature based on probe sets with good pre-analytical and analytical performance facilitated our customization of an accurate targeted RNAseq assay to measure both phenotype and genotype of ER-related transcription. Elevated SET ER/PR was associated with prolonged sensitivity to endocrine therapy in patients with metastatic HR+/HER2- breast cancer, especially in the absence of mutated ESR1 transcript.

We tested SET ER/PR index in biopsies of metastastic HR+/HER2- breast cancer against the treatment outcomes in 140 patients. Then we customized the SET ER/PR assay to measure 18 informative, 10 reference transcripts, and sequence the ligand binding domain (LBD) of ESR1 using droplet-based targeted RNAseq, and tested that in residual RNA from 53 patients.   Higher SET ER/PR index in metastatic samples predicted longer progression-free (PFS) and overall survival (OS) when patients received endocrine therapy as next treatment, even after adjustment for clinical-pathologic risk factors (PFS: HR 0.485, 95% CI 0.265 to 0.889, p = 0.019; OS: HR 0.314, 95% CI 0.155 to 0.637, p = 0.001). Mutated ESR1 LBD was detected in 8/53 (15%) of metastases, involving 1% to 98% of ESR1 transcripts (all had high SET ER/PR index). A signature based on probe sets with good pre-analytical and analytical performance facilitated our customization of an accurate targeted RNAseq assay to measure both phenotype and genotype of ER-related transcription. Elevated SET ER/PR was associated with prolonged sensitivity to endocrine therapy in patients with metastatic HR+/HER2- breast cancer, especially in the absence of mutated ESR1 transcript.

overall_design: 140 biopsy samples from metastases from patients with stage IV breast cancer were used for RNA extraction and hybridization on affymetrix microarrays.

last: Symmans


title: Single cell expression analysis reveals anatomical and cell cycle-dependent transcriptional shifts during heart development

city: Pittsburgh

first: Guang

last: Li

state: PA

address: 530 45th St. 8116 Rangos Research Center

department: Developmental Biology

institute: University of Pittsburgh

summary: The heart is a complex organ composed of multiple cell and tissue types. During early developmental stages, heart cells from different regions of the heart exhibit different patterns of gene expression, which are thought to significantly contribute to heart development and morphogenesis. Until recently, the lack of adequate tools prevented our ability to systematically profile gene expression in a cell type and anatomically-specific manner during heart development. Single cell RNA sequencing has emerged as a powerful approach that allows genome-wide analysis of gene expression in single cells. Using microfluidic-chip and droplet-based single-cell RNA sequencing platforms, we analyze cardiac cells during the early stages of heart development. We found, by principle component analysis, that the expression of cell cycle genes represents a major determinant of transcriptional variation in all analyzed cardiac cell types. Interestingly, when single cardiomyocytes (CMs) from different heart chambers were analyzed, we found that atrial ventricular canal derived CMs have reduced cell cycle activity compare with CMs from the left and right ventricular chambers. In addition, CMs in the trabecular myocardium exhibit reduced cell cycle activity than CMs in the compact myocardium. When CMs within the same chamber were segregated by their cell cycle phase, we found that CMs in the G2/M phase downregulate their sarcomeric and cytoskeletal markers. Finally, we revealed the expression of a signaling ligand from the endocardium that may repress trabecular CM proliferation, and an epicardial-derived ligand that can promote compact CM proliferation. Together these data highlight the variations in cell cycle activity to selectively promote cardiac chamber growth during development and the profound transcriptional shift within the same cell at different phases of cell cycle. Identifying alterations in the expression of key signaling molecules that drive CM proliferation may lead to greater understanding of the onset or progression of congenital heart disease.

overall_design: Single cell transcriptional analysis of embryonic cardiac cells using 10x Genomics 3' solution.

first: Sean

last: Wu


title: Discovery cohort for SET ER/PR

summary: Samples from hormone-receptor positive breast cancer to identify transcripts related to ESR1 and PGR expression.

overall_design: 147 samples from patients with stage I to IV hormone receptor-positive breast cancer prior to any systemic treatment were profiled on Affymetrix U133A microarrays.


summary:
 There is clinical need to predict sensitivity of metastatic hormone receptor-positive and HER2-negative (HR+/HER2-) breast cancer to endocrine therapy, and targeted RNA sequencing (RNAseq) offers diagnostic potential to measure both transcriptional activity and functional mutation.
We developed the SETER/PR index to measure gene expression microarray probe sets that were correlated with hormone receptors (ESR1 and PGR) and robust to pre-analytical and analytical influences. We tested SETER/PR index in biopsies of metastastic HR+/HER2- breast cancer against the treatment outcomes in 140 patients. Then we customized the SETER/PR assay to measure 18 informative, 10 reference transcripts, and sequence the ligand binding domain (LBD) of ESR1 using droplet-based targeted RNAseq, and tested that in residual RNA from 53 patients.   Higher SETER/PR index in metastatic samples predicted longer progression-free (PFS) and overall survival (OS) when patients received endocrine therapy as next treatment, even after adjustment for clinical-pathologic risk factors (PFS: HR 0.534, 95% CI 0.299 to 0.955, p = 0.035; OS: HR 0.315, 95% CI 0.157 to 0.631, p = 0.001). Mutated ESR1 LBD was detected in 8/53 (15%) of metastases, involving 1% to 98% of ESR1 transcripts (all had high SETER/PR index).
A signature based on probe sets with good pre-analytical and analytical performance facilitated our customization of an accurate targeted RNAseq assay to measure both phenotype and genotype of ER-related transcription. Elevated SETER/PR was associated with prolonged sensitivity to endocrine therapy in patients with metastatic HR+/HER2- breast cancer, especially in the absence of mutated ESR1 transcript.


title: CXCR4 is a host factor that regulates Plasmodium development in hepatocytes

status: Public on May 29 2019

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: The liver stage of the etiological agent of malaria, Plasmodium, is obligatory for successful infection of its various mammalian hosts. Differentiation of the rod-shaped sporozoites of Plasmodium into spherical exoerythrocytic forms (EEFs) via bulbous expansion is essential for parasite development in the liver. However, little is known about the host factors regulating the morphological transformation of Plasmodium sporozoites in this organ. Here, we show that sporozoite differentiation into EEFs in the liver involves protein kinase Cζ-mediated NF-κB activation, which robustly induces the expression of C-X-C chemokine receptor type 4 (CXCR4) in hepatocytes and subsequently elevates intracellular Ca2+ levels, thereby triggering sporozoite transformation into EEFs. Blocking CXCR4 expression by genetic or pharmacological intervention profoundly inhibited the liver stage development of the P. berghei rodent malaria parasite and the human P. falciparum parasite also. Collectively, our experiments show that CXCR4 is a key host factor for Plasmodium development in the liver, and CXCR4 warrants further investigation for malaria prophylaxis.

overall_design: To explore the molecular mechanisms by which the HGF/MET/PKCζ/NF-κB pathway regulates P. berghei sporozoite development in hepatocytes, we compared the gene expression patterns in wild-type and PKCζ-KO Huh7 cells treated or not treated with HGF. We also analyzed the gene expression profiles in wild type and PKCζ-KO Huh7 cells uninfected or infected with P. berghei sporozoites.

