title: Single-cell analysis of Crohn’s disease lesions identifies a pathogenic cellular module associated with resistance to anti-TNF therapy

status: Public on Aug 29 2019

city: new york

first: Mamta

last: Giri

state: new york

address: 1470 madison ave

department: Institute of Personalized medicine

institute: Mount Sinai hospital

summary: Clinical benefits of cytokine blockade in ileal Crohn’s disease (iCD) are limited to a subset of patients. Here we applied single cell technologies to iCD lesions to address whether cellular heterogeneity contributes to treatment resistance. We found that a subset of patients expressed a unique cellular module in inflamed tissues that consisted of IgG plasma cells, inflammatory mononuclear phagocytes, activated T cells and stromal cells, which we named the GIMATS module. Analysis of ligand-receptor interaction pairs identified a distinct connectivity network that likely drives the GIMATS module. Strikingly, the GIMATS module was also present in a subset of patients in 4 independent iCD cohorts (n=441), and its presence at diagnosis correlated with failure to achieve corticosteroid-free durable remission upon anti-TNF therapy. These results emphasize the limitations of current diagnostic assays and the potential for single cell mapping tools to identify novel biomarkers of treatment response and tailored therapeutic opportunities

overall_design: Single cell seq analysis of paired resection ileal samples from inflamed and uninflamed area

first: Judy

last: Cho

first: Jerome

last: Martin

first: Miriam

last: Merad

first: Ephraim

last: Kenigsberg


title: Gene expression profiling of CHIR99021-induced skeletal myogenesis in human pluripotent stem cells

status: Public on Sep 13 2019

city: Ottawa

first: Alexandre

last: Blais

state: ON

address: 451 Smyth Road

country: Canada

institute: University of Ottawa

summary:
Human pluripotent stem cell- (hPSC)-derived skeletal muscle progenitors (SMP)—defined as PAX7-expressing cells with myogenic potential—can provide an abundant source of donor material for muscle stem cell therapy owing to the near-infinite replication potential of PSCs. As in vitro myogenesis is decoupled from in vivo timing and the 3D-embryo structure, it remains difficult to definitively characterize what stage or type of muscle is modeled in culture. Here, gene expression profiling is analyzed in hPSCs over a 50 day skeletal myogenesis protocol and compared to gene expression datasets of other hPSC-derived skeletal muscle and adult murine satellite cells. Furthermore, day 2 cultures differentiated with high or lower concentrations of CHIR99021 were contrasted.
Expression profiling of the 50 day time course identified successively expressed gene subsets involved in mesoderm/paraxial mesoderm induction, somitogenesis, and skeletal muscle commitment/formation which could be regulative by a putative cascade of transcription factors. Initiating differentiation with higher CHIR99021 concentrations resulted in significantly higher expression of MSGN1 and TGFB-superfamily genes, notably NODAL, resulting in enhanced paraxial mesoderm and reduced ectoderm/neuronal gene expression. Comparison to adult satellite cells revealed that genes expressed in day 50 cultures correlated better with those expressed by quiescent or early activated satellite cells, which have a greater therapeutic potential than late activated satellite cells. Day 50 cultures were similar to other hPSC-derived skeletal muscle and both expressed known and novel SMP surface proteins.

overall_design: 24 samples were analyzed, reflecting 8 experimental conditions with 3 biological replicates each. Day 0 samples were used as a reference in downstream analysis to establish altered levels of gene expression at the later stages of differentiation.

first: Michael

last: Shelton


title: Transcriptome analysis using RNA sequencing conducted for wild type (Col-0) and a stable transgenic line with ectopic expression of AT3G11290 (35S:HIN1) under control conditions and after 96 hours at moderate low water potential stress (-0.7 MPa)

status: Public on Oct 01 2019

city: Taipei City

first: Paul

last: Verslues

address: No.128, Sec.2, Academia Rd., Nangang Dist.

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

type: Expression profiling by high throughput sequencing

summary: RNA sequencing was used to identify alternative splicing events and differentially expressed genes (DEG) in 35S:HIN1 stable transgenic line compared to Col-0 wild type. Two treatments were analyzed for each genotype: unstressed control and a 96 hours moderate severity low water potential (-0.7 MPa) treatment. RNA sequencing analysis found that overexpression of HIN1 in unstressed plants was sufficient to duplicate the effects of stress on nearly 40% of the genes where intron retention was normally suppressed by stress in wild type. Differentially expressed genes (DEGs) were also analyzed (P < 0.05 and fold change ≥ 1.5 used as cut off values for DEGs). Differentially expressed genes in 35S:HIN1has limited overlap of DEGs between 35S:HIN1and wild type. This indicated that HIN1 plays a lesser role in stress-regulated gene expression than in splicing regulation.

overall_design: Wild type (Col-0) and 35S:HIN1 stable transgenic line Arabidopsis thaliana seedlings were germinated on half strength Murashige-Skoog agar plates. After seven days of growth, seedlings were transferred either to fresh plates of control media or to moderate low water potential (-0.7 MPa) imposed using agar plates of the control media infiltrated with PEG-8000. Samples were collected 96 hours after transfer to unstressed control and stress treatments. Three independent biological experiments and RNA extractions were performed for each genotype/treatment. After quality check and quantitation, the samples were used for RNA sequencing. This sequencing experiment was conducted at the same time as analysis of ahl10 describe in Wong et al. (PNAS 2019 116 (6) 2354-2363; https://doi.org/10.1073/pnas.1819971116).  Thus the wild type data in this submission are the same as for the ahl10 GEO submission (accesion no. GSE112368).

first: Geeng

last: Chong


title: ChIP-seq of p63 and RNA-seq of knockdown and overexpression of p63

status: Public on Aug 06 2019

city: Hefei

first: Ge

last: Shan

state: Anhui

address: 443 Huangshan Road

department: School of Life Sciences

country: China

institute: University of Science and Technology of China

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We performed ChIP-seq of p63 in ME-180 cell line and RNA-seq of knockdown and overexpression of p63

overall_design: Examination of binding sites and RNA level for p63

first: Fei

last: Xu


title: Transcriptome analysis of HPV-induced warts and healthy skin in humans

status: Public on Aug 27 2019

city: Ar Ramtha

first: Laith

last: Al-Eitan

state: Irbid

address: Petra Street

country: Jordan

institute: Jordan University of Science and Technology

summary: The main purpose of this study is to investigate the differences between the gene expression profiles of common warts and healthy skin in HPV-positive individuals by RNA sequencing on the Illumina HiSeq 2500. After obtaining shave biopsies of common warts and healthy skin from twelve Arab males, we were able to analyze the transcriptomes of 24 paired cases and controls.

overall_design: Investigation of transcriptomic differences between warts and normal skin

first: Amneh

middle: H

last: Tarkhan

first: Mansour

middle: A

last: Alghamdi

first: Firas

last: Al-Qarqaz

first: Hadeel

middle: S

last: Al-Kofahi


title: β-catenin/Tcf7l2 dependent transcriptional regulation of GLUT1 gene expression by Zic family proteins in colon cancer

status: Public on Aug 20 2019

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

country: USA

institute: Northwestern University Feinberg School of Medicine

summary: The Zinc finger of the cerebellum (ZIC) proteins have been implicated to function in normal tissue development. Mutations or deletions of ZIC genes have been found to be associated with neural-related abnormalities. Recent studies point out the critical functions of Zic proteins in cancers and the potential tumor suppressive functions in colon cancer development and progression. To elucidate the functional roles of Zic proteins in colorectal cancer, we employed CRISPR/Cas9 genome editing to knock out the Zic5 gene and analyze the chromatin localization pattern and transcriptional regulation of target gene expression. Zic5 regulates glucose metabolism through the regulation of expression of the GLUT1/SLC2A1 gene. Zic5 knockout is accompanied by an increased glycolytic state, tolerance to a low glucose condition, and derepression of metabolic genes especially GLUT1 gene expression. Reciprocally, the loss of Zic2 partially restored the glucose uptake by decreasing GLUT1 gene expression, pointing out the balance between the different Zic family proteins. Mechanistically, Zic5 is recruited by the β-catenin/TCF7l2 complex to the promoters of the target genes. Loss of β-catenin or TCF7l2 significantly diminishes the chromatin binding of Zic5 globally. Our studies suggest that the Wnt/β-catenin signaling pathway has a strong influence on the function of Zic proteins and glucose metabolism in colorectal cancers through GLUT1, thus interfering Wnt/β-catenin - Zic5 axis regulated aerobic glycolysis represents a potentially effective strategy to selectively target colon cancer cells.

overall_design: To characterize the functions of glucose metabolism regulated by Zic family proteins using Zic5 knockout human cancer cell lines

first: Zibo

last: Zhao

first: Elizabeth

last: Bartom


title: A conserved kinase-based body temperature sensor globally controls alternative splicing and gene expression

status: Public on Feb 14 2020

city: Berlin

first: Marco

last: Preussner

address: Takustrasse 6

country: Germany

institute: FU berlin

summary: Homoeothermic organisms maintain their core body temperature in a narrow, tightly controlled range. Whether and how subtle circadian oscillations or disease-associated changes in core body temperature are sensed and integrated in gene expression programs remains elusive. Furthermore, a thermo-sensor capable of sensing the small temperature differentials leading to temperature-dependent sex determination (TSD) in poikilothermic reptiles has not been identified. Here we show that the activity of CDC-like kinases (CLKs) is highly responsive to physiological temperature changes, which is conferred by structural rearrangements within the kinase activation segment. Lower body temperature activates CLKs resulting in strongly increased phosphorylation of SR-proteins in vitro and in vivo. This globally controls temperature-dependent alternative splicing and gene expression, with wide implications in circadian, tissue-specific and disease-associated settings. This temperature sensor is conserved across evolution and adapted to growth temperatures of diverse poikilotherms. The dynamic temperature range of reptilian CLK homologs suggests a role in TSD.

overall_design: HEK293 cells were pre-entrained to 39°C for 12 hours. After addition of DMSO or TG003 cells were shifted to 35°C (or maintained at 39°C); RNA was extracted after 6 hours and analyzed by RNA-Seq.

first: Florian

last: Heyd


title: Epigenome-wide Association study of individuals conceived by Assisted Reproduction Technologies at birth and adulthood

status: Public on Jul 29 2019

city: Parkville

first: Boris

last: Novakovic

state: Victoria

address: Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road

country: Australia

institute: Murdoch Children's Research Institute

summary: Genome wide DNA methylation profiling of whole blood at birth (Guthrie blood spots) and adulthood of individuals conceived by assisted reproductive technology (ART) and matched non-ART controls. The Illumina Infinium MethylationEPIC BeadChip was used to obtain DNA methylation profiles across approximately 850,000 CpGs in guthrie cards and whole adult blood.

overall_design: Bisulphite converted DNA from the 440 samples were hybridised to the Illumina Infinium MethylationEPIC BeadChip.

first: Jane

last: Halliday

first: Richard

last: Saffery


title: Acidification of tumor: stromal boundaries drive transcriptome alterations associated with aggressive phenotypes

status: Public on May 29 2019

city: Cambridge

first: Dunaduan

last: Ma

state: Ma

address: 77 Massachusetts Ave

department: Koch Institute

institute: MIT

summary: We report RNA splicing changes in response to extracellular acidification

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: MDA-MB-231 and 4T1 mammary carcinoma cell lines were exposed to 48hrs of low pH conditions generated by changes in sodium bicarbonate concentrations.

