title: Induction of DISE by tumor suppressive microRNAs

city: Bethesda

first: Markus

last: Hafner

address: 50 South Drive

department: NIAMS

institute: NIH

summary: Many siRNAs and shRNAs induce a form of cell death in all cancer cells by silencing a set of critical survival genes in a process called death induced by survival gene elimination (DISE). Mechanistically, a 6mer seed sequence (position 2-7 of the guide strand) is sufficient to confer DISE-inducing activity. We have now performed a strand-specific screen testing the toxicity of all 4096 possible 6mer seed sequences in a neutral double-stranded siRNA backbone. We found an asymmetric preference for guanine in positions 1-3 and a G content of >80% of the 6mer seed in the most toxic siRNAs, which target survival genes that are GC rich in their 3'UTR. During over 800 million years of evolution, miRNAs have evolved to avoid guanine in their seed sequences. However, two tumor suppressive miRNAs were found to be killing cancer cells through DISE using G rich toxic 6mer seeds in cells exposed to genotoxic stress: 1) the p53 inducible miR-34 family; and 2) miR-320a, a noncanonical miRNA that is still expressed in cancer cells when miRNA processing genes are mutated. Our data suggest that most miRNAs have evolved to avoid induction of DISE but certain tumor suppressive miRNAs utilize this mechanism to kill cancer cells.

overall_design: Pan Argonaute immunoprecipitation and small RNA cloning in HeyA8 and HCT116 wild-type and Drosha KO cells treated with doxorubicin

first: Quan

middle: Q

last: Gao

first: William

middle: E

last: Putzbach

first: Andrea

last: Murmann

first: Siquan

last: Chen

first: Aishe

middle: A

last: Sarshad

first: Giovanna

last: Ambrosini

first: Elizabeth

last: Bartom

first: Marcus

last: Peter


title: mRNA sequencing of msh1 memory line in Arabidopsis

status: Public on Jan 12 2019

city: State College

first: Sally

last: Mackenzie

state: PA

address: 362 North Frear

department: Biology

country: USA

institute: Penn State University

type: Expression profiling by high throughput sequencing

summary: Germination of the memory line and isogenic Col-0 wild type on media containing 100 uM 5-azacytidine alleviated the phenotype differences between the two lines, resulting in similar growth rates, here we generate gene expression profile for wild type and  msh1 memory line under 100 uM 5-azacytidine treatment to investigate the  effect of 5-azacytidine on msh1 memory gene expression profile

overall_design: At least two blogical replicates and technological replicates for each genotype has been sequenced. Technological replicate means same RNA, but different library

first: Xiaodong

last: Yang


title: Differentially expressed RNAs in the skin tissue of IRF1 knockout mice following radiation

status: Public on Jan 11 2019

city: suzhou

first: zhang

middle: shu

last: yu

state: Jinagsu

address: 199 Ren'ai Rd

department: Radiation Medicine

country: China

institute: soochow University

summary: This study aims to compared RNA expression  profiles between  the skin tissues of IRF1 knockout (IRF-/-) mice and wild-type mice by microarray analysis. Male  IRF1 knockout (IRF-/-) mice and wild-type mice (8 weeks old) were irradiated with a single 35-Gy dose of irradiation was administered to the treatment area at a rate of 750 cGy/min using a 6-MeV electron beam accelerator (Clinac 2100EX, Varian Medical Systems, Inc., CA). Skin tissues from irradiated areas were collected and subjected to RNA expression analysis.

overall_design: Male  IRF1 knockout (IRF-/-) mice and wild-type mice (8 weeks old) were irradiated with a single 35-Gy dose of irradiation was administered to the treatment area at a rate of 750 cGy/min using a 6-MeV electron beam accelerator (Clinac 2100EX, Varian Medical Systems, Inc., CA). Skin tissues from irradiated areas were collected and subjected to microarray analysis.

first: Shuyu

last: Zhang


title: Gallus gallus reference-based transcriptome analysis of SRSF1-3 knock-in clones in DT40-ASF cells

city: Indore

first: Amit

middle: Kumar

last: Singh

state: Madhya Pradesh

address: SB-215, School Building, IIT Indore, Khandwa Road, Simrol, Indore

department: Biosciences and Bio-medical Engineering

country: India

institute: Indian Institute of Technology, Indore

summary: To identify the differential gene expression between the Control (Untransfected) and treated (transfected clone 41 and 47) samples using RNA sequencing data

overall_design: Examination of two different SRSF1-3 knock in clones in DT40-ASF cells

last: Kumar Singh

first: Anubhav

last: Tamrakar

first: Ankit

last: Jaiswa

first: Naoki

last: Kanayama

first: Prashant

last: Kodgire


title: RNAseq analysis of the N. punctiforme transcriptome during hormogonium development in wild type, and three sigma-factor deletion strains

city: Stockton

first: Douglas

middle: D

last: Risser

state: California

address: 3601 Pacific Ave

institute: University of the Pacific

summary: Change in gene expression for wild-type Nostoc punctiforme ATCC 29133, or three derivative strains with sigma factors deleted, over the time course of hormogonium development

