title: The impact of aging on beta-cell functionality and structural integrity under metabolic stress conditions in diabetes-prone and diabetes-resistant mice.

status: Public on Nov 02 2020

city: Nuthetal

first: Richard

last: Kehm

address: Arthur-Scheunert-Allee 114-116

department: Molecular Toxicology

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

summary: Overnutrition contributes to insulin resistance, obesity and metabolic stress, initiating a loss of functional beta-cells and diabetes development. Whether these damaging effects are amplified in advanced age is barely investigated. Therefore, New Zealand Obese (NZO) mice, a well-established model for the investigation of human obesity-associated type 2 diabetes, were fed a metabolically challenging diet with a high-fat, carbohydrate restricted period followed by a carbohydrate intervention in young as well as advanced age. Interestingly, while young NZO mice developed massive hyperglycemia in response to carbohydrate feeding, leading to beta-cell dysfunction and cell death, aged counterparts compensated the increased insulin demand by persistent beta-cell function and beta-cell mass expansion. Beta-cell loss in young NZO islets was linked to increased expression of thioredoxin-interacting protein (TXNIP), presumably initiating an apoptosis-signaling cascade via caspase-3 activation. In contrast, islets of aged NZOs exhibited a sustained redox balance without changes in TXNIP expression, associated with higher proliferative potential by cell cycle activation. These findings support the relevance of a maintained proliferative potential and redox homeostasis for preserving islet functionality under metabolic stress, with the peculiarity that this adaptive response emerged with advanced age in diabetes-prone NZO mice.

overall_design: Metabolic stress-induced gene expression in murine pancreatic islets of diabetes-prone New Zealand Obese (NZO) mice was determined at week 18 (young) and 39 (aged) of -CH (carbohydrate-free, high-fat diet) feeding as well as 2 days after an additional +CH (carbohydrate-rich diet) intervention (n = 5 mice per group).

first: Annika

last: Höhn

first: Tilman

last: Grune


title: RNA sequencing of tomato seed tissues during seed development

status: Public on Dec 11 2020

city: Beaucouze

first: Julia

last: Buitink

address: 42 rue Georges Morel

department: BAP

country: France

institute: INRAE

type: Expression profiling by high throughput sequencing

summary: During maturation seeds acquire several physiological traits to enable them to survive drying and disseminate the species. Few studies have addressed the regulatory networks controlling acquisition of these traits at the tissue level particularly in endospermic seeds such as tomato, which matures in a fully hydrated environment and does not undergo maturation drying. Using temporal RNA-seq analyses of the different seed tissues during maturation, gene network and trait-based correlations were used to explore the transcriptome signatures and identify hubs associated with desiccation tolerance, longevity, germination under water stress and dormancy.

overall_design: Three replicates of 10-20 fresh tomato seeds were harvested at 14 stages throughout seed development from 15 DAF to overripened fruits (red plus 14 days (R14)). RNA-seq data series of whole seeds and isolated seed tissues was obtained from 15 to 28 DAF for entire seeds, from 35 DAF to stage R14 for embryo and endosperm, and from 35 to 49 DAF for seed coat.

first: Elise

last: Bizouerne

first: Olivier

last: Leprince


title: miRNA Profiling of Exosomes from Spontaneous Hypertensive Rats by Next-Generation Sequencing

status: Public on Oct 30 2020

city: Beijing

first: Xiaoyan

last: Liu

address: 8 Gongren Tiyuchang Nanlu, Chaoyang District

country: China

institute: Beijing Chao-Yang Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: The role and miRNA expression profile of exosomes in hypertension remain largely unknown, therefore, next generation sequencing was used to define the miRNA expression profile of plasma exosomes in spontaneously hypertensive rats (SHRs), the most widely used animal model of human essential hypertension, and their controls, normotensive Wistar-Kyoto rats (WKYs). Results revealed that percentages of miRNA in the total small RNA isolated from WKYs and SHRs were not significantly different. Twenty-seven miRNAs were significantly differentially expressed (DE) between WKY and SHR exosomes, among which 23 were upregulated and 4 were downregulated in SHR exosomes compared with WKY exosomes. Gene Ontology analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis of top 10 DE miRNAs identified hypertension-specific target genes/signaling pathways. In conclusion, our findings indicate the selective packing of miRNA cargoes into exosomes under hypertensive status, while facilitating the development of potential targets for the diagnosis, prevention and treatment of hypertension.

overall_design: Exosome miRNA profiles of Wistar-Kyoto rats and spontaneously hypertensive rats were generated by next-generation sequencing, in sextuplicate, using Illumina Hiseq 2500.

first: Wen

last: Yuan

first: Lei

last: Yang

first: Jing

last: Li

first: Jun

last: Cai


title: A transcriptomic analysis reveals novel patterns of gene expression during 3T3-L1 adipocyte differentiation

status: Public on Oct 02 2020

city: Shenzhen

first: SHAO

middle: MIN

last: YANG

state: guangdong

address: Nanshan

department: Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center

institute: Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine

summary: this study analyzed the transcriptomic changes of 3T3-L1 adipocytes during differentiation, which is important for better understand the molecular mechanisms of obesity. The purpose of the current study is to provide a comprehensive understanding at the transcriptome level of adipocyte differentiation. The transcriptomic profies in 3T3-L1 adipocytes from different differentiation stage were examined using RNAseq technique.

overall_design: Examination of the transcriptomic changes of 3T3-L1 adipocytes during differentiation

first: Wuping

last: Sun

first: Shaomin


title: Gender-specific transcriptional profiles identified in β-thalassemia patients

status: Public on Aug 25 2020

city: Athens

first: Eleni

last: Katsantoni

address: Soranou tou Ephessiou 4

department: Basic Research

country: Greece

institute: Biomedical Research Foundation, Academy of Athens

summary: Lifelong treatment and major complications characterize β-thalassemia patients, whether they suffer from the milder type of the disease (β-thalassemia intermedia, TI) or the severe type (β-thalassemia major, TM). This study aimed to ascertain the differences in the transcriptional profiles of TI and TM patients to identify targets for stratification and the development of personalized therapeutic strategies. RNA-seq of 49 participants (16 TI, 16 TM, 17 healthy) identified a higher number of differentially expressed genes in TM than in TI patients when compared to healthy participants portraying accurately the clinical observations. When TI patients were compared to TM, the absence of significantly differentially expressed genes highlighted the increased variability seen in the TI expression profiles suggesting that a continuous spectrum describes the disease and not distinct conditions. Although no confounding effect was seen due to different centers, age groups and various clinical characteristics, when male and female patients were compared to healthy participants of the same gender, it was evident that males and females are affected in distinctive ways by β-thalassemia. TI triggers a pronounced and consistent transcriptional signature in males, whereas a small effect is seen in females reflecting increased biological variability. TM induces transcriptional changes of similar magnitude in both genders with limited overlap between them emphasizing that different pathways are affected. Our study provides a framework for further stratification studies in β-thalassemia and highlights the need to consider gender as an important variable for developing differential diagnostic and therapeutic strategies.

overall_design: We have analysed the gene expression profiles of erythroid progenitor cultures derived from 16 TI and 16 TM patients using RNA-seq and we studied the differentially expressed genes and pathways irrespective to patient genotype. The aim of this study was to identify biomarkers for patient stratification and therapeutic management, identify confounding factors, pinpoint the targets that dictate each phenotype and possibly develop therapeutic strategies focused on these targets.

first: Aikaterini

last: Nanou


title: Epigenetic changes in human DIPG cells with histone H3K27M mutations [ATAC-seq]

status: Public on Jun 24 2020

city: Ann Arbor

first: Sriram

last: Venneti

state: MI

address: 3520E MSRB 1, 1150 W. Medical Center Dr.

country: USA

institute: University of Michigan

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We assessed changes in chromatin accessibility in H3.3K27M DIPG cell lines on knockdown of metabolic enzymes including HK2, GDH and IDH1

overall_design: Hexokinase-2 (HK2), Glutamate dehydrogenase (GLUD1) or insocitrate dehydrogenase (IDH1) were knocked down in H3.3K27M HSJD-DIPG007 cells. Genomic changes in chromatin accessibility were assessed between each shRNA and non-targeted NT controls.

first: S


title: RNA-seq analysis dataset: Hippocampal tissues from Emx1-Cre;Auts2-flox/flox  and Auts2-flox/flox mice at P14

status: Public on Jun 17 2020

city: Okazaki

first: SHOJI

last: TATSUMOTO

address: Myodaiji

country: Japan

institute: The National Institutes of Natural Sciences NINS

summary: Previous studies have revealed that AUTS2 regulates cytoskeletal organization as well as gene expression during prenatal brain development. Its involvement in controlling synapses, however, remains unclear. Here, we report the increased dendritic spine formation in Auts2 mutant mice as well as the primary cultured neurons from Auts2 mutant mice. To investigate the involvement of AUTS2 function in the regulation of gene expression, we performed transcriptome analysis. RNA-seq on total RNA from the hippocampal tissues of Emx1Cre/+;Auts2flox/flox homozygous conditional KO mice at P14 reveals changes in gene associated with brain development including synapse formation. These results suggest that AUTS2 regulates the expression of genes that are related to synapse formation/function, and some of which may be involved in spine number restriction. Aberrant expression of such synaptic genes may cause synaptic dysfunction in patients with AUTS2 mutations.

overall_design: The mRNA profiles of the hippocampal tissues from four  Emx1-Cre;Auts2-flox/flox homozygous mutant mice and four Auts2-flox/flox control mice at P14 were generated using the Illumina HiSeq platforms.

first: Mikio

last: Hoshino

first: Kei

last: Hori

first: Yasuhiro

last: Go


title: Epigenetic changes in mouse neuronal stem cells and human DIPG cells with histone H3K27M mutations

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Genome-wide maps of H3K27me3 and H3K27ac in cells treated with HDAC inhibition, EZH2 inhibition, or combined HDAC/EZH2 inhibition

status: Public on May 12 2020

city: Boston

first: Ryan

middle: P

last: Kuzmickas

state: MA

address: 77 Avenue Louis Pasteur, NRB458B

department: Genetics

institute: Brigham and Women's Hospital

summary: Investigation of the mechanism by which combined EZH2 and HDAC inhibition kills PC3 prostate cancer cells. Next-generation sequencing was used to identify changes in genome localization of HDAC targets (H3K27ac) and EZH2 targets (H3K27me3) upon treatment with each inhibitor alone or in combination.

