title: Differential expression study in heterogeneous tumoral cell clones

city: Barcelona

first: Ana

last: Martín-Pardillos

address: Passeig de la Vall d'Hebron, 119-129

country: Spain

institute: Vall d´Hebron Institut de Recerca

summary: Cancer is a rapidly evolving, multifactorial disease that accumulates numerous genetic alterations. This results in phenotypic and molecular heterogeneity within the tumor, the complexity of which is further amplified through specific interactions between cancer cells. We aimed at dissecting the molecular mechanisms underlying the cooperation between different clones. We produced clonal cell lines derived from the MDA-MB-231 breast cancer cell line, using the UbC-StarTrack system, which allows tracking of multiple clones by colour: GFP C3, mKO E10 and Sapphire D7. Characterization of these clones in vitro revealed clear differences at genetic levels, that induce differences in growth rate, morphology and cytokine expression among them. In vivo, all clonal cell lines were able to form tumors, however an injection of an equal mix of clones, led to the formation of tumors where mKO E10 was almost depleted. Additionally, the mKO E10 clonal cell line showed a significant deficiency in the formation of lung metastasis. These results confirm that even in stable cell lines heterogeneity is present. In vitro the complementation of growth medium with medium or exosomes from either parental or clonal cell lines, increased the growth rate of the other clones. Co-growth and co-injection of mKO E10 and GFP C3 clonal cell lines increased the efficiency of invasion and migration, respectively. These findings support a model where the interplay of clones confers aggressiveness and may allow to identify factors involved in cellular communication which can be involved in clonal cooperation and be new targets preventing tumor progression.

overall_design:
Tumoral cell line has been labeled with a plasmid harboring a fluorescent protein gene (transposon). Cells has been sorted to single cell and cultured again (clones). We have observed different properties in each clone when they are injected in mice. We are interested in study if different gene expression among the clones, is the responsible of the heterogeneity in the properties.
We used microarray to study different gene expression among clones.
1.5 million cells were seeded in 100x17mm-dish in triplicate. After 72 hours cells were trypsinized and centrifuged. RNA was extracted using the PureLink™ RNA Mini Kit (ThermoFisher).


title: Expression data from reconstructed human epidermis

status: Public on Jul 01 2019

city: Kizugawa

first: Md

middle: Zobaer

last: Hasan

state: Kyoto

address: Kunimidai 6-5-4

department: Safety Design Center

country: Japan

institute: Rohto Pharmaceutical CO.,Ltd

summary:
Gene expression profiles of reconstructed human epidermis following exposure to lactic acid or methylparaben for 1, 6, or 24 hours
We used microarrays to study the changes in gene expression of reconstructed human epidermis after exposure to lactic acid or methylparaben during 1, 6, and 24 hours

overall_design: Reconstructed human epidermal tissue samples at 14 days of culture at the air-liquid interface were treated with either lactic acid or methylparaben, for 1, 6, or 24 hours. At the end of the experiments, the total RNA of each sample were extracted using the Qiagen RNeasy kit and processed for hybridization on GeneChip Human Gene 2.0 ST arrays (Affymetrix, 902112)

first: Hubaux

last: Roland

first: Hasan

last: Zobaer


title: ARPCs Can Revert Lps-Induced Endothelial-to-Mesenchymal Transition of Endothelial Cells

city: Bari

first: Fabio

last: Sallustio

state: Bari

address: Piazza G. Cesare N°11

country: Italy

institute: University of Bari

summary:
Endothelial dysfunction is a hallmark of  LPS-induced acute kidney injury (AKI).  Endothelial cells (EC) acquired a fibroblast-like phenotype and contributed to myofibroblasts generation through Endothelial to Mesenchymal Transition (EndMT) process. Noteworthy, ARPCs enhance tubular regenerative mechanism during AKI, but little is known about their effects on EC. Here we investigated whether ARPCs could prevent sepsis-induced EndMT and the related mechanism.
When activated by LPS, Human endothelial cells (EC) proliferated and decreased specific EC markers such as CD31 and VE-cadherin and up-regulated myofibroblast markers such as Collagen I and Vimentin. The co-culture with ARPCs normalized EC proliferation rate and abrogated the LPS-induced EndMT by restoring the high expression of EC markers and the low expression of myofibroblast markers. Gene set enrichment analysis showed that most of genes modulated in LPS-stimulated ARPCs belongs to cell activation and defense response pathways. In particular, among most up-regulated genes we found BPIFA2, SAA2, SAA4 and CXCL6. BPIFA2 is recently described as an early biomarker of AKI but little is known about its function in the kidney. The other genes are frequently involved in the response to bacterial infection and kidney injury. Finally, in a swine model of LPS-induced AKI, we observed an increase of CD133+ARPCs that expressed BPIFA2 respect to healthy pigs. Taken together, these results suggest an underestimate role of ARPCS in preventing endothelial dysfuncton by the production of several proteins. The identification of these molecules may offer novel strategies to protect endothelial compartment and promote kidney repair.

overall_design: Renal stem cells stimulated by LPS for 24 hours

first: Alessandra

last: Stasi

first: Rossana

last: Franzin

first: Claudia

last: Curci

first: Giuseppe

last: Castellano

first: Loreto

last: Gesualdo


title: Acsl mutants repress neuroblast development

city: BEIJING

first: DANQING

last: MENG

state: BEIJING

address: 1 BEICHEN WEST ROAD, CHAOYANG DISTRICT

department: Institute of Genetics and Developmental Biology

country: China

institute: Chinese Academy of Science

type: Expression profiling by high throughput sequencing

summary: We found Acsl mutants have deficient neuroblast development. Further experiment confirmed that genes related to cell cycle and pluripotency were supressed in Acsl mutants.

overall_design: We used wild-type and Acsl mutant flies to study the developmental changes in mutants.

first: Danqing

last: Meng

first: Yongqing

last: Zhang


title: Identification of NMD regulated genes in Nicotiana benthamiana

city: Godollo

first: Daniel

last: Silhavy

state: US and Canada only

address: Szent-Gyorgyi 4

department: Agricultural Biotechnology Intsitute

country: Hungary

institute: National Agricultural Research and Innovation Cen.

summary: Nonsense mediated decay (NMD) is a translation termination coupled quality control system. NMD identifies and degrades aberrant mRNAs containing premature termination codons, thereby preventing the accumulation of detrimental truncated proteins. NMD also controls the expression of several normal mRNAs and non-coding transcripts. RNA-seq assays were conducted to identify the NMD regulated genes in Arabidopsis. However, NMD targets have not been studied in other plants. To identify the conserved NMD targets, we wanted to identify the NMD regulated genes in Nicotiana benthamiana model species. Virus induced gene silencing was used to inactivate UPF1 NMD key factor in N. benthamiana, and then comparative RNA-seq experiment was carried out using UPF1-silenced and control–silenced plants. We found that in N. benthamiana significantly more genes are controlled by NMD than in Arabidopsis and that, surprisingly few conserved NMD targets can be recognized. These results suggest that while the mechanism of NMD is highly conserved, the set of NMD controlled genes can be quickly changed in plants.

overall_design: Comparative Illumina RNA-seq experiments were conducted from leaf samples isolated from three UPF1-silenced and three control silenced plants. Virus induced gene silencing was used to generate the silenced plants. In the control lines, only the phytoene desaturase (PDS) silencing monitor gene was inactivated, while in the UPF1-silenced plants, both PDS and UPF1 genes were silenced. Sequencing libraries were prepared from polyA enriched RNA samples.

first: Andor

last: Auber

first: Mátyás

last: Medzihradszky

first: Farkas

last: Kerényi

first: Dániel


title: Agilent data from Arabidopsis thaliana enriched guard cell tissues (GC) treated with high CO2 and darkness

city: Würzburg

first: Marcus

last: Dittrich

address: Biozentrum, Am Hubland

department: Biozentrum

country: Germany

institute: University of Würzburg

summary: Genes of the of Arabidopsis thaliana guard cells transcriptome that respond to high CO2 and darkness were identified and compared to the ABA- and low humidity treated samples of Experiment GSE41054 in Arabidopsis thaliana enriched guard cell samples.

overall_design: Total samples analysed are 16: 4 biological independent replicates each of Arabidopsis thaliana (COL-0) enriched guard cells : 4h light  vs. 2h light followed by 2h darkness at ambient CO2; 5h ambient CO2 (380ppm) vs. 1h ambient followed by 4h high CO2 (1000ppm).

first: Peter

last: Ache


title: Transcriptome Profiling of Wild-type vs. A1CF -/- Mouse Whole Kidneys

city: Chicago

first: Jennie

last: Lin

address: 303 E Superior

country: USA

institute: Northwestern University

summary:
Purpose: A1CF is an RNA binding protein that has not been extensively studied on a transcriptome-wide scale. Here we profile the whole kidneys of wild-type and A1cf knockout mice to detect differences in gene expression.
Methods: mRNA profiles of 6-8 week old wild-type and A1cf knockout mice were generated by deep sequencing using Illumina HiSeq 2500.  Reads that passed quality filters were aligned to mm10 genome and analyzed for differential expression using CuffDiff2 and DESeq2.
Results: We mapped reads to the mm10 genome and found a subset of fewer than 500 differentially expressed genes in A1CF deficiency.
Conclusions: Our study represents the first transcriptomic profiling of A1CF deficiency in the kidney.

overall_design: Kidney mRNA profiles of 6-8 week old wild-type and A1cf -/- mice were generated by deep sequencing of 6 biological replicates in each group, using Illuminar HiSeq 2500


title: Genome-scale DNA methylation analysis of tissue-of-origin of plasma cell-free DNA

city: Chengdu

first: xiaomeng

last: liu

address: No.55,Section 4,South Renmin Road

country: Colombia

institute: Sichuan Cancer Hospital & Institute, Sichuan Cancer Center

type: Methylation profiling by high throughput sequencing

summary: Current methods for mapping the tissue-of-origin of circulating cell-free DNA (cfDNA) are still insufficient. Here, we have extended a previously developed methylated CpG tandems amplification and sequencing (MCTA-Seq) method for quantitative analysis of tissue-of-origin of plasma cfDNA. By comparing paired plasma cfDNA and white blood cell genomic DNA, we have demonstrated that the liver is the major non-hematopoietic tissue contributing to plasma cfDNA in healthy adults, accounting for approximately 2%. Furthermore, we have detected changes in liver-derived DNA in patients with benign  liver diseases and increases in pancreas-derived DNA in acute pancreatitis patients. Interestingly, our results suggest that DNA derived from pathological tissues makes a minor contribution to the increased cfDNA in many clinical cases. Finally, we have identified a tissue-specific hypermethylated cfDNA marker located in the intragenic regions of tissue-specifichighlyexpressed genes. This study represents valuable progress in the field of cfDNA and offers promise for clinical research and medical diagnostics using the described method.

overall_design: We performed MCTA-Seq on paired cfDNA and WBC gDNA obtained from 14 healthy individuals to find the significantly differentially methylated CGCGCGGs(dmCGCGCGGs) between plasma and WBC. To obtain the tissue-specific methylation pattern, we performed MCTA-Seq on eight major tissues, including liver, lung, stomach, colon, kidney, pancreas, muscle and skin. We found that most plasma dmCGCGCGGs were hypermethylated in the liver. Next, we sought to quantify the non-hematopoietic tissue DNA fractions in plasma cfDNA using deconvolution analysis. We quantify the tissue DNA fractions in plasma cfDNA from healthy individuals and non-malignant liver disease patients.