first: Nazaninn

last: Rohani

first: Frank

middle: B

last: Gertler


title: Developmental switch within the bacterial cell cycle regulator CtrA

status: Public on Nov 25 2019

city: Geneva 4

first: Patrick

middle: H.

last: Viollier

address: Rue Michel Servet 1

department: Dept.  Microbiology and Molecular Medicine

country: Switzerland

institute: University of Geneva, Faculty of Medicine / CMU

summary: Many bacteria acquire dissemination and virulence traits in G1-phase. CtrA, an essential and conserved cell cycle transcriptional regulator identified in the dimorphic alpha-proteobacterium Caulobacter crescentus, mysteriously switches from activating promoters in late S-phase to a different set in G1-phase. We found that a core and highly conserved determinant in the DNA-binding domain (DBD) of CtrA governs this promoter switch and that it is also required for promoter reprogramming in stationary phase in response to a (p)ppGpp alarmone signal perceived by the RNA polymerase beta subunit. A simple side chain modification in one critical residue of this DBD confers opposing developmental phenotypes and transcriptional activities. This region is also central to understanding the developmental reprogramming in the obligate intracellular Rickettsiae where replicative cells develop into dispersal cells and a naturally occurring polymorphism in the rickettsial DBD resembles a mutation that drives CtrA towards activation of the dispersal (G1-phase) program in Caulobacter.

overall_design: Examination of CtrA whole genome binding/occupancy (ChIP-Seq) in WT Caulobacter crescentus and mutants

first: Marie

last: Delaby

first: Gaël

last: Panis


title: Novel role for the T-helper 17 signature cytokine IL-17: CD4 resistance to immune suppression

status: Public on Aug 26 2020

city: Iowa City

first: Nitin

last: Karandikar

state: Iowa

address: C673 General Hospital

department: Pathology

institute: University of Iowa

summary: Important immune regulatory mechanisms mediated by CD4+ and CD8+ T-cells keep untoward CD4+ T-cell responses in check. CD4+ T-helper 17 (Th17) cells, characterized by IL-17 production, play critical roles in the body’s response to infections and cancer and in the pathogenesis of autoimmune diseases such as multiple sclerosis, psoriasis, arthritis, IBD, among others. Here we demonstrate that human CD4+ T-cells cells exposed to a Th17-differentiating milieu are highly resistant to immune suppression by CD8+ T-cells, compared to control Th0 cells. This resistance is mediated, in part, through the action of IL-17A, IL-17F and IL-17AF heterodimer through their receptors (IL-17RA and IL-17RC) on CD4+ T-cells themselves, but not through their action on CD8+ T-cells or APC. We further show that IL-17 can directly act on non-Th17 effector CD4+ T-cells to induce suppressive resistance and this resistance can be reversed by blockade of IL-1, IL-6 or STAT3. These studies reveal a novel function for IL-17 cytokines in a CD4-intrinsic mechanism of immune resistance. The pathways induced in this process may serve as a critical target for intensive investigation and therapeutic intervention.

overall_design: Ex vivo-purified bulk CD4+CD25- T-cells isolated from 3 healthy donors and sequenced after in vitro for 48 hours in the presence of media alone (control), or 10 ng/ml of IL-17A, IL-17F or IL-17AF

first: Michael

middle: P

last: Crawford

first: Sushmita

last: Sinha

first: Pranav

last: Renavikar

first: Nicholas

last: Borcherding

middle: J


title: Moderate maternal folic acid supplementation ameliorates adverse embryonic and epigenetic outcomes associated with assisted reproduction

status: Public on May 15 2019

city: Montreal

first: Jacquetta

last: Trasler

state: Quebec

address: 1001 Decarie Boul, Block E, ES1.4380

department: Pharmacology & Therapeutics; Human Genetics

institute: McGill University

type: Methylation profiling by high throughput sequencing

summary:
STUDY QUESTION:  Could clinically-relevant moderate and/or high dose maternal folic acid supplementation prevent aberrant developmental and epigenetic outcomes associated with assisted reproductive technologies (ART)?

SUMMARY ANSWER:  Our results demonstrate dose-dependent and sex-specific effects of folic acid supplementation in ART and provide evidence that moderate dose supplements may be optimal for both sexes.

WHAT IS KNOWN ALREADY:  Children conceived using ART are at an increased risk for growth and genomic imprinting disorders, often associated with DNA methylation defects. Folic acid supplementation is recommended during pregnancy to prevent adverse offspring outcomes; however, the effects of folic acid supplementation in ART remain unclear.

STUDY DESIGN, SIZE, DURATION:  Outbred female mice were fed 3 folic-acid supplemented diets, control (rodent daily recommended intake or DRI; CD), moderate (4-fold DRI; 4FASD) or high (10-fold DRI; 10FASD) dose, for six weeks prior to ART and throughout gestation. Mouse ART involved a combination of superovulation, in vitro fertilization, embryo culture and embryo transfer.

PARTICIPANTS/MATERIALS, SETTING, METHODS:  Upon collection of midgestation embryos and placentas (n=74-99 embryos/group), all embryos were assessed for developmental delay and gross morphological abnormalities. Embryos and placentas were also examined at the epigenetic level. We assessed methylation at four imprinted genes (Snrpn, Kcnq1ot1, Peg1, and H19) in matched midgestation embryos and placentas (n=31-32/group) using bisulfite pyrosequencing. In addition, we examined genome-wide DNA methylation patterns in midgestation placentas (n=6 normal placentas per sex/group) and embryos (n=6 normal female embryos/group; n=3 delayed female embryos/group) using reduced representation bisulfite sequencing.

MAIN RESULTS AND THE ROLE OF CHANCE:  Moderate, but not high dose supplementation, was associated with a decrease in the proportion of developmentally delayed embryos. Although moderate dose folic acid supplementation reduced DNA methylation variance at certain imprinted genes in embryonic and placental tissues, high dose supplementation exacerbated the negative effects of ART at imprinted loci. Furthermore, folic acid supplements resolved female-biased aberrant imprinted gene methylation. Supplementation was more effective at correcting ART-induced genome-wide methylation defects in male versus female placentas; however, folic acid supplementation also led to additional methylation perturbations which were far more pronounced in males.

LIMITATIONS, REASONS FOR CAUTION:  Although the combination of mouse ARTs utilized in this study consisted of techniques commonly used in human fertility clinics, there may be species differences. Therefore, human studies, designed to determine the optimal levels of folic acid supplementation for ART pregnancies, and taking into account fetal sex, are warranted.

WIDER IMPLICATIONS OF THE FINDINGS:  Taken together, our findings support moderation in the dose of folic acid supplements taken during ART.

overall_design: 84 samples in total; Embryos/Placenta derived following ART or Natural matings; n=3-6 per group; comparison of treatment (4x or 10x folic acid supplemented) vs. CD for ART samples; comparison of Natural Matings (on CD) vs. ART (on CD); comparisons done within the same sex of embryo/placenta

first: Sophia

last: Rahimi

first: Josée

last: Martel

first: Gurbet

last: Karahan

first: Camille

last: Angle

first: Nathalie

last: Behan

first: Donovan

last: Chan

first: Amanda

last: MacFarlane

middle: M


title: Thyroid hormone regulates distinct paths to maturation in pigment cell lineages

status: Public on May 14 2019

city: Charlottesville

first: David

last: Parichy

state: VA

address: 409 McCormick Road, Department of Biology, PLSB 339

department: Biology

institute: University of Virginia

summary: Early and post-embryonic neural crest-derived lineages in the zebrafish trunk in response to thyroid hormone modulation

overall_design: Single-cell RNA-seq experiments were performed on the 10X Genomics platform from FAC sorted, Sox10:CRE positive cells from 5dpf and post-embryonic zebrafish trunks with and without thyroid hormone.

first: L

last: Saunders

first: D

first: C

last: Trapnell


title: Single-cell RNA-sequencing of spinocerebellar tract neuron populations in cervical and thoracic sections of mouse spinal cord

status: Public on Apr 26 2019

city: New York

first: Vilas

last: Menon

state: NY

department: Neurology

institute: Columbia University Medical Center

summary: We profiled single cells from mouse spinocerebellar tract neurons (SCTNs) in cervical and thoracic sections of mouse spinal cord, as defined by retrograde projection labeling. For each sample, SCTNs were labeled by injecting CTB (Alexa555 conjugated form, 1µg/µl in PBS) into  the cerebellum using NanojetII at P4 and examined at P6-P7.  Labeled SCTNs were collected manually from 150-300µm transverse spinal cord, and slices were generated using a razor blade. Labelled cells were manually collected from each injection experiment and then profiled using a plate-based SMART-SCRB protocol (see Baek et al. 2019 for detailed methods)

overall_design:
We collected four populations of spinal cord cells: 3 control populations comprising Rostral Cervical (CRC), Caudal Cervical (CCC), Rostral Thoracic (CRT), and 1 population of rostral thoracic cells from the Hocx9-/- mutant (MRT).  In addition, each plate contains wells with ERCC spike-in controls only (ERCC) and wells with a control mRNA spike-in (qRNA), which contains 10 picograms of whole mouse brain mRNA. Each library was prepared using the SMART-SCRB protocol (see Baek et al. 2019 for details), and paired-end sequenced. Read 1 contains the cell barcode (nucleotides 2-9, see BCs_4x96well.csv file) and Unique Molecular Identifier (subsequent 10 nucleotides). Read 2 contains the transcript sequence, and was aligned to the mouse transcriptome (GRCm38) using the STAR aligner with default parameters. Quantification was carried out by collapsing reads with the same UMI from the same cell mapping to the same gene, thus generating transcript counts tables.

The 'all_sc_data_annotation_20180724.csv' contains the cluster identities assigned to each single-cell sample.