overall_design: Total RNA from 3 biological replicates at 0,1,6,12, and 18 hours after hormogonium induction was ribodepleted, converted to cDNA, apended with adapters and sequenced in 6 lanes of a flow cell on an illumina HiSeq 4000 instrument


title: Effect of IL-13 on transcriptome of differentiated human airway mucociliary epithelium

status: Public on Jan 10 2019

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: We used microarrays to detail the global programme of gene expression that occurs in response to treatment of IL-13 on fully-differentiated human airway mucociliary epithelium

overall_design: Human nasal epithelial cells isolated from nasal turbinates were cultured in air-liquid interface (ALI) until the full differentiation was complete. Differentiated cells at ALI-D47 were  incubated with 100 ng/mL of  IL-13 for 3 days

first: Brice

last: Marcet

first: Benoit

last: Chevaliert

first: Pascal

last: Barby

first: Agnes

last: Paquet

first: Geraldine

last: Rios


title: Liver transcriptome analysis of juvenile largemouth bass under lead exposure by RNA-seq

city: Taizhou

first: Baoying

last: Qian

state: Zhejiang

address: 1139 Shifu Road, Jiaojiang, Taizhou, Zhejiang 318000, P. R. China

department: School of life science

institute: Taizhou University

summary: We sequenced mRNA from 9 liver samples of juvenile largemouth bass (Micropterus salmoides) taken from different lead concentration exposure treatment fish and control fish to investigate the transcriptome and comparative expression profiles of largemouth bass liver undergoing lead exposure.

overall_design: Liver mRNA prolfiles of control group (L0), low lead concentration exposure group (17.8 mg/L) (L2) and high lead concentration exposure group (100 mg/L) (L5)  were generated by RNA-seq, using Illumina HiSeq 2000.


title: Expression data from the constitutive expression of TaSIN in Arabidopsis

city: Qingdao

first: Mei

last: Wang

state: Shandong

address: Binhai road 72

institute: Shandong University

summary:
To gain further insight into the possible signaling pathways in which TaSIN participates, constitutive lines of TaSINFL and TaSIN∆C were generated in Arabidopsis. ∆COE seedlings survived organellar oxidative stress better than the FLOE ones.
A microarray experiment was designed to identify the downstream target genes of TaSIN.

overall_design: Constitutive expression lines of TaSINFL (FL3) and TaSIN∆C (∆C26 and ∆C27) were generated in Arabidopsis, and grown under non-stressed conditions for 12 days. The seedlings were used for RNA extraction and hybridization on Affymetrix microarrays. Arabidopsis transgenic line carrying an empty vector (VC) and wild type Col-0 were used as controls. Two independent biological replicates were performed for each genotype.

first: Guangmin

last: Xia


title: Molecular definition of high grade B cell lymphoma: a centroblast-like group with potential for more effective therapy

status: Public on Jan 15 2019

city: Leeds

first: Chulin

last: Sha

address: Woodhouse Lane

department: School of Mole&Cell Biology

country: United Kingdom

institute: University of Leeds

summary: A retrospective analysis of whole transcriptome data for 928 DLBCL patients from REMoDLB clinical trial, identifies a subgroup of molecular high grade (MHG) class that present centroblast-like gene expression, enriched for MYC rearrangement, double-hit (MYC rearrangement accompanied with BCL2 and/or BCL6 rearrangement) and associated with adverse clinical outcome.

overall_design: Gene expression profiling was carried out for RNA extracted from Formalin-fixed, paraffin embedded (FFPE) biopsies of 928 diagnosed DLBCL using the Illumina Whole-Genome DASL HT version 4 array.

first: Sharon

middle: L

last: Barrans


title: Expression data from cav1-/+apcmin/+ mouse intestinal tissue

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

summary: We used microarrays to decipher the global programme of gene expression in normal colon tissue versus colorectal tumor tissue explants from 6 months old cav1-/+ apcmin/+ mice and identified distinct classes of differentially regulated genes.

overall_design: Mouse tissues were selected by genotype for RNA extraction and hybridization on Affymetrix microarrays.

first: Elke

last: Burgermeister

first: Henrik

last: Einwächter


title: Gene expression patterns of 52 hpf and 7 dpf zebrafish hearts

city: Bad Nauheim

first: Didier

last: Stainier

address: Ludwigstrasse 43

department: Developmental Genetics

institute: Max Planck Institute for Heart and Lung Research

summary: To assess gene expression patterns in zebrafish hearts at different developmental time points

overall_design: Hearts from Tg(myl7:GFP) zebrafish were extracted, total RNA was then isolated and used for microarrays to examine global gene expression

first: Ayele

middle: T

last: Tsedeke

first: Vanesa

middle: J

last: Amilburu


title: Prediction of functional microRNA targets by integrative modeling of microRNA binding and target expression data

city: Chicago

first: Xiaowei

state: IL

address: 909 S Wolcott Ave, Rm 5137

institute: University of Illinois at Chicago

summary: We perform a large-scale RNA sequencing study to experimentally identify genes that are downregulated by 25 miRNAs. This RNA-seq dataset is combined with public miRNA target binding data to systematically identify miRNA targeting features that are characteristic of both miRNA binding and target downregulation. By integrating these common features in a machine learning framework, we develop and validate an improved computational model for genome-wide miRNA target prediction. All prediction data can be accessed at miRDB (http://mirdb.org).

