title: Identification and Temporal Expression Analysis of Conserved and Novel MicroRNAs in the Leaves of Winter Wheat Grown in the Field

city: xinxiang

first: kangning

last: wei

state: henan

address: jianshe road

institute: Henan Normal University

summary: MicroRNAs (miRNAs) are small non-coding RNAs that regulate target mRNAs by inducing degradation or preventing translation of their target mRNAs. Winter wheat, Triticum aestivum., is an important crop plant, yet there are only a few studies on the association of miRNAs and growth and development of winter wheat grown in the field. Here we carried out experimental analysis of miRNAs in wheat leaves by analyzing small RNA profiles at different growth stages.

overall_design: To identify miRNAs involved in winter wheat growth and development, we performed high-throughput sequencing of sRNA libraries from leaves at  4 different growth and development stages: three leaf stage, winter dormancy stage, spring greenup stage and jointing stage.Winter wheat cultivar Shimai 22 was grown in the field under natural weather condition;BGISEQ500 RS (BGI, China)platform  was used.

first: Yong

last: Li


title: Chromatin Decondensation Data of SREBP2(N) Overexpression in Human Umbilical Vein Endothelial Cells

status: Public on Oct 01 2019

city: La Jolla

first: John

last: Shyy

state: California

address: 9500 Gilman Dr., BRF2 Rm 1217 Bay LL

department: Medicine

country: USA

institute: University of California, San Diego

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Sterol regulatory element-binding protein 2 (SREBP2) is a transcription factor that has been recently discovered to mediate vascular endothelial cell (EC) dysfunction. We therefore investigated the role of SREBP2 in the epigenetic function of EC biology through comparing ATAC-seq of human umbilical vein endothelial cells (HUVECs) that were infected with adenovirus overexpressing SREBP2 (Ad-SREBP2) or with empty vector (Ad-null) control.  Gene ontology analysis revealed that SREBP2 not only decondenses chromatin for cholesterol biosynthesis, but also mediates the TGF pathway.  Among the responsive promoter, SREBP2 exhibited the induction of genes related to mesenchymal transition.

overall_design: ATAC-seq data of HUVECs overexpressing SREBP2 using adenovirus followed by deep sequencing, in biological duplicate, using Illumina HiSeq 2000.

first: Marcy

last: Martin

middle: Y


title: Highly efficacious antiviral protection of plants by siRNAs identified in vitro

city: Halle

first: Claus

last: Weinholdt

address: Von-Seckendorff-Platz 1

department: Institute of Computer Science

country: Germany

institute: Martin Luther University Halle-Wittenberg

type: Non-coding RNA profiling by high throughput sequencing

summary:
In response to a viral infection, the plant’s RNA silencing machinery processes viral RNAs into a huge number of small interfering RNAs (siRNAs). However, very few of these siRNAs actually interfere with viral replication. A reliable approach to define the characteristics underlying the activity of these immunologically effective siRNAs (esiRNAs) has not been available so far.
We developed a novel screening approach that enables a rapid functional identification of antiviral esiRNAs. The approach is essentially based on the use of a cytoplasmic extract from Nicotiana tabacum BY-2 protoplasts (BY-2 lysate, BYL), that shows Dicer-like (DCL) activity and facilitates the assembly of active RNA-induced silencing complexes (RISC) with an in vitro-translated Argonaute (AGO) protein of choice.
We exposed double-stranded (ds) RNA of Tomato bushy stunt virus (TBSV) to the BYL to generate viral siRNAs (DCL assay). Total RNA was isolated from the reactions and DCL-generated TBSV siRNAs were identified by NGS. In another approach, AGO1/RISC- or AGO2/RISC-associated siRNAs were isolated using FLAG-AGO immunoprecipitation (AGO-IP) and analyzed by NGS. Subsequently, the antiviral activity of siRNAs with high affinity to AGO proteins was characterized in vitro and in vivo.

overall_design: siRNA sequence data was obtained from three different DCL assays, two AGO1-IPs and three AGO2-IPs

first: Selma

last: Gago-Zachert

first: Jana

last: Schuck

first: Marie

last: Knoblich

first: Vitantonio

last: Pantaleo

first: Ivo

last: Grosse

first: Torsten

last: Gursinsky

first: Sven-Erik

last: Behrens


title: Open Array Mouse Inflammation Real-time quantitative PCR analysis of mouse colonic mucosa

city: Jouy en Josas, France

first: Unai

middle: Escribano

last: Vazquez

state: --- Sélectionner ---

address: Domaine de Vilvert Bat 440

department: MICALIS

country: France

institute: INRA

summary: Intrarectally DNBS-treated groups, to provoke colitis, were treated orally with the commensal CEC (CEC) or probiotic Nissle 1917 (Nissle) E. coli strains. Healthy control group was treated intrarectally and orally with PBS (PP). Sick control group was treated intrarectally with DNBS and orally with PBS (DP). Mice were sacrificed 24 days post first DNBS injection and the colonic gene expression profiles analyzed by high-throughput qPCR using TaqMan OpenArrays Mouse Inflammation Panel.

overall_design: qPCR gene expression profiling.  Colonic mucosa from healthy control groups mice were used as control. Equal amount total RNA from each mouse was pooled prior to gene expression analysis.

last: Escribano-Vazquez


title: Open Array Mouse Inflammation Real-time quantitative PCR analysis of mouse ileal mucosa

summary: Intrarectally DNBS-treated groups, to provoke colitis, were treated orally with the commensal CEC (CEC) or probiotic Nissle 1917 (Nissle) E. coli strains. Healthy control group was treated intrarectally and orally with PBS (PP). Sick control group was treated intrarectally with DNBS and orally with PBS (DP). Mice were sacrificed 24 days post first DNBS injection and the ileal gene expression profiles analyzed by high-throughput qPCR using TaqMan OpenArrays Mouse Inflammation Panel.

overall_design: qPCR gene expression profiling.  Ileal mucosa from healthy control groups mice were used as control. Equal amount total RNA from each mouse was pooled prior to gene expression analysis.


title: Open Array Custom Real-time quantitative PCR analysis of mouse colonic mucosa

summary: Germ-free wild-type mice (GFWT) were inoculated with the commensal CEC (CECWT) or probiotic Nissle 1917 (NissleWT) E. coli strain. Mono-colonized mice, CECWT and NissleWT, were sacrificed 21 days post-inoculation and the colonic gene expression profiles analyzed by high-throughput qPCR using TaqMan OpenArrays.

overall_design: qPCR gene expression profiling.  Colonic mucosa from germfree mice were used as control. Equal amount total RNA from each mouse was pooled prior to gene expression analysis.


title: Genome-wide RNA-Seq of rRNA depleted total RNA from Arabidopsis thaliana WT (Col-0) and pumpkin mutant

city: Strasbourg

first: Kamel

last: Hammani

address: 12 Rue du général Zimmer

institute: IBMP-CNRS

type: Expression profiling by high throughput sequencing

summary: Purpose: Analyses of transcriptomes of WT and pumpkin mutants, in order to compare gene expression of typically NEP or PEP-transcribed plastid genes.

overall_design: Examination of gene expression in WT (Col-0) versus pumpkin mutant

first: Nikolay

last: Manavski

first: Jörg

last: Meurer

first: Lisa-Marie

last: Schmid

first: Andreas

last: Brachmann

first: Jose

middle: M

last: Muiño


title: Identification of PUMPKIN RNA targets using RIPSeq

summary: Stroma extracts were isolated from 2-week-old WT plants and incubated with either PUMPKIN-specific antibodies or with the pre-immune serum. IgGs were captured with SiMAG-Protein G beads (Chemicell) and recovered RNA was used for generation of libraries with the ScriptSeq v2 RNA-seq Library Preparation Kit (Epicentre). Primary reads were aligned to the Arabidopsis chloroplast genome (accession number NC_000932.1) using CLC Genomics Workbench, the mean RPKM values of the replicates as well as the ratio of PUMPKIN vs Pre-immuneserum were calculated. Five prominent RNA targets (trnG-UCC, trnV-UAC, petB, petD and ndhA) were identified and validated via Slot Blot analyses.

overall_design: RNA Immunoprecipitation with PUMPKIN-specific antibody and the respective pre-immuneserum as control using WT stroma extract. As PUMPKIN represents a soluble chloroplast-localized protein, stroma extract was used for RNA-Immunoprecipitation to identify the plastid RNA targets of the PUMPKIN protein.


title: RNA-Seq and RIP-seq studies for A. thaliana WT and pumpkin mutant

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

overall_design: Refer to individual Series


title: RNA-seq data from wildtype, STAT5A-knockout and STAT5B-knockout BCR/ABLp185+ transformed mouse bone marrow cell lines

city: Vienna

first: Veronika

last: Sexl

address: Veterinaerplatz 1

department: Pharmacology / Toxikology

country: Austria

institute: University of Veterinary Medicine Vienna

summary: RNA-Seq of immortalized Stat5a-/-, Stat5b-/-, and wildtype BCR/ABLp185+ cell lines was used to identify STAT5A and STAT5B specific target genes.

overall_design: mRNA from immortalized Stat5a-/-, Stat5b-/-, and wildtype BCR/ABLp185+ cell lines (3 technical replicates) were prepared using the Lexogen SENSE mRNA-Seq library preparation kit. Single-end, 50bp sequencing was performed on an Illumina HiSeq-2500 sequencer. Reads were mapped to the GENECODE M13 genome.

first: Eva

last: Grundschober

first: Sebastian

last: Kollmann

first: Barbara

last: Maurer

first: Reinhard

last: Grausenburger

first: Andrea

last: Hoelbl-Kovacic


title: FLASH: ultra-fast protocols to identify RNA-protein interactions in cells

city: Freiburg

first: Daniel

last: Maticzka

state: BW

address: Georges-Köhler-Allee 106

department: Department of Computer Science

institute: University of Freiburg

summary: Determination of the in vivo binding sites of RNA-binding proteins (RBPs) is paramount to understanding their function and how they affect different aspects of gene regulation. With hundreds of RNA-binding proteins identified in human cells, a flexible, high-resolution, high-throughput, highly multiplexible and radioactivity-free method to determine their binding site has not been described to date. Here we report FLASH (Fast Ligation of RNA after some sort of Affinity Purification for High-throughput Sequencing), which uses a special adapter design and an optimized protocol to determine protein-RNA interactions in living cells. We demonstrate the flexibility, speed and versatility of FLASH by using it to determine binding sites of both tagged and endogenously expressed proteins under diverse conditions. The entire FLASH protocol, starting from cells-on-plates to a sequencing library, takes 1.5 days.

overall_design: FLASH (Fast cloning of RNA After some Sort of affinity purification for High-throughput sequencing). This experiment investigates binding of two isoforms of the RNA-binding protein QKI (QKI-A and QKI-B) and a non-RNA-binding control (GFP), expressed using transiently transfected plasmids and performed with two biological replicates per condition.

first: Ibrahim

last: Ilik


title: Transcriptomic Profiles of Immortalized Human Hepatocytes Overexpressing  Intracellular Domain of NOTCH1

city: Bangkok

first: Tanapat

last: Palaga

address: Payathai Road, Pathumwan

department: Microbiology

country: Thailand

institute: Chulalongkorn University

summary: To investigate the effect of hyperactivation of Notch signaling in hepatocytes, an immortalized human hepatocyte cell line THLE-2 was stably transduced with control vector or plasmid harborning intracellular domain of NOTCH1 (NICD1) and the transcriptomic profiles were analyzed by RNA-seq.