first: Xiaomeng

last: Liu

first: Jie

last: Ren

last: Luo

first: Lu

last: Wen

first: Fuchou

last: Tang

first: Jirui

last: Peng


title: Gene expression in mouse RPE in wild-type and MFRP mutants

city: Cleveland

first: Joseph

last: Fogerty

state: OH

address: 9500 Euclid Ave, i3-179

department: Ophthalmic Research

institute: Cleveland Clinic - Cole Eye Institute

summary: We compared gene expression in retinal pigment epithelium (RPE) isolated from wild-type mice and two different membrane-type frizzled-related protein (Mfrp) mutants. The rd6 mutant is described in Hawes, et al. (2000) IOVS 41:3149-3157. The 174delG mutant is described in Fogerty, et al (2011) IOVS 52:7256-7266.

overall_design: Total RNA was collected from RPE and hybridized to a mouse whole genome array.

last: Besharse


title: Impact of ERBB inhibitors on erythroid progenitors

city: Boston

first: Melissa

last: Kinney

state: MA

address: 1 Blackfan Circle

institute: Boston Children's Hospital

summary: RNA-seq was performed to determine the genome-wide changes in expression upon treatment with different classes of ERBB inhibitors

first: James

last: Collins

first: Patrick

last: Cahan

first: Douglas

last: Lauffenburger

first: George

last: Daley


title: The olfactory molecular snapshot of Tg2576 mice at early stages of amyloid pathology

city: Pamplona

first: Victor

last: Segura

state: Navarra

address: Avda. Pío XII, 55

department: Unit of Proteomics, Genomics and Bioinformatics

institute: FIMA

summary: Olfaction is often deregulated in Alzheimer's disease (AD) patients, being also impaired in transgenic Tg2576 AD mouse model, which overexpress the Swedish mutated form of human amyloid precursor protein (APP). However, little is known about the molecular mechanisms that accompany the neurodegeneration of olfactory structures in Tg2576 mice. For that, we have applied proteome- and transcriptome-wide approaches to probe molecular disturbances in the olfactory bulb (OB) dissected from Tg2576 mice (2, and 6 months of age) respect to age-matched wild-type (WT) littermates.

overall_design: Olfactory bulbs from 3 WT mice vs. olfactory bulbs from 3 Tg2576 transgenic mice in each time point.

first: Enrique

last: Santamaría


title: Corpus luteum (CL) transcriptome of non pregnant bitches

city: São Paulo

first: Paula

middle: de Carvalho

last: Papa

state: São Paulo

address: Av. Prof. Dr. Orlando Marques Paiva, 87

department: Surgery

country: Brazil

institute: School of Veterinary Medicine and Animal Science, University of São Paulo

summary:
Purpose:We used transcriptome sequencing to characterize CL function during diestrus in non-pregnant female dogs. The aim of this study was to identify genes (and their respective pathways) that are differentially expressed (DE) during diestrus in order to obtain a broader understanding of CL function and developmental control.
Methods:The CL were obtained from non-pregnant bitches (n=30) on days 10, 20, 30, 40, 50 and 60 (n=3/group) post-ovulation (p.o.). Sequencing was performed on an Illumina HiSeq 2000 using the paired-end reads protocol and the Illumina TruSeq PE cluster kit v3-cBotHS (Illumina). The reads were mapped against the reference genome (Canis_familiaris. CanFam 3.1.75.dna.toplevel.fa) using TopHat v2.0.9, and the transcripts were assembled using Cufflinks and identified by their Ensembl name. The relative abundance of transcripts of RNA-seq fragments was measured by Cufflinks in fragment per kilobase of exon model per million mapped reads (FPKM). We performed real-time PCR (qPCR) to validate the RNAseq results using Taqman assays.
Results: A total of 771,208,718 reads (approximately 42 million per sample) was generated, with size of 100 bp. The software TopHat v2.0.9 assigned the reads to 34,408 genes, of which 9,000 were not annotated in the canine genome. 5,116 genes were differentially expressed (DEGs), although 1,106 of those were not yet annotated in the canine genome. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that many of the DE genes were related to cell proliferation, cell survival, angiogenesis, and immune system, which may regulate luteal formation and regression.
Conclusion: This study provides fundamental data that could prove useful in reproductive research regarding the regulation of CL lifespan.

overall_design: Corpus luteum mRNA profiles collected during diestrus on days 10,20,30,40,50 and 60 post-ovulation (n=3/group) were generated by deep sequencing, using Illumina HiSeq 2000.

first: Ana

middle: P

last: Cardoso

first: Renata

middle: S

last: Silva

first: Liza

middle: M

last: Sousa

first: Ines

middle: C

last: Giometti

first: Jochen

last: Bick

first: Stefan

last: Bauersachs


title: Interactome (iCLIP) and Translatome ( Polysome profiling) of Musashi 2 (MSI2) targets in K562

city: NEW HAVEN

first: MANOJ

last: PILLAI

state: CT

address: 300 GEORGE STREET #786

institute: YALE UNIVERSITY

summary: iCLIP was performed for FLAG-tagged MSI2 in K562 cells. Polysome profiling was performed for MSI2-knockdown and control shRNA K562 cells

overall_design: iCLIP and Polysome profiling

first: Manoj

last: Pillai


title: The gene regulation of miR-10a* in lung cancer (mRNA)

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

summary:
This study aimed to investigate the metastasis-related prognostic gene signature in lung cancer. We started from the genowide miRNAs profiling of 16 lung adenocarcinoma cells. We identified that miR-10a* is an invasion-based prognostic gene in lung adenocarcinoma.
Besides, we used expression beadsarray to identify the global gene alterations in HOP-62 cells after ectopic introducing miR-10a* and ectopic expressing HDAC5 genes.

overall_design: All 16 lung adenocarcinoma cells were parental. Ectopic introducing miR-10* mimics and expressing HDAC5 in HOP-62 cells.

first: Pin-Yen

last: Hsu

first: Bing-Ching

last: Ho

first: Hsuan-Yu

last: Chen


title: The gene regulation of miR-10a* in lung cancer (microRNA)


title: The gene regulation of miR-10a* in lung cancer

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

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

overall_design: Refer to individual Series


title: NF-Y controls fidelity of transcription initiation at gene promoters through maintenance of the nucleosome-depleted region

city: RTP

first: Raja

last: Jothi

state: NC

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

institute: National Institutes of Health

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Faithful transcription initiation is critical for accurate gene expression, yet the mechanisms underlying specific transcription start site (TSS) selection in mammals remain unclear. Here, we show that the histone-fold domain protein NF-Y, a ubiquitously expressed transcription factor, controls the fidelity of transcription initiation at gene promoters. We report that NF-Y maintains the region upstream of TSSs in a nucleosome-depleted state while simultaneously protecting this accessible region against aberrant and/or ectopic transcription initiation. We find that loss of NF-Y binding in mammalian cells disrupts the promoter chromatin landscape, leading to nucleosomal encroachment over the canonical TSS. Importantly, this chromatin rearrangement is accompanied by upstream relocation of the transcription pre-initiation complex and ectopic transcription initiation. Further, this phenomenon generates aberrant extended transcripts that undergo translation, disrupting gene expression profiles. These results demonstrate that NF-Y is a central player in TSS selection in metazoans and highlight the deleterious consequences of inaccurate transcription initiation.

overall_design: MNase-Seq, RNA-Seq, Start-Seq, Ribo-Seq, and ATAC-seq experiments on control knockdown (KD) and NF-YA KD mouse ESCs.

first: A

middle: J

last: Oldfield

first: T

last: Henriques

middle: B

last: Burkholder

first: D

last: Paulet

first: C

last: Cinghu

first: P

last: Yang

first: B

last: Scruggs

middle: A

last: Lavender

last: Kumar

last: Bennett

first: E

last: Rivals

first: K

last: Adelman

first: R


title: Tpl-2 small molecule project

city: South San Francisco

first: Mark

last: McCreary

state: California

address: 1 DNA Way, MS 93

department: Bioinformatics

institute: Genentech

summary: Tpl-2 is a serine/threonine kinase that has been studied extensively in monocytes. Tpl-2 is believed to phosphorylate MEK1/2, which is upstream of ERK1/2, and regulates inflammatory gene expression in response to TLR and IL-1b receptor signaling. In the course of performing proof-of-concept studies using a small molecule inhibitor (SMI) of Tpl-2, we were surprised to see the inhibitor affect cytokine production in human neutrophils. Unlike human monocytes, which respond at least some degree to both Tpl-2 and MEK inhibitors, neutrophils showed a disconnect between Tpl-2 and MEK. A panel of genes in this cell type can be fully blocked by a Tpl-2 SMI, and yet show no response to a MEK SMI, suggesting Tpl-2 mediates its effect through substrates other than MEK.

overall_design: The goal of this study is to compare the gene expression profiles of LPS-treated human neutrophils treated with vehicle, Tpl-2 SMI, or MEK SMI, in order to shed light on the MEK-independent arm of the Tpl-2 response. Purified neutrophils from 5 healthy donors were split into 4 groups: Unstimulated neutrophils, vehicle treated for 6.5 hrs; Neutrophils pretreated 30 min with vehicle, then stimulated 6 hrs with 10 ng/ml LPS; Neutrophils pretreated 30 min with G-432, then stimulated 6 hrs with 10 ng/ml LPS; and Neutrophils pretreated 30 min with G-573, then stimulated 6 hrs with 10 ng/ml LPS. This yields a total of 20 samples (5 donors x 4 conditions).

first: Kate

last: Senger

first: Victoria

last: Pham

first: Eugene

last: Varfolomeev

first: Jason

last: Hackney

first: Jenna

last: Collier

first: Kajal

last: Hamidzhadeh

first: Zhiyu

last: Huang

first: Ivan

last: Peng

first: Cesar

last: Corzo

first: Francesca

last: Setiadi

first: Youngsu

last: Kwon

first: Yonglian

last: Sun

first: Patrick

last: Caplazi

first: Surinder

last: Jeet

first: Kai

middle: H

last: Barck

first: Anna

first: Connie

last: Ha

first: Jeremy

last: Stinson

first: Joseph

last: Guillory

first: Lucinda

last: Tam

first: Zora

last: Modrusan

first: Brent

last: McKenzie

first: Michael

last: Townsend

first: Richard

last: Carano

first: Søren

last: Warming

first: Domagoj

last: Vucic

last: DeVoss

first: Wyne

last: Lee

first: Jennie

middle: R

last: Lill

first: Ali

last: Zarrin


title: Regulation of germline gene expression in C. elegans germline stem cells.

city: Madison

first: Elena

last: Sorokin

state: WI

address: 433 Babcock Drive

department: Biochemistry

institute: UW-Madison

summary: ChIP-Seq study to understand regulation of germline stem cell gene expression by immunoprecipitation of stem-cell factor Notch and associated transcriptional cofactor LAG-1 in C. elegans.

overall_design: ChIP-Seq of Notch protein plus input DNA samples in quadruple biological replicates; LAG-1 cofactor IP and input in quadruple replicates; control Flag and Myc-tagged GFP IP and input in triple biological replicates.