overall_design: RNA-seq to identify transcript targets that are downregulated by overexpression of 25 individual miRNAs.

first: Weijun

last: Liu


title: Alteration of circRNA Expression in rDFCs During Osteogenic Differentiation

city: Guangzhou

first: Jing

last: Li

address: Zhongshan Road

institute: Zhongshan university

summary: Circular RNAs (circRNAs) are novel among noncoding RNAs and play crucial roles in various biological processes. However, little is known about the functions of circRNAs during osteogenic differentiation. The current study aimed to investigate the differential expression of circRNAs in rat dental follicle cells (rDFCs) upon osteogenic medium culture. Those potential circRNAs were identified by RNA high-throughput sequencing and quantitative real-time polymerase chain reaction (qRT-PCR). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to further explore circRNA biofunctions. 266 differentially-expressed circRNAs were revealed and involved in several important signaling pathways, which include MAPK and TGF-β signaling pathways. Among these, circFgfr2 and its predicted downstream targets, miR-133 and BMP6, were identified both in vivo and in vitro. For further validation, circFgfr2 was overexpressed during osteogenic differentiation, bringing about the down-regulation of miR-133 and the up-regulation of BMP6. Taken together, the results revealed the circRNA expression profiles and indicate the importance of circRNAs during the osteogenic differentiation of rDFCs. In addition, circFgfr2 might promote osteogenesis by controlling miR-133/BMP6, which possibly provide new target to manipulate tooth regeneration and bone formation.

overall_design: dental follicle cells were collected from4 SD rats and were grouped into control groups and ostepgenic induction groups.After 28-day incubation, RNA was collected from each group and RNA high throughput sequencing was conducted.

first: Yu

last: Du


title: Gene Expression Profiling of Gastric Cancer-Associated Myofibroblasts

city: Liverpool

first: Hanna

last: Najgebauer

address: Crown Street

department: Cellular and Molecular Physiology

institute: University of Liverpool

summary: The Illumina HumanHT-12v4 Expression BeadChip arrays were performed on a collection of primary gastric cancer-associated myofibroblasts (CAM) and their patient-matched adjacent tissue myofibroblasts (ATM) as well as unrelated normal tissue myofibroblasts (NTM). CAM and ATM samples were obtained from patients undergoing gastric cancer surgery; whereas NTM samples were generated from deceased transplant donors with normal morphology.

overall_design: Total RNA obtained from gastric stromal myofibroblasts, including 3 CAMs, 3 ATMs and 3 NTMs, were hybridised to theIllumina HumanHT-12v4 Expression BeadChip

first: Chris

last: Sanderson


title: DNA methylation directs microRNA biogenesis

city: Tel Aviv

first: Carmit

last: Levy

address: Ramat Aviv

department: Human Genetics and Biochemistry

country: Israel

institute: Tel Aviv University

summary: MicroRNA (miRNA) biogenesis initiates co-transcriptionally, but how the Microprocessor machinery pinpoints the locations of short precursor miRNA sequences within long flanking regions of the transcript is not known. Here we show that miRNA biogenesis depends on DNA methylation. We found that miRNAs whose corresponding coding sequence’s flanking regions are highly methylated are expressed more, have greater sequence conservation, and are more likely to drive cancer-related phenotypes than miRNAs encoded by unmethylated loci. Accordingly, the removal of DNA methylation from miRNAs leads to their downregulation. Further, we found that MeCP2 binding to the DNA of methylated miRNAs halts RNA polymerase II elongation, an inactivation that leads to enhanced processing of primary miRNA by Drosha. Taken together, our data reveal that DNA methylation directly affects miRNA biogenesis.

overall_design: miRNA profiling in mouse ESC(R1) and in mouse ESC without DMNTs(TKO). R1 and TKO cells were obtain from: Akiko Tsumura et al, Maintenance of self‐renewal ability of mouse embryonic stem cells in the absence of DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b (Genes to Cell 2006). Two biological replicates were performed for the miRNA profiling.

first: Ohad

last: Glaich

first: Shivang

last: Parikh

first: Rachel

last: Bell

first: Keren

last: Mekahel

first: Maya

last: Donyo

first: Ronna

last: Shayevitch

first: Danna

last: Sheinboim

first: Sivan

last: Yannai

first: Dror

last: Hollander

first: Ze'ev

last: Melamed

first: Galit

last: Lev-Maor

first: Gil

last: Ast


title: miRNA expression in oxygen-stable HIF1 transgenic mice

status: Public on Jan 09 2019

city: Honolulu

first: Allison

middle: Lesher

last: Williams

state: HI - Hawaii

address: 651 Ilalo St BSB 311

institute: University of Hawaii

summary: Oxygen-stable HIF1 was inducibly expressed in cardiomyocytes of double transgenic mice. Specifically, tetracycline-inducible HIF-PPN mice (Pro402, Pro564 and Asn803 of HIF1a were mutated to Ala residues to limit degradation, termed HIF-PPN) were crossed to a-MHC-tTA expressing mice. HIF-PPN expression was induced by removal of doxycycline for 3 days and  compared to control hearts that remained on doxycycline (uninduced).