first: Hironori

last: Bando

first: Masahiro

last: Yamamoto


title: Microbiota-driven regulation and epigenetic alterations in intestinal epithelial cells

status: Public on May 26 2019

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center


title: Microbiota-driven epigenetic alterations in intestinal epithelial cells [ChIP-seq]

summary:
We compare H3K9Ac enrichment in intestinal epithelial cells from intestine of germ-free and microbiota-replete (conventionally-housed) mice.
Intestinal epithelial cells were harvested from the intestine of conventional or germ-free C57Bl6J mice. Chromatin immunoprecipitation was performed with anti-H3K9Ac.  Sequencing was performed using the Illumina HiSeq2500. Reads were mapped to the mm10 genome using Bowtie.
Microbiota induce loss of H3K9Ac within mulitple sites of the Clec2e gene.

overall_design: Intestinal epithelial cells were harvested from the intestine of conventional or germ-free C57Bl6J mice,  and ChIPseq was performed using H3K9Ac.

first: Theresa

last: Alenghat

first: Vivienne

last: Woo


title: Mimicking immune signatures of flavivirus infection with targeted adjuvants improves dengue subunit vaccine immunogenicity in mice and primates

first: Ahmad Nazri

last: Mohamed Naim

address: 60 Biopolis Street, Genome, #02-01

department: Infectious disease

institute: Genome institute of Singapore

summary: Comparison of gene expression profiles after infection with flaviviruses or tratment with toll-like receptor agonists

overall_design: Human PBMCs for four individual healthy donors were treated for 48 hours with flaviviruses (dengue viruses and yellow fever) and adjuvants (alum, Pam3CSK4, PolyI:C, LPS, R848 and ODN2006)

first: Katell

last: Bidet

first: Victor

last: Ho

first: Collins

middle: W

last: Chu

first: Ahmad

middle: N

first: Khaing

last: Thazin

first: Kuan

middle: R

last: Chan

first: Jenny

middle: G

last: Low

first: Milly

last: Choy

first: Lan

last: Wong

first: Paola

last: Florez de Sessions

first: Yie

last: Lee

first: Martin

last: Hibberd

first: Eng

last: Ooi

first: Katja

last: Fink

first: Jianzhu

last: Chen


title: Transcriptome maps of general eukaryotic RNA degradation factors

status: Public on May 28 2019

city: Goettingen

first: Katharina

middle: Bettina

last: Hofmann

address: Am Fassberg 11

department: Molecular Biology

institute: Max Planck Institute for Biophysical Chemistry

summary: RNA degradation pathways underlie RNA processing, the regulation of RNA levels, and the surveillance of aberrant or poorly functional RNAs in cells. Here we provide transcriptome-wide RNA-binding profiles of 30 general RNA degradation factors in the yeast S. cerevisiae. The profiles define the distribution of factors between RNA classes. They are also consistent with the canonical degradation pathway for closed-loop forming mRNAs after deadenylation. Modeling based on mRNA half-lives suggests that most degradation factors bind already to intact mRNAs, whereas decapping factors are recruited only for mRNA degradation, consistent with decapping being a rate-limiting step. Global analysis suggests that the nuclear surveillance machinery, including the complexes Nrd1/Nab3, TRAMP4, and the exosome, targets aberrant nuclear RNAs, pre-processes snoRNAs, and regulates attenuated genes. Finally, mRNA transcript optimality is the most predictive feature for binding of decapping factors and the Xrn1 exonuclease to mRNA, consistent with rapid 5´-degradation of inefficiently translated mRNAs.

overall_design: We used photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) to systematically generate transcriptome-wide protein binding profiles for 30 general RNA degradation factors in the yeast Saccharomyces cerevisiae. Biological replicates are collected for all 30 degradation factors.

first: Salma

last: Sohrabi-Jahromi

middle: B

first: Andrea

last: Boltendahl

first: Saskia

last: Gressel

first: Carlo

last: Baejen

first: Christian

last: Roth

first: Johannes

last: Soeding

first: Patrick

last: Cramer


title: Expression data from Malpighian tubules of wild type and dVHL +/- Drosophila 5-days old female

city: Bologna

first: Giuseppe

last: Gargiulo

address: Via Selmi, 3

institute: University of Bologna

summary:
Mutations in VHL tumor suppressor gene are the cause of the familial VHL disease that displays multiple benign and malignant tumors such as clear cell renal cell carcinoma. The VHL gene is similar in Drosophila melanogaster (dVHL) and humans.
We used microarrays to compare the gene expression profile between yellow white (used as control) and heterozygous dVHL +/- Malpighian tubes dissected from adult Drosophila female with the aim to identify distinct classes of up-regulated and downregulated genes in a sensitized (haploinsufficient) genetic background.

overall_design: Drosophila female of the appropriated genotype were transfered each day into new vials with supplemented yeast for 5 days. Malpighian tubules were then dissected for RNA extraction and hybridization on expression microarrays. Each sample was composed of Malpighian tubules dissected from 50 females of the same age.

first: Marilena

last: Ignesti

first: Davide

last: Andrenacci

first: Bettina

last: Fischer

first: Valeria

last: Cavaliere


title: Vitamin D and Wnt3A have additive and partially overlapping modulatory effects on gene expression and phenotype in human colon fibroblasts

city: Madrid

first: Maria Jesus

last: Larriba

state: Madrid

address: Arturo Duperier 4

department: Cancer Biology

country: Spain

institute: Instituto de Investigaciones Biomedicas "Alberto Sols"

summary: The Wnt/b-catenin signalling pathway is essential for intestinal epithelium homeostasis, but its aberrant activation is a hallmark of colorectal cancer (CRC). Several studies indicate that the bioactive vitamin D metabolite 1a,25-dihydroxyvitamin D3 (1,25(OH)2D3) inhibits proliferation and promotes epithelial differentiation of colon carcinoma cells in part through antagonism of the Wnt/b-catenin pathway. It is now accepted that stromal fibroblasts are crucial in healthy and pathologic intestine: pericryptal myofibroblasts are constituents of the stem cell niche and cancer-associated fibroblasts (CAFs) contribute to CRC progression. However, studies on the combined action of 1,25(OH)2D3 and Wnt factors in colon fibroblasts are lacking. Here we show by global transcriptomic studies that 1,25(OH)2D3 and Wnt3A have profound, additive, partially overlapping effects on the gene expression profile of CCD-18Co human colon myofibroblasts. Moreover, 1,25(OH)2D3 and Wnt3A inhibit CCD-18Co cell proliferation and migration, while 1,25(OH)2D3 reduces, but Wnt3A increases, their capacity to contract collagen gels (a marker of fibroblast activation). These data were largely confirmed in patient-derived primary colon normal fibroblasts and CAFs, and in fibroblasts from other origins. Our results indicate that 1,25(OH)2D3 and Wnt3A are strong regulators of colon fibroblast biology and contribute to a better knowledge of intestinal homeostasis and stromal fibroblast action in CRC.

overall_design: RNA-sequencing analysis of three independent experiments of CCD-18Co human normal colon myofibroblasts treated with 1a,25-dihydroxyvitamin D3, Wnt3A, both, or vehicle for 24 hours

first: Gemma

last: Ferrer-Mayorga

first: Núria

last: Niell

first: Ramón

last: Cantero

first: José

middle: M

last: González-Sancho

first: Luis

last: del Peso

first: Alberto

last: Muñoz

first: María

middle: J


title: Transcriptome analysts of a growth domain and a differentiated domain of the medaka gill.