overall_design: Immortalized human hepatocyte cell line THLE-2 cells were transduced with retrovirus vector containing empty vector or NICD1 plasmid. The mRNA profiles from NICD1-overexpressed THLE2 cell line were generated by deep sequencing using Illumina NextSeq 500. The results were compared between empty vector and NICD1-overexpressed cells.

first: Pornrat

last: Kongkavitoon

first: Patarin

last: Tangtanatakul

first: Pinidphon

last: Prombutara


title: Long non-coding RNA profile of the liver across three developmental stages in chickens

city: Chengdu

first: Kequan

last: Li

state: Sichuan

address: 172 shun sheng road, zhengxing street, tianfu new district

country: China

institute: Sichuan Eagene Technology services co. LTD

summary: We have defined a timeline of functional transcriptome transition from prenatal to adult in Lohmann laying hens. A total of ~161.17 Gb of raw data were obtained, with 4,127 putative and 539 differentially expressed lncRNAs.

overall_design: Here, we used RNA-Sequencing to analyze the transcriptome of chicken liver from prenatal (at embryonic day of 13) to postnatal stages (at 5 weeks and 42 weeks of age)

first: Yingping

last: Xiao

first: E

last: Xu


title: DNA-dependent protein kinase drives prostate cancer progression through transcriptional regulation of the Wnt signaling pathway

city: San Francisco

first: vishal

last: kothari

state: California(CA)

address: HD300 1450 Third street, PO Box #3110

department: Radiation Oncology

institute: university of California, San francisco

summary:
DNAPK was identified as the most significantly expressed kinase associated with metastatic progression in high-risk prostate cancer. GSEA analysis on DNAPK knockdwon samples and on patient data nominated Wnt signaling as the top pathway associated with DNAPK
Our data indicates that DNAPK regulates Wnt signaling pathway.

overall_design: Cell lines were transcfected with either the non-targeting siRNAs or with the siRNAs targeting DNAPK. Gene Set Enrichment Analysis was performed to identify the pathways associated with DNAPK

first: Shuang

middle: G

last: Zhao

first: Felix

last: Feng

first: Vishal

last: Kothari


title: Open Array Custom Real-time quantitative PCR analysis of mouse ileal mucosa

first: Unai

last: Vazquez

summary: Germ-free wild-type mice (GFWT) were inoculated with the commensal CEC (CECWT) or probiotic Nissle 1917 (NissleWT) E. coli strain. Mono-colonized mice, CECWT and NissleWT, were sacrificed 21 days post-inoculation and the ileal and colonic gene expression profiles analyzed by high-throughput qPCR using TaqMan OpenArrays.

overall_design: qPCR gene expression profiling.  Ileal mucosafrom germfree mice were used as control. Equal amount total RNA from each mouse was pooled prior to gene expression analysis.

last: Escribano-Vazquez


title: Anti-PD-L1 antibody direct activation of macrophages contributes to an abscopal response in murine brain tumors

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

summary: Immunotherapy approaches for glioblastoma multiforme have been thus far largely unsuccessful, suggesting unappreciated complexity in glioma biology and immunology. The intra-tumoral heterogeneity of these intrinsic brain tumors results in therapies killing only a subset of the tumor cells; therefore, therapeutic success will require achieving and optimizing an “abscopal effect” where tumor cells not specifically targeted are recognized and attacked as bystanders by the immune system. We have modified an immune-competent, genetically-driven mouse glioma model where a portion of the tumor burden is treated and another untreated portion is used as a readout of therapeutic efficacy. We find that following radiation of one lesion, anti-PD-L1 therapy enhances the abscopal response (macrophages and T-cells) to the un-irradiated lesion.  In gliomas with few baseline T-cells, the anti-PD-L1-enhanced abscopal response occurs as an anti-PD-L1-driven, macrophage-mediated, and ERK-dependent increase in phagocytosis of tumor cells. Our results indicate that combined radiation and anti-PD-L1 therapy for gliomas results in peripherally-derived macrophages being responders in tumors with few baseline T-cells in the microenvironment.

overall_design:
We established Proneural (PN) gene set-enriched gliomas with luciferase expression by injecting 2x10e5 RCAS vector producing DF-1 cells bearing RCAS-PDGF and RCAS-Cre vectors into the cortex of adult Ntva Ink4a/Arf-/- Ptenflox/flox mice with an additional Lox-Stop-Lox luciferase cassette. Here, the second vector RCAS-Cre activates the luciferase gene and is selected for with simultaneous deletion of Pten (allowing for positive selection of luciferase expressing tumor cells). We also generated a CL/MES-gene set enriched glioma by injecting 2x10e5 RCAS vector producing DF-1 cells bearing RCAS-PDGF and RCAS-Cre vectors into the cortex of adult Ntva Ink4a/Arf-/- Ptenflox/flox mice with  Lox-Stop-Lox EGFRvIII.
EGFR Normal = Proneural (PN) gene set-enriched gliomas
EGFR Tumor = CL/MES-gene set enriched glioma

first: Chibawanye

middle: I

last: Ene

first: Shannon

middle: A

last: Kreuser

first: Huajia

last: Zhang

first: Kara

middle: W

last: Moyes

first: Frank

last: Szulzewsky

first: Hans-Georg

last: Wirsching

first: Anoop

last: Patel

first: Paul

last: Kong

first: Timothy

middle: R

last: Woodiwiss

first: McGarry

last: Houghton

first: Terreia

middle: S

last: Jones

first: Robert

middle: H

last: Pierce

first: Courtney

last: Crane

first: Eric

middle: C

last: Holland


title: Whole Genome Bisulfite Sequencing of Botrytis cinerea

city: Beijing

first: Chang

last: He

address: No.20 Nanxincun, Xiangshan

department: Key Laboratory of Plant Resources

institute: Institute of Botany, the Chinese Academy of Sciences

type: Methylation profiling by high throughput sequencing

summary: Analysis of the genome-wide DNA methylation pattern of Botrytis cinerea. Results provide new and important information that DNA methylation is critical for pathogenicity and development of Botrytis cinerea by regulating gene expression.

overall_design: Bisulphite converted DNA from the 4 samples were sequenced by using the HighSeq4000.


title: Mutant KRAS/BRAF Reprograms the Enhancer Landscape via GATA1 to Drive Chemoresistance

city: Rochester

first: Rentian

last: Wu

address: 200 1st Street SW

institute: Mayo Clinic

summary: Despite advances in the detection and management of colorectal cancers, resistance to anti-cancer therapies remains a significant challenge. Activating mutations in KRAS and BRAF are frequently observed in colorectal cancers and have been associated with aggressive tumors and poor survival after chemotherapy. In the present study, we demonstrate that mutations in KRAS/BRAF alter the enhancer landscape of tumor cells, which leads to the resistance of the cornerstone colorectal cancer chemotherapeutic agent 5-fluorouracil (5-FU) through activation of transcription factor GATA1. Targeted inhibition of GATA1 reverses epigenetic changes in KRAS mutant cells and restores sensitivity to 5-FU. These results indicate a novel therapeutic opportunity for tailoring individualized therapy in human colorectal cancer.

overall_design: RNA-seq and H3K4me1- H3K27ac-ChIP-seq were performed on GATA1 KO HCT116 cells. RNA-seq was performed on K7174-treated HCT116 cells and Colo320 cells expressing vector, wildtype and G12V KRAS.

middle: B

last: Diasio


title: DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development

city: Tel Aviv

first: Assaf

last: Zemach

address: Haim Levanon

department: School of Plant Sciences and Food Security

country: Israel

institute: Tel Aviv University

summary: DNA methylation of active genes, also known as gene body methylation, is found in many animal and plant genomes. Despite this, the transcriptional and developmental role of such methylation remains poorly understood. Here, we explore the dynamic range of gene body methylation and its association with transcription and splicing in honey bee, an organism that targets methylation specifically to gene bodies. Our data show that gene body methylation globally fluctuates during honey bee development, with relatively high CG methylation in the embryo and adult stages and lower methylation in the larvae. We did not find a significant correlation between developmentally associated genic methylation dynamics and gene expression profiles. Furthermore, most developmentally regulated gene expression alterations occur in unmethylated genes. Tissue-specific methylation patterns, either at the level of complete genes or exons, are rare, implying robust maintenance of gene body methylation throughout the honeybee life cycle. Additionally, we show that CG methylation maintenance fluctuates in somatic cells, while reaching maximum fidelity in sperm cells. Finally, we report a Dnmt3-associated non-CG methylation signal in the gene bodies of adult bee heads that resembles the methylation patterns of mammalian brain tissue. Based on these results, we suggest that honey bee DNA methylation is distinctly regulated in the soma and germline. In the germline, methylation is efficiently maintained to preserve methylation patterns across generations. In contrast, methylation can fluctuate in somatic cells with limited division potential, as long as overall methylation of exons and genes remains at an adequate functional level. Additionally, we propose that heightened non-CG methylation may be a conserved characteristic of animal nervous systems.

overall_design:
To investigate the dynamics of DNA methylation during honey bee development, we profiled the genome wide methylomes of eight developmental stages: sperm, worker embryo, worker larva, drone larva, worker pupa, worker head, drone head, and queen head. Quantification of the averaged CG methylation level of two biological replicates, either separately or combined, in the whole nuclear genome, as well as within specific genetic elements, including exons, introns, and repeats, revealed two main characteristics of DNA methylation in honey bee.
BS-seq and RNA-seq samples.

first: James

middle: P

last: Lloyd

first: Keith

middle: D

last: Harris

first: Daniel

last: Zilberman


title: NHR-14 loss of function couples intestinal iron uptake with innate immunity in C. elegans through PQM-1 signaling

city: Salt lake city

first: Elizabeth

last: Leibold

state: Utah

address: 15 North 2030 East

department: Molecular Medicine

institute: University of Utah

summary: We report that NHR-14 coordinates iron uptake and an innate immune response in C. elegans.

overall_design: Transcriptome comparison between N2 wild-type and nhr-14 null worms

first: Cole

last: Anderson

first: Malini

last: Rajan


title: RNA sequencing of WT and Hmgb2-/- mice liver treated with CCL4

city: Indianapolis

first: Zhihong

last: Yang

institute: Indiana University

summary: loss of Hmgb2 in vivo in mouse liver largely prevented CCl4-induced liver fibrosis. The goal of the RNA-seq is to identify the Hmgb2 regulated genes in CCL4 induced liver fibrosis.

overall_design: Liver 5' capped RNA samples from WT-Oil, WT-CCL4, Hmgb2-/-Oil and Hmgb2-/-CCL4 mice were sequenced with Illumina HiSeq 2500.

first: Li

last: Wang


title: Phf21b is a novel histone reader essential for epigenetic silencing of cell cycle genes during neurogenesis

city: Mainz

first: Hyobin

last: Jeong

state: Germany

address: Richard shirrmann Str 12.

institute: IMB

summary: The role of chromatin-mediated regulation in cell-fate specification during mammalian development is been increasingly appreciated. However, very little is known about epigenetic regulatory networks during embryonic neurogenesis. In search for novel epigenetic regulators of neuronal development, we find that Phf21b is specifically expressed in the cortex during embryonic neurogenesis. Interestingly, knockdown of Phf21b during cortical development leads to a defective neurogenesis. Immunoprecipitation assay combined with mass-spectrometry revealed that Phf21b associates with the repressive chromatin machinery including histone deacetylases as well as Lsd1, suggesting that it likely functions in gene repression. Biochemical analysis revealed that Phf21b has higher affinity for H3K4me1 compared to other modifications states of histone H3 at Lysine 4 (K4). Our data suggests that Phf21b targets the regulatory regions of the cell cycle genes where they recruit Lsd1 and Hdac2 to repress them via loss of H3K4me1 and H3K27ac. Overall, we identify Phf21b as a novel essential regulator of neurogenesis, which mediates epigenetic silencing of cell cycle genes during cortical development.

