title: Transcriptomic profile of brain endothelial cells after stroke w/o chronic stress

city: Berlin

first: Stephanie

last: Wegner

address: Charitéplatz 1

department: Experimental Neurology

institute: Charité - Universitätsmedizin Berlin

summary: Our previous studies demonstrate that chronic stress leads to worse stroke outcome with increased brain lesion sizes after experimental brain ischemia. These effects were mediated by endothelial dysfunction and altered cerebral blood flow regulation. RNA-sequencing was performed to further investigate the underlying molecular mechanisms of stress-induced endothelial dysfunction.

overall_design: Chronic stress and control animals were exposed to 30 min MCAo followed by reperfusion. At 72h after stroke endothelial cells from the MCAo territory and the corresponding contralateral tissue were isolated. Brain tissue from 3-5 animals were pooled per condition and 4 replicates per condition were used for RNA-Sequencing.

first: Ria

last: Uhlemann

first: Golo

last: Kronenberg

first: Karen

last: Gertz


title: Genome-wide DNA methylation comparison reveals epigenetically regulated regeneration capacity of Boea hygrometrica during development

status: Public on Nov 25 2019

city: Beijing

first: Run-Ze

last: Sun

address: No.20 Nanxincun, Xiangshan, Haidian District

department: Institute of Botany

country: China

institute: Chinese Academy of Sciences

type: Expression profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

summary: Plants are competent to regenerate new individuals from differentiated tissues under appropriate culture conditions. Although the molecular basis of shoot regeneration has steadily been unraveled, role of DNA methylation in the regulation of plant regeneration capacity remains practically unknown. Here, we established an effective auxin/cytokinin-induced regeneration system of the Chinese resurrection plant Boea hygrometrica through direct organogenesis, and observed that the potential regeneration capacity of leaf explants was gradually decreased with increased age of donor plants. Global transcriptome analysis revealed significant up-regulation of genes required for phenylpropanoid biosynthesis and phytohormone signaling while inhibition of photosynthetic activity in leaf explants during regeneration. Transcriptional changes of positive regulators HY5, STM, EMK and FLA, and negative regulators TSD and CDK involved in plant regeneration, were positively correlated with the regeneration process of B. hygrometrica, implicating their conserved functions across plant species. Comparison of global DNA methylation profiles between expanding young leaves and fully expanded mature leaves with different regeneration capability using whole-genome bisulfite sequencing revealed that increased asymmetrical methylation in mature leaves were predominant distributed in promoter regions, demonstrating their putative inhibitory function for downstream gene expression in B. hygrometrica leaves during maturation. Moreover, the predicted possible DNA methylation control for genes encoding GRCWP1 and BGS40L essential for cell wall architecture, CENL1 controlling extend shoot meristem phases, ANL2 and WRKY75 mediating root hair development, as well as HY5 and two members of ABA signaling components ABF and PP2C also provide new insights into the association of DNA methylation dynamics with regeneration capacity.

overall_design: To investigate the transcriptome changes during regeneration process of B. hygrometrica, we collected leaf explants cultured in induction medium for 0, 5, 10 and 15 days (YL-0d, YL-5d, YL-10d and YL-15d) to conduct the whole-genome transcriptome analysis. Each sample has three biological replicates. In order to further understand the potential role of genomic DNA methylation during shoot regeneration, high-throughput sequencing was performed on bisulfite-treated DNA fragments of young leaves (YL) and mature leaves (ML) of B. hygrometrica to determine the DNA methylation profiles at single nucleotides, yielding a total of 44.49 and 41.19 Gb of clean bases, respectively.


title: Co-Culture of CD8+ T cells and Breast Cancer Cells

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

country: Germany

institute: University Hospital Würzburg

summary: Targeting of tumor immune escape mechanisms holds enormous therapeutic potential. Still, most patients progress under immune checkpoint blockade and some even become hyper-progressors. To investigate how cancer cells respond to activated but ineffective T cells, we challenged peptide-loaded MCF-7 breast cancer cells with antigen-specific CD8+ T cells in which Perforin had been destroyed by pre-treatment with Concanamycin A.

overall_design: Gene expression analysis after coculture in presence of antigen and control peptide.

first: Laura

last: Schlahsa

first: Stefan

last: Ebert

middle: J

first: Jörg

last: Wischhusen


title: The immunogenic potential of bacterial flagella for Salmonella-mediated tumor therapy

city: Braunschweig

first: Matthias

last: Preusse

address: Inhoffenstr. 7

institute: Helmholtz Centre for Infection Research

summary:
Genetically engineered Salmonella Typhimurium are potent vectors for prophylactic and therapeutic measures against pathogens as well as cancer. This is based on the potent adjuvanticity that supports strong immune responses. The physiology of Salmonella is well understood. It simplifies engineering of both enhanced immune-stimulatory properties as well as safety features, thus, resulting in an appropriate balance between attenuation and efficacy for clinical applications. A major virulence factor of Salmonella is the flagellum. It is also a strong pathogen-associated molecular pattern recognized by extra- and intracellular receptors of immune cells of the host. At the same time, it represents a serious metabolic burden. Accordingly, the bacteria evolved tight regulatory mechanisms that control flagella synthesis in vivo. Here, we systematically investigated the immunogenicity and adjuvant properties of various flagella mutants of Salmonella in vitro and in a mouse cancer model in vivo. We found that mutants lacking the flagellum-specific ATPase FliHIJ or the inner membrane ring FliF displayed the greatest stimulatory capacity and strongest anti-tumor effects, while remaining safe in vivo. Scanning electron microscopy revealed the presence of outer membrane vesicles in the ΔfliF and ΔfliHIJ mutants.
Finally, the combination of the ΔfliF and ΔfliHIJ mutations with our previously described attenuated and immunogenic background strain SF102 displayed strong efficacy against the highly resistant cancer cell line RenCa. We thus conclude that manipulating flagella biosynthesis has great potential for the construction of highly efficacious and versatile Salmonella vector strains.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: The samples of Salmonella Typhimurium strain SF102 (ΔlpxR9 ΔpagL7 ΔpagP8 ΔaroA) and derivates (EM6331 (SF102 + ΔfliHIJ), EM6333 (SF102 + ΔfliF)) were analyzed by RNA-seq. The control samples were cultivated in the LB medium until they reached the exponential phase. Four biological replicas were pooled in pairs to get two replicas for RNA extraction, library preparation and sequencing.

first: Sebastian

last: Felgner

first: Imke

last: Spöring

first: Vinay

last: Pawar

first: Dino

last: Kocijancic

first: Christine

last: Falk

first: Manfred

last: Rohde

first: Sausanne

last: Haeussler

first: Siegfried

last: Weiss

first: Marc

last: Erhardt


title: The effect pregnane receptor X (PXR) agonist PCN on hepatic gene expression in mouse liver with and without glucose

city: Kuopio

first: Jaana

last: Rysae

address: Yliopistonranta 1C

department: School of Pharmacy

country: Finland

institute: University of Eastern Finland

summary: The mice were treated i.p. with pregnenolone-16-α-carbonitrile (PCN, 50mg/kg dissolved in DMSO-corn oil 1:3) or vehicle (DMSO-corn oil 1:3) once daily for four days. The mice were fasted for four hours and then administered glucose (2g/kg) by oral gavage or further kept on fasting. The mice were sacrificed 1 hour after glucose administration.

overall_design: The effect of prototypical pregnane receptor X (PXR) agonist (pregnenolone 16α-carbonitrile) PCN on hepatic gene expression was studied in male C57BL/6 mice. PCN and DMSO-corn oil (30%:70%) as a control were given for 4 days. After 6 hours of fasting, glucose (2 mg/g) was given orally. After one hour mice were sacrificed and tissues were collected. Total RNA isolated from mouse liver tissue

first: Jukka

last: Hakkola

last: Rysä


title: Expression data from differentially responsive Toll-like receptor 4 (Tlr4)-normal mice infected with respiratory syncytial virus (RSV)

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

country: USA

institute: NIEHS

summary:
In airway epithelial cells, Tlr4 mediates both innate and adaptive immune responses to viral pathogens  through the surface fusion glycoprotein (RSV F), however the mechanism is not well characterized.
We used microarrays to identify differential gene expression pathways induced by RSV infection.

overall_design: Tlr4-normal mice were infected intranasally with RSV19 (10^6 PFU) or vehicle.  Lungs were collected at 1 and 5 days post infection for RNA extraction and hybridization on Affymetrix arrays.

first: Jacqui

last: Marzec

first: Hye-Youn

last: Cho

first: Steven

last: Kleeberger


title: Characterization of the growth-related transcriptome in family selection of Silurus lanzhouensis through RNA-Seq analysis

status: Public on Nov 24 2019

city: Lan Zhou

first: Wei

last: Xiao

state: Gan Su

address: No. 1, Ying Men Village, Anning District

department: College of Animal Science and Technology

institute: Gansu Agricultural University

summary: The catfish (Silurus lanzhouensis), a popular scaleless fish, is highly nutritious and of great commercial importance. However, transcriptome information related to growth traits in S.lanzhouensis are still unknown. In this study, muscle transcriptome data was used to study this issue by RNA-Seq. In total 44,176,578 to 52,345,588 raw reads were generated for each sample, 163,949 transcripts and 89,579 genes were obtained from the two groups. 843 DEGs showed significant differential expression among 89579 unigenes between two groups, of these, 366 DEGs were up-regulated while 477 DEGs were down-regulated.

overall_design: The experiment was conducted at Ningxia Fisheries Research Institute in May 2016 using F3 S. lanzhouensis fingerlings generated by F2 selectd female parent and wild male of S. lanzhouensis, following the procedures conducted in Nile tilapia [1,2] with modiﬁcations according to growth regime of S. lanzhouensis and available equipment.The ﬁsh were reared for 16 wk prior to challenge in an experimental tank (diameter 1.2m, and depth 1.5m).Tanks were set up with a constant ﬂow-through system (0.5 l/s) with fresh pond water at oxygen levels (8.0–10.0 ppm) and ambient temperature (～24°C). Meanwhile, according to the growth trait of S. lanzhouensis, the heaviest three fish and the lightest three fish from the tank were selected and divided into SLA and SLB. Muscle was withdrawn from the back of the ﬁsh (1.5–2.0g) for RNA extraction. Tissues were placed into RNAlater, and then moved to -80°C for storage until use.Then,RNA-Seq was carried out.


title: p38-MK2 regulate RNA metabolism after UV light-induced DNA damage

city: Mainz

first: Petra

last: Beli

address: Ackermannweg 4

institute: Institute of Molecular Biology (IMB)

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Droplet-based single-cell RNA-sequencing of mouse and naked mole-rat spleen and circulating immune cells, in natural conditions, following lipopolysaccharide (LPS) challanege, and saline control

city: South San Francisco

first: Nimrod

middle: Daniel

last: Rubinstein

state: CA

address: 1170 Veterans blvd

institute: Calico

summary: Single-cell RNA-sequencing was performed in the mouse and naked mole-rat immune systems in order to map and compare their immune cell repertoirs and their cell-specific gene-expression responses to LPS challenge

sample_organism:
Mus musculus
Heterocephalus glaber

platform_organism:
Mus musculus
Heterocephalus glaber

overall_design: Single-cell RNA-sequencing was obtained from: 1. 4 adult mouse and 4 adult naked mole-rat spleens in duplicate; 2. 4 adult mouse and 3 adult naked mole-rat circulating immune cells; 3. 2 adult mouse and 2 adult naked mole-rat spleens following LPS challenege in duplicate; 4. 2 adult mouse and 2 adult naked mole-rat spleens following saline administration in duplicate; 5. 2 adult mouse and 2 adult naked mole-rat circulating immune cells following LPS challenege in duplicate; 4. 2 adult mouse and 2 adult naked mole-rat circulating immune cells following saline administration in duplicate;

first: Hugo

last: Hilton

first: Rochelle

last: Buffenstein


title: The role of ATG16L1 in the intestinal epithelium

status: Public on Nov 23 2019

city: New York

first: Yu

last: Matsuzawa

state: NY

address: 430 East 29th Street, 4th Floor, Lab 424

institute: New York University School of Medicine

summary: The ATG16L1-deficient intestinal organoids display increased IFN-I signature.