city: Sevilla

first: Lorena

last: Buono

state: Sevilla

address: Carretera de Utrera km 1

institute: CABD

summary: Medaka gill filaments contain stem cells in their most apical domains and differentiated cells of diverse lineages in central and basal domains. We aim at identifying differentially expressed genes among these two functionally different regions.

overall_design: The apical and central domain of filaments were extracted using surgery scissors under a dissection binocular. Total RNA was obtained from both samples and used to prepare poliA libraries.

first: Lazaro

last: Centanin


title: Microbiota-driven regulation in small intestinal epithelial cells [RNA-seq]

first: Rebekah

last: Karns

summary:
We compare transcriptomic profiles of intestinal epithelial cells obtained from the small intestine of germ-free and conventionally-caged mice.
Intestinal epithelial cells were harvested from the intestine of conventional or germ-free C57Bl6J mice.  Directional polyA RNA-seq was performed on RNA fom cells using standard Illumina protocols.
Microbiota induce decreased expression of the Clec2e gene.

first: Theresa

last: Alenghat

first: Vivienne

last: Woo


title: Cancer-cell transcriptional signatures associated with Socs1 knockdown in an immunocompetent and orthotopic mouse model of non-small lung cancer

status: Public on May 23 2019

city: Aurora

first: Joanna

last: Poczobutt

institute: University of Colorado Denver

summary: How cancer cells respond to signals coming from the tumor microenvironment cannot be fully elucidated in vitro. Additionally, RNA-Sequencing data from bulk human tumors does not assess the contribution of cancer cells alone, but from a complex mixture of both host and cancer cells. Using an immunocompetent and orthotopic mouse model of human Non-small Cell Lung Cancer, we sought to determine cancer cell specific transcriptomes from bulk tumors and compared these to cancer cells grown in vitro. We hypothesized that knockdown of Socs1, or suppressor of cytokine signaling 1 in Lewis Lung Carcinoma (LLC) cells would not only impact their response to single-agent immunotherapy, but also lead to complex changes in the tumor microenvironment. First, we harvested RNA from either LLC-NT (LLC cells transduced with a non-targeting control vector) or LLC-sh21 (LLC cells transduced with a Socs1 knockdown vector) cell lines grown in vitro. To determine the transcriptome of these cells grown in vivo, we injected LLC-NT or LLC-sh21 cells into the left lung of transgenic GFP-expressing C57BL/6J mice. After three weeks, tumor-bearing lung lobes were isolated from mice and were made into single cell suspensions. The GFP-negative cancer cell population was sorted from GFP-positive host cells by fluorescence activated cell sorting. RNA was extracted from freshly isolated cancer cells grown in vitro or from cancer cells isolated from tumors. Our RNA-seq analysis shows that LLC-sh21 cells respond to IFNg coming from the microenvironment relative to LLC-NT cells which have a blunted response due to high basal expression of SOCS1. These data suggest that specific genes in the IFNg response pathway are important for response to immunotherapy.

overall_design: The following conditions were analyzed: (1) LLC-NT In Vitro. RNA was extracted from LLC-NT cells cultured in vitro. This condition has 3 independently cultured and harvested replicates.(2) LLC-NT In Vivo. RNA was extracted from LLC cells that were injected into transgenic GFP-expressing C57BL/6J mice, formed a primary tumor and after three weeks, the GFP-negative cancer cell population was isolated by fluorescence activated cell sorting. This condition has 3 independently injected and harvested replicates. Each replicate is a pool of 5 tumor-bearing lung lobes. (3) LLC-sh21 In Vitro. RNA was extracted from LLC-sh21 cells cultured in vitro. This condition has 3 independently cultured and harvested replicates.(4) LLC-sh21 In Vivo. RNA was extracted from LLC-sh21 cells that were injected into transgenic GFP-expressing C57BL/6J mice, formed a primary tumor and after three weeks, the GFP-negative cancer cell population was isolated by fluorescence activated cell sorting. This condition has 3 independently injected and harvested replicates. Each replicate is a pool of 5 tumor-bearing lung lobes.

first: Bonnie

last: Bullock

first: Abigail

middle: K

last: Kimball

first: Alexander

last: Neuwelt

first: Howard

last: Li

first: Amber

last: Johnson

first: Jeff

last: Kwak

first: Emily

last: Kleczko

first: Rachael

last: Kaspar

last: Wagner

first: Katharina

last: Hopp

first: Erin

last: Schenk

first: Mary

middle: C

last: Weiser-Evans

first: Eric

last: Clambey

first: Raphael

middle: A

last: Nemenoff


title: Wt1 regulates proliferation and differentiation of neural progenitors during brain development

status: Public on May 24 2019

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary:
Purpose: To gain a total insight into how Wt1 regulates embryonic neurogenesis, RNA-seq was performed to compare the different expressed genes ar E13
Methods: Total RNA were extracted from E13 telencephalic tissue of Wt1fl/fl and Wt1CKO mice. Then the total RNA was quality controlled and quantified using an Agilent 2100 Bioanalyzer. After converting to cDNA and building library, high-throughput sequencing was performed using the Illumina HiSeq 2500 platform in Annoroad Genomics.
Results: Approximately approximately one thousand transcripts showed differential expression between the Wt1fl/fl and Wt1CKO mice brain cortex, with a fold change ≥1.5 and p value <0.05. These results indicated the importance of Wt1 in cortical development.
Conclusions：RNA-seq based transcriptome characterization would provide a global understanding how Wt1 gene contribute to brain cortical development.

overall_design: Total 4 samples including 2 Wt1fl/fl and 2 Wt1CKO at E13 were sequenced; CKO1_WT1.anno.txt was generated from WT_R1.fq.gz files and CKO_R1.fq.gz files; CKO2_WT2.anno.txt was generated from WT_R2.fq.gz files and CKO_R2.fq.gz.

first: Fen

last: Ji


title: Loss of TLE3 promotes the mitochondrial program in beige adipocytes and improves glucose metabolism

city: Odense M

first: Anne

last: Loft

address: Campusvej 55

department: Biochemistry & Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: Prolonged cold exposure stimulates the recruitment of beige adipocytes within white adipose tissue. Beige adipocytes depend on mitochondrial oxidative phosphorylation to drive thermogenesis. The transcriptional mechanisms that promote remodeling in adipose tissue during the cold are not well understood. Here we demonstrate that the transcriptional coregulator transducin-like enhancer of split 3 (TLE3) inhibits mitochondrial gene expression in beige adipocytes. Conditional deletion of TLE3 in adipocytes promotes mitochondrial oxidative metabolism and increases energy expenditure, thereby improving glucose control. Using chromatin immunoprecipitation and deep sequencing, we found that TLE3 occupies distal enhancers in proximity to nuclear-encoded mitochondrial genes and that many of these binding sites are also enriched for early B-cell factor (EBF) transcription factors. TLE3 interacts with EBF2 and blocks its ability to promote the thermogenic transcriptional program. Collectively, these studies demonstrate that TLE3 regulates thermogenic gene expression in beige adipocytes through inhibition of EBF2 transcriptional activity. Inhibition of TLE3 may provide a novel therapeutic approach for obesity and diabetes.