overall_design: (1) mRNA expression profiles of mESC, N2a, and IUE mouse embryonic cortex upon depletion of Phf21b were examined by Illumina Hi-seq 2500 and Next seq 500. (2) ChIP-seq of Phf21b was examined using mESC and N2a day2 differentiated system (3) ATAC-seq of N2a Undifferentiated and Day2 differentiated system upon depletion of Phf21b was profiled

first: Amitava

last: Basu


title: IFNγ/IL10 ratio stratifies corticosteroids therapy for septic shock

city: Jena

first: Amol

last: Kolte

address: Am Klinikum 1

institute: Center for Sepsis Control and Care, University Clinic, Jena

summary: To stratify hydrocortisone application in septic shock, we investigated an immune sub-study of the CORTICUS trial (Sprung et.al 2008, NEJM) employing machine learning to a panel of 120 parameters of 84 patients (n=24 non-survived, n=60 survived, 28 days) with special emphasis on potentially disadvantageous corticosteroids effects in the context of sepsis including clinical parameters, organ failure scores, lymphocyte counts and plasma protein concentrations of cytokines. We identified the ratio of IFNγ/IL10 in serum before randomization to serve as a valid biomarker for treatment stratification. This was validated with cytokine serum levels of patients (n=49) from the SISPCT study (Bloos et.al 2016, JAMA) and the early arm (n=20) of a hydrocortisone cross-over study (Keh et.al. 2003, Am J Respir Crit Care Med). Integrating these three studies, we yielded an odds ratio of 2.1 and a 95% confidence interval of 0.99-4.52 (P=0.03).In vitro assays revealed IFNγ/Il10 to reflect the burden or severity of systemic infection. Severity was evidencedbyserum levels of these cy-tokines in the patients with septic shock we observed, and also in patients with less severe sepsis. Elucidating the molecular regulation of leukocytes during treatment and placebo by a transcriptomics analysis pointed to induced recovery of immune cell function due to hydro-cortisone treatment, particularly in the predicted hydrocortisone responders. IFNγ/IL10 is a molecular marker with high potential for support of hydrocortisone therapy decision. IFNγ/IL10 is reasonable for this as it reflects the burden and recovery of the immune system which seems to be indicative for corticosteroids treatment of septic shock.

overall_design: Paired samples of 47 septic shock patients from the CORTICUS-trial (ClinicalTrials.gov number, NCT00147004) treated with either Placebo or Hydrocortisone (HC) were included. Whole blood from patients was collected in the morning (pre) and 24 hours (post) later. Total cellular RNA from circulating leukocytes was isolated using PaxGene Blood RNA Kit (PreAnalytix) for transcriptome profiling. The first analysis compared the pre-treatment samples of 28 patients with IFNg/IL10 high versus 19 patients with IFNg/IL10 low. Genes with standard deviation or average expression above the 25% quantile were tested for significant up- or downregulation using two sided t-tests. In the second analysis, the effect of HC on 7 IFNg/IL10 low-ratio patients (benefitting from HC therapy) was observed by comparing gene expression 24h post start of the treatment versus pre-treatment (0h). Differentially expressed genes were obtained using two sided t-tests followed by multiple testing correction (Benjamini-Hochberg, FDR < 0.1). A similar comparison was made with 12 low-ratio patients treated with placebo. Genes distinctly up or down regu-lated in patients of the HC arm compared to the placebo arm were selected for gene set enrichment analysis.

first: Michael

last: Bauer

first: Rainer

last: König


title: Gene expression profiling of Antarctic krill in LD condition

city: Padova

first: Cristiano

last: De Pitta

address: Via U. Bassi, 58/B

department: Biology

country: Italy

institute: University of Padova

summary: This work represents the first characterization of the krill circadian transcriptome under laboratory conditions and provides a first insight into the genetic regulation of physiological changes, which occur around the clock in light-dark (LD) and in constant darkness (DD) condition.

overall_design: Gene expression profiling was performed with the ‘‘Krill 2.0’’ custom platform (Agilent) in specimens collected at regular intervals throughout the 24 hours cycle (external times: 06:00, 09:00, 12:00, 15:00, 18:00, 21:00, 24:00, 03:00 and 06:00) in light-dark (LD) condition.

first: Alberto

last: Biscontin

first: Paolo

last: Martini

first: Bettina

last: Meyer

first: Rodolfo

last: Costa

first: Mathias

last: Teschke


title: Gene expression profiling of Antarctic krill in DD condition

overall_design: Gene expression profiling was performed with the ‘‘Krill 2.0’’ custom platform (Agilent) in specimens collected at regular intervals throughout the 24 hours cycle (external times: 06:00, 09:00, 12:00, 15:00, 18:00, 21:00, 24:00, 03:00 and 06:00) in constant darkness (DD) condition.


title: Photobiomodulation by blue light induces a dose dependent biphasic proliferation curve in human keratinocytes [exp2]

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

institute: University Heidelberg

summary: Photobiomodulation (PBM) with blue light induces a biphasic dose response curve in proliferation of immortalized human keratinocytes (HaCaT), with a maximum proliferative effect reached with 7.5min (10.35J/cm2). The aim of this study was to test the photobiomodulatory effect of 10.35J/cm2 blue light irradiation on cell proliferation, ROS production and gene expression at different time points after irradiation of HaCaT cells in vitro and to compare the results with the anti-proliferative phase of PBM using blue light with 41.4J/cm2. For 10.35J/cm2 cell proliferation was increased for all measured harvesting time points up to at least 24h after irradiation. ROS concentration was increased 30min after irradiation. However, already 1h after irradiation, cells were able to decrease ROS and stabilize the concentration to the basal level. The sudden increase in ROS was even higher when compared to 41.4J/cm2. However, gene expression analysis did not indicate any sign of apoptosis and even indicated an activation of cell survival mechanisms. Furthermore, comparable to 41.4J/cm2, aryl hydrocarbon receptor (AHR) “battery genes” showed a deregulation after blue light irradiation strengthening the hypothesis of AHR as possible target for blue light irradiation.

overall_design: 6 samples: 3x 96 well plates per experiment, each plate contains irradiated cells and not light control cells to exclude a plate effect (systematic error),  therefore there are 3 replicates for irradiated cells and 3 replicates of no light conotrol cells

first: Anja

last: Becker

last: De La Torre

first: Carsten

last: Sticht

first: Norbert

last: Gretz


title: Photobiomodulation by blue light induces a dose dependent biphasic proliferation curve in human keratinocytes [exp3]

overall_design: 6 samples: 3x 96 well plates per experiment, each plate contains irradiated cells and not light control cells to exclude a plate effect (systematic error),  therefore there are 3 replicates for irradiated cells and 3 replicates of no light contol cells


title: Photobiomodulation by blue light induces a dose dependent biphasic proliferation curve in human keratinocytes [exp1]

overall_design: 6 samples: 3x 96 well plates per experiment, each plate contains irradiated cells and not light control cells to exclude a plate effect (systematic error),  therefore there are 3 replicates for irradiated cells and 3 replicates of no light control cells


title: Analysis of the circadian transcriptome of the Antarctic krill Euphausia superba

summary:
Antarctic krill (Euphausia superba) is a high latitude pelagic organism which plays a central role in the Southern Ocean ecosystem. E. superba shows daily and seasonal rhythms in physiology and behaviour, which are synchronized with the environmental cycles of its habitat. Recently, the main components of the krill circadian machinery have been identified and characterized. However, the exact mechanisms through which the endogenous timing system operates the control and regulation of the overt rhythms remains only partially understood. Here we investigate the involvement of the circadian clock in the temporal orchestration of gene expression by using a newly developed version of a krill microarray platform. The analysis of transcriptome data from krill exposed to both light-dark cycles (LD 18:6) and constant darkness (DD), has led to the identification of 1,564 putative clock-controlled genes. A remarkably large proportion of such genes, including several clock components (clock, period, cry2, vrille, and slimb), show oscillatory expression patterns in DD, with a periodicity shorter than 24 hours. Energy-storage pathways appear to be regulated by the endogenous clock in accordance with their ecological relevance in daily energy managing and overwintering. Our results provide the first representation of the krill circadian transcriptome under laboratory, free-running conditions.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Photobiomodulation by blue light induces a dose dependent biphasic proliferation curve in human keratinocytes

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


title: The metabolism of colorectal cancer adapting to nutritional stress

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

summary: Tumor cells respond to their microenvironment, which includes hypoxia and malnutrition, and adapt their metabolism to survive and grow. Some oncogenes are associated with cancer metabolism via regulation of the related enzymes or transporters. However, the importance of metabolism and precise metabolic effects of oncogenes in colorectal cancer remain unclear. We found that colorectal cancer cells could survive under the condition of glucose depletion and that their resistance to such conditions was dependent on not KRAS mutation alone but whole genomic alterations. Metabolome analysis of those cells demonstrated the maintenance of tricarboxylic acid (TCA) cycle activity and anabolic processes under such conditions. Furthermore, we revealed a pivotal role of GLUD1, a key enzyme related to glutaminolysis, and SLC25A13 coding the aspartate–glutamate carrier (AGC) that composed malate–aspartate shuttle in cells. Colorectal cancer cells that are resistant to glucose depletion positively regulate GLUD1 to replenish TCA cycle metabolites and produce energy. Furthermore, they negatively regulate SLC25A13 to decrease reactive oxygen species (ROS) production. High expression of Glud 1 or low expression of Slc25a13 was associated with tumor aggressiveness and worse prognosis by immunohistochemistry of colorectal cancer specimens. Furthermore, high expression of Glud1 combined with low expression of Slc25a13 had a higher association with tumor aggression and poor prognosis than did individual expression of each. In conclusion, Glud1 and Slc25a13 may serve as new targets in treating refractory colorectal cancer. Understanding the inherent metabolism of each cancer type can result in development of cancer therapy.