UPDATE: Prior to 2 May 2023, the design description above stated that the cell barcode was the first 8 nucleotides in Read 1. The barcodes are actually found in positions 2-9 of Read 1. This has now been corrected.

first: Myungin

last: Baek


title: Condensin II inactivation in interphase does not affect chromatin folding or gene expression

status: Public on May 05 2019

first: Nezar

last: Abdennur

state: MA

summary: Condensin complexes have been proposed to play a prominent role in interphase chromatin organization and control of gene expression. Here, we report that the deletion of the central condensin II kleisin subunit Ncaph2 in differentiated mouse hepatocytes does not lead to significant changes in chromosome organization or in gene expression. Both observations challenge current views that implicate condensin in interphase chromosomal domain formation and in enhancer-promoter interactions. Instead, we suggest that the previously reported effects of condensin perturbation may result from their structural role during mitosis, which might indirectly impact the re-establishment of interphase chromosomal architecture after cell division.

overall_design: This submission contains 2 biological replicates of Hi-C (TCC) , 4 replicates of RNA-seq from hepatocytes isolated from Ncaph2-/- mice.

first: Wibke

last: Schwarzer

first: Aleksandra

last: Pekowska

first: Indra

last: Shaltiel

first: Wolfgang

last: Huber

first: Christian

last: Haering

first: Leonid

last: Mirny

first: Francois

last: Spitz


title: Transcriptome Analysis Reveals Distinct Responses to Physiologic versus Toxic Manganese Exposure in Human Neuroblastoma Cells

status: Public on Jun 20 2019

city: Atlanta

first: Dean

middle: P.

last: Jones

address: 615 Michael Street Room 205

department: Department of Medicine

institute: Emory University

summary: We report the application of RNA-Seq analysis to determine the transcriptional responses to Mn dose, ranging from physiological to toxicological levels in human SH-SY5Y neuroblastoma cells. We find that Mn dose showed widespread effects in abundance of protein coding genes for metabolism of reactive oxygen species, energy sensing, glycolysis, protein homeostasis including the unfolded protein response and transcriptional regulation. Adaptive responses at physiological Mn concentration-10 μM Mn for 5 h, a concentration that did not result in cell death after 24 h increased abundance of differentially expressed genes (DEGs) in the protein secretion pathway that function in protein trafficking and cellular homeostasis.These include BET1 (Golgi vesicular membrane trafficking protein), ADAM10 (ADAM metallopeptidase domain 10) and ARFGAP3 (ADP-ribosylation factor GTPase activating protein 3). In contrast, 5 h exposure to 100 μM Mn, a concentration that caused cell death after 24 h, increased abundance of DEGs for components of the mitochondrial oxidative phosphorylation pathway. In conclusion, this study provides a framework  for Mn dose dependent exposure in a human in vitro cell culture model and provides a testable hypothesis for in vivo studies. Importantly, the transcriptome responses at toxic Mn dose demonstrated patterns observed with neurological diseases and suggest that differential functions of the secretory pathway and mitochondria could provide a basis to improve detection and management of adverse environmental and occupational Mn exposures.

overall_design: Examination of transcriptomic responses to Mn dose (0,1,5,10,50,100 μM MnCl2 for 5 h) in human SH-SY5Y neuroblastoma cells with three biological replicates per Mn treatment using Illumina HiSeq 2500.

first: Jolyn

last: Fernandes

first: Joshua

middle: D

last: Chandler

first: Loukia

middle: N

last: Lili

first: Karan

last: Uppal

first: Xin

last: Hu

first: Li

last: Hao

first: Young-Mi

last: Go


title: ATAC-Seq and ChIP-Seq studies in PLC-PRF cells

status: Public on Dec 13 2019

city: Tianjin

first: Heng

last: Zhang

address: 38 Rd.Tongyan

institute: Nankai University

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

overall_design: Refer to individual Series


title: Prenatal hypoxia exposure induced methylomic and transcriptomic alterations in rat hearts

status: Public on Apr 25 2019

city: Loma Linda

first: Charles

last: Wang

state: CA

address: 11021 Campus St

institute: Loma Linda University


title: Prenatal hypoxia exposure induced methylomic and transcriptomic alterations in rat hearts [BiSulfite-seq]

summary: Antenatal hypoxia has critial impacts on fetal heart development. The molecular mechanism of the antenaltal hypoxia effect on the heart development is still unknown. We performed DNA methylome and transcriptome analyses of antenatal hypoxia induced rat fetal and adult offspring hearts to understand the hypoxia-mediated epigenomic programming in the heart development. Heart tissue from fetal (E21) and adult rat (5 months old) were collected. mRNA and genomic DNA methylation profiles of the heart tissue were generated by RNAseq and reduced representation bisulfite seuqencing (RRBS) techniques. We found 323 and 112 differential expressed genes between control and hypoxia groups in the fetal and adult hearts, respectively. Meanwhile, 2828 and 2193 differential methylated regions were identified in the fetal and adult hearts. Furthermore, opposite gobal DNA methylation pattern changes in transcription start site regions (TSS ± 1kb) were observed between fetal and adult hearts. Combining transcriptome, data indicates a significant difference in the responding genes and pathways between fetal and adult hearts in responding to the antenatal hypoxia. Our study provides an initial framework and new insights into fetal hypoxia-mediated epigenetic programming of pro-inflammatory phenotype in the heart development, linking antenatal stress, and developmental programming of heart vulnerability to disease later in life.

overall_design: Fetal (E21) heart tissues from control (n=3) and hypoxia (n=3) Sprague-Dawley (SD) rats were collected for methylome and transcriptome analysis. Adult male (5 months old) heart tissues from control (n=6) and hypoxia (n=6) SD rats were obtained for methylome analysis. Adult male and female (5 months old) heart tissues from control (n=5 per gender) and hypoxia (n=5 per gender ) SD rats were used for transcriptome analysis.

last: Chen

first: Lubo


title: Prenatal hypoxia exposure induced methylomic and transcriptomic alterations in rat hearts [RNA-seq]

overall_design: Fetal (E21) heart tissues from control (n=3) and hypoxia (n=3) Sprague-Dawley (SD) rats were collected for transcriptome analysis. Adult male and female (5 months old) heart tissues from control (n=5 per gender) and hypoxia (n=5 per gender ) SD rats were used for transcriptome analysis.


title: Nonhuman primate iPSCs and embryonic inner cell mass transcriptome

status: Public on Sep 30 2020

city: Atherton

first: Morteza

last: Roodgar

address: 26 Selby Ln

department: Genetics

institute: Stanford University

summary: Induced pluripotent stem cells (iPSCs) hold promise for generating personalized xenogenic organs via development of cross-species chimeric animals. However, whether human and other primate iPSCs are capable of establishing cross-species chimeras remains unknown. Recognizing the ethical concerns of cross-species chimerism using human iPSCs, we explored the capacity for cross-species chimerism between distinct, non-human primates. Injection of either pig-tailed macaque iPSCs or chimpanzee iPSCs into the rhesus macaque blastocyst embryos demonstrated that these cells survive, proliferate, and integrate near the rhesus inner cell mass (ICM). Ectopic expression of BCL2 in pig-tailed and chimpanzee iPSCs greatly improved the success rate of establishing cross-species blastocyst chimerism. This study represents the first successful cross-species blastocyst chimerism between distinct, non-human primate species, and highlights critical factors that may be necessary to unlock the broad potential of primate iPSCs to form cross-species chimeras, with diverse applications for basic research and translational medicine.

sample_organism:
Macaca mulatta
Macaca nemestrina
Pan troglodytes
Homo sapiens
Mus musculus

overall_design: A total of 29 samples were used in this study which includes biological and technical replicates from each of the study species. The RNA-seq library preperation and sequencing for all the samples/species were conducted at the same time to minimize potential batch effect. We compared transcriptome profiles of chimpanzee iPSCs, pig-tailed macaque iPSCs, rhesus macaque iPSCs and ESCs with the transcriptome of rhesus macaque and mouse embryonic inner cell mass.


title: Transcriptomic analysis of mice treated with Lactobacillus rhamnosus CNCM i-3690 and different mutants and variants generated from this strain

status: Public on Apr 17 2019

city: Jouy en Josas

first: Rebeca

last: Martin Rosique

state: Yvelines

address: Domaine de Vilvert bat 440 R-2

department: MICALIS

country: France

institute: INRA

summary: we have performed transcriptomic analysis of colonic samples of mice  challenged with DNBS twice in a chronic model of inflammation and treated with CNCM -I3690 strain and several mutants and variants generated from it. colonic transcriptome analysis at the endpoint revealed that CNCM I 3690 enhances the expression of genes related to healthy gut permeability, motility (Ghrelin (GHR)), and absorption (guanylate cyclase activator 2B (Guca 2b)); cell proliferation (amino acid transporter SLC7A7); and protective functions (endogenous protease inhibitor kazal-type4). Focusing on inflammation, both GHR and Guca 2B have been found to act as anti-inflammatory, protecting the gut against a wide range of threats. Besides, CNCM I-3690 also up regulated TRAF-interaction protein with a forkhead-associated domain (TIFA), an important signaling adaptor in the NF-κβ pathway.

overall_design: To further analyze the mechanisms of action of CNCM I-3690 in a murine model of gut inflammation we have performed transcriptomic analysis of colonic samples of mice  challenged with DNBS and treated with this strain and several mutants and variants generated from it

last: Martin

first: Philippe

last: Langella

first: Tamara

last: Smokvina


title: Transcriptome profiling of the early response to   volumetric muscle loss repair strategies

status: Public on Jan 31 2019

city: Fayetteville

first: Kevin

last: Roberts

state: AR

address: 700 W Research Ctr Blvd

department: Cell and Molecular Biology Program

institute: University of Arkansas

summary: We report the transcriptomic profiles of rat tibialis anterior following VML injury and three repair strategies in the early period following injury

overall_design: Transcriptome profiles of rat tibialis anterior following VML injury and three repair strategies generated at three and fourteen days post-injury.

first: Jeffrey

middle: C

last: Wolchok


title: Genome-wide fetalization of enhancer architecture in heart disease [RNA-Seq]

status: Public on Apr 02 2019

city: Berkeley

first: Axel

last: Visel

address: 1 Cyclotron Road

institute: Lawrence Berkeley National Laboratory

summary: Heart disease is associated with re-expression of key transcription factors normally active only during prenatal development of the heart.  However, the impact of this reactivation on the genome-wide regulatory landscape in heart disease has remained obscure.  Here we show that pervasive epigenomic changes occur in heart disease, with thousands of regulatory sequences reacquiring fetal-like chromatin signatures.  We used RNA-seq and ChIP-seq targeting a histone modification associated with active transcriptional enhancers to generate genome-wide enhancer maps from left ventricle tissue from 18 healthy controls and 18 individuals with idiopathic dilated cardiomyopathy (DCM).  Healthy individuals had a highly reproducible epigenomic landscape, consisting of more than 31,000 predicted heart enhancers.  In contrast, we observed reproducible disease-associated gains or losses of activity at more than 7,500 predicted heart enhancers.  Next, we profiled human fetal heart tissue by ChIP-seq and RNA-seq.  Comparison with adult tissues revealed that the heart disease epigenome and transcriptome both shift toward a fetal-like state, with more than 3,400 individual enhancers sharing fetal regulatory properties.  Our results demonstrate widespread epigenomic changes in DCM, and we provide a comprehensive data resource (http://heart.lbl.gov) for the mechanistic exploration of heart disease etiology.

overall_design: Total RNA-seq of adult left ventricle tissue from healthy hearts, adult explanted hearts with ideopathic dilated cardiomyopathy, and embryonic/fetal hearts

first: Cailyn

last: Spurrell

first: Iros

last: Barozzi

first: Yoko

last: Yuzawa

first: Sarah

last: Afzal

first: Brandon

last: Mannion

first: Jennifer

last: Akiyama

first: Veena

first: Stella

last: Tran

first: Ingrid

last: Plajzer-Frick

first: Catherine

last: Pickle

first: Momoe

last: Kato

first: Elizabeth

last: Lee

first: Thomas

last: Cappola

first: Michael

last: Morley

first: Ken

last: Margulies

first: Steve

last: Lisgo

first: Diane

last: Dickel

first: Len

last: Pennacchio


title: Innate-like activation of mucosal-associated invariant T cells in mycobacterial infection

status: Public on Mar 31 2019

city: Cincinnati

first: Shouxiong

last: Huang

state: OH

address: 160 Panzeca Way

department: Environmental Health

institute: University of Cincinnati College of Medicine

summary: Gene expression of Va7.2+CD161+CD4-CD8+MAIT cells from two subsets (CD69+CD26++ and CD69-CD26+/-).

overall_design: Human blood mononuclear cells were magnetically sorted to enrich MAIT cells, which were stimulated with M. bovis-incubated MR1-expressing cells or anti-CD3 antibody and further sorted to CD69+CD26++ and CD69-CD26+/- subsets from Va7.2+CD161+CD4-CD8+ -gated MAIT cells.