overall_design: Comparison between WT and ATG16L1-deficient small intestinal organoids with or without TNFa stimulation.

first: Ken

last: Cadwell

first: Eugene

last: Rudensky


summary: Ultraviolet (UV) light induces the formation of bulky UV photoproducts in the genome that interfere with DNA replication and transcription. It is well-established how human cells repair UV light-induced DNA lesions, however the signaling pathways and mechanisms that regulate transcription after exposure to UV light are poorly understood. Here, we provide a systematic view on dynamic protein phosphorylation patterns induced by UV light and uncover the dependencies of phosphorylation events on canonical DNA damage kinases and the p38 MAP kinase pathway. Notably, we demonstrate that p38 and its downstream effector kinase MK2 are responsible for one quarter of protein phosphorylation induced by UV light. We identify RNA binding proteins as primary targets and 14-3-3 family proteins as direct readers of UV light-induced, p38-MK2-dependent phosphorylation. Importantly, we demonstrate that UV light triggers rapid and dynamic phosphorylation of the negative elongation factor (NELF) complex subunit NELFE on serine 115 that mediates its binding to 14-3-3. NELFE interaction with 14-3-3 stabilizes NELFE and RNA pol II interaction on the chromatin and inhibits transcriptional elongation, thereby promoting cell survival after UV light.

overall_design: Analysis of NELFE occupancy genome-wide in U2OS cells by ChIP-seq.

first: Beli

last: Petra


overall_design: Analysis of RNA pol 2 occupancy genome-wide in mock-treated U2OS cells, cell exposed to UV light and cells pre-treated with the p38 inhibitor and exposed to UV light by ChIP-seq.


title: Large-scale in vitro production of red blood cells from human peripheral blood mononuclear cells

city: Amsterdam

first: Emile

last: van den Akker

address: Plesmanlaan 126

country: Netherlands

institute: Sanquin Blood Supply

summary: We provide the first full account of transcriptional changes during terminal erythroid differentiation for cells grown under conditions of stress erythropoiesis. Samples were generated from PBMC's in three-stage culture system in Cellquin, an IMDB based culture medium optimized for erythroid outgrowth. The first two stages rely on presence of EPO Stem Cell Factor and dexamethasone (mimmicking stress erythropoiesis), followed by a terminal differentiation stage in presence of EPO and Holotransferrin. This culture set up allows for generation of large number of cultured Red Blood Cells that ar functionally and morphologically similar to ex-vivo red blood cells.

overall_design: RNA sequencing accross 10 sampling points in erythroid differentiation (4 donors each).

first: E

first: M

last: von Lindern


title: Real-time quantitative PCR analysis of human total blood tissue from athletes or sedentary controls

city: Granada

first: Jorge

last: Molina

state: Granada

address: Campus de la Cartuja S/N

department: Physiology

country: Spain

institute: University of Granada

summary: Thirteen elite handball athletes and 13 sedentary controls. Three timepoints were established: T0 (baseline conditions); T8 (after 8 weeks of supplementation); and T16 (after 8 weeks in the absence of supplementation). The dietary intervention consisted of the oral administration of one daily multivitamin/mineral complex capsule (Multicentrum® Pfizer, Barcelona, Spain) before exercise during the controlled dietary intervention period. Multivitamin/mineral complex intervention adherence/compliance was defined as the percentage of all of the supplement capsules ingested throughout the study period. The expressions of a total 112 of genes were evaluated by RT-qPCR analysis with the QuantStudioTM 12K Flex Real-Time PCR System. 78 genes were finally analized.

overall_design: qPCR gene expression profiling.  Total blood from 13 athletes and 13 sedentary subjects were used and treated separately as indicated in the summary. Equal amount total RNA from each subject was pooled prior to gene expression analysis.

last: Molina-López

middle: A

last: Quispe Ricalde


title: Bone marrow B cell transcriptomic profile in humanized NSG mice injected with KU55933

city: New Haven

first: Kofi

last: Mensah

state: CT

address: 300 George Street

department: Rheumatology, Allergy and Clinical Immunology

institute: Yale University School of Medicine

summary: RNA Sequencing was performed on RNA extracted from human bone marrow B cells from NSG humanized mice that had been transplanted with human hematopoietic stem cells and then injected or not with the ATM inhibitor KU55933.

overall_design: RNA was extracted from batch sorted human CD45+CD19+CD10+IgM+ bone marrow B cells isolated from humanized NSG injected or not with ATM inhibitor KU55933

first: Eric

last: Meffre


title: Impaired ATM Activation in B Cells Promotes Osteoclastogenic Cytokine Production and Bone Erosion in Patients with Rheumatoid Arthritis

summary: Rheumatoid arthritis (RA) patients may display atypical CD21-/lo B cells in their blood but the significance of this observation remains unclear. We report here that the group of RA patients with elevated frequencies of CD21-/lo B cells shows decreased ataxia-telangiectasia mutated (ATM) expression and activation in B cells compared with other RA patients and healthy donor controls. In agreement with ATM involvement in the regulation of V(D)J recombination, RA patients with defective ATM function displayed a skewed B cell receptor (BCR) Igk repertoire, which resembled that of ataxia-telangiectasia (AT) patients. This repertoire was characterized by increased Jk1 and decreased upstream Vk gene segment usage, suggesting improper secondary recombination processes and selection. In addition, altered ATM function in B cells was associated with decreased osteoprotegerin (OPG) and increased RANKL production. These changes favor bone loss and correlated with a higher prevalence of erosive disease in RA patients with impaired ATM function. Using a humanized mouse model, we also show that ATM inhibition in vivo induces an altered Igk repertoire and RANKL production by immature B cells in the bone marrow, leading to decreased bone density. We conclude that dysregulated ATM function in B cells promotes bone erosion and the emergence of circulating CD21-/lo B cells, thereby contributing to RA pathophysiology.

overall_design: RNA was extracted from batch sorted CD19+CD21+CD10-CD27- naïve B cells isolated from donors using the Absolutely RNA microprep kit (Stratagene). 100-200 ng of RNA was obtained per sample, and the quality of the purified RNA was assessed by the Bioanalyzer from Agilent. Using the Ovation biotin system kit from Nugen, 30-50ng of RNA was amplified and labeled to produce cDNA. Labeled cDNA was hybridized on chips containing the whole human genome (Human Genome U133 2.0 from Affymetrix).

first: Isabelle

last: Isnardi


title: Affymetrix SNP array data for a pediatric acute lymphoblastic leukemia samples

city: MONZA

first: MARTA

last: GALBIATI

address: VIA CADORE

country: Italy

institute: TETTAMANTI RESEARCH CENTER

summary: First evidence of a Cornelia de Lange Syndrome patient with a novel cohesin mutation and Acute Lymphoblastic Leukemia

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved diagnostic bone marrow samples.
Copy number analysis of Affymetrix Cytoscan HD arrays was performed on ALL diagnostic sample and remission sample

first: Grazia

last: Fazio

first: Valentina

last: Massa

first: Andrea

last: Grioni

first: Vojtech

last: Bystry

first: Silvia

last: Rigamonti

first: Claudia

last: Saitta

first: Marta

last: Galbiati

first: Carmelo

last: Rizzari

first: Caterina

last: Consarino

last: Biondi

first: Angelo

last: Selicorni

first: Giovanni

last: Cazzaniga


title: Inhibition of Lysine-Specific Demethylase-1 in Myelodysplastic Syndrome Progenitors Restores Differentiation of CD141Hi Conventional Dendritic Cells

city: BUFFALO

first: Eduardo

last: Cortes

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

summary: Immunotherapeutic approaches to treat patients with myelodysplastic syndromes (MDS) show promise but progress is hindered by our incomplete knowledge of the immunologic milieu. In a recent phase I trial, we found that vaccination of MDS patients against the tumor antigen NY-ESO-1 activated antigen-specific adaptive immune responses in patients with higher numbers of CD141Hi conventional dendritic cells (cDCs). In solid tumor models, the CD141Hi cDC is critical for initiating anti-tumor immune responses but its impact in myeloid malignancies is unknown. In a series of studies using human samples and mouse models, we tested the hypothesis that MDS patients would exhibit decreased quantity and quality of CD141Hi cDCs due to myeloid dysplasia. Overall, we found CD141Hi cDCs were decreased in MDS patients’ bone marrow and that decreased numbers of CD141Hi cDCs were associated with reduced overall survival. MDS patients had reduced numbers of DC committed progenitors and their progenitors expressed lower levels of the transcription factor interferon regulatory factor-8 (IRF8), a master regulator of CD141Hi cDC differentiation. Induction of IRF8 expression in mouse, healthy human and MDS patient progenitors using an inhibitor of lysine-specific demethylase-1 (LSD1) increased CD141Hi cDC differentiation. These data reveal a previously unrecognized factor of the immune microenvironment in MDS and suggest intriguing connections between epigenetic regulation of CD141Hi cDC differentiation in MDS and the ability to translate these mechanisms to improve immunotherapy for MDS patients.

overall_design: 32 samples; 18 NBM and 14 VP; 10 CD141Hi, 11 CD1c and 11 CD34 cell types.

first: Pragya

last: Srivastava

first: Stephanie

last: Tzetzo

first: Kevin

last: Eng

first: Prashant

last: Singh

first: Kitty

last: de Jong

first: Sheila

last: Sait

first: Miranda

last: Lynch

first: Jennifer

last: Peresie

first: Kyle

last: Wiatrowski

first: Jianming

last: Wang

first: Scott

middle: I

last: Abrams

first: Elizabeth

last: Griffiths

first: Michael

last: Nemeth


title: Integrative analysis of microRNAs and mRNAs in liver tissue and exosomes from blood of hepatitis C virus (HCV) related hepatocellular carcinoma (HCC) patient to identify biomarker and regulators of HCC [Total RNA-Seq]

city: Kolkata

first: Soma

last: Banerjee

state: West Bengal

address: 244, A.J.C Bose Road

department: School of Digestive & Liver Diseases

country: India

institute: Institute of Post Graduate Medical Education & Research

summary: Chronic hepatitis C (CHC) is one of the major risk factor for the progressive development of end stage liver diseases including liver cirrhosis (LC) and HCC worldwide. A deep insight into the molecular mechanism of development and progression of liver fibrosis into cirrhosis and HCC following chronic HCV infection leads to characterization of multiple cellular processes and the underlying regulatory mechanisms. Non-coding RNAs (sncRNAs) including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are found to be the prime regulators of multiple cellular pathways. Using such tools several studies have identified myriads of differentially regulated non-coding RNAs and genes in HCV disease progression to HCC. Our study attempted to look into the integrative network of regulatory non-coding RNAs and target genes involved in HCV related HCC and thereby identify a potential diagnostic molecule as well as therapeutic target for HCC surveillance and management.