first: Erika

last: Sorensen

first: Amy

last: Groth

first: Judith

last: Kimble


title: Tpl-2 and MEK small molecule inhibitors

first: Mark

last: McCreary


title: Multifaceted stoichiometry control of bacterial operons revealed by data-independent acquisition mass spectrometry

city: guangzhou

first: zhang

last: hong

state: guangdong province

address: Huangpu Boulavard West Jinan uinversity

institute: zhanghong

summary: More than half of the protein-coding genes in bacteria are organized in polycistronic operons composed of two or more genes. Whether the operon organization maintains the stoichiometric expression of the genes within an operon remain under debate. In this study, we performed a label-free data-independent acquisition hyper reaction monitoring mass-spectrometry (HRM-MS) experiment to quantify the Escherichia coli proteome in exponential phase and quantified 93.6% of the cytosolic proteins, covering 67.9% and 56.0% of the translating polycistronic operons in BW25113 and MG1655 strains, respectively. We found the shorter operons tend to be more tightly controlled for stoichiometry than longer operons, and those operons for metabolic pathways are less controlled for stoichiometry compared with operons for protein complexes, illustrating the multifaceted nature of the operon-wise regulation: the operon-wise unified transcriptional level and gene-specific translational level. This multi-level regulation benefits the host by optimizing the efficiency of the productivity of metabolic pathways and maintenance of different types of protein complexes.

overall_design: RNA-seq and Ribo-seq of E. coli strain BW25113 in M9 minimal medium

first: Hong

last: Zhang

first: Gong


title: The  transcriptional basis of a developmental transition from brown to white adipose tissue.

city: Saint Lucia, Brisbane

first: Tony

last: Vuocolo

state: Queensland

address: 306 Carmody Road

country: Australia

institute: CSIRO

summary: Next Generation Sequencing (NGS) was used to measure the levels of gene transcription in perirenal adipose tissue (PRAT) in late gestation sheep fetuses (~ 2 weeks before birth) and in 12 week old lambs.

overall_design: mRNA profiles of PRAT from sheep fetuses at 132 days of gestation (132 d post conception (dpc); term =150±3d) and lambs 80 days after birth  were generated by deep sequencing using Illumina HiSeq2000 sequencing platform. Three biological replicates for each developmental timepoint were analysed. The sequence reads that passed quality filters were mapped to sheep genome  ENSEMBL gene models for assembly OARv3.1.74 using the mapping protocol in the CLC Genomics Workbench (v7.0). Differential expression was measured using the method EdgeR implemented as DGE in CLCBio Genomics Workbench.

first: Ross

last: Tellam


title: Short-term Akt activation in cardiac muscle cells improves contractile dysfunction in failing hearts.

city: Ulm

first: Stephan

last: Schiekofer

address: Robert Koch Str. 8

department: Department of Internal Medicine I

institute: Ulm University

summary:
Akt is a serine/threonine protein kinase that is activated by a variety of growth factors or cytokines in a PI3-kinase dependent manner. Using a conditional transgenic system in which Akt signaling can be turned on or off in the adult heart, we have recently demonstrated that short-term Akt activation induces a ‘physiological’ form of cardiac hypertrophy with enhanced coronary angiogenesis and maintained contractility. Here we tested the hypothesis that induction of physiological hypertrophy by short-term Akt activation might improve contractile function in failing hearts. When Akt signaling was transiently activated in murine hearts with impaired contractility induced by pressure overload or adriamycin treatment, contractile dysfunction was attenuated in both cases. Importantly, improvement of contractility was observed before the development of cardiac hypertrophy, indicating that Akt improves contractile dysfunction independently of its growth-promoting effects. To gain mechanistic insights into Akt-mediated positive inotropic effects, transcriptional profiles in the heart were determined in a pressure overload-induced heart failure model. Biological network analysis of differentially expressed transcripts revealed significant alterations in the expression of genes associated with cell death, and these alterations were reversed by short-term Akt activation. Thus, short-term Akt activation improves contractile dysfunction in failing hearts. This beneficial effect of Akt on contractility is hypertrophy-independent and may be mediated in part by inhibition of cell death associated with heart failure.
Keywords: transgenic mice, Akt1, cardiac hypertrophy after ascending aortic constriction and contractile dysfunction, DNA microarrays

overall_design: Transcriptional profiles were determined in pressure overload-induced heart failure models. Mice were sacrificed at predetermined time points, and hearts were excised and snap-frozen in liquid nitrogen. RNA extraction, cDNA synthesis, biotinylated cRNA preparation, and hybridization of cRNA to microarrays (Affymetrix GeneChip Mouse Expression Set 430A and B) were performed. Data were obtained at three time points (before AAC, 4 weeks after AAC, and 6 weeks after AAC (2 weeks after Akt activation)), and three independent sets of hybridizations were performed at each time point.

first: Ichiro

last: Shiojima

first: Kaori

last: Sato

first: Gennaro

last: Galasso

first: Kenneth

last: Walsh


title: Genome wide chromatin modification associated with the developmental transition from brown to white adipose tissue

summary: Chromatin immunoprecipitation coupled with Next Generation Sequencing (NGS) was used to find regions enriched for  the histone modifications, H3K27me3, H3K27ac and H3K4me3 in perirenal adipose tissue  in late gestation sheep fetuses, (i.e.~ 2 weeks before birth) and 12 week old lambs.  This was undertaken to investigate the epigenetic changes that occur as a result of development during this key period where the perirenal adipose tissue transitions from a primarily brown adipose tissue state to a primarily white adipose tissue state.  The former tissue has a primary role in maintaining thermogenesis in new-born mammals while the latter acts as an energy storage vehicle that enhances survival when food is limiting. Both tissues are involved in maintaining energy homeostasis in adults and are strongly implicated in chronic metabolic diseases associated with obesity in humans. Little is known about this developmental process in terms of mechanism and changes in gene expression.  This developmental contrast revealed that this developmental transition is associated with large changes in chromatin modifications associated with the morphological change of the tissue during this brief period.

overall_design: Genome wide chromatin modification  profiles  for H3K27me3, H3K27ac and H3K4me3 of perirenal adipose tissue from sheep fetuses at 132 days of gestation (132 d post conception (dpc); term =150±3d) and lambs 80 days after birth  were generated by deep sequencing using Illumina GA11X or HiSeq2000 sequencing platform. Two biological replicates for each developmental timepoint were analyzed except for H3K4me3, where n=3/gp was used for the lamb sample and n=2/gp for the fetal sample. The sequence reads that passed quality filters were mapped to sheep genome  assembly OARv3.1.74 using the mapping protocol in the CLC Genomics Workbench (v7.0).


title: MEK-dependent and -independent signaling events downstream of Tpl-2

summary: Comparison of Tpl-2 small molecule inhibitor (SMI) versus MEK SMI activities in LPS-treated human monocytes will reveal a subset of genes that require Tpl-2 but are independent of MEK. Tpl-2 is a highly conserved (94% human versus mouse) serine-threonine kinase expressed in cells important to the inflammatory response, including monocytes, macrophages, dendritic cells, and B/T cells. The role of Tpl-2 in monocytes and macrophages has been especially well-studied. It has been shown in these cells that Tpl-2 is required for the expression of cytokines in response to Toll-like receptor ligands, including LPS. In resting cells, Tpl-2 forms a complex with p105 and ABIN-2. Upon stimulation, this complex dissociates. Dissociated p105 is processed to p50, which impacts transcription. Dissociated Tpl-2 phosphorylates MEK, which, in turn, phosphorylates ERK. ERK activates the transcription factor AP-1 and its downstream gene targets. An open question in the field is whether Tpl-2 acts solely through MEK to drive gene expression, or does Tpl-2 have any MEK-independent targets. Answering this question is important both for understanding basic Tpl-2 biology as well as its role in disease. Based on published data, Tpl-2 is important for inflammatory cytokine production, and in animal models where these cytokines contribute to disease (septic shock, IBD), blocking Tpl-2 ameliorates disease symptoms. We have a highly selective SMI of Tpl-2 that effectively blocks cytokine production in purified human monocytes. This SMI can block production of the same cytokines that a MEK inhibitor blocks, which is expected given that Tpl-2 lies upstream of MEK. However, the MEK SMI only partially inhibits certain cytokines, while the Tpl-2 SMI fully blocks them, suggesting there are additional factors downstream of Tpl-2 that are not MEK-dependent.

overall_design: Human monocytes will be purified from buffy coats (total of 5 donors) using a negative selection kit (Miltenyi 130-091-153) and plated at 1 x 10^6/ml in RPMI + 10% FBS + 100 ng/ml rhM-CSF. The next day, media will be aspirated and substituted with low-serum media (RPMI + 0.5% FBS). Tpl-2 and MEK inhibitors will be added to a subset of the plates at concentrations of 2.8 uM and 0.31 uM, respectively (the amounts required to fully inhibit the expression of several cytokines based on our cell-based assays), and allowed to be taken up by the cells for 1 hr. Then, 10 ng/ml of LPS will be added to a subset of the plates to activate the cells. After 6 hrs, RNA will be harvested from all of the plates. Supernatants will be saved and analyzed by ELISA to confirm cell activity/cytokine expression.

first: Kate

last: Senger

first: Victoria

last: Pham

first: Eugene

last: Varfolomeev

first: Jason

last: Hackney

first: Jenna

last: Collier

first: Kajal

last: Hamidzhadeh

first: Zhiyu

last: Huang

first: Ivan

last: Peng

first: Cesar

last: Corzo

first: Francesca

last: Setiadi

first: Youngsu

last: Kwon

first: Yonglian

last: Sun

first: Patrick

last: Caplazi

first: Surinder

last: Jeet

first: Kai

last: Barck

first: Anna

first: Connie

last: Ha

first: Jeremy

last: Stinson

first: Joseph

last: Guillory

first: Lucinda

last: Tam

first: Zora

last: Modrusan

first: Brent

last: McKenzie

first: Michael

last: Townsend

first: Richard

last: Carano

first: Søren

last: Warming

first: Domagoj

last: Vucic

last: DeVoss

first: Wyne

last: Lee

first: Jennie


title: Expression analysis of plants with altered GEM mRNA levels, with and without ABA treatment (2 hours).

city: Madrid

first: Crisanto

last: Gutierrez

address: Nicolas Cabrera 1

department: Genome Dynamics and Function

institute: Centro de Biologia Molecular Severo Ochoa

summary: Investigation of whole genome gene expression levels of plants with altered GEM mRNA levels, with and without ABA treatment (2 hours).

overall_design: A twelve whole genome chip study using total RNA recovered from two separate biological replicates of wild-type plants, with altered GEM mRNA levels, with and without ABA treatment (2 hours).

