title: Transcriptome profile of Trichoderma asperellum challenged with Organophosphorus Pesticide Dichlorvos

status: Public on Jul 19 2018

city: Fuyang

first: Mi

last: NI

state: Anhui

address: No.100 Qinghe West Road

institute: Fuyang Normal Univ

summary: We report the application of RNA sequencing technology for transcriptome profiling of Trichoderma asperellum challenged with Organophosphorus Pesticide Dichlorvos.  Based on RNA-seq analysis, in T. asperellum TJ01 treated with 100 μg/mL, 500 μg/mL, and 1000 μg/mL dichlorvos, 204, 490, and 872 genes were significantly upregulated, respectively, while 37, 177, and 383 genes were significantly downregulated, respectively. This study provides a framework for the application of transcriptome profiling towards characterization of trichoderma under stress of Organophosphorus Pesticide.

overall_design: Examination of differential response of Trichoderma in Dichlorvos treated group or control .

first: Jun

last: Tang

last: Ni


title: Comparative analyses of human saliva and plasma IgG antibody reactivities

status: Public on Jul 17 2018

city: Vienna

first: Peter

last: Hettegger

address: Giefinggasse 4

department: Center for Health and Bioresources

country: Austria

institute: Austrian Institute of Technology

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

platform_organism:
human gammaherpesvirus 4
Hepatitis B virus adw/991

overall_design: Refer to individual Series


title: Comparative analyses of human saliva and plasma IgG antibody reactivities [HBV]

summary: Saliva based diagnostics is a rapidly evolving field due to the large potential of saliva and the simple sample collection. A systematic comparison of IgG antibody profiles in saliva and plasma is currently lacking in scientific literature. Our hypothesis is that IgG profiles are equal in blood and saliva. By showing the equality of the profiles and relative IgG antigenic reactivities towards proteins and peptides we provide evidence that plasma IgG reactivities can be inferred from saliva IgG reactivities. IgG antibodies were isolated from human saliva and plasma samples. The reactivities of IgG isolates were analysed on peptide microarrays displaying linear epitopes of EBV (EBNA1 protein) and HBV (Large envelope protein) virus. Peptide arrays were printed by JPT Peptide Technologies (Berlin, Germany). We show high similarity of saliva and plasma IgG profiles on these two platforms and argue for generalisation from this subset to the whole immunological IgG antibody profile.

overall_design: IgG antibodies were isolated from paired plasma and saliva samples of 20 individuals.

first: Jasmin

last: Huber

first: Katharina

last: Paßecker

first: Lisa

last: Milchram

first: Regina

last: Soldo

first: Ulrike

last: Kegler

first: Christa

last: Nöhammer

first: Andreas

last: Weinhäusel


title: Transcriptome dynamics Associated with Resistance and Susceptibility against Fusarium Head Blight in Four Wheat Genotypes

status: Public on Aug 09 2018

city: Ottawa

first: Ziying

last: Liu

state: ON

address: 1200 Montreal Road

country: Canada

institute: National Research Council, Canada

type: Expression profiling by high throughput sequencing

summary: We report differentially expressed genes in four wheat genotypes, Nyubai, Wuhan 1 and their progeny line HC374, shaw associated with resistance and susceptibility against Fusarium Head Blight (FHB). Our result indicates an early up-regulation of LRR-RKs distinct between susceptible and resistant genotypes; subsequently, different sets of genes associated with defense response were up-regulated. Differences in expression profiles among the resistant genotypes indicate genotype specific defense mechanisms. This study also showed a greater resemblance in transcriptomics of HC374 to Nyubai, consistent with their sharing of two type II FHB resistant QTLs on 3BS and 5AS, than to Wuhan 1 which carries one QTL on 2DL in common with HC374.

overall_design: The four genotypes were subjected to challenge by the pathogenic fungus Fusarium graminearum and water mock treatment as a control

first: Youlian

last: Pan

first: Hélène

last: Rocheleau

first: François

last: Fauteux

first: Yunli

last: Wang

first: Curt

last: McCartney

first: Thérèse

last: Ouellet


title: Transcriptional profiling of Hepa1-6-bearing mouse model

status: Public on Aug 02 2018

city: Shanghai

first: Qilong

last: Chen

address: 1200, Cailun Road

country: China

institute: TCM center

summary: Hepa1-6-bearing C57BL/6 mouse model was established to evaluate the therapeutic efficacy of Ganoderma lucidum extract (GLE) in HCC. The GLE treated and untreated mice were used for transcriptioanl profiles detection, and 126 differentially expressed lncRNAs and 558 DE mRNAs were identified, respectively. The bioinformatics analysis shows that the GLE could suppress the growth and proliferation of HCC by PI3K/Akt/mTOR and MAPK signaling pathway, and also could induce apoptosis of tumor cell by mitochondrial and death receptor pathway.

overall_design: 6 samples, including 3 GLE treated Hepa1-6-bearing C57 BL/6 mice and 3 GLE untreated Hepa1-6-bearing C57 BL/6 mice were performed to analyze

first: Ruolin

last: Zhao


title: Alteration in the transcriptome of lung resident fibroblast upon genetic knockdown of Wilms' tumor1 transcription factor

status: Public on Aug 01 2018

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

country: USA

institute: University of Cincinnati

summary: Pulmonary fibrosis (PF) is associated with many chronic lung diseases including Systemic sclerosis (SSc), Idiopathic Pulmonary Fibrosis (IPF) and Cystic Fibrosis (CF) which are characterized by the progressive accumulation of stromal cells and formation of scar tissue. Pulmonary fibrosis is a dysregulated response to alveolar injury which causes a progressive decline in lung function and refractory to current pharmacological therapies. Airway and alveolar epithelial cells and stromal cells contribute to pulmonary fibrosis but the cell-specific pathways and gene networks that are responsible for the pathophysiology are unknown. Recent published reports from our lab demonstrated the aberrant activation of Wilms' tumor1 (WT1) transcription factor in lung resident fibroblast and myofibroblast in IPF lung biopsies and the mouse model of transforming growth factor-α (TGFα) and bleomycin induced fibrosis. In this study, we sought to determine the role of WT1 in transcriptome changes in lung resident fibroblast during pulmonary fibrosis. Our results showed that WT1 regulates the transcriptional changes that are required for the fibroblast activation processes such fibroproliferation, myofibroblast transformation and extracellular matrix deposition during pulmonary fibrosis. Finally, this study demonstrates that WT1 is a critical regulator of fibroblast activation in IPF and hence serve as a target for therapeutic intervention.

overall_design: mRNA profiles of cultured fibrotic lung resident fibroblast isolated from TGFα mice and treated with Control or WT1-specific siRNA.

first: Vishwaraj

last: Sontake

first: Jenny

first: Satish

middle: K

last: Madala


title: CD73 knockdown effect in pancreatic cancer cell lines

status: Public on Jul 13 2018

city: Hangzhou City, Zhejiang Province

first: Liangjing

last: Zhou

address: no. 3,QingChun east road,Jianggan District, Hangzhou City, Zhejiang Province

department: Department of General Surgery

institute: Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China

summary: Recent studies have shown that non-enzymatic function of CD73 play a key role in tumor progression, but this function of CD73 in pancreatic cancer cells has not been studied. In the present study, PANC-1 cell lines were transfected with CD73 siRNA, and proliferation ability and cell cycle was significantly inhibited. However, little is known about the mechanisms involved in CD73 regulation in tumors.

overall_design: Six sampels including three CD73 knockdown cells by siRNA and three negative control cell lines were used.

first: Shengnan

last: Jia


title: Comparative analyses of human saliva and plasma IgG antibody reactivities [EBV]

first: Peter

last: Hettegger

overall_design: IgG antibodies were isolated from paired plasma and saliva samples of 20 individuals. Technical replicates (repeated IgG purification and microarray processing from the same sample) and sample replicates (repeated sampling from one individual) are included.

first: Jasmin

last: Huber

first: Katharina

last: Paßecker

first: Lisa

last: Milchram

first: Regina

last: Soldo

first: Ulrike

last: Kegler

first: Christa


title: Alternative RNA processing events in a double NSR mutant Arabidopsis

status: Public on Jul 12 2018

city: Gif Sur Yvette

first: Jeremie

last: Bazin

address: Bâtiment 630, rue de Noetzlin Plateau du Moulon

country: France

institute: CNRS

summary: We analyze the effect of a double deletion mutant for alternative-splicing regulators nsra and nsrb (Nuclear Speckle RNA binding proteins), on the Arabidopsis thaliana transcriptome.

overall_design: RNA-seq experiments (polyA+ RNA) in triplicates for each condition WT and nsrab mutants.

first: N

last: Romero-Barrios

first: Federico

last: Ariel

first: Martin

last: Crespi


title: Human peripheral blood mononuclear cells (PBMC): post- ECP treatment vs. pre-treatment (baseline)

status: Public on Jul 02 2018

city: Houston

first: Xiao

last: Ni

state: TX

address: 1515 Holcombe Blvd.

department: Dermatology

institute: MD Anderson Cancer Center

summary: Transcriptional profiling of human peripheral mononuclear cells in patients with leukemic cutaneous T-cell lymphoma (CTCL): a pilot study of effects of extracorporeal photopheresis (ECP) in clinically responsive and non-responsive/resistant patients

overall_design: Four-condition experiment: Day 2 post-ECP vs. baseline, non-responsive; I month post-ECP vs. baseline, non-responsive; Day 2 post-ECP vs. baseline, responsive; I month post-ECP vs. baseline, responsive. Five biological replicates in each condition; 2 technical replicates.


title: Transcriptomic profiles of Senegalese sole in response to infection with different reassortant strains of betanodavirus

status: Public on Jul 25 2018

city: Malaga

first: Alejandro

last: Labella

state: Malaga

address: Boulevard Louis Pasteur campus teatinos Faculty of Sciences

department: Microbiology

country: Spain

institute: University of Malaga

summary: Betanodaviruses (VNNV) are the causative agents of the viral nervous necrosis, a disease that affects cultured Senegalese sole (Solea senegalensis). VNNV reassortant strains, combining genomic segments from the RGNNV and SJNNV genotypes, have previously been isolated from wild and farmed several fish species. The wild reassortant wSs160.03 isolated from sole has been proved to be more virulent for sole than the parental genotypes (RGNNV and SJNNV), causing 100% mortality. Mutations of wSs160.03 strain performed by reverse genetic, have allow to obtain a mutant reassortant strain (rSs160.03247+270) with mutations at amino acids 247 (serine to alanine) and 270 (serine to asparagine), which provoke a 40% decreased mortality. In the current study, the RNA-Seq technology has been used to compare the Senegalese sole transcriptomes in two organs (head-kidney and eye/brain) after infection with the wild reassortant strain and the mutant reassortant strain. A total of 633 genes were differentially expressed (DEGs) in animals infected with the wSs160.03 strain, whereas only 393 genes were differentially expressed in animals infected with the rSs160.03247+270 strain, indicating a 37.9% decrease in the number of DEGs after infection with the mutated reassortant strain. An inversion in the proportion of genes up/down-regulated in nervous tissue of these animals was also obtained for both reassortants. To understand the biological functions of identified DEGs involved in VNNV infection, a gene ontology (GO) enrichment analysis was performed with fold change > 1.5 (up- or down-regulated) and p-value < 0.05. Different profiles of GO were obtained in the subclasses biological process, cellular component, and molecular function for each reassortant strains. Regarding the immune response, genes coding for proteins acting as mediators of IFN type I expression (DHX58, IRF3, IRF7) and IFN-stimulated genes (ISG15, Mx, PKR, Gig1, ISG12, IFI44, IFIT-1, to name a few) were up-regulated in animals infected with the wild type reassortant, whereas no-differential expression of these genes was observed in animals infected with the mutant reassortant. The different transcriptomic profiles obtained could help to better understand VNNV pathogenesis in Senegalese sole, setting up the importance as virulence determinants of amino acids at positions 247 and 270 within the RNA2 segment.