overall_design:
Our study attempted to look into the integrative network of regulatory non-coding RNAs and target genes involved in HCV related HCC.
[contributor] Medgenome Inc.

first: Shaleen

last: Aggarwal

first: Subash

last: Gupta

first: Sukanta

last: Ray

first: Raghunath

last: Chatterjee


title: Role of Ikaros in Early B-cell Development: Studies of IkZnF1-/- and IkZnF4-/- mutant mice

city: San Francisco

first: Hilde

last: Schjerven

address: 513 Parnassus Ave

department: Laboratory Medicine

institute: UCSF

summary: Ikaros is a zinc finger (ZnF) transcription factor critical for B-cell development. The C2H2 zinc finger is the most prevalent DNA-binding motif in the mammalian proteome, with DNA-binding domains usually containing more tandem fingers than are needed for stable sequence-specific DNA recognition. To examine the reason for the frequent presence of multiple zinc fingers, we generated mice lacking finger 1 or finger 4 of the 4-finger DNA-binding domain of Ikaros (Schjerven et al., Nat Immunol, 2013; PMID: 24013668). Each mutant strain exhibited a specific subset of the phenotypes observed with Ikaros null mice, and revealed that different subsets of fingers within multi-finger transcription factors can regulate distinct target genes and biological functions. We here study the effect of these mutants on early B-cell development in the bone marrow (BM) with transcriptome profiling of sorted proB-cells (Hardy fractions B+C+C') from BM of wt and the two ZnF mutants (this GEO submission: RNA-Seq).

overall_design: RNA-Seq from sorted primary proB cells of combined Hardy Fractions B+C+C' (BC), comparing wt, Ikaros-ZnF1-/- mutant and Ikaros-ZnF4-/- mutant (B220+, CD19+, IgM-, CD24+, BP1+/-).

first: Stephen

middle: T

last: Smale


title: Differential gene expression profiles in imatinib-resistant cell lines

status: Public on Nov 22 2019

city: Hyderabad

first: Ramakrishna

last: Kancha

address: Osmania University Main Campus

institute: Osmania University

summary: The study reports deregulated gene expression profiles underlying imatinib resistance in leukemic cell lines

overall_design: Comparison of differentially expressed genes between wild type and  imatinib-resistant cell lines

first: Rama

last: Krishna Kancha

first: Utsa

last: Bhaduri


title: Transcriptomic, epigenetic and functional analyses implicate neutrophil diversity in the pathogenesis of systemic lupus erythematosus [ATAC-seq]

city: Bethesda

first: Hong-wei

last: Sun

state: MD

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

summary: Two subpopulations of low density granulocytes (LDGs) were defined in terms of different gene expression patterns, transcriptional and epigenetic features as well as functions. This study provides insights into the mechanism of immune dysregulation and the vascular damage characteristic of lupus.

overall_design: Transcriptomics and epigenetic assessment of lupus PBMCs, LDGs, autologous normal-density neutrophils (NDN) and healthy control (HC) neutrophils was performed by mRNA sequencing and assay for transposase-accessible chromatin sequencing. NET formation, chemotaxis, phagocytosis, degranulation, induction of endothelial dysfunction and release of oxidized nucleic acids were compared among subsets. This metadata sheet includes the 24 ATAC-Seq samples of this project.

first: P

last: Mistry

first: S

last: Nakabo

first: L

last: O’Neil

first: R

middle: R

last: Goel

first: K

last: Jiang

last: Dell’Orso

first: G

last: Gutierrez-Cruz

first: H

middle: W

first: M

last: Kaplan


title: Increased Muscleblind levels by chloroquine treatment improves myotonic dystrophy type 1 phenotypes in in vitro and in vivo models

city: Burjassot

first: Ruben

last: Artero

state: Valencia

address: C/ Doctor Moliner, 50

department: Genetics

institute: Universidad de Valencia

summary: Myotonic dystrophy type 1 (DM1) is a life-threatening and chronically debilitating neuromuscular disease caused by the expansion of a CTG trinucleotide repeat in the 3'UTR of the DMPK gene. The mutant RNA forms insoluble structures capable of sequestering RNA binding proteins of the Muscleblind-like (MBNL) family, which ultimately originates phenotypes. In this work we demonstrate that treatment with the anti-autophagic drug chloroquine in Drosophila and mouse (HSALR) models, and patient-derived myoblasts, was sufficient to upregulate MBNL1 and 2 proteins. Extra Muscleblind was functional at the molecular level and improved splicing events regulated by MBNLs in all disease models. In vivo, chloroquine rescued locomotion and average crossectional muscle area, and extended median survival of DM1 flies. In HSALR mice the drug recovered muscular strength and histopathology signs, and reduced myotonia grade. Taken together these results offer a novel means to replenish the critically low levels of MBNLs in DM1.

overall_design: We have 3 replicas of each treatment: Control, Disease, TreatmentConcentration1, TreatmentConcentration2

first: Ariadna

last: Bargiela

first: Maria

last: Sabater-Arcis

first: Jorge

last: Espinosa-Espinosa

first: Miren

last: Zulaicad

first: Adolfo

last: Lopez de Munain


title: The short time-series transcriptome profiles of a human adipose mesenchymal stem cell by electrical stimulation of enzymatic biofuel cell

city: Pocheon-si

first: Jae Ho

last: Lee

state: Gyeonggi-do

address: 120, Haeryong-ro

department: Department of biomedical Science

country: South Korea

institute: CHA University

summary:
We investigate the mRNA expression properties of hAD-MSCs by electrical stimulation using EBFC as an electrical regulator. We set up three different electrical currents, at 120±10.2, 250±11.5, and 500±16.2 nA/cm2 in hAD-MSCs. We performed transcriptome profiling to analyze the impact of EBFC-derived electrical current on gene expression using next-generation sequencing (NGS).
Among the 166 up-regulated genes, 98 genes were significantly enriched into the UniProtKB functional categories such as ribosomal protein, alternative splicing, ribonucleoprotein, and amino-acid biosynthesis. This indicate that the genes highly associated with metabolic regulation of cell growth and proliferation have been changed by electrical stimulation in the EBFCs.

overall_design: mRNA profiles of wild-type human adipose-derived mesenchymal stem cells (hAD-MSCs) and hAD-MSCs under nano-scale electrical stimulation at 120±10.2, 250±11.5, and 500±16.2 nA/cm2, using Illumina HiSeq2500.

first: Keunsoo

last: Kang

first: Kyudong

last: Han

first: Seyoung

last: Mun


title: Early quantification of systemic inflammatory (INF) and cardiovascular disease (CVD) proteins predicts long-term treatment response to Tofacitinib and Etanercept (INF data set)

first: Lewis

middle: Elwood

last: Tomalin

state: New York

address: 303 East 71st Street, Apt1B

department: Population Health Science & Policy

institute: Icahn School of Medicine at Mount Sinai

summary:
Proteomic profiles of 92 inflammatory proteins were measured in the blood of psoriasis patients both before and after treatment with tofacitanib or etanercept.
These proteomic profiles were used to develop statistical classifiers for predicting PASI75 responses to tofacitinib and etancercept

overall_design: A cohort of 266 psoriasis patients used in this study (Table1) was randomly selected from a phase-3 clinical trial comparing efficacy of tofacitinib 10 mg QD and etanercept 50 mg BIW for the treatment of moderate-to-severe chronic plaque psoriasis (ClinicalTrials.gov: NCT01241591) (Bachelez et al., 2015), 30% of non-responders were taken from each group.

first: Jaehwan

last: Kim


title: Early quantification of systemic inflammatory (INF) and cardiovascular disease (CVD) proteins predicts long-term treatment response to Tofacitinib and Etanercept (CVD data set)

summary:
Proteomic profiles of 91 cardiovascular disease proteins were measured in the blood of psoriasis patients both before and after treatment with tofacitanib or etanercept.
These proteomic profiles were used to develop statistical classifiers for predicting PASI75 responses to tofacitinib and etancercept


title: Early quantification of systemic inflammatory (INF) and cardiovascular disease (CVD) proteins predicts long-term treatment response to Tofacitinib and Etanercept

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

overall_design: Refer to individual Series


title: Mucosal Profiling of Pediatric-Onset Colitis and IBD Reveals Common Pathogenics and Therapeutic Pathways

city: Guangzhou

first: Yuxia

last: Zhang

address: Jinsui Road

department: Guangzhou Institute of Pediatrics

institute: Guangzhou Women and Children's Medical Center, Guangzhou Medical University

summary: Pediatric-onset colitis and inflammatory bowel disease (IBD) have significant effects on the growth of infants and children, but the etiopathogenesis underlying disease subtypes remains incompletely understood. Here, we report single-cell clustering, immune phenotyping, and risk gene analysis for children with undifferentiated colitis, Crohn’s disease, and ulcerative colitis. We demonstrate disease-specific characteristics, as well as common pathogenesis marked by impaired cyclic AMP (cAMP)-response signaling. Specifically, infiltration of PDE4B- and TNF-expressing macrophages, decreased abundance of CD39-expressing intraepithelial T cells, and platelet aggregation and release of 5-hydroxytryptamine at the colonic mucosae were common in colitis and IBD patients. Targeting these pathways by using the phosphodiesterase inhibitor dipyridamole restored immune homeostasis and improved colitis symptoms in a pilot study. In summary, comprehensive analysis of the colonic mucosae has uncovered common pathogenesis and therapeutic targets for children with colitis and IBD.

overall_design: Single cell suspensions of colonic biopsies from eight patients were stained with antibodies and sorted by FACS. Single cell 5’ gene expression libraries were prepared for CD45+CD3+CD19- (HB1), CD45+CD3-CD19+ (HB2), CD45+CD3-CD19- (HB3-1) and CD45- (HB4) cells obtained from pooled cells of 4 patients. Single cell 5’ gene expression library was prepared for CD45+CD3-CD19- (HB3-2) cells from pooled cells of 2 patients. Single cell 3’ gene expression libraries were prepared for CD45+ (S279 and S280) cells obtained from 2 patients respectively. All libraries were constructed according to the 10X Chromium instructions and sequenced on Illumina Hiseq X Ten instrument.

first: B

last: Huang

first: Z

last: Chen

first: L

last: Geng

first: J

last: Wang

last: Liang

first: Y

last: Cao

first: W

last: Su

last: Xu

last: Liu

last: Lu

last: Xian

last: Li

last: Ren

last: Xie

last: Ye

last: Zhao

first: P

first: S

first: T

first: D

last: Che

last: Si

first: X

last: Gu

last: Zeng

last: Zhan

last: Delfouneso

first: A

middle: M

last: Lew

last: Cui

last: Tang

last: Gong

first: F

last: Bai

last: Yang


title: Chromatin-seq and RNA-seq of dREAM subunit deficient Drosophila S2R+ cells

city: Cardiff

first: Helen

last: White-Cooper

address: Museum Avenue

country: United Kingdom

institute: Cardiff University

summary: dREAM is a multi-functional complex which activates and represses genes involved in the G2/M transition and is involved in maintaining chromatin boundaries through interactions with CTCF and BEAF-32, however the mechanisms by which it carries out gene and chromatin regulation is yet to be uncovered. Applying a novel Mnase-seq technique, RNAi and RNA-seq we report links between transcriptional changes in S2R+ cells deficient for dREAM subunits and changes in chromatin structure. The most distinct chromatin phenotype of these cells are at CTCF binding sites, several of which are located between divergent gene pairs which show impaired regulation in cells deficient for a dREAM component.