overall_design: Two hearts per condition (3 days off dox and control- on dox) were pooled and hybridized on same array. Representative HIF induced hearts were selected based on significant increase in heart weight/body weight ratio compared to control hearts.

first: Chad

last: Walton


title: Dopamine D2L Receptor Deficiency Causes Stress Vulnerability through 5-HT1A Receptor Dysfunction in Serotonergic Neurons

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

summary: Mental disorders are caused by genetic and environmental factors. We here show that deficiency of an isoform of dopamine D2 receptor (D2R), D2LR, causes psychosocial stress vulnerability in mouse. This occurs through dysfunction of type 1A serotonin (5-hydroxytryptamine, 5-HT) receptor (5-HT1AR) on serotonergic neurons in the mouse brain. Exposure to forced swim stress significantly increased anxiety- and depressive-like behaviors in D2LR knockout (D2LR-KO) male mice as compared with wild-type mice. Treatment with 8-OH-DPAT, a 5-HT1AR agonist, failed to alleviate the stress-induced behaviors in D2LR-KO mice. In forced swim-stressed D2LR-KO mice, 5-HT release in the medial prefrontal cortex was elevated and the expression of genes related to 5-HT levels was up-regulated by the transcription factor PET1 in the dorsal raphe nucleus. Notably, D2LR formed a heteromer with 5-HT1AR in serotonergic neurons, thereby suppressing 5-HT1AR–activated G-protein–activated inwardly rectifying potassium (GIRK) conductance in D2LR-KO serotonergic neurons. Finally, D2LR overexpression in serotonergic neurons in the dorsal raphe nucleus alleviated stress vulnerability observed in D2LR-KO mice. Taken together, we conclude that disruption of the negative feedback regulation by the D2LR/5-HT1A heteromer causes stress vulnerability.

overall_design: To identify differentially expressed genes following forced swim stress (FS), we compared three FS-stressed mouse groups (WT, D2R-KO, and D2LR-KO) with non-stressed control WT group.   The mice were submitted to 6-min FS stress on four consecutive days, and the dorsal raphe nucleus (DRN) was dissected 12 h after the last FS stress exposure and gene expression analyzed. n = 5 mice per group per pool.

first: Norifumi

last: Shioda

first: Kohji

last: Fukunaga


title: Brief Local Application of Progesterone via a Wearable Bioreactor Induces Long-Term Regenerative Response in Adult Xenopus Hindlimb

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

summary: The induction of limb repair depends on signals that initiate regeneration and the successful transmission of those signals in vivo. Here, we characterize the effects of an integrated device-based in vivo delivery of drug compounds in adult Xenopus laevis, which normally regenerate only a cartilaginous spike after limb amputation. A wearable bioreactor containing a silk protein-based hydrogel containing progesterone that was applied to the wound site immediately after hind-limb amputation for 24 hours induced regeneration of flattened paddle-like structures in adult frogs. Molecular assays (ELISA and NGS), Morphometric analysis (soft-tissue patterning), X-ray imaging (bone regrowth), immunofluorescence (cell proliferation, immune response, neuro/vascular tissues), and behavioral data (functional use of regenerates) were used to characterize the differences between the paddle-like structures and the hypomorphic spike observed in untreated animals. Initially, treated animals exhibited an extensive wound epithelium, and increased nerve supply compared to controls. Subsequently, flattened structures with robust bone remodeling were formed, resembling comparable tissues of adult limbs at the early and middle stages of regeneration. The limbs ceased regeneration at the position where the digits usually form. Functional tests revealed that the response to the paddle-like structures was similar to that of uncut limbs. Analysis of the blastema transcriptome identified a number of key genes related to the combined intervention, and also revealed regulated transcripts related to hormonal and neural pathways, representing novel targets for emerging regenerative therapies. Our experiments (1) establish a new model for testing of therapeutic cocktails in vertebrate limb regeneration; (2) identify pro-regenerative activities of progesterone, and (3) provide proof-of-principle of using integrated device-based delivery of small molecule drugs as a viable strategy to induce and maintain a regenerative response.