overall_design: Evaluation of amino acid positions 247 and 270 of the capsid protein as virulence determinants of VNNV.

middle: M

first: Juan

middle: J

last: Borrego

first: Esther

last: García-Rosado


title: Targeting oncogenic β-catenin/CBP activity for the treatment of head and neck squamous cell carcinoma

status: Public on Jul 03 2018

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: Head and neck squamous cell carcinoma (HNSCC) presents primarily as oral squamous cell carcinoma (OSCC), an aggressive malignancy characterized by heterogeneity, locoregional metastases and resistance to existing treatments. Although a number of molecular alterations associated with OSCC have been identified, they have had limited impact on clinical management. A frequent feature of OSCC is the inappropriate activation of nuclear β-catenin. Here, we provide a comprehensive characterization of the effects of blocking the interaction between nuclear β-catenin and the cAMP-responsive element binding (CREB)-binding protein (CBP) using the small molecule inhibitor ICG-001. We demonstrate that ICG-001 inhibits cell proliferation and aggressive OSCC cell phenotypes in cellular, zebrafish and murine models, and that its inhibition-associated transcriptional signature tracks with advanced tumor grade and poor survival in human patients. Our results suggest that targeting the β-catenin/CBP interaction in the nucleus represents a new and effective therapy for OSCC.

overall_design:
Microarray gene expression profiling pertaining to ICG-001 or DMSO (control) treatment in HSC-3 and CAL27 cells, and siCTNNB1 or scrambled siRNA control in HSC-3 cells ; n=3 per treatment group, per cell line).

Note: the preprocessed data were generated from two normalizations: 1) samples GSM2522361-GSM2522372, and 2) samples GSM2522373-GSM2522378, plus six other arrays that are not included in this Series.  The preprocessed data for samples GSM2522373-GSM2522378 therefore cannot be reproduced entirely from this Series alone.

first: Vinay

last: Kartha

first: Maria

last: Kukuruzinska


title: Identification of the targets of RNA binding protein NSRa [RIP-seq]

summary: We used RNA immunoprecipitation and sequencing to identify NSRa targets

overall_design: rRNA depleted RNA was isolated from immunoprecipitation eluate of pNSRa:NSRa:HA and input samples


title: Overlapping activities of SRRM3 and SRRM4 regulate vital pre-mRNA splicing events for neuromuscular synaptogenesis and neuron-specific gene expression

status: Public on Jul 01 2018

city: Coralville

first: Botond

last: Banfi

state: Iowa

address: 2501 Crosspark Road

department: Anatomy and Cell Biology

institute: University of Iowa


title: Expression profiling of microRNAs in oxygen-induced retinal neovascularization in mice

status: Public on Jun 19 2018

city: Changsha

first: Yedi

last: Zhou

state: Hunan

address: No. 139, Middle Renmin Road

department: Department of Ophthalmology

institute: The Second Xiangya Hospital, Central South University

summary: The purpose of this study is to identify disease-related miRNAs in retinas of a mouse model of oxygen-induced retinopathy (OIR). OIR pups were exposed to 75% oxygen at postnatal day (P)7 for 5 days, and were returned to room air at P12. The miRNAs expression profiles in the retinas from OIR mice at P17 and room air controls were determined through microarray analysis. Expressions of significantly upregulated and downregulated miRNAs in the OIR retinas and controls were confirmed through quantitative real-time RT-PCR (qPCR). Compared to the room air controls, 3 miRNAs were significantly up-regulated, and 8 miRNAs were down-regulated in OIR retinas. Our findings indicated that several miRNAs were differentially expressed in the oxygen-induced retinal neovascularization, which might provide novel therapeutic targets in regulating retinal neovascular diseases.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: In this study, three samples from OIR mice retinas and another three samples from room air control mice retinas at postnatal day 17 were used to acquire the miRNA expression profiling.

first: Lusi

last: Zhang

first: Tantai

last: Zhao


title: Expression from C. elegans L1 animals

status: Public on Jun 04 2018

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary:
Nutrient-driven O-GlcNAcylation of key components of the transcription machinery may epigenetically modulate gene expression in metazoans. Knockouts of the O-GlcNAc cycling enzymes in C. elegans are viable and fertile, allowing a global analysis of the impact of GlcNAcylation.  Here we compare gene expression in wild type and O-GlcNAc mutants (ogt-1 and oga-1) in synchronized, fed L1 animals.
Whole genome transcriptional profiling of the O-GlcNAc cycling mutants confirmed dramatic deregulation of genes in these key pathways. As predicted, the O-GlcNAc cycling mutants show phenotypically altered lifespan and susceptibility to UV stress.

overall_design: L1 larvae were synchronized by starvation for two days after hatching in sterile buffer and then plated on NGM with E. coli (OP50) and allowed to feed for 3 hours at room temperature.  Wild type and mutant animals were collected and total RNA isolated for gene expression analysis.

first: Michael

last: Krause

first: John

last: Hanover


title: Uterine microbiome in postpartum dairy cows: Associations with ovarian cyclicity and endometrial transcriptome at five and nine weeks after calving

city: Columbia

first: Matthew

last: Lucy

state: Missouri

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: University of Missouri

summary: We hypothesized that the uterine microbiome postpartum would affect the endometrial transcriptome in “real-time” (implicating a direct interaction between microbial products and the endometrium and also that the microbiome could program the future function of the endometrium (implicating a uterine programming perhaps through mechanisms similar to inflammatory memory). To test this hypothesis, we performed 16S rRNA gene sequencing of the endometrial microbiome at one, five and nine weeks after calving and tested for an effect of the microbial population on the endometrial transcriptome at five and nine weeks after calving using mRNA-sequencing. As expected, the initiation of cyclicity and elevated circulating progesterone (P4) affected the endometrial transcriptome. We also report evidence for both “real-time” and long-term programming of the endometrial transcriptome by the microbiome. An unexpected result was that some of the affected genes in the endometrial microbiome on the endometrial transcriptome were identical to those affected by ovarian cyclicity. This unexpected observation may implicate an indirect mechanism through which the endometrial microbiome can act in a systemic manner to mediate endometrial function through a pathway that involves restoration of ovarian cyclicity postpartum.

first: Stephen

middle: G

last: Moore

middle: C


title: Next-generation sequencing of PDLSC transcriptome

status: Public on Jul 11 2018

city: Beijing

first: Yunfei

last: Zheng

state: Beijing

address: 22 Zhongguancun Avenue South, Haidian District

department: Oral and Maxillofacial Surgery

institute: Peking University School and Hospital of Stomatology

type: Non-coding RNA profiling by high throughput sequencing

summary: We performed RNA-sequencing and miRNA-sequencing to detect the whole transcriptome of periodontal ligament stem cells (PDLSCs) at different stages during osteogenic differentiation.

overall_design: PDLSCs were isolated and cultured in osteogenic medium. Total RNA from cells at D0, D3, D7, and D14 were extracted, and submitted to RNA-sequencing and miRNA-sequencing.

first: Lingfei

last: Jia

first: Weiran

last: Li


title: ILC1 lineage identity is determined by a cis-regulatory element marked by a novel lncRNA [ATAC-seq]

status: Public on Jul 14 2018

city: Farmington

first: Asli

last: Uyar

state: CT

address: 10 Discovery Dr

department: Computational Sciences

institute: The Jackson Laboratory

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Innate lymphoid cells (ILCs) comprise three groups of recently identified tissue resident immune cell lineages that play critical roles in protective immune responses and tissue homeostasis. While significant progress has been made in defining the key protein mediators of ILC development and function, how cis-acting epigenetic regulatory elements or long non-coding RNAs (lncRNAs) regulate ILCs is unknown. Herein, we describe a cis-regulatory element demarcated by a novel lncRNA that controls the maturation, function and lineage identity of group 1 ILCs while being dispensable for early ILC development and homeostasis of mature ILC2s and ILC3s. We named this ILC1-restricted lncRNA Rroid. The Rroid locus controls the functional specification and lineage identity of ILC1 by promoting chromatin accessibility and STAT5 deposition at the promoter of its neighboring gene, Id2, in response to the ILC1-specific cytokine IL-15.

overall_design: Examination of chromatin accessibility in mouse NK cells.

first: Walter

last: Mowel

first: Sam

last: McCright

first: Jonathan

last: Kotzin

first: Magalie

last: Collet

first: Xin

first: Alexandra

last: DeLaney

first: Sean

middle: P

last: Spencer

first: Anthony

middle: T

last: Virtue

first: Enjun

last: Yang

first: Alejandro

last: Villarino

first: Makoto

last: Kurachi

first: Margaret

last: Dunagin

first: Gretchen

last: Harms Pritchard

first: Judith

last: Stein

first: Cynthia

last: Hughes

first: Diogo

last: Fonseca-Pereira

first: Henrique

last: Veiga-Fernandes

first: Arjun

last: Raj

first: Taku

last: Kambayashi

first: Igor

middle: E

last: Brodsky

last: O’Shea

first: E

last: Wherry

first: Loyal

middle: A

last: Goff

middle: L

last: Rinn

first: Adam

last: Williams

first: Richard

last: Flavell

first: Jorge

last: Henao-Mejia


title: Cytochrome P450 Monooxygenase Mediated Metabolic Utilization of Benzo(a)pyrene by Fungi

status: Public on Jul 10 2018

city: Madison

first: Jae-Hyuk

last: Yu

state: Wisconsin

address: 1550 LInden Dr.

department: Bacteriology

institute: UW-Madison

summary: Soil dwelling Aspergillus fungi possess the versatile metabolic capability to utilize complex organic compounds which are toxic to humans, yet the mechanisms they employ remain largely unknown. Benzo(a)pyrene is a common carcinogenic contaminant, posing a significant concern for human health. Here, we report that Aspergillus fungi can degrade benzo(a)pyrene effectively. In Aspergillus nidulans, exposure to benzo(a)pyrene results in transcriptomic and metabolic changes associated with cellular growth and energy generation, implying that the fungus utilizes benzo(a)pyrene as a food. Importantly, we identify and characterize the conserved bapA gene encoding a cytochrome P450 monooxygenase that exerts the first step in the degradation of benzo(a)pyrene. We further demonstrate that the fungal NF-κB-type global regulators VeA and VelB are required for benzo(a)pyrene degradation in A. nidulans, which occurs through expression control of bapA in response to nutrient limitation. Our study illuminates fundamental knowledge of fungal benzo(a)pyrene metabolism and provides novel insights into enhancing bioremediation potential.