overall_design: Genome-wide ChIP-seq profiling of TLE3 binding in eWAT, iWAT, and BAT adipocytes.

first: Stephanie

last: Pearson

first: Susanne

last: Mandrup

first: Claudio

last: Villanueva


title: Functional role of SLIT2 and ROBO1 in trophoblasts

status: Public on May 27 2019

city: Oulu

first: Antti

last: Haapalainen

address: Aapistie 5A

department: CRC

country: Finland

institute: University of Oulu

summary: Analysis of the effect of SLIT2 and ROBO1 siRNA experiment

overall_design: RNA-seq analysis of silenced SLIT2 (n = 3), ROBO1 (n = 3) and negative control (n=3) samples

first: Heli

last: Tiensuu


title: Evaluation of ultra-low input RNA sequencing for the study of human T cell transcriptome

city: Gaithersburg

first: Jingya

last: Wang

state: Maryland

address: 1 Medimmune Way

department: Early respiratory and immunology

institute: Astrazeneca

summary: Deeper understanding of T cell biology is crucial for the development of new therapeutics.  Human naïve T cells have low RNA content and their numbers can be limiting; therefore we set out to determine the parameters for robust ultra-low input RNA sequencing.  We performed transcriptome profiling at different cell inputs and compared three protocols: Switching Mechanism at 5’ End of RNA Template technology (SMART)  with two different library preparation methods (Nextera (SMART_Nxt) and Clontech (SMART_CC)), and AmpliSeq technology.  As the cell input decreased the number of detected coding genes decreased with SMART, while stayed constant with AmpliSeq. However, SMART enables detection of non-coding genes, which is not feasible for AmpliSeq. The detection is dependent on gene abundance, but not transcript length. The consistency between technical replicates and cell inputs was comparable across methods above 1K but highly variable at 100 cell input. Sensitivity of detection for differentially expressed genes decreased dramatically with decreased cell inputs in all protocols, support that additional approaches, such as pathway enrichment, are important for data interpretation at ultra-low input.  Finally, T cell activation signature was detected at 1K cell input and above in all protocols, with AmpliSeq showing better detection at 100 cells.

overall_design: Primary human naïve CD4 T cells were treated with a-CD3 only or a-CD3 and B7-1 Fc, which stimulate T cell activation, for 2 hours.  Next, the cells were collected and serially diluted to achieve 100K, 5K, 1K and 100 cells. Finally, RNA was extracted and transcriptome library was generated with two different protocols: SMART-Seq and AmpliSeq.  For SMART-Seq technology, two different library preparation kits were utilized: Nextera Library Preparation Kit (SMART_Nxt) and Clontech Library Preparation kit (SMART_CC)

first: Rajiv

last: Raja

first: Sadiye

last: Rieder


title: ARID1A regulates condensin II distribution and chromosomal partition [HiC]

status: Public on May 21 2019

city: Philadelphia

first: Priyankara

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: ARID1A, a subunit of the switch/sucrose non-fermentable (SWI/SNF) chromatin remodeling complex, influences gene accessibility. However, the role of ARID1A in spatial genomic organization and chromosomal interaction remains elusive.  We showed that the SWI/SNF complex interacts with condensin II and they show significant overlapping distributions in enhancers.  ARID1A inactivation drives redistribution of condensin II preferentially at enhancers without affecting the interaction between the SWI/SNF and condensing II complexes.   ARID1A and condensin II contribute to transcriptionally inactive B compartments, while ARID1A weakens the borders of topologically associated domains.  ARID1A inactivation decreases the frequency of genomic interactions over distance, but increases the intermixing of interphase small chromosomes, which was validated by three dimensional chromosome painting.  These results demonstrated ARID1A spatially partitions genome and chromosomes.

overall_design: RNA-seq, CHIP-seq and HiC in ARID1A/CAPH2 WT, ARID1A KO and CAPH2 KD cell lines

first: Rugang

last: Zhang

first: Shuai

last: Wu


title: NOMe-seq of mouse embryonic stem cells

city: Granada

first: Jordi

last: Martorell-Marugan

address: Avenida de la Ilustración 114

department: Bioinformatics Unit

institute: GENyO

summary: We report NOMe-seq data obtained from mouse embryonic stem cells

overall_design: NOMe-seq analysis of mouse embryonic stem cells to be used as input in NOMePlot sofware.

first: Francisco

last: Requena

first: Helena

first: Pedro

last: Carmona-Saez

first: David

last: Landeira


title: Mowing Alters Nutrient Element Accumulation Patterns and Reprograms Root Transcriptional Regulation in Brachypodium distachyon Bd21

city: Shanghai

first: Hailing

last: Zi

address: Chenhua road3888

institute: Shanghai center for plant stress biology

summary: Mowing is a common practice to agricultural and horticultural grass species. Nonetheless, it has been unclear how mowing may affect roots at the levels of nutrient accumulation and transcriptional regulation. Hereby we report a comprehensive investigation on molecular  impacts of mowing by using a model grass species, Brachypodium distachyon Bd21.

overall_design: We sequenced 3 replicates for both control and treatment. The DNA was extracted from the root of Brachypodium distachyon Bd21.

first: Wei

first: Hui

last: Sun

first: Sunil

last: Singh

first: Yu

last: Yang

first: Renyi

last: Liu

first: Huiming

first: Zhaoqing

last: Chu


title: Lgr5+ stem and progenitor cells reside at the apex of a heterogeneous embryonic hepatoblast pool

city: Dresden

first: Meritxell

last: Huch

address: Pfotenhauerstrasse 108

institute: Max Planck Institute of Molecular Cell Biology and Genetics

summary: During mouse embryogenesis, progenitors within the liver known as hepatoblasts give rise to adult hepatocytes and cholangiocytes. Hepatoblasts, which are specified at E8.5-E9.0, have been regarded as a homogeneous progenitor population that initiate differentiation from E13.5. Recently, scRNA-seq analysis has identified sub- populations of transcriptionally distinct hepatoblasts at E11.5. Here, we show that hepatoblasts are not only transcriptionally but also functionally heterogeneous, and that a subpopulation of E9.5-E10.0 hepatoblasts exhibit a previously unidentified early commitment to cholangiocyte fate. Importantly, we also identify a sub-population constituting 2% of E9.5-E10.0 hepatoblasts that express the adult stem cell marker Lgr5, and generate both hepatocyte and cholangiocyte progeny that persist for the lifespan of the mouse. Combining lineage tracing and scRNA-seq, we show that Lgr5 marks E9.5-E10.0 bipotent liver progenitors residing at the apex of a hepatoblast hierarchy. Notably, isolated Lgr5+ hepatoblasts can be clonally expanded in vitro into embryonic liver organoids, which can commit to either hepatocyte or cholangiocyte fates. Our study demonstrates functional heterogeneity within E9.5 hepatoblasts and identifies Lgr5 as a marker for a sub-population of bipotent liver progenitors.