overall_design: Samples from 3 treatment groups were RNA sequenced (Control, Sham or Silk, and Prog) via NGS, n= 9 per group, n=3 for three tissues (brain, stump, and blastema)

first: Celia

last: Herrera-Rincon

first: Mike

last: Levin


title: TOC1 silencing in roots only changes transcriptional responses to drought in Nicotiana attenuata

status: Public on Jan 08 2019

city: Jena

first: Klaus

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

institute: Max-Planck-Institute for Chemical Ecology

summary: Identification of transcripts that change expression in TOC1-silenced Nicotiana attenuata plants leaves and roots under drought

overall_design: Gene expression in rosette stage of grafted EV/EV (EE), EV/irTOC1 (ET), and irTOC1/irTOC1 (TT) plants in control and drought conditions

first: Henrique

last: Valim

first: Meredith

last: Schuman

first: Ian

last: Baldwin


title: Differential functional effects of Ibuprofen in the human fetal ileum

status: Public on Jan 07 2019

city: Sherbrooke

first: Jean-François

last: Beaulieu

state: Québec

address: 3001, 12ème avenue nord

department: Anatomie & biologie cellulaire

country: Canada

institute: Université de Sherbrooke

summary:
Transcriptional profiling of small intestinal explants cultured in the absence or in the presence of Ibuprofen (100 µM).
Two-condition experiment, control intestinal explants vs Ibuprofen intestinal explants

overall_design: Differential gene expression

first: Emanuela

last: Ferretti

first: Eric

last: Tremblay

first: Nancy

last: Perron

first: Babakissa

last: Corentin

first: Mandy

last: Malik

first: Ernest

last: Seidman

first: Emile

last: Levy

first: Daniel

last: Ménard


title: miRNA expression profile is related to vestibular schwannoma growth rate

city: Copenhagen OE

first: Hjalte

middle: Christian Reeberg

last: Sass

address: Blegdamsvej 9

department: Department of Otorhinolaryngology, Head and Necksurgery & Audiology

country: Denmark

institute: Copenhagen University Hospital Rigshospitalet

summary:
Tumor miRNA expression is related to the growth rate of sporadic vestibular schwannomas. Rapid tumor growth is associated with deregulation of several miRNAs, including up-regulation of miR-29abc, miR-19, miR-340-5p, miR-21 and miR-221 and down-regulation of miR-744 and let-7b. Gene ontologies affected by the deregulated miRNAs included neuron development and differentiation, gene silencing and negative regulation of various biological processes, including cellular and intracellular signalling and metabolism.
We used microarray to determine the miRNA expresison in vestibular schwannoma their relation to the growth rate.

overall_design: Tumor tissue was sampled during surgery of patients with a sporadic vestibular schwannoma. Tumor growth rate was determined by tumor measurement on the two latest pre-operative MRI scans. Tumor miRNA expression was analysed using the Affymetrix Gene Chip® protocol, and CEL files were generated using GeneChip® Command Console® Software and normalized using Partek Genomics Suite 6.5. The CEL files were analyzed using the statistical software program R. Principal component analysis, affected gene ontology analysis and analysis of miRNA expression fold changes were used for analysis of potential relations between miRNA expression profile and tumor growth rate.

middle: C

first: Rehannah

last: Borup

first: Morten

last: Nielsen

first: Finn

first: Per

last: Cayé-Thomasen


title: Generation Sequencing Facilitates Quantitative Analysis of Wild Type and TaD27 Transcriptomes

city: Taian

first: Fang

last: Wang

address: No. 61 Dai Zong Street

institute: Shandong Agricultural University

summary: To further dissect the molecular basis of tiller generation, we performed an RNA-seq analysis of TaD27-RNAi axillary bud primordia at the three-week old. The axillary buds of wild type KN199 at the same development stage were used as the control. A total of 4,947 differentially expressed genes (DEGs) between the WT and TaD27-RNAi were identified using a fold-change of 2 and FDR<0.05. Among them, 4,124 genes were expressed at a low level, 823 genes were highly expressed in TaD27-RNAi compared to the WT.

overall_design: Wheat mRNA profiles of 3-week old wild type (WT) and TaD27-RNAi were generated by deep sequencing, in triplicate, using Gene Denovo.

first: BIN

last: Zhao

first: FANG


title: Chromatin changes induced by a Plasmodium falciparum infection in Anopheles gambiae

city: Granada

first: Jose

middle: Luis

last: Ruiz Rodriguez

state: Granada

address: Avda. del Conocimiento 17. P. T. Ciencias de la Salud

country: Spain

institute: IPBLN-CSIC

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Background: Infection by the human malaria parasite leads to important changes in mosquito phenotypic traits related to vector competence. However, we still lack a clear understanding of the underlying mechanisms and, in particular, of the epigenetic basis for these changes. We have examined genome-wide distribution maps of H3K27ac, H3K9ac, H3K9me3 and H3K4me3 by ChIP-seq and the transcriptome by RNA-seq, of midguts from Anopheles gambiae mosquitoes blood-fed uninfected and infected with natural isolates of the human malaria parasite Plasmodium falciparum in Burkina Faso.

Results: We report 15,916 regions containing differential histone modification enrichment between infected and uninfected, of which 8339 locate at promoters and/or intersect with genes. The functional annotation of these regions allowed us to identify infection-responsive genes showing differential enrichment in various histone modifications, such as CLIP proteases, antimicrobial peptides-encoding genes, and genes related to melanization responses and the complement system. Further, the motif analysis of regions differentially enriched in various histone modifications predicts binding sites that might be involved in the cis-regulation of these regions, such as Deaf1, Pangolin and Dorsal transcription factors (TFs). Some of these TFs are known to regulate immunity gene expression in Drosophila and are involved in the Notch and JAK/STAT signaling pathways.