overall_design: Aspergillus nidulans hyphae were incubated in 0.1% glucose media with 200 µM benzo(a)pyrene or solvent only control (DMSO) and samples were taken at 6, 24, and 48 hours post incubation. Timepoint zero represents spore inoculation in 1% glucose media and growth for 18 hours. Transcripts were sequenced using Illumina HiSeq2500

first: Erin

last: Ostrem Loss


title: Deconstructive SCNT reveals heterogeneity within Treg population [single-cell]

status: Public on May 30 2018

city: Freiburg

first: Manching

last: Ku

address: Mathildenstrasse 1

department: Hematology and Oncology

country: Germany

institute: Medical Center - University of Freiburg

summary: Thymic-derived Treg cells consist of heterogeneous subsets with different characteristics and development.

overall_design: Previously, we used somatic cell nuclear transfer (SCNT) to generate a naturally occurring Treg (nTreg) model. Given our surprising findings relating to the TCR strength of nTreg cells, and the many additional conflicting hypotheses that have evolved around Treg cells, we hypothesized that the Treg population might be heterogeneous and consist of subsets with different characteristics. Hence, we generated another SCNT Treg model, T143. T143 developed in the thymus similar to nTreg T138, but showed evidence of an agonist-induced (aTreg) development contrary to nTreg T138. Strikingly, bulk and single-cell transcriptomic analyses revealed that nTreg T138 and aTreg T143 are two distinct subsets out of four potential Treg subsets.

first: Oktay

last: Kirak

first: Eugene

last: Ke


title: Deconstructive SCNT reveals heterogeneity within Treg population

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

overall_design: Refer to individual Series


title: Deconstructive SCNT reveals heterogeneity within Treg population [bulk]


title: Transcriptome analysis of the glioma stem cells  infected with ZIKV

status: Public on May 26 2018

city: Suzhou

first: feng

last: ma

state: Jiangsu

address: 218 Xinghu Street, B5-527

department: Suzhou Institute of Systems Medicine

institute: CAMS

summary: Glioma stem cells derived from patient samples were infected with ZIKV at MOI of 1 for 48hrs, total RNA was extracted and deep sequenced to compare the gene expression  profiles between mock and ZIKV infected cells

overall_design: Triplicated 3 Mock samples and 3 ZIKV-infected samples were sequneced and compared

first: Cheng-Feng

last: Qin

first: Feng

last: Ma


title: Hepatic transcriptome of pediatric hepatoblastoma.

first: Rebekah

last: Karns

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary: The mechanisms underlying hepatoblastoma are not well defined.  To address this, we generated transcriptomic profiles of normal, background, and hepatoblastoma liver samples from patients aged 0.01 months to 6 years, using RNA-sequencing.  Hepatoblasoma was histologically confirmed.  Here we focus on the elevation of stem cell markers and the loss of tumor suppressor proteins leading to the development of hepatoblastoma in very young children.

overall_design: Hepatic mRNA profiles of normal (n=3), background (n=6), and hepatoblastoma (n=23) tissues were generated through RNAsequencing using the Illumina HiSeq2500.

first: Nikolai

last: Timchenko

first: Leila

last: Valanejad


title: MJAY analysis of cortical RNA obtained from Srrm3-Srrm4 double mutant mice and wild-type mice

first: Botond

last: Banfi

summary:
The Bronx waltzer mutation in Srrm4, a gene that encodes a neuronal Ser/Arg (SR)-rich splicing factor, disrupts the expression of several alternative exons specifically in the inner ear. Here we show that the expression of SRRM3 in neurons limits the distribution of SRRM4-dependent splicing. In vitro, SRRM3 and SRRM4 regulated the same alternative exons, yet in vivo Srrm3 deficiency caused neuronal splicing alterations and motor dysfunction, indicating that SRRM3 has non-redundant functions. Mice harboring mutations in both Srrm3 and Srrm4 failed to breathe, and their neuromuscular junctions (NMJ) were malformed. Transcriptome-wide analysis revealed a large network of SRRM3/SRRM4-dependent splicing changes, including the skipping of key exons in the NMJ organizer Agrin. Furthermore, SRRM3/SRRM4 regulated gene expression through neuron-specific switches in chromatin regulatory complexes and by altering the reading frame in several mRNAs. Our findings reveal that the SRRM3/SRRM4 subfamily of SR proteins is central to regulation of the neuronal transcriptome.
In this dataset, we include probe-set level data obtained from brain cortex samples. The processed data represent probe-set intensities that have been normalized to gene expression levels.

overall_design: 8 samples were analyzed: brain cortex from 4 wild-type (WT) and 4 homozygous Srrm3-Srrm4 double mutant (dMut) mice on E19.

first: Yoko

last: Nakano


title: MJAY analysis of cerebellar RNA obtained from Srrm3 gene-trapped mice and wild-type mice

summary:
The Bronx waltzer mutation in Srrm4, a gene that encodes a neuronal Ser/Arg (SR)-rich splicing factor, disrupts the expression of several alternative exons specifically in the inner ear. Here we show that the expression of SRRM3 in neurons limits the distribution of SRRM4-dependent splicing. In vitro, SRRM3 and SRRM4 regulated the same alternative exons, yet in vivo Srrm3 deficiency caused neuronal splicing alterations and motor dysfunction, indicating that SRRM3 has non-redundant functions. Mice harboring mutations in both Srrm3 and Srrm4 failed to breathe, and their neuromuscular junctions (NMJ) were malformed. Transcriptome-wide analysis revealed a large network of SRRM3/SRRM4-dependent splicing changes, including the skipping of key exons in the NMJ organizer Agrin. Furthermore, SRRM3/SRRM4 regulated gene expression through neuron-specific switches in chromatin regulatory complexes and by altering the reading frame in several mRNAs. Our findings reveal that the SRRM3/SRRM4 subfamily of SR proteins is central to regulation of the neuronal transcriptome.
In this dataset, we include probe-set level data obtained from cerebellar samples. The processed data represent probe-set intensities that have been normalized to gene expression levels.

overall_design: 8 samples were analyzed: cerebellums from 4 wild-type (WT) and 4 homozygous Srrm3 gene-trapped (gt/gt) mice on P16.


title: Histone deacetylase inhibitors in alveolar rhabdomyosarcoma

status: Public on Jun 13 2018

city: Beaverton

first: Noah

last: Berlow

address: 12655 SW Beaverdam Rd

institute: CC-TDI

summary: Multiple histone deacetylase inhibitors were tested on multiple alveolar rhabdomyosarcoma cell lines and multiple patient-derived xenograft models of alveolar rhabdomyosarcoma

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Alveolar rhabdomyosarcoma cell lines were treated with various histone deacetylase inhibitors or with vehicle. Post experiment cells were snap frozen and had RNA isolated from cell pellets. Isolated RNA was sequenced and quantified

first: Charles

last: Keller

first: Narendra

last: Bharathy


title: Genome-wide effect of constitutive IFN-signaling

status: Public on Jun 01 2018

first: Alexander

last: Poltorak

state: Massachusetts

address: 150 Harrison avenue

institute: Tufts University

summary: Using wild type mice and mice deficient for either IFNb1 or IFN-receptor, we analysed the effect of the constitutive IFN on genome-wide expression

overall_design: To look for the role of constitutive interferon, we compared levels of expression of Interferon-stimulated genes (ISGs) in alveolar macrophages or liver in three mouse lines that is, C57BL6, IFNb1-KO, and IFN-receptor KO mice. Specifically, we isolated RNA from rested alveolar macrophages or liver and made library using Illumina TruSeq kit for the library construction. One replica of each sample is provided.

first: Caitlin

last: Beiyun


title: Response by Fusarium oxysporum f.sp. lycopersici 4287 to 28 and 37 degrees celcius

status: Public on May 23 2018

city: Amherst

first: Gregory

middle: Alan

last: DeIulio

address: 240 Thatcher Road

department: Biochemistry and Molecular Biology

institute: Umass Amherst

summary: Temperature shift experiment to assay heat stress response

sample_organism: Fusarium oxysporum f. sp. lycopersici 4287

overall_design: 3 replicates per condition at two temperatures, 28 degrees C and 37 degrees C

first: Li

last: Guo

first: Li-Jun

first: Greg


title: Methylation analysis of human embryonic stem cells (hESCs), hESC-derived splanchnic mesoderm and hESC-derived mesothelium (mesenchymal form)

status: Public on Oct 06 2018

city: Athens

first: Stephen

last: Dalton

state: GA

address: 325 Riverbend Rd

department: Biochemistry & Molecular Biology

institute: University of Georgia

type:
Methylation profiling by array
Third-party reanalysis

summary: Genome wide DNA methylation profiling of hESC-derived mesothelium (MesoT), hESCs and hESC-derived splanchnic mesoderm (SplM) compared to primary human tissue samples. The Illumina Infinium HumanMethylation450 BeadChip kit was used to obtain DNA methylation profiles across approximately 450,000 methylation sites. Samples include 2 WA09 hESCs, 2 hESC-derived splanchnic mesoderm and 3 hESC-derived mesothelium replicates.

overall_design: Bisulphite converted DNA from the 38 samples were hybridized to the Illumina Infinium HumanMethylation450 BeadChip.  This series includes re-analyzed data from GSE31848. Processed data for all samples (new and re-analyzed) are available in the file METH_FINAL_SWAN.txt at the foot of this record.

first: Jeanne

last: Loring

first: Kristopher

last: Nazor

first: Miranda

last: Hayworth

first: Thomas

last: Colunga


title: Deficiency in SUMOylation, by injection of Gam1 mRNA into one cell embryos, leads to differential expression of genes in Xenopus

status: Public on Jun 23 2018

city: Notre Dame

first: Paul

last: Huber

state: IN

address: University of Notre Dame

institute: University of Notre Dame

summary:
Background: Adenovirus protein Gam1 triggers the proteolytic destruction of the E1 SUMO-activating enzyme. Microinjection of an empirically determined amount of Gam1 mRNA into one-cell Xenopus embryos can reduce SUMOylation activity to undetectable, but nonlethal levels, enabling an examination of the role of this post-translational modification during early vertebrate development.
Results: We find that SUMOylation-deficient embryos consistently exhibit defects in neural tube and heart development. We have measured differences in gene expression between control and embryos injected with Gam1 mRNA at three developmental stages: early gastrula (immediately following the initiation of zygotic transcription), late gastrula (completion of the formation of the three primary germ layers), and early neurula (appearance of the neural plate). Although changes in gene expression are widespread and can be linked to many biological processes, three pathways, non-canonical Wnt/PCP, snail/twist, and Ets-1, are especially sensitive to the loss of SUMOylation activity and can largely account for the predominant phenotypes of Gam1 embryos. SUMOylation appears to generate different pools of a given transcription factor having different specificities with this post-translational modification involved in the regulation of more complex as opposed to housekeeping processes.
Conclusions: We have identified changes in gene expression that underlie the neural tube and heart phenotypes resulting from depressed SUMOylation activity. Notably, these developmental defects correspond to the two most frequently occurring congenital birth defects in humans, strongly suggesting that perturbation of SUMOylation, either globally or of a specific protein, may frequently be the origin of these pathologies.

overall_design: Three different time points (early gastrula-9 hours post fertilization, late gastrula- 13.5 hours post fertilization, and early neurula- 16.5 hours post fertilization). Twenty embryos from each time point. Three replicate experiments. Samples from control (injected with water) and experimental (injected with Gam1 mRNA).