overall_design: Examination of genome-wide localization of 2 different histone modifications in PC3 prostate cancer cells following treatment with Vehicle (DMSO), HDAC inhibition (VOR, Vorinostat), EZH2 inhibition (GSK126), or combined HDAC and EZH2 inhibition (COMBO)


title: Functional regeneration and repair of tendons using biomimetic scaffolds loaded with recombinant Periostin

status: Public on Sep 23 2020

first: yu

last: Wang

state: Beijing

address: 22 South Zhongguancun Street, Haidian District

department: Peking University School and Hospital of Stomatology

institute: Peking University

summary:
Although the biological events that modulate tendon embryonic development are widely studied, how they orchestrate postnatal tendon maturation that is similar to tendon regeneration is still largely unknown
For molecular profiling of tendon maturation, we performed mRNA microarray analyses of total rat tendon tissue harvested from normal neonatal and 6-8w Achilles’ tendons and identified meaningful  genes in down-regulated group

overall_design: Tendon tissues from the neonatal (1day) and  6-8 week rats were harvested.Then total RNA was extracted using Trizol reagen, and following labeling, fragmented cDNA was hybridized for 16 h at 45 oC on GeneChip Affymetrix Rat Transcriptome Array 1.0 (Affymetrix))

first: Yan

first: Yu


title: SMG1, a Nonsense-Mediated mRNA Decay (NMD) regulator, as a therapeutic target in multiple myeloma

status: Public on Jul 01 2020

city: San Francisco

first: Esther

middle: T

last: Chan

state: California

address: 1500 Owens Street, Suite 500

institute: Celgene Corporation

summary: RNA expression was profiled in B-cell lymphoma cell lines treated with CC0483115 (CC-115) using strand-specific RNA-sequencing. The following cell lines were tested: GRANTA (mantle cell lymphoma, resistant to CC-115), JEKO (mantle cell lymphoma, sensitive), Jiyoye (Burkitt lymphoma, resistant), RAMOS (Burkitt lymphoma, sensitive), RPMI8226 (multiple myeloma (MM), sensitive), and U-266 (MM, resistant).

overall_design:
Strand-specific RNA-seq was performed on 6 B-cell lymphoma cell lines, untreated and treated with CC-115
Various B-cell lymphoma cell lines were cultured, treated with CC-115 or vehicle (DMSO), and harvested. Samples were transferred to NeoGenomics for library preparation withTruSeq Stranded mRNA kits and paired-end sequencing on Illumina HiSeq 2500.

first: Eric

last: Eldering

first: Ingrid

middle: A

last: Derks

first: Brett

last: Garrick

first: Aldo

last: Jongejan

first: Martino

last: Colombo

first: Timon

last: Bloedjes

first: Torsten

last: Trowe

first: Jim

last: Leisten

first: Michelle

last: Howarth

first: Mehnaz

last: Mahlek

first: Deborah

last: Mortensen

first: Kate

last: Blease

first: Matthew

last: Groza

first: Rama

middle: K

last: Narla

first: Remco

last: Loos

first: Marie

middle: J

last: Kersten

first: Perry

last: Moerland

first: Jeroen

last: Guikema

first: Arnon

last: Kater

first: Ellen

last: Filvaroff


title: Next Generation sequencing revealed the quantitative transcriptome analysis of the preimplantation embryos (3 d.p.c) generated from the cross between L13a+/- mice

status: Public on Apr 30 2020

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

summary: Comparative study of the genomewide transcriptome analysis with reference to the regression scale of ribosomal protein L13a transcript level i.e in the absence of L13a (-/-), intermediate level of L13a (+/-) and wild type (+/+)

overall_design: Preimplanted embryos at the morula stage were collected by flashing the oviduct/uterus of pregnant L13a(+/-) mice at 3 d.p.c Each embryos were washed in PBS and transferred to 10ml of Cells-to-CDNA II Cell lysis buffer (Cat#AM8723 invitrogen) and boiled at 75 degree Centrigrade for 10 minutes, lysates were centrifuged briefly and transferred immediately on ice. RNA purification was performed using PicoPure RNA isolation it (Cat# KIT0214) following users manual. These samples were submitted for library construction and next generation sequencing.

first: R

last: Kour

first: B

last: Richardson

first: M

last: Mazumder


title: In vivo transcriptomic responses to mercury chloride exposure in rat kidney tissue

status: Public on Jul 07 2020

city: Frederick

first: Patric

last: Schyman

state: Maryland

address: 2405 Whittier Drive, Suite 200

institute: Biotechnology HPC Software Applications Institute (BHSAI)

summary: In this study we tested the ability to predict organ injury from transcriptomics data in Sprague-Dawley rats at early time points after exposure to mercury chloride (10 and 34 hours). We selected mercury chloride, a compound extensively used in animal studies for its ability to cause acute kidney and liver damage.

overall_design: We treated 30 Sprague-Dawley rats with saline solution (control), 0.25 mg/kg (low dose), and 0.50 mg/kg (high dose) to produce different degrees of injury. RNA samples for gene expression analysis were collected from the kidney at 10 and 34 hours. Number of repicates were five.

first: Richard

middle: L

last: Printz

first: Mohamed

middle: D

last: AbdulHameed

first: Shanea

last: Estes

first: Tracy

last: O’Brien

first: Masakazu

last: Shiota

first: Anders

last: Wallqvist


title: Effect of Ramoplanin treatment on hESC-RPE transcriptome during POS phagocytosis

status: Public on Nov 25 2020

city: Dresden

first: Seba

last: Almedawar

address: Fetscherstrasse 105

country: Germany

institute: CRTD- TU Dresden

summary: we report the effect of Ramoplanin on the transcription profile of RPE cells in comparison to DMSO (Vehicle) or MFGE8+GAS6 treated cells in the presence and absence of POS

overall_design: The experiment contained 7 differently treated samples with 3 biological repeats

first: Sven

last: Schreiter


title: Co-option of the lineage-specific LAVA retrotransposon in the gibbon genome

status: Public on Jul 20 2020

city: Portland

first: Mariam

last: Okhovat

state: Oregon

address: 3030 S Moody Ave.

department: Medicine

institute: Oregon Health and Science University

sample_organism:
Hylobates lar
Hylobates muelleri
Hylobates pileatus
Symphalangus syndactylus
Nomascus gabriellae
Nomascus leucogenys
Hylobates moloch
Hoolock leuconedys


title: Multiple roles of H2A.Z in regulating promoter chromatin architecture in human cells

status: Public on Jun 01 2020

city: TALLAHASSEE

first: LAUREN

last: COLE

state: Florida

address: 319 STADIUM DR

institute: FLORIDA STATE UNIVERSITY


title: Expression data in PC3 prostate cancer cells treated with DMSO, HDAC inhibitor, EZH2 inhibitor, or combined HDAC and EZH2 inhibitors.

status: Public on May 05 2020

first: Ryan

last: Kuzmickas

summary: Transcriptional profiles were examined in PC3 prostate cancer cells treated with vehicle (DMSO), vorinostat (VOR, HDACi), GSK126 (GSK126, EZH2i) or all 3 agents (COMBO) at 72 hours, prior to the commencement of cell death, to investigate the molecular mechamism by which these drugs and their combinations are functioning.

overall_design: RNA was isolated from PC3 cells 72 hours after treatment with the indicated drugs (3 replicates per treatment arm)


title: Knocking out non-muscle myosin II in retinal ganglion cells promotes long-distance optic nerve regeneration (RNA-Seq II)

status: Public on Mar 24 2020

city: Tampa

first: Xuewei

last: Wang

state: FL

address: 4001 E Fletcher Ave, ALZ 339

department: Molecular Medicine

institute: University of South Florida

summary: In addition to altered gene expression, pathological cytoskeletal dynamics in the axon are another key intrinsic barrier for axon regeneration in the central nervous system (CNS). Here we showed that knocking out myosin IIA/B in retinal ganglion cells alone either before or after optic nerve crush induced significant optic nerve regeneration. Combined Lin28a overexpression and myosin IIA/B knockout led to additive promoting effect and long-distance axon regeneration. Immunostaining, RNA sequencing and western blot analyses revealed that myosin II deletion did not affect known axon regeneration signaling pathways or the expression of regeneration associated genes. Instead, it abolished the retraction bulb formation and significantly enhanced the axon extension efficiency. The study provided clear evidence that directly targeting neuronal cytoskeleton was sufficient to induce significant CNS axon regeneration, and combining altered gene expression in the soma and modified cytoskeletal dynamics in the axon was a promising approach for long-distance CNS axon regeneration

overall_design: Lumbar 4 and 5 Dorsal root ganglia mRNA profiles of Myh9/10 double-floxed mice (WT) and Advillin-Cre:Myh9/10 double-floxed mice (dKO) 3 days following sham surgery or sciatic nerve axotomy were generated by RNA-seq in duplicate.

first: Xue-Wei

first: Shu-Guang

last: Yang

first: Chi

last: Zhang

first: Ming-Wen

last: Hu

first: Jiang

last: Qian

first: Jin-Jin

last: Ma

first: Yingchi

first: Bin-Bin

first: Yi-Lan

last: Weng

first: Guo-Li

last: Ming

first: Anish

middle: R

last: Kosanam

first: Saijilafu

last: XXX

first: Feng-Quan

last: Zhou


title: Dynamic Regulation of Tfh Clonal Selection During the Germinal Center Reaction

status: Public on Mar 19 2020

city: NEW YORK

first: Thiago

middle: Y

last: Oliveira

state: New York

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University

summary: The Germinal center is a dynamic microenvironment wherein B cells expressing high affinity antibody variants produced by hypermutation are selected for clonal expansion by limiting numbers of T follicular helper cells. Although a great deal is known about the mechanisms that control B cell selection in the germinal center, far less is understood about the clonal behavior of the T follicular helper cells that regulate this process. Here we report on the dynamic behavior of clones of T follicular helper cells during the germinal center reaction. We find that like germinal center B cells, T follicular helper cells undergo antigen dependent selection during the germinal center reaction resulting in differential proliferative expansion and contraction. Increasing the amount of antigen presented in the germinal center leads to increased T follicular cell division. Competition between T follicular helper cell clones is mediated by T cell receptor affinity for peptide-MHC ligand. Higher affinity T cells expanding preferentially in the germinal center show increased expression of genes downstream of the T cell receptor, genes required for metabolic reprogramming, cell division and cytokine production. These dynamic changes lead to dramatic remodeling of the functional T follicular cell repertoire during the germinal center reaction.

overall_design: OTII-Fucci cells were adoptively transferred into C57Bl/6 mice that were immunized with NP-OVA and then boosted on day 7 with high and low affinity aDEC-APLs or nothing and analyzed after 18 hours. To examine the transcriptional programs associated with increased TCR affinity driven Tfh division we performed bulk mRNA sequencing. To determine whether there is dynamic redistribution of Tfh clones during a polyclonal immune response we followed clonotypes in the same mouse longitudinally by performing hemi-splenectomy on days 7 and 21 after immunization with NP-OVA. To ensure that we assayed T cells entering the spleen during the initial immune response we used mice that carry a tamoxifen inducible Cre in the CD62L locus and a tdTomato indicator (SellCreERT2 ROSAtdTmice). Tamoxifen injection into SellCreERT2 ROSAtdT reporter mice labels naïve T cells, but not Tfh cells and immunization recruits labeled naïve cells into the Tfh compartment. Naïve cells were labeled in reporter mice before immunization and following immunization tdTomato expressing Tfh were purified from hemisplectomized mice on days 7 and 21 after NP-OVA injection. Single cell RNA sequencing was carried out using Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-Seq) method.