first: Manju

last: Sharma

first: Liang

last: Niu

first: Xiang

last: Zhang


title: Total RNA profiles in response to four tyrosine kinase inhibitors in human induced pluripotent stem cell-derived cardiomyocytes

status: Public on Mar 23 2019

city: Boston

first: Robert

middle: Patrick

last: Sheehan

state: Massachusetts

address: 200 Longwood Ave

department: Systems Biology

institute: Harvard Medical School

summary: To define molecular markers of tyrosine kinase inhibitor-induced cardiotoxicity, we measured transcriptome changes in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) treated with one of four tyrosine kinase inhibitors (Erlotinib, Lapatinib, Sorafenib, or Sunitinib) displaying a range of mild to severe cardiotoxicity or a vehicle-only control (DMSO). Gene expression changes were assessed at the cell population level using total RNA-seq, which measured levels of both mRNAs and non-coding RNAs. hiPSC-CMs used in this study were the Cor.4U cells purchased from Ncardia.

overall_design: hiPSC-CMs were treated with each TKI (Erlotinib, Lapatinib, Sorafenib or Sunitinib) at three doses (1, 3 and 10 µM) for 24 hours and the intermediate dose (3 µM) for an additional three time points (6h, 72h and 168h). hiPSC-CMs were also treated with the DMSO vehicle-only control at four time points (6h, 24h, 72h and 168h). Each treatment condition had three biological replicates, collected from three independent experiments using three different lots of hiPSC-CMs. Total RNA was collected from all these samples.

first: Huan

last: Wang

first: Sarah

last: Boswell

first: Peter

middle: K

last: Sorger


title: Genome-wide fetalization of enhancer architecture in heart disease [ChIP-Seq]

first: Axel

last: Visel

overall_design: H3K27ac ChIP-seq of adult left ventricle tissue from healthy hearts, adult explanted hearts with ideopathic dilated cardiomyopathy, and embryonic/fetal hearts

first: Cailyn

last: Spurrell

first: Iros

last: Barozzi

first: Yoko

last: Yuzawa

last: Afzal

first: Brandon

last: Mannion

first: Jennifer

last: Akiyama

first: Veena

first: Stella

last: Tran

first: Ingrid

last: Plajzer-Frick

first: Catherine

last: Pickle


title: Epigenetic profiling of Fetal Alcohol Spectrum Disorder (FASD) Discovery

status: Public on Mar 18 2019

city: Amsterdam

last: Henneman

state: Noord Holland

address: Meibergdreef 9

department: Clinical Genetics

country: Netherlands

institute: Academic Medical Center Amsterdam

summary: Genome wide DNA methylation profiling of FASD patients versus healthy unexposed controls. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 485,000 CpGs in peripheral blood samples. Samples included 64 healthy controls and 39 FASD patients.

overall_design: Bisulfite converted DNA from the 103 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip

first: J

last: Cobben

first: I

last: Krzyzewska

first: A

last: Venema

last: Mul

last: Polstra

middle: V

last: Postma

first: R

last: Smigiel

first: K

last: Pesz

last: Niklinski

first: M

last: Chomczyk

first: P

last: Mannens


title: RNA_Seq-based global transcriptome analysis of S. pneumoniae mutants lacking PhpP and StkP

status: Public on Apr 13 2019

city: Columbus

first: Vijay

last: Pancholi

address: 420W 12th Ave, TMRF-288

institute: Ohio State University

summary: We report the mRNA expression profile of Streptococcus pneumoniae Type 2 D39 strain-derived mutant lacking the phpP gene encoding eukaryote-type ser/thr phosphatase and the stkP gene  encoding Ser/Thr protein kinase.

overall_design: Measuring transcriptome profiling in D39DphpP mutants vs D39-WT pneumococcus wild-type strain


title: Epigenetic profiling of Fetal Alcohol Spectrum Disorder (FASD)

first: Peter


title: RNA-seq of Arabian horses

status: Public on Jan 23 2019

city: East Lansing

first: Stephanie

last: Valberg

state: MI

address: 736 Wilson Road, D202

department: LACS

institute: Michigan State University

summary: Report transcritpome analysis of Arabian horses before and after exercise

overall_design: Looking at muscle RNA expression in horses at 2 different conditions, before and after exercise


title: RNA partitioning into stress granules is independent of G3BP

status: Public on Jan 30 2019

city: Boulder

first: Roy

middle: Robert

last: Parker

state: CO

address: 3415 Colorado Ave

department: Chemistry and Biochemistry

institute: University of Colorado at Boulder

summary: Stress granules (SGs) are stress induced RNA-protein assemblies formed from untranslating mRNPs.  Mammalian SGs are non-uniform and contain “cores”, which are stable in lysates and heterogenous in protein composition.  The interactions defining RNA recruitment into SGs, and whether the RNA composition varies between different cores remains unclear.  Herein, we determine the SG transcriptome through purification of both PABPC1 and G3BP SG cores during both arsenite and sorbitol stress.  We observe that similar RNAs are recruited to SGs independent of the protein used for core purification, suggesting individual RNA-binding proteins (RBPs) may play a limited role in defining the SG transcriptome. Analysis of the sorbitol-induced SG transcriptome reveals G3BP1/2 has little effect on RNAs recruited to SGs suggesting RNAs localize to SGs independent of individual RBPs.  Taken together, we suggest that partitioning of RNAs to SGs is independent of at least some proteins, consistent with SGs forming through intermolecular RNA-RNA interactions.

overall_design: Stress granule core RNA was purified from U-2 OS cells via differential centrifugation and immunoprecipitation using a PABP antibody or GFP antibody (in the case of GFP-G3BP U-2OS cells).  In addition, we collected total cytoplasmic RNA (nuclei were spun out) from stressed and unstressed cells.  Stressed cells were either stressed with .5mM arsenite or .5M sorbitol.

first: Tyler

last: Matheny


title: IRF5 regulates unique subset of genes in mouse dendritic cells during West Nile virus infection (BMM_RNA-Seq)

status: Public on Dec 14 2018

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

summary: Using integrative bioinformatics analyses, we identified new IRF5 primary target genes in mouse DCs in response to virus infection. This study provides novel insights into the distinct and unique innate immune and immune gene regulatory program directed by IRF5.

overall_design: Total RNA-seq profiling of mouse bone marrow-derived macrophages infected with WNV and mock infection at 6h and 12h

first: Kwan

middle: T

last: Chow

first: Connor

last: Driscoll

first: Yueh-Ming

last: Loo

first: Megan

last: Knoll

last: Gale Jr.


title: IRF5 regulates unique subset of genes in mouse dendritic cells during West Nile virus infection (ChIP-Seq)

overall_design: ChIP-exo profiling of mouse bone marrow-derived dendritic cells infected with WNV and mock infection at 6h and 12h


title: IRF5 regulates unique subset of genes in mouse dendritic cells during West Nile virus infection


title: Nuclear receptor corepressor (NCOR) and HDAC3 in hypothalamus [RNA-Seq]

status: Public on Oct 29 2018

city: Houston

first: Ying-Wooi

last: Wan

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: We determined genomic binding of HDAC3 in mouse hypothalamus by ChIP-seq, and identified target genes of the NCOR/HDAC3 complex in hypothalamus of NS-DADm (mutated deacetylase activation domain in NCORs) mice by RNA-seq.

overall_design: Hypothalamus from 7-8 mice were pooled for one ChIP. Multiple independent ChIP samples and Input samples were pooled to generate 1 ChIP library and 1 input library followed by sequencing. For RNA-seq, total RNAs from hypothalamus of 3 WT mice and 3 NS-DADm mice were separately prepared to generate 6 libraries, followed by sequencing


title: Nuclear receptor corepressor (NCOR) and HDAC3 in hypothalamus [ChIP-Seq]

first: Zheng

last: Sun

first: Hari

last: Yalamanchili


title: Nuclear receptor corepressor (NCOR) and HDAC3 in hypothalamus

overall_design: Refer to individual Series


title: IRF5 regulates unique subset of genes in mouse dendritic cells during West Nile virus infection (RNA-Seq)

overall_design: Total RNA-seq profiling of mouse bone marrow-derived dendritic cells infected with WNV and mock infection at 6h, 12h, and 24h


title: Genetics, sex and life experience influence DNA methylation in the mouse

status: Public on Oct 24 2018

city: Research Triangle Park

first: Paul

last: Wade

state: NC

address: 111 TW Alexander Drive

department: Laboratory of Molecular Carcinogenesis

institute: NIEHS

summary: Methylation of DNA is an essential epigenetic mark in mammals, intimately involved in gene regulation. The extent to which genetics, sex, and life experience influence genomic DNA methylation patterns are matters of intense current interest.    We addressed this issue by intercrossing inbred mouse strains and analyzing DNA methylation at the base-pair level across the genome in somatic tissue from parents and from age-matched offspring of multiple families.  In comparison across genotype, tens of thousands of differentially methylated CpG residues and thousands of differentially methylated regions were detected.  Differential methylation at these loci was preserved on parental alleles in offspring, suggesting that CpG methylation is a very stable epigenetic mark largely preserved across generation, correlating with DNA sequence. In comparison of autosomal DNA methylation patterns across sex, thousands of differentially methylated CpG residues and hundreds of differentially methylated regions were detected, consistent with known biological parameters that differ between males and females.  Finally, comparison of individual groups of animals within our study revealed a CpG methylation pattern that likely results from pregnancy and/or lactation that was restricted to female animals who had borne offspring, signifying that CpG methylation may provide a record of major life events.  Collectively, our results demonstrate the stability of CpG methylation across generation, clarify the interplay of epigenetics with genetics and sex, and suggest that CpG methylation may serve as an epigenetic record of life events.

overall_design: Methylation profiles of C57BL/6N mice, C3H/HeN mice, and their offspring were determined by whole-genome bisulfite sequencing.