first: Michelle

last: Bertke

first: Laura

last: Cronin

first: Erliang

last: Zeng

middle: W


title: Genome-wide DNA methylation of survival outliers of glioblastoma

status: Public on May 17 2018

city: Seoul

first: Chul-Kee

last: Park

address: 101 Daehak-ro, Jongno-gu

department: Department of Neurosurgery

country: South Korea

institute: Seoul National University College of Medicine

summary: In this study, we aimed to characterize the global DNA methylation pattern of mainly IDH1 wild type survival outliers of glioblastoma.

overall_design: We compared IDH1 WT gliobliastoma patients who lived longer than 3 years (N=17) with the patients who lived less than 1 year (N=12). For validation, additional 10 glioblastoma samples were also profiled.

first: Taeyoung

last: Hwang

first: Dimitrios

last: Mathios

first: Kerrie

last: McDonald

first: Irene

last: Daris

first: Sung-Hye

first: Peter

last: Burger

first: Sojin

last: Kim

first: Yun-Sik

last: Dho

first: Hruban

last: Carolyn

first: Chetan

last: Bettegowda

first: Joo

last: Shin

first: Michael

last: Lim


title: Establishment and characterization of prostate cancer organoids [RNA-seq]

status: Public on May 10 2018

first: Adam

middle: G.

last: Sowalsky

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

summary:
Prostate cancer translational research has been hampered by the lack of comprehensive and tractable models that represent the genomic landscape of clinical disease.
Metastatic castrate-resistant prostate cancer (mCRPC) patient derived xenografts (PDXs) recapitulate the genetic and phenotypic diversity of the disease.
We sought to establish a representative, preclinical platform of PDX-derived organoids that is experimentally facile for high throughput and mechanistic analysis.

overall_design:
To investigate the effects of organoid establishment on clonal selection and drift, we assessed patterns of gene expression from PDX and organoids from the same individual.

Total RNA was extracted from fresh organoids, using a Qiagen AllPrep DNA/RNA Mini Kit. RNA from each sample was quality checked using an Agilent TapeStation 2200 and RiboGreen Assay, and an aliquot of up to 3 micrograms of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility. After adaptor trimming, reads were simultaneously aligned to the hg19 genome (human) or mm10 genome (mouse) using Bowtie2 and Tophat version 2.1.1 without novel junction discovery, based on species-specific gene predictions downloaded from the UCSC genome table browser in January 2018. Each accepted-hits BAM file was sorted by read name and then processed by Disambiguate, which deposited species-specific read pairs into corresponding BAM files. Reads aligning equally well to both species' transcriptomes were discarded. The BAM file of reads preferentially aligning to the human transcriptome were processed by the PICARD SamToFastq tool to recover the FASTQ files, discarding all secondary alignments and singletons. The pre-processed data were then filtered to remove low quality reads, followed by the trimming of low quality bases. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count. Transcripts per million (TPM) were then normalized to the 75th percentile for each sample.

The FASTQ raw data for these samples are being submitted to dbGaP study phs001587 due to patient privacy concerns.

NIH grant(s):
ZIA BC011782 Mechanisms of Pathogenesis in Patient Derived Organoid Models of Prostate Cancer NATIONAL CANCER INSTITUTE KATHLEEN SIEBENLIST
ZIA BC011679 Mechanisms Driving Evolution of Aggressive Prostate Cancer NATIONAL CANCER INSTITUTE ADAM SOWALSKY

last: Beshiri

first: Eva

last: Corey

first: Kathleen

last: Kelly


title: Expression data of sheep exposed to Mycobacterium avium subsp. Paratuberculosis

status: Public on May 15 2018

city: Camden

first: Auriol

middle: Cecilia

last: Purdie

state: NSW

address: 402 Werombi Rd

department: Faculty of Science, Sydney School of Veterinary Sciences

country: Australia

institute: University of Sydney

summary: In this study, consistent gene expression changes were analysed to identify gene-to-gene interaction and functional pathway relationships associated with the MAP exposure outcomes of either a paucibacillary or a multibacillary disease form or sheep resilient to disease. The results suggest that although groups of genes are differentially changed in the MAP exposed sheep regardless of clinical outcome, there are distinct variations in gene expression patterns between the paucibacillary and multibacillary forms of disease and of particular note was the finding that MAP exposed animals with evidence of recovery or resilience respond to MAP exposure with a pattern of gene and molecular pathway interactions distinct from those animals that progress to clinical paratuberculosis.

overall_design: Transcriptomic analysis was carried out on samples from all twenty of the MAP inoculated sheep and five of the control sheep at 2, 10, 18, 32 and 56 weeks post MAP inoculation. Each animal contributed 5 samples and in total 125 samples were processed using the Bovine Affymetrix® GeneChip® 3’IVT array

first: Karren

last: Plain

first: Douglas

last: Begg

first: Kumudika

last: de Silva

first: Richard

last: Whittington


title: Environmental enrichment prevents transcriptional disturbances induced by alpha-Synuclein overexpression

status: Public on May 14 2018

city: Saarbrücken

first: Julia

middle: Maria

last: Schulze-Hentrich

address: Campus, Building A2.4

department: Genetics and Epigenetics

institute: Saarland University

summary: Using a mouse model overexpressing human SNCA and profiling the hippocampal transcriptome, we assessed gene-environment interactions to reveal perturbations in gene expression and their modulation through long-term enriched environment (EE) exposure. We observed that EE prevented perturbations of genes attributed to neuronal and glial cell types and linked to glutamate signaling, calcium homeostasis, inflammation, and related processes of SNCA biology. Cluster and promoter analyses suggested driver genes that specifically responded to the EE, and pointed to a pivotal role of Egr1 to have hierarchically activated other drivers. We suggest a model in which EE-induced driver genes prevent and counter-balance perturbations of SNCA overexpression, restoring a largely normalized gene expression profile and system state.

overall_design: Using a 2x2 factorial design, we cross-compared a line of transgenic mice overexpressing human SNCA with wildtype animals, and the effects of a long-term EE with standard housing conditions. Employing RNA-seq, we profiled gene expression in the hippocampus of 12-month-old female animals.

first: Thomas

last: Hentrich


title: KIF20A/MKLP2 regulates the division modes of neural progenitor cells during cortical development

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary: Balanced symmetric and asymmetric divisions of neural progenitor cells (NPCs) are crucial for orderly progression of brain development, but the underlying mechanisms are not fully understood. Here, we report that mitotic kinesin KIF20A/MKLP2 interacts with RGS3 and plays a crucial role in controlling the division modes of NPCs during the mouse cortical neurogenesis. KIF20A is selectively expressed by daughter progenitors in NPC divisions. Knockdown of KIF20A causes dislocation of RGS3 from the intercellular bridge (ICB) of dividing NPCs, impairs the function of EphrinB-RGS cell fate signaling complex, and leads to a transition in NPCs from proliferative to differentiative divisions. Germ-line and inducible knockout of KIF20A causes a loss of progenitor cells and neurons and results in thinner cortex and ventriculomegaly. Interestingly, loss-of-function of KIF20A induces early cell cycle exit and precocious neuronal differentiation without causing substantial multinucleation or apoptosis in mutant NPCs. Our results thus uncover a novel RGS-KIF20A axis in regulation of cell division mode and suggest a potential link of cytokinesis control within the ICB to regulation of cell fate determination.

overall_design: Transcriptome analyses in Kif20a wild-type and knock-out forebrains were performed.

first: Anqi

last: Geng

first: Jiancheng

last: Liu

first: Qiang

last: Lu


title: RNA-seq Analyzes Transcriptomes of dnaB-Ts and dnaB-Ts ΔahpC at Both Permissive and Non-permissive Temperature

status: Public on May 12 2018

city: Newark

first: Yuzhi

last: Hong

state: NJ

address: 225 Warren St

department: PHRI, New Jersey Medical School

institute: Rutgers, the University of New Jersey

summary: To generate a bona fide model to study post-stress baterial programmed cell death (PCD), we used a temperature-sensitive E. coli mutant (dnaB-Ts) since temperature stress can be rapidly reversed while other stress, such as antibotic treatment, is difficult to be rapidly and completely stopped and removed for post-stress PCD analysis. When cells were shifted from permissive (30 °C) to non-permissive temperature (42 °C), the dnaB-Ts ΔahpC double mutant maintained full surival while survival of the dnaB-Ts single mutant dropped 3 orders of magnitude; similarly, the double mutant showed much higher survival during treatments with quinolones and β-lactams at permissive temperature.  The purpose of the RNA-seq analyses is to uncover molecular mechanisms underlying the increased survival of the dnaB-Ts ΔahpC double mutant by comparing its transcriptional profiles with that of the dnaB-Ts single mutant at both permissive and non-permissive temperature. The results showed that multiple antioxidative systems and stress response pathways were highly upregulated due to a deficiency of ahpC when combined with a dnaB-Ts mutation.  The high expression of these genes are consistent with the lower levels of toxic reactive oxygen species (ROS) in the dnaB-Ts ΔahpC mutant than in the dnaB-Ts single mutant. Thus, the RNA-seq data supported that ROS are an important lethal factor in bacterial suicide pathways when bacterial cells are exposed to harsh stress.

overall_design: Two independent early log-phase cells of a dnaB-Ts mutant or a dnaB-Ts ΔahpC mutant, incubated at 30 °C or at 42 °C for 60 min, were collected and mixed together for total RNA extraction and subsequenct RNA-seq sequencing.

first: Xilin

last: Zhao


title: Proliferation pause as an early blockade of human cellular reprogramming toward pluripotency [ChIP-seq analysis]

status: Public on Apr 10 2018

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

summary: Human induced Pluripotent Stem cells (iPSCs) can be generated by enforced-expression of OCT3/4, SOX2, KLF4 and c-MYC (OSKM) via intermediate state that is labeled with a surface antigen TRA-1-60.  However the event during conversion of somatic cells to TRA-1-60 positive (+) fate by OSKM is still unclear. Here we show that TRA-1-60 (+) cells emerged from ESRG (+) cells with proliferation independent manner.   Overcoming the proliferation pausing phase is crucial for further progression of reprogramming. Inactivation of RB pathway is associated with the expansion of early TRA-1-60 (+) cells. Indeed, extended RB activation   drastically decreased the proportion of TRA-1-60 (+) cells with marked premature senescence. An RNA-binding protein LIN41 promotes the RB inactivation and facilitates reprogramming efficiency in early stage via   post-transcriptional suppression of cycline dependent kinase inhibitor p21. This LIN41/p21/RB axis was invalidated in immortalized cells which showed a resistance to oncogene-induced senescence. Thus, LIN41-  mediated RB inactivation promotes to bail out of transient quiescence as a major blockade in initial phase of reprogramming.

overall_design: ChIP-seq profiles for 4 histone marks of an Human induced Pluripotent Stem cell line (201B7) and Human dermal fibroblasts (TIG120) were generated by deep sequencing.