overall_design:
scRNAseq of 471 E10.5 and 472 E13.5 mouse liver hepatoblast cells to investigate heterogeneity within the hepatoblast population
We used male Lgr5-EGFP-IRES-creERT2 mice maintained on a C57BL/6 background, these males were mated with MF1 females to generate experimental embryos

first: Nicole

last: Prior

first: Christopher

last: Hindley

first: Fabian

last: Rost

first: Elena

last: Meléndez

first: Winnie

last: Lau

first: Berthold

last: Göttgens

first: Benjamin

middle: D

last: Simons

first: Steffen

last: Rulands


title: Single-cell RNA-Seq Analysis of Retinal Development Identifies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specification

status: Public on May 22 2019

city: St. Louis

first: Brian

middle: Stewart

last: Clark

state: Missouri

address: 660 S Euclid Ave; Campus Box #8096

department: Ophthalmology and Visual Sciences

institute: Washington University

summary: Single cell RNA sequencing using either an adapted Smart-seq2 protocol on Chx10-GFP (+) retinal progenitor cells; 10x Genomics Chromium Single Cell system across 10 timepoints of mouse retinal development to examine retinal progenitor cell heterogeneity across retinal development and global changes in gene expression from early retinal neuroepithelial cells through specification and differentiation of retinal cell types; 10X Genomics Chromium Single Cell on P14 Nfia/b/x het control or Nfia/b/x tCKO (Chx10-Cre-GFP) retinas

overall_design: Examination of transcript expression within 120,840 cells across 10 developmental time-points (14 experiments) via 10x Genomics and 864 cells via an adapted Smart-Seq2 protocol; Characterization of Nfia/b/x mutant phenotypes using single-cell RNA-seq

middle: S

first: Seth

last: Blackshaw


title: ARID1A regulates condensin II distribution and chromosomal partition

first: Priyankara

last: Wickramasinghe

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

overall_design: Refer to individual Series


title: ARID1A regulates condensin II distribution and chromosomal partition [ChIP-seq]

first: Rugang

last: Zhang

first: Shuai

last: Wu


title: ARID1A regulates condensin II distribution and chromosomal partition [RNA-seq]


title: Whole transcriptomic analysis of zebrafish embryos of dyrk1aakrb1, dyrk1aa knock out mutant and Wild Type (WT) (+/+) in the background of Tg(kdrl:egfp)

status: Public on May 20 2019

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary: Purpose: The goals of this experiments are to analyze the transcriptomic change in dyrk1aakrb1 mutants compared with WT embryos by mRNA-seq technique.          Methods: Whole mRNA profiles of 48 hpf WT(+/+) and dyrk1aakrb1 mutants zebrafish embryos were generated by mRNA-seq techinque, in duplicate, using HiSeq 2500 (Illumina, Inc., USA).  Results: This analysis identified 222 transcripts as differentially regulated genes (DEG), of which 101 were up-regulated and 121 were down-regulated in dyrk1aakrb1 mutant (more than 2 fold and less than 0.5 fold respectively,; p value< 0.05).

overall_design: Whole transcriptomic analysis of zebrafish embryos of dyrk1aakrb1, dyrk1aa knock out mutant and WT (+/+) in the background of Tg(kdrl:egfp) at 48 hpf.

first: Hyun-Ju

last: Cho

first: Jeong-Soo

last: Lee

first: Jong

middle: H

first: Seon

middle: Y


title: Impact of acute aerobic exercise on genome-wide DNA methylation in natural killer cells - a pilot study

city: Cologne

first: Alexander

last: Schenk

address: Am Sportpark Müngersdorf 6

institute: German Sports University Cologne

type: Methylation profiling by genome tiling array

summary: This pilot study investigates the influence of an acute bout of exercise on DNA-methylation on isolated natural killer (NK-) cells. Therefore, 5 healthy women performed a graded exercise test with blood sampling before and 1 Min after. After NK-cell separation, DNA was isolated and DNA-methylation was analyszed usind the Ilumina Infinium MethylationEPIC BeadChip.

overall_design: NK-cell DNA isolated before and after an acute bout of exercise was analyzed using the Infinium MethylationEPIC BeadChip.

first: Christine

last: Koliamitra

first: Claus

last: Bauer

first: Robert

last: Schier

first: Michal-Ruth

last: Schweiger

first: Wilhelm

last: Bloch

first: Philipp

last: Zimmer


title: A comparison of RNA extraction and sequencing protocols for detection of small RNAs in plasma

city: Belfast

first: David

middle: Arthur

last: Simpson

state: N. Ireland

address: The Wellcome – Wolfson Institute for Experimental Medicine, 97 Lisburn Road

department: Wellcome-Wolfson Institite for Experimental Medicine

country: United Kingdom

institute: Queen's University Belfast

type: Non-coding RNA profiling by high throughput sequencing

summary: We compared 3 small RNA library prep kits (CleanTag, NEXTflex, QIAseq) and two RNA extraction methods (miRNeasy and MagnaZol) on plasma. We report that library preparation has a significant effect upon the miRNA profile detected, with QIAseq libraries exhibiting the least sequencing bias of the three library kits. RNA extraction methods also contribute, to a lesser extent, to the miRNA profile detected, with MagnaZol RNA extraction increasing the percentage of reads mapping to miRNAs and the number of individual miRNAs detected.

overall_design: Comparison of miRNA profiles detected in plasma by commercially available library prep kits.

first: Ryan

last: Wong

first: Meabh

last: MacMahon

first: Jayne

middle: V

last: Woodside


title: An atlas of vagal sensory neurons and their molecular specialization

city: Solna

first: Patrik

last: Ernfors

address: Biomedicum, Solnavägen 9

department: MBB/Molneuro

country: Sweden

institute: Karolinska Institutet

summary: Sensory functions of the vagus nerve are critical for specific aware perceptions and for monitoring visceral functions in the cardio-pulmonary and gastrointestinal systems. Here we present a comprehensive identification, classification, and validation of the neuron types in the neural crest (jugular) and placode (nodose) derived vagal ganglia by single cell transcriptomic (scRNA-seq) analysis. Our results reveal major differences between neurons derived from different embryonic origins. Jugular neurons exhibit fundamental similarities to the somatosensory spinal neurons, including major types such as C-low threshold mechanoreceptors (C-LTMRs), A-LTMRs, Aδ-nociceptors, cold-, and mechano-heat C-nociceptors. In contrast, the nodose ganglion contains 18 distinct types dedicated to surveying the physiological state of the internal body. Our results reveal a vast diversity of vagal neuron types including many previously unanticipated types as well as proposed types that are consistent with chemoreceptors, nutrient detectors, baroreceptors, and stretch and volume mechanoreceptors of the respiratory, gastrointestinal, and cardiovascular systems.

overall_design: Single-cell RNA-seq from 1896 vagal ganglion cells derived from wild-type and Vglut2Cre-Tomato animals originating from four replicates and consisting of the neuronal and non-neuronal cells that make up the ganglionic tissue.

first: Jussi

last: Kupari

first: Martin

last: Häring

first: Eneritz

last: Agirre

first: Gonçalo

last: Castelo-Branco


title: 4C on Sox2 Locus with tetO/cuO Modifications

status: Public on May 16 2019

city: San Francisco

first: Jeffrey

middle: Michael

last: Alexander

state: CA

address: 1650 Owens St

institute: Gladstone Institutes

summary: We have profiled the chromosomal contacts of the Sox2 promoter in wild-type ESCs as well as cell lines with a genetically altered Sox2 locus.