overall_design: Colorectal cancer cell line DLD1 and HT29 under glucose- and glutamine-containing conditions and glucose-deprived conditions

first: Masaaki

last: Miyo

first: Masamitsu

last: Konno

first: Naohiro

last: Nishida

first: Jun

last: Koseki

first: Koichi

last: Kawamoto

first: Hugh

last: Colvin

first: Junichi

last: Nishimura

first: Taishi

last: Hata

first: Noriko

last: Gotoh

first: Fumio

last: Matsuda

first: Taroh

last: Satoh

first: Tsunekazu

last: Mizushima

first: Hiroshi

last: Shimuzu

first: Yuichiro

last: Doki

first: Masaki

last: Mori

first: Hideshi

last: Ishii


title: Large-scale gene expression profiling  of hepatocellular adenomas

city: Paris

first: Sandrine

last: Imbeaud

address: 15 rue de l'Ecole de Médecine

department: INSERM UMRS1138-EQUIPE 28, Sorbonne Université-Inserm-Université de Paris

institute: Centre de Recherche des Cordeliers

summary: Hepatocellular adenomas (HCA) are rare benign tumors mainly developed in women after 2 years of oral contraceptive use (Rooks et al., 1979). HCA are also related to other risk factors (obesity, vascular diseases, androgen and alcohol intake) or to different genetic diseases (Mac Cune Albright syndrome, glycogen storage diseases type 1a and MODY3 diabetes caused by HNF1A germline mutation) (Calderaro et al., 2013; Nault et al., 2013a). Bleeding and malignant transformation to hepatocellular carcinoma (HCC) can occur as severe complications observed respectively in 30-50% and 5% of the cases. In the past 10 years, we identified 4 major molecular subgroups of HCA defined by (1) mutations inactivating HNF1A (H-HCA, 35% of the HCA) (Bacq et al., 2003; Bluteau et al., 2002; Jeannot et al., 2010), (2) activation of ß-catenin by mutations in exon 3 (bHCA, 15%) (Chen et al., 2002), (3) inflammatory phenotype with STAT3 activation (IHCA, 50%) (Bioulac-Sage et al., 2009; Zucman-Rossi et al., 2006), (4) a tumor subgroup of HCA with Sonic Hedgehog pathway activation due to recurrent focal deletions (shHCA) (Nault et al. ,in preparation) and (5) the remaining unclassified tumors (UHCA, 10%) (Bioulac-Sage et al., 2009). Among bHCA, half displayed both inflammatory and ß-catenin activated phenotypes (bIHCA). Inflammatory adenomas (IHCA) are caused by IL6ST somatic mutation activating gp130 in 60% of the cases (Rebouissou et al., 2009) whereas other IHCA are mutated for STAT3 itself (Pilati et al., 2011) or GNAS (Nault et al., 2012) but in the remaining 30% cases no mutation (NM) were identified yet. This molecular classification is currently accepted in clinical practice using either immunohistochemical markers (Bioulac-Sage et al., 2009; Bioulac-Sage et al., 2007) or in radiology at MRI (Laumonier et al., 2008) and it has dramatically improved the diagnosis and prognostic assessment of HCA. HCC derived from HCA malignant transformation (HCC on HCA, 5%)

overall_design: HCA liver tumors corresponding to 35 patients. In all cases, tumor samples were frozen (-80°C) after hepatic resection at diagnosis. Normal liver samples were used as reference samples. Comparative gene expression analysis was done using Affymetrix U133plus v2 array (GPL570)

first: Jessica

last: Zucman-Rossi

first: Julien

last: Calderaro

first: Stefano

last: Caruso

first: Gabrielle

last: Couchy

first: Eric

last: Letouzé

first: Jean-Charles

last: Nault

first: Camilla

last: Pilati

first: Sandra

last: Rebuissou


title: Transcriptome analysis of peripheral blood monocytes

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: RNA sequencing data of peripheral blood monocytes to assess their transcriptomic differences, in particular metabolics, compared to ascites fluid-derived tumor associated macrophages (datasets publicly available; E-MTAB-3167 and E-MTAB-4162)

overall_design: Isolation of CD14+ peripheral blood monocytes from 8 independent healthy donors

first: Sander

last: Tuit

first: Thomas

last: Ulas

middle: L

last: Schulze

first: Lisardo

last: Bosca

first: Subhra

middle: K

last: Biswas


title: Differentially expressed genes in Naa10p knockout mouse embryos

city: Taipei

first: Li-Jung

last: Juan

address: 128 Academia Road, Section 2, Nankang

department: Genomic Research Center

country: Taiwan

institute: Academia Sinica

summary: Mammalian Naa10p, encoded by NAA10, is the only known enzyme capable of catalyzing both N-α-acetylation of nascent proteins in cytosol and ε-acetylation of internal lysines of proteins. Both enzyme-dependent and -independent functions of Naa10p are associated with cancer and some genetic diseases with developmental defects. To examine the function of Naa10p in development, we generated Naa10-KO mice by deleting exons 2 to 6 of Naa10 gene, which encode all putative isoforms of Naa10p. RNA sequencing (RNA-seq) analysis of 2 WT and 2 Naa10p-KO embryos from the same litter was performed.

overall_design: mRNA profiles of 2 Naa10-KO and 2 littermate WT embryos were generated by deep sequencing, using Illumina HiSeq 2000.

first: Li

middle: J

first: Chen

last: Lee

first: Shih

last: Peng


title: Effects on gene expression of RNA polymerase I inhibitor CX-5461 in control and TP53-knockout cell lines of multiple myeloma

city: Houston

first: Wencai

last: Ma

address: 7455 Fannin st

institute: MD Anderson Cancer Center

summary:
Multiple myeloma cell lines MM1S and MOLP8 were modified by zinc finger nucleases targeting exon 7 of the TP53 DNA binding domain. Knockout (KO) clones were isolated by limiting dilution, identified by TP53 resequencing, and confirmed by Western blotting.
KO and unmodified (WT) clones were then either treated with vehicle or 200 nM CX-5461 for 48 hours for gene expression profiling (GEP).

overall_design: Genes were ranked according to their average change in expression by CX-5461 in multiple KO clones, and then examined by Gene Set Enrichment Analysis.

first: Hans

first: Hua

last: Wang

first: Isere

last: Kuiatse

first: Robert

middle: Z

last: Orlowski

first: Zhiqiang

first: R

middle: E

last: Davis


title: Transcriptomic analysis of Col and ein3eil1 under Cd stress.

city: Jinan

first: Xiangpei

last: Kong

address: 27 Shanda South Road

institute: Shandong University

summary: To reveal the molecular mechanism underlying EIN3-mediated Cd tolerance, we performed RNA sequencing (RNA-seq) analysis to identify Cd-regulated genes that are differentially expressed in ein3 eil1 double mutant.

overall_design: Examination of  primary root  of Col and ein3eil1 mutant with or without Cd stress

first: Zhaojun

last: Ding


title: microRNA and mRNA gene expression signature in JK and JinB8 cell lines [mRNA]

status: Public on Sep 30 2019

city: BETHESDA

first: abdel

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

summary: microRNA and mRNA gene expression signature in JK and JinB8 cell lines.

overall_design: 3 cell culture replicates of JK  and JINB8 cell lines. mRNA from exosomes.

first: Abdel

first: Sukhbir

last: Kaur


title: Global surveillance of somatic alterations in triple negative breast cancers by whole exon sequencing analyses

city: Tokushima

first: Yosuke

last: Matsushita

address: 3-18-15 Kuramoto

department: Institute for Genome Research

institute: Tokushima University

summary: Triple negative breast cancers (TNBC), defined by lacking the expression of oestrogen receptor-alpha (ERa), progesterone receptor, and HER2, is considered to be one of the most aggressive subtypes of all breast cancers. To elucidate the genomic and molecular aberrations in TNBC, we performed whole exon sequencing (WES) analysis on 36 TNBC, and identified 117 genes that significantly mutated (q < 0.05) in TNBC including MUC4, MUC6, TP53, and PIK3CA. Interestingly, genes associated with chromatin regulators including the subunits of SWI/SNF complex were frequently mutated in 44.7% of the cases. Furthermore, from the aspect of the possible association of epigenetic dysregulation and TNBC carcinogenesis, we focused on epigenome and genetic alterations of SALL3, an intrinsic inhibitor of DNMT3A, and identified the role of its dysfunction on cancer cell growth. Our study suggests that epigenetic aberrations caused by somatic alterations including DNA methylation might be a potential pathogenesis of TNBC in a certain number of cases.

overall_design: Human TNBC cell line, BT-20, was seeded at a density of 2.5x10^5 cells per 3.5 cm dish. Cells were transfected with 50nM siRNA (siEGFP or siSALL3) by Lipofectamine RNAiMAX reagent. Total RNA was extracted 48h and 96h after transfection. 100 ng of total RNA from each sample was amplified using T7 RNA polymerase with simultaneous Cy3-labeled CTP incorporation. Then, 2 μg of Cy3-labeled cRNA was fragmented, and hybridized onto the Agilent Whole Human Genome Microarray 8x60K slide. Then, a slide was scanned by the Agilent Microarray scanner system. The data were analyzed using GeneSpring. We identified up- and down-regulated genes common to siSALL3_48h and siSALL3_96h compared with siEGFP_48h. The fold change was >2.0.

first: Masato

last: Komatsu

first: Kazuma

last: Kiyotani

first: Tetsuro

last: Yoshimaru

first: Toyomasa

last: Katagiri


title: Pre-existent adult sox10+ cardiomyocytes contribute to myocardial regeneration in the zebrafish

city: Bern

first: Nadia

last: Mercader

address: Baltzerstrasse 2

country: Switzerland

institute: University of Bern

summary: During heart regeneration in the zebrafish, fibrotic tissue is replaced by newly formed cardiomyocytes derived from pre-existing ones. It is unclear whether the heart is comprised of several cardiomyocyte populations bearing different capacity to replace lost myocardium. Here, using sox10 genetic fate mapping, we identified a subset of pre-existent cardiomyocytes in the adult zebrafish heart with a distinct gene expression profile that expanded massively after cryoinjury. Genetic ablation of sox10+ cardiomyocytes severely impaired cardiac regeneration revealing that they play a crucial role for heart regeneration.

overall_design: Adult zebrafish heart tg(sox10:CreERT2;vmhcl:loxP-tagBFP-loxP-mCherry-NTR) were disassociated and 20 CMs were FAC-sorted in single tubes for DESeq2 Library preparation

first: Marcos

last: Sande-Melon

first: David

middle: M

last: Ferreira-Francisco

first: Marius-Alexandru

last: Botos


title: Sirena1: The most abundant lncRNA in mouse oocytes brings together post-transcriptional regulations and mitochondrial distribution (mouse dev_stages)

city: Prague

first: Filip

last: Horvat

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

summary: Long non-coding RNAs (lncRNAs) are a large group of rapidly evolving non-coding RNAs. Tens of thousands of lncRNAs were identified but function has been assigned to relatively few. LncRNAs expressed in mouse oocytes have been annotated but their contribution to oocyte development and early development remains unknown. Here, we report evolutionary history and functional analysis of Sirena1, maternal lncRNA that is the most expressed maternal lncRNA and 10th most abundant Pol II transcript in mouse oocytes.

overall_design:
Bulk RNA-seq of 13 mouse developmental stages samples:
- GV oocyte: 3x WT and 3x Sirena1 KO
- MII egg: 3x WT and 4x Sirena1 KO

first: Petr

last: Svoboda

first: Radek

last: Malik

first: Sravya

last: Ganesh


title: Polyamine synthesis effects capsule expression in Streptococcus pneumoniae TIGR4

city: Starkville

first: Bindu

last: Nanduri

state: MS

address: P.O. Box 6100, 240 Wise Center Drive

department: Basic Science

institute: Mississippi State University

summary:
Purpose: We recently reported that isogenic deletion of lysine decarboxylase (ΔcadA/SP_0916), an enzyme that catalyzes the biosynthesis of polyamine cadaverine in Streptococcus pneumoniae TIGR4 results in loss of capsular polysaccharide (CPS), which constitutes a novel mechanism of regulation of CPS. Here, we conducted RNA-Seq to elucidate molecular mechanisms of CPS regulation in polyamine synthesis impaired pneumococci.
Result: Significantly differentially expressed genes in  ΔcadA represent pneumococcal pathways involved in the biosynthesis of precursors for CPS and peptidoglycan.
Conclusion: We establish a possible link and interchange between two cellular processes such as high energy demanding capsule production and oxidative stress responses in polyamine synthesis impaired pneumococci (ΔcadA).

overall_design: Comparing the gene expression changes between  S. pneumoniae TIGR4 wild type and polyamine synthesis impaired isogenic deletion strain ΔcadA.

first: Moses

last: Ayoola

first: Leslie

last: Shack


title: Transcriptome Data of SREBP2(N) Overexpression in Human Umbilical Vein Endothelial Cells

city: La Jolla

first: John

last: Shyy

address: 9500 Gilman Dr., BRF2 Rm 1217 Bay LL

department: Medicine

institute: University of California, San Diego

summary: Sterol regulatory element-binding protein 2 (SREBP2) is a transcription factor that has been recently discovered to mediate vascular endothelial cell (EC) dysfunction. We therefore investigated the role of SREBP2 in EC function through comparing the transciptional profiling of human umbilical vein endothelial cells (HUVECs) that were infected with adenovirus overexpressing SREBP2 (Ad-SREBP2) or with empty vector (Ad-null) control.  Gene ontology analysis revealed that SREBP2 not only regulates cholesterol biosynthesis, but also mediates the TGF, WNT, and cytoskeleton remodeling pathways.  Among the responsive genes, SREBP2 exhibited the induction of mesenchymal transition.