first: Nuria

last: Mauri


title: Expression Data for Cisplatin Treated Dorsal Root Ganglia from A/J and C57BL/6J Mice

city: Baltimore

first: Susan

middle: G

last: Dorsey

state: MD

address: 655 W. Lombard Street, Room 727A

department: University of Maryland School of Nursing

institute: University Of Maryland, Baltimore

summary:
Peripheral sensory neuropathy is a common complication to cisplatin treatment in cancer patients. Multiple signaling pathways are likely to be implicated in the pathophysiology, there are no explicit treatments and little is known about predictive factors associated with the onset or progression of cisplatin induced peripheral neuropathy. The transcriptional profiles of differentially senesitive strains of dorsal root ganglion across two inbreed strain of mice will promote better understanding of progression and risk factors assocciated with cisplatin induced peripheral neuropathy. Peripheral neuropathy was induced with a bi-weekly treatment of 4mg/kg cisplatin.
We used microarrays to detail the transciptional profile underlying cisplatin induced peirperal neuropathy in two differentailly sensitve inbreed strains of mice: A/J and C57BL/6J

overall_design: L4-L5 dorsal root ganglia from untreated, vehicle treated and cisplatin treated mice for one and four weeks from A/J and C57BL/6J mice

first: Cameron

last: Lassiter


title: Blocking oncogenic Ras-induced β-catenin degradation and prosenescent inflammation redirects premature senescence to mesenchymal transformation

status: Public on Jun 30 2019

city: Guangzhou

first: junchao

last: Cai

address: zhongshan er road

institute: Sun-yat sen university

sample_organism:
Homo sapiens
Mus musculus


title: MiRNA profiling of adult Mouse Grey Matter versus GFAP-HaV12-Ras Astrocytoma (tumor)

city: San Francisco

first: Anders

middle: I

last: Persson

state: CA

address: 675 Nelson Rising Lane

department: Neurology

institute: University of California San Francisco

summary: The goal of the experiment was to determine global miRNA expression in adult mouse neocortex versus mouse astrocytoma tissue (GFAP-HaV12-Ras)

overall_design: nCounter nanostring miRNA profiling assay (version 1.3) of postnatal day 60 mouse neocortex versus tumor tissue from postnatal day 60-150 astrocytoma tissue (GFAP-HaV12-Ras)

first: Hanna

last: Sabelstrom


title: Blocking oncogenic Ras-induced β-catenin degradation and prosenescent inflammation redirects premature senescence to mesenchymal transformation (miRNA expression)

summary: We constructed LSL-KrasG12D/+ and Spc-Cre;LSL-KrasG12D/+ mice to investigate the role of microRNA in the pathogenesis of lung cancer

overall_design: LSL-KrasG12D/+ and Spc-Cre;KrasLSL-G12D/+ mice at 9 months were anesthetized and resected for lung tissue, followed by PBS wash for 3 times.  The lung tissues from indicated mice were subject to RNA extraction and human microRNA array detection to identify those miRNAs having identical sequences in both human and mouse.

first: Junchao

first: Mengfeng

last: Li


title: The epigenetic and transcriptional basis of the developmental transition from brown to white adipose tissue

first: Tony

last: Vuocolo


title: Nuclear speckles as a key regulator for the 3D genome organization [HiC]

city: Shanghai

first: Bo

last: Wen

address: 130 DongAn Road

department: Institutes of Biomedical Sciences

institute: Fudan University

summary: The nuclei of eukaryotes contain various higher-order chromatin architectures and nuclear bodies (NBs), which are critical for proper nuclear functions. By using mouse hepatocytes as the model, we knocked-down SRRM2, a core protein component scaffolding NSs, and performed Hi-C experiments to examine genome-wide chromatin interactions. We found that Srrm2 depletion disrupted the NSs and changes expression of about 1,000 genes. The intra-chromosomal interactions were decreased in type A (active) compartments and increased in type B (repressive) compartments. Furthermore, upon Srrm2 knockdown, the insulation of TADs was decreased specifically in active compartments, and the most significant reduction was found in the A1 sub-compartments. We showed that disruption of NSs by Srrm2 knockdown led to a global decrease of chromatin interactions in active compartments, indicating critical functions of NSs in the organization of the 3D genome.

overall_design: HiC data in Control and SRRM2 KD AML12 cells.

first: S

last: Hu

first: P

last: Lv

first: B


title: Nuclear speckles as a key regulator for the 3D genome organization [RNA-Seq]

overall_design: RNAseq data in Control and SRRM2 KD AML12 cells.


title: Epigenome-wide study of widespread hypomethylated loci associated with early-onset preeclampsia

first: Xinzhi

last: Zhao

address: No. 138, Yixueyuan Rd.

department: Fudan University

institute: Institutes of Biomedical Sciences

summary: For understanding the relationship of preeclampsia and placental methylation,we performed an epigenome-wide association study in a Chinese cohort containing 22 early-onset preeclampsia patients and 20 normal controls. We used Illumina Infinium HumanMethylation450k BeadChip for detecting the methylation level, and used placental genomic DNA as sample. most of the significant CpG sites were hypomethylated in EOPE in the Chinese cohort.

overall_design: placental genomic DNA from 22 early-onset preeclampsia patients and 20 normal controls was bisulfate converted in 450k platform and measured with Illumina HiScan.

first: Teng

last: Wang

first: Yuqian

last: Xiang


title: Investigation of the timing of secondary small RNA biogenesis during programmed DNA elimination in Tetrahymena

city: Montpellier

first: Kazufumi

last: Mochizuki

address: 141 rue de la Cardonille

country: France

institute: Institute of Human Genetics, CNRS

summary: Signal amplification of the initial small RNA trigger is important to ensure the silencing of repetitive transposable elements (TEs). Curiously, secondary small RNA biogenesis occurs by various mechanisms that are coupled with distinct steps of TE silencing in different eukaryotes, such as nucleolytic cleavage of TE transcripts, recruitment of RNA-dependent RNA polymerase, and heterochromatin-directed transcription. How such a variety of small RNA amplification mechanisms has evolved has not been thoroughly elucidated to date. Ciliated protozoa perform small RNA-directed programmed DNA elimination of thousands of TE-related internal eliminated sequences (IESs) in the newly developed somatic nucleus. In the ciliate Paramecium, secondary small RNAs are produced after primary small RNAs induce the excision of IESs. To examine whether such post-excision production of secondary small RNAs is conserved, we investigate the causality between the excision of IESs and the biogenesis of secondary small RNAs in another ciliate, Tetrahymena. We show that secondary small RNAs accumulate at least a few hours before their derived IESs are excised and that DNA excision is dispensable for their biogenesis in this ciliate. Therefore, unlike the situation in Paramecium, small RNA amplification occurs prior to IES excision in Tetrahymena. This study reveals remarkable mechanistic diversity of secondary small RNA biogenesis mechanisms, even among ciliates showing similar DNA elimination processes, and thus raises the possibility that the evolution of TE-targeting small RNA amplification can be traced by investigating the DNA elimination mechanisms of ciliates.

overall_design: To understand the timing of secondary small RNA biogenesis during programmed DNA elimination in Tetrahymena, 1) we compared the timing of the appearance of small RNAs that uniquely map Type-B IES with that of excised IES circles (IES5, IES737, IES4092); and 2) we analyzed small RNA biogenesis in the absence of TPB2.

first: Masatoshi

last: Mutazono

first: Tomoko

last: Noto


title: Abundance and localization of human UBE3A isoforms

first: Carissa

middle: L

last: Sirois

address: 1500 Highland Ave T515

department: Waisman Center

institute: University of Wisconsin-Madison

summary: We performed ChIPseq for UBE3A to determine whether it had any direct binding to chromatin in human cells

overall_design: ChIPseq for UBE3A and H3K27ac was performed in H9 hESC-derived neuronal progenitors, H9 hESC-derived neurons, and UBE3A-null H9 hESCs using two antibodies against UBE3A.

first: Stormy

last: Chamberlain

first: Justin

last: Cotney

first: Noelle

last: Germain


title: U-BIOPRED blood transcriptomics from children with asthma or wheeze

city: Stevenage

first: Adam

last: Taylor

address: Medicine Research Center

country: United Kingdom

institute: GalxoSmithKline

summary:
Asthma is an inflammatory disease of the airways characterised by episodic airway obstruction resulting in cough, episodic shortness of breath. It is, and is clinically and physiologically heterogeneous. It is estimated that around 300 million people worldwide have the diseaseare diagnosed with asthma, including up to 20% of children (Asher et al, 2006), with 5–10% of these children believed to have severe or difficult-to-treat asthma. Asthma has often been classified in terms of severity and based on clinical diagnostic criteria, but it is now apparent that the heterogeneity that exists at the physiological level is also a feature of the underlying pathological mechanisms (Lotvall et al, 2011).   The aim of this study was to identify blood transcriptomics profiles for children diagnosed with asthma or wheeze, and establish whether these profiles suggested endotypes or mechanisms that could underlie disease, or be related to disease severity, in these children. Importantly, given that children are currently treated with the same medicines as adults, we also aimed to compare profiles of children to those of adults with asthma to help determine whether efforts should be directed to the development of medicines targeting pathways and mechanisms that may be unique to children. To this end, we used gene transcriptome data generated from blood samples from adults and children from the U-BIOPRED consortium to ask how similar or different the differential gene expression profiles were between groups of adults and pre-school or school-aged children with severe or mild-moderate asthma (or wheeze for the pre-school aged children) using current definitions.
The Unbiased Biomarkers for the Prediction of Respiratory Disease Outcomes (U-BIOPRED) project was set up as a public-private partnership within the framework of the Innovative Medicines Initiative (IMI), engaging academia, the pharmaceutical industry and patient groups. The goal of this investigation was to identify transcript fingerprints in whole blood that characterize patients with severe asthma and to determine whether subgroups of severe asthmatics can be identified.

overall_design: This is a cross-sectional study of school age children with severe asthma or mild moderate asthma, and pre-school age children with severe wheeze or mild moderate wheeze. Blood was collected at baseline.

first: Karen

last: Affleck

first: John

last: Riley

first: Stewart

last: Bates

first: Stelios

last: Pavlidis

first: Louise

last: Fleming

first: Ian

last: Adcock

first: James

last: Schofield

first: Charles

last: Auffray

first: Jeanette

last: Bigler

first: Hans

last: Bisgaard

first: Michael

last: Boedigheimer

first: Klaus

last: Bonnelykke

first: Andrew

last: Bush

first: K

middle: F

last: Chung

first: Ratko

last: Djukanovic

first: Urs

last: Frey

first: Stephen

last: Fowler

first: Simone

last: Hashimoto

first: Anna

middle: T

last: Bansal

first: Gunila

last: Hedlin

first: X

first: Clare

last: Murray

last: Nordlund

first: Dominick

last: Shaw

first: Florian

last: Singer

first: Peter

last: Sterk

last: Sousa

first: W

last: Van Aalderen

first: Scott

last: Wagers


title: Blocking oncogenic Ras-induced β-catenin degradation and prosenescent inflammation redirects premature senescence to mesenchymal transformation (mRNA expression)

first: junchao

last: Cai

summary: This experiment is designed to evaluate gene expression alteration and significant pathway(s) following HRasV12 transduction in BEAS-2B the immortalized human bronchial epithelial cell line, which causes senescence-like phenotype.

overall_design: Total RNA were extracted from BEAS-2B cells stably transduced with HRasV12 or vector control and subjected to whole transcripts microarray (Agilent_HUMAN_G3V2) analysis.  Expression profiling of coding RNA is provided.