first: Julia

last: Merkenschlager

first: Shlomo

last: Finkin

first: Victor

last: Ramos

first: Carla

last: Nowosad

first: Anna

last: Gazumyan

first: Melissa

last: Cipollac

first: Michel

middle: C

last: Nussenzweig


title: Co-option of the lineage-specific LAVA retrotransposon in the gibbon genome [WGS]

first: Mariam

last: Okhovat

summary: Co-option of transposable elements (TEs) to become part of existing or new enhancers is an important mechanism for evolution of gene regulation. However, contributions of lineage-specific TE insertions to recent regulatory adaptations remain poorly understood. Gibbons present a suitable model to study these contributions as they have evolved a lineage-specific TE called LAVA (LINE-AluSz-VNTR-AluLIKE), which is still active in the gibbon genome. The LAVA retrotransposon is thought to have played a role in the emergence of the highly rearranged structure of the gibbon genome by disrupting transcription of cell cycle genes. In this study, we investigated whether LAVA may have also contributed to the evolution of gene regulation by adopting enhancer function. We characterized fixed and polymorphic LAVA insertions across multiple gibbons and found 96 LAVA elements overlapping enhancer chromatin states. Moreover, LAVA was enriched in multiple transcription factor binding motifs, was bound by an important transcription factor (PU.1), and was associated with higher levels of gene expression in cis. We found gibbon-specific signatures of purifying/positive selection at 27 LAVA insertions. Two of these insertions were fixed in the gibbon lineage and overlapped with enhancer chromatin states, representing putative co-opted LAVA enhancers. These putative enhancers were located within genes encoding SETD2 and RAD9A, two proteins that facilitate accurate repair of DNA double-strand breaks and prevent chromosomal rearrangement mutations. Co-option of LAVA in these genes may have influenced regulation of processes that preserve genome integrity. Our findings highlight the importance of considering lineage-specific TEs in studying evolution of gene regulatory elements.

platform_organism:
Hylobates lar
Hylobates muelleri
Hylobates pileatus
Symphalangus syndactylus
Nomascus gabriellae
Nomascus leucogenys
Hylobates moloch
Hoolock leuconedys

overall_design: WGS: 23 samples

first: Lucia

last: Carbone


title: Redundant type II cadherins define neuroepithelial cell states for cytoarchitectonic robustness

status: Public on Sep 16 2020

first: SHOJI

last: TATSUMOTO

summary: Individual cell shape and integrity must precisely be orchestrated during morphogenesis. Here, we determine function of type II cadherins, Cdh6, Cdh8, and Cdh11, whose expression combinatorially demarcates the mouse neural plate/tube. While CRISPR/Cas9-based single type II cadherin mutants show no obvious phenotype, Cdh6/8 double knockout mice develop intermingled forebrain/midbrain compartments as these two cadherins’ expression opposes at the nascent boundary. Cdh6/8/11 triple, Cdh6/8 double or Cdh8/11 double knockout mice further cause exencephaly just within the cranial region where mutated cadherins’ expression merges. In the Cdh8/11 double knockout midbrain, we observe less-constricted apical actin meshwork, ventrally-directed spreading, and occasional hyperproliferation among dorsal neuroepithelial cells as origins for exencephaly. These results provide rigid evidence that, by conferring distinct adhesive codes to each cell, redundant type II cadherins serve essential and shared roles in compartmentalization and neurulation, both of which proceed under the robust control of the number, positioning, constriction, and fluidity of neuroepithelial cells.

overall_design: The mRNA profiles of the forebrain and midbrain tissues from type II cadherin double and triple knockout mice (E9.5) were generated using the Illumina HiSeq platforms. The numbers of each replicate are three to six, and the total number of samples is 32.

first: Takayoshi

last: Inoue

first: Kou

last: Hiraga

first: Shoji

last: Tatsumoto

first: Yasuhiro

last: Go


title: Identification of tissue regulatory T cell precursors in lymphoid organs

status: Public on Jan 01 2020

city: Mainz

first: Michael

last: Delacher

state: Rhineland-Palatinate

address: Langenbeckstrasse 1

department: Institute for Immunology

institute: University Medical Center of the Johannes Gutenberg-University Mainz


title: Dissecting molecular mediators of TGFb- and HGF-induced cell mechanical enhancement in NSCLC

status: Public on Dec 26 2019

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

summary: Importance of growth factor (GF) signaling in cancer progression is widely acknowledged. Transforming growth factor beta (TGFβ) and and hepa- tocyte growth factor (HGF) are known to play a key role in epithelial-to- mesenchymal transition (EMT) and metastatic cell transformation that are characterized by distinctive alterations in cell mechanical architecture and behavior towards a more robust and motile single cell phenotype. How- ever, molecular mechanisms mediating cancer type specific enhancement of cell mechanical properties in response to growth factors remain unlighted. Here, we combine high-throughput mechanical cell phenotyping, microarray analysis and gene-silencing to dissect molecular mediators of GF-induces cell mechanical enhancement in non-small-cell lung adenocarcinoma (NSCLC). Our experimental results show that both growth factors elevate cell rigidity, size and migratory activity, however, effects of TGFβ stimulation on cell mechanical phenotype and differential gene expression turn out to be significantly stronger. Our microarray analysis reveals that TGFβ-treated NSCLC cells exhibit upregulation of migration-, adhesion-related and down- regulation of cytokinesis-related groups of genes. In addition to vimentin, a canonical marker of EMT, a large number of cytoskeletal and motor proteins including previously reported MYL9, MYLK, TMP1 but also less-known un- conventional myosins are overexpressed in lung adenocarcenoma cells upon treatment with TGFβ. Selective probing of gene-silenced cells lead to identi- fication of unconventional myosin MYH15 as a novel mediator of elevated cell rigidity and invasiveness in TGFβ-stimulated NSCLC cells. In comparison to TGFβ, HGF-treated NSCLC cells respond with upregulation of a relatively small number of genes that are related to actin cyskeleton, microtubules and caveolae. Our results provide insights into phenotypic effects and molecular mechanisms of TGFβ- and HGF-induced mesenchymal cell transformation in NSCLC, and suggest that mediators of cell mechanical enhancement such as unconventional cytoskeletal and motor proteins represent promising phar- maceutical targets for restraining invasive spread of lung cancer.

overall_design: To observe the dynamic transcriptome and pathway response in the non-small cell lung cancer cell line H1975 after treatment with TGF-b or HGF we extracted RNA from biological duplicates and triplicates at t=[0h,0.5h,1h,2h,4h,6h,8h,12h,18h,24h,48h] after stimulation and compared the gene regulation relative to untreated cells at the same time points.

first: Melanie

last: Boerries

first: Ursula

last: Klingmüller

first: Evgeny

last: Gladilin

first: Kai

last: Breuhahn

first: Ruth

last: Merkle

first: Dmytro

last: Dvornikov


title: Whole transcriptome profiles during sheep skeletal muscle development

status: Public on Nov 18 2019

first: Tianpei

last: Shi

address: No. 2, Yuanmingyuan West Road, Huangzhuang, Haidian

institute: Chinese Academy of Agricultural Sciences

summary: Herein we present spatialtemporal profiles and performed a detailed data analysis in longissimum dorsi muscle of Chinese merino sheep at embryonic ages D85, D105, and D135. This is the first report of myogenic differentiaion and muscle fibre formation at the whole transcriptome level. The objective herein was to evaluate the whole transcriptome profiles and to develop an indepth and systematic understanding of molecular genetic controls underlying myofibre proliferation and differentiation in sheep. This report provides an effective reference for the study of non-coding RNA in other agricultural animals.

overall_design: The whole trancriptome profiles of 85,105 and 135-day old fetal skeletal muscle were generated by deep sequencing using Illumina Hiseq 4000 and Illumina Hiseq 2500.

first: Zhang

last: Li


title: Multiple roles of H2A.Z in regulating promoter chromatin architecture in human cells (Mnase-seq & ChIP-seq)

first: LAUREN

last: COLE

summary: We employed an MNase-Transcription Start Site Sequence Capture method to map and determine the accessibility of all nucleosomes, including those that contain H2A.Z, at high coverage for all human Pol II promoters. We uncovered unexpected features of nucleosomal organization in epithelial cells and following transition to a mesenchymal and malignant state. In contrast to the prevailing model, we observe many different types of active and inactive promoter structures that differ in their nucleosome organization and sensitivity to MNase digestion. Further, we found that  H2A.Z has an important role in the assembly of repressed promoters into an inaccessible state. Finally, we uncovered a new promoter type in which a stable H2A.Z nucleosome occupies the TSS of an active promoter.

overall_design: Nucleosome mapping via Mnase-seq and parallel ChIP-seq of H2A.Z in MCF10A and MCF10A-CA1a cells

first: Jonathan

last: Dennis

first: Lauren

last: Cole

first: Sebastian

last: Kurscheid

first: David

last: Tremethick


title: Knocking out non-muscle myosin II in retinal ganglion cells promotes long-distance optic nerve regeneration (RNA-Seq I)

status: Public on Mar 22 2020

first: Xuewei

last: Wang

overall_design: We compared the transcriptomic profiles of wild type and Myh9/10 double knockout retinal ganglion cells purified by FACS in triplicate.

first: Xue-Wei

first: Shu-Guang

last: Yang

first: Chi

last: Zhang

first: Ming-Wen

last: Hu

first: Jiang

last: Qian

first: Jin-Jin

last: Ma

first: Yingchi

first: Bin-Bin

first: Yi-Lan

last: Weng

first: Guo-Li

last: Ming

first: Anish

last: Kosanam

first: Saijilafu

last: XXX

first: Feng-Quan

last: Zhou


title: hNSCs siRNA NOVA2, PQBP1, BRPF1 and DYRK1A

status: Public on Oct 12 2019

city: Strasbourg

first: Amélie

last: Piton

address: 1 rue Laurent Fries

institute: IGBMC

summary: inactivation of NOVA2 gene in human neural stem cells (hNSCs). Two independent series

overall_design: hNSCs siRNA NOVA2

first: Amelie


title: Identification of tissue regulatory T cell precursors in lymphoid organs [scRNA]

first: Michael

last: Delacher

summary: Regulatory T (Treg) cells maintain self-tolerance in lymphoid tissues, and specialized Treg cells accumulate and perform homeostasis and regenerative functions in non-lymphoid tissues. A common differentiation pathway of homeostasis-promoting Treg cells in non-lymphoid tissues from a putative precursor remains elusive. By using novel reporter mice and single-cell RNA-sequencing, we identified precursor stages of the IL-33 receptor ST2-expressing non-lymphoid tissue Treg population in spleen and lymph nodes. Molecular profiling of these precursors versus mature tissue Treg cells revealed their sequence of differentiation on a single-cell level. Global chromatin profiling of non-lymphoid tissue Treg cells and progenitor populations revealed a stepwise acquirement of open chromatin accessibility at tissue Treg genes. Mechanistically, we identified and validated the basic leucine zipper transcription factor, ATF-like (Batf) as a driver of the molecular tissue Treg program. Understanding this tissue program will help to harness regenerative properties of tissue Treg cells for therapy.

overall_design: RNA-seq and scRNA-seq on FACS purified T cell subpopulatinos from different organs

first: Charles

last: Imbusch

first: Christian

last: Schmidl

first: Markus

last: Feuerer


title: The PedBE clock accurately estimates DNA methylation age in pediatric buccal cells [dataset 11,UCI]

status: Public on Sep 25 2019

city: Vancouver

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

type: Methylation profiling by genome tiling array

summary: The development of current biological markers of aging has primarily focused on adult samples. The epigenetic clock is one promising tool for measuring biological age that shows impressive accuracy across most tissues and age ranges. In adults, deviations from the DNA methylation (DNAm) age prediction are correlated with several agerelated phenotypes, such as mortality and frailty. In children, however, fewer such associations have been made, possibly because DNAm changes are more dynamic in pediatric populations as  compared to adults. To address this crucial gap, we aimed to develop a highly accurate, noninvasive biological measure age specific to pediatric samples by using buccal epithelial cell DNAm. We gathered 1,721 genome-wide DNAm profiles from 11 different cohorts of typically developing individuals aged 0 to 20 y old. Elastic net penalized regression was used to select 94 CpG sites from a training dataset (n = 1,032) and the performance was assessed in a separate dataset (n = 689). The DNAm at 94 CpG sites was highly predictive of age in the test cohorts (median absolute error = 0.35 y). The Pediatric-Buccal-Epigenetic (PedBE) clock was characterized in additional cohorts, showcasing the accuracy in longitudinal data, the performance in nonbuccal tissues and adult age ranges, and the association with obstetric outcomes. The PedBE tool for measuring biological age in children might help in understanding the environmental and contextual factors that shape the DNA methylome during child development, and how it, in turn, might relate to child health and disease.