overall_design: Comparison of 4C profiles between WT and modified cell lines

first: Jeff


title: Small RNA profiling of extracellular vesicles secreted by A549 cells infected with West Nile virus and treated with interferon alpha

city: St Lucia

first: Andrii

last: Slonchak

state: QLD

address: Bldg 76 Cooper Rd

department: School of Chemistry and Molecular Biosciences

country: Australia

institute: The University Of Queensland

summary: The goal of this study is to determine if infection with flavivirus (West Nile virus) and action of proinflamatory cytokine interferon alter incorporation of host RNAs into extracellular vesicles secreted by human cells.

overall_design: Human lung carcinoma cells A545 were infected with Kunjin strain of West Nile virus at multiplicity of infection (MOI)=1 or incubated in the media containing 300u/ml IFN alpha 2a. Cells were then maintained in exosome free media for the next 24h. At 24 h post infection extracellular vesicles were isolated from culture fluids of infected or uninfected (Mock) cells using ExoQuick TC Exosomes isolation reagent. Enriched fractions of small RNAs were isolated from extacellular vesicles using mirVana miRNA isolation Kit (Ambion, USA) and used for library construction and RNA-Seq on Illumina HiSeq platform.

first: Brian

last: Clarke

first: Alex

last: Khromykh


title: Differential pathogenic Th17 profile in mesenteric lymph nodes of Crohn's disease and ulcerative colitis patients

status: Public on May 17 2019

city: Montreal

first: Marika

last: Sarfati

state: Qc

address: 900 Rue St Denis

institute: CRCHUM

summary: The drug targets IL23 and IL12 regulate pathogenicity and plasticity of intestinal Th17 cells in Crohn’s disease (CD) and ulcerative colitis (UC), the two most common inflammatory bowel diseases (IBD). However, studies examining Th17 dysregulation in mesenteric lymph nodes (mLNs) of these patients are rare. We showed that in mLNs, CD could be distinguished from UC by increased frequencies of CCR6+CXCR3-RORg+Tbet-CD4+ (Th17) memory T cells enriched in CD62Llow effector memory T cells (TEM), and their differentially expressed molecular profile. Th17 TEM cells (expressing IL17A, IL17F, RORC and STAT3) displayed a higher pathogenic/cytotoxic (IL23R, IL18RAP, and GZMB, CD160, PRF1) gene signature in CD relative to UC, while non-pathogenic/regulatory genes (IL9, FOXP3, CTLA4) were more elevated in UC. In both CD and UC, IL12 but not IL23, augmented IFNg expression in Th17 TEM and switched their molecular profile towards an ex-Th17 (Th1*)-biased transcriptomic signature (increased IFNG, and decreased TCF7, IL17A), suggesting that Th17 plasticity occurs in mLNs before their recruitment to inflamed colon. We propose that differences observed between Th17 cell frequencies and their molecular profile in CD and UC might have implications in understanding disease pathogenesis, and thus, therapeutic management of patients with IBD.

overall_design: For microarray study, we sorted CCR6+CXCR3-CD62LlowCD45RO+CD45RA-CD25-CD8-CD4+ Th17 TEM cells from mesenteric lymph nodes of Crohn's disease and ulcerative colitis patients. Th17 TEM cells were stimulated with anti-CD3/CD28 beads and cultured with or without IL12 for 6 days. NanoString Human Immunology v2 panel was performed on samples.

first: Marwa

last: Bsat


title: Codon usage optimization in pluripotent embryonic stem cells

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine


title: Codon usage optimization in pluripotent embryonic stem cells [tRNA sequencing]

summary: The uneven use of synonymous codons in the transcriptome regulates the efficiency and fidelity of protein translation rates. Yet, the importance of this codon bias on regulating cell state-specific expression programs is currently debated. Here, we asked whether the gene expression program in the well-defined cell states of self-renewal and differentiation in embryonic stem cells is driven by optimized codon usage. Using ribosome and transcriptome profiling, we identified distinct codon signatures for human self-renewing and differentiating embryonic stem cells. One driver for the cell state-specific codon bias was the genomic GC-content of the differentially expressed genes and thus, determined by transcription rather than translation. However, by measuring the codon frequencies at the ribosome’s active sites interacting with transfer RNAs (tRNA), we discovered that the wobble position tRNA modification inosine strongly influenced the codon optimization in self-renewing embryonic stem cells. This effect was conserved in mice and independent of the differentiation stimulus. In summary, we newly reveal how translational mechanisms based on RNA modifications can shape optimized codon usage in embryonic stem cells.

overall_design: tRNA sequencing of self-renewing and differentiating human H9 cells, 4 biological replicates per condition

first: Susanne

last: Bornelöv

first: Tommaso

last: Selmi

first: Sophia

last: Flad

first: Michaela

last: Frye


title: Differentially and co-expressed genes in embryo, germ-line and somatic tissues of Tribolium castaneum

city: COLLEGE STATION

first: SHER AFZAL

last: KHAN

state: TX

address: 370 Olsen Blvd

department: Entomology

institute: Texas A&M University

summary: Transcriptomic studies of Tribolium castaneum have led to significant advances in our understanding of co-regulation and differential expression of genes in development. However, previously used microarray approaches have covered only a subset of known genes. The aim of this study was to investigate gene expression patterns of beetle embryo, germ-line and somatic tissues. We identified 12,302 expressed genes and determined differentially expressed up and down-regulated genes among all samples. For example, 1624 and 3639 genes were differentially increased in expression greater than or equal to twofold change (FDR<0.01) in testis vs ovary (virgin female) and ovary vs embryo (0-5 hour), respectively. Of these, many developmental, somatic and germ-line differentially expressed genes were identified. Furthermore, many maternally deposited transcripts were identified, whose expression either decreased rapidly or persisted during embryogenesis. Genes with the largest change in expression were predominantly decreased during early embryogenesis as compared to ovary or were increased in testis compared to embryo. We also identify zygotic genes induced after fertilization. The genome wide variation in transcript regulation in maternal and zygotic genes could provide additional information on how the anterior posterior axis formation is established in Tribolium embryos as compared to Drosophila. Together, our data will facilitate studies of comparative developmental biology as well as help identify candidate genes for identifying cis-elements to drive transgenic constructs.

overall_design: Poly A mRNA profiles of 4 day old wild type (WT) male and female Tribolium castaneum adults from tissues (carcasses, ovary and testis) and embryos (0-5 hrs and 6-11 hrs) were generated by deep sequencing, in triplicate, using Illumina NextSeq 500 .

first: Sher

last: Afzal Khan

first: Heather

last: Eggleston

first: Zach

middle: N

last: Adelman


title: Linking cell dynamics with coexpression networks to characterize key events in chronic virus infections

status: Public on May 15 2019

city: Barcelona

first: Anna

last: Esteve-Codina

address: Carrer Baldiri Reixac 4-8

institute: CNAG-CRG

summary: The host immune response against an infection requires the coordinated action of many diverse cell subsets that dynamically adapt to the pathogen threat. Here we combined WGCNA and DCQ to analyse time-resolved mouse splenic transcriptomes in acute and chronic LCMV infections. This approach allowed to better characterize the dynamic cell events occurring in complex tissues such as the induction of the adaptive T cell response which requires the coordination of monocytes/macrophages and CD8+ T cells.