first: K

last: Sutou

last: Tanabe

first: A

first: M

last: Narita

last: Takahashi


title: Proinflammatory cytokines and response to molds in mononuclear cells of patients with Meniere disease, vestibular migarine and Healthy controls

status: Public on Apr 18 2018

city: Granada

first: Jose

middle: Antonio

last: Lopez-Escamez

state: Granada

address: Av. Ilustracion 114

department: Genomics of vestibular disorders

institute: Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research (GENYO)

summary: Analysis of PBMC gene expression level before and after stimulation with Aspergillus or Penicillium

overall_design: Total RNA obtained from isolated PBMC from subjected to 16 hours stimulation with Aspergillus, Penicillium or nothing

first: Lidia

last: Frejo


title: Proliferation pause as an early blockade of human cellular reprogramming toward pluripotency

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Towne induced changes to human foreskin fibroblast transcriptional activity.

status: Public on Mar 31 2018

city: Detroit

first: Philip

middle: E.

last: Pellett

state: MI

address: 540 E Canfield St

department: Biochemistry, Microbiology, and Immunology

institute: Wayne State University School of Medicine

summary:
Human fibroblasts infected with human cyotmegalovirus strain Towne at a multiplicity of infection equal to 6. Host transcriptional levels were quantitated at 12 and 96 hours post infection using Illumina HT-12 beadarrays.
These array depostions are an extension of a previous submission, GSE50955.

overall_design: Cells were infected in biological triplicate then harvested at 12 and 96 hpi time points when they were assayed for transcriptional activity.

first: William

last: Close

first: Stephen

last: Gurczynski


title: Proliferation pause as an early blockade of human cellular reprogramming toward pluripotency [single cell RNA-seq analysis]

overall_design: Single cell RNA-seq profiles of Human dermal fibroblasts, Human induced Pluripotent Stem cell, intermediate reprogrammed cells.


title: Ribotag analysis of proprioceptive dorsal root ganglion neurons in cell culture

status: Public on Apr 25 2018

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

summary: We analyzed ribosome-associated RNA (raRNA) in dorsal root ganglion neurons in TrkC+ proprioceptive dorsal root ganglion neurons in cell culture.

overall_design: All DRG neurons from young adult (3-6 mo) male mice expressing Rpl22HA/HA Runx3-Cre+ and age/sex matched Cre negative littermates (Rpl22HA/HA Runx3-Cre-) were harvested using density purification on Percoll and grown for 24h in serum-supplemented F12 medium. Ribosome-associated RNA was isolated using immunoprecipitation targeting the HA epitope. 10% of pre-immunoprecipitation lysates were used for input samples reflecting total RNA profile of the tissue. Cre negative samples were sequenced to control for background.  N=3 for all four groups (Pulldown/Cre+, Pulldown/Cre-, Input/Cre+, Input/Cre-).


title: Transcriptome analysis of the mRNAs and lncRNAs in porcine alveolar macrophages in response to porcine reproductive and respiratory syndrome virus or IFN-a at different time points

city: Beijing

middle: Fang

last: Zeng

address: Yuanmingyuan West Road No. 2 Haidian district

department: college of veterinary medicine

institute: China Agriculture University

summary:
Purpose:We performed next-generation RNA sequencing and a comprehensive bioinformatics analyses to characterize the transcriptome landscapes, including mRNAs and long noncoding RNAs (lncRNAs) in PRRSV-infected PAMs or IFN-stimulated PAMs at different time points.
Conclusions: We showed that PRRSV infection displays different transcriptome profiles of PAMs, and the aberrant function of PAMs may be reflected by significant down-regulation of essential genes at the transcriptome levels. In addition, we discovered a great amount of differentially expressed lncRNAs, including lncRNA XR_297549.1, which is highly expressed and predicted to both cis- and trans-regulate its neighboring gene PTGS2.In addition, In order to expand our understanding of these IFN-induced non-coding transcripts, especially long non-coding RNAs (lncRNAs), we performed next-generation RNA sequencing and a comprehensive bioinformatics analysis of porcine alveolar macrophages (PAMs) stimulated with pig-IFN-? for 6h and 12h, respectively. A great amount of differentially expressed mRNAs and lncRNAs were identified, and several lncRNAs are of great interest for further investigation as their potential role in regulation of the well-characterized antiviral genes, such as OAS1, PML and ISG15.

overall_design: Examination of the differential expression profiles of primary porcine alveolar macrophages infected with porcine reproductive and respiratory syndrome virus or stimulated with IFN-a with two biological replicates, using Illumina Higseq 2500.

first: Nanfang


title: Deciphering the regulon of the alternative extracytoplasmic function (ECF) sigma factor DvdS and its dependence on the regulatory proteins CarD and CarG

city: Murcia

first: Montserrat

last: Elías-Arnanz

state: Please Select

address: Campus Espinardo

department: Departamento de Genética y Microbiología

institute: University of Murcia

summary: This study addresses the key role of the extracytoplasmic function (ECF) sigma factor DdvS in the Gram-negative bacterium Myxococcus xanthus.  It allows us to determine its regulon and it shows that the expression of ddvS and its regulón depends on the global regulatory complex CarD-CarG.

overall_design: Four loop experiment, each test and its reference were repeated and analyzed twice. At least three biological replicates were used for each condition (wild type DK1622 and its derivative strains MR1543, MR1544 and MR1545)

first: Javier

last: Abellón-Ruiz


title: Discovery of a Drug Candidate for GLIS3-Associated Diabetes

status: Public on May 05 2018

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

summary: Through development and use of a minimal component protocol for derivation of late stage pancreatic progenitors and beta-like cells, we compared WT and GLIS3-/- pancreatic cells at different stages and discovered that GLIS3-/- cells show an ectopic activation of TGF-beta signaling.

overall_design: Comparison of WT and GLIS3-/- cells at various stages of human pancreatic differentiation

first: Sadaf

last: Amin


title: Translational Regulation in Initial Stages of the Neuronal Injury Response

summary: Transcriptional events leading to outgrowth of neuronal axons have been intensively studied, but the role of translational regulation in this process is not well understood. Here we use translatome analyses by ribosome pull-down and protein synthesis characterization by metabolic isotopic labeling to study nerve injury and axon outgrowth proteomes in rodent dorsal root ganglia (DRG) and sensory neurons. We identify over 1600 gene products that are primarily translationally regulated in DRG neurons after nerve injury, many of which contain a 5’UTR CERT motif, implicating the translation initiation factor Eif4e in the injury response. We further identified approximately 200 proteins that undergo robust de novo synthesis in the initial stages of axon growth. ApoE is one of the highly synthesized proteins in neurons, and inhibition of its signaling affects axon outgrowth. These findings suggest prominent roles for translational regulation in initial stages of the neuronal injury response and axon extension.

overall_design: Use Ribotag mice to identify cell type specific translatomes within dorsal root ganglia and observe their change following an injury to the sciatic nerve

first: Meir

last: Rozenbaum

first: Marek

last: Rajman

first: Ida

last: Rishal

first: Sandip

last: Koley

first: Katalin

middle: F

last: Medzihradszky

first: Juan

last: Oses-Prieto

first: Paul

middle: S

last: Amieux

first: Giovanni

last: Coppola

first: Alma

last: Burlingame

first: Mike

last: Fainzilber


title: Longitudinal Multi’omics of the Human Microbiome in Inflammatory Bowel Disease

status: Public on Mar 17 2018

city: Boston

first: Curtis

last: Huttenhower

state: MA

address: 677 Huntington Ave

department: Biostatistics

institute: Harvard T.H. Chan School of Public Health

summary:
Purpose: The main Inflammatory Bowel Disease (IBD) Multi'omics Database (IBDMDB) study includes multi’omics measurements from over 100 subjects, sampled biweekly over up to a year in both adult and pediatric patients with IBD (Crohn’s disease and ulcerative colitis), along with non-IBD controls. Data types include fecal metagenomes, metatranscriptomes, metabolomes, and proteomes, as well as host genetics, intestinal biopsy transcriptomes, epigenetics, and 16S amplicon profiles. Subjects’ medical histories and demographics are collected at baseline and medication, diet, and disease activity profiled longitudinally.
Methods: Methods: Total RNA was quantified using theQuant-iT™ RiboGreen® RNA Assay Kit and normalized to 5ng/ul. Following plating, 2 uL of ERCC controls (using a 1:1000 dilution) were spiked into each sample. An aliquot of 200ng for each sample was transferred into library preparation which was an automated variant of the Illumina TruSeq™ Stranded mRNA Sample Preparation Kit. This method preserves strand orientation of the RNA transcript. It uses oligo dT beads to select mRNA from the total RNA sample.  It is followed by heat fragmentation and cDNA synthesis from the RNA template. The resultant 500bp cDNA then goes through library preparation (end repair, base ‘A’ addition, adapter ligation, and enrichment) using Broad designed indexed adapters substituted in for multiplexing. After enrichment the libraries were quantified using Quant-iT PicoGreen (1:200 dilution). After normalizing samples to 5 ng/uL, the set was pooled and quantified using the KAPA Library Quantification Kit for Illumina Sequencing Platforms.  The entire process is in 96-well format and all pipetting is done by either Agilent Bravo or Hamilton Starlet. Pooled libraries were normalized to 2nM and denatured using 0.1 N NaOH prior to sequencing. Flowcell cluster amplification and sequencing were performed according to the manufacturer’s protocols using either the HiSeq 2000.

overall_design:
RNA-seq analysis of biopsy samples retrieved from CD, UC and non-IBD patients enrolled in the HMP2 project.
NOTE: Submitter declares that the raw data will be submitted to dbGaP (https://www.ncbi.nlm.nih.gov/gap) because of patient privacy concerns.

first: Cesar

last: Arze

first: Damian

last: Plichata

first: Jason

last: Bishai


title: Whole blood transcriptome analysis in amyotrophic lateral sclerosis: a biomarker study [HT12_V3]

status: Public on Apr 05 2018

city: Utrecht

first: Jan

middle: Herman

last: Veldink

state: Utrecht

address: Heidelberglaan 100, F.02.230

department: Neurology, Brain Center Rudolf Magnus

country: Netherlands

institute: University Medical Center Utrecht

summary: Transcriptome-wide analysis of whole blood gene expression profiles of ALS patients, gender- and age-matched controls and patients diagnosed with diseases mimicking ALS at a tertiary referral center for motor neuron diseases.

overall_design: mRNA was obtained from whole blood around the time of diagnosis and expression profiles were compared between ALS patients, controls and mimics in a biomarker design.

first: Wouter

last: van Rheenen

first: Frank

last: Diekstra

first: Oliver

last: Harschnitz

first: Kristel

middle: R

last: van Eijk

first: Henk-Jan

last: Westeneng

first: Christiaan

middle: G

last: Saris

first: Ewout

middle: J

last: Groen

first: Michael

last: van Es

first: Hylke

middle: M

last: Blauw

last: van Vught

middle: H

first: Leonard

last: van den Berg


title: Tabula Muris: Transcriptomic characterization of 20 organs and tissues from Mus musculus at single cell resolution

status: Public on Mar 19 2018

city: San Francisco

first: Angela

last: Oliveira Pisco

address: 499 Illinois St

department: Data Science

institute: Chan Zuckerberg Biohub

summary:
We have created a resource of single cell transcriptome data from the model organism Mus musculus.