first: Sara

last: Grimm

first: Motoki

last: Takaku


title: Coronary artery disease genes SMAD3 and TCF21 promote opposing interactive genetic programs that regulate smooth muscle cell differentiation and disease risk [RNA-seq]

status: Public on Sep 11 2018

city: Stanford

first: Thomas

last: Quertermous

address: 300 Pasteur Drive

department: Medicine Cardiology

summary:
Although numerous genetic loci have been associated with coronary artery disease (CAD) with genome wide association studies (GWAS), efforts are needed to identify the causal genes in these loci and link them into fundamental signaling pathways. Toward that end, experiments reported here extend our investigation of the disease mechanism of CAD associated gene SMAD3, a central transcriptional intermediate in the TGFb pathway, investigating its role in smooth muscle biology. In vitro studies in human coronary artery smooth muscle cells (HCASMC) revealed that SMAD3 modulates cell state decisions in this cell type, promoting expression of differentiation marker genes and migration while inhibiting proliferation. RNA and chromatin immunoprecipitation sequencing (ChIPseq) studies in HCASMC identified downstream genes that reside in pathways which mediate vascular development and disease processes, including those related to atherosclerosis pathophysiology, expanding understanding of the TGFb canonical pathway in this cell type. ChIPseq studies also found colocalization of SMAD3 binding in loci targeted by TCF21, a CAD associated transcription factor that has been shown to produce a CAD protective de-differentiation program in HCASMC. In loci where these factors are juxtaposed on DNA, SMAD3 binding was anti-correlated with TCF21, and increased in cells depleted of TCF21, as shown by ChIPseq and ChIP experiments. Further, reporter gene studies revealed that while SMAD3 increased transcription at a SERPINE1 enhancer, and this effect was blocked by TCF21. Together, these data suggest that SMAD3 regulation of gene expression is modulated by TCF21, through independent regulation of jointly occupied genes and through epigenetic and possibly direct protein-protein interactions. Finally, eQTL studies in HCASMC indicated that SMAD3 expression is directly associated with increased disease risk, opposing the known protective effect of TCF21. We propose that the pro-differentiation function of SMAD3 inhibits HCASMC dedifferentiation of these cells as they respond to vascular stresses and expand and migrate to stabilize the plaque, and that SMAD3 function is directly opposed at the transcriptional level by the disease protective expression of TCF21, which promotes dedifferentiation and phenotypic modulation.
Methods: Primary human coronary artery smooth muscle cells (HCASMCs) were purchased from three different manufacturers, PromoCell, Lonza and Cell Applications at passage 2 and were cultured in smooth muscle cell basal media along with hEGF, insulin, hFGF-B and fetal bovine serum (FBS) (Lonza # CC-3182) according to the manufacturer’s instructions. HCASMCs between passages 5-8 were used for all the experiments. SMAD3 (s8401 and s8402) silencer select siRNAs were purchased from Life Technologies. siRNA transfection was performed using Lipofectamine RNAiMAX (Life Technologies). For each well treated with the SMAD3 siRNA or scrambled control (Life technologies, #4390843), the final concentration was 20 nM. HCASMCs were seeded in 6 well plates and grown to 75% confluence before siRNA transfection. HCASMCs were transfected with the SMAD3 siRNA or scrambled control for 12 hours and subsequently collected and processed for RNA isolation after 48 hrs of transfection using the RNeasy kit (Qiagen). Three experimental and three control samples were generated and sequenced on a HiSeq 4000 machine, 125 bp paired end reads. Reads were processed using rnaSeqFPro, a workflow for full processing of RNASeq data starting from fastq files. In brief, the quality control was performed using FastQC, mapping to the human genome hg19 was performed using STAR second pass mapping to increase the percentage of mapped reads, and counting was done with featureCounts using GENCODE gtf annotation. Next, rnaSeqFPro performed differential analysis using DESeq2, conducted principal component analysis and hierarchical clustering using standard R functions, plotPCA and heatmap.2 and generated graphs using gglot2. DESeq2 gave 493 differentially expressed (DE) genes (FDR < 0.05).

overall_design: Human coronary artery smooth muscle cells were grown in culture in the presence of serum. Three control replicates and three SMAD3 siRNA knockdown replicates were studies, RNA was extracted, libraires prepared, and sequenced on a HiSeq 4000 machine.

first: Dharini

last: Iyer

first: Milos

last: Pjanic

first: Quanyi

last: Zhao


title: Transcriptome profiles of female and male mouse liver

status: Public on Oct 25 2018

summary: Sexual dimorphism of gene expression is commonly observed in mammalian tissues, including liver. To assess sexual dimorphisms in gene expression, we profiled the transcriptome of liver tissue from 20-week old male and female mice of the C57BL/6N (B6) and C3H/HeN (C3) inbred mouse strains using RNA-seq. These two inbred mouse strains exhibit phenotypic differences in liver biology, as they are at opposite ends of the spectrum of spontaneous hepatocellular carcinoma incidence; C3 mice are highly susceptible to develop spontaneous liver tumors as a function of age, while B6 mice are extremely resistant. Overall, these datasets provide insight into the underlying gene expression patterns that should be considered when assessing sex differences in mouse liver.

overall_design: Transcriptome profiles of adult female and male liver tissues from C57BL/6N and C3H/HeN mice, using RNA-seq


title: Transcriptome analysis using RNA sequencing conducted for wild type (Col-0) and ahl10-1 mutant under control conditions and after 96 h at moderate low water potential (-0.7 MPa)

status: Public on Jul 20 2018

city: Taipei City

last: Verslues

address: No.128, Sec.2, Academia Rd., Nangang Dist.

department: Institute of Plant and Microbial Biology

institute: Academia Sinica

summary: RNA sequencing was used to identify genes differentially expressed (DEG) in ahl10-1 mutant compared to Col-0 wild type. Two treatments were analyzed for each genotype: unstressed control and a 96 hour low water potential (-0.7 MPa) treatment. P<0.05 and fold change ≥ 1.25 used as cut off value for DEG. Approximately 2000-3000 genes were found to be significantly up and down-regulated in the wild type stress versus control treatment using . In control treated seedlings, 10 or less than 10 genes are up and down-regulated in ahl10-1 mutant. In the stress treatment, ahl10-1 has 19 and 42 genes that are up and downregulated, respectively.

overall_design: Wild type (Col-0) and ahl10-1 Arabidopsis thaliana seedlings were germinated on agar plates and after seven days of growth, seedlings were transferred either to fresh plates of control media or to moderate severity low water potential (-0.7 MPa) imposed using agar plates of the control media infiltrated with PEG-8000.  Samples were collected 96 h after transfer (Control and stress treatments). Three independent biological experiments and mRNA extractions were performed for each genotype/treatment. After quality check and quantitation, the samples were used for sequencing

first: Min

last: Wong


title: Effect of Nkx2.5 mutation on gene expression profiles of mouse embryonic stem cells undergoing cardiac differentiation.

status: Public on Dec 31 2017

city: Ottawa

first: Alexandre

last: Blais

state: ON

address: 451 Smyth Road

institute: University of Ottawa

summary: The purpose of this study was to determine the effect of Nkx2.5 mutation (R141C) on gene expression in mouse embryonic stem cells during their differentiation into cardiac progenitors.

overall_design: Mouse embryonic stem cells (wild-type or heterozygous for the Nkx25-R141C mutation) were analyzed before or after their differentiation into cardiac progenitors. Two biological replicates of each sample were analyzed.

first: Abeer

last: Zakariyah

first: Ellias

last: Horner

first: Ilona

last: Skerjanc


title: Identifying urinary RNA as non-invasive biomarkers for progression of chronic kidney disease

status: Public on Oct 31 2018

city: Ann Arbor

first: Markus

last: Bitzer

address: 1500 E Medical Center Dr SPC 5361

institute: University of Michigan

type: Non-coding RNA profiling by high throughput sequencing

summary: To identify urinary RNA as non-invasive biomarkers for progression of chronic kidney disease

overall_design: Urine samples from patients with nephrotic syndrome due to different types of glomerular diseases and stages of kidney disease. No controls.

last: Tuschl

first: Jian

last: Shi

first: Klaas

last: Max

first: Kimberly

last: Bogardus

first: Anuoluwapo

last: Sopeyin


title: Genome-wide mapping of binding sites of the MADS domain protein FRUITFULL in Arabidopis thaliana

status: Public on Feb 13 2018

city: Berlin

first: Dijun

last: Chen

address: Philippstr. 13 (House 22)

department: Plant Cell and Molecular Biology

institute: Humboldt University

summary: FUL has a dual role in regulating floral transition and fruit development. We used ChIP-seq to map and compare the FUL binding events in the two different tissues.

overall_design: We used a pFUL:FUL-GFP line to conduct chromatin immuno-precipitation experiments with GFP-specific antibodies sampling two different tissue types, inflorescence meristems and pistils/siliques. The IP was followed by library preparation and deep-sequencing (ChIP-seq) to determine the FUL binding sites on a genome-wide scale. Inflorescence meristems were harvested from 4-5 weeks old 35S:AP1-GR ap1 cal pFUL:FUL-GFP lines, while stage 12-16 pistils/siliques were harvested from ful-1 pFUL:FUL-GFP lines. The tissue was fixed for 15-30’ and the immunoprecipitation was performed according to Kaufmann et al., 2010 (doi: 10.1038/ nprot.2009.244.). Experiments were done in two biological replicates with the according input sample as control.

first: Hilda

last: van Mourik

first: Jose

last: Muiño

first: Cezary

last: Smaczniak

first: Marian

last: Bemer

first: Gerco

last: Angenent

first: Kerstin

last: Kaufmann


title: Genome-wide maps of chromatin state in naïve CD4+ T cells, WT/EZH2-null TFH and TH1 cells

status: Public on Dec 31 2018

city: Chicago

first: Jun

last: Huang

state: IL

address: Eckhardt, 5640 S Ellis Ave

department: Institute for Molecular Engineering

institute: University of Chicago

summary: ATAC-Seq experiments were performed to elucidate the chromatin state changes among naïve CD4+ T cells, WT follicular helper T (TFH) cells and WT type 1 helper T (TH1) cells Day2 (D2), Day5 (D5), Day8 (D8) post-LCMV-Armstrong infection, as well as EZH2-null (KO) TFH and TH1 at Day8 post-LCMV-infection. The analysis suggested stringent lineage-specific mode of chromatin accessibility in each group, indicating chromatin remodeling is tightly associated with TFH versus TH1 lineage differentiation in response to acute viral infection. Furthermore, the comparison between wild-type and EZH2-null TFH cells showed that less-opening state of certain chromatin accessible region in TFH-differentiation associated genes in the formers, suggesting EZH2 led to permissive chromatin accessibility primarily at specific regions of TFH-associated genes. H3K27me3-ChIP-seq was performed in WT TFH and TH1 cells to confirm the deposition of the histone marks at those loci.

overall_design: SMARTA TFH and TH1 cells at D2, D5, D8 post-LCMV-Armstrong infection and EZH2-null TFH and TH1 cells at day 8-post LCMV Armstrong infection, and naïve CD4+ T cells were sorted (2 or 3 samples per group, each sample was pooled from at least 5 mice). The ATAC-Seq libraries of the sorted cells were then prepared by using the Nextera DNA Sample Preparation Kit (FC-121-1030, Illumina), followed by next-generation sequencing. H3K27me3-ChIP-seq was also performed on D3 post-LCMV-Armstrong infection SMARTA TFH and TH1 cells, as well as CD4+ Naive T cells.

first: Daniel

last: Cao

first: Xinagyu


title: Genome-wide fetalization of enhancer architecture in heart disease

status: Public on Apr 02 2019

first: Axel

last: Visel

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


title: Coronary artery disease genes SMAD3 and TCF21 promote opposing interactive genetic programs that regulate smooth muscle cell differentiation and disease risk

first: Thomas

last: Quertermous

institute: Stanford University


title: GLIS3 is indispensable for TSH/TSHR-dependent thyroid hormone biosynthesis and follicular cell proliferation

status: Public on Aug 30 2017

city: RTP

first: Raja

last: Jothi

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

institute: National Institutes of Health

summary: Deficiency in Krüppel-like zinc finger transcription factor, GLI-Similar 3 (GLIS3) in humans is associated with the development of congenital hypothyroidism. However, the functions of GLIS3 in the thyroid gland and by what mechanism GLIS3-dysfunction causes hypothyroidism are unknown. In this study, we demonstrate that GLIS3 acts downstream of thyroid stimulating hormone (TSH)/TSHR and is indispensable for TSH/TSHR-mediated induction of thyroid follicular cell proliferation and thyroid hormone biosynthesis. ChIP-Seq and promoter analysis revealed that GLIS3 is critical for the transcriptional activation of several genes required for thyroid hormone biosynthesis, including the iodide transporters Nis and Pds, indicating that these genes are directly regulated by GLIS3. The repression of cell proliferation regulatory genes is due to the inhibition of TSH-mediated activation of the mTORC1/RPS6 pathway as well as direct transcriptional regulation of several cell division-related genes by GLIS3. Consequently, GLIS3-deficiency prevents the development of goiter as well as the induction of inflammatory and fibrotic genes during chronic elevation of circulating TSH. Our study identifies GLIS3 as a new and key regulator of TSH/TSHR-mediated thyroid hormone biosynthesis and proliferation of thyroid follicular cells, and uncovers a mechanism by which GLIS3-deficiency causes congenital hypothyroidism and prevents goiter development.