overall_design: S2R+ cells treated with dsRNA against GFP (control), mip40, E2F2, mip120 or mip130 where harvested for chromatin digestion by Micrococcal nuclease, or for total RNA purification. Purified DNA or RNA was then sequenced using an Illumina HiSeq 2000 machine. All samples were carried out in duplicate except E2F2, of which there is a single sample.

first: Gordon

last: Beattie

first: Nick

last: Kent


title: Transcriptomic analysis of adhesive capsulitis of the shoulder

status: Public on Nov 21 2019

city: Waurn Ponds

first: Nima

last: Kamal

state: VIC

address: 75 Pigdons Rd

department: School of Medicine

country: Australia

institute: Deakin University

summary: We compared genes from tissue of patients with adhesive capsulitis (AC) with those having surgery for shoulder instability to determine potential biomarkers specific to AC through transcriptomic analysis. Our results presented increased expression of PDGFB, COL18A1 and MMP9 in patients with AC, while TNFA expression was reduced.

overall_design: Tissue samples were collected from the anterior capsule and rotator interval during surgery. Total RNA was extracted and RNA-sequencing-based transcriptomics were performed. Bioinformatic analyses were carried out to identify biological processes and pathways enriched in this dataset. A number of genes deemed differentially expressed in RNA-sequencing analysis were validated using real time RT-PCR.

first: Sean

middle: L

last: McGee

first: Graeme

last: Brown

first: Sally

first: Kevin

last: Eng

first: Fiona

last: Collier

first: Stephen

last: Gill

first: Richard

last: Page


title: Impact of ETV7 activity on interferon-stimulated gene expression in 293T cells treated with interferon alpha

city: Durham

first: Nicholas

last: Heaton

address: 213 Research Drive, 426 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

summary: 293T cells constitutively expressing ETV7 have reduced expression of interferon-stimulated genes.

overall_design: 293T cells were transfected with plasmids expressing ETV7 or a control (mCherry) and then treated with interferon alpha 9 h before total RNA collection and RNAseq.

first: Heather

last: Froggatt

middle: S


title: Microarrays after exposure in Caco-2 cells to titanium dioxide food additive E171 and titanium dioxide nanoparticles and microparticles

city: Maastricht

first: Héloïse

last: Proquin

address: Universiteitssingel 50

institute: Maastricht University

summary: Exposure to titanium dioxide (TiO2) food additive by ingestion increased over the years. TiO2 is used in food to give a brighter, fresher colour to sweets, cookies, salad dressing under the name E171. New studies on E171 showed that after ingestion in a colorectal cancer mouse model, a significant increased number of colorectal tumours were found. In addition, short-term exposure to E171 induces gene expression changes in relation to oxidative stress responses, an impairment of the immune system, activation of signalling and cancer-related genes. Furthermore, dysregulation of the immune system was also observed after ingestion of E171 in rats. E171 comprises nanoparticles (NPs) and microparticles (MPs). Previous in vitro studies showed the capacity of E171, TiO2 NPs and MPs to induce oxidative stress, DNA damage, and induction of the micronuclei. The aim of our study was to investigate the relative contribution of the NPs and MPs fractions to the effects of E171 at the molecular level. This investigation was performed using in vitro exposure of Caco-2 cells to E171 as well as the NPs and MPs fractions of TiO2 and assessing effects with genome wide gene expression analysis. Results showed that the E171, TiO2 NPs and MPs induce gene expression changes in signalling, inflammation, immune system, transport, and cancer. Contribution of NPs was observed on genes involved in TLR cascade, MHC class I and II presentation, late cornified envelope, potassium channels, and cell cycle. MPs contribution was observed with changes in gene expression on a target to Hedgehog family, α-defensins, cadherin and cholinergic receptors. The gene expression changes associated with the immune system and inflammation induced by E171, MPs, and NPs suggest the creation of a favourable environment for cancer development.

overall_design: Total of 76 samples, 3 biological replicates plus every sample in duplicate. One time course exposure to TiO2 NPs for 2, 4, and 24h and exposure to MPs and E171 for 24h. Samples of MPs and E171 also have a time 0h exposure. First pre-processing was performed with the samples of the time course experiment with NPs. For this, six groups were defined: NPs 2h, 4h, and 24h for the exposed samples and control 2h, 4h, and 24h for the controls. The second pre-processing was split in 2 parts in which the first part was a pre-processing of the NPs 24h with its time-matched control and the second part was a pre-processing of E171 24h and MPs 24h with their time-matched control. The second pre-processing was split in 2 because the experiments were performed independently.

first: Marlon

last: Jetten

first: Marloes

middle: C

last: Jonkhout

first: Luis

middle: G

last: Garduño-Balderas

first: Jacob

last: Briedé

first: Theo

last: de Kok

first: Yolanda

last: Chirino

first: Henk

last: van Loveren


title: Chromatin fiber invasion and nucleosome displacement by the Rap1 transcription factor

city: Geneva

first: Sevil

last: Zencir

address: 30, quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

summary: Pioneer transcription factors (pTFs) bind to target sites within compact chromatin initiating chromatin remodeling and controlling the recruitment of downstream factors. The mechanisms by which pTFs overcome the chromatin barrier are not well understood. Here we reveal, using single-molecule fluorescence, how the yeast transcription factor Rap1 invades and remodels chromatin. Using a reconstituted chromatin system replicating yeast promoter architecture we demonstrate that Rap1 can bind nucleosomal DNA within a chromatin fiber, but with shortened dwell times compared to naked DNA. Moreover, we show that Rap1 binding opens chromatin fiber structure by inhibiting inter-nucleosome contacts. Finally, we reveal that Rap1 collaborates with the chromatin remodeler RSC to displace promoter nucleosomes, paving the way to form long-lived bound states on now exposed DNA. Together, our results provide a mechanistic view of how Rap1 gains access and opens chromatin, thereby establishing an active promoter architecture and controlling gene expression.

overall_design: RSC remodeling and Rap1 binding experiments were performed on either 601 (S1/S2) or RPL30 nucleosomes, and mapped nucleosome positioning using MNase-seq

first: Maxime

last: Mivelaz

first: Anne-Marinette

last: Cao

first: Slawomir

last: Kubik

first: Ruud

last: Hovius

first: Iuliia

last: Boichenko

first: Anna

last: Stachowicz

first: Christoph

middle: F

last: Kurat

first: David

last: Shore

first: Beat

last: Fierz


title: ETV7 and interferon response

first: Nicholas

last: Heaton


title: Absolute quantification of cohesin, CTCF and their regulators in human cells

city: Vienna

first: Roman

last: Stocsits

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP - Research Institute of Molecular Pathology

summary: We have measured absolute copy numbers and dynamics of cohesin, CTCF and their regulators NIPBL, WAPL and sororin by mass spectrometry, fluorescence-correlation spectroscopy and fluorescence recovery after photobleaching in HeLa cells before and after DNA replication. Comparison of these numbers with chromatin immunoprecipitation-sequencing data implies that some genomic cohesin and CTCF enrichment sites are unoccupied in single cells at any one time.

overall_design: Absolute quantification of cohesin copy number by liquid chromatography mass spectrometry and fluorescence-correlation spectroscopy.

first: Wen

last: Tang

first: Georg

last: Busslinger


title: A genome-wide CRISPR activation screen identifies ETV7 as a negative regulator of the interferon response

summary: Identification of factors that negatively regulate the interferon response

overall_design: A549 cells containing an interferon responsive reporter and CRISPR activation technology were transduced with the complete sgRNA library and then treated with interferon alpha. Next, cells that were not responsive to interferon were collected and the sgRNAs enriched in these populations was sequenced.

first: Alfred

last: Harding

first: Heather

last: Froggatt


city: Chicago

first: zhike

last: lu

state: IL

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

summary: FMRP facilitates the nuclear export of N6-methyladenosine-containing mRNAs.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
We used PAR-CLIP followed by m6A-IP to determine direct binding sites of FMRP. We used m6A-seq to determine methylated transcripts in cortices of WT and Fmr1KO mice. We used RNAseq to determine abundance of transcripts in cytoplasmic and nuclear portions of cortices of WT and Fmr1KO mice.
HEK293T cells were treated with control and FMR1 siRNAs for 48 hours, and collected for RNA-seq.

first: Phillip

last: Hsu

first: Hailing

last: Shi

first: Zhike

last: Lu

first: Brittany

last: Edens

first: Nimrod

last: Miller

first: Yongchao

last: Ma

first: Chuan

last: He


city: NANJING

first: SENLIN

last: JI

state: Jiangsu

address: No. 1, Weigang Road

department: College of Veterinary Medicine

institute: Nanjing Agricultural University

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

summary: Rabies, caused by the rabies virus (RABV), is the oldest known zoonotic infectious disease. Although the molecular mechanisms of RABV pathogenesis have been investigated extensively, the interactions between host and RABV are not clearly understood. It is now known that long non-coding RNAs (lncRNAs) participate in various physiological and pathological processes, but their possible roles in the host response to RABV infection remain to be elucidated. To better understand the pathogenesis of RABV, RNAs from RABV-infected and uninfected human neuroblastoma cells (SK-N-SH) were analyzed using human lncRNA microarrays. We identified 896 lncRNAs and 579 mRNAs that were differentially expressed after infection, indicating a potential role for lncRNAs in the immune response to RABV. Differentially expressed RNAs were examined using Gene Ontology (GO) analysis and were tentatively assigned to biological pathways using the Kyoto Encyclopedia of Genes and Genomes (KEGG). A lncRNA-mRNA-transcription factor co-expression network was constructed to relate lncRNAs to regulatory factors and pathways that may be important in virus-host interactions. The network analysis suggests that E2F4, TAF7 and several lncRNAs function as transcriptional regulators in various signaling pathways. This study is the first global analysis of lncRNA and mRNA co-expression during RABV infection, provides deeper insight into the mechanism of RABV pathogenesis, and reveals promising candidate for future investigation.

overall_design: Examine the different of mRNA and lncRNA expression profiles between rabies virus infected and untreated human neuroblastoma cells

first: Senlin

last: Ji

first: Jiyong

last: Zhou


title: RNA-seq data for salivary glands and midgut sections from adult Nezara viridula on corn and green bean diets

city: Gainesville

first: Pablo

middle: Emiliano

last: Canton

state: Florida

address: Natural Area Dr.

department: Entomology and Nematology

institute: University of Florida

summary: Transcriptomic data was obtained from adults of the stink bug Nezara viridula to complement biochemical enzymatic activity analysis performed for digestive enzymes. Pooled reads from all sample types were used for de novo assembly of a reference transcriptome. After mapping reads to reference, differential expression was performed between the different tissues of the same diet or between the same tissue in different diets.