overall_design: mRNA profiles of CD8 T cells and macrophages (in duplicate days 0 and 7 post-infection) from C57BL/6 mice infected with 2x10E2 pfu of LCMV strain Docile, generated by deep sequencing.

first: Jordi

last: Argilaguet


title: Codon usage optimization in pluripotent embryonic stem cells [RNA-seq]

overall_design: Ribosome profiling and total RNA from self-renewing and differentiating human H9 cells, 4 biological replicates per condition

last: Bomelov


title: Transcriptome profiling of the aging fly brain

city: Jupiter

first: Ronald

middle: L

last: Davis

state: Florida

address: 130 Scripps Way

department: Neuroscience

institute: The Scripps Research Institute - Scripps Florida

summary: Cognitive decline is a common occurrence of the natural aging process in animals, and studying age-related changes in gene expression in the brain might shed light on disrupted molecular pathways that play a role in this decline. The fruit fly is a useful neurobiological model for studying aging due to its short generational time and relatively small brain size. We investigated age-dependent changes in the Drosophila melanogaster whole-brain transcriptome by comparing 5-, 20-, 30- and 40-day-old flies of both sexes. We used RNA-Sequencing of dissected brain samples followed by differential expression, temporal clustering, co-expression network and gene ontology enrichment analyses. Our study provides the first transcriptome profile of aging brains from fruit flies of both sexes, and it will serve as an important resource for those who study aging and cognitive decline in this model.

overall_design: 24 biological sample replicates (3 per age per sex), each consisting of pooled dissected whole-brains from 18 flies, were processed for total RNA extraction and sequencing. Age groups were 5, 20, 30 and 40 days old. One sample from the 30-day-old male group had to be removed from analysis due to sample contamination.

first: Rodrigo

last: Pacifico

first: Courtney

last: MacMullen


title: ChIP-Seq and ATAC-Seq analysis for Hox protein binding in Drosophila Kc167 cells

city: Cambridge

first: Rob

last: White

address: Downing Street

department: Physiology, Development and Neuroscience

institute: University of Cambridge

summary:
Hox protein transcription factors specify segmental diversity along the anterior-posterior body axis in metazoans. Understanding the basis of Hox function has long faced the problem that, while the different members of the Hox family show clear functional specificity in vivo, they all show very similar binding specificity in vitro. Based on in vitro studies, Hox cofactors may increase Hox binding selectivity but a satisfactory understanding of in vivo Hox target selectivity is still lacking.
We have carried out a systematic analysis of the in vivo genomic binding profiles of all eight Drosophila Hox proteins using transient transfection in Kc167 cells to examine Hox protein targeting. We find that Hox proteins show considerable binding selectivity in vivo in the absence of the canonical Hox cofactors Extradenticle and Homothorax. Hox binding selectivity is strongly associated with chromatin accessibility; binding sites in less accessible chromatin show the highest selectivity and the different Hox proteins exhibit different propensities to bind less accessible chromatin. High Hox binding selectivity is also associated with high affinity binding regions, leading to a model where Hox proteins derive binding selectivity through an affinity-based competition with nucleosomes. Provision of the Extradenticle/Homothorax cofactors generally leads to an increase in the number of Hox binding regions and promotes the binding to regions in less accessible chromatin, however the provision of these cofactors has little effect on the overall selectivity of Hox targeting.
These studies indicate that chromatin accessibility plays a key role in Hox selectivity and we propose that relative chromatin accessibility provides a basis for subtle differences in binding specificity and affinity to generate significantly different sets of genomic targets for different Hox proteins. We suggest that this mechanism may also be relevant to other transcription factor families.
This SuperSeries is composed of the SubSeries listed below.


title: Taenia crassiceps excreted/secreted products alters the microRNA profile and regulates the pro-inflammatory response of M1 macrophages

city: Tlalnepantla de Baz

first: Luis

middle: Ignacio

last: Terrazas Valdes

state: Estado de Mexico

address: Av. de los Barrios 1, colonia Los Reyes Iztacala

institute: UNAM

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


title: Characterization of the Bovine Salivary Gland Transcriptome Associated with Mycobacterium avium subsp. paratuberculosis Experimental Challenge

city: Guelph

first: Sanjay

last: Mallikarjunappa

state: ON

address: 50 Stone Road East

department: Animal Biosciences

institute: University of Guelph

summary: We report mandibular and parotid salivary gland RNA-Seq transcriptome profiles in MAP exposed and control cattle

overall_design: comparison of salivary gland transcriptome profiles between MAP exposed and control cattle

first: Kieran

middle: G

last: Meade


title: PRC2-mediated H3K27me3 contributes to transcriptional regulation of FIT-mediated iron deficiency response

city: Amherst

first: Jeeyon

last: Jeong

state: MA

address: 25 East Drive

department: Biology

institute: Amherst College

summary: We report that H3K27me3 attenuates the induction of FIT-target genes under iron deficiency response

overall_design: RNA-seq analysis of transcripts from wild type and clf root tissue grown under iron sufficient and deficient conditions


title: Mapping genomic binding sites of Drosophila Hox proteins and Hox cofactors, Extradenticle and Homothorax, in Kc167 cells with transient expression [ChIP-seq_Transient]

summary: We have carried out a systematic analysis of the in vivo genomic binding profiles of all eight Drosophila Hox proteins using transient transfection in Kc167 cells to examine Hox protein targeting. In addition, we have examined Hox protein binding in cells transfected  with both Hox and the cofactor, Homothorax. Provision of Homothorax also recruits the cofactor Extradenticle.

overall_design: We have examined the binding of all 8 Drosophila Hox proteins both in the absence and presence of the cofactor Homothorax. We also examine the binding of Homothorax and Extradenticle. For each sample type there are two biological replicates and one input sample.

first: Damiano

last: Porcelli

first: Bettina

last: Fischer

first: Steven

last: Russell

first: Robert


title: Suppressive and stimulatory host processes during virus infection fate decisions

summary: The processes and mechanisms of virus infection fate decisions that are the result of a dynamic virus - immune system interaction with either an efficient effector response and virus elimination or an alleviated immune response and chronic infection are poorly understood. Here we characterized the host response to acute and chronic lymphocytic choriomeningitis virus (LCMV) infections by gene coexpression network analysis of time-resolved splenic transcriptomes. We found first, an early attenuation of inflammatory monocyte/macrophage prior to the onset of T cell exhaustion and second, a critical role of the XCL1-XCR1 communication axis during the functional adaptation of the T cell response to the chronic infection state. These findings not only reveal an important feedback mechanism that couples T cell exhaustion with the maintenance of a lower level of effector T cell response but also suggest therapy options to better control virus levels during the chronic infection phase.

overall_design: mRNA profiles of spleens (in duplicate, days 0, 3, 5, 6, 7, 9 and 31 post-infection) and macrophages (in triplicate, day 6 post-infection) from C57BL/6 mice infected with 2x10E2 (acute) or 2x10E6 (chronic) pfu of LCMV strain Docile, generated by deep sequencing.

first: Andreas

last: Meyerhans

first: Mireia

last: Pedragosa


title: Total RNA-Seq data from leukemic patients with complex structural variants

status: Public on May 13 2019

city: Brno

first: Karla

last: Plevova

address: Kamenice 5

department: Central European Institute of Technology

country: Czech Republic

institute: Masaryk University

summary: Structural variants can lead to an alteration of gene expression which may be associated with disease worsening. In our study we attempted to describe expression changes associated with the presence of extensive genomic rearrangements in chronic lymphocytic leukemia.