first: Junchao

first: Mengfeng

last: Li


title: Coordinate regulation of expression of SdsR toxin and its downstream pphA gene by RyeA antitoxin expression in Escherichia coli

city: Daejeon

first: Younghoon

last: Lee

address: KAIST 291 Daehak-ro, Yuseong-gu

department: Chemistry

country: South Korea

institute: KAIST

summary:
RNA-seq analysis of cells with an ryeA or sdsR promoter mutation
In Escherichia coli, SdsR and RyeA, a unique pair of mutually cis-encoded sRNAs, act as toxin and antitoxin, respectively. They are located in the same intergenic region, but transcribed in bidirectional way. Expression of SdsR is reciprocally related to that of RyeA; however, it remains unclear how their syntheses are regulated by each other.
Here, using sdsR and ryeA promoter mutant strains, we characterized biosynthesis of the two sRNAs during growth and their coordinate regulation. RyeA transcription occurs even when cells enter the stationary phase, but its apparent expression is restricted to exponentially growing cells because of its degradation by SdsR. The appearance of SdsR was similarly delayed due to its RyeA-mediated degradation. We also found that the sdsR promoter was mostly responsible for transcription of the downstream pphA gene encoding a phosphatase and that pphA mRNA was synthesized through transcriptional read-through over the sdsR terminator. Transcription from the sigma70-dependent ryeA promoter inhibited transcription from the ?S-dependent sdsR promoter through transcriptional interference. This transcription inhibition also downregulated pphA expression, but RyeA itself did not downregulate pphA expression. Our results show that expression of the toxin SdsR and its downstream pphA gene are regulated by expression of the antitoxin RyeA, but differently.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: E. coli cells (wild type, ryeA promoter mutant, and sdsR promoter mutant) were grown at 37℃ for 3 h and 8 h post-inoculation, and total RNAs were extracted using an RNeasy mini kit (Qiagen). For DNase treatment of 10 μg of total RNA, a Turbo DNA free kit (Ambion) was used according to the manufacturer’s guidelines. All RNA sequencing and alignment procedures were conducted by ChunLab. The Ribo-Zero rRNA removal kit (Epicentre) was used for ribosomal RNA depletion according to manufacturer instructions. Libraries for Illumina sequencing were generated using a TruSeq Stranded mRNA sample prep kit (Illumina) according to the manufacturer’s protocol. RNA sequencing was performed on the Illumina HiSeq 2500 platform using single-end 50 bp sequencing. The sequence data for the reference genome were retrieved form the NCBI database. Quality-filtered reads were aligned to the reference genome sequence using Bowtie2. The relative transcript abundance was measured in Relative Log Expression (RLE). To screen for mRNAs whose levels differed by more than two-fold versus that wild-type cells, we filtered for mRNAs with EdgeR p values < 0.05.

first: Jee Soo

last: Choi

first: Hongmarn

last: Park

first: Wonkyong

last: Kim


title: Predicting Postoperative Liver Dysfunction Based on Blood Derived MicroRNA Signatures

city: Vienna

first: Matthias

last: Hackl

state: Austria

address: Leberstrasse 20

country: Austria

institute: TAmiRNA GmbH

summary: Treatment options and reliable predictive marker to determine patients at risk to develop postoperative LD and to define the optimal time point of liver resection are limited. Accordingly, there is an urgent need for an easily assessable preoperative test to predict postoperative liver function recovery, specifically as current markers are often expensive, time consuming and sometimes invasive. Emerging evidence suggests that microRNA (miRNA) signatures represent potent diagnostic, prognostic and treatment response biomarkers for several diseases. Using next-generation sequencing as an unbiased systematic approach 554 miRNAs were detected in preoperative plasma of 21 patients suffering from postoperative LD after liver resection and 27 matched controls. Subsequently, we identified a miRNA signature - consisting of miRNAs 151a-5p, 192-5p and 122-5p - that highly correlated with patients developing postoperative LD after liver resection. The predictive potential for postoperative LD was subsequently confirmed using real-time PCR in an independent validation cohort of 98 patients. Ultimately, a regression model of the two miRNA ratios 151a-5p to 192-5p and 122-5p to 151a-5p was found to reliably predict postoperative LD, severe morbidity, prolonged intensive care unit and hospital stay and even mortality prior to surgery with a remarkable accuracy, thereby outperforming established markers of postoperative LD. Ultimately, we documented that miRNA ratios closely followed liver function recovery after partial hepatectomy. Conclusion: Given the clinical relevance of predicting potentially fatal postoperative clinical outcome after liver resection, our data demonstrate the clinical utility of a novel miRNA-based biomarker to support the selection of patients undergoing partial hepatectomy. The dynamical changes during liver function recovery indicate a possible role in tailoring the optimal time point of surgery to each individual patient. Thereby, our data might help to tailor surgical strategies to the specific risk profile of individual patients.

overall_design:
Examination of 48 baseline plasma samples by Illumina NextSeq 500 sequencing taken prior to partial hepatectomy. 21 samples from patients with post-operative liver dysfunction. 27 samples from patients without post-operative liver dysfunction.

Please note that there are two patients who received hepatic surgery because of liver cirrhosis, but did not suffer from a cancerous disease (characteristics: cancer type = none). The main outcome of this study was post-operative liver dysfunction (characteristics: Liver Dysfunction) and the type of cancer was provided as supporting information to give background about the reason why patients required liver surgery. Mostly, lesions due to three types of cancer were the reason for surgery, and, in only two cases, cirrhosis.

first: Patrick

last: Starlinger

first: Hubert

first: David

last: Pereyra

first: Susanna

last: Skalicky

first: Elisabeth

last: Geiger

first: Michaela

last: Finsterbusch

first: Dietmar

last: Tamandl

first: Christine

last: Brostjan

first: Thomas

last: Grünberger

first: Alice

last: Assinger


title: Fibroblasts in cholesteatoma activate osteoclasts.

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Cholesteatoma arises from a tympanic membrane and expands in the middle ear. It erodes the surrounding bone and leads to hearing loss or brain abscess which is lethal complication. Currently, the only effective treatment is the complete surgical removal of cholesteatoma. However, possibility of recurrence is not satisfactory, other clinical treatment is desired. A mechanism of bone erosion in rheumatoid arthritis, which is one of the bone destructive disease, is progressing to be clarified. Receptor activator of NF-κB ligand (RANKL) secreted by synovial fibroblasts, T cells, and B cells lead to differentiation and activation of osteoclast precursor in rheumatoid arthritis. In contrast it has been still unclear why cholesteatoma erodes bone. In the current study we studied that osteoclasts statistically increased in cholesteatoma, and that fibroblasts in the prematrix of cholesteatoma express RANKL. In this study we studied that osteoclasts statistically increased in cholesteatoma, and that fibroblasts in the prematrix of cholesteatoma express RANKL. We investigated upstream of RANKL from RNA sequence results by Ingenuity Pathways Analysis, which is data base of abundance information about molecular biology.

overall_design: To generate the transcriptome profiles of the permatrix of cholesteatoma and dermis cut by laser micro dissection from cholesteatoma, three pairs of both sample from the same patients were adapted to RNA sequencing.

first: Ryusuke

last: Imai

first: Takashi

last: Sato


title: Effect of matrix deprivation on breast cancer cells Part-2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: Gene expression analysis of MDA-MB-231 breast cancer cells cultured in suspension {and stably expressing control shRNA, shPHLPP2 or GFP-Akt DD (GFP-HA-Akt-T308D S473D)}. Results provide insights into regulation of molecular pathways by PHLPP2 and Akt signaling in matrix deprived condition.

overall_design:
Organism : Homo sapiens, Agilent's Human Gene Expression  8x60k Array (AMADID: 072363)
MDA-MB-231_Suspension (24 hrs)
MDA-MB-231_Suspension/shPHLPP2 (24 hrs)
MDA-MB-231_Suspension/shPHLPP2+LY (24 hrs)
MDA-MB-231_Suspension/GFP-HA-Akt-T308D S473D (24 hrs)

first: Manipa

last: Saha

first: Saurav

last: Kumar

first: Shoiab

last: Bukhari

first: Sai

last: Balaji

first: Prashant

first: Sravanth

middle: K

last: Hindupur

first: Annapoorni

last: Rangarajan


title: Nuclear speckles as a key regulator for the 3D genome organization

first: Bo

last: Wen

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

overall_design: Refer to individual Series


title: Leo1 is essential for dynamic regulation of heterochromatin and gene expression during cellular quiescence [ChIP microarray]

city: Huddinge

first: Eriko

last: Oya

address: Blickagången 16

country: Sweden

institute: Karolinska Institutet

type: Genome binding/occupancy profiling by genome tiling array

summary: Cellular quiescence is a reversible differentiation state when cells are changing the gene expression programme to reduce metabolic functions and adapt to a new cellular environment. The epigenetic changes that accompany these alterations are not so well understood. Here we investigate the role of Leo1, a subunit of the conserved Paf1 (RNA polymerase-associated factor 1) complex, in the quiescence process using fission yeast as a model organism. Fission yeast cells enter the G0 phase of the cell cycle when exposed to nitrogen starvation and the heterochromatin regions become very dynamic. The reduction of heterochromatin in early G0 correlates with the reduced activity of target of rapamycin, TORC2, signalling. Cells lacking the Leo1 show reduced survival in G0.  In these cells heterochromatin regions including subtelomeres are stabilized and many genes, including membrane transport genes, fail to be expressed. Our results suggest that Leo1 is essential for dynamic regulation of heterochromatin and gene expression during cellular quiescence.

overall_design: Gemone-wide mapping of H3K9me2 in wt/leo1D/clr4D during quiescence; In total 48 samples; 20 Input files (duplicates) with the corresponding 20 ChIP samples

first: Mickaël

middle: D

last: Dubief

first: Adiel

last: Cohen

first: Catherine

last: Schurra

first: Jun-ichi

last: Nakayama

first: Ronit

last: Weisman

first: Benoit

last: Arcangioli

first: Karl

last: Ekwall


title: Effect of matrix deprivation on breast cancer cells Part-1

first: Genotypic

summary: Gene expression analysis of MDA-MB-231 breast cancer cells cultured in attached (treated with vehicle DMSO or A76) or suspension (and stably expressing control shRNA or shAMPKα2). Results provide insights into changes in molecular pathways and its regulation by AMPK

overall_design:
Organism : Homo sapiens, Agilent's Human Gene Expression  8x60k Array (AMADID: 039494)
Gene expression of attached cells treated with DMSO
Gene expression of attached cells treated with A76
Gene expression of suspension cells stable for scr
Gene expression of suspension cells stable for shAMPK alpha 2


title: Expression data from classical dendritic cells isolated from mouse lymph nodes

city: Lille

first: Denis

last: Mogilenko

address: 1 Rue du Professeur Calmette, BP245

institute: INSERM

summary:
Dendritic cells increase expression of pro-inflammatory cytokines and chemokines and undergo metabolic reprogramming upon TLR activation. Mice fed conventional diet (CD) or 60% high-fat diet (HFD) were treated by skin application of imiquimod (IMQ) during 6 days and classical dendritic cells (cDC) were isolated from inguinal lymph nodes (iLN) to reveal inflammatory and metabolic pathways that are sensitive to TLR7/8 activation and a high fatty acid environment.
We used microarray to identify pathways in classical dendritic cells from IMQ-treated mice that link inflammation and metabolism in a high fatty acid environment.

overall_design: cDC were isolated from skin-draining iLN from IMQ-treated mice. Mice were fed CD or 60% HFD and belly skin was treated with a daily dose of cream (62.5 mg) containing 5% IMQ during 6 days. CD3−CD19−CD64−Ly6G−CD11c+MHCII+ cDC were sorted from mouse iLN using BD Influx Cell Sorter (BD Biosciences) and used for RNA isolation.