overall_design: The Illumina Infinium HumanMethylation450 Beadchip was used to obtain genome-wide DNA methylation measures in human buccal epithelial swabs (n = 250) from the   University of California, Irvine cohort (UCI, Dataset 11) which is longitudinal cohort of newborns and infants for which their mothers were recruited  during the first trimester of pregnancy. All women had singleton, intrauterine pregnancies. Women were not  eligible for study participation if they met the following criteria: corticosteroids, or illicit  drugs during pregnancy (verified by urinary cotinine and drug toxicology). Exclusion  criteria for the newborn were early preterm birth (i.e., less than 34 weeks of gestational  age at birth), as well as any congenital, genetic, or neurologic disorders at birth. Buccal swabs were collected twice, once at newborn and again at 12 months.

first: Lisa

middle: M

last: McEwen

first: Kieran

last: O’Donnell

first: Megan

middle: G

last: McGill

first: Rachel

last: Edgar

first: Meaghan

last: Jones

first: Julia

last: MacIsaac

first: David

last: Lin

first: Katia

last: Ramadori

first: Alexander

last: Morin

first: Nicole

last: Gladish

first: Elika

last: Garg

first: Eva

last: Unternaehrer

first: Irina

last: Pokhvisneva

first: Neerja

last: Karnani

first: Michelle

middle: Z

last: Kee

first: Torsten

last: Klengel

first: Nancy

middle: E

last: Adler

first: Ronald

last: Barr

last: Letourneau

first: Gerald

middle: F

last: Giesbrecht

first: James

middle: N

last: Reynolds

first: Darina

last: Czamara

first: Jeffrey

last: Armstrong

first: Marilyn

last: Essex

first: Carolina

last: de Weerth

first: Roseriet

last: Beijers

first: Marieke

middle: S

last: Tollenaar

first: Bekh

last: Bradley

first: Tanja

last: Jovanovic

first: Kerry

last: Ressler

first: Meir

last: Steiner

first: Sonja

last: Entringer

first: Pathik

last: Wadhwa

first: Claudia

last: Buss

last: Bush

first: Elisabeth

middle: B

last: Binder


title: Gene expression profiling of tankyrase-inhibited mouse articular chondrocytes

status: Public on Sep 24 2019

city: Seoul

first: Jin-Hong

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

summary: Osteoarthritis (OA) is a prevalent degenerative disease, which involves progressive and irreversible destruction of cartilage matrix. Despite efforts to reconstruct cartilage matrix in osteoarthritic joints, it has been a difficult task as adult cartilage exhibits marginal repair capacity. Here we report the identification of tankyrase as a regulator of the cartilage anabolism axis based on systems-level factor analysis of mouse reference populations. Tankyrase inhibition drives the expression of a cartilage-signature matrisome and elicits a transcriptomic pattern that is inversely correlated with OA progression. Furthermore, tankyrase inhibitors ameliorate surgically-induced OA in mice, and stem cell transplantation coupled with tankyrase knockdown results in superior regeneration of cartilage lesions. Mechanistically, the pro-regenerative features of tankyrase inhibition are mainly triggered by uncoupling SOX9 from a poly(ADP-ribosyl)ation (PARylation)-dependent protein degradation pathway. Our findings provide insights into the development of future OA therapies aimed at reconstruction of articular cartilage.

overall_design: Gene expression profiling of primary cultured mouse articular chondrocytes treated with DMSO, XAV939, or IWR-1 or transfected with control siRNA or Tnks and Tnks2 siRNAs. Three biological replicates were used for each group.

first: Sangbin

last: Han

first: Sukyeong

first: Young-Ran

last: Gu


title: The PedBE clock accurately estimates DNA methylation age in pediatric buccal cells [dataset 15, MAVAN mothers cohort]

status: Public on Oct 18 2019

first: Michael

last: Kobor

summary: The development of current biological markers of aging has primarily focused on adult samples. The epigenetic clock is one promising tool for measuring biological age that shows impressive accuracy across most tissues and age ranges. In adults, deviations from the DNA methylation (DNAm) age prediction are correlated with several age-related phenotypes, such as mortality and frailty. In children, however, fewer such associations have been made, possibly because DNAm changes are more dynamic in pediatric populations as compared to adults. To address this crucial gap, we aimed to develop a highly accurate, noninvasive biological measure age specific to pediatric samples by using buccal epithelial cell DNAm. We gathered 1,721 genome-wide DNAm profiles from 11 different cohorts of typically developing individuals aged 0 to 20 y old. Elastic net penalized regression was used to select 94 CpG sites from a training dataset (n = 1,032) and the performance was assessed in a separate dataset (n = 689). The DNAm at 94 CpG sites was highly predictive of age in the test cohorts (median error = −0.35 y). The Pediatric-Buccal-Epigenetic (PedBE) clock was characterized in additional cohorts, showcasing the accuracy in longitudinal data, the performance in nonbuccal tissues and adult age ranges, and the association with obstetric outcomes. The PedBE tool for measuring biological age in children might help in understanding the environmental and contextual factors that shape the DNA methylome during child development, and how it, in turn, might relate to child health and disease.

overall_design: Human buccal epithelial cells from 250 women in the Maternal Adversity, Vulnerability and Neurodevelopment (MAVAN) cohort (dataset 15) were collected using the Illumina Infinium HumanMethylation450 Beadchip. Samples were taken at one timepoint with an age range of 25.5 to 51.4 years.

first: Lisa

last: McEwen

first: Kieran

last: O’Donnell

first: Megan

last: McGill

first: Rachel

last: Edgar

first: Meaghan

last: Jones

first: Julia

last: MacIsaac

first: David

middle: T

last: Lin

first: Katia

last: Ramadori

first: Alexander

last: Morin

first: Nicole

last: Gladish

first: Elika

last: Garg

first: Eva

last: Unternaehrer

first: Irina

last: Pokhvisneva

first: Neerja

last: Karnani

first: Michelle

last: Kee

first: Torsten

last: Klengel

first: Nancy

last: Adler

first: Ronald

last: Barr

last: Letourneau

first: Gerald

last: Giesbrecht

first: James

last: Reynolds

first: Darina

last: Czamara

first: Jeffrey

last: Armstrong


title: Genome wide expression profiles (RNAseq) of human CD8+ T cells in resting, activated (CD3+CD28) and PD-1-stimulated cells (CD3+CD28+PD-L1-Fc) at diferent time points

status: Public on May 29 2019

city: Madrid

first: Santos

last: Mañes

state: Madrid

address: C/Darwin, 3

department: Immunology and Oncology

country: Spain

institute: National Center of Biotechnology (CNB/CSIC)

summary: Background: Binding of the programmed death-1 (PD-1) receptor to its ligands (PD-L1/2) transduces inhibitory signals that promote exhaustion of activated T cells. Blockade of the PD 1 pathway is widely used for cancer treatment, yet the inhibitory signals transduced by PD-1 in T cells remain elusive. Methods: Expression profiles of human CD8+ T cells in resting, activated (CD3+CD28) and PD-1-stimulated cells (CD3+CD28+PD-L1-Fc) conditions were evaluated by RNA-seq. Bioinformatic analyses were used to identify signaling pathways differentially regulated in PD 1-stimulated cells.

overall_design: Total RNA was isolated from T control (IgG1-coated beads were used as control , N=3), T activadas (N=3) and Tactivadas+PD1 (N=3) at 6, 24 and 48 h post-stimulation.

last: Manes


title: LEDGF and HDGF2, histone H3K36 methyl-binding proteins that assist RNA polymerase II transcription through nucleosomes

status: Public on Sep 01 2019

city: Monterotondo

first: nicolas

last: descostes

address: via Ramarini 32

department: Bioinformatics

country: Italy

institute: EMBL

summary: FACT (facilitates chromatin transcription) is a protein complex that allows RNAPII to overcome the nucleosome-induced barrier to transcription.  While abundant in stem cells and many cancer cells, FACT it is not very abundant in most tissues.  Therefore, we screened for additional factors that might replace FACT in such tissues.  Here we report the identification of two such proteins, LEDGF and HDGF2, each containing two HMGA-like AT-hooks and a PWWP methyl-lysine reading domain known to bind to H3K36me2 and H3K36me3.  LEDGF and HDGF2 localize with H3K36me2/3 at genomic regions containing active genes, usually adjacent to H3K27me3 domains.  In myoblasts, where FACT expression is low, LEDGF and HDGF2 are enriched on most active genes.  Upon differentiation to myotubes, HDGF2 is recruited to the majority of myotube up-regulated genes and is required for their expression.  We propose that LEDGF and HDGF2 substitute for FACT in differentiated tissues and that their distribution on the genome helps maintain transcriptional programs unique to particular cell types.

overall_design:
Characterization of two new proteins having FACT-like activity
ChIP-seq and RNA-Seq for studying the role of LEDGF and HDGF2 in 293TRex and two differentiation systems
PRO-Seq of WT, HDGF2KO, and 'HDGF2KO rescued by WT' myoblast cells

first: Gary

last: LeRoy

first: Ozgur

last: Oksuz

first: Nicolas

last: Descostes

first: Rais

middle: A

last: Ganai

first: Havva

middle: O

last: Kara

first: Jia-Ray

last: Yu

first: Chul-Hwan

last: Lee

last: Stafford

first: Yuki

last: Aoi

first: Ali

last: Shilatifard

first: Danny

last: Reinberg


title: Ribo-tag translatomic profiling of Drosophila oenocyte reveals down-regulation of peroxisome and mitochondria biogenesis under aging and oxidative stress

status: Public on Dec 29 2018

city: Ames

first: Kerui

last: Huang

state: IA

address: 2437 Pammel Drive

department: Genetics and Genomics

institute: Iowa State University

summary: We used cell-type-specific ribosome profiling (Ribo-tag) to study the impacts of aging and oxidative stress on the expression of actively translated mRNA in adult Drosophila oenocytes. Polysome associated mRNAs from oenocyte were extracted from young flies and aged flies, treated with water or paraquat. Restults provide insight into aging mechanism and tissue specific response to stress in oenocyte.

overall_design: Drosophila melanogaster expressing FLAG tagged Rpl13A under oneocyte driver (PromE-Gal4 > Rpl13A-FLAG) was used in the experiment. Samples were collected in three replicate from sexually-mature freely-mated adults. Young (1-2 weeks old) and aged (4 weeks old) adults were transferred on control food or paraquat (10mM) food for 24 hours prior to mRNA extraction. Polysome were pulled down using anti-FLAG antibody and total RNAs were extracted. PolyA+ RNA was obtained from the total RNAs and was prepared to RNA-seq libraries. We further multiplexed RNA-seq libraries with indexed adaptors and pooled for sequencing.