overall_design: Tissues were collected from adults fed on corresponding diet for 24 hours post molt. Each tissue (salivary glands, M1, M2, M3) was dissected from 4-10 individuals. Each sample type ( tissue in specific diet) was obtained in triplicate from a biological replicate of experiment

middle: E

last: Cantón

first: Bryony

middle: B

last: Bonning


title: Transcriptomic analysis of race L Botryococcus braunii AC768 revealed a race L-specific protein resembling the lycopaoctaene synthase

city: Zhoushan

first: Jianhua

last: Liu

state: Zhejiang

address: 10 Tiyu Road, Room 502

department: Ocean Research Centre of Zhoushan

institute: Zhejiang University

summary: The green algal Botryococcus braunii (Chlorophyte) is known for accumulating high levels of hydrocarbons that are a useful alternative to fossil fuels.  B. braunii is categorized into three groups based on types of their accumulated hydrocarbons: alkadiene/triene in race A, botryococcenes in race B, and lycopadiene in race L.  Transcriptomic studies in race A and race B have discovered tremendous information related to the genes encoding proteins involved in hydrocarbon biosynthesis.  However, transcriptome of race L has not been reported.  In this study, we report a transcriptome of race L B. braunii AC768 through the de novo assembly using Hiseq platform.  Our analyses indicate that photosynthesis and protein biosynthesis are the most abundantly transcribed in actively growing race L B. braunii.  We show that the transcriptome of race L shares similar amounts (~20%) of mutual best-hits with that of race A or race B.  Sequence homologous analyses indicate that enzymes involved in squalene and phytoene biosynthesis are well separated into geranyl-diphosphate synthase, farnesyl-diphosphate synthase, geranylgeranyl-diphosphate synthase, phytoene synthase, and squalene synthase.  Both B. braunii specific enzymes botryococcene synthase SSL3 and lycopaoctaene synthase LOS are found to form distinctive subgroups in the group of squalene synthase.  One of the ESTs in AC768 transcriptome that falls into the subgroup with LOS and shares >88% identity with that of LOS.  Together, our results show that SSL and LOS are unique to race B and race L B. braunii subspecies, respectively.  We propose that phytoene synthase in race L shares higher homolog to squalene synthase than phytoene synthase in other algae.

overall_design: 1 biological samples

first: Zhenyu

last: Xu


title: Transcriptomic changes of Arabidopsis plants subjected to high light, heat stress and their combination

city: Memphis

first: Soham

last: Sengupta

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

summary: Transcriptomic analysis by RNAseq of Col leaves subjected to high light, heat stress and the combination of high light and heat stress

overall_design: 30-day-old Arabidopsis thaliana Col-0  plants were subjected to high light (600 µmol m-2 s-1), heat stress (42°C) and the combination of high light and heat stress during 7h.

first: Damián

last: Balfagón

first: Aurelio

last: Gómez-Cadenas

first: Felix

last: Fritschi

first: Rajeev

middle: K

last: Azad

first: Ron

last: Mittler

first: Sara

last: Zandalinas


title: Gene expression of Skeletal muscle in Tacrolimus-Induced Post-transplantation Diabetes Mellitus model

status: Public on Nov 20 2019

city: wenzhou

first: chenlei

last: zheng

address: wenzhou medical university

institute: wenzhou medical university

summary: Post-transplantation diabetes mellitus (PTDM) is a known complication of transplantation which affected the prognosis. Tacrolimus (Tac, or FK506) is a widely used immunosuppressant, has been reported as a risk factor for PTDM and further develops complications in heart and skeletal muscle , while the mechanism is still largely unknown. The gene expression of  rat muscles of control group and Tac induced PTDM group were analyzed.

overall_design: In the study presented here, 3 rat muscles of control group and 3 rat muscles of Tac induced PTDM group were used to acquire expression profiles of a total of 275 different expression genes, followed by bioinformatics analyses.

first: Chen

last: Zheng

first: Bi

last: Chen


title: Genome-wide mapping of SET-Nup214, mutant NPM1 (NPM1c), and CRM1-binding sites in human leukemia or mouse ES cell lines

city: Ibaraki

first: Masahiro

last: Oka

state: Osaka

address: 7-6-8 Saito-Asagi

country: Japan

institute: National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN)

summary: We used ChIP-seq to examine the genome-wide binding of CRM1, SET-Nup214, and NPM1c in leukemia cell lines. Our analysis revealed that CRM1, SET-Nup214, and NPM1c are preferentially targeted to HOX cluster regions.

overall_design: chromatin immunoprecipitation

first: Yoshihiro

last: Yoneda

first: Jumpei

last: Nogami

first: Kazumitsu

last: Maehara

first: Akihito

last: Harada

first: Yasuyuki

last: Ohkawa


title: Transcriptional profiling of ependymal cells lining the ventricles in the central nervous system of a Dcdc2a-TRAP (ES2575) mouse line

city: New York

first: Laura

last: Kus

address: 1230 York Avenue # 260

department: Heintz Laboratory

institute: The Rockefeller University

summary: TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain.  Using this technique we obtained RNA-Seq data from actively translating transcripts present in ependymal cells lining the ventricles in the central nervous system of adult Dcdc2a-EGFP/Rpl10a (ES2575) mice

overall_design: TRAP-Seq of ependymal cells lining the CNS ventricles of adult Dcdc2a-EGFP/Rpl10a (ES2575) mice

first: Eric

last: Schmidt

first: Jim

last: Li

first: Nathaniel

last: Heintz


title: Expression data from huh28 cells

city: Nanjing

first: Shen

last: Gu

address: Hankou Road 22

institute: nanjing university

summary:
Intrahepatic cholangiocarcinoma (iCCA) has over the last 10 years become the focus of increasing concern largely due to its rising incidence and high mortality rates worldwide. Microcystin-leucine-arginine (MC-LR) have been reported to be carcinogenic but there are no data on the linkage between MC-LR and iCCA.
We used microarrays to detail the change of gene expression in iCCA cells(huh28) treated with MC-LR.

overall_design: Cells incubated in the absence or presence of 500 nM MC-LR for 24 h were harvested and total RNA was isolated immediately from 106 cells. The mRNA microarray analysis was performed by Affymetrix GeneChip® Human Genome U133 Plus 2.0 Array according to the manufacturer’s instructions.

first: Yudong

last: Qiu


title: Wide spread and efficient co-transcriptional splicing facilitated by multiple exons

city: Fuzhou

first: mao

last: fei

state: Fujian

address: Shangxiadianlu NO.15

department: National Engineering Research Center of JUNCAO

institute: Fujian Agriculture and Forestry University

summary: Pre-mRNA splicing is important for gene expression in most eukaryotic organisms. Regulation occurs during pre-mRNA splicing greatly expanded the transcriptome complexity. Recent studies from Mammals, Drosophila and Yeast showed that the majority of introns are spliced co-transcriptionally. However, in plant the nature of co-transcriptionally splicing (CTS) and its regulation is still largely unknown. Here, through sequencing the chromatin-bound RNA (CB-RNA-seq), we studied the feature of CTS in Arabidopsis. We found CTS is widespread in Arabidopsis seedlings and a large proportion of alternative splicing events are determined co-transcriptionally. We found the CTS efficiency correlate with gene expression level, chromatin landscape and most surprisingly, the number of intron/exon of individual genes, whilst independent of gene length.  In combination with iCLIP analysis, we found splicing regulator RZ-1B/1C promotes efficient CTS of thousands genes involving direct binding mainly to the exonic sequences. Interestingly, for many cases, the splicing promotion activity of RZ-1C does not associate with its binding to the regions immediately adjacent to the regulated intron. We propose a model of plant gene splicing, where multiple exon of individual gene is in favour of efficient CTS likely involving RZ-1C cooperative interactions with many exons and splicing factors. Our work uncovers the robustness of plant CTS and highlighted the role of RZ-1C in this process.

overall_design: chromatin-bound RNA sequencing and iCLIP-seq were used to investigate the basic feature and regulation of co-transcriptional pre-mRNA splicing

first: Danling

last: Zhu

first: Fei

last: Mao

first: Yuanchun

last: Tian

first: Xiaoya

last: Lin

first: Lianfeng

first: Hongya

first: Li-jia

last: Qu

first: Yufeng

last: Wu

first: Zhe


title: Epigenetic regulation of iASPP-p63 feedback loop in cutaneous squamous cell carcinoma

city: Biella

first: Paola

last: Ostano

address: via Malta 3

institute: Fondazione Edo ed Elvo Tempia

summary: Keratinocyte skin cancer, comprising cutaneous squamous (cSCC) and basal cell carcinoma, is the most common malignancy in the UK. P53 is frequently mutated in cSCC. iASPP is a key inhibitor of p53 and NF-kB signalling pathways and has been documented as highly expressed in several types of human cancer. We have previously identified an autoregulatory feedback loop between iASPP and p63, which is critical in epidermal homeostasis. We hypothesised a potential role for dysregulation of this axis in the pathogenesis of keratinocyte malignancies. Immunostaining of 116 cSCC clinical samples revealed increased iASPP and ΔNp63 expression but also highlighted a significant alteration of iASPP cellular localisation, with consequent deregulation of its function. Expression patterns, functionality, gene and microRNA expression analysis were further investigated in 10 cSCC cell lines. Our data suggest that whilst direct effects of iASPP and p63 upon each other’s expression are maintained in cSCC, epigenetic dysregulation of the feedback loop occurs at the microRNA level by a novel mechanism controlling p63 expression. We demonstrate that this autoregulatory feedback loop controls cell migration in cSCC by blocking EMT and promoting proliferation, and provides future directions for clinical biomarker and therapeutic target discovery in cutaneous SCC.

overall_design: miRNA expression profiling of si-iASPP or non-targeting siRNA treated cSCC cell lines and keratinocytes cSCC cell lines.

first: Deborah

middle: J

last: Robinson

first: Ankit

last: Patel

first: Karin

last: Purdie

first: Jun

last: Wang

first: Hasan

last: Rizvi

first: Martin

last: Hufbauer

first: Baki

last: Akgül

first: Giovanna

last: Chiorino

first: Catherine

last: Harwood

first: Daniele

last: Bergamaschi


title: Collagen type-V is a danger signal associated with primary graft dysfunction in lung transplantation

city: Indianapolis

first: Robert

last: Stearman

state: IN

address: 950 W Walnut St

department: Medicine/Pulmonary

institute: Indiana Univeristy School of Medicine

summary: Primary graft dysfunction (PGD) is the leading cause of early mortality after lung transplantation. Anti-collagen type-V (col(V)) immunity has been observed in animal models of ischemia-reperfusion injury (IRI) and in PGD. We hypothesized that collagen type-V is an innate danger signal contributing to PGD pathogenesis. Methods: Anti-col(V) antibody production was detected by flow cytometric assay following cultures of murine CD19+ splenic cells with col(V). Responding murine B cells were phenotyped using surface markers. RNA-Seq analysis was performed on murine CD19+ cells. Levels of anti-col(V) antibodies were measured in 188 recipients from the Lung Transplant Outcomes Group (LTOG) after transplantation. Results: Col(V) induced rapid production of anti-col(V) antibodies from murine CD19+ B cells. Subtype analysis demonstrated innate B-1 B cells bound col(V). Col(V) induced a specific transcriptional signature in CD19+ B cells with similarities to, yet distinct from, B cell receptor (BCR) stimulation. Rapid de novo production of anti-col(V) Abs was associated with an increased incidence of clinical PGD after lung transplant. Conclusions: This study demonstrated that col(V) is an rapidly recognized by B cells and has specific transcriptional signature. In lung transplants recipients the rapid seroconversion to anti-col(V) Ab is linked to increased risk of grade 3 PGD.

overall_design: Three biological replicate harvest of C57BL/10 male mouse spleens were used in 7 different experimental conditions. CD19+ cells (1×106 ml) were then resuspended in 6 well plates in a total volume of 4 ml, and incubated for 3 h. Conditions included media (RPMI 1640 (Invitrogen) containing 10% heat-inactivated FBS (HyClone) and 1% penicillin/streptomycin, 1% glutamine (Invitrogen)), media plus 5mM HOAc, or media plus 5mM HOAc with either 200 μg/ml col(I), 200 μg/ml col(V), 10 μg/ml LPS (E. coli 0111:B4 (Sigma L4391), or 10 μg/ml goat anti-mouse F(ab’)2 anti-IgM (Jackson ImmunoResearch 115-006-075). Purified col(I) and col(V) were soluble in 50mM or 100mM HOAC, respectively, so the culture media had 20mM HEPES pH 7.5 added to restore the pH to neutrality.