overall_design: Peripheral blood samples from leukemic patients were used for RNA extraction. Gene expression profiles were correlated to chromosomal abnormalities identified in the cohort.

first: Jakub

last: Hynst


title: Mapping genomic binding sites of Drosophila Hox proteins, Hox cofactors Extradenticle and Homothorax, and the pioneer factor Glial cells missing in stable cell lines [ChIP-seq_Stable]

summary: We have carried out  analysis of the in vivo genomic binding profiles of  Drosophila Hox proteins using stable cell lines to examine Hox protein targeting. We have also examined Hox protein binding in stable cell lines expressing both Hox and the cofactor, Homothorax. Provision of Homothorax also recruits the cofactor Extradenticle.In addition, we have  examined Hox protein binding in stable cell lines expressing both Hox and the pioneer factor, Glial cells missing in the absence or presence of Homothorax.

overall_design: We have examined the genomic binding of selected Drosophila Hox proteins in the absence and presence of the cofactor Homothorax, in the presence of the pioneer factor Glial cells missing and in the presence of both Homothorax and Glial cells missing. We also examined the genomic binding of Homothorax and Glial cells missing. For each sample type there are two biological replicates and one input sample.


title: microRNA modulated networks of adaptive and innate immune response in pancreatic ductal adenocarcinoma

city: Botucatu

first: Tainara

middle: Francini

last: Felix

state: SP

address: Av. Prof. Mário Rubens Guimarães Montenegro, s/n, s/n

department: Surgery and Orthopedics

country: Brazil

institute: UNESP

summary: Despite progress in treatment strategies, only ~24% of pancreatic ductal adenocarcinoma (PDAC) patients survive >1 year. Our goal was to elucidate deregulated pathways modulated by microRNAs (miRNAs) in PDAC and Vater ampulla (AMP) cancers.

overall_design: Global miRNA expression was identified in 19 PDAC, 6 AMP and 25 paired, histologically normal pancreatic tissues using the GeneChip® 4.0 miRNA arrays. Computational approaches were used for miRNA target prediction/identification of miRNA-regulated pathways.

middle: F

first: Rainer

middle: M

last: Lopez Lapa

first: Márcio

last: de Carvalho

first: Natália

last: Bertoni

first: Tomas

last: Tokar

first: Rogério

last: Oliveira

first: Maria

last: Rodrigues

first: Cláudia

last: Hasimoto

first: Walmar

first: Leonardo

last: Pelafsky

first: César

middle: T

last: Spadella

first: Juan

last: Llanos

first: Giovanni

last: Silva

first: Wan

last: Lam

first: Silvia

last: Regina Rogatto

first: Luciana

last: Schultz Amorim

first: Sandra

last: Drigo

first: Robson

last: Carvalho

first: Patricia

middle: P

last: Reis


title: Taenia crassiceps excreted/secreted products alters the microRNA profile and regulates the pro-inflammatory response of M1 macrophages [mRNA]

first: Luis

last: Terrazas Valdes

summary: We tested the ability of helminth Taenia crassiceps parasite excreted/secreted products (TcES) to induce a regulatory-associated profile in bone-marrow derived macrophages (BMDMs). We also compared gene expression and microRNA profile of BMDMs exposed to TcES with those exposed to LPS which elicits a well-known inflammatory program.

overall_design: Mature macrophages were exposed for 4 or 24 hr to LPS (1 ug/ml), T. crassiceps excreted/secreted products (25ug/ml) or T. crassiceps excreted/secreted products plus LPS. After these time points, total RNA were collected. Next, 15ng of mRNA or microRNA from each group were hybridized overnight following manufacturer's instructions and gene expression was compared to unstimulated BMDMs.

first: Diana

last: Martínez-Saucedo

middle: A

last: Terrazas


title: Transcriptional control of subtype switching ensures adaptation and growth of pancreatic cancer

first: Rushika

last: Perera

address: 513 Parnassus Ave, HSW1321

department: Anatomy

institute: UCSF

summary:
Purpose: The goal of this study is to determine whether ectopic expression of the GLI2 transcription factor in the human pancreatic cancer cell line, YAPC is sufficient to cause gene expression changes associated with a EMT switch.
Methods: RNA was isolated from YAPC cells engineered to express a doxycycline inducible cassette for ectopic expression of GLI2 following treatment with 1ug/ml of Dox for 6 days. Control YAPC cells expressing an "empty vector" dox inducible cassette were similarly treated for 6 days with 1ug/u Dox and RNA was collected. Three biologically destinct replicates were submitted for library preparation and RNA-sequencing on an Illumina hiseq 2000. The sequence reads that passed quality filters were analyzed at the transcript level using TopHat followed by Cufflinks. qRT–PCR validation was performed using SYBR Green assays
Results: RNA-seq data confirmed stable over-expression of GLI2 in the YAPC-rtta-GLI2 cells and not in the EV control cells treated with Dox. Target genes of interest were validated by qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR for all target genes tested.  Gene set enrichment analysis of differentially expressed genes showed enrichment of EMT associated pathways which was further validated using functional assays. In addition a statistically significant alteration in SPP1 transcript was discovered in GLI2 overexpressing cells which formed the basis of ongoing experiments in the study.
Conclusions: Our data support a role for GLI2 in regulation of genes associated with basal-like subtype switching including SPP1

overall_design: mRNA profiles from human pancreatic cancer cell lines YAPC-rtta-GLI2 and YAPC-rtta-EV treatment with doxycyline for 6 days were compared, in triplicate.


title: CarD contributes to diverse gene expression outcomes throughout the genome of Mycobacterium tuberculosis

status: Public on May 11 2019

city: St. Louis

first: Dennis

last: Zhu

address: 4905 Children’s Place

department: Molecular Microbiology

institute: Washington University

summary: We examined the role of the RNA polymerase binding factor CarD on gene expression throughout the Mycobacterium tuberculosis genome. We performed RNA-seq on a panel of M. tuberculosis strains with point mutations in CarD that either enhance or disrupt its ability to stabilize RNA polymerase-promoter DNA open complexes in vitro.

middle: X

first: Ashley

last: Garner

first: Eric

last: Galburt

first: Christina

last: Stallings


title: Group 3 innate lymphoid cells mediate early protective immunity against Mycobacterium tuberculosis

city: Durban

first: Alasdair

last: Leslie

address: 719 Umbilo Road

country: South Africa

institute: African Health Research Institute

summary: We report the phenotype of human lung ILC2 and ILC3 populations from individuals with tuberculosis (TB) and non-TB cancer controls. We find that ILC2s demonstrate moderate transcriptional differences in TB infection, whereas ILC3s demonstrate large differences.

overall_design: ILC2s and ILC3s were purified by FACS from lung biopsies from TB infected lung tissue and peripheral healthy lung tissue from individuals with cancer. Low-input RNA-seq was performed on 1-3 replicates (dependent on cell number) on 5 individuals with TB infection and 2 controls.

first: Shabaana

last: Khader


title: Taenia crassiceps excreted/secreted products alters the microRNA profile and regulates the pro-inflammatory response of M1 macrophages [miRNA]

first: César