first: Wenhao

last: Chen

first: Hua

last: Bai

first: Zhu

last: Fang

first: Pankaj

last: Kapahi


title: Identification and characterization of a transcribed distal enhancer involved in cardiac Kcnh2 regulation

status: Public on Aug 01 2019

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

summary: The human ether-a-go-go-related gene KCNH2 encodes the voltage-gated potassium channel underlying IKr, a current critical for the repolarization phase of the cardiac action potential. Mutations in KCNH2 that cause a reduction of the repolarizing current can result in cardiac arrhythmias associated with long QT syndrome. Here, we investigated the regulation of this critical cardiac gene and identified multiple active enhancers in the Kcnh2 locus. An enhancer ~85 kbp downstream of Kcnh2 physically contacted the promoters of two Kcnh2 isoforms in a cardiac-specific manner in vivo. Knockdown of a ncRNA controlled by this enhancer results in reduced expression of Kcnh2b and two neighboring mRNAs, Nos3 and Abcb8, in vitro. Genomic deletion of the enhancer, including the ncRNA transcription start site, from the mouse genome caused a modest downregulation of both Kcn2a and Kcn2b in the ventricles. These findings establish that the regulation of Kcnh2a and Kcnh2b is governed by a complex regulatory landscape that involves multiple partially redundantly acting enhancers.

overall_design: 4C-seq on adult murine hearts and livers to identify contact profiles of the Kcnh2 promoter and or cis-regulatory element Kcnh2_CRE11

first: Malou

last: van den Boogaard

first: Jan

middle: H

last: van Weerd

first: Harmen

middle: J

last: van de Werken


title: A comparison of the transcriptional profiles of invariant NKT cells derived from Wild type  and Eomes conditional knockout mice

status: Public on May 09 2019

city: Yokohama

first: Shin-ichiro

last: Fujii

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: IMS

institute: RIKEN

summary: Functional subsets of iNKT cells, NKT1, NKT2 and NKT17, have been reported to arise during the thymus to peripheral differentiation stages. The key transcription factors for NKT1, NKT2 and NKT17 development in the thymus have been identified as T-bet, Gata3 and Rorγt, respectively. In contrast, these iNKT cell subsets can also undergo further differentiation in the periphery. Eomesodermin (Eomes) is a T-box transcription factor with high homology to T-bet and is expressed by activated CD8+ T cells as well as in resting and activated NK cells. However, its role in invariant (i)NKT cells remains unknown. Here, we show the impact of Eomes on iNKT cells in the thymus and peripheral tissue using conditional knockout (Eomes-cKO) mice. Eomes regulates the differentiation of NKT1 cells in the thymus. In the peripheral tissue, Klrg1+ iNKT1 cells are generated in lung after vaccination with -GalCer-pulsed DCs (DC/Gal) as memory like iNKT cells. In the current study, we found that Eomes also regulates their differentiation into memory-like KLRG1+iNKT cells in the periphery.

overall_design: RNA-seq of invariant Natural Killer T cell population in steady state and primed state from 2 genotypes of mice

first: Kanako

last: Shimizu


title: Profiling of PML-body associated regions

status: Public on Aug 14 2019

city: Okazaki

first: Misuzu

last: Kurihara

state: Aichi

address: 5-1 Higashiyama, Myodaiji

institute: National Institute for Basic Biology

summary: The promyelocytic leukemia (PML) body is a phase-separated nuclear structure composed of various proteins including several chromatin regulators, and physically associates with chromatin. To address functional roles of the PML-chromatin association, we conducted genome-wide profiling of PML body-associated regions.

overall_design:
We performed genome-wide profiling of genomic regions associated with PML bodies in mESCs. Cells were treated with H2O2 to trigger labeling of chromatin with biotin (H2O2+). Experimental negative controls (H2O2-), where the H2O2 treatment was omitted, were also analyzed. Sequence reads were trimmed by using Trimmomatic, then mapped to repeat masked mm10 using bowtie2 version 2.3.5.1 with parameter -N1. ENCODE blacklisted regions and grey list prepared by chipseq-greylist were subsequently removed using bedtools.
BigWig files were generated by using bamCompare with option --scaleFactorsMethod SES --operation subtract.

first: Kagayaki

last: Kato

first: Chiaki

last: Sanbo

first: Shuji

last: Shigenobu

first: Yasuyuki

last: Ohkawa

first: Takeshi

last: Fuchigami

first: Yusuke

last: Miyanari


title: UBR7 is a novel E3 ubiquitin ligase for H2BK120 and acts as a tumor-suppressor in breast cancer

status: Public on Feb 08 2019

city: Houston

first: Kunal

last: Rai

state: TX

address: 1801 East Rd

department: Genomic Medicine

institute: MD Anderson Cancer Center

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

overall_design: Refer to individual Series


title: In vivo transcriptomic responses to thioacetamide exposure in rat liver, kidney, and heart tissue

status: Public on Sep 20 2018

city: Frederick

first: Patric

last: Schyman

address: 2405 Whittier Drive, Suite 200

institute: Biotechnology HPC Software Applications Institute (BHSAI)

summary: In this study we tested the ability to predict organ injury from transcriptomics data in Sprague-Dawley rats at early time points after exposure to thioacetmide (8 and 24 hours). We selected thioacetamide, an organosulfur compound extensively used in animal studies as a hepatotoxin and carcinogen for its ability to cause acute liver damage.

overall_design: We treated 30 Sprague-Dawley rats with saline solution (control), 25 mg/kg (low dose), and 100 mg/kg (high dose) to produce different degrees of injury. RNA samples for gene expression analysis were collected from the liver, kidney, and heart at 8 and 24 hours. Number of repicates were five.

first: Richard

middle: L

last: Printz

first: Shanea

middle: K

last: Estes

first: Kelli

last: Boyd

first: Masakazu

last: Shiota

first: Anders

last: Wallqvist


title: A systematic evaluation of the design, orientation, and sequence context dependencies of massively parallel reporter assays

status: Public on Dec 30 2019

city: South San Francisco

first: Vikram

last: Agarwal

state: CA

address: 1130 Veterans Blvd

institute: Calico Life Sciences

summary: Enhancers play important roles in evolution and disease. However, traditional assays to test enhancers are low throughput and not scalable to the >100,000 enhancers in the human genome. To better prioritize variants associated with disease and to study the role of enhancers, our group and others developed massively parallel reporter assays (MPRAs), which functionally screen thousands of sequences for regulatory activity in parallel. Although MPRAs have been applied to address diverse questions in gene regulation, there has been no systematic comparison of how differences in experimental design influence findings, making it difficult to interpret results and compare between groups. Here, we screen a library of 2,440 sequences, representing candidate liver enhancers and controls, in HepG2 cells for regulatory activity using nine different approaches (including conventional episomal, STARR-seq, and lentiviral MPRA designs). We identify subtle but significant differences in the resulting measurements that correlate with epigenetic and sequence-level features. We also test this library in both orientations with respect to the promoter, validating en masse that enhancer activity is robustly independent of orientation. Finally, we develop and apply a novel method to assemble and functionally test libraries of the same putative enhancers as 192-mers, 354-mers, and 678-mers, and observe surprisingly large differences in functional activity. This work provides a framework for the experimental design of high-throughput reporter assays, suggesting that the extended sequence context of tested elements, and to a lesser degree the precise assay, influence MPRA results.

overall_design: We systematically cloned the same library of 2,440 candidate enhancers into nine different MPRA designs. These included episomal vs lentivirally integrated constructs as well as STARR-seq and traditional upstream reporter assays. We also synthesized a subset of the 2,440 candidate sequences as 192bp, 354bp, and 678bp sequences to test for the effect of added sequence context on activity. Finally, we directionally cloned the full library in both directions to compare effects of direction on activity. All libraries were transfected into the human liver hepatocellular carcinoma cell line, HepG2.

first: Jason

last: Klein

first: Fumitaka

last: Inoue

first: Aidan

last: Keith

first: Beth

last: Martin

first: Martin

last: Kircher

first: Nadav

last: Ahituv

first: Jay

last: Shendure


title: UBR7 is a novel E3 ubiquitin ligase for H2BK120 and acts as a tumor-suppressor in breast cancer [ChIP-Seq]

summary: Plant Homeo Domain (PHD) is a versatile chromatin reader/effector module which recognizes methylated, acetylated or unmodified histone substrates and regulates cellular gene expression programs. Although PHD domains shows selective epigenetic recognition of methylated, acetylated and unmodified histone substrates, there has been no previous report on its catalytic function regulating malignant transformation of cells. Here we report that PHD finger of UBR7 (Ubiquitin Protein Ligase E3 Component N-Recognin 7 (Putative)), in isolation or in context of full length protein, harbors E3 ubiquitin ligase activity towards monoubiquitination of histone H2B at lysine 120 . Knockdown of UBR7 in MCF10a and breast cancer cells decreased H2BK120ub both at the global levels and on specific genes. Conversely, overexpression of wild type, but not catalytic mutant, rescued H2BK120ub levels. Low UBR7 expression was associated with basal-like and triple negative breast cancers as well as showed poor expression in metastatic tumors. Consistently, UBR7 loss resulted in invasion properties, induced epithelial-to-mesenchymal transition and promoted metastasis. Conversely, ectopic expression of UBR7 reduced cell growth, invasion and tumor growth in mouse fat pad. Mechanistically, UBR7 reduced H2BK120ub gene body of cell-adhesion related genes as well as gene expression including on CDH4 gene. Importantly, rebuilding CDH4  levels rescued invasion phenotypes seen in UBR7-low cells. Collectively, our results establish that UBR7 PHD has novel H2B ubiquitin ligase activity and it suppresses tumor growth in basal-like breast cancers.

overall_design: Examination of 7 different histone modifications in Wild Type and UBR7-shRNA MCF10A Cell Line

first: Christopher

last: Terranova


title: Bulk RNA sequencing of kidney tubuloids and the tissue that the tubuloids were derived from

status: Public on Dec 20 2018

city: Utrecht

first: Frans

last: Schutgens

address: Uppsalalaan 8

institute: Hubrecht Institute / UMC Utrecht

summary: Adult Stem Cell (ASC )-derived organoids are 3D epithelial structures that recapitulate essential aspects of their organ of origin. We have developed conditions for the long-term growth of primary kidney tubular epithelial organoids (‘tubuloids’). Cultures can be established from mouse and human kidney tissue, as well as from urine and can be expanded for at least 20 passages (> 6 months). The structures retain a normal number of chromosomes. Human tubuloids represent proximal as well as distal nephron segments, as evidenced by gene expression, immunofluorescence and tubular functional analyses. BK virus infection of tubuloids recapitulates in vivo phenomena. "Tumoroids" can be established from Wilms nephroblastoma. Kidney tubuloids from urine from a subject with Cystic Fibrosis (CF) allows ex vivo assessment of treatment efficacy. Finally, tubuloids cultured on microfluidic organ-on-a-chip plates adopt a tubular conformation and display active (trans-)epithelial transport function. Adult kidney-derived epithelial tubuloids allow studies of hereditary, infectious and malignant kidney disease in a personalized fashion.

overall_design: We generated transcriptome data of kidney tubuloids (n=3) and the tissue that the tubuloids were derived from (n=3).