overall_design: Genome-wide mapping of endogenous GLIS3 in thyroid glands from GLIS3-EGFP mice fed a low-iodine diet (LID) for 2 weeks; RNA-Seq profiling of wild-type (WT) and Glis3KO thyroid glands from mice fed a LID.

first: Hong

last: Kang

first: Dhirendra

last: Kumar

first: Grace

last: Liao

first: Kristin

last: Lichti-Kaiser

first: Kevin

last: Gerrish

first: Xiao-Hui

first: Samuel

last: Refetoff

first: Anton

last: Jetten


title: A novel nucleoid-associated protein coordinates asymmetric chromosome replication and chromosome partitioning

status: Public on Nov 01 2017

city: Geneva 4

first: Patrick

last: Viollier

address: Rue Michel Servet 1

department: Dept.  Microbiology and Molecular Medicine

institute: University of Geneva, Faculty of Medicine / CMU

summary: We searched for regulators of chromosome replication in the cell cycle model Caulobacter crescentus and found a novel DNA-binding protein that selectively aids both the initiation of chromosome replication and the initial steps of chromosome partitioning. We identified and purified a protein (OpaA) that binds the chromosome origin of replication (Cori) and its higher-affinity binding to mutated Cori-DNA that increases Cori-plasmid replication in vivo. opaA gene expression is essential for normal growth and sufficient OpaA levels are required for the correct timing of chromosome replication. Whole genome ChIP-seq identified dynamic DNA-binding distributions for OpaA, with the strongest associations at the partitioning (parABS) locus near Cori. Using molecular-genetic and fluorescence microscopy experiments, we showed that OpaA also promotes the first steps of chromosome partitioning, the initial separation of the duplicated parS loci following Cori replication. This separation occurs before the parABS-dependent partitioning and it coincides with the poorly defined mechanism(s) that establishes chromosome asymmetry: C. crescentus chromosomes are partitioned to distinct cell-poles which develop into replicating and non-replicating cell-types. We propose that OpaA coordinates chromosome replication with asymmetry-establishing chromosome separation, noting that both roles are consistent with the phylogenetic restriction of opaA to asymmetrically dividing bacteria that avoid multi-fork replication.

overall_design: Examination of OpaA whole genome binding/occupency (ChIP-Seq) in WT (2 replicates) or ΔopaA supp+ Caulobacter crescentus backgrounds. In addition, we addressed OpaA whole genome peaks redistribution from WT growing cultures treated with rifampicin, novobiocin or chloremphenicol (3 ChIP-Seq samples).

first: James

last: Taylor

first: Gaël

last: Panis

middle: H

first: Gregory

last: Marczynski


title: Transcriptional regulation of adaptive NK and CD8 T cell responses [RNA-Seq]

status: Public on Dec 20 2017

city: Ithaca

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

institute: Cornell University

summary: Natural killer (NK) cells are innate lymphocytes that possess features of adaptive immunity such as clonal expansion and generation of long-lived memory. Here we look at transcriptional profiles of NK cells throughout several time points during MCMV infection, ex-vivo cytokine stimulation, and/or deficiency of key transcription factors such as STAT4, STAT1, and Runx1. In addition, we profile parallel time points of MCMV-specific CD8 T cells during infection and memory formation.

overall_design: RNA-seq was performed on ex-vivo NK cultured overnight in cytokines or NK cells and CD8 T cells harvested during in-vivo infection. Cytokine conditions are as follows: unstim, IL-12 (20 ng/ml), IL-12 (20 ng/ml) and IL-18 (10 ng/ml), IFNa (100 U/ml) stim, IL-15 (10 ng/ml).

first: Joseph

last: Sun


title: Regulation of natural killer cells during MCMV infection

status: Public on Dec 21 2017


title: Transcriptomics of Human Alveolar Macrophages and Peripheral Blood Monocytes in Acute Respiratory Distress Syndrome

status: Public on Apr 30 2017

city: Seattle

first: Sina

last: Gharib

state: WA

address: 850 Republican St.

department: Medicine

institute: University of Washington

summary:
Rationale: Serial measurements of genome-wide transcriptional changes in alveolar macrophages (AM) and peripheral blood monocytes (PBM) from patients with acute respiratory distress (ARDS) could clarify the biologic programs activated in ARDS and the relationship of these changes to clinical outcomes.
Objectives: To identify transcriptional programs activated in purified AM and PBM over the course of ARDS, and determine the relationship of these programs with patient outcomes.
Methods: We performed transcriptional profiling of total RNA isolated from AMs and PBMs purified from bronchoalveolar lavage fluid (BALF) and peripheral blood respectively, collected from patients (n = 26) with ARDS previously enrolled in a phase-II clinical trial.  Cells were obtained at baseline (day 0) after enrollment.
Measurements and Main Results: Using an unbiased gene set enrichment analysis (GSEA), we found highly divergent patterns of gene expression in AMs and PBMs.  Notably, immuno-inflammatory gene sets were enriched in AMs isolated on day 0 in those who survived and had more ventilator-free days (VFD); however, this association between inflammatory and immune gene sets and good outcomes was not seen in PBMs.
Conclusion: Transcriptional responses during ARDS are remarkably different between AMs and PBMs.
Rationale: Serial measurements of genome-wide transcriptional changes in alveolar macrophages (AM) and peripheral blood monocytes (PBM) from patients with acute respiratory distress (ARDS) could clarify the biologic programs activated in ARDS and the relationship of these changes to clinical outcomes.
Objectives: To identify transcriptional programs activated in purified AM and PBM over the course of ARDS, and determine the relationship of these programs with patient outcomes.
Methods: We performed transcriptional profiling of total RNA isolated from AMs and PBMs purified from bronchoalveolar lavage fluid and peripheral blood respectively, collected from patients (n = 26) with ARDS previously enrolled in a phase-II clinical trial.  Cells were obtained at baseline (day 0) after enrollment.
Measurements and Main Results: Using an unbiased gene set enrichment analysis (GSEA), we found highly divergent patterns of gene expression in AMs and PBMs.  Notably, immuno-inflammatory gene sets were enriched in AM isolated on day 0 in those who survived and had more ventilator-free days (VFD); however, this association between inflammatory and immune gene sets and good outcomes was not seen in PBMs.  Conclusion: Transcriptional responses during ARDS are remarkably different between AM and PBM.

overall_design: 1. Total RNA from human alveolar macrophages was isolated and hybridized  to Illumina HumanRef-8 BeadChip (n =  26) 2. Total RNA from human peripheral monocytes was isolated and hybridized  to Illumina HumanRef-8 BeadChip (n = 26)

middle: A

first: Eric

last: Morrell


title: Functional interactors of genomewide association study genes are differentially expressed in severe chronic obstructive pulmonary disease lung tissue

status: Public on Mar 29 2017

city: Boston

first: Jarrett

last: Morrow

address: 181 Longwood Ave.

department: Channing Division of Network Medicine

institute: Brigham and Women's Hospital

summary: Multiple gene expression studies have been performed in lung or airway tissues from subjects with chronic obstructive pulmonary disease (COPD). However, in comparison to genome-wide association studies (GWAS), there has been poor replication across these studies. We sought to perform gene expression profiling on a large sample of severe COPD cases and control smokers and use network methods to identify interacting genes and pathways. We collected surgically-resected lung tissue samples from subjects with severe COPD and controls with normal lung function; all subjects were former smokers. Gene expression profiling on homogenized lung tissue was performed using Illumina HumanHT-12 BeadChips. Protein and RNA binding studies, RNA-interference, a murine smoking model, and expression quantitative trait locus analyses were used to identify genes and proteins that may interact with three known COPD GWAS genes: IREB2, HHIP and FAM13A. Weighted Gene Co-Expression Network Analysis (WGCNA) was used to define co-expressed gene modules. Comparing 111 COPD cases and 40 control smokers, 214 genes were differentially expressed; none of these genes were at significant GWAS loci. However, the top differentially expressed gene was HMGB1, which interacts with AGER, a gene implicated through COPD GWAS. The genes differentially expressed in lung tissue showed strong enrichment for putative interactors of IREB2 and HHIP, with less support for FAM13A, based on the gene sets from the in vitro, in vivo, and in silico studies. In the WGCNA, the module most highly associated for COPD was enriched for B-cell pathways, which shared seventeen genes with the results of the Hhip+/- mouse smoking model. As in other common diseases, genes at COPD GWAS loci were not differentially expressed with COPD status; however, using a combination of network methods, experimental studies of interaction and careful phenotype definition, we found differential expression of putative interactors of these genes, and we replicated previous human and mouse microarray results involving B cell pathways.

overall_design: Lung tissue samples were snap frozen and stored at -80oC.  RNA and DNA were simultaneously extracted from the homogenized lung tissue using the AllPrep kit (Qiagen, Valenica, CA). RNA quality was assessed on a BioAnalyzer (Agilent, Santa Clara, CA). Gene expression profiling was performed using HumanHT-12 BeadChips (Illumina, San Diego, CA).

first: Xiaobo

last: Zhou

first: Taotao

last: Lao

first: Zhiqiang

last: Jiang

first: Dawn

middle: L

last: DeMeo

first: Michael

last: Cho

first: Weiliang

last: Qiu

first: Suzanne

last: Cloonan

first: Victor

last: Pinto-Plata

first: Bartholome

last: Celli

first: Nathaniel

last: Marchetti

first: Gerard

last: Criner

first: Raphael

last: Bueno

first: George

middle: R

last: Washko

first: Kimberly

last: Glass

first: John

last: Quackenbush

first: Augustine

last: Choi

first: Edwin

last: Silverman

first: Craig

last: Hersh


title: RNA-seq profiling of cortical collecting ducts in rats undergoing vasopressin escape

status: Public on Jun 10 2017

city: Bethesda

first: Jae Wook

last: Lee

state: MD

address: 10 Center Drive, 6N314

summary: We sequenced mRNAs in cortical collecting ducts microdissected from rats undergoing vasopressin escape.

overall_design: Rats were given subcutaneous DDAVP for 5 days via subcutaneous osmotic minipumps. Rats in treatment group (n=3-4) were given high water load (50 mL/day) and rats in control group were given normal water load (25 mL/day). After 1, 2, and 4 days, rats were sacrificed and cortical collecting ducts were microdissected and collected from collagenase-digested left kidney for RNA-seq profiling of mRNAs.