Contributor: The Tabula Muris Consortium

The full list of contributors to this dataset can be found in the corresponding publication.

overall_design: Single cell RNA sequencing of single cells across 20 tissues of 3 month aged mice


title: Gene expression profile of tumors developed in the spleen of p53-haploinsufficient mice

status: Public on Apr 01 2018

city: Shimotsuke

first: Yusuke

last: Furukawa

state: Tochigi

address: 3311-1 Yakushiji

department: Center for Molecular Medicine

institute: Jichi Medical University

summary: We aimed to ivestigate the effects of LSD1 on the gene expression program of p53-haploinsufficient mice to understand the molecular mechanisms underlying the development of lymphoid malignancies.

overall_design: We isolated mRNA from tumors developed in the spleen of p53+/−, LSD1 × p53+/− #2, and LSD1 × p53+/− #3 mice, and subjected them to gene expression analysis using an Agilent Gene Expression Array.

first: Taeko

last: Wada


title: TCRβ+ vs. TCRβ- CD11bhighCD14+F4/80+ splenic macrophages (Mf)

status: Public on Mar 09 2018

city: Silver Spring

first: Miranda

middle: Sarah Melissa

last: Oakley

state: MD

address: 10993 New Hampshire Avenue

institute: FDA

summary: Measure the effect of TCRβ expression on the transcriptional profile of CD11bhighCD14+F4/80+ macrophages sorted from mouse spleen on day 6 post-infection with Plasmodium berghei ANKA malaria

overall_design: One condition experiment (presence or absence of TCRβ); quadruplicate replicates

first: Timothy

last: Myers


title: Transcriptome of tumor biopsy sample of patient with granulosa cell tumor of the ovary

status: Public on Apr 02 2018

city: Moscow

first: Maria

middle: Vladimirovna

last: Suntsova

address: Miklukho-Maklaya, 16/10

department: Department of Genetics and Postgenomic Technologies

country: Russia

institute: M.M. Shemyakin and Yu.A. Ovchinnikov  Institute of  bioorganic chemistry of the Russian Academy of Sciences

type:
Expression profiling by array
Third-party reanalysis

summary: We profiled gene expression in formalin-fixed, paraffin-embedded (FFPE) tumor biopsy sample of the patient with granulosa cell tumor of the ovary.

overall_design: Microrray analysis was perrformed for single biopsy sample. Sample was evaluated by a pathologist to confirm the diagnosis and estimate the tumor cell numbers (sample should contain at least 80% of tumor cells).

first: Elena

last: Ilnitskaya


title: Proliferation pause as an early blockade of human cellular reprogramming toward pluripotency [Methylation analysis]

first: Akira

last: Watanabe

overall_design: DNA methylation analysis of Human dermal fibroblasts (N=3) and Teratoma (N=3).

first: K

last: Sutou

last: Tanabe

first: A

first: M

last: Narita

last: Takahashi


title: Effect of human CD5 molecule-like (CD5L) overexpression on PMA-differentiated THP1 human monocyte-like cells

status: Public on Mar 29 2018

city: Badalona

first: Maria Rosa

last: Sarrias

address: Ctra Can Ruti camí de les escoles, s/n

department: Innate Immunity Group

institute: Health Sciences Research Institute Germans Trias i Pujol (IGTP)

summary:
To assay the differential gene expression in human THP1-PMA differentiated macrophages expressing human CD5 molecule-like (CD5L) compared to THP1 empty vector control cells.   Abstract from associated publication: Lucía Sanjurjo, Gemma Aran, Érica Téllez, Núria Amézaga, Carolina Armengol, Daniel López, Clara Prats and Maria-Rosa Sarrias. CD5L Promotes M2 Macrophage Polarization Through Autophagy-Mediated Upregulation of ID3. Frontiers in Immunology. 9:480. doi: 10.3389/fimmu.2018.00480 (2018).
ABSTRACT: CD5L (CD5 molecule-like) is a secreted glycoprotein that controls key mechanisms in inflammatory responses, with involvement in processes such as infection, atherosclerosis, and cancer. In macrophages, CD5L promotes an anti-inflammatory cytokine profile in response to TLR activation. In the present study, we questioned whether CD5L is able to influence human macrophage plasticity, and drive its polarization towards any specific phenotype. We compared CD5L-induced phenotypic and functional changes to those caused by IFN/LPS, IL4 and IL10 in human monocytes. Phenotypic markers were quantified by RT-qPCR and flow cytometry, and a mathematical algorithm was built for their analysis. Moreover, we compared ROS production, phagocytic capacity and inflammatory responses to LPS. CD5L drove cells towards a polarization similar to that induced by IL10. Furthermore, IL10- and CD5L-treated macrophages showed increased LC3II content and colocalization with acidic compartments, thereby pointing to the enhancement of autophagy-dependent processes. Accordingly, siRNA targeting ATG7 in THP1 cells blocked CD5L-induced CD163 and MERTK mRNA and efferocytosis. In these cells, gene expression profiling and validation indicated the upregulation of the transcription factor ID3 by CD5L through ATG7. In agreement, ID3 silencing reversed polarization by CD5L. Our data point to a significant contribution of CD5L-mediated autophagy to the induction of ID3 and provide the first evidence that CD5L drives macrophage polarization.

overall_design: 2 samples THP1-Vector (duplicates), control. 3 samples THP1-CD5L (triplicates), reference

first: Nuria

last: Amégaga

first: Lucía

last: Sanjurjo

first: Maria-Rosa


title: Genome-wide analysis of PDX1 target genes in human pancreatic progenitors [expression profiling]

status: Public on Feb 27 2018

city: Neuherberg

first: Heiko

last: Lickert

address: Ingolstaedter Landstraße 1

department: Institute of Diabetes and Regeneration Research

institute: Helmholtz Zentrum München German Research Center for Environmental Health

summary:
Objective: Homozygous loss-of-function mutations in the gene coding for the homeobox transcription factor (TF) PDX1 leads to pancreatic agenesis, whereas heterozygous mutations can cause Maturity-Onset Diabetes of the Young 4 (MODY4). Although the function of Pdx1 is well studied in pre-clinical models during insulin-producing β-cell development and homeostasis, it remains elusive how this TF controls human pancreas development by regulating a downstream transcriptional program. Furthermore, many studies reported the association between single nucleotide polymorphisms (SNPs) and T2DM and it has been shown that islet enhancers are enriched in T2DM-associated SNPs. Whether regions, harboring T2DM-associated SNPs are PDX1 bound and active at the pancreatic progenitor stage has not been reported so far.

Methods: In this study, we have generated a novel induced pluripotent stem cell (iPSC) line that efficiently differentiates into human pancreatic progenitors (PPs). Furthermore, PDX1 and H3K27ac chromatin immunoprecipitation sequencing (ChIP-seq) was used to identify PDX1 transcriptional targets and active enhancer and promoter regions. To address potential differences in the function of PDX1 during development and adulthood, we compared PDX1 binding profiles from PPs and adult islets. Moreover, combining ChIP-seq and GWAS meta-analysis data we identified T2DM-associated SNPs in PDX1 binding sites and active chromatin regions.

Results: ChIP-seq for PDX1 revealed a total of 8088 PDX1-bound regions that map to 5664 genes in iPSC-derived PPs. The PDX1 target regions included important pancreatic TFs, such as PDX1 itself, RFX6, HNF1B and MEIS1, which were activated during the differentiation process as revealed by the active mono-acetylated chromatin mark H3K27ac and mRNA expression profiling, suggesting that auto-regulatory feedback regulation maintains PDX1 expression and initiates a pancreatic TF program. Remarkably, we identified several PDX1 target genes that have not been reported in human so far, including RFX3, required for ciliogenesis and endocrine differentiation in mouse, and the ligand for the Notch receptor, DLL1, which is important for endocrine induction and tip-trunk patterning. The comparison of PDX1 profiles from PPs and adult human islets identified sets of stage-specific target genes, associated with early pancreas development and adult β-cell function. Furthermore, we found an enrichment of T2DM-associated SNPs in active chromatin regions from iPSC-derived PPs. Two of these SNPs fall into PDX1 occupied sites that are located in the intronic regions of TCF7L2 and HNF1B. Both of these genes are key transcriptional regulators of endocrine induction and mutations in cis-regulatory regions predispose to diabetes.

Conclusions: Our data provides stage-specific target genes of PDX1 during in vitro differentiation of stem cells into pancreatic progenitors that could be useful to identify pathways and molecular targets that predispose for diabetes. In addition, we show that T2DM-associated SNPs are enriched in active chromatin regions at the pancreatic progenitor stage, suggesting that the susceptibility to T2DM might originate from imperfect execution of a β-cell developmental program.

overall_design: We performed Affymetrix microarray analysis on XM001 cells at the pluripotency and PP stages

first: Xianming

last: Wang

first: Michael

last: Sterr

first: Ingo

last: Burtscher

first: Shen

last: Chen

first: Anja

last: Hieronimus

first: Fausto

last: Machicao

first: Harald

last: Staiger

first: Hans-Ulrich

last: Häring

first: Gabriele

last: Lederer

first: Thomas

last: Meitinger

first: Filippo

last: Cernilogar

first: Gunnar

last: Schotta

first: Martin

last: Irmler

first: Johannes

last: Beckers

last: Hrabě de Angelis

first: Christopher

last: Wright

first: Mostafa

last: Bakhti


title: Genome-wide analysis of PDX1 target genes in human pancreatic progenitors [ChIP-seq]

first: Heiko

last: Lickert

summary: We performed ChIP-seq of PDX1 and H3K27ac on XM001 cells at PP stage

last: Wang

middle: V


title: Whole blood transcriptome analysis in amyotrophic lateral sclerosis: a biomarker study

first: Jan

last: Veldink

overall_design: Refer to individual Series


title: Establishment and characterization of prostate cancer organoids

status: Public on May 10 2018

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

overall_design:
Refer to individual Series
NIH grant(s):
ZIA BC011782 Mechanisms of Pathogenesis in Patient Derived Organoid Models of Prostate Cancer NATIONAL CANCER INSTITUTE KATHLEEN SIEBENLIST
ZIA BC011679 Mechanisms Driving Evolution of Aggressive Prostate Cancer NATIONAL CANCER INSTITUTE ADAM SOWALSKY


title: Transcriptomic profiling of rhesus macaques vaccinated with Ad26/ALVAC+gp120 or DNA/ALVAC+gp120

status: Public on Feb 23 2018

city: Chicago

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

department: Medicine

institute: Northwestern University

summary: We contrasted innate and adaptive immune responses of HIV vaccine candidates of varying efficacy in macaques that shared the ALVAC+gp120 protein boost with an ALVAC, DNA or Ad26 prime modality. The vaccine efficacies of the DNA/ALVAC+gp120 and ALVAC/ALVAC+gp120 vaccine regimens, both protective, were associated with qualitative temporal-spatial differences in the innate CD14+ and CD16+ cells in blood and tissues. The activation of hypoxia and the inflammasome in CD14+ DR+ CD16- classical monocytes and CD4+ Th2 responses correlated with a decreased risk of SIVmac251 acquisition. CD4+ Th2 cells, in turn, correlated with mucosal NKp44+ cells and mucosal protective antibodies to V2. In contrast, the Ad26/ALVAC+gp120 vaccine resulted in increased de novo differentiated CX3CR1+ CD163+ macrophages in lymph nodes, increased CD4+ Th17 cells in blood and rectal mucosa, and a lack vaccine efficacy. These data posit that the engagement of classical monocytes and inflammasome activation is central for the elicitation of protective innate and adaptive responses by the ALVAC-based HIV vaccine platform.