first: Maarten

last: Rookmaaker

first: Carola

last: Ammerlaan

first: Jitske

last: Jansen

first: Marco

last: Viveen

first: Linda

last: Gijzen

first: Annelotte

last: Vonk

first: Karin

last: de Winter-de Groot

first: Benedetta

last: Artegiani

first: Ruben

last: van Boxtel

first: Edwin

last: Cuppen

first: Antoni

middle: P

last: Hendrickx

first: Marry

last: van den Heuvel-Eibrink

first: Ellen

last: Heitzer

first: Henriette

last: Lanz

first: Jeffrey

last: Beekman

first: Jean-Luc

last: Murk

first: Rosalinde

last: Masereeuw

first: Jarno

last: Drost

first: Marianne

middle: C

last: Verhaar

first: Hans

last: Clevers


title: Single-cell RNA-seq of murine thymic Treg cell progenitors and mature Treg cells

status: Public on Dec 31 2018

city: MInneapolis

first: Michael

last: Farrar

state: MN

address: 2101 6th Street SE

department: Lab Medicine and Pathology

institute: University of Minnesota

summary: We use single-cell RNA-seq to determine distinct selection phenotypes of 2 rare thymic Treg cell progenitors as well as mature thymic Treg cells

overall_design: A single cell suspension was generated from murine thymus then magnetically depleted for CD8/Ter119 before sorting CD25+Foxp3-, CD25-Foxp3lo and CD25+Foxp3+ cells from CD4+CD73- thymocytes on a BD Aria II. The 10x Genomic platform…

first: David

last: Owen

first: Rebecca

last: LaRue


title: Cellular and Molecular Changes in Psoriasis Lesions Induced by Ustekinumab: Distinct Differences in Responders vs. Non-Responders

status: Public on Feb 01 2019

city: Spring House

first: K

last: Li

state: PA

address: 1400 McKean Road

institute: Janssen R&D

summary:
A gene expression profiling sub-study was conducted in which skin biopsy samples (n=192) were collected for RNA extraction and hybridization to microarrays from patients with moderate-to-severe psoriasis who participated in ACCEPT, an IRB-approved Phase 3, multicenter, randomized trial.
This analysis identified gene expressions significantly modulated in psoriasis lesions (LS) following ustekinumab or etanercept treatment at week 12 compared to baseline.  Molecular expression of mRNA was found to be different in ustekinumab PASI75 responders vs. nonresponders. Differential modulation of selected mRNAs was also observed between ustekinumab and etanercept PASI75 responders.

overall_design: Skin biopsy samples (n=192) were collected at baseline and 12 weeks after ustekinumab or etanercept treatment for RNA extraction and microarray analysis from patients with moderate-to-severe psoriasis.

first: Carrie

last: Brodmerkel

first: Katherine

first: Sandra

last: Garcet

first: Karen

last: Hayden

first: Andrea

last: Chiricozzi

first: Inna

last: Novitskaya

first: Judilyn

last: Fuentes-Duculan

first: Mayte

last: Suárez-Fariñas

first: Kim

last: Campbell

first: James

middle: G

last: Krueger


title: Real-time quantitative PCR analysis of human stroke patients recovering from upper extremity hemiparesis

status: Public on Aug 31 2018

city: Washington

first: Matthew

last: Edwardson

state: DC

address: 4000 Reservoir Rd NW, Building D, Room 207

department: Neurology

institute: Georgetown University

summary: Fasting blood samples were collected from 27 stroke patients in EDTA tubes mean 19 days post-stroke, plasma was extracted and frozen at -80C, then 200uL of plasma sent for qPCR.

overall_design: qPCR microRNA expression profiling. Expression profiles from participants with good arm recovery, as assessed by a change in the Action Research Arm Test (ARAT) score >=6  from baseline to 6 mo. post-stroke were compared to those with poor recovery (ΔARAT < 6).


title: Transcriptome profiling of normal and transformed mouse urothelial cells

status: Public on Jan 01 2019

city: New York

first: Tomasz

middle: Boguslaw

last: Owczarek

state: NY

address: 1130 St. Nicolas Av.

department: Hematology and Oncology

institute: Columbia University

summary:
Transcriptome analysis of urothelial KRT5-traced and KRT8-traced YFP-sorted cells with and without combinatorial loss of Trp53 and Pten.
Bladders from 2-month-old KRT5-CreERT2, Rosa26YFP/LacZ mice, 2-month-old KRT8-CreERT2, Rosa26YFP/LacZ mice, 5-month-old KRT5-CreERT2, p53flox/flox, Ptenflox/flox, Rosa26YFP/+ mice, and 5-month-old KRT8-CreERT2, p53flox/flox, Ptenflox/flox, Rosa26YFP/+ mice were enzymatically dissociated, sorted for YFP by FACS, harvested, resuspended in Trizol and snap frozen for subsequent molecular analysis.

overall_design: Total RNA obtained from YFP-sorted urothelial cells were harvested and processed for RNA isolation and transcriptome analysis using the MagMAX RNA isolation kit (Ambion). RNA was amplified using SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara # 634891).

first: Chioma

last: Madubata

first: Raul

last: Rabadan

middle: M

last: Shen

first: Cory

last: Abate-Shen


title: Transcriptome analysis of kidney organoids

first: Frans

last: Schutgens


title: Genome-wide mapping of 8-oxodG and gH2AX in growing MCF10A cells and MEFs

status: Public on Nov 28 2018

city: Naples

first: Stefano

last: Amente

address: via pansini, 5

department: Department of  Molecular Medicine and Medical Biotechnologies

institute: University of Naples "FEDERICO II"

summary: 8-oxo-7,8-dihydro-2’-deoxyguanine (8-oxodG) is one of the major DNA modifications and a potent pre-mutagenic lesion prone to mispair with deoxyadenine (dA). Several thousand residues of 8-oxodG spread constitutively in the genome of human cells, but their genomic distribution has not yet been characterized. Here, by using OxyDIP-Seq, a highly sensitive methodology that uses high-throughput sequencing, we report the first genome-wide distribution of 8-oxodG in human cells, using the non-tumorigenic epithelial breast cells MFC10A. Results were compared with those we obtained in mouse embryo fibroblasts. OxyDIP-Seq revealed sites of 8-oxodG accumulation overlapping with gH2AX ChIP-Seq signals within gene bodies of long transcribed genes.

overall_design: Genome-wide maps of 8-oxodG and gH2AX in growing MCF10A and MEF cells.

first: Giacomo

last: Di Palo

first: Giovanni

last: Scala

first: Tiziana

last: Castrignanò

first: Sergio

last: Cocozza

first: Luigi

last: Lania

first: Pier

last: Pelicci

first: Gaetano

middle: I

last: Dellino

first: Barbara

last: Majello


title: Heart expression data from WT mice at ZT12 after short ischemia/reperfusion +/- Reverb alpha antagonist treatment

status: Public on Mar 15 2018

city: Lille

first: Lefebvre

last: Philippe

state: Nord

address: Blvd Pr. J.Leclerc

institute: Inserm

summary:
Nuclear receptor Reverb alpha is a component of circadian rythm which could be evolved in cardioprotection strategy. We test if pharmacological modulation of these target could be suitable for cardioprotection after ischemia reperfusion injury
We used microarrays to detail the global programme of gene expression

overall_design: heart ischemia reperfusion were performed using Langendorff isolated heart model and twenty minutes stop flow ishemia with twenty minutes reperfusion.

first: Xavier

last: Marechal

first: David

last: Montaigne

first: Celine

last: Gheeraert

first: Philippe

last: Lefebvre


title: Multi-axial self-organisation properties of mouse embryonic stem cells into gastruloids

status: Public on Jun 01 2018

city: Geneva

first: Leonardo

last: Beccari

address: 30 Quai Ernest Ansermet

department: Genetics and Evolution

country: Switzerland

institute: University of Geneva


title: Multi-axial self-organisation properties of mouse embryonic stem cells into gastruloids [individual]

summary: Gastruloids, small aggregates of murine Embryonic Stem (ES) cells stimulated to undergo gastrulation-like symmetry breaking events in vitro (van den Brink, S. C. et al. 2014, Simunovic, M. & Brivanlou, A. H 2017).  Analysis of the transcriptional profiles from pools of gastruloids collected at different time-points after aggregation (AA) revealed that gastruloids are capable of organizing an axially integrated post-occipital pattern of neural, mesodermal and endodermal derivatives that mimics that of the embryo in terms of gene expression. To test the homogeneity and reproducibility of the transcriptional programs uncovered by our bulked RNAseq experiments, we performed RNAseq analysis of individual gastruloids collected at different time-points AA (10 biological replicates per time-point). Our results indicates that the transcriptional profiles of gastruloid were highly reproducible at each time points and that each gastruloid implement the full diversity of transcriptional programs detected in our bulked RNAseq experiments.

overall_design: RNA-seq analysis of individual gastruloids collected at different time-points after aggregation

first: L

first: N

last: Moris

first: M

last: Girgin


title: ChIP-seq for H3K4me3, H3K27me3, H3K79me2 in MCF10A cells

status: Public on Feb 01 2018

city: Cambridge

first: Dexter

middle: X

last: Jin

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute

summary: We performed ChIP-Seq against histones H3K4me3, H3K27me3, and H3K79me2 in MCF10A cells to identify transcription factors with bivalent and pseudo-bivalent epigenetic modifications.

overall_design: Performing ChIP-Seq on MCF10A cells

first: Daniel

last: Miller

first: Ethan

last: Sokol


title: DNMT and HDAC inhibitors globally induce cryptic TSSs encoded in long terminal repeats

status: Public on May 29 2017

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

type: Methylation profiling by high throughput sequencing

summary: By mapping global transcription start site (TSS) and chromatin dynamics, we observed the activation of thousands of cryptic, currently non-annotated TSSs (TINATS) following DNMTi and/or HDACi treatment. The resulting transcripts encode truncated or chimeric open reading frames that can be translated into products with predicted abnormal functions or immunogenic potential. TINAT activation after DNMTi coincided with DNA hypomethylation and gain in H3K4me3, H3K9ac, and H3K27ac histone marks. In contrast, HDACi induced only canonical TSSs in association with histone acetylation, but TINATs via a yet unknown mechanism. Nevertheless, both inhibitors convergently induced unidirectional transcription from identical sites since TINATs are encoded in solitary long-terminal repeats of the endogenous retrovirus-9 family, epigenetically repressed in virtually all normal cells.

overall_design: CAGE-, ChIP-, and WGB-sequencing of NCI-H1299 EGFP-NEO reporter cells after treatment with DMSO, DAC, SB939, or DAC+SB

last: Brocks

first: Christopher

middle: R

last: Schmidt

first: Michael

last: Daskalakis

last: Oakes

first: Ting

last: Wang

first: Christoph

last: Plass


title: Sex-specific Transcriptional Signatures in Human Depression

status: Public on Aug 12 2017

first: Eddie

last: Loh

address: 1425 Madison Avenue

department: Department of Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary:
Rational: Major depressive disorder (MDD) is a leading cause of disease burden worldwide. While the incidence, symptoms and treatment of MDD all point toward major sex differences, the molecular mechanisms underlying this sexual dimorphism remain largely unknown.
Methods: Here, combining differential expression and gene coexpression network analyses, we provide a comprehensive characterization of male and female transcriptional profiles associated with MDD across 6 brain regions. We overlap our human profiles with those from a mouse model of chronic variable stress and capitalize on converging pathways to define molecular and physiological mechanisms underlying the expression of stress susceptibility in males and females.
Results: Our results show a major rearrangement of transcriptional patterns in MDD, with limited overlap between males and females, an effect seen in depressed humans and in stressed mice. We identify key regulators of sex-specific gene networks underlying MDD and confirm their sex-specific impact as mediators of stress susceptibility. For example, downregulation of the female-specific hub gene DUSP6 in prefrontal cortex mimics stress susceptibility in females only by increasing ERK signaling and pyramidal neuron excitability. Such DUSP6 downregulation also recapitulates the transcriptional remodeling that occurs in PFC of depressed females.
Conclusions: Together, our findings reveal dramatic sexual dimorphism at the transcriptional level in MDD and highlight the importance of studying sex-specific treatments for this disorder.

overall_design:
RNA sequencing data from (1) 6 human postmortem brain regions in males and females with and without major depression and (2) 2 epuivalent brain regions in males and female mice with and without 21 days of chronic varibale stress (CVS).