Conclusions: The analysis of malaria infection-induced chromatin changes in mosquitoes is important not only to identify regulatory elements and genes underlying mosquito responses to P. falciparum infection, but also for possible applications to the genetic manipulation of mosquitoes and to other mosquito-borne systems.

overall_design: Genome-wide profiling of histone modifications enrichment (ChIP-seq) in mosquito tissues infected and non-infected by P.falciparum coupled with transcriptome profiling (RNA-seq)

first: José

last: Ruiz

first: Rakiswendé

middle: S

last: Yerbanga

first: Thierry

last: Lefèvre

first: Jean

middle: B

last: Ouedraogo

first: Victor

middle: G

last: Corces

first: Elena

last: Gómez-Díaz


title: Transcriptomic and metabolomic analysis of the heat-stress response of Populus tomentosa

city: Yangzhou

first: Biao

last: Jin

state: Jiangsu

address: Wenhui east road no. 48

department: College of Horticulture and Plant Protection

institute: Yangzhou University

summary: We sequenced mRNA from the control and heat treatments leaves of Populus tomentosa using the Illumina HiSeq4000 platform to generate the transcriptome dynamics that may serve as a gene expression profile blueprint for different response patterns under control and heat stress in Populus tomentosa.

overall_design: Transcriptome sequencing in control and heat treatments leaves of Populus tomentosa

first: Shixiong

last: Ren


title: PBDE-47 and PBDE mixture (DE-71) toxicities and liver transcriptomic changes at PND 22 after in utero/postnatal exposure in the rat.

status: Public on Jan 05 2019

city: Morrisville

first: June

last: Dunnick

state: NC

address: 530 Davis Dr.

department: NIEHS

institute: NIH

summary: Test articles used: DE-71 (Pentabromodiphenyl Ether Mixture [Technical Grade), CAS Number 32534-81-9, DTXSID2024246); PBDE-47 (CAS Number 5436-43-1); PB (Phenobarbital, CAS Number 50-06-6 ); PCB (PCB126, CAS Number 57465-28-8)

overall_design:
PBDE-47 and the PBDE mixture were evaluated at PND 22 in Wistar Han rat (Crl: WI (Han)) pups after in utero/postnatal exposure (0, 0.1, 15, or 50 mg/kg; dams, GD6-21; pups, PND 12-PND 21; oral gavage daily dosing)
contributor: National Toxicology Program


title: PGC1a and Exercise Adaptations in Zebrafish

status: Public on Jan 06 2019

city: Lausanne

first: Philipp

last: Gut

address: EPFL Innovation Park, building H

country: Switzerland

institute: Nestlé Institute of Health Sciences SA

summary: Fish species display huge differences in physical activity ranging from lethargy to migration of thousands of miles, making them an interesting model for human exercise.  Here, we show a remarkable plasticity of zebrafish in response to exercise and induction of PGC1α (encoded by PPARGC1A), a dominant regulator of mitochondrial biogenesis.  Forced expression of human PPARGC1A induces mitochondrial biogenesis, an exercise-like gene expression signature, and physical fitness comparable to wild-type animals trained in counter-current swim tunnels.  We quantify a stoichiometric induction of the electron transport chain (ETC) in response to exercise or PGC1α expression, identified by a proteomic SWATH-MS workflow.  Exercise or PGC1α expression induce the re-organization of the ETC into respiratory supercomplexes, and we show that ndufa4/ndufa4l, previously assigned to complex I, associates to free and supramolecular complex IV in vivo.  Thus, zebrafish is a useful and experimentally tractable vertebrate model to study exercise biology, including ETC expression and assembly.

overall_design: RNA-Seq from total RNA of skeletal muscle of adult zebrafish. Transcriptomic profiles of wild-type fish not trained (Lazy_WT), wild-type fish trained in chronic exercise (Trained_WT) and transgenic fish overexpressing PGC1α not trained (Lazy_TG)

first: Alice

last: Parisi

first: Peter

last: Blattmann

first: Giulia

last: Lizzo

first: Vivienne

last: Stutz

first: Laura

last: Strohm

first: Joy

last: Richard

first: Gabriele

last: Civiletto

first: Aline

last: Charpagne

first: Frederic

last: Raymond

first: Cedric

last: Gobet

first: Benjamin

last: Weger

first: Eugenia

last: Migliavacca

first: Ruedi

last: Aebersold

first: Bruce

last: Spiegelman


title: Comparative transcriptomic analysis reveal the regulation mechanism underlying MeJA-induced accumulation of alkaloids in Dendrobium officinale

city: hangzhou

first: chengchao

last: zhang

address: Xuelin Street No.16

institute: Hangzhou Normal University

summary: Dendrobium officinale is a traditional medicinal herb with a mount of bioactive components. Alkaloid is one of the major active ingredients of Dendrobium plants, and its immune regulatory effects have been well-studied. A total of 4857 DEGs, including 2943 up- and 1932 down-regulated genes, were identified between the control and MeJA-treated groups. Several shikimate and methylerythritol 4-phosphate pathway genes and a number of MeJA-induced P450 family genes, aminotransferase genes and methyltransferase genes were identified, providing several important candidates to further elucidate the alkaloid biosynthetic pathway of D. officinale. Furthermore, a large number of MeJA-induced transcript factor encoding genes were identified, suggesting a complex genetic network affecting the alkaloid metabolism in D. officinale.