overall_design: Transcriptome data of HUVECs overexpressing SREBP2 using adenovirus followed by deep sequencing, in biological duplicate, using Illumina NextSeq 500.

first: Marcy

last: Martin

middle: Y


title: microRNA and mRNA gene expression signature in JK and JinB8 cell lines [miRNA]

first: abdel

middle: G

last: Elkahloun

sample_organism:
Homo sapiens
Mus musculus

overall_design: 3 cell culture replicates of JK  and JINB8 cell lines

first: Abdel

first: Sukhbir

last: Kaur


title: Calcaneal tendon plasticity following gastrocnemius muscle injury in rat

city: Brasíia

first: Fabrício

middle: Reichert

last: Barin

address: Centro Metropolitano, Conjunto A, Lote 01

country: Brazil

institute: Universidade de Brasília

summary: We investigated calcaneal tendon extracellular matrix (ECM) remodeling after gastrocnemius muscle injury using a rat model. Wistar rats were randomly divided into four groups: control group (C; animals that were not exposed to muscle injury) and harvested at different time points post gastrocnemius muscle injury (3, 14 and 28 days) for gene expression analysis. qRT-PCR was performed using TaqMan Universal PCR Master Mix system (Applied Biosystems, CA, USA - Cat.  4304437).

overall_design: For the evaluation of CT gene expression, a total of 1 μg of RNA extracted from each tendon were converted into cDNA (final volume 20 μL) using SuperScript ™ VILO ™ MasterMix reverse transcriptase (Invitrogen-Cat. 11755-010) according to the manufacturer's protocol. To perform reverse transcription, the samples were incubated at 25°C for 10 minutes, at 42°C for 60 minutes, and at 85°C for 5 minutes before being stored at -20°C in a freezer.

last: Reichert Barin

first: Ivo

middle: V

last: de Sousa Neto

first: Graciele

last: Ramos

first: Alexander

last: Szojka

first: Amanda

last: Ruivo

first: Carla

middle: T

last: Mota Anfror

first: José

last: Hurtado Agualimpia

first: Allan

last: Domingues

first: Octávio

last: Franco

first: Adetola

last: Adesida

first: João

last: Quaglioti Durigan1

first: Rita

last: de Cassia Marqueti1


title: Transcriptional landscape of pulmonary lymphatic endothelium during late gestation

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary:
Maturation of lung cell types occurs during late gestation to ensure lung function and optimal gas exchange at birth.  The pulmonary lymphatic endothelium is an understudied cell type and is essential for immune regulation and interstitial fluid removal.  Here we provide the first characterization of the pulmonary lymphatic endothelium during late gestation prior to birth.
We used microarrays to detail the global transcriptional programme underlying maturation of pulmonary lymphatic endothelium and identified 1,281 genes with significant changes in gene expression over time. Gene expression was validated by qPCR and in situ hybridization, which indicated a potential role for IFN-I signaling in pulmonary lymphatic endothelial cell (PLEC) maturation prior to birth.

overall_design: After microdissection in ice-cold PBS, we combined 10-21 embryonic lungs from two litters for each sample at E16.5, E17.5, and E18.5 fetal time points (n=3 samples/time point). After tissue digestion and immunostaining, we sorted CD45-/Epcam-/CD31+/Vegfr3+/Lyve1+/Pdpn+ cells from the fetal murine lungs directly into QIAzol on a FACS Aria SORP.  RNA extraction was performed using the miRNeasy kit (Qiagen). RNA (RIN>7.5) was used to profile gene expression with Affymetrix Mouse Gene 2.0 microarrays in the Boston University Microarray and Sequencing Resource.

first: Timothy

last: Norman

first: Alan

last: Fine


title: Expression profiling of Histoplasma capsulatum G217B yeast to filament transition in GlcNAc or glucose for wild type, msb2, and complemented strains

city: San Francisco

first: Mark

last: Voorhies

state: CA

address: 513 Parnassus, S472

department: Microbiology and Immunology

institute: University of California

summary: Dimorphic fungi are temperature-sensitive organisms that couple their cell shape with their environment. One of these fungi, Histoplasma capsulatum, exists as both a soil-dwelling hypha and a host-associated yeast. Here we examine the role of the previously uncharacterized gene MSB2 in filamentous growth. We performed a genetic screen to identify insertion mutants that are unable to transition from the yeast form to the hyphal form. One yeast-locked mutant has an insertion upstream of the MSB2 gene. This mutant strain (SG1) fails to express MSB2, whose ortholog in the model yeast Saccharomyces cerevisiae is a known signaling component in the high osmolarity glycerol (HOG) pathway and filamentous growth (FG) pathway. Here, we profiled gene expression by RNA-seq to characterize transcriptional differences between wild type and msb2 mutant strains during the yeast to hyphal transition.

overall_design: Samples were were prepared in two distinct experiments and sequenced in three distinct sequencing runs.  In the first experiment, two biological replicates each of Histoplasma capsulatum G217B ura5 (WU15) or an msb2 mutant derived from WU15 (SG1) were grown in liquid culture with glucose or GlcNAc as the carbon source at 37C. After taking t=0 samples, the cultures were moved to room temperature (RT) and additional samples were taken at 2, 6, 8, or 10 days. One sample was not usable for sequencing, giving a total of 2*2*2*5-1 = 39 samples. The GlcNAc samples were sequenced in part of a lane of one HiSeq 4000 run (batch 1) and the glucose samples were sequenced in part of a lane of a second run (batch 2). Because these samples were grown at the same time, they were treated as a single batch in our limma analysis.  In the second experiment, two biological replicates each of WU15, SG1, or SG1 episomally complemented with MSB2::PaURA5 (SG1cMSB2) were grown in liquid culture with glucose or GlcNAc as the carbon source at 37C. After taking t=0 samples, the cultures were moved to RT and additional samples were taken at 2, 6, or 8 days, for a total of 2*3*2*4 = 48 samples. These samples were sequenced in a full lane of a HiSeq 4000 run (batch 3). In this second experiment, WU15 and SG1 were episomally complemented with PaURA5 to control for the selectable PaURA5 marker in the SG1cMSB2 strain.

first: Lauren

last: Rodriguez

first: Anita

last: Sil


title: In vitro maturation of intestinal organoids differentiated from wild type and STAT3 knock out human embryonic stem cells

city: Daejeon

first: Mi-Young

last: Son

address: 111 Gwahangno, Yuseong-gu

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology (KRIBB)

summary: Human intestinal organoids (hIOs) resemble the human intestine physiologically and structurally. We recently present an in vitro maturation technique for generating mature and functional hIOs from human pluripotent stem cells (hPSCs). Here, we investigated the mechanisms of STAT3 for inducing in vitro maturation of hIOs. Using CRISPR/Cas9-mediated gene editing, STAT3 knockout (KO) human embryonic stem cell (hESC) lines were generated and characterized. By genome-wide microarray analyses, STAT3 KO hIOs showed markedly different profiles from the in vitro matured hIOs and human small intestine and the majority of genes, which are associated with intestinal development and functions, were downregulated by STAT3 KO. This study reveals important signaling pathways for the maturation of hIOs derived from hPSCs.

overall_design: Gene expression profile of hIOs differentiated from WT and STAT3 KO hESCs with or without in vitro maturation, and adult human small intestine (hSI).

first: Kwang-Bo

last: Jung

first: Ohman

last: Kwon


title: Identification of the gene profiling of Wt1GFP expressing cardiomyocytes at different stages of embryonic heart development [M]

city: Guildford

first: Fernando

middle: O

last: Martinez Estrada

state: Surrey

address: Stag Hill

department: Faculty of Health & Medical Sciences

country: United Kingdom

institute: University of Surrey

summary: Detailed FACS analyses of enzymatically disaggregated embryonic hearts from Wt1GFPKI mice revealed two distinct types of Wt1-GFP-positive cells based on their GFP expression levels: a Wt1-GFP bright population (H) and a Wt1-GFP dim (M) population. Interestingly, when viewed under the microscope, cultured Wt1GFP+ (M) cells were shown to exhibit synchronous contractions that suggest a cardiomyocyte identity. These observations also imply that a population of low Wt1-expressing cardiomyocytes contributes to the formation of the myocardium.

overall_design: In order to characterise the gene expression profile of the Wt1GFP expressing cardiomyocytes , RNA from the Wt1-GFP+ (M) population sorted cells from heart ventricles were isolated each day from E11.5 to E16.5.

last: Martinez

first: Ofelia

last: Estrada

first: Víctor

last: Velecela


title: DNA Methylation Identifies Genetically and Prognostically Distinct Subtypes of Myelodysplastic Syndromes

city: la jolla

first: Brian

last: Reilly

address: 3855 Health Sciences Drive

department: Moores Cancer Center

institute: UC San Diego

summary: We report the identification of five subtypes of myelodysplastic syndromes (MDS) identified via unsupervised classification of DNA methylation (DNAm) profiles. Bisulfite padlock probe sequencing (BSPP) was used to measure DNAm of ~500,000 unique CpGs covering 140,749 non-overlapping regulatory regions across the genome in bone marrow DNA samples from 141 patients with MDS. Application of a non-negative matrix factorization (NMF) decomposition of DNAm profiles identified five consensus clusters described by five NMF components as the most stable grouping solution.

overall_design:
DNA methylomes were generated from bone marrow mononuclear cells of 141 myelodysplastic syndrome patients using targeted bisulfite sequencing approach, bisulfite padlock probes, and sequenced on an Illumina HiSeq 2500.

Submitter declares that the raw data will be submitted to dbGaP (or EGA) because of patient privacy concerns.

first: Rafael

last: Bejar


title: Effect of Miz1 POZ domain deletion on expression profiles of B and T leukemia cells

city: Montreal

first: Möröy

last: Tarik

state: Quebec

address: 110 Pine avenue West

country: Canada

institute: Insititut de Recherches Cliniques

summary: Acute lymphoblastic leukemia (ALL) is an aggressive blood cancer mainly affecting children. Relapse rates are high and toxic chemotherapies that block DNA replication and induce DNA damage cause health problems later in life, underlining the need for improved therapies. c-Myc is a transcription factor that is hyperactive in a large proportion of cancers including leukemia but is difficult to target in therapy. We show that ablation of the function of the BTB/POZ domain factor Miz-1, an important co-factor of c-Myc, significantly delays T- and B-ALL/lymphoma in mice and interferes with c-Myc oncogenic transcriptional activity. Leukemic cells that still emerge in this system activate DNA replication pathways, which are those targeted by current chemotherapeutic drugs such as cytarabine. We found that the combination of acute ablation of the Miz-1 POZ domain enhances the effect of cytarabine treatment. This combination was effective in both Eµ-Myc and Notch ICN driven leukemia models and prolonged survival of tumor bearing animals by accelerating apoptosis of leukemic cells. These observations suggest that targeting Miz-1 could render current ALL chemotherapies more effective with a better outcome for patients.

overall_design: mRNA was extracted from 2 miz1 wt and 2 miz1 deltaPOZ B cell and 2 miz1 wt and 2 miz1 deltaPOZ T cell leukemic samples.

first: Julie

last: Ross

first: Tarik

last: Möröy

first: Charles

last: Vadnais


title: Genome-wide analysis of hepatic gene expression in patients with non-alcoholic steatohepatitis (NASH) before and after 1 year supplementation with n-3 polyunsaturated fatty acids (PUFA) from fishoil

city: Toronto

first: Johane

middle: P.