Note: The raw data for Samples GSM2740709-GSM2740726, GSM2740805, and GSM2740808 were updated in January 2018. The processed data have not changed.

first: Benoit

last: Labonte

first: Olivia

last: Engmann

first: Immanuel

last: Purushothaman

first: Caroline

last: Ménard

first: Junshi

first: Chunfeng

last: Tan

first: Joseph

last: Scarpa

first: Gregory

last: Moy

first: Yong-Hwee

middle: E

last: Cahill

first: Zachary

middle: S

last: Lorsch

first: Peter

last: Hamilton

first: Erin

last: Calipari

first: Georgia

last: Hodes

first: Orna

last: Issler

first: Hope

last: Kronman

first: Madeline

last: Pfau

first: Aleksandar

last: Obradovic

first: Yan

last: Dong

first: Rachael

last: Neve

first: Scott

last: Russo

first: Andrew

last: Kazarskis

first: Carol

last: Tamminga

first: Naguib

last: Mechawar

first: Gustavo

last: Turecki

first: Bin

last: Zhang

first: Li

last: Shen

first: Eric

last: Nestler


title: Enhanced Protein Translation Underlies Improved Metabolic and Physical Adaptations to Different Exercise Training Modes in Young and Old Humans

status: Public on Mar 28 2017

city: Rochester

first: Surendra

last: Dasari

address: 200 First Street SW

department: Quantitative Health Sciences Research

institute: Mayo Clinic

summary: The molecular transducers of benefits from different exercise modalities remain incompletely defined. Here we report that 12 weeks of high-intensity aerobic interval (HIIT), resistance (RT), and combined exercise training enhanced insulin sensitivity and lean mass, but only HIIT and combined training improved aerobic capacity and skeletal muscle mitochondrial respiration. HIIT revealed a more robust increase in gene transcripts than other exercise modalities, particularly in older adults, although little overlap with corresponding individual protein abundance was noted. HIIT reversed many age-related differences in the proteome, particularly of mitochondrial proteins in concert with increased mitochondrial protein synthesis. Both RT and HIIT enhanced proteins involved in translational machinery irrespective of age. Only small changes of methylation of DNA promoter regions were observed. We provide evidence for predominant exercise regulation at the translational level, enhancing translational capacity and proteome abundance to explain phenotypic gains in muscle mitochondrial function and hypertrophy in all ages.

overall_design: The prospective exercise training study was approved by the Mayo Clinic Institutional Review Board, registered at https://clinicaltrials.gov (#NCT01477164) and conducted in accordance with the Declaration of Helsinki. All participants provided informed written consent. Participants were recruited into two distinct age groups: young (18–30 years) or older (65–80 years) with a goal of an equal number of men and women. The final groups were approximately balanced for sex, and all women in the older group were post-menopausal. Exclusion criteria were structured regular exercise (>20 min, twice weekly), cardiovascular disease, metabolic diseases (type 2 diabetes mellitus, fasting blood glucose > 110 mg/dL, and untreated hypothyroidism or hyperthyroidism), renal disease, high body mass index (BMI > 32 kg/m2), implanted metal devices, pregnancy, smoking, and history of blood clotting disorders. Exclusionary medication included anticoagulants, insulin, insulin sensitizers, corticosteroids, sulfonylureas, barbiturates, peroxisome proliferator-activated receptor γ agonists, β blockers, opiates, and tricyclic antidepressants. Following baseline measurements, the participants were randomized to three groups (HIIT, RT, or CT) using gRand (v1.1, Peter A. Charpentier) following a permuted block strategy with block length of 15 and 2 factors (age and sex). HIIT was 3 days per week of cycling (4 × 4 min at >90% of peak oxygen consumption [VO2 peak] with 3 min pedaling at no load) and 2 days per week of treadmill walking (45 min at 70% of VO2 peak). RT consisted of lower and upper body exercises (4 sets of 8–12 repetitions) 2 days each per week. CT participants first underwent a 12-week sedentary period (SED) and wore accelerometers to record any structured activity. Following SED, participants underwent metabolic studies and began CT of 5 days per week cycling (30 min at 70% VO2 peak) and 4 days per week weight lifting with fewer repetitions than RT. Both baseline and post-training studies were performed in all participants.

first: Matthew

last: Robinson

first: Sree

last: Nair


title: Transcriptome analysis on wild type and ddx39a mutant zebrafish embryos by Next Generation Sequencing

city: Nanjing

first: Yuxi

last: Yang

state: Jiangsu

address: Room 402, 12 Xuefu Road, Nanjing University

department: Medical School

institute: Nanjing University

summary: DEAD box RNA helicase DDX39A has been shown to regulate RNA metabolism; however its role in vertebrate development has not previously been examined. To determine the impact of loss of ddx39a on transcriptome during vertebrate early development, we pursued transcriptome analysis (RNA-Seq) on wild type and ddx39a mutant zebrafish embryos at 24 hour-post-fertilization. And by using RIP-seq to identify targeted RNA which were DDX39A binded.

overall_design: Using RNA-seq to identify the changes in the transcriptomic landscape in ddx39a mutants. Using RIP-seq to identify DDX39A binding RNAs.

first: Xin

last: Lou


title: Identification of microRNAs in sheep heart

status: Public on Sep 15 2017

city: Singapore

first: Lee Lee

last: Wong

address: 14 Medical Drive, 08-01

department: Medicine

country: Singapore

institute: National University of Singapore

summary: MicroRNA sequencing of myocardium of ovine comparing normal (Control), paced-induced heart failure (HF) and heart failure recovery (HF-R) after discontinuation of pacing.

overall_design: Three RNA groups were generated from the pooling of 4 Cont, 6 HF and 4 HF-R samples, and 100 ng of total RNA from each group converted into three small RNA libraries using a NEBNEXT library generation kit (New England Biolabs Inc., Ipswich, MA, USA) according to the manufacturer’s instructions. Each pooled RNA sample was ligated with adaptors to its 3’ and 5’ ends and converted into cDNA before pre-amplification with specific primers containing sample-specific indexes. After 15 cycles, pre-PCR cDNA was purified on QiaQuick columns (Qiagen, Hombrechtikon, Switzerland) and the insert efficiency evaluated by the 2100 Bioanalyzer on high sensitivity DNA chips (Agilent Inc., Waldbronn, Germany). The miRNA cDNA were size fractionated (LabChip XT, Caliper Inc., Hopkintin, MA, USA) and bands representing adaptors and 15-50 base pair (bp) inserts were excised and collected. Based on quality of the inserts and the concentration measurements the 3 libraries were assembled in equal concentrations. The libraries were finally quantified again with qPCR and sequenced on the Illumina NextSeq 500 system (Illumina Inc., San Diago, CA, USA).

first: Lee

first: Peipei

last: Wang


title: The PedBE clock accurately estimates DNA methylation age in pediatric buccal cells

status: Public on Sep 17 2019

city: Vancouver

first: Michael

middle: S.

last: Kobor

address: 950 West 28th Avenue

department: Medical Genetics

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

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

overall_design: Refer to individual Series


title: Effect of selection on residual feed intake and diet on gene expression in whole blood of pig

status: Public on Jul 01 2016

city: Saint-Gilles

first: Annie

last: Vincent

address: domaine de la prise

institute: INRA

summary: Transcriptional profiling in the whole blood of 48 pigs (132 days of age) originated from two lines divergently selected for residual feed intake (RFI) : low-RFI pigs (RFIneg), high-RFI pigs (RFIpl). Both lines were offered isocaloric and isoproteic diets with contrasted energy source and nutrients:  low fat, low fiber (LF) diet or a high fat, high fiber (HF)diet during 10 weeks. Effects of RFI selection, diet and interaction between diet and line were investigated.

overall_design: Four experimental groups : low-RFI pigs fed high fat, high fiber diet (HF_RFIneg), high-RFI pigs fed high fat, high fiber diet(HF_RFIpl),  low-RFI pigs fed low fat, low fiber diet (LF_RFIneg) and high-RFI pigs fed low fat, low fiber diet(LF_RFIpl). 12 pigs per condition. One replicate per array.

first: Maëva

last: Jégou

first: Isabelle

last: Louveau

first: Florence

last: Gondret


title: Calcifying vascular smooth muscle cells and osteoblasts: independent cell types exhibiting extracellular matrix and biomineralization-related mimicries

status: Public on Oct 10 2014

city: Rotterdam

first: Jeroen

last: van de Peppel

address: 's Gravendijkwal 230

institute: ErasmusMC

summary:
Background: Ectopic vascular calcifications represent a major clinical problem associated with cardiovascular disease and mortality. However, the mechanisms underlying pathological vascular calcifications are largely unknown hampering the development of therapies to tackle this life threatening medical condition.
Results: In order to gain insight into the genes and mechanisms driving this pathological calcification process we analyzed the transcriptional profile of calcifying vascular smooth muscle cells (C-VSMCs). These profiles were compared to differentiating osteoblasts, cells that constitute their physiological calcification counterparts in the body. Overall the transcriptional program of C-VSMC and osteoblasts did not overlap. Several genes, some of them relevant for bone formation, were distinctly modulated by C-VSMCs which did not necessarily lose their smooth muscle cell markers while calcifying. Bioinformatics gene clustering and correlation analysis disclosed limited bone-related mechanisms being shared by two cell types. Extracellular matrix (ECM) and biomineralization genes represented common denominators between pathological vascular and physiological bone calcifications. These genes constitute the strongest link between these cells and represent potential drivers for their shared end-point phenotype.
Conclusions: the analyses support the hypothesis that VSMC trans-differentiate into C-VSMCs keeping their own identity while using mechanisms that osteoblasts use to mineralize. The data provide novel insights into groups of genes and biological processes shared in MSC and VSMC osteogenic differentiation. The distinct gene regulation between C-VSMC and osteoblasts might hold clues to find cell-specific pathway modulations, opening the possibility to tackle undesired vascular calcifications without disturbing physiologic bone formation and vice versa.

overall_design: Total RNA obtained from hMSC and hVSMC cultured in osteogenic differentiation medium supplemented with 1.8  mM Ca2+ for 0, 2, 8, 12 or 25 days respectively. For each timepoint 3 replicates were used, with exception for day 0 where 4 replicates were collected.