first: David

last: Dombrowicz


title: Expression data from BMDC

summary:
Dendritic cells increase expression of pro-inflammatory cytokines and chemokines and undergo metabolic reprogramming upon TLR activation. We treated mouse BMDC with TLR7/8 ligand imiquimod (IMQ) and palmitic acid (PA) to reveal inflammatory and metabolic pathways that are sensitive to TLR7/8 activation and a high fatty acid environment.
We used microarray to identify pathways in dendritic cells that link inflammation and metabolism in  a high fatty acid environment.

overall_design: Bone marrow-derived dendritic cells differentiated in the presence of GM-CSF (GM-DC) were used for RNA extraction and hybridization on Affymetrix microarrays.  GM-DC were treated with mock or 3 uM IMQ during 24 hr with or without 0.5 mM PA conjugated with BSA.


title: Gene expression in uninvolved and involved epidermis from patients with atopic dermatitis (laser capture microdissection): set 1

summary: We performed microarray analysis on laser-microdissected epidermis from patients with atopic dermatitis to identify genes dysregulated in uninvolved and involved lesional epidermis

overall_design: Epidermis and dermis were obtained from human skin biopsies by laser capture microdissection using Arcturus XT (MDS Analytical Technologies) system, followed by RNA isolation with Arcturus Picopure RNA isolation Kit. 10 ng RNA were amplified with ExpressArt Kit and labeled with One-color microarray-based Gene Expression Analysis Low Input Quick Amp WT Labeling (Agilent Technologies) and hybridized with Human Gene Expression Microarray 8x60K chip (Agilent Technologies).


title: Gene expression in uninvolved and involved lesional epidermis from human skin biopsies from patients with atopic dermatitis (laser capture microdissection)


title: Expression analysis of AR-positive, ER-/PR-negative breast cancer and normal tissues

city: Nanjing

first: Yan

last: Wang

state: Jiangsu

address: No. 121 Jiangjiayuan Rd

department: Department of Pathology

institute: The Second Affiliated Hospital of Nanjing Medical University

summary: This study is intended to investigate the differences in biological molecular expression upon HER2 status (HER2-positive and –negative) in AR-positive, ER-/PR-negative breast cancer. Results indicate that differentially expressed genes were involved in olfactory transduction, major histocompatibility complex, ECM-receptor interaction, focal adhesion, adherens junction, as well as protein processing in endoplasmic reticulum.

overall_design: A total of 9 samples are analyzed. Of which, 3 samples (T39, T40 and T54) were AR-positive, ER-/PR-negative, HER2-positive breast cancer, and 3 samples (B13, B29 and B32) were AR-positive, ER-/PR-negative, HER2-negative breast cancer, and other 3 samples were normal breast tissues. The three normal breast samples (N39, N40 and N54) were used for gene expression analysis as a reference group.

first: Wenwen

last: Guo


title: Genome-wide analysis of drug resistance gene expression by twist1 overexpression

city: Tianjin

first: Yan Liu

last: Rong

address: Tianjin

institute: Tianjin International Biomedical Research Institute

summary: Analysis of the mechanism of drug resistance regulated by Twist 1 at gene expression level. The hypothesis tested in the present study was that Twist 1 regulated the expression of drug resistance related genes. Results provide important information of the response of drug resistance related genes to Twist 1, either up- or down-regulated.

overall_design: Total RNA obtained from cells transferred with pcDNA3.1-Twist after 48h.

first: Tao

last: Sun


title: Evidence against tetrapod-wide digit identities and for a limited frame shift in bird wings

city: West Haven

first: Cong

last: Liang

address: 300 Heffernan Dr.

institute: Yale University

summary: In crown group tetrapods, individual digits are homologized in relation to a pentadactyl ground plan. However, testing hypotheses of digit homology is challenging because it is unclear whether digits develop with distinct and conserved gene regulatory states. Here we show dramatic evolutionary dynamism in the gene expression profiles of digits, challenging the notion that five digit identities are conserved across amniotes. Transcriptomics of developing limbs shows diversity in the patterns of genetic differentiation of digits, although the anterior-most digit has a unique, conserved expression profile. Further, we identify a core set of transcription factors that are differentially expressed among the digits of amniote limbs; their spatial expression domains, however, vary between species. In light of these results, we reevaluate the frame shift hypothesis of avian wing evolution and conclude that only the anterior-most digit has shifted position, suggesting a 1,3,4 digit identity in the bird wing.

sample_organism:
Alligator mississippiensis
Mus musculus
Anolis carolinensis

overall_design: Examination of mRNA profiles of developing digits and their associated posterior interdigital messenchyme from forelimbs of mouse, green anole (Anolis), and American alligator.

first: Thomas

last: Stewart

first: Gunter

last: Wagner


title: Gene expression in uninvolved and involved epidermis from patients with atopic dermatitis (laser capture microdissection): set 2


title: Genome-wide DNA methylation profile in the peripheral blood of cocaine and crack dependents

city: São Paulo

first: Caroline

middle: Perez

last: Camilo

address: Rua Doutor Ovídio Pires de Campos, 785

department: Institute of Psychiatry

institute: University of São Paulo

type: Methylation profiling by genome tiling array

summary: Objective: Cocaine use disorders (CUD) represent a major public health problem in many countries. To better understand the interaction between the environmental modulations and phenotype, the aim of the present study was to investigate the DNA methylation pattern of CUD patients, which were concomitant dependents of cocaine and crack, and healthy controls. Methods: We studied DNA methylation profiles in the peripheral blood of 23 CUD patients and 24 healthy control subjects using the Illumina Infinium HumanMethylation450 BeadChip arrays. Results: Comparison between CUD patients and controls revealed 186 differentially methylated positions (DMPs, adjP<10-5) related to 152 genes, with a subset of CpGs confirmed by pyrosequencing. DNA methylation patterns discriminated CUD patients and control groups. A gene network approach showed that EHMT1, EHMT2, MAPK1, MAPK3, MAP2K1 and HDAC5 genes, which are involved in transcription and chromatin regulation cellular signaling pathways, were also associated with cocaine dependence. Conclusion: The investigation of DNA methylation patterns in CUD patients may contribute to a better understanding of the biological mechanisms involved in cocaine use disorders.

overall_design: Comprehensive methylation analysis in the peripheral blood of 23 cocaine and crack dependents and 24 control subjects, using the Illumina Infinium Human Methylation 450K Bead Chips.

first: Mariana

last: Maschietto

first: Henrique

last: Vieira

first: Ana

last: Tahira

first: Gisele

last: Gouveia

last: Feio dos Santos

first: André

last: Negrão

first: Marcelo

last: Ribeiro

first: Ronaldo

last: Laranjeira

first: Homero

last: Vallada

first: Helena

last: Brentani


title: Transcriptomes analysis of mammary tumors induced by overexpression of the Ret receptor tyrosine kinase from a new transgenic mouse model

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

summary: Model: The activation of Ret receptor tyrosine kinase regulates mammary tumor growth, tumor-associated inflammation and metastasis. To uncover Ret’s function, we have generated a new transgenic mouse mammary tumor model, in which the human wild type Ret is expressed in the mammary epithelium of mice in a doxycycline (Dox)-inducible manner (system developed by Dr. Chosdosh). Induction of constitutive Ret expression leads to the development of mammary tumors in 60% of the mice. We have found that the Ret-induced tumors have histologic characteristics of the human DCIS. Purpose:  The goals of this study are to compare Next-generation sequencing (NGS)-derived transcriptome profiling (RNA-seq) of Ret-induced tumors to human breast cancer databases in order to determined which cancer subtype is represented by this new tumor model. Additionally, to further analyze the mechanisms underlying Ret-induced tumorigenesis, we will also examine the transcriptome by NGS: in this case, this analysis will be performed on tumors that regress upon dox-food withdrawal, in comparison to the growing tumors. We will also perform similar analysis with the hyperplastic glands, a step before of tumor development. Later, the RNA-seq differential expression data will be analyzed using pathway analysis software as Ingenuity and public available datasets as the Gene Set Enrichment Analysis (GSEA) or the Integrating Motif Response Activity Analysis (ISMARA).

overall_design: Tumor or mammary tissue mRNA profiles of  bitransgenic Ret/MTB mice or control (Ret/- or MTB/-) mice were generated by deep sequencing, N=3-6, using Illumina HiSeq 2500.

first: Kirsten

last: Jacobeit

first: Ina

last: Nissen

first: Albana

last: Gattelli

first: Nancy

last: Hynes


title: Methylation in Adaptive Natural Killer cells after exposure to NKG2C agonist antibodies for 7 days

city: Minneapolis

first: Aimee

last: Merino

state: MN

address: 420 Delaware Street SE

institute: University of Minnesota

summary: Natural Killer cells from cytomegalovirus positive individuals (i.e. adaptive NK) where cultured for seven days with either control antibody, an NKG2C agonist antibody, or an antibody agonist to NKG2C and NKG2A

overall_design:
NK cells were isolated from peripheral blood by Ficoll-Paque and then a Miltenyi bead kit. They were cultured for seven days in B0 media with 10 ng/mL IL-15 and platebound isotype antibody, anti-NKG2C, or anti-NKG2A. After seven days cells were pelleted and DNA extracted for bisulfite sequencing and  analysis by Ilumina Infinium methylationEPIC Beadchips
NA10858_batch 2 (control nucleic acid) and NA10858_batch 1 (control nucleic acid) should not have beta values as they are controls, not samples. We did not generate Beta values for samples  1215 (A,B,C) and 1233 (A,B,C) because the raw data did not have good quality control across the three experimental conditions. Therefore we did not use these for analysis for our paper but submitted the raw data for transparency sake.

first: Bin

last: Zhang

first: Philip

last: Dougherty

first: Jinhua

last: Wang

first: Bruce

last: Blazar

first: Jeffrey

last: Miller

first: Frank

last: Cichocki


title: BR-body enrichment for RNA substrate identification.

status: Public on Jun 29 2019

city: Bloomington

first: Jared

middle: Michael

last: Schrader

state: IN

address: 212 S Hawthorne Dr

department: Biology

institute: Indiana University

summary: BR-body RNA substrates were identified by RNA-seq of enriched BR-body samples compared to cell lysate.

overall_design: BR-bodies from JS299 cells were enriched by differential centrifugation, and prepared for RNA-seq.  As a comparison, whole cell lysate from the same strain was used to prepare RNA-seq libraries.


title: Regionally specified human pluripotent stem cell-derived astrocytes

city: Middleton

first: Robert

last: Bradley

address: 8460 Market Street Apt 412

institute: University of Wisconsin - Madison

summary: Bulk RNA-seq of highly pure regionally specified human pluripotent stem cell-derived astrocytes

overall_design: Transcriptomic profiling of human regional astrocytes differentiated from hPSCs

first: Su-Chun


title: Expression data from mouse abdominal skin

first: Denis

last: Mogilenko

summary: Psoriasis-like skin inflammation was indused by 5 daily topical applications of imiquimod (IMQ), a TLR7/8 agonist, or vehicle, in mice fed a high fat diet (HFD) or control chow diet (CD). Skin samples were collected at day 6.

overall_design: 5 mice in CD-vehicle group, 5 mice in HFD-vehicle group, 5 mice in CD-IMQ group, 5 mice in HFD-IMQ group

first: David

last: Dombrowicz


title: BR-body mutant mRNA half-life profiling.