last: Allard

state: Ontario

address: 585 University Ave, 9-NU-973

institute: University Health Network

summary:
Fishoil or n-3 PUFA supplementation has shown some beneficial effects in patients with NASH. It is known that n-3 PUFA can influence hepatic gene expression. However, the effect of n-3 PUFA supplementation on hepatic gene expression has not been examined in patients with NASH. Aim of this pilot study was to examine the effect of n-3 PUFA supplementation on liver n-3 PUFA levels, hepatic gene expression and liver histology in patients with NASH.
In a single-arm pilot intervention study, the effect of a one year n-3 PUFA supplementation on hepatic gene expression (Illumina Microarray), liver histology, and liver and erythrocyte PUFA was examined in 11 adult patients with NASH. For the intervention trial, NASH patients received n-3 PUFA supplementation from fish oil (2 g fish oil per day, containing 740-840 mg eicosapentaenoic acid (EPA) and 400-440 mg docosahexaenoic acid (DHA) quantified as ethyl ester) for one year. The supplement was produced by Ocean Nutrition Canada Ltd. (Dartmouth, NS, Canada) (product code 4020PB1000CT, Lots # 21211, 24168, and 31639). The selected supplement was within the range used in previous studies, where doses of n-3 PUFA and the EPA/DHA balance varied widely. Effects of n-3 PUFA on liver steatosis were observed in other studies by ultrasound within 6 to 12 months. To increase safety and acceptance of the second liver biopsy, an intervention period of 12 months was selected. During the intervention, patients were asked to maintain their habitual diet and physical activity.   Fishoil supplementation lead to increased n-3 PUFA in erythrocyte total lipids and hepatic lipids. However, there was no significant change in liver histology or hepatic gene expression between baseline and post-intervention.

overall_design: Single-arm open-label pilot study , including patients with biopsy-proven NASH. Eleven patients completed the intervention and had paired liver biopsies (baseline and 12 months) available for measurements. In 1 of them, the tissue was insufficient for fatty acid measurements and in 2 of them, one sample did not pass quality control for gene expression data, resulting in a total of 10 and 9 patients who were included in the analysis for hepatic fatty acids and hepatic gene expression, respectively..

first: Bianca

last: Arendt

first: Elena

last: Comelli

first: David

middle: W

last: Ma

first: Wendy

last: Lou

first: Anastasia

last: Teterina

first: TaeHyung

last: Kim

first: Scott

last: Fung

last: Wong

first: Ian

last: McGilvray

first: Sandra

last: Fischer


title: Identification of the gene profiling of Wt1GFP enriched epicardial cells at different stages of embryonic heart development [H]

first: Fernando

last: Martinez Estrada

summary: Detailed FACS analyses of enzymatically disaggregated embryonic hearts from Wt1GFPKI mice revealed two distinct types of Wt1GFP-positive cells based on their GFP expression levels: a Wt1GFP bright population (H) and a Wt1GFP dim (M) population. Quantitative RT-PCR analyses for epicardial genes demonstrated an enrichment in epicardial genes in the  Wt1GFP bright population (H)

overall_design: In order to characterise the gene expression profile of Wt1GFP enriched epicardial cells, RNA from Wt1-GFP bright population (H) sorted cells from heart ventricles was isolated each day from E11.5 to E16.5.

last: Martinez

first: Ofelia

last: Estrada

first: Víctor

last: Velecela


title: Identification of the gene profiling of Wt1GFP expressing cardiomyocytes at different stages of embryonic heart development

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

overall_design: Refer to individual Series


title: Transcriptome analysis of Enzalutamide-resistant C4-2B (C4-2B MDVR) cells treated with Indocin.

status: Public on Sep 29 2019

city: Sacramento

first: Clifford

middle: G.

last: Tepper

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

summary: The overall goal of this study was to identify genes that were differentially-expressed in C4-2B MDVR cells treated with Indocin. C4-2B MDVR were either treated with Indocin (20 uM) or DMSO vehicle control for 3 days, followed by isolation of total cellular RNA. Transcriptome analysis was performed with RNA-Sequencing (RNA-Seq) in order to identify differentially-expressed genes (DEGs) induced by Indocin treatment.

overall_design: Two samples were analyzed by RNA-Seq analysis: Indocin (20 uM)-treated C4-2B MDVR cells, and DMSO-treated C4-2B MDVR cells as a control.

first: Chengfei

last: Liu

first: Allen

middle: C

last: Gao


title: Loss of Bap1 leads to an increased global methylation and decrease in H3K27AC enhancer marks around key lineage commitment genes in Xenopus laevis embryos [ChIP-seq]

status: Public on Sep 26 2019

city: Miami

first: Michael

last: Durante

state: FL

department: Ophthalmology

institute: University of Miami Miller School of Medicine

summary: We performed morpholino-mediated knockdown of Bap1 protein expression in Xenopus laevis developing embryos, and analyzed inhibiting  and activating histone marks . We find that inhibition of Bap1 leads to decrease in H3K27AC activating makrs around lineage  commitment genes, and increased global methylation.

overall_design: Control and Bap1-depleted stage 12 frog embryos were analyzed by ChIP-seq for expression of H3K27AC, H3K27me3, H2Aub and H3K4me3 histone marks.

first: Jeffim

middle: N

last: Kuznetsov

first: Stefan

last: Kurtenbach


title: Genetic expression of stage IV oral squamous cell carcinoma according to the recurrence

city: Ansan

first: Yoon Chan

last: Rah

address: 123 Jeokgeum-ro, Danwon-gu

department: Otorhinolaryngology

institute: Korea University

summary: To characterize differential gene expression patterns and their actual expression in tissues for recurrent and non-recurrent tumors to identify independent prognostic markers for oral squamous cell carcinoma (OSCC).

overall_design: cDNA microarray analysis was performed to identify differentially expressed genes in both primary tumors and regional normal lymph nodes from patients with and without recurrence. Four patients for each recurrent/non-recurrent group were included. All of them were diagnosed with stage IV oral squamous cell carcinoma and the study group was allocated according to the presence of recurrence after successful surgical resection.

first: Yoon

first: Jae-Cheul

last: Ahn

first: Eun-Hui

last: Jeon

first: Hyojin

first: Jin

middle: H

last: Paik

first: Woo-Jin

last: Jeong

first: Soon-Hyun


title: PESCA: A scalable platform for the development of cell-type-specific viral drivers

status: Public on Sep 27 2019

first: Mark

middle: Aurel

last: Nagy

state: Massachusetts

address: 220 Longwood Ave

department: Department of Neurobiology

institute: Harvard Medical School

summary: Highly paralleled functional evaluation of enhancer activity in single cells generates new cell-type-specific tools with broad medical and scientific applications.

overall_design: For INTACT we crossed Sst-IRES-Cre (The Jackson Laboratory Stock # 013044), Vip-IRES-Cre (The Jackson Laboratory Stock # 010908) and Pv-Cre (The Jackson Laboratory Stock # 017320) with SUN1-2xsfGFP-6xMYC (The Jackson Laboratory Stock # 021039) and used adult (6-12 wk old) male and female F1 progeny. Nuclear purifications were performed from whole cortex of adult mice as previously described using anti-GFP antibodies (Fisher G10362). Isolated nuclei were gently resuspended in cold L1 buffer (50 mM Hepes pH 7.5, 140 mM NaCl, 1 mM EDTA, 1 mM EGTA, 0.25% Triton X-100, 0.5% NP40, 10% Glycerol, protease inhibitors), and pelleted at 800g for 5 minutes at 4°C. DNA libraries were prepared from the nuclei using the Nextera DNA Library Prep Kit (Illumina) according to manufacturer’s protocols.  The final libraries were purified using the Qiagen minelute kit and sequenced on a Nextseq 500 benchtop DNA sequencer (Illumina). 2 replicates were generated and sequenced for each mouse strain.     For PESCA screening we used adult (6-10 wk) C57BL/6J (The Jackson Laboratory, Stock # 000664) mice. Animals were anesthetized with isofluorane (1–3% in air) and placed on a stereotactic instrument (Kopf) with a 37°C heated pad. The PESCA library (AAV9, 1.9 x 1013 genome copies/mL) was stereotactically injected in V1 (800 nL per site at 25 nL/min) using a sharp glass pipette (25-45 μm diameter) that was left in place for 5 min prior to and 10 min following injection to minimize backflow. Two injections were performed per animal at coordinates 3.0 and 3.7 mm posterior, 2.5 mm lateral relative to bregma, and 0.6 mm ventral relative to the brain surface.  Individual rAAV-GRE constructs were stereotactically injected at a titer of 1 x 1011 genome copies/mL. (250 nL per site at 25 nL/min).  All injections were performed at two depths (0.4 and 0.7 mm ventral relative to the brain surface) to achieve broader infection across cortical layers. The injection coordinates relative to bregma were 3.0 or 3.7 mm posterior, 2.5 or -2.5 mm lateral. Single-nuclei suspensions were generated as described previously(1)  , with minor modifications. V1 was dissected and placed into a Dounce with homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, pH 7.8, 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors). The sample was homogenized using a tight pestle with 10 stokes. IGEPAL solution (5%, Sigma) was added to a final concentration of 0.32%, and 5 additional strokes were performed. The homogenate was filtered through a 40-μm filter, and OptiPrep (Sigma) added to a final concentration of 25% iodixanol.  The sample was layered onto an iodixanol gradient and centrifuged at 10,000g for 18 minutes as previously described. Nuclei were collected between the 30% and 40% iodixanol layers and diluted to 80,000-100,000 nuclei/mL for encapsulation. All buffers contained 0.15% RNasin Plus RNase Inhibitor (Promega) and 0.04% BSA. Single nuclei were captured and barcoded whole-transcriptome libraries prepared using the inDrops platform as previously described(5, 6), collecting five libraries of approximately 3,000 nuclei from each animal. For enrichment of virally-derived transcripts, a fraction (3 μL) of the amplified RNA intermediate was reverse transcribed with random hexamers without prior fragmentation. PCR was next used to amplify virally derived transcripts. The forward primer was designed to introduce the R1 sequence and anneal to a sequence uniquely present 5’ of the viral-barcode sequence present in the viral transcripts (5’- GCATCGATACCGAGCGC). The reverse primer was designed to anneal to a sequence present 5’ of the cell-barcode (5’- GGGTGTCGGGTGCAG). The result of the PCR is preferential amplification of the viral-derived transcripts, while simultaneously retaining the cell-barcode sequence necessary to assign each transcript to a particular cell/nucleus. Following PCR amplification (18 cycles, Hot Start High-Fidelity Q5 polymerase) all the libraries were indexed, pooled, and sequenced on a Nextseq 500 benchtop DNA sequencer (Illumina).