overall_design: In the present study, a number of differential expressed genes were identified to elucidate the regulation mechanism underlying the MeJA-induced accumulation of alkaloids in D. officinale.

first: Chenjia

last: Shen


title: Transcriptional changes following cellular knockdown of the schizophrenia risk gene SETD1A are enriched for common variant association with the disorder

city: Cardiff

first: Matthew

middle: James

last: Hill

address: Maindy Road

institute: Cardiff University

summary: Loss of function mutations in SETD1A are the first experiment-wide significant findings to emerge from exome sequencing studies of schizophrenia. Although SETD1A is known to encode a histone methyltransferase, the consequences of reduced SETD1A activity on gene expression in neural cells have, to date, been unknown. To explore transcriptional changes through which genetic perturbation of SETD1A could confer risk for schizophrenia, we have performed genome-wide gene expression profiling of a commonly used human neuroblastoma cell line in which SETD1A expression has been experimentally reduced using RNA interference (RNAi). We identified 1031 gene expression changes that were significant in two separate RNAi conditions compared with control, including effects on genes of known neurodevelopmental importance such as DCX and DLX5. Genes that were differentially expressed following SETD1A knockdown were enriched for annotation to metabolic pathways, peptidase regulator activity and integrin-mediated regulation of cell adhesion. Moreover, differentially expressed were enriched for common variant association with schizophrenia, suggesting a degree of molecular convergence between this rare schizophrenia risk factor and susceptibility variants for the disorder operating more generally.

overall_design: siRNA mediated knock down of SETD1A in SH-SY5Y cells. 4 controls, 4 siRNA1, 4 siRNA2

first: Darren

last: Cameron

first: Derek

last: Blake

first: Nicholas

last: Bray


title: IRCC Breast Cancer dataset

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

country: Italy

institute: Candiolo Cancer Institute, University of Torino

summary: Dataset of frozen breast cancer surgical specimens collected between 1988 and 2001, and profiled at IRCC (Institute for Cancer Research and Treatment (IRCC), Candiolo, Italy).

overall_design: Expression profiling of frozen breast tumor samples annotated with clinical information

first: Claudio

last: Isella

first: Tommaso

last: Renzulli

first: Michele

last: De Bortoli


title: Genome-wide analysis of cfDNA fragmentation patterns and nucleosome positioning in dual enzyme-digested NIPT quality control materials (DENQCMs) and maternal plasma

city: Wenzhou

first: Ziyang

last: Li

state: Zhejiang Province

address: University-town, Chashan

institute: Wenzhou Medical University

summary: The genome-wide analysis of cfDNA fragmentation patterns in DENQCMs and maternal plasma was performed by deep sequencing using Illumina Novaseq to confirm their biological characteristics. We first performed deep whole genome sequencing of the cfDNA extracted from DENQCMs and maternal plasma cfDNA. Then we analyzed the sequencing data and compared various characteristics of cfDNA fragmentation patterns, such as dinucleotide composition, nucleosome protection length, and nucleosome occupancy based on a windowed protection score (WPS), to the submitter-provided processed data from a healthy individual IH01 (GEO accession GSM1833276).

overall_design: cfDNA profiles of 2 samples were generated by deep sequencing using Illumina NovaSeq.

first: Rui

last: Zhang

first: Jiansheng

last: Ding


title: RNA-seq analysis of cry vvd wc-1 triple knockout(△cry,△vvd,△wc-1) strain in the filamentous fungus neurospora crassa

city: Guangzhou

first: Ma

last: Huan

state: Guangdong

address: 132 East Waihuan Rd, Rm 438 Higher Education Mega

institute: Sun Yat-Sen University

summary: Analysis of genes differentially expressed in △cry,△vvd,△wc-1 strain under different light intensity

overall_design: Total RNA obtained from isolated Neurospora crassa strains(△cry,△vvd,△wc-1 strain) grown in dark, 1000lux or 5000lux with 2 replicates.

first: Huan

last: Ma

first: Jinhu

last: Guo


title: Cardiac Muscle Ring Finger-1 (MuRF1) and Transcriptional Regulation of Ischemia-Reperfusion Injury In Vivo