first: Jae

middle: W

first: Carolyn

last: Ecelbarger

first: Mark

last: Knepper


title: α-linolenic acid and long-chain n-3 polyunsaturated fatty acids modulate colitis operating with a different gene set

status: Public on Oct 12 2016

city: Mysore

first: Vijay kumar Reddy

last: Kondreddy

state: None Selected

address: Lab-115, B&N department, CFTRI, Mysore, India

department: Biochemistry

country: India

institute: CSIR-Central Food Tehnological research institute

summary: Adult Wistar rats were fed diet enriched with either α-linolenic acid (ALA) or fish oil for 8 (n=10) weeks. Colitis was induced in rats using 5% dextran sulfate sodium for 7 days. The rats were dissected and RNA was isolated from the colon tissues of rats, the samples from 6 rats were pooled and used for the microarray experiments. Global gene expression analysis was done in duplicates in each group and the results were compared to n-6 fatty acid group. α-linolenic acid (ALA) and fish oil rich in eicosapentaenoic acid and docosahexaenoic acid significantly attenuated the symptoms of colitis, compared to n-6 fatty acid group. Gene expression analysis has revealed that there is no common gene signature in the two groups.

overall_design:
Agilent Custom Rat Gene Expression 8X60K (AMADID: 28279) designed by Genotypic Technology Private Limited , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)
Adult Wistar rats were fed diet enriched with either α-linolenic acid (ALA) or fish oil for 8 (n=10) weeks. The results were compared to n-6 fatty acid group.

first: Vijay

first: Jhansi

last: Magisetty


title: Heterogeneity in neurodegenerative disease

city: South San Francisco

first: Brad

last: Friedman

state: CA

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

summary:
RNA was purified from fusiform gyrus tissue sections of autopsy-confirmed Alzheimer's cases and neurologically normal age-matched controls.
The "SAM.ID" sample characteristic is a sample identifier internal to Genentech.
The ID of this project in Genentech's ExpressionPlot database is PRJ0007261

overall_design: RNA from fusiform gyrus of Alzheimer's or Neurologically Normal post-mortem tissue.

first: Marcel

last: van der Brug

first: Melanie

last: Huntley

first: Yi

last: Cao


title: High-Fat High-Sugar Diet Induces Polycystic Ovary Syndrome in a Rodent Model

status: Public on Jun 01 2017

city: Lexington

first: Gregg

middle: Brooks

last: Whitworth

state: VA

address: 204 West Washington St

department: Biology

institute: Washington and Lee Unversity

summary: Obesity has been linked with a host of metabolic and reproductive disorders including polycystic ovary syndrome (PCOS). While a distinct link exists between obesity and PCOS, the exact pathogenesis of the disease remains less understood and limited research has explored the impact of diet on the development of PCOS. With the primary symptoms of PCOS including hyperandrogenism, anovulation, and polycystic ovaries, most animal models utilize androgen treatment to effectively induce PCOS. However, these models fail to address the underlying causes of disease symptoms and do not effectively demonstrate the metabolic features of the disease such as hyperinsulinemia. Here, we present a novel rodent model of diet-induced obesity that recapitulates both the metabolic and reproductive phenotypes of human PCOS. In utilizing a high-fat high-sugar (HFHS) diet, we have created a model of PCOS that allows for the study of metabolic parameters and their impact on ovarian follicle development and reproductive health. Animals on the HFHS diet not only demonstrated signs of metabolic impairment, but they also developed polycystic ovaries and experienced irregular estrous cycling marked by an extended period spent in estrus. Though hyperandrogenism was not characteristic of HFHS diet animals as a group, testosterone levels were predictive of a polycystic ovarian morphology. Importantly, PCOS was induced similarly to the disease etiology in humans, allowing this model to offer the unique opportunity to study PCOS at its genesis rather than following the development of disease symptoms.

overall_design: Female Sprague-Dawley rats (n = 60; P17) were randomly assigned to either a HFHS (n = 32) or control diet (n = 28) group. The control group had ad libitum access to water and standard rat chow (Envigo – LM-485, 3.1 kcal/g, 17% calories from fat). Rats were bilaterally ovariectomized after 11 weeks of diet exposure.  For RNA-Seq analysis, two ovaries were collected from two different animals in each experimental group.

first: Jacob

middle: S

last: Roberts

last: Bowman

first: Patrick

last: Ozark

first: Sarah

last: Blythe

first: Natalia

last: Toporikova

middle: B


title: VHL Substrate Transcription Factor ZHX2 As An Oncogenic Driver In Clear Cell Renal Cell Carcinoma

status: Public on Jul 19 2018

first: Jeremy

last: Simon

state: MA

address: 450 Brookline Ave

department: Department of Data Science

institute: Dana-Farber Cancer Institute

summary: Inactivation of the von Hippel-Lindau (VHL) E3 ubiquitin ligase protein is a hallmark of clear cell renal cell carcinoma (ccRCC). Identifying how pathways affected by VHL loss contribute to ccRCC remains challenging. We used a genome-wide in vitro expression strategy to identify proteins that bound VHL only when hydroxylated. Zinc fingers and homeoboxes 2 (ZHX2) was found as a VHL target and its hydroxylation allowed VHL to regulate its protein stability. Tumor cells from ccRCC patients with VHL loss-of-function mutations usually had increased ZHX2 amount and nuclear localization. Functionally, depletion of ZHX2 inhibited VHL-deficient ccRCC cell growth in vitro and in vivo. Mechanistically, integrated ChIP-Seq and microarray analysis showed that ZHX2 promoted NF-kB activation. These studies reveal ZHX2 as a potential therapeutic target for ccRCC.

overall_design: ZHX2 is identified as a VHL substrate from a genome-wide screen, which promotes NF-kB pathway activation and ccRCC tumorigenesis. We profiled NFkB-p65 and ZHX2 occupancy genome-wide using ChIP-seq in ccRCC 786-0 cells

middle: M

first: Qing

last: Zhang


title: Separation of circulating microRNAs using apheresis in patients with systemic lupus erythematosus

status: Public on Apr 11 2016

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

summary:
Examined the removal or reduction of circulating miRNAs with apheresis. The levels of expression of a large number of circulating miRNAs were measured in the plasma samples separated by the primary membranes from all 3 patients with systemic lupus erythematosus.
This is the first report that circulating miRNAs in peripheral blood can be separated and possibly directly removed using membrane separation apheresis.

overall_design: Collected blood and separated plasma samples from 3 patients with systemic lupus erythematosus who were undergoing plasmapheresis at our hospital. Peripheral blood was collected before and after it was passed through a primary membrane, centrifuged, and used to extract circulating miRNAs.

first: Makio

last: Kusaoi

first: Ken

last: Yamaji


title: Gene expression profiling on C3H/10T1/2 fibroblasts during their myogenic conversion in case of Six4 ablation

status: Public on Dec 31 2015

first: Alexandre

last: Blais

summary: In this study, we used C3H/10T1/2 cells, a well known model of myogenic conversion, to study the effect of Six4 knockdown on the expression of genes during fibroblasts to myocytes conversion induced by ectopic expression of MyoD

overall_design: We established C3H/10T1/2 cell line with stable Six4 knockdown  by short hairpin RNA (shSix4) vs a control cell line (shLuc) and converted these cells into myogenic lineage by retroviral transduction of plasmid encoding Flag-MyoD-myc (pBABE-MyoD) or empty plasmid (pBABE). Cells were then induced to differentiate for 24 hours before RNA extraction.

first: Imane

last: Chakroun


title: Modulation of reactive oxygen species and inflammatory cytokines by FoxO3a promotes host survival against Salmonella typhimurium

status: Public on Aug 11 2016

summary:
We employed microarray expression profiling to identify genes which are differentially regulated in the absence of FoxO3a, upon Salmonella typhimurium (ST) infection. ST induced gene expression changes were measured in Wild-type and FoxO3a-/- bone marrow derived macroophages at 6 hours post infection. The array showed an enrichment of MAPK signaling and alterations in inflammatory cytokines and ROS regulators in the absence of FoxO3a.
Gene expression changes in bone marrow derived macrophages was measured after infection with 10 MOI of Salmonella typhimurium. Control samples were left untreated. Two mice from each genotype were used for the experiment.

first: Julie

last: Joseph

first: Subash

last: Sad

first: Daniel

last: O'Neil

first: Emmanuelle

last: Ametepe


title: Control, low water potential (drought) stress and stress release transcriptome analysis of mutants impaired in proline (Delta1-pyrroline-5-carboxylate synthase1-4; p5cs1-4) or abscisic acid (aba2-1) synthesis.

status: Public on Aug 05 2016

first: Paul

last: Verslues

summary: mRNA sequencing was used to identify genes differentially expressed in  Delta1-pyrroline-5-carboxylate synthase1-4 (p5cs1-4) mutants deficient in low water potential-induced proline accumulation and the Abscisic Acid (ABA) deficient mutant aba2-1 compared to Col-0 wild type.  Three treatments were analyzed for each genotype: unstressed control, a 96 hour low water potential (-1.2 MPa) treatment and a stress-release treatment where seedlings were removed from the stress treatment and transferred back to control media for 10 hours.  Approximately 100 genes were found to be significantly up-regulated in p5cs1-4 compared to wild type in both the control and stress treatments with an equal number down regulated.  There was also a substantial transcription response to the stress release treatment which varied between wild type, p5cs1-4 and aba2-1.

overall_design: Wild type (Col-0), p5cs1-4 and aba2-1 Arabidopsis thaliana seedlings were germinated on agar plates and after seven days of growth, seedlings were transferred either to fresh plates of control media or to low water potential (-1.2 MPa) stress plates.  Samples were collected 96 h after transfer (Control and stress treatments).  At 96 h, additional seedlings were transferred from the stress treatment back to control agar plates and samples collected 10 h after this stress release.  Three independent biological experiments and mRNA extractions were performed for each genotype/treatment (27 mRNA extractions.  After quality check and quantitation, the mRNA samples were pooled to produce a set of 9 samples for sequencing.

first: Sandeep

last: Sharma


title: Leucegene: AML sequencing (part 6)

status: Public on Jan 01 2019

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

institute: Institute for Research in Immunology and Cancer

summary: RNA-sequencing of human acute promyelocytic leukemias

overall_design: The goals of this project are to obtain a comprehensive study of mutations and gene expression in human acute myeloid leukemia (AML). Methods: AML cells were thawed. DNA and RNA (polyA) was extracted and sequences were obtained with an illumina HiSeq 2000 sequencer.

first: Vincent-Philippe

last: Lavallée

first: Josée

last: Hébert

first: Sébastien

last: Lemieux

first: Anne

last: Marinier

first: Jana

last: Krosl

first: Jalila

last: Chagraoui

first: Tara

last: McRae

first: Miriem

last: Marquis

first: Caroline

last: Pabst


title: Genome-wide map of Six4 in C2C12 cells 24 hours post-differentiation

first: Alexandre

last: Blais

summary: In this study, we used ChIP-seq to map Six4 binding profile in different C2C12 cell lines 24 hours after differentiation (T24). We performed ChIP-seq using two different antibodies: anti-Flag antibody in Flag-Six4 C2C12 cell line  or in parental C2C12 cells; a custom-made anti-Six4 antibody in shNS C2C12 cell line (a control cell line) or shSix4 C2C12 (C2C12 with stable Six4 knockdown using short hairpin RNA). We also performed ChIP-seq in parental C2C12 cells using normal rabbit IgG. We were able to identify Six4-bound loci in C2C12 T24 that were recognized by two different antibodies and showed a decrease in peak intensity in shSix4 C2C12 compared to shNS C2C12 cells.