first: Sinisa

last: Hrvatin

first: Christopher

middle: P

last: Tzeng

middle: A

first: Hume

last: Stroud

first: Charalampia

last: Koutsioumpa

first: Oren

middle: F

last: Wilcox

first: Elena

last: Assad

first: Jonathan

last: Green

first: Eric

last: Griffith

last: Greenberg


title: Unique and redundant function of SOX2 and SOX17 in regulating the germ cell tumour fate

status: Public on Sep 28 2019

city: Bonn

first: Sina

last: Jostes

address: Venusberg Campus 1

department: Department of Developmental Pathology

institute: Institute of Pathology

summary: Embryonal carcinomas (ECs) and seminomas are testicular germ cell tumours. ECs display expression of SOX2, while seminomas display expression of SOX17. In somatic differentiation, SOX17 drives endodermal cell fate. However, seminomas lack expression of endoderm markers, but show features of pluripotency. Here, we use ChIP-sequencing to report and compare the binding pattern of SOX17 in seminoma-like TCam-2 cells to SOX2 in EC-like 2102EP cells and SOX17 in somatic cells. In seminoma-like cells, SOX17 was detected at canonical (SOX2/OCT4), compressed (SOX17/OCT4) and other SOX family member motifs. SOX17 directly regulates TFAP2C, PRDM1 and PRDM14, thereby maintaining latent pluripotency and suppressing somatic differentiation. In contrast, in somatic cells canonical motifs are not bound by SOX17. In sum only 10% of SOX17 binding sites overlap in seminoma-like and somatic cells. This illustrates that binding site choice is highly dynamic and cell type specific. Deletion of SOX17 in seminoma-like cells resulted in loss of pluripotency, marked by a reduction of OCT4 protein level and loss of alkaline phosphatase activity. Further, we found that in EC-like cells SOX2 regulates pluripotency-associated genes, predominantly by partnering with OCT4. In conclusion, SOX17 (in seminomas) functionally replaces SOX2 (in ECs) to maintain expression of the pluripotency cluster.

overall_design: Chromatin immunoprecipitation (ChIP) was carried out using 200 µg chromatin lysate and 5 µg antibody (anti-SOX2: #ab59776 (abcam); anti-SOX17: #AF1924 (R&D)). SOX17 ChIP was performed on chromatin lysate of TCam-2 seminoma-like cells for three biological replicates. SOX2 ChIP was performed on chromatin lysate of 2102EP EC-like cells for three biological replicates. The protocol was performed according to the Simple ChIP Enzymatic Chromatin IP Kit (Cell Signaling Technology). 2% Input (= 2 µg chromatin) served as control. ChIP-seq libraries were generated using the MicroPlex Library Preparation Kit v2 (Diagenode). Quality of the ChIP-seq libraries was assessed on a 2400 Tapestation (Agilent, Santa Clara, USA) and library pools were quantified using Qubit (Thermo Fisher Scientific). Samples were then sequenced on the Illumina High Seq 2500 v4 (Illumina, San Diego, USA) in rapid mode using 25 M single-end reads (1 x 75 bp) per sample. Reads were mapped to the human genome (hg38) using CLC Genomics Workbench 12 (Qiagen, Hilden, Germany) and data was analysed using HOMER (Hypergeometric Optimization of Motif EnRichment) Software (http://homer.ucsd.edu/homer/).

first: Martin

last: Fellermeyer

first: Lena

last: Arévalo

first: Gina

last: Merges

first: Glen

last: Kristiansen

first: Daniel

last: Nettersheim

first: Hubert

last: Schorle


title: Viral miRNA adaptor differentially recruits miRNAs to target mRNAs through alternative base-pairing

city: Salt Lake City

first: Demian

middle: E

last: Cazalla

state: UT

address: 15 N Medical Drive East, Rm 4100

department: Biochemistry

institute: University of Utah

summary: The viral non-coding RNA HSUR2 regulates apoptosis by recruiting host microRNAs to host mRNAs encoding apoptotic factors. The mechanism whereby HSUR2 targets specific host mRNAs is unknown. Here we developed iRICC to identify sequences mediating RNA-RNA interactions in vivo between a single RNA of interest and its binding RNAs. Sequences that mediate HSUR2-mRNA interactions identified by iRICC-seq were functionally validated by mutational analyses. Unlike other small regulatory non-coding RNAs, HSUR2 does not contain a “seed” region responsible for interaction with most target mRNAs, but rather uses different sequences to bind to different targets. Our findings describe a mode of interaction that provides HSUR2 with flexibility both in target recognition and in the selection of trans-acting miRNAs that are recruited for target mRNA repression.

sample_organism:
Callithrix jacchus
Saimiriine gammaherpesvirus 2

overall_design: Polyadenylated (polyA+) RNA was selected and hybridized to an antisense DNA oligonucleotide complementary to full-length HSUR2 (anti-H2 DNA) followed by limited single-strand S1 endonuclease digestion to fragment polyA+ RNA while maintaining HSUR2 integrity. After removal of anti-H2 DNA by DNAse I digestion, samples were split into two samples and hybridization with anti-H2 DNA was repeated in one (Control) sample, followed by digestion of both samples with RNAse H, which resulted in removal of HSUR2 only from the Control sample. Following a second digestion with DNAse I, HSUR2 and crosslinked RNAs were purified in both samples under stringent conditions with a biotinylated RNA oligonucleotide antisense to HSUR2. High-throughput sequencing libraries were prepared for both samples using random primers. HSUR2 target mRNAs were identified by comparison of pull downs from HSUR2 samples with Control samples in three independent replicate experiments

first: Demián

first: Carlos

last: Gorbea

first: Tim

last: Mosbruger

first: David

last: Nix


title: Loss of Bap1 in Xenopus laevis embryos

first: Michael

last: Durante


title: Bap1 loss leads to decreased expression of lineage specific commitment genes, and increased expression of pluripotency genes [RNA-seq]

summary: We performed morpholino-mediated knockdown of Bap1 protein expression in Xenopus laevis developing embryos, and analyzed gene expression at stage 12. We find that inhibition of Bap1 leads to decrease in lineage specific commitment genes, and increased expression of pluripotency genes.

overall_design: RNA profiles of stage 12 embryos injected with either Ctrl morpholino (CtrlMO) or mopholino targeting Bap1 (Bap1MO), in triplicate, using Illumina Nextseq500.

first: Jeffim

last: Kuznetsov

first: Matthew

last: Field


title: Glycine Cleavage System Determines the Fate of Pluripotent Stem Cells via the Regulation of Senescence and Epigenetic Modifications

status: Public on Sep 25 2019

city: Hefei

first: junru

last: feng

address: huangshan road #443

institute: USTC

summary: To investigate whether embryonic stem cells exhibit a metabolic state different from that of somatic cells, we performed RNA-seq  in mouse embryonic fibroblasts (MEFs), induced pluripotent stem cells (iPSCs) and mouse embryonic stem cells (mESCs). To further investigate the effect of Gldc in mESCs, we performed  RNA-seq in V6.5 cells with Gldc knockdown.

overall_design: RNA-seq for MEF,IPS and V6.5 cells was performed to analyze the gene expression of these lines. mouse ES cell were transfected with Gldc shRNA or non-targeting control shRNA followed by RNA extraction and sequenced on HiSeq X Ten (Mus musculus).

first: Shengya

last: Tian

first: Junru

last: Feng

first: Shengqi

last: Shen

first: Huafeng

last: Zhang

first: Xiuying

last: Zhong

first: Ping

last: Gao


title: Biological effect of chronic mistranslation in mammalian cells

status: Public on Sep 24 2019

city: Zürich

first: Youjin

last: Teo

address: Gloriastrasse 30

department: Institut für Medizinische Mikrobiologie

institute: Universität Zürich

summary: Analysis of HEK293 cells lines  expressing mutant ribosomal protein RPS2 (human A226Y). RPS2 A226Y mutation has been shown to cause misreading and readthrough. Results provide insight into the response to chronic mistranslation in mammalian cells.

overall_design: mRNA profiles of RPS2 wild-type and RPS2 A226Y mutant HEK293 cell culture samples generated by deep sequencing.

first: Dimitri

last: Scherbakov

first: Erik

last: Böttger


title: Super-enhancer-guided decoding of gene regulatory networks in trophoblast stem cells

city: Austin

first: Bum-Kyu

last: Lee

state: TX

address: 2506 Speedway Stop A5000

institute: University of Texas at Austin

summary: Cells belonging to trophoblast lineage are required for proper implantation and placentation, as well as the vascular, hematopoietic, and immunological properties of the placenta, a crucial organ mediating dynamic interactions between maternal and fetal tissues. Defects in trophoblast lineage development can cause early pregnancy failure or other pregnancy-related disorders. Despite its pivotal roles, the placenta remains as one of the least studied organs. Until now, only a handful of trophoblast-specific transcription factors (TFs) have been characterized, and underlying regulatory mechanisms modulating trophoblast lineage development remain poorly understood. Here we explore trophoblast stem cell (TSC)-specific super-enhancers (SEs) and subsequently identify SE-associated factors enriched with previously known and many unknown TFs modulating trophoblast lineage development. By mapping direct targets of 28 TSC-specific TFs in TSCs, we construct highly intertwined transcriptional regulatory networks where TFs are co-regulated and linked with signaling pathways, and which function as cellular modules dedicated to trophoblast lineage development. Additionally, we reveal that TSC-specific TFs alter their target sites corresponding to the reshaped enhancers during TSC differentiation. These findings advance our understanding on placenta biology.

overall_design: ChIP sequenicngs were performed for p300, Med12, various trophoblast-specific transcription factors, and diverse histone marks using native antibodies in self-renewing and differentiated trophoblast stem cells (TSCs). Mock ChIP was also performed for a control. ATAC-seq was performed for both self-renewing embryonic stem cells(ESCs) and TSCs. RNA-seq was performed with samples from knockdown of either Meis1, Hopx, Maff, Mafk, Pou3f1, and a control in both TSC and differentiated TSCs (dTSCs) for 3 days.

first: Jonghwan

last: Kim


title: MicroRNA Dynamics and Functions During Arabidopsis Embryogenesis

city: Wageningen

middle: D

last: Nodine

state: Gelderland

address: Radix West

department: Plant Sciences

country: Netherlands

institute: Wageningen University & Research

summary: MicroRNAs (miRNAs) are short non-coding RNAs that mediate the repression of target transcripts in plants and animals. Although miRNAs are required throughout plant development, relatively little is known regarding their embryonic functions. To systematically characterize embryonic miRNAs in Arabidopsis thaliana, we developed or applied high-throughput sequencing based methods to profile hundreds of miRNAs and associated targets throughout embryogenesis. We discovered dozens of miRNAs that dynamically cleave and repress target transcripts including 30 that encode transcription factors. Transcriptome analyses indicated that these miRNA:target interactions have a profound impact on embryonic gene expression programs, and we further demonstrated that the miRNA-mediated repression of six transcription factors were individually required for embryo morphogenesis. These data indicate that the miRNA-directed repression of multiple transcription factors is critically important for the establishment of the plant body plan, and provide a foundation to further investigate how miRNAs contribute to these initial cellular differentiation events.

overall_design: sRNA-seq libraries were constructed for three biological replicates of nine tissues/genotypes and single biological replicates of six additional tissues/conditions. nanoPARE libraries were constructed for three biological replicates of eleven tissues/genotypes. mRNA-seq libraries were generated for three biological replicates of one tissue/genotype.


title: Single cell RNA-seq Analysis of Wild Type(WT), Dux knockout(KO) and Dux overexpression(OE) embryos

city: Shanghai

first: Mingyue

last: Guo

state: Shanghai

address: Siping

department: School of Life science and technology

institute: Tongji University

summary: We tested the transcriptome of embryos from WT and Dux KO mice including zygotes (hCG 28h), early 2-cell (hCG 31-32h), middle 2-cell(hCG 41-42h), late 2-cell(hCG 47-48h) and, Dux mRNA injected embryos including zygote(5h after injection, hCG 28h), early 4-cell(6h after injection, hCG 54h) and late 4-cell (17h after injection, hCG 65h) using the Covaris DNA shearing protocol for Smart-seq sequence library generation. We found that the activation of Dux is important but not essential for ZGA, but the silencing and elimination of Dux is strictly necessary for early embryonic development.

overall_design: Embryos mRNA profiles of WT,Dux KO and Dux OE were generated by deep sequencing, using Illumina NovaSeq 6000.