title: Single cell RNA sequencing identifies the developmental origin of C-Myc dependent T-bet+thymic intraepithelial lymphocyte precursor

city: Freiburg

first: Patrice

last: Zeis

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Natural intraepithelial lymphocytes (IELs) are thymus-derived adaptive immune cells, which are important contributors to intestinal immune homeostasis. Similar to other innate-like T cells they are induced in the thymus through high-avidity interaction that would otherwise lead to clonal deletion in conventional CD4 and CD8 T cells. By applying single-cell RNA-sequencing (scRNA-seq) on a heterogeneous population of IEL precursors (IELPs) we define a developmental trajectory that identifies Id3 as a novel regulator of IELP development and shows that all natural TCRαβ+ IELPs progress through a PD-1 stage as a result of strong agonist selection. Furthermore, with the use of newly developed PD-1 fate map and conditional T-bet knockout mice we demonstrate that this PD-1 stage precedes the induction of T-bet. The transition from PD-1 to T-bet is regulated by the transcription factor C-Myc, as T cell-specific conditional C-myc knockout mice lack PD-1-T-bet+ IELPs, while PD-1+T-bet- IELPs are still present. In summary, our results provide a high-resolution molecular framework for thymic IEL development and deepen our understanding of this still elusive cell type.

overall_design:
Single cell RNA sequencing was performed on thymic intraepithelial lymphocytes by sorting CD4-CD8-TCRb+NK1.1+ fresh isolated thymocytes from one TBGR mouse. A replicating experiment was executed by comparing fresh isolated IELPs from one TBGR and TGBR C-mycD/DCd4 mouse.
Please note that some of the readme_*.coutt.txt files are identical, because the same cell barcodes have been used but different illumina barcodes.

first: Jonas

last: Hummel

first: Dominic

last: Grün

first: Yakup

last: Tanriver


title: Differential expression of Hdc-GFP+/hi HSC VS Hdc-GFP-/lo hematopoetic stem cells (HSCs) from bone marrow.

first: Timothy

middle: Cragin

state: NY

address: 1130 St. Nicholas Ave

department: Medicine- Liver and Digestive Diseases

institute: Columbia University Medical Center

summary: Bone marrow Hdc-GFPhi and  Hdc-GFPlo HSPC (SLAM-LSK, Lin-c-kit+Sca-1+CD150+CD48-) HSCs were isolated from mouse femur and tibia from histidine decarboxylase (Hdc) green fluorescent protein (Hdc-GFP) mice. Hdc-GFPhi HSC and Hdc-GFPlo HSC cells were sorted by combinations of GFP and the cell surface markers of HSC. total RNA was isolated from sorted 2,500 HSPCs using ARCTURUS PicoPure RNA isolation kit (Life Technologies). cDNA was amplified and libraries were constructed by using SMARTer Ultra Low Input RNA kit (Clontech Laboratories) and Nextera XT DNA Library Preparation kit (Illumina) according to manufacturer’s instructions respectively. Sequencing was performed on the Illumina HiSeq2000 platform.

overall_design:
a. Hdc-GFPhi bone marrow HSC cells (n=3)
b. Hdc-GFPlo bone marrow HSC cells (n=4)

first: Xiaowei

last: Chen

first: Alexander

first: Richard

middle: A

last: Friedman

first: Siddhartha

last: Mukherjee


title: Alteration of renal gene expression following miR-22 inhibition in rhabdomyolysis (24 h) induced acute kidney injury

city: Berlin

first: Michael

last: Fähling

address: Charitéplatz 1

department: Institut für Vegetative Physiologie

institute: Charité - Universitätsmedizin Berlin

summary:
In acute kidney injury (AKI) regions of the kidney are hypoxic. However, for reasons yet unknown, adaptation to hypoxia through hypoxia inducible factor (HIF) is limited. Here we seek for potential HIF repressors, their amenability to intervention, and assess the consequences for AKI outcome
Renal miR-22 is up-regulated in AKI. In vitro, miR-22 is inducible by hypoxia, represses HIF, and this repression is offset by specific anti-miR-22 molecules. Inhibition of miR-22 in AKI leads to a complex regulation of more than 3,000 renal genes, most of which are unrelated to the HIF pathway.

overall_design: Anti-miR-22 (I-mmu-miR-22-3p, sequence 5’-3’ CTTCAACTGGCAGCT, Exiqon, Denmark) or mock molecules (I-mmu-miR-22-3p MM, sequence 5’-3’ CTACTACAGGCTGCT, Exiqon, Denmark) were dissolved in 0.9% saline, and injected SC at a dose of 20 mg/kg of body weight 24 h prior to glycerol injection. 50% glycerol injection into the gastrocnemic muscle causes rhabdomyolysis and subsequently acute kidney injury (AKI). 24 h after glycerol injection, animals were euthanized by cervical dislocation under isoflurane narcosis, and kidneys were rapidly removed, halved, and snap frozen in liquid nitrogen

first: Christian

last: Rosenberger

first: Susanne

last: Mathia


title: BCL6 evolved in vertebrates as a stress tolerance gene and is broadly used by cancer cells to adapt to stress

first: Tharu

last: Fernando

address: 413 East 69th St BB1462

department: Medicine, Heme-Onc

institute: Weill Cornell Medical College

summary: We have found that BCL6 is a component of the conserved stress response program regulated by HSF1. BCL6 mediates cellular adaptation to stress by repressing genes through its BTB domain. These genes fail to be repressed after stress in a murine model with point mutations in the BCL6 BTB domain that disrupt its repressor activity.

overall_design: Splenic B220+ cells from wild-type and BCL6BTBmut mice were heat shocked for 12 hs. Total RNA was harvested from cells before and 12 h after heat shock and used for expression profiling via mRNA-seq.

first: Ari

last: Melnick


title: DNA methylation and histone H1 jointly repress transposable elements and aberrant intragenic transcripts

city: Norwich

first: Jaemyung

last: Choi

address: Norwich Research Park

department: Cell and Developmental Biology

institute: John Innes Centre

summary: DNA methylation and histone H1 mediate transcriptional silencing of genes and transposable elements, but how they interact is unclear. In plants and animals with mosaic genomic methylation, functionally mysterious methylation is also common within constitutively active housekeeping genes. Here we show that H1 is enriched in methylated sequences, including genes, of Arabidopsis thaliana, yet this enrichment is independent of DNA methylation. Loss of H1 disperses heterochromatin, globally alters nucleosome organization, and activates H1-bound genes, but only weakly de-represses transposable elements. However, H1 loss strongly activates transposable elements hypomethylated through mutation of DNA methyltransferase MET1. Hypomethylation of genes also activates antisense transcription, which is enhanced by H1 loss. Our results demonstrate that H1 and DNA methylation jointly maintain transcriptional homeostasis by silencing transposable elements and aberrant intragenic transcripts. Such functionality plausibly explains why DNA methylation, a well-known mutagen, has been maintained within coding sequences of crucial plant and animal genes.

overall_design: Bisulfite and RNA sequencing was performed using wt, h1, met1, h1met1, h1;met1 +/- plants (5-6 replicates, one sample for h1;met1 +/-) to examine the effect of DNA methylation and histone H1 loss on RNA expression. Decap-seq was performed using wt, met1, h1met1, and h1;met1+/- plants (2-3 replicates, one sample for h1;met1+/-). H1 ChAP and H3K9me2 ChIP sequencing: pH1-H1-BLRP transgenic plants were generated in wt and met1 plants to monitor H1 distribution change. Antibody against H3K9me2 (Abcam, cat. No. AB1220) was used to enrich chromatin bound to modified histones in wt and met1 plants.

first: David

last: Lyons

first: M

middle: Y

last: Kim


title: De novo assembly and transcriptome analysis of Litopenaeus vannamei gill response to different salinity cultivated conditions

city: Qingdao

first: Dan

last: Zhang

address: Yushan Road 5

department: Fisheries College

institute: Ocean University of China

summary: We provided a step forward in examining the transcriptomic response of L. vannamei to different salinity conditions following the application of the next-generation sequencing techniques and was first to explain osmoregulation of L. vannamei at a transcriptome-wide scale based on three practical cultivated models with different salinities. The assembled sequence data comprising 349,012 unique transcripts were obtained, and the established transcriptional database provided a comprehensive sequence source for this non-model organism.

overall_design: Gill mRNA profiles of L. vannamei cultured in seawater, brackish water and fresh water, respectively, were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Fang

last: Wang


title: Plag1 in the mouse Epididymis

status: Public on Nov 19 2019

city: Melbourne

first: Joanne

last: Wong

address: Kingsbury Drive

department: PAM

institute: La Trobe University

summary: RNA sequencing of Plag1 mouse epididymides. 5 each of Plag1 WT, HET and KO whole epididymis tissues were sequenced.

overall_design: Transcriptome analysis of Plag1 WT, HET and KO whole epididymis


title: Transcriptomic analysis of cyanobacterial alkane production

city: Tucson

first: Kerry

middle: Kevin

last: Cooper

state: AZ

address: 1117 E. Lowell St.

department: School of Animal and Comparative Biomedical Sciences

institute: University of Arizona

summary: To identify transcriptional adaptations associated with increased alkane production in Nostoc punctiforme, we performed comparative transcriptomic analysis of an alkane overproduction strain. RNA-seq data identified a large number of highly up-regulated genes in the overproduction strain potentially involved in rRNA processing, mycosporine-glycine production, and synthesis of non-ribosomal peptides including nostopeptolide A.  Other up-regulated genes encoding helical carotenoid proteins, stress-induced proteins, and those for microviridin synthesis were also up-regulated.  The presence of several up-regulated genes or operons on multi-copy plasmids resulted in reduced alkane production, indicating possible targets for mutagenesis that might limit lipid droplet and alkane production.

overall_design: Comparison of gene expression patterns of wild type Nostoc punctiforme versus alkane overexpressing strain

first: Daisy

last: Arias

first: Kevin

last: Pinto

last: Summers


title: MYC predetermines the sensitivity of gastrointestinal cancer to antifolate drugs through regulating TYMS transcription

city: Shanghai

first: Jingyu

last: Lang

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences

summary: The goal of this study is to dig out the downstream gnens of NIPBL

overall_design: mRNA profiles of NUGC3 cell transfected with shNIPBL and scramble were detected by RNA-sequencing.