first: Alves

last: Rodrigo

first: Marco

last: Eijken

first: Johannes

last: van Leeuwen


title: Core oxidative stress response (COSR) in Aspergillus nidulans

status: Public on Dec 31 2015

city: Debrecen

first: Tamas

last: Emri

address: Egyetem ter 1

country: Hungary

institute: University of Debrecen

summary: Genome wide transcriptional changes induced by various types of oxidative stresses as well as salt stress were studied in a DatfA mutant and the appropriate control A. nidulans strains. Although a significant number of stereotypically regulated genes was identified (Core Oxidative Stress Response or COSR genes) when the global transcriptional effects of five different oxidative stress conditions were compared the number of co-regulated genes decreased to 13 when NaCl stress was included into the analyses. The appearance of only a few co-regulated genes and the great number of genes regulated merely by one certain type of stress do not support the existence of a S. cerevisiae-type Environmental Stress Response in A. nidulans. Deletion of atfA, a true functional ortholog of fission yeast’s “all-purpose” stress response transcription factor, increased the oxidative stress sensitivity of A. nidulans and affected the transcription of several genes under both unstressed and stressed conditions. The number of genes under AtfA control was quite stress-type dependent; e.g. deletion of atfA altered the transcription of a wide spectrum of genes under menadione sodium bisulfite stress but had only a minor effect on the transcriptome profiles when A. nidulans cultures were exposed to H2O2, tBOOH, NaCl and, especially, to diamide stress. These observations suggest that the function of AtfA in the regulation of various stress responses is much smaller than we thought before or other transcription factors can take over a number of AtfA’s functions when the atfA gene is deleted. It is noteworthy that both oxidative and salt stress induced the transcription of some secondary metabolite gene clusters and the deletion of atfA enhanced the stress responsiveness of further clusters. Surprisingly, certain clusters were down-regulated by the stress conditions tested and the majority of them were not stress-responsive at all. Therefore, stress dependent regulation seems to be a frequent but far not a general feature of the regulation of secondary metabolism in A. nidulans.

overall_design: 14 samples, 7 with the control strain and 7 with an DatfA strain (each series contains samples from untreated as well as menadione, low concentration hidrogen-peroxide, high concentration hidrogen-peroxide, tert-butylhydroperoxide, diamide and NaCl treated cultures)

first: Tamás

first: Vera

last: Szarvas

first: Erzsébet

last: Orosz

first: Károly

last: Antal

first: HeeSoo

last: Park

first: Kap-Hoon

last: Han

first: Jae-Hyuk

last: Yu

first: István

last: Pócsi


title: Context-dependent role of ARF for response to chemotherapy in muscle invasive bladder cancer

status: Public on Nov 15 2016

first: Tomasz

last: Owczarek

summary: Gene expression profiling analysis (RNAseq) of mouse bladder epithelium from wildtype mice (Arf+/+; p53+/+; Pten+/+) or bladder tumors from Arf-wild-type (Arf+/+; p53f/f; Ptenf/f) or Arfnull (Arff/f; p53f/f; Ptenf/f) mice that had been treated with vehicle or cisplatin

overall_design: Total RNA obtained from bladder epithelium or bladder tumors. Bladder tissues or tumors were harvested and processed for RNA isolation and transcriptome analysis using the MagMAX RNA isolation kit (Ambion).

middle: B

first: Takashi

last: Kobayashi

first: Ricardo

last: Ramirez

first: David

last: Solit

first: Cory

last: Abate-Shen


title: Genome-wide blood transcriptional profiling in critically ill patients - MARS consortium

status: Public on Jul 06 2015

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

summary: The host response in critically ill patients with sepsis, septic shock remains poorly defined. Considerable research has been conducted to accurately distinguish patients with sepsis from those with non-infectious causes of disease. Technological innovations have positioned systems biology at the forefront of biomarker discovery. Analysis of the whole-blood leukocyte transcriptome enables the assessment of thousands of molecular signals beyond simply measuring several proteins in plasma, which for use as biomarkers is important since combinations of biomarkers likely provide more diagnostic accuracy than the measurement of single ones or a few. Evidence suggests that genome-wide transcriptional profiling of blood leukocytes can assist in differentiating between infection and non-infectious causes of severe disease. Of importance, RNA biomarkers have the potential advantage that they can be measured reliably in rapid quantitative reverse transcriptase polymerase chain reaction (qRT-PCR)-based point of care tests.

overall_design: PAXgene blood RNA was isolated at intensive-care unit (ICU) admission and throughout ICU length-of-stay. Through the use of genome-wide microarrays we aimed to identify molecular features that enbale the adequate discrimination of infectious and non-infectious sources of critical illness. Patient diagnoses include community-acquired pneumonia (cap), hospital-acquired pneumonia (hap) and non-infectious cap control patients (no-cap) (characteristics: pneumonia diagnoses). The influence of variable degrees of thrombocytopenia were also assessed (characteristics: thrombocytopenia).

first: Tom

last: van der Poll


title: Effects of selection on residual feed intake and diet on gene expression in pig tissues

first: Annie

last: Vincent


title: Gene expression profiling in skeletal muscle 3 hours following the performance of an eccentric exercise

status: Public on Oct 04 2010

city: Amherst

first: Robert

last: Hyldahl

address: Totman Building 30 Eastman Lane

department: Department of Kinesiology

institute: University of Massachusetts Amherst

summary: Eccentric exercise (ECC) can result in ultra-structural and histological damage to skeletal muscle. The damage incurred following ECC is typically followed by a subsequent regenerative and adaptive response. The specific mechanisms that drive this response, particularly in human muscle, are not well understood. The objective of this study was to characterize the early molecular response in skeletal muscle following ECC in humans. We used an Agilent whole human genome microarray to assess global gene expression in male subjects (N=35) at 3 hours post-100 eccentric contractions of the knee extensors. ANCOVA (age and BMI covariates) was used to compare mRNA expression between the ECC and non-exercised (CON) legs of each subject. Novel transcripts from IPA identified networks were confirmed with quantitative real-time (qRT)-PCR. qRT-PCR analysis of 3 of these transcripts (IkBα, TNFRSF1A and ICAM-1) confirmed changes observed in the microarray analysis.

overall_design: 35 male subjects performed an eccentric exercise protocol consisting of 100 maximal eccentric contrations of the knee extensors.  3 hours after the completion of the exercise regimen, a muscle biopsy was taken from the vastus lateralis of both legs. The non-exercised leg served as the control. Gene expresssion was analyzed using an ANCOVA, with covariates for age and BMI.

middle: D

first: Ling

last: Xin

first: Stuart

last: Chipkin

first: Monica

last: Hubal

first: Priscilla

last: Clarkson


title: Cell-type transcriptomes of the multicellular green alga Volvox carteri yield insights into the evolutionary origins of germ and somatic differentiation programs

status: Public on Dec 11 2017

city: Saint Louis

first: James

last: Umen

address: 975 N Warson Rd

institute: Donald Danforth Plant Science Center

summary: Germ-soma differentiation is a hallmark of complex multicellular organisms, yet its origins are not well understood. Volvox carteri is a simple multicellular green alga that has recently evolved a simple germ-soma dichotomy with only two cell types: large germ cells called gonidia and small terminally differentiated somatic cells. Here, we provide a comprehensive characterization of the gonidial and somatic transcriptomes of Volvox to uncover fundamental differences between the molecular and metabolic programming of these cell types. We found extensive transcriptome differentiation between cell types, with somatic cells expressing a more specialized program overrepresented in younger, lineage-specific genes and gonidial cells expressing a more generalist program overrepresented in more ancient genes that shared striking overlap with metazoan stem-cell-specific genes. Directed analyses of metabolic pathways revealed a strong dichotomy between cell types with gonidial cells expressing growth-related genes and somatic cells expressing an altruistic metabolic program geared towards the assembly of flagella, which support organismal motility, and the conversion of storage carbon to sugars, which act as donors of extracellular matrix glycoproteins whose secretion enables massive organismal expansion. Volvox orthologs of Chlamydomonas diurnally regulated genes were analyzed for cell-type distribution and found to be strongly partitioned, with expression of dark-phase genes overrepresented in somatic cells and light-phase genes overrepresented in gonidial cells, a result that is consistent with cell type programs in Volvox arising by cooption of temporal regulons in a unicellular ancestor. Together our findings reveal fundamental molecular, metabolic, and evolutionary mechanisms that underlie the origins of germ-soma differentiation in Volvox and provide a template for understanding the acquisition of germ-soma differentiation in other multicellular lineages.

overall_design: Gonidial cells and somatic cells of Volvox were separated and RNA was extracted from each cell type pool. RNA-seq libraries were generated from the extracted RNA and sequenced using high-throughput Illumina sequencing. A total of 4 RNA-seq samples were generated, 2 gonidial cell biological replicates and 2 somatic cell biological replicates.

first: Gavriel

middle: Y

last: Matt


title: Genome-wide analysis of EGR2/SOX10 binding in myelinating peripheral nerve

status: Public on Apr 01 2012

city: Madison

first: John

last: Svaren

state: WI

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

summary: We provide ChIP-Seq analysis of Egr2 and Sox10 transcription factor binding in Schwann cells of rat peripheral nerve

overall_design:
ChIP-Seq analysis of Egr2 and Sox10 binding in P15 rat sciatic nerve.
Wiggle files of negative log of posterior probability determined by Mosaics using rat genome Rn4

first: Sunduz

last: Keles

first: Guannan

last: Sun

first: Rajini

last: Srinivasan


title: Early Pregnancy Gene Expression Profiling of Women with Preeclampsia: The “Vitamin D Antenatal Asthma Reduction Trial” (VDAART) Study

status: Public on Aug 24 2017

city: Boston

first: Alvin

middle: T.

last: Kho

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

type:
Expression profiling by array
Other

summary: Peripheral whole blood transcriptome profiles of pregnant women with normal pregnancy and preeclampsia from 10-18 weeks of gestational age enrolled in the “Vitamin D Antenatal Asthma Reduction Trial” (VDAART).

overall_design:
Comparing the whole blood (PAXgene) transcriptome from 10-18 weeks of gestational age of 110 mothers with normal pregnancies versus 47 mothers with preeclampsia.
Whole blood transcriptome, disease state analysis

first: Hooman

last: Mirzakhani

first: Augusto

middle: A

last: Litonjua

first: Thomas

middle: F

last: McElrath

first: George

last: O’Connor

first: Aviva

last: Lee-Parritz

first: Ronald

last: Iverson

last: Macones

first: Leonard

last: Bacharier

last: Zeiger

first: Bruce

middle: W

last: Hollis

first: Diane

last: Handy

first: Amitabh

last: Sharma

first: Nancy

last: Laranjo

first: Vincent

middle: J

last: Carey

first: Weilliang

last: Qiu

first: Marc

last: Santolini

first: Shikang

last: Liu

first: Divya

last: Chhabra

first: Daniel

last: Enquobahrie

first: Michelle

last: Williams

first: Joseph

last: Loscalzo

first: Scott

middle: T

last: Weiss


title: Human annulus disc cells grown in a 3D collagen sponge and exposed to TNF-a

status: Public on Oct 31 2012

city: Charlotte

first: Helen

last: Gruber

state: NC

address: 1542 Graden Terrace

department: Orthopaedic Surgery

institute: Carolinas HealthCare System

summary:
The objective of this study was to determine how TNF-a, an important proinflammatory cytokine, affects gene expression in the human annulus.
Cells were grown in a 3D collagen construct for 14 days with TNF-a. mRNA was isolated and  subjected to microarray. Fold changes in gene expression were determined via GeneSifer software.

overall_design: Human disc tissue samples were obtained from surgical disc procedures performed on patients with herniated discs and degenerative disc disease. Cultured annulus cells were grown in a 3D collagen construct with or without 10e3 pM TNF-a for a total of 14 days. Following homogenization in TRIzol reagent, total RNA was isolated and analyzed via mircoarray.

first: Gretchen

middle: L

last: Hoelscher

first: Jane

last: Ingram

first: Edward

middle: N

last: Hanley Jr