summary: BR-body mutant strains were globally profiled for mRNA half-lives using rifampicin treatment followed by RNA-seq.  JS38 (wild type) was compared to JS221 (lacking the intrinsically disordered CTD and unable to form BR-bodies), JS233 (unable to recruit degradosome components into BR-bodies), and JS299 (active site mutant of RNase E).

overall_design: BR-body mutant strains were globally profiled for mRNA half-lives using rifampicin treatment followed by RNA-seq.  Biological samples were taken before treatment, then at 1, 3, and 9 minutes after rifampicin treatment.


title: Transcriptome profiling for floral bud development in reblooming cultivar 'High Noon' of Paeonia suffruticosa

city: Beijing

first: Yanting

last: Chang

address: Futongdong Rd, Wang Jing, Chaoyang District

department: State Forestry Administration, Institute of Horticultural Flower and Landscape

institute: International Centre for Bamboo and Rattan

summary: To examine the mechanisms that control flower development, we sequenced the flower bud transcriptomes of ‘High Noon’, a reblooming cultivar of P. suffruticosa × P. lutea. Both full-length isoforms and RNA-seq were sequenced in 3 floral developmental stages. A total of 15.94 Gb raw data and 457.0 million reads were generated in full-length transcript sequencing and RNA-seq.

overall_design: The 3 stage of the floal development in tree peony was sequenced and analyzed, each stage with 3 repeats.

first: Tao

last: Hu

first: Wenbo

first: Zehui

last: Jiang


title: Beauveria bassiana abaA (BbabaA) and brlA (BbbrlA) regulating genes involved in conidiation

city: Hangzhou

first: Shenghua

last: Ying

state: Zhejiang

address: Yu-hang-tang Road 688

institute: Zhejiang University

summary: Gene BbabaA and BbbrlA play an essential role in conidation, a determinant to the biocontrol  potential of entomopathogenic fungi.  The genome-wide exprssion analysis involved in fungal conidiation was analyzed by using high throughput sequencing (RNA-Seq). Our transcriptional profiles revealed that numerous differentially expressed genes (DEGs), of which involved in metabolism, cell transport and cell rescue, were significantly involved in deveopment of fungal conida.

overall_design: Total RNA obtained from ∆BbabaA and BbbrlA mutant strains were compared to that of wild type strain (WT) grown on SDA plates (Glucose 4%, Peptone 1%, and Yeast extract 1% plus 1.5% Agar).

first: Ming-Guang

last: Feng

first: Sheng-Hua


title: Differential c-Kit expression identifies two subsets of ILC2s with IL-17 producing capabilities that may contribute to IL-17 mediated pathologies

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

summary: Group 2 innate lymphoid cells (ILC2s) are linked to type 2 immune diseases but can also molecularly change phenotype and provide type 1 immunity towards pathogens. Here we identify an ILC2 subset which can convert into IL-17 producing NKp44‒ ILC3-like cells. c-Kit and CCR6 define this ILC2 subpopulation which exhibit ILC3 features, including RORγt, which enables the conversion into IL-17 producing cells in response to IL-1β and IL-23. We also report a novel but critical role for TGF-β in promoting the conversion of c-kit‒ ILC2s into RORγt expressing c-Kit+ ILC2s by inducing the upregulation of IL23R, CCR6 and KIT mRNA in these cells. This switch was dependent on RORγt and down-regulation of GATA-3. IL-4 was able to reverse this event supporting a role for this cytokine in maintaining ILC2 identity. Notably, this plasticity has physiological relevance as a subset of RORγt+ ILC2s express the skin homing receptor CCR10 and the frequencies of IL-17‒producing ILC3s are increased at the expense of ILC2s within the lesional skin of psoriatic patients compared to healthy individuals.

overall_design: c-kit‒ and c-Kit+ ILC2 subsets purified from PBMC by flow cytometry were stimulated with different combinations of IL-1β, IL-23 and TGF-β to induce IL-17A production

first: Jochem

last: Bernink

first: Marcel

last: Teunissen

first: Jan

last: Koster

first: Hergen

last: Spits


title: Progressive dosage compensation during Drosophila embryogenesis is reflected by gene arrangement on the X chromosome

status: Public on Jun 28 2019

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

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

overall_design: Refer to individual Series


title: Placental transcriptome in pregnancies complicated by Intrauterine growth restriction (IUGR) and preeclampsia (PE)

city: London

first: Victor

last: Han

state: Ontario

address: 1151 Richmond Street

department: Biochemistry

country: Canada

institute: Western University

summary: Purpose: Identify differentially expressed genes in placental samples from early-onset (EO) IUGR, EO-PE, as well as pregnancies complicated by both EO-PE and EO-IUGR

overall_design: Methods: Isolated total RNA from human placenta at birth and used it for RNA-sequencing on the Hiseq2000. Sequences were aligned to the human transcriptome (hg19/genome_build37) . Aligned sequences were then used to obtain abundance measurements and conduct differential expression analysis.

first: Z

last: Awamleh

first: G

last: Gloor

first: V


title: The intestine harbours functionally distinct tissue-resident and inflammatory Th17 cells

first: Gavin

last: Kelly

state: London

address: 1 Midland Road

institute: Francis Crick institute

summary: Th17 cells are extensively studied because of their known pathogenic role in many inflammatory diseases, but are also important to support the integrity of the intestinal barrier in a non-inflammatory manner. Since therapeutic targeting of Th17 cell mediated pathologies carries the risk of inadvertently affecting protective Th17 cells, we set out to define the major distinctions between homeostatic tissue-resident Th17 cells and Th17 cells engaged in inflammatory reactions, focusing on the gut. We show here that homeostatic Th17 cells exhibit little plasticity towards expression of inflammatory cytokines, are characterised by a metabolism typical for quiescent or memory T cells, and do not participate in inflammatory processes. Infection-induced Th17 cells, on the other hand, show extensive plasticity towards pro-inflammatory cytokines, disseminate widely into the periphery and engage aerobic glycolysis in addition to oxidative phosphorylation typical for inflammatory effector cells.

overall_design: RNA-seq study comparing the gene expression of SFB-induced homeostatic vs. C. rodentium-induced inflammatory intestinal Th17 cells

first: Sara

last: Omenetti

first: Brigitta

last: Stockinger


title: Placental microRNA expression in pregnancies complicated by Intrauterine growth restriction (IUGR) and preeclampsia (PE)

type: Non-coding RNA profiling by high throughput sequencing

summary: Purpose: Identify differentially expressed miRNAs in placental samples from early-onset (EO) IUGR, EO-PE, as well as pregnancies complicated by both EO-PE and EO-IUGR

overall_design: Methods: Isolated total RNA from human placenta at birth and used it for miRNA-sequencing on the Hiseq2000. Sequences were aligned to the mature microRNAs human index available on miRbase. Aligned sequences were then used to obtain abundance measurements and conduct differential expression analysis using multiple bioconductor packages.

first: Zain

first: Gregory


title: A conditionally immortalized Gli1-positive kidney mesenchymal cell line models myofibroblast transition

status: Public on Jun 27 2019

city: St. Louis

first: Haojia

last: Wu

state: Missouri

address: 600 S Euclid Ave

department: Renal Division/Internal Medicine

institute: Washington University in St. Louis

summary: Glioma-associated oncogene homolog-1 (Gli1)-positive resident mesenchymal stem cell-like cells are the predominant source of kidney myofibroblasts in fibrosis, but investigating Gli1-positive myofibroblast progenitor activation is hampered by the difficulty of isolating and propagating primary cultures of these cells. Using a genetic strategy with positive and negative selection, we isolated Kidney-Gli1 (KGli1) cells that maintain expression of appropriate mesenchymal stem cell-like cell markers, respond to hedgehog pathway activation, and display robust myofibroblast differentiation upon treatment with transforming growth factor-β (TGF-β). Coculture of KGli1 cells with endothelium stabilizes capillary formation. Single-cell RNA sequencing (scRNA-seq) analysis during differentiation identified autocrine ligand-receptor pair upregulation and a strong focal adhesion pathway signal. This led us to test the serum response factor inhibitor CCG-203971 that potently inhibited TGF-β-induced pericyte-to-myofibroblast transition. scRNA-seq also identified the unexpected upregulation of nerve growth factor (NGF), which we confirmed in two mouse kidney fibrosis models. The Ngf receptor Ntrk1 is expressed in tubular epithelium in vivo, suggesting a novel interstitial-to-tubule paracrine signaling axis. Thus, KGli1 cells accurately model myofibroblast activation in vitro, and the development of this cell line provides a new tool to study resident mesenchymal stem cell-like progenitors in health and disease.

overall_design: DropSeq on primary culture kidney Gli1+ cells harvasted from 0, 6, 12, and 24 hrs after TGF-beta treatment

first: Benjamin

last: Humphreys


title: Systematic evaluation of RNA-Seq preparation protocol performance (RNASeq: TruSeq)

city: Houston

first: Yue

last: Lu

state: TX

address: 1881 East Road

department: Epigenetics & Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

summary: In this study, we present a comprehensive evaluation of four RNA-Seq library preparation methods. We used three standard input protocols, the Illumina TruSeq Stranded Total RNA and TruSeq Stranded mRNA kits, and a modified NuGEN Ovation v2 kit; and an ultra-low-input RNA protocol, the TaKaRa SMARTer Ultra Low RNA Kit v3. Our evaluation of these kits included quality control measures such as overall reproducibility, 5’ and 3’ end-bias, and the identification of DEGs, lncRNAs, and alternatively spliced transcripts. Overall, we found that the two Illumina kits were most similar in terms of recovering DEGs, and the Illumina, modified NuGEN, and TaKaRa kits allowed identification of a similar set of DEGs. However, we also discovered that the Illumina, NuGEN and TaKaRa kits each enriched for different sets of genes.

overall_design: Three mESC cell lines (biological replicates) from Zbtb24 knockout (1lox/1lox) clones are compared with three wild-type (2lox/+) clones (biological replicates) using the TruSeq mRNA protocol.

first: Hsueh-Ping

last: Chao

first: Yueping

last: Chen

first: Yoko

last: Takata

first: Mary

middle: W

last: Tomida

first: Kevin

last: Lin

first: Jason

middle: S

last: Kirk

first: Melissa

last: Simper

first: Carol

last: Mikulec

first: Joyce

middle: E

last: Rundhaug

first: Susan

last: Fischer

first: Taiping

first: Dean

last: Tang

first: Jianjun

last: Shen


title: Lipid-associated macrophages control metabolic homeostasis in a Trem2-dependent manner

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Immune cells residing in white adipose tissue have been highlighted as important factors contributing to the pathogenesis of metabolic diseases, but the molecular regulators that drive adipose tissue immune cell remodeling during obesity remain largely unknown. Using index and transcriptional single-cell sorting, we comprehensively map all adipose tissue immune populations in both mice and humans during obesity. We describe a novel and conserved Trem2+ lipid-associated macrophage (LAM) subset and identify markers, spatial localization, and functional pathways associated with these cells. Genetic ablation of Trem2 in mice globally inhibits the downstream LAM molecular program during obesity, leading to adipocyte hypertrophy and both tissue-level and systemic hypercholesterolemia and glucose intolerance. These findings identify Trem2 signaling as a major pathway by which macrophages respond to loss of tissue-level lipid homeostasis, highlighting Trem2 as a key sensor of metabolic pathologies across multiple tissues and a potential therapeutic target in metabolic diseases.