overall_design: We established a C2C12 cell line with stable Six4 knockdown  by short hairpin RNA (shSix4) vs. a control cell line (shNS).  We also established a C2C12 cell line with stable expression of Flag-Six4-myc  by infection of retroviruses expressing  pBABE-Flag-Six4-myc  (Flag-Six4 C2C12) vs. parental C2C12. We differentiate these cells for 24 hours before using them for ChIP-seq.

first: Imane

last: Chakroun


title: Gene modulation in acetic acid-induced oral ulcerative mucositis

status: Public on Jun 15 2016

city: Inashiki-gun

first: Kiyoshi

last: Terawaki

state: Ibaraki

address: 3586 Yoshiwara, Ami-machi

institute: Tsumura & Co.

summary: To reveal the molecular mechanisms underlying oral ulcerative mucositis-induced pain, we investigated putative pain-associated mediators, pain-related behaviors and gene modulation in a rat oral mucositis model. On day 1 after acetic acid treatment, the mucosal area showed slight redness and swelling but no evidence of ulceration or pain induction. On day 2, oral ulcers were obvious, as was the induction of spontaneous and mechanical pain. In the treated mucosal area, bacterial loading and prostaglandin E2 increased beginning on day 2; no significant changes were observed on day 1. DNA microarray analysis of trigeminal ganglion tissue collected on day 2 identified 32 significantly regulated genes (>1.5-fold change in expression). The up-regulation of the top 3 genes, Hamp (hepcidin antimicrobial peptide), Reg3b (regenerating islet-derived 3β) and Serpina3n (serine peptidase inhibitor A3N), was validated through quantitative RT-PCR. Systemic antibiotic pre-treatment did not increase the mRNA levels. Therefore, we conclude that the oral ulcerative mucositis-induced pain is caused by infectious inflammation of the ulcerative area and stimulates anti-bacterial and anti-peptidase gene expressions in sensory neurons.

overall_design: Oral ulcerative mucositis-induced gene expression in trigeminal ganglion tissue was measured. Ten Wistar rats were divided into the following two groups, control, oral ulcerative mucositis (stomatitis). Five rats were anesthetized with sodium pentobarbital. A piece of filter paper was soaked in 50% acetic acid diluted with water and placed in the labial fornix region of the inferior incisors of rats for 30 sec. Other five rats received only anesthesia without any treatment were used as a control. On day 2 after acetic acid treatment, oral ulcerative mucositis was obvious and trigeminal ganglion tissues in two groups were collected for DNA microarray analysis.

first: Suzuro

last: Hitomi

first: Kentaro

last: Ono

first: Kiyotoshi

last: Inenaga

first: Keita

last: Mizuno

first: Chinami

last: Matsumoto

first: Yuji

last: Omiya

first: Yoshio

last: Kase


title: Genomic mapping of E2F3 and E2F4 binding sites in neurospheres

status: Public on Jun 01 2015

address: 451 Smyth Road

institute: University of Ottawa

type: Genome binding/occupancy profiling by genome tiling array

summary: Neural precursor cells from the ganglionic eminence at E14.5 were isolated and cultured as neurospheres. E2F3 and E2F4 genomic binding sites are mapped by ChIP-on-Chip on wild type or mutant cells.

overall_design: All cells used in this study were cultured as neurospheres. Neural precursors were obtained by dissection of the ganglionic eminence from developing embryos at gestational age E14.5 from either wild type mice or germline E2f3a and E2f3b deficient mice, and cells were cultured as neurospheres. 3 independent biological replicates were used for each experiment. The customized microarray design counts approximately 1 million probes covering the proximal promoter of most mouse genes.

first: Lisa

last: Julian

first: Ruth

last: Slack

first: Yubing

last: Liu


title: mRNA differential expression analysis in a human ex vivo model of chronic wounds

status: Public on Dec 16 2015

city: Berkeley

first: Claire

last: Dugast-Darzacq

state: California

address: LI KA SHING Center

department: Molecular and Cell Biology

institute: UC Berkeley

summary: To study the fibroblast to myofibroblast differentiation in a normal or pathological situation, NHDF (Normal human dermal fibroblast) obtained from two different healthy donors (donors A and B) were either left untreated (T-E-) either treated with TGF-beta alone (T+E-), or with exudate from chronic wounds (T-E+) or both (T+E+). For each different treatment we performed mRNA deep sequencing 3 times : twice with cells from donor A and once with cells from donor B.We focused our study on gene expression profile as a representation of cell fate. We performed mRNA deep sequencing analysis of the 4 different conditions. For each condition, mRNA deep sequencing was performed 3 times : twice with cells from donor A and once with cells from donor B.Comparing the mRNA abundance between the different treatments, we identified 3 lists of genes characterizing the different gene expression states: 171 genes in List I representing the genes differentially expressed during normal fibroblast to myofibroblast differentiation, 409 genes in List II representing the genes differentially expressed upon exudate-only treatment and 1006 genes in List III representing the genes differentially expressed upon the combination of exudate and TGF-beta treatments.

overall_design: 4 different treatments are compared : (T-E-) NHFD left untreated, (T+E-) NHDF treated with TGFbeta  for 4 days, (T-E+) NHDF treated with exudate for 4 days and (T+E+) NHDF treated with both TGFbeta and exudate. NHDF : Normal Human Dermal Fibroblast

first: Maïté

last: Noizet

first: Emilie

last: Lagoutte

first: Marlène

last: Gratigny

first: Marielle

last: Bouschbacher

first: Isabelle

last: Lazareth

first: Hugues

last: Roest Crollius

first: Xavier

last: Darzacq


title: Leucegene: AML sequencing (part 4)

status: Public on Jul 09 2015

first: Guy

last: Sauvageau

summary: RNA sequencing of human leukemia

overall_design: The goals of this project are to obtain a comprehensive study of mutations and gene expression in human acute myeloid leukemia (AML). Methods: AML cells were thawed. DNA and RNA (polyA) was extracted and sequences were obtained with an illumina HiSeq 2000 sequencer. Results are pending.

first: Vincent

last: Lavallée

first: Jana

last: Krosl

first: Brian

last: Wilhelm

first: Frédéric

last: Barabé

first: Patrick

last: Gendron

first: Geneviève

last: Boucher

first: Raphaëlle

last: Lambert

first: Claude

last: Rondeau

first: Annie

last: Bilodeau

first: Sylvie

first: Caroline

last: Pabst

first: Jonathan

last: Yeh

first: Bernhard

last: Lehnertz

first: Radia

last: Johnson

first: Clarisse

last: Thiollier

first: Giovanni

last: D'Angelo

first: Sébastien

last: Lemieux

first: Josée

last: Hébert


title: Activation of beta-catenin in hepatocellular carcinoma (HCC patients)

status: Public on May 21 2015

city: Houston

first: Sangbae

last: Kim

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

summary: CTNNB1 is the most frequently mutated gene in hepatocellular carcinoma (HCC). However, its clinical relevance remains controversial. We determined an evolutionarily conserved β-catenin signature by comparative analysis of gene expression data from human HCC and a mouse model (GSE43628). We generated gene expression data from the tumors of 88 HCC patients who underwent surgical resection as the primary treatment. We used these gene expression data to develop a new prognostification model for prognosis of HCC after surgery.

first: Ji

first: Koo

middle: J

last: Kang

first: Ju

last: Lee

first: Yun

middle: Y

last: Park


title: Leucegene: AML sequencing (part 3)

first: Guy

last: Sauvageau

summary: RNA sequencing of human leukemia

first: Camille

last: Simon

first: Jalila

last: Chagraoui

first: Jana

last: Krosl

first: Patrick

last: Gendron

first: Brian

last: Wilhelm

first: Geneviève

first: Pierre

last: Chagnon

first: Simon

last: Drouin

first: Raphaëlle

last: Lavallée

first: Martin

first: Anne

last: Bergeron

first: Vincent

first: Eric

last: Deneault

first: Jessica

last: Simard

first: Frédéric

last: Barabé


title: Human Lung Adenocarcinoma Cells: control vs. mAb NJ001 treated

status: Public on Aug 01 2014

city: Nanjing

first: Shiyang

last: Pan

state: Jiangsu

address: 300 Guangzhou Road

department: Department of Laboratory Medicine

institute: the First Affiliated Hospital of Nanjing Medical University

summary: Transcriptional profiling of human lung adenocarcinoma cells comparing control untreated SPC-A1 cells with SPC-A1 cells treated with 300 µg/ml mAb NJ001 for 36h

overall_design: Two-condition experiment, SPC-A1 vs. NJ001-SPC-A1 cells. Biological replicates: 3 control, 3 treated, independently grown and harvested. One replicate per array.


title: A role for Widely Interspaced Zinc finger (WIZ) in retention of the G9a methyltransferase on chromatin

status: Public on Sep 03 2015

city: Chapel Hill

first: Ian

middle: Jonathan

last: Davis

address: 450 West Drive

department: Genetics, Pediatrics

institute: University of North Carolina

summary: G9a and GLP lysine methyltransferases form a heterodimeric complex that is responsible for the bulk of cellular mono- and di-methylation on histone H3 lysine 9 (H3K9me1/me2).  Widely Interspaced Zinc finger (WIZ) associates with the G9a/GLP protein complex, but its role in lysine methylation is poorly defined.  Here, we show that WIZ regulates global H3K9me2 levels through a mechanism that involves retention of G9a on chromatin.  We also show that WIZ-mediated chromatin loss of G9a/GLP results in altered gene expression and protein-protein interactions that are distinguishable from that of using a molecule-induced enzymatic inhibitor towards G9a/GLP – thus providing evidence that the G9a/GLP/WIZ complex has unique functions when bound to chromatin that are independent of the H3K9me2 mark

overall_design: DMSO, UNC0638, NS, and siWIZ treatments to HEK293T cells, assessing G9a and H3K9me2 localization, each performed in duplicate, plus one input control for each cell condition. 30 samples total.

first: Samantha

middle: G

last: Pattenden

first: Jeremy

first: Joel

last: Parker


title: Evolutionary Engineering and Transcriptomic Analysis of Phenylethanol-resistant Saccharomyces cerevisiae

status: Public on Jul 12 2014

city: TOULOUSE

first: CEREN

last: ALKIM

address: Laboratoire d'Ingénierie des Systèmes Biologiques & des Procédés

institute: INRA

summary: Phenylethanol-resistant S. cerevisiae mutants were obtained by using evolutionary engineering strategy. Briefly, a chemically mutagenized culture was used as the initial population for the selection procedure. Gradually increasing levels of phenylethanol stress was applied through 56 successive batch cultivations. Individual mutants were selected from the final population. The mutant with the highest phenylethanol resistance could resist up to 3 g/L phenylethanol concentrations. Whole-genome transcriptomic analyses of the phenylethanol-resistant mutant strain and the reference strain were performed by using DNA microarray technology, in the absence of phenylethanol stress.

overall_design: Agilent yeast DNA microarray systems were used for whole-genome transcriptomic analyses of the reference strain and the selected phenylethanol-resistant mutant. Three replicates of each culture were grown in 100 mL yeast minimal medium using 500 mL flasks, at 30°C and 150 rpm. Cells at logarithmic phase of growth (~1.0 OD600) were used for total RNA isolation.

first: Can

last: Holyavkin

first: Ulku

last: Yılmaz

first: Ceren

last: Alkım

first: Burcu

last: Turanlı-Yıldız

first: Halil

middle: I

last: Kısakesen

first: Jean-Marie

last: François

first: Gustavo

last: de Billerbeck

first: Zeynep

middle: P

last: Cakar