first: Tingting

last: Liu

first: Jing-Yu


title: The neurogenomic transition from territory establishment to parenting in a territorial female songbird

city: Bloomington

first: Kimberly

last: Rosvall

address: 1001 E Third Street

department: Biology

institute: Indiana University

summary: The brain plays a critical role in upstream regulation of processes central to mating effort, parental effort, and self-maintenance. For seasonally breeding animals, the brain is likely mediating trade-offs among these processes within a short breeding season, yet research thus far has only explored neurogenomic changes from non-breeding to breeding states or select pathways (e.g., steroids) in male and/or lab-reared animals. Here, we use RNA-seq to explore neural plasticity in three behaviorally relevant neural tissues (ventromedial telencephalon [VmT], hypothalamus [HYPO], and hindbrain), comparing free-living female tree swallows (Tachycineta bicolor) as they shift from territory establishment to incubation. We additionally highlight changes in candidate aggression-related genes to explore the potential for a neurogenomic shift in the mechanisms regulating aggression, a critical behavior both in establishing and maintaining a territory and in defense of offspring. We found hundreds of differentially expressed genes in the VmT and HYPO. Enrichment analyses for the VmT revealed higher expression of genes related to neuroplasticity and processes beneficial for competition during territory establishment, but down-regulated immune processes. The HYPO showed signs of high neuroplasticity during incubation, and a decreased potential for glucocorticoid signaling. Furthermore, expression of aggression-related genes shifted from steroidal to non-steroidal pathways across the breeding season. Altogether, we found genomic signatures suggestive of trade-offs between enhanced activity and immunity in the VmT and between stress responsiveness and parental care in the HYPO, along with a potential shift in the mechanisms regulating aggression. These data highlight important gene regulatory pathways that may underlie behavioral plasticity in females.

overall_design: 3 tissues (hindbrain, ventromedial telencephalon, and hypothalamus) were collected from 10 female tree swallows (n=5 during territory establishment and n=5 during incubation) and total RNA was extracted and run on a Nextseq platform.

first: Alexandra

last: Bentz

first: Gregg

middle: W

last: Thomas

first: Douglas

last: Rusch


title: Effect of high fat diet on phenotype, brain transcriptome and lipidome in Alzheimer's model mice

city: Pittsburgh

first: Iliya

last: Lefterov

state: PA

address: 130 De Soto Street

department: Enviromantal and Occupational health

institute: University of Pittsburgh

summary: We examined the effect of chronic high fat diet (HFD) on amyloid deposition and cognition of 12-months old APP23 mice, and correlated the phenotype to brain transcriptome and lipidome. HFD significantly increased amyloid plaques and worsened cognitive performance compared to mice on normal diet (ND).

overall_design: Male and female APP23 mice (mean age 11.7 months) were randomly assigned to ND (Prolab Isopro RMH 3000, Lab Diet) or HFD (D12079B RD Western Diet, Research Diets). HFD supplemented 40% calories from fat; 16.8% from protein and 42.6% from carbohydrates. Fat was provided as anhydrous milk fat and corn oil. The mice had free access to water and food. After 3 months of feeding, behavior was assessed at mean age of 14.7 months.

first: Kyong

middle: N

last: Nam

first: Anais

last: Mounier

first: Cody

last: Wolfe

first: Nicholas

last: Fitz

first: Alexis

last: Carter

first: Emilie

last: Castranio

first: Hafsa

middle: I

last: Kamboh

first: Valerie

last: Reeves

first: Jianing

first: Xianlin

last: Han

first: Jonathan

last: Schug

first: Radosveta

last: Koldamov


title: Effects of darunavir upon gene expression in kidney tubular cells after transduction with HIV or EGFP-control lentivirus

first: Weijia

last: Zhang

address: 1 Gustave L. Levy Pl

department: Renal

institute: Icahn School of Medicine at Mount Sinai

summary: To determine the effect of darunavir upon HIV-induced gene regulation in renal epithelial cells, immortalized human renal tubular epithelial cells (HPT1b) were transduced with VSV-pseudotyped gag/pol-deleted HIV lentivirus or EGFP control lentivirus. 4 days later, cells were treated with darunavir (3uM) or vehicle control from 4-7 days post transduction. Primary comparisons in gene expression were between HIV and control-transduced cells at 4 days post transduction, and between DRV and control-treated HIV-transduced cells at 7 days post transduction.

overall_design: All experiments (including controls) were performed in triplicate at all time points.

first: Michael

last: Ross

first: Xiaobo

last: Gao

first: Alan

last: Rosales

first: Zhengzi

last: Yi


title: The role of cardiac transcription factor NKX2-5 in regulating the human cardiac miRNAome.

first: Katrina

middle: M

last: Bell

state: Victoria

address: RCH, Flemington Rd, Parkville

institute: MCRI

type: Non-coding RNA profiling by high throughput sequencing

summary:
Aims: MiRNAs are post-transcriptional regulatory molecules with recognized roles in human heart development and disease. The purpose of this study was to define human miRNA expression profile in cardiac progenitors and early-differentiated cardiomyocytes and to determine if these miRNAs that are governing cardiogenesis is dependent on NKX2-5, a highly conserved pan-cardiac transcription factor.
Methods: MiRNA expression profiles of pre-NKX2-5 mesoderm, cardiac progenitors and early cardiomyocytes derived from heterozygous HES3 NKX2-5eGFP/w  and null NKX2-5eGFP/eGFP hESC lines were generated by small RNA sequencing in triplicates, using Illumina HiSeq. Reads between 17-28 base pairs were selected for sequence alignment to the human genome (hg19) using Bowtie2. FeatureCounts (Subread, R package) was used to count the number of reads mapping to miRNAs and analysis of statistically differentially expressed miRNA was carried out using Limma (Bioconductor) through the statistical language R. qRT–PCR validation was performed using Taqman MicroRNA Assays.
Results: We identified 11 miRNAs that were differentially expressed between pre-NKX2-5 mesoderm and cardiac progenitors, and 112 differentially expressed miRNAs between cardiac progenitors and early cardiomyocytes. Four of which were validated with qRT–PCR, including canonical myogenic miRNAs such as MIR-1-1, -133A1 and 208A that were enriched in both the cardiac progenitor and early cardiomyocyte populations. Strikingly, deletion of NKX2-5 did not result in gross changes in cardiac miRNA profile either at progenitor or cardiomyocyte stage. Instead, non-hierarchical clustering and principal component analysis demonstrated that the different stages of differentiation (day 6 vs day 10) was a larger discriminator between samples than NKX2-5 genotype.
Conclusion: Our study demonstrates the application of human embryonic stem cells as an in vitro model to investigate the role of miRNAs in human cardiac development. We conclude that while specific miRNAs have been identified in our study to have a role in the early stages cardiac cell fate specification, the majority of cardiac myogenic miRNA program is regulated separately from the highly conserved NKX2-5 -dependent gene network. This study provides a framework for further investigation of other key transcription factors of cardiac muscle development that might drive cardiomyogenic expression of miRNAs.

overall_design: miRNA expression profiles of pre-NKX2-5 mesoderm, cardiac progenitors and early cardiomyocytes derived from heterozygous HES3 NKX2-5eGFP/w  and null NKX2-5eGFP/eGFP hESC lines were generated by small RNA sequencing in triplicates

first: David

last: Elliott

first: Deevina

last: Arasaratnam


title: Coinfection of monocyte derived dendritic cells with HSV2 and HIV

city: Linköping

first: Rada

last: Ellegård

state: Ostergotlands Lan

address: Vallmogatan 16

country: Sweden

institute: Linköping University

overall_design:
RNA-seq of coinfected of monocyte derived dendritic cells with HSV2 and HIV

Definitions:
HIV = single infection with free HIV-1
CHIV = single infection with complement opsonized HIV-1
HSV2HIV = Dual infection with free HSV2 and free HIV-1
CHSV2CHIV = Dual infection with complement opsonized HSV2 and complement opsonized HIV-1

>>>Submitter states that raw data are not available due to patient privacy concerns<<<

first: Marie

last: Larsson


title: Coagulation FXIII-A protein expression defines three novel sub-populations in pediatric B-cell progenitor acute lymphoblastic leukemia characterized by distinct gene expression signatures

city: Debrecen

first: Szilard

last: Poliska

address: Egyetem ter 1.

department: Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

summary:
Leukemic B-cell precursor (BCP) lymphoblasts were recently identified as a novel expression site for coagulation factor XIII subunit A (FXIII-A). The FXIII-A negative subgroup was significantly associated with the ‘B-other’ genetic category and had an unfavorable disease outcome
RNA was extracted from bone marrow lymphoblasts of 42 pediatric patients with BCP-acute lymphoblastic leukemia (ALL). FXIII-A expression was determined by multiparameter FC. Genetic diagnosis was based on conventional cytogenetic method and fluorescence in situ hybridization. Affymetrix GeneChip Human Primeview array was used to analyze global expression pattern of 28869 well-annotated genes.

overall_design: Sub-groups were createdtwo way: 1)  based on the protein expression of FXIII-A:  FXIII-A negative group (<20% FXIII-A positive lymphoblasts),  FXIII-A dim group (20%-79% FXIII-A positive lymphoblasts),  FXIII-A positive group (≥80% FXIII-A positive lymphoblasts) 2) based on genetic sub-type: non-B-other: - low-risk including t(12;21)/ETV6/RUNX1(TEL-AML1) and high hyperdiploidy (51-65 chromosome), - high-risk including MLL translocations, iAMP21, complex karyotype, near haploidy (chromosome number 23-29), and low hypodiploidy (chromosome<45) - intermediate risk with  t(1;19) translocations, B-other: anything else not belonging to the upper categories which are currently genetically unclassified

first: Katalin

last: Gyurina

first: Bettina

last: Kárai

first: Anikó

last: Ujfalusi

first: Zsuzsanna

last: Hevessy

first: G

last: Barna

first: Pál

last: Jáksó

first: Gyöngyi

last: Pálfi-Mészáros

first: Szilárd

last: Póliska

first: Beáta

last: Scholtz

first: János

last: Kappelmayer

first: Gábor

last: Zahuczky

first: Csongor

last: Kiss


title: Integrative analysis of microRNAs and mRNAs in liver tissue and exosomes from blood of hepatitis C virus (HCV) related hepatocellular carcinoma (HCC) patient to identify biomarker and regulators of HCC

city: Kolkata

first: Soma

last: Banerjee

state: West Bengal

address: 244, A.J.C Bose Road

department: School of Digestive & Liver Diseases

institute: Institute of Post Graduate Medical Education & Research

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

overall_design: Refer to individual Series


title: Early epigenomic and transcriptional changes reveal Elk-1 transcription factor as a therapeutic target in Huntington’s disease

first: Ferah

last: Yildirim

address: Charitéplatz 1, Virchowweg 6

institute: Charité Berlin


title: Vanilla planifolia Jacks., transcriptomic response towards Fusarium oxysporum f. sp. vanillae infection

city: Cuernavaca

first: Veronica

last: Jimenez-Jacinto

state: Morelos

address: Av. Universidad 2001. Col. chamilpa

department: Unidad Universitaria de Secuenciación Masiva y Bioinformática

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

summary: Upon exposure to unfavorable environmental conditions, plants need to respond quickly to maintain their homeostasis. For instance, physiological, biochemical and transcriptional changes occur during plant-pathogen interaction. In the case of Vanilla planifolia Jacks., a worldwide economically important crop, it is susceptible to Fusarium oxysporum f. sp. vanillae. This pathogen causes root and stem rot in vanilla plants that lead to plant death. To investigate how vanilla plants, respond at the transcriptional level upon infection with F. oxysporum f. sp. vanillae, here we employed the RNA-Seq approach to analyze the dynamics of whole-transcriptome changes during two-time frames of the infection. Analysis of global gene expression profiles indicated that the major transcriptional change occurred at 2 dpi, in comparison to 10 dpi. Whereas 3420 genes were found with a differential expression at 2 dpi, only 839 were identified at 10 dpi. The analysis of the transcriptional profile at 2 dpi suggests that, among other responses, vanilla plants prepare to counter the infection by gathering a pool of translational regulation-related transcripts. The screening of transcriptional changes of V. planifolia Jacks upon infection by F. oxysporum f. sp. vanillae provides insights into the plant molecular response, particularly the upregulation of ribosomal proteins at early stages. Thus, we propose that the plant-pathogen interaction between V. planifolia Jacks and F. oxysporum f. sp. vanillae causes a transcriptional reprogramming coupled with a translational regulation. Altogether, this study provides the identification of molecular players that could help to fight the most damaging disease of vanilla.