platform_organism:
Homo sapiens
Mus musculus

overall_design:
At age 8-9 weeks, for some mice the normal chow was replaced with a high fat diet. Founding Trem2-/- knockout (KO) breeder mice were crossed with wild-type (WT) mice to produce second-generation cohorts of WT and KO littermates. F1 offspring was bred to produce homozygous WT or KO, some of which were also set to feed on HFD. Mice were euthanized and nd perfused immediately through the left ventricle of the heart The epididymal (visceral) adipose tissue (EAT) was readily located and excised right above the epididymis. The subcutanous adipose tissue (SAT) was obtained from the inguinal fat depot.
The 'metadata.txt' contains the details associating each single cell with its amplification batch and index sorting readouts
To comply with the institutional review board, the raw files for human samples have been uploaded to the European Genome-phenome Archive (EGA) at the European Bioinformatics Institute (EBI).

first: Diego

last: Jaitin

first: Lorenz

last: Adlung

first: Christoph

last: Thaiss

first: Assaf

last: Weiner

first: Eran

last: Elinav


title: Microarray expression profiling data for Trp53/Brca1-null mammary tumors derived from K8+ luminal cells

city: Boston

first: Zhe

last: Li

state: MA

address: 77 Avenue Louis Pasteur, Room 466

department: Medicine, Genetics Division

institute: Brigham and Women's Hospital

summary: BRCA1 mutation-carriers are predisposed to develop Basal-like breast cancer (BLBC), and p53 mutations are present in the majority of human BLBC cases, suggesting loss of these two tumor suppressors play key roles in development of BLBC.  Recent studies suggest that the majority of human breast cancers, including BLBC, may originate from mammary epithelial cells (MECs) in the luminal lineage.  However, how loss of p53 and BRCA1 contributes to development of BLBC from luminal MECs remains largely elusive.  We developed a novel genetic targeting and lineage tracing approach based on intraductal injection of Cre-expressing adenovirus under the control of the pan-luminal Keratin 8 (K8) promoter (Ad-K8-Cre).  We performed intraductal injection of Ad-K8-Cre to female mice carrying conditional knockout alleles of Brca1 and Trp53.  The injected females developed mammary tumors within 12 months after injection.  Microarray expression profiling of these tumors showed that they most closely resembled human BLBC.

overall_design: Total RNAs from YFP+ wild-type luminal mammary epithelial cells (i.e., cells of origin) sorted from Rosa26-Stop-YFP female mice 10-14 days after intraductal induction of Ad-K8-Cre adenovirus, or from mammary tumors developed in Trp53L/L;Brca1L/L females several months after intraductal injection of Ad-K8-Cre, were prepared and subjected to microarray expression profiling.

first: Dongxi

last: Xiang


title: Systematic evaluation of RNA-Seq preparation protocol performance

first: Yue

last: Lu


title: Azithromycin induces epidermal differentiation and   multivesicular bodies in airway epithelia

city: Reykjavik

first: Zuzana

last: Budkova

address: Vatnsmyrarvegi 14

department: BioMedical Center, School of Health Sciences

country: Iceland

institute: University of Iceland

summary: Azm affects the integrity of the bronchial epithelial barrier. To better understand these unexpected effects of Azm on bronchial epithelium we have now investigated global changes in gene expression in VA10 cells

overall_design: VA10 cells were cultivated in air-liquid interphase (ALI) conditions for 22 days with and without Azm. RNA was isolated at days 4, 10 and 22 and run through high-throughput RNA sequencing.

first: Jennifer

last: Kricker

first: Ari

middle: J

last: Arason


title: Comparative DNA methylomic analyses reveal insight into potential origins of novel monocyte epigenetic biomarkers of insulin resistance

status: Public on Jun 25 2019

city: Honolulu

first: Christian

middle: Ka'ikekuponoaloha

last: Dye

state: HI

address: 641 Ilalo St. BSB 222K

department: Native Hawaiian Health

institute: University of Hawaii at Manoa

summary: Genome wide DNA methylation profiling of monocytes from insulin sensitive and insulin resistant HIV-infected patients. The Illumina Infinium Human Methylation 450k Beadchip was used to obtain DNA methylation profiling across 450,000+ CpGs. Samples included monocytes from 37 HIV-infected individuals, of which 14 were insulin resistant and 23 were insulin sensitive, monocytes from 9 HIV-seronegative individuals, of which 4 were insulin sensitive and 5 insulin resistant, and FACS monocyte subsets (classical, intermediate, and non-classical monocytes) from two healthy donors.

overall_design: 500+ng of DNA was bisulfite converted from all 46 samples and hybridized to the Illumina Infinium Human Methylation 450K Beadchip

first: Michael

last: Corley

first: Razvan

last: Sultana

first: Alika

last: Maunakea


title: Differental DNA methylation in Nicolaides-Baraitser syndrome

city: Toronto

first: Eric

last: Chater-Diehl

state: ON

address: 686 Bay St.

institute: SickKids Research Institute

summary: Nicolaides-Baraitser syndrome (NCBRS) is a neurodevelopmental disorder caused by pathogenic sequence variants in SMARCA2 which encodes the catalytic component of the chromatin remodeling BAF (SWI/SNF) complex. We identified an NCBRS-SMARCA2 DNA methylation (DNAm) signature of 429 differentially methylated CpG sites in blood cells of individuals with NCBRS (n=8) compared to neurotypical controls (n=23) using the Illumina MethylationEPIC array. The genes to which these CpGs mapped were enriched for roles in cell differentiation, calcium signaling, and neuronal function consistent with NCBRS pathophysiology. The DNAm signature, demonstrating 100% sensitivity and specificity, was used to generated a model enabling classification of variants of unknown significance (VUS) in SMARCA2 as pathogenic (like NCBRS cases) or benign (like controls). Model assignments were concordant with the clinical phenotype and predicted protein effects for most cases; variants within the SMARCA2 ATPase/helicase domain classified as pathogenic and those outside as benign. A patient with a mild NCBRS phenotype and a SMARCA2 VUS distal to the ATPase/helicase domain demonstrated an intermediate DNAm signature profile, suggesting the signature output reflects the phenotype of individual cases. At most of the signature sites, the methylation values for this patient resembled those of either NCBRS cases or controls; the ontology of the genes overlapping these NCBRS- or control-like CpG sites were consistent with the patient?s unique clinical presentation. The NCBRS-SMARCA2 DNAm signature provides alternate means of functional molecular classification of SMARCA2 VUS as benign or pathogenic, as well as providing insight into downstream BAF complex targets.

overall_design: NCBRS blood samples (SMARCA2_1, SMARCA2_2, SMARCA2_5, SMARCA2_6, SMARCA2_7, SMARCA2_8, SMARCA2_9, SMARCA2_11), SMARCA2 test variants (SMARCA2_4, SMARCA2_10, SMARCA2_12, SMARCA2_14, SMARCA2_15, SMARCA2_16, SMARCA2_17, SMARCA2_18, SMARCA2_19)  control blood samples (n=23)  have DNA methylation measured on the Infinium MethylationEPIC Bead Chip array (GPL21145). Test cases with vairants of unknown significane Pyrosequencing in cases and matched controls was done as described in the associated publication. There are no replications in this submission.

first: Resham

last: Ejaz

first: Michelle

last: Siu

first: Andrei

last: Turinsky

first: Sanaa

last: Choufani

first: Cheryl

last: Cytrynbaum

first: Sarah

last: Goodman

first: Omar

last: Abdul-Rahman

first: Melanie

last: Bedford

first: Naghmeh

last: Dorrani

first: Kendra

last: Engleman

first: Josue

last: Flores-Daboub

first: David

last: Genevieve

first: Robert

last: Greenstein

first: Roberto

last: Mendoza-Londono

first: Wendy

last: Meschino

first: Laurence

last: Perrin

first: Nicole

last: Safina

first: Sharron

last: Townshend

first: Stephen

last: Scherer

first: Jean-Louis

last: Mandel

first: Amelie

last: Piton

first: Evdokia

last: Anagnostou

first: Matthew

middle: A

last: Deardorff

last: Brudno

last: Chitayat

first: Rosanna

last: Weksberg


title: Profiling microRNA expression in murine bone healing and nonunion formation: Role of miR-140 during the early stage of bone healing

city: Homburg

last: Ludwig

address: Kirrberger Strasse

department: Human Genetics

country: Germany

institute: Saarland University

summary: Although cellular and molecular mechanisms during the course of bone healing have been thoroughly investigated, the regulation of gene expression by microRNA during bone regeneration is still poorly understood. We hypothesized that nonunion formation is associated with different microRNA expression patterns and that target proteins of these microRNAs are differently expressed in callus tissue of nonunions compared to physiologically healing bones. In a well-established femoral osteotomy model in CD-1 mice osteotomies were induced which result either in healing or in nonunion formation. MicroRNA and target protein expression was evaluated by microarray, quantitative real-time polymerase chain reaction (qrt-PCR) and Western blot. Microarray analyses demonstrated 44 microRNAs to be relevant for nonunion formation compared to physiological bone healing. In nonunions qrt-PCR could validate a higher expression of microRNA-140-3p and microRNA-140-5p. This was associated with a reduced expression of Dnpep and stromal cell-derived factor (SDF)-1α, which are both known to be target proteins of microRNA-140 and also to be involved in the process of bone healing. These data suggest that an increased expression of microRNA-140-3p and mi-croRNA-140-5p markedly contributes to the development of nonunions, most probably by affecting bone morphogenetic protein (BMP)-2 function during the early stage of healing due to a reduced SDF-1α expression.

overall_design: To study miRNA expression during physiological bone healing, mice were assigned to two groups: A surgical procedure was performed to create a gap (0.25mm in the union group, 1.8mm in the non-union group) in the femur of the mice as model for bone healing. To avoid secondary dislocation, the gap was fixed using metallic clips. After 7 days, callus tissue at the gap site was harvested and miRNA expression was measured using microarrays.

first: Marcel

last: Orth


title: Genome-wide transcript structure resolution in murine gammaherpesvirus 68: 3T12 BGI RNA-Seq

city: Gainesville

first: Scott

last: Tibbetts

state: FL

department: Molecular Genetics & Microbiology

country: USA

institute: University of Florida

summary: Strand-specific RNA-Seq was used in conjunction with Pacific Biosciences Iso-Seq and deepCAGE to globally resolve transcript structures in lytic murine gammaherpesvirus 68.

overall_design: Strand-specific BGI RNA-Seq of MHV68-infected fibroblasts

first: Tina

last: O'Grady

first: April

last: Feswick

first: Brett

last: Hoffman

first: Yiping

last: Wang

first: Erik

last: Flemington


title: Genome-wide transcript structure resolution in murine gammaherpesvirus 68: HE 2.1 BGI RNA-Seq


title: Genome-wide transcript structure resolution in murine gammaherpesvirus 68: HE 2.1 deepCAGE

summary: deepCAGE was used in conjunction with Pacific Biosciences Iso-Seq and Illumina RNA-Seq to globally resolve transcript structures in lytic murine gammaherpesvirus 68.

overall_design: deepCAGE of B cells with latent or reactivated MHV68


title: Muscle stem cell function

city: PHILADELPHIA

first: Arndt

last: Siekmann

state: Pennsylvania

address: 421 Curie Boulevard, 1114 Biomedical Research Building II/III

department: Perelman School of Medicine

institute: UNIVERSITY OF PENNSYLVANIA