overall_design: Twenty four (24) rhesus macaques were randomized to two vaccination groups. One group (n=12) was primed once with Ad26 (at week 0) and boosted twice with ALVAC-SIV/gp120 in Alum adjuvant (at week 12 and week 24). The second group (n=12) was primed twice with DNA (at week 0 and week 4) and boosted twice with ALVAC-SIV/gp120 in Alum adjuvant (at week 12 and week 24). Blood samples were taken pre-vaccination, 24 hours after the first boost (week 12), 2 weeks after the first boost (week 14), 24 hours after the second boost (week 24) and 1 week after the second boost (week 15). All the samples were taken before SIV challenge. One animal (R270) who received the Ad26/ALVAC+gp120 vaccine was not included in the transcriptomic study because of a lack of blood samples. Blood samples were conserved in PAXgene tubes. RNA was extracted and hybridized to Illumina beadchips.

first: Monica

last: Vaccari

first: Shari

last: Gordon

first: Rafick-Pierre

last: Sékaly

first: Genoveffa

last: Franchini


title: Single cell RNA-seq analysis of K27M-mutant glioma

status: Public on Apr 21 2018

city: Rehovot

first: Itay

last: Tirosh

address: Herzl 234

country: Israel

institute: WEIZMANN INSTITUTE OF SCIENCE

summary: To understand the diversity of expression states within K27M-mutant gliomas, we profiled 4058 single cells, primarily from 6 K27M-mutant gliomas, by single cell RNA-seq

overall_design:
Tumors were disaggregated, sorted into single cells, and profiled by Smart-seq2.
------------------------------------------------------
Authors state that  "We are currently unable to deposit the raw data
due to privacy concerns, but will have the raw data available once
we obtain permission from our institution."
Please contact the submitter directly regarding access to raw data on a case-by-case basis.

first: Volker

last: Hovestadt

first: Mario

last: Suva

first: Mariella

last: Filbin


title: Transcriptomic analysis of the biocontrol fungus Trichoderma atroviride overgrowing Verticilluim dahliae provides the identification of mycoparasitic candidate genes aganinst this plant pathogenic fungus

city: Villamayor

first: Marta

last: Montero-Barrientos

state: Salamanca

address: Río Duero 12

institute: CENIT SUPPORT SYSTEMS

summary: A Trichoderma microarrays composed of 385,000 probes, designed against the genomes of Trichoderma reesei (= Hypocrea jecorina), ID: 431241 (9,129 genes) + Trichoderma virens (= Hypocrea virens), ID: 413071 (11,643 genes) + Trichoderma atroviride (= Hypocrea atroviridis) ID: 197014A (11,643 genes), was constructed (Roche-NimbleGen, Inc., Madison, WI, USA). Probes contained entere transcript sequence. This microarray was used to analyze the transcriptomic changes of T. atroviride IMI 352941 (T11) in three conditions: T11 growing alone, T11 growing at ca 5 mm of V. dahliae V-138I and T11 overgrowing V-138I.

platform_organism:
Trichoderma virens
Trichoderma reesei
Trichoderma atroviride

overall_design: Three samples were analyzed as follows: T. atroviride IMI 352941 (T11) grown alone (SOM05CVT), used as control, T11 grown at ca. 5 mm of V. dahliae V-138I (SOM05CVV) and T11 overgrowing V-138I (SOM05CVW). Three replicates for each sample were performed.

first: Rosa

last: Hermosa

first: Enrique

last: Monte


title: Expression data from doxorubicin-treated Myxoid Liposarcoma cells and untreated control cells

city: Göteborg

first: Emma

last: Jonasson

address: Medicinaregatan 1F, floor 5

department: Sahlgrenska Center for Cancer Research

country: Sweden

institute: University of Gothenburg

summary:
Despite an improved survival of myxoid liposarcoma (MLS) patients, existing therapies have shortcomings including therapy resistance.
To study the characteristics of therapy resistance in MLS, we treated three MLS cell lines with the commonly used chemotherapy drug doxorubicin and compared their gene expression profiles with untreated control cells.

overall_design: Doxorubicin-treated and untreated samples from three different MLS cell lines were analyzed using an affymetrix array platform.

first: Soheila

last: Dolatabadi

first: Anders

last: Ståhlberg


title: Transcriptional alterations in response to insulin and glucagon in the murine liver

status: Public on Mar 06 2018

city: Nankoku

first: Katsumi

last: Toda

state: Kochi

address: Oko-cho, Kohasu

department: Biochemistry

institute: Kochi University, School of Medicine

summary: The analysis identified 122 genes displaying responses to insulin and/or glucagon administration in the liver of WT male mice.  Of 122 genes, 75 genes responded in a insulin-selected manner, 29 genes in a glucagon-selected manner, and 18 genes were regulated by both of insulin and glucagon 60 min after stimulation with each hormone.  Insulin upregulated expression of 45 genes including  Btg2, Ddit4, and Rasgef1b, downregulated 30 genes such as Arrdc3 Rgs16, and Txnip. Glucagon upregulated expression of 15 genes including Chordc1 and Gck, and downregulated expression of 14 genes such as Mt2 and Lcn2. Seventeen genes showed transcriptional upregulation in response to both insulin and glucagon including Hspa1b, Nr4a1 Trp53inp1, and one gene, Orm2, displayed downregulation after stimulation of insulin or glucagon.

overall_design: The livers were removed from mice (C57BL6/j) 60 min after intraperitoneal injection with PBS, with 0.75 IU of recombinant human insulin, or with glucagon 50 ng/g body weight.  Total RNA extracted from the livers of five mice of each experimental group and mixed for the microarray analysis.


title: Proliferation pause as an early blockade of human cellular reprogramming toward pluripotency [RNA-seq analysis]

status: Public on Apr 10 2018

city: Kyoto

first: Akira

last: Watanabe

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

institute: CyberomiX Inc

summary: Human induced Pluripotent Stem cells (iPSCs) can be generated by enforced-expression of OCT3/4, SOX2, KLF4 and c-MYC (OSKM) via intermediate state that is labeled with a surface antigen TRA-1-60.  However the event during conversion of somatic cells to TRA-1-60 positive (+) fate by OSKM is still unclear. Here we show that TRA-1-60 (+) cells emerged from ESRG (+) cells with proliferation independent manner.   Overcoming the proliferation pausing phase is crucial for further progression of reprogramming. Inactivation of RB pathway is associated with the expansion of early TRA-1-60 (+) cells. Indeed, extended RB activation   drastically decreased the proportion of TRA-1-60 (+) cells with marked premature senescence. An RNA-binding protein LIN41 promotes the RB inactivation and facilitates reprogramming efficiency in early stage via   post-transcriptional suppression of cycline dependent kinase inhibitor p21. This LIN41/p21/RB axis was invalidated in immortalized cells which showed a resistance to oncogene-induced senescence. Thus, LIN41-  mediated RB inactivation promotes to bail out of transient quiescence as a major blockade in initial phase of reprogramming.

overall_design: RNA-seq profiles of Human dermal fibroblasts (N=3), Teratoma-derived fibroblasts (N=3).

first: K

last: Sutou

last: Tanabe

first: A

first: M

last: Narita

last: Takahashi


title: Comprehensive mapping of transcriptional networks specifying lactogenic differentiation of murine mammary epithelial stem like cells

status: Public on Feb 09 2018

city: Hyderabad

first: Sreenivasulu

last: Kurukuti

state: Telangana

address: Gachibowli

department: Animal Biology

country: India

institute: University of Hyderabad

summary:
Purpose:  Understanding of gene transcriptional networks specifying murine mammary epithelial cells (HC11) during lactogenic differentiation and its comparision with murine embryonic stem cells
Methods: RNA-sequencing after ribosomal RNA depletion followed by cDNA synthesis, adaptor ligation and sequencing in duplicate of each sample using Illumina Hi-seq 2500 paired end sequencing. Sequence reads with adapters, over-represented and low-quality reads were discarded. High quality reads were mapped to reference mouse genome (mm10) using Bowtie followed derivation of FPKM values using cufflinks and DE-seq to observe differentially expressed genes.
Results: Using standard analysis methods which were published recently we uniquely mapped more than 50 million sequence reads out of which total 11961 transcripts were from ESC, 11045 from Normal, 11243 from Primed and 10719 from prolactin stage. When we did DE-seq differential gene expression analysis we observed that for Normal to primed transition 1141 and 1026 transcripts were Up and Down regulated respectively where as upon transition from Primed to Prolactin stage 385 and 655 transcripts were Up and Down regulated respectively. We also did pathway analysis to interpret the transcript activation and its function during lactogeinc differentiation; we found that the pathways which are highly up regulated are related to carbohydrate, lipids, nucleic acid and protein metabolism. We also observed that most of the up regulated pathways were related to maintenance of mammary cells differentiated state and nutrition of the infants. Our study concludes that overall differentiation requires priming with glucocorticoids followed by prolactin stimulation of HC11 cells, which tunes the cells for the secretion of milk and its maintenance of the differentiated state till the lactation period.
Conclusions: Transcriptome analysis by next generation sequencing allowed us to explore global gene expression during lactogenic differentiation of HC11 cells in presence of glucocortiocids in primed state. Glucocorticoids are activating genes, transcription factors, epigenetic modifiers and metabolic pathways which are required for later stages of lactation. On other hand gene expression analysis of prolactin stage revealed that there is a focused gene expression exclusively related to lactation process. We also observed that HC11 stem like marker are highly expressed in undifferentiated state whose expression was down regulated in primed and prolactin state indicating that HC11 are partially bipotent cells; when these cells receive differentiation signals they loose their stem cell like characteristics and are differentiated.

overall_design: Paired end sequencing of transcriptome in replicates of embyonic stem cells, normal, primed and prolactin. Analysis of data and validation by real-time pcr analysis.

first: TrinadhaRao

last: Sornapudi

first: Rakhee

last: Nayak

first: Vanita

last: Uppada

first: Prashanth

middle: K

last: Guthikonda

first: Srinivas

last: Kethavath

first: Sailu

last: Yellaboina

first: Anil

last: Pasupulati


title: Massively parallel dissection of human accelerated regions in human and chimpanzee neural progenitors [chimpanzee]

status: Public on Feb 17 2018

city: Luebeck

first: Martin

last: Kircher

state: SH

address: Ratzeburger Allee 160

department: Humangenetics

institute: University of Luebeck

summary: Human accelerated regions (HARs) are evolutionarily conserved sequences that acquired human-specific nucleotide changes and reside in genomic regions associated with unique human traits and disease. The majority of HARs (96%) are noncoding, a few of which have been shown to be functional enhancers. Here, we comprehensively tested human and chimpanzee sequences of HARs (N=714) for enhancer activity using a lentivirus-based massively parallel reporter assay (lentiMPRA) in human and chimpanzee iPSC derived neural progenitors at two differentiation time points. We found that 43% (306/714) function as enhancers and over two-thirds (204/306) showed consistent differences in activity between human and chimpanzee sequences across conditions. We also tested all possible permutations of substitutions in seven HARs and found significant positive and negative interactions. Our study provides a comprehensive resource of functional neurodevelopmental HAR enhancers and shows that multiple interacting sites drive evolutionary activity differences.

overall_design:
We applied a lentivirus-based massively parallel reporter assay (lentiMPRA) to directly compare the enhancer activities of the human and chimpanzee alleles of 714 human-accelerated regions in human and chimpanzee iPSC-derived neural progenitor cell lines (N2 and N3 cell stages).