first: Yanping

first: Yixuan

last: Wang


title: HRPK-1, a conserved KH-domain protein, modulates microRNA activity during Caenorhabditis elegans development

city: Beer-Sheva

first: Isana

last: Veksler-Lublinsky

address: P.O.B. 653 Beer-Sheva

institute: Ben-Gurion university of the Negev

summary: microRNAs (miRNAs) are potent regulators of gene expression that function in diverse developmental and physiological processes. Argonaute proteins loaded with miRNAs form the miRNA Induced Silencing Complexes (miRISCs) that repress gene expression at the post-transcriptional level. miRISCs target genes through partial sequence complementarity between the miRNA and the target mRNA’s 3’ UTR. In addition to being targeted by miRNAs, these mRNAs are also extensively regulated by RNA-binding proteins (RBPs) through RNA processing, transport, stability, and translation regulation. While the degree to which RBPs and miRISCs interact to regulate gene expression is likely extensive, we have only begun to unravel the mechanisms of this functional cooperation. An RNAi-based screen of putative ALG-1 Argonaute interactors has identified a role for a conserved RNA binding protein, HRPK- 1, in modulating miRNA activity during C. elegans development. Here, we report the physical and genetic interaction between HRPK-1 and ALG-1/miRNAs. Specifically, we report the genetic and molecular characterizations of hrpk-1 and its role in C. elegans development and miRNA-mediated target repression. We show that loss of hrpk-1 causes numerous developmental defects and enhances the mutant phenotypes associated with reduction of miRNA activity, including those of lsy-6, mir-35-family, and let-7-family miRNAs. In addition to hrpk-1 genetic interaction with these miRNA families, hrpk-1 is required for efficient regulation of lsy-6 target cog-1. We report that hrpk-1 plays a role in processing of some but not all miRNAs and is not required for ALG-1/AIN-1 miRISC assembly. We suggest that HRPK-1 may functionally interact with miRNAs by both affecting miRNA processing and by enhancing miRNA/miRISC gene regulatory activity and present models for its activity.

overall_design: Small RNA libraries were generated and sequenced from total RNA obtained from wild type (N2) and hrpk-1(zen17) and hrpk-1(tm5522) mutant animals at the embryo and L4 stages.

first: Anna

last: Zinovyeva

first: Li

last: Li


title: Genome-wide DNA methylation analysis in autism spectrum disorders (ASD patients vs Controls)

status: Public on Sep 23 2019

city: Kyoto

first: Ryo

last: Kimura

address: Yoshida-Konoe-cho

department: Anatomy and Developmental Biology

institute: Kyoto University Graduate School of Medicine

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA methylation profiling of ASD and controls using peripheral blood samples.

overall_design: Bisulfite converted DNA was hybridized onto the Illumina Infinium HumanMethylation450 BeadChip array

first: Masatoshi

last: Hagiwara


title: Effects of social isolation stress on miRNA expression in the bed nucleus of stria terminalis (BNST) in male and female rats

city: Boston

first: Lorena

last: Pantano

address: 655 Huntington Ave

department: Biostatistics

country: USA

institute: Harvard Chan School of Public Health

summary:
Purpose: This study assessed putative sex differences in miRNA expression in the bed nucleus of the stria terminalis (BNST)—a sexually dimorphic brain region implicated in anxiety—of adult male and female rats that had been exposed throughout adolescence to social isolation (SI) stress.
Methods: Male and female Sprague-Dawley rats underwent SI during adolescence or remained grouped housed (GH) till adulthood. Small RNA sequencing was performed on tissue extracted from the anterodorsal BNST.
Results: SI compared to GH induced more anxiogenic-like effects in females compared to males and sex-dependent changes in miRNA expression in the BNST.
Conclusions: The current study shows that housing conditions (either SI or GH) during adolescence regulates miRNA expression in a sex-specific manner in the sexually dimorphic area of the adBNST

overall_design: Small RNA sequencing results were generated from the anterodorsal bed nucleus of stria terminalis (adBNST) of male and female group housed (GH) and socially isolated (SI) rats.

first: Maria

last: Mavrikaki

first: David

last: Potter

first: Max

last: Rogers-Grazado

first: Sami

last: Amr

first: Elena

last: Chartoff


title: Endogenous fluctuations of OCT4 and SOX2 bias pluripotent cell fate decisions

city: Lausanne

middle: Michael

last: Suter

address: EPFL SV-IN Station 19

department: Institute of Bioengineering

institute: École polytechnique fédérale de Lausanne

summary: SOX2 and OCT4 are pioneer transcription factors playing a key role in embryonic stem (ES) cell self-renewal and differentiation. How temporal fluctuations in their expression levels bias lineage commitment is unknown. Here we generated knock-in reporter fusion ES cell lines allowing to monitor endogenous SOX2 and OCT4 protein fluctuations in living cells and to determine their impact on mesendodermal and neuroectodermal commitment. We found that small differences in SOX2 and OCT4 levels impact cell fate commitment in G1 but not in S phase. Elevated SOX2 levels modestly increased neuroectodermal commitment and decreased mesendodermal commitment upon directed differentiation. In contrast, elevated OCT4 levels strongly biased ES cells towards both neuroectodermal and mesendodermal fates. Using ATAC-seq on ES cells gated for different endogenous SOX2 and OCT4 levels, we found that high OCT4 levels increased chromatin accessibility at differentiation-associated enhancers. This suggests that small endogenous fluctuations of pioneer transcription factors can bias cell fate decisions by concentration-dependent priming of differentiation-associated enhancers.

overall_design: Cells were subjected to ATAC-seq by Tn5 transposition or to ChIP-seq by immunoprecipitation

middle: M

first: Elias

last: Friman


title: CGGBP1 regulates chromatin barrier activity and CTCF occupancy at repeats

city: Gandhinagar

first: Umashankar

last: Singh

state: Gujarat

address: Acad Block 4 Room 317 IIT Gandhinagar Palaj

department: Biological Sciences and Engineering

country: India

institute: IIT Gandhinagar

summary: To study the role of CGGBP1 in regulation of CTCF occupancy, we performed CTCF ChIP-seq in HEK293T cells with three different levels of CGGBP1: (i) endogenous levels of CGGBP1 (ii) CGGBP1 knockdown, and (iii) CGGBP1 overexpression. Here, we show that CTCF binds to repeats as well as canonical CTCF-motifs and CGGBP1 determines the CTCF occupancy preference for repeats over canonical CTCF-motif. By combining CTCF ChIP-seq with histone modifications ChIP-seq (for H3K4me3, H3K9me3 and H3K27me3) under conditions of normal or CGGBP1 knockdown, we demonstrate that CTCF binding sites regulated by CGGBP1 correspond to chromatin barrier elements with profound effects on H3K9me3 distribution. In conclusion, these finding shows that CGGBP1 is a regulator of CTCF occupancy and serve as a regulator of barrier functions of CTCF-binding sites.

overall_design: CTCF occupancy was compared in HEK293T cells through ChIP-seq under conditions of normal CGGBP1 expression, CGGBP1 knockdown and overexpression. Histone modifications ChIP-seq (H3K4me3, H3K9me3 and H3K27me3) were performed under endogenous levels of CGGBP1 and CGGBP1 knockdown.

first: Divyesh

last: Patel

first: Manthan


title: RNA-seq data from Cdk8∆/∆  and wildtype BCR-ABL1p185+ transformed bone marrow cell lines either untreated or treated  with SenexinB (4 biological replicates each)

status: Public on Sep 20 2019

city: Vienna

first: Veronika

last: Sexl

address: Veterinaerplatz 1

department: Pharmacology / Toxikology

institute: University of Veterinary Medicine Vienna

summary: RNA-seq data from Cdk8∆/∆  and wildtype BCR-ABL1p185+ transformed cell lines either untreated or treated  with SenexinB was used to identify kinase-dependent and independent target genes of CDK8

overall_design: mRNA from immortalized Cdk8∆/∆  and wildtype BCR-ABL1p185+ cell lines either untreated or treated  with SenexinB (4 biological replicates each) were prepared using the Lexogen SENSE mRNA-Seq library preparation kit. Single-end, 50bp sequencing was performed on an Illumina HiSeq-2500 sequencer. Reads were mapped to the GENECODE M13 genome.

first: Ingeborg

last: Menzl

first: Reinhard

last: Grausenburger


title: Functional genomics of Caspase-3 deficiency or proficiency in MCF-7 cells or MDA-MB-231 tumors after docetaxel treatment

status: Public on Sep 22 2019

city: Dijon

first: Romain

last: Boidot

address: 1, rue Pr Marion

country: France

institute: CGFL

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

overall_design: Refer to individual Series


title: Postmortem Cortex Samples Identify Distinct Molecular Subtypes of ALS: Retrotransposon Activation, Oxidative Stress, and Activated Glia [eCLIP]

city: New York

first: Oliver

last: Tam

state: New York

address: 435 E 30th St

department: Institute for Systems Genetics

institute: NYU Grossman School of Medicine

summary: Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease characterized by the progressive loss of motor neurons. While several inherited pathogenic mutations have been identified as causative, the vast majority of cases are sporadic with no family history of disease. Thus, for the majority of ALS cases, a specific causal abnormality is not known and the disease may be a product of multiple inter-related pathways contributing to varying degrees in different ALS patients. Using unsupervised machine learning algorithms, we stratified the transcriptomes of 148 ALS decedent cortex tissue samples into three distinct and robust molecular subtypes. The largest cluster, identified in 61% of patient samples, displayed hallmarks of oxidative and proteotoxic stress. Another 20% of the ALS patient samples exhibited high levels of retrotransposon expression and other signatures of TDP-43 dysfunction. Finally, a third group showed predominant signatures of glial activation (19%). Together these results demonstrate that at least three distinct molecular signatures contribute to ALS disease. While multiple dysregulated components and pathways comprising these clusters have previously been implicated in ALS pathogenesis, unbiased analysis of this large survey demonstrated that sporadic ALS patient tissues can be segregated into distinct molecular subsets.

overall_design: eCLIP analysis of TARDBP In SH-SY5Y cells (2 replicates) compared against a size matched input

first: Nikolay

middle: V

last: Rozhkov

first: Regina

last: Shaw

first: Molly

last: Gale Hammell


title: Postmortem Cortex Samples Identify Distinct Molecular Subtypes of ALS: Retrotransposon Activation, Oxidative Stress, and Activated Glia [motor cortex]

overall_design: RNA-seq analysis of sporadic ALS patient samples against those from individuals without neurological disorders

first: John

last: Ravits

first: Josh

last: Dubnau


title: Postmortem Cortex Samples Identify Distinct Molecular Subtypes of ALS: Retrotransposon Activation, Oxidative Stress, and Activated Glia [shRNA]

overall_design: RNA-seq of shRNA knockdown of TARDBP in SH-SY5Y cells (2 replicates), compared against two control shRNA (2 replicates each)


title: Postmortem Cortex Samples Identify Distinct Molecular Subtypes of ALS: Retrotransposon Activation, Oxidative Stress, and Activated Glia


title: Genome-wide analysis of Corsican population reveals a close affinity with Northern and Central Italy

status: Public on Sep 19 2019

city: Tartu

first: Tuuli

last: Reisberg

address: Riia 23

country: Estonia

institute: University of Tartu

summary: We combined new data with previously published data to characterize the population structure of Corsican population in the context of their geographic neighbors across Eurasia and North Africa.

overall_design: 49 samples were analyzed with the Illumina Human660W-Quad Genotyping BeadChips and are described herein.

first: Erika

last: Tamm

first: Francesco

last: Montinaro

first: Mait

last: Metspalu