overall_design: 2-step analysis of Fusarium infection in vanilla roots. 2 days after incubation (DPI) and 10 days after inoculation respectively.

first: Marco

middle: T

last: Solano de la Cruz

first: Jacel

last: Adame-García

first: Josefat

last: Gregorio-Jorge

first: Verónica

last: Jiménez-Jacinto

first: Leticia

last: Vega-Alvarado

first: Lourdes

last: Iglesias-Andreu

first: Esteban

last: Escobar-Hernández

first: Mauricio

last: Luna-Rodríguez


title: Early epigenomic and transcriptional changes reveal Elk-1 transcription factor as a therapeutic target in Huntington’s disease [ChIP-seq]

summary: Huntington’s disease (HD) is a chronic neurodegenerative disorder characterized by a late clinical onset despite ubiquitous expression of the mutant Huntingtin gene (HTT) from birth. Transcriptional dysregulation is a pivotal feature of HD. Yet, the genes that are altered in the prodromal period and their regulators, which present opportunities for therapeutic intervention, remain to be elucidated. Using transcriptional and chromatin profiling, we found aberrant transcription and changes in histone H3K27 acetylation in the striatum of R6/1 mice during the presymptomatic disease stages. Integrating these data, we identified the Elk-1 transcription factor as a candidate regulator of prodromal changes in HD. Exogenous expression of Elk-1 exerted beneficial effects in a primary striatal cell culture model of HD, and adeno-associated virus-mediated Elk-1 overexpression alleviated transcriptional dysregulation in R6/1 mice. Collectively, our work demonstrates that aberrant gene expression precedes overt disease onset in HD, identifies the Elk-1 transcription factor as a key regulator linked to early epigenetic and transcriptional changes in HD, and presents evidence for Elk-1 as a target for alleviating molecular pathology in HD.

overall_design: ChIP-seq for H3K27ac and Elk-1 in R6/1, CHL2 and wild type animals.

first: Christopher

last: Ng

first: Tobias

last: Ehrenberger

first: Anthony

middle: R

last: Soltis

first: David

last: Housman

first: Ernest

last: Fraenkel


title: Effects of human adipose tissue-derived and umbilical cord tissue-derived mesenchymal stem cells in a dextran sulfate sodium-induced mouse model

city: Shinagawa-ku

first: KATSUHIDE

last: IGARASHI

state: Tokyo

department: Life Science Tokyo Advanced Research center (L-StaR)

institute: Hoshi University School of Pharmacy and Pharmaceutical Science

summary:
Background: Mesenchymal stem cells (MSCs) can be acquired from medical waste. MSCs are easily expanded and have multiple functions, including anti-inflammatory effects. We evaluated the effects of human adipose tissue-derived MSCs (AD-MSCs) and umbilical cord tissue-derived MSCs (UC-MSC) in a dextran sulfate sodium (DSS)-induced mouse model.

Methods: Human AD-MSCs and UC-MSCs (1 × 106 cells) were injected intravenously into a 7-day DSS-induced colitis model. The therapeutic effects of cell origin, injection timing, and supernatants obtained from MSC cultures were evaluated. We also analyzed mRNA expression in MSCs, tissues, and intestinal flora.

Results: AD-MSCs and UC-MSCs had strong anti-inflammatory effects when injected on day 3 in a mouse model. On day 11, mRNA levels of inflammatory factors in colon tissues were significantly decreased after injection of MSCs on day 3. Supernatants from MSCs culture decreased mRNA levels of tumor necrosis factor (Tnf)-α, but had reduced therapeutic effects compared with MSC cell injection. RNA sequencing using colon tissues obtained the day after cell injection revealed changes in the TNF-α/nuclear factor-κB and T-cell receptor signaling pathways. Additional analyses showed that several factors, including chromosome 10 open reading frame 54, stanniocalcin-1, and TNF receptor superfamily member 11b were increased in MSCs after adding serum from DSS colitis mice. Furthermore, both AD-MSCs and UC-MSCs maintained the balance of intestinal flora.

Conclusion: AD-MSCs and UC-MSCs showed therapeutic effects against inflammation after early cell injection while maintaining the intestinal flora. Although supernatants showed therapeutic effects, cell injection was more effective against inflammation.

overall_design: Examination of RNA expression in 3 conditions each having 3 biological replicates.

first: Shunzo

last: Ikarashi

first: Masayuki

last: Oki

first: Katsuhide

last: Igarashi


title: RNA-Seq Analysis of transcriptome network effects of dual-trait selection for ethanol preference and withdrawal using SOT and NOT genetic models

city: Portland

first: Priscila

last: Darakjian

state: OR

address: 3181 SW Sam Jackson Park Road, L470

department: Behavioral Neuroscience

institute: Oregon Health and Science University

summary:
Purpose: Genetic factors significantly affect alcohol consumption and vulnerability to withdrawal. Some genetic models that show predisposition to severe withdrawal are also predisposed to low ethanol consumption and vice versa, even when tested independently in naïve animals.  The study was undertaken to understand gene and network differences between mice selectively bred for high withdrawal/low withdrawal or low withdrawal/high consumption.
Methods: Beginning with a C57BL/6J×DBA/2J F2 intercross founder population, animals were simultaneously selectively bred for both high alcohol consumption and low acute withdrawal (SOT line), or vice versa (NOT line). Using randomly chosen fourth selected generation (S4) mice (N= 18-22/sex/line), RNA-Seq was employed to assess genome-wide gene expression in the ventral striatum. The Mega-MUGA array was used to detect genome-wide genotypic differences. Differential gene expression and the weighted gene co-expression network analysis (WGCNA) were implemented.
Results: The new selection of the SOT and NOT lines was similar to that reported previously (Metten et al. 2014). One thousand eight hundred and fifteen transcripts were detected as being differentially expressed between the lines. For the genes overexpressed in the SOT line there was enrichment in genes associated with cell adhesion, synapse organization and post-synaptic membrane. The genes with a cell adhesion annotation included 23 protocadherins, Mpdz & Dlg2. Genes with a postsynaptic membrane annotation included Gabrb3, Gphn, Grid1, Grin2b, Grin2c & Grm3. The genes overexpressed in the NOT line were enriched in a network module (red) with annotations associated with mitochondrial function. Several of these genes were module hub nodes and these included Nedd8, Guk1, Elof1, Ndufa8, & Atp6v1f.
Conclusions: Marked effects of selection on gene expression were detected. The NOT line was characterized by the increased expression of hub nodes associated with mitochondrial function. Genes overexpressed in the SOT aligned with previous findings e.g. Colville et al. (2017) that high ethanol preference and consumption is associated with effects on cell adhesion and glutamate synaptic plasticity.

overall_design: Ventrolateral Striatal mRNA profiles of S4 adult SOT and NOT mouse strains  were generated. Differential gene expression and GO annotations were assessed.  Differential variance, differential wiring of Networks modules were also assessed.

first: Laura

last: Kozell

first: Denesa

last: Lockwood

first: Stephanie

last: Edmunds

first: Karen

last: Shepherdson

first: Kari

last: Buck

first: Robert

last: Hitzemann


title: Tissue specific human fibroblast differential expression based on RNAsequencing analysis

city: Madison

first: Ziyue

last: Wang

state: WI

address: 425 Henry Mall

institute: UW Madison

summary:
Background:Physical forces, such as mechanical stress, are essential for tissue homeostasis and influence geneexpression of cells. In particular, the fibroblast has demonstrated sensitivity to extracellular matrices with assumedadaptation upon various mechanical loads. The purpose of this study was to compare the vocal fold fibroblastgenotype, known for its unique mechanically stressful tissue environment, with cellular counterparts at various otheranatomic locales to identify differences in functional gene expression profiles.
Results:By using RNA-seq technology, we identified differentially expressed gene programs (DEseq2) among sevennormal human fibroblast primary cell lines from healthy cadavers, which included: vocal fold, trachea, lung, abdomen,scalp, upper gingiva, and soft palate. Unsupervised gene expression analysis yielded 6216 genes differentially expressedacross all anatomic sites. Hierarchical cluster analysis revealed grouping based on anatomic site origin rather thandonor, suggesting global fibroblast phenotype heterogeneity. Sex and age-related effects were negligible. Functionalenrichment analyses based on separate post-hoc 2-group comparisons revealed several functional themes within thevocal fold fibroblast related to transcription factors for signaling pathways regulating pluripotency of stem cells andextracellular matrix components such as cell signaling, migration, proliferation, and differentiation potential.
Conclusions:Human fibroblasts display a phenomenon of global topographic differentiation, which is maintained inisolation via in vitro assays. Epigenetic mechanical influences on vocal fold tissue may play a role in uniquely modellingand maintaining the local environmental cellular niche during homeostasis with vocal fold fibroblasts distinctlyspecialized related to their anatomic positional and developmental origins established during embryogenesis.

overall_design: Comppared mRNA profiles of a total of 34 samples from 7 different locations controlling for age and sex effect.

first: Alexander

middle: G

last: Foote

first: Susan

middle: L

last: Thibeault

first: Christina

last: Kendziorski


title: ChIP-Seq Worm_Lonp1_IP_vs_IgG

city: Worcester

first: pengpeng

last: liu

state: Massachusetts

address: 436 Plantation St

department: MCCB

institute: umassmed

summary: We performed the CHIP-SEQ assay for LONP1 in C.elegans. Our findings suggest an evolutionary conserved mechanism where mtDNA-bound LONP1 serves as an internal sensor of organelle function that promotes mtDNA replication in dysfunctional compartments. We propose that if LONP1 activity declines, ATFS-1 avoids degradation and binds mtDNA to promote replication in an effort to recover the dysfunctional compartment, which inadvertently promotes ∆mtDNA replication in heteroplasmic cells.

overall_design: Synchronized worms were cultured in liquid and harvested at early L4 stage by sucrose flotation.  The worms were lysed via Teflon homogenizer in cold PBS with protease inhibitors (Roche). Cross-linking of DNA and protein was performed by treating the worms with 1.85% formaldehyde for 15 min. Glycine was added to a final concentration of 125mM for 5 min at room temperature to quench the formaldehyde. The pellets were resuspended twice in cold PBS with protease inhibitor. Samples were sonicated in Bioruptor (Diagenode) for 15 min at 4°C on high intensity (30s on and 30s off). Samples were transferred to microfuge tubes and spun at 15,000*g for 15 min at 4°C. The supernatant was precleaned with pre-blocked ChIP-grade Pierce™ magnetic protein A/G (Thermo Scientific) and then incubated with Monoclonal ANTI-FLAG® M2 antibody (Sigma, F1804) or Mouse mAb IgG1 Isotype Control (Cell Signaling Technology, G3A1) rotating overnight at 4°C. Then, the antibody-chromatin complex was precipitated with magnetic beads. After washing, the crosslinks were reversed by incubation at 65 °C overnight and further treated with RNaseA 37 °C for 1 hour and then proteinase K 55 °C for 2 hours, respectively. Finally, immunoprecipitated and input DNA were purified with ChIP DNA Clean & Concentrator (Zymo Research, D5205) and used as templates for qPCR or next generation sequencing.

first: Qiyuan

last: Yang

first: Pengpeng

last: Liu