Pt2A and Pt5C refer to two iPSC cell lines, each derived from a different individual.

first: Katherine

last: Pollard

first: Nadav

last: Ahituv

first: Jay

last: Shendure

first: Arnold

last: Kriegstein


title: Massively parallel dissection of human accelerated regions in human and chimpanzee neural progenitors [human]

overall_design:
We applied a lentivirus-based massively parallel reporter assay (lentiMPRA) to directly compare the enhancer activities of the human and chimpanzee alleles of 714 human-accelerated regions in human and chimpanzee iPSC-derived neural progenitor cell lines (N2 and N3 cell stages).

WTc and HS1-11 refer to two iPSC cell lines, each derived from a different individual.


title: Massively parallel dissection of human accelerated regions in human and chimpanzee neural progenitors

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

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens


title: CREB Coactivators CRTC2 and CRTC3 Modulate Bone Marrow Hematopoiesis

status: Public on Feb 01 2018

city: San Diego

first: Ezra

last: Wiater

address: 10010 N Torrey Pines Rd

department: PBL

institute: Salk Institute For Biological Studies

summary: Populations of circulating immune cells are maintained in equilibrium through signals that enhance the retention or egress of hematopoietic stem cells (HSCs) from bone marrow (BM). Prostaglandin E2 (PGE2) stimulates HSC renewal and engraftment, for example, via induction of the cAMP pathway. Triggering of PGE2 receptors increases HSC survival in part via the PKA-mediated induction of the CREB signaling pathway. PKA stimulates cellular gene expression by phosphorylating CREB at Ser133 and by promoting the dephosphorylation of the cAMP Responsive Transcriptional Coactivators (CRTCs). We show here that disruption of both CRTC2 and CRTC3 causes embryonic lethality, and that a single allele of either CRTC2 or CRTC3 is sufficient for viability. CRTC2 knockout mice that express one CRTC3 allele (CRTC2/3m mice) develop neutrophilia and splenomegaly in adulthood due to the up-regulation of Granulocyte-Colony Stimulating Factor (G-CSF); these effects are reversed following administration of neutralizing anti-G-CSF antiserum. Adoptive transfer of CRTC2/3m BM conferred the splenomegaly/neutrophilia phenotype on WT recipients. Indeed, targeted disruption of both CRTC2 and CRTC3 in stromal cells with a mesenchymal Prx1-Cre transgene also promoted this phenotype.  Depletion of CRTC2/3 was found to decrease the expression of Suppressor of Cytokine Signaling 3 (SOCS3), leading to increases in STAT3 phosphorylation and to the induction of CEBPb, a key regulator of the G-CSF gene. As small molecule inhibition of JAK activity disrupted CEBPb induction and reduced G-CSF expression in CRTC2/3m stromal cells, our results demonstrate how cross-coupling between the CREB/CRTC and JAK/STAT pathways contributes to BM homeostasis.

overall_design: Primary mouse SVF cells from wild-type or CRTC2/CRTC3 compound heterozygote mice were used to interrogate the impact of FSK exposure and CREB activity on cAMP dependent gene regulation in primary SVF cells

first: Jeong-Ho

last: Kim

first: Susan

last: Hedrick

first: Wen-Wei

last: Tsai

first: John

middle: L

last: Lay

first: Klaus

last: Kaestner

first: Mathias

last: Leblanc

first: Andrew

last: Loar

first: Marc

last: Montminy


title: bigSCale: An Analytical Framework for Big-Scale Single Cell Data

status: Public on Apr 15 2018

city: Barcelona

first: giovanni

last: iacono

state: Spain

address: Baldiri Reixac, 4

department: single cell sequencing

institute: CNAG,Centro Nacional de Análisis Genómico

summary: Single-cell RNA sequencing significantly deepened our insights into complex tissues and latest techniques are capable to analyze ten-thousands of cells simultaneously. With bigSCale, we provide an analytical framework being scalable to analyze millions of cells, addressing challenges of future large data sets. Unlike other methods, bigSCale does not constrain data to fit an a priori-defined distribution and instead uses an accurate numerical model of noise. We evaluate the performance of bigSCale using a biological model of aberrant gene expression and simulated data sets, which underlined its speed and accuracy. We further apply bigSCale to analyze 1.3 million cells from the mouse developing forebrain. The directed down-sampling strategy identified rare populations, such as Reelin positive Cajal-Retzius neurons, for which we determined a previously not recognized heterogeneity associated to distinct differentiation stages, spatial organization and cellular function. Together, bigSCale presents a perfect solution to address future challenges of large single-cell data sets.

overall_design: Single cell transcriptomes from 1847 neuronal progenitors differentiated from iPSC of one healthy donor, two patients with Williams-Beuren syndrome and two patients with 7q11.23 microduplication syndrome.

first: Giovanni

last: Iacono

first: Holger

last: Heyn


title: Early dynamics of ERa and GRHL2 binding on stimulation with estradiol

status: Public on Jan 30 2018

city: York

middle: Nicholas

last: Holding

address: Wentwork Way

department: Biology

country: United Kingdom

institute: University of York

summary: We measured ER binding by ChIP-Seq at three time-points (0, 45, 90 minutes after activation with E2) and overlaid the binding information on a co-expression network. Our approach, called VULCAN, rediscovered many known components of the ER complex and additionally found that the activation ER results in the reprogramming of the transcriptional role of the GRHL2 cofactor.

overall_design: ChIP-seq data in MCF7 at three time-points for ERa and two time points for GRHL2 after stimulation with 100 nM E2

middle: N

first: Florian

last: Markowetz


title: Whole blood transcriptome analysis in amyotrophic lateral sclerosis: a biomarker study [HT12_V4]

status: Public on Apr 05 2018

city: Utrecht

first: Jan

last: Veldink

address: Heidelberglaan 100, F.02.230

institute: University Medical Center Utrecht

summary: Transcriptome-wide analysis of whole blood gene expression profiles of ALS patients, gender- and age-matched controls and patients diagnosed with diseases mimicking ALS at a tertiary referral center for motor neuron diseases.

overall_design: mRNA was obtained from whole blood around the time of diagnosis and expression profiles were compared between ALS patients, controls and mimics in a biomarker design.

first: Wouter

last: van Rheenen

first: Frank

middle: P

last: Diekstra

first: Oliver

last: Harschnitz

first: Kristel

last: van Eijk

first: Henk-Jan

last: Westeneng

first: Christiaan

last: Saris

first: Ewout

last: Groen

first: Michael

middle: A

last: van Es

first: Hylke

last: Blauw

first: Paul

middle: W

last: van Vught

first: Leonard

last: van den Berg


title: Predictive computational obesity risk framework through integration of gene expression profiles and genetic risk score.

status: Public on Jan 25 2018

first: Wendy

middle: A.

last: Henderson

address: 10 Center Drive, 2-1341

department: Intramural Research Program

institute: National Institutes of Health, NINR, DHHS

summary: We aimed to predict obesity risk with genetic data, specifically, obesity-associated gene expression profiles. Genetic risk score was computed. The genetic risk score was significantly correlated with BMI when an optimization algorithm was used. Linear regression and built support vector machine models predicted obesity risk using gene expression profiles and the genetic risk score with a new mathematical method.

overall_design:
Microarrays n = 90 whole blood peripheral human samples were assayed by Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. Fasting morning blood samples (2.5 mL) were collected from healthy controls and overweight participants using PAXgeneTM RNA (Qiagen, Valencia, CA) tubes and frozen at -80ºC. Total RNA was extracted and purified with RNA PAXgene kit (Qiagen, Valencia, CA)  and stored at -80oC.  RNA quantity, purity, and integrity were assessed via spectrometry and by RNA 6000 Nano LabChip kit on a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Total RNA passed quality control criteria prior to microarray analysis.

Grant Information: 1ZIANR000018  NIH Intramural Research Program, NINR, DHHS; Henderson, W.A. (PI)
The Rockefeller University,  Heilbrunn Nurse Scholar Award; NIH Office of Workforce Diversity; Joseph, P.V. (PI)
NIH Intramural Research Training Award; Fourie, N.F.

first: Paule

last: Joseph

first: Yupeng

last: Wang

first: Nicolaas

last: Fourie


title: Respecifying human iPSC-derived blood cells into highly engraftable hematopoietic stem and progenitor cells with a single factor

status: Public on Jan 31 2018

city: San Francisco

first: Yuet Wai

last: Kan

state: CA

address: 513 Parnassus Avenue, HSW901E

institute: University of California, San Francisco

summary:
Purpose: We designed this study to evaluate the feasibility of using only one factor to respecify human induced pluripotent stem cells (iPSCs)-derived blood cells into long-term engraftable hematopoietic stem and progenitor cells (HSPCs).
We also parallelly compared iPSC-derived HSPCs (iHSPCs) with primary HSPCs under the same induction and transplantation condition in order to examine the functional equivalency between iHSPCs and bona fide HSPCs.

Methods: In vitro derived human iPSC-HSPCs are induced with or without (w/o) doxycycline for the expression of MLL-AF4. In vivo derived bone marrow cells are harvested and FACS-sorted for human populations from primary transplants over nine to sixteen weeks after transplantation. Either iPSC-HSPCs or primary HSPCs, both of which are induced by MLL-AF4, is used for the transplantation experiments. iPSCs are either derived from peripheral blood mobilized CD34+ HSPCs (CD34-iPSC) or mononuclear cells (MN-iPSCs). Normal human CD34+ HSPCs and mononuclear cells are set as control groups.

Results: MLL-AF4 can impart HSC and lymphoid potential to iPSC-derived blood cells in vitro, and induction of MLL-AF4 leads to the cellular identity transition from common myeloid progenitors to hematopoietic stem and progenitor cells. MLL-AF4 alone is sufficient to realize the potent engraftment of induced HSPCs (iHSPCs) from iPSCs, and multilineage and long-term hematopoiesis could be observed. Primary HSPCs with the induction of MLL-AF4 could gain significantly enhanced engraftability. During the long-term engraftment period, leukemic mutations with a bias to B-cell leukemia could be found in the iHSPCs and their derivatives. By contrast, MLL-AF4 induced primary HSPCs maintain the normal hematopoiesis without leukemic transformation.

Conclusions: Our study has demonstrated for the first time, to our knowledge, that the pluripotency-dependent conversion of somatic cells to long-term engraftable HSPCs can be achieved by using a single factor in a non-integrative way. This study also suggests that iPSC-derived HSPCs are more prone to leukemic mutations during the long-term engraftment period, which provides a necessary caveat of using them in the actual therapies.

overall_design: Human mRNA profiles of either in vitro derived iPSC-HSPCs or engrafted NSG mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000.

first: Yu-Ting

last: Tan

first: Yuet


title: Genome-wide analysis of PDX1 target genes in human pancreatic progenitors

first: Heiko

last: Lickert

overall_design: Refer to individual Series