city: Chapel Hill

first: Monte

middle: Shaw

last: Willis

address: 103 Mason Farm Road, MBRB 2340B

department: Pathology & Laboratory Medicine

institute: University of North Carolina

summary: We previously identified a role for the muscle-specific ubiquitin ligase MuRF1 (Muscle Ring Finger-1) in cardiac ischemia-reperfusion (I/R) injury. We found that cardiomyocyte-specific (alphaMHC-) MuRF1 transgenic mice (MuRF1 Tg+) mice were significantly protected from I/R injury. As we discovered MuRF1’s regulation of other transcriptions factors, we sought to identify other ways in which MuRF1 was cardioprotective in I/R injury. In the present study, we first identified the regulation of MuRF1 expression by qPCR in a porcine model of I/R injury. MuRF1 mRNA significantly increased within 90 minutes of I/R injury. We next assayed MuRF1 Tg+ ventricular tissue after I/R reperfusion injury by microarray (44K transcripts) to identify how MuRF1 regulates the transcriptome. We identified 71 significantly altered genes having a >1.5-fold (p<0.01) in MuRF1 Tg+ and wildtype hearts challenged with I/R injury (or sham operation). Functional annotation of the top upregulated genes found enrichment for myogenesis, cell adhesion, and nucleic acid metabolism. TRANSFAC analysis of MuRF1 Tg+ significant genes identified enrichment for genes (30-53%) with promoter regions recognized by the transcription factors MAZ, PIT1, VMW65, and BACH2. The transcription factor MAZ binds muscle creatine kinase (MCK) promoter in skeletal and cardiac myocytes, known most for its regulation of myogenin and MEF2C in cardiomyocytes. While the role of PIT1 and BACH2 in adult cardiomyocytes is not clear, VMW65 is a powerful transactivator with functions in chromatin remodeling. In neonatal cardiomycoyte I/R injury, VMW65 associates with HIF1alpha to upregulate cardioprotective VEGF, Glut-1, Glut-4, HSP70, and iNOS expression. These findings elucidate the MuRF1-specific regulation of genes in cardiac I/R injury that are associated with cardioprotection and may represent multiple additional direct or indirect mechanisms that MuRF1 regulates cardiomyocyte signaling.

overall_design: Four strain-matched groups of 12-16 week old mice were investigated: 1) Wild-type (MuRF1+/+) sham operated; 2) MuRF1 Tg+ sham operated; 3) Wild-type (MuRF1+/+) ischemia reperfusion (I/R) injury; 4) MuRF1 Tg+ I/R injury. Biological replicates: 3 per genotype per surgery group. Whole hearts were harvested and the tissue above the LAD ligation and below the LAD ligation (or potential ligation site in sham surgery animals) were analyzed by microarray (two samples from each heart, above and below).


title: Protective effects of SGLT2 inhibitors in human proximal tubular cells

status: Public on Jan 04 2019

city: Innsbruck

first: Johannes

last: Leierer

address: Anichstr. 35

department: Internal Medicine IV - Nephrology

country: Austria

institute: Medical University Innsbruck

summary: Effects of SGLT2 inhibitors on gene expression were evaluated in two independent human proximal tubular cell lines using microarray hybridization analysis followed by pathway analysis as well as qPCR- and ELISA-based verification on mRNA and protein level

overall_design:
Human renal proximal tubular cells (HK2 and RPTEC/TERT1) were cultured in the respective medium. All cells were grown at 37 °C in a humidified atmosphere with 5% CO2.
After growth to confluency, cells were serum- and supplement starved for 24 hours. Thereafter, cells were treated with either Empagliflozine (500nM), Canagliflozine (500nM) or TGF-beta1 (10ng/ml) for 24 hours in the absence of serum and any other growth supplements. Unstimulated control cells were grown in serum- and supplement-free medium.

first: Markus

last: Pirklbauer

first: Herbert

last: Schramek

first: Petra

last: Staudinger


title: LncRNA expression in 95C/95D lung cancer cell line

city: xian

first: yingxuan

last: tian

state: Xi'an, Shaanxi

address: Xiwu road No.36

institute: the Second Affiliated Hospital

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

summary: To determine the lncRNA expression profile inexpression differences with metastasis characteristics, we uesed lncRNA microArray analysis form Arraystar to examine the expression of lncRNAs in  in 95c/95D lung cancer cell lines.

overall_design: The Arraystar LncRNA V3.0 chip were used to detect differential LncRNA in two lung cancer cell lines with different metastatic characteristics, 95c with low metastatic characteristics and 95D cell lines with corresponding high metastatic characteristics.

first: Shuanying

last: Yang


title: Comparative analysis of miRNA transcriptome in tobacco under cold stress

city: Changsha

first: Xianwen

state: Hunan

address: 1 Nongda Road Furong district

institute: Hunan Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: The study aims to elucidate the cold response mechanism of miRNAs for tobacco

overall_design: Examination of miRNA profile in different tobacco genotypes under cold stress

first: Hu

last: Risheng

first: Zhang

last: Xianwen


title: Comparative analysis of mouse CD8+ Teff cells infiltrating distinct organ targets of aGVHD by gene expression profiling

city: Budapest

first: Nikolett

last: Lupsa

state: Pest

address: Nagyvárad tér 4

department: Genetics, Cell-and Immunbiology

country: Hungary

institute: Semmelweis University

summary: This study seeks a better understanding of the functional differences emerging between mouse CD8+ T effector (Teff) cells infiltrating three distinct mucosal environments; the small intestine, the lung and the liver. CD8+ Teff cells immigrating in the target organs were generated using a murine experimental acute graft versus host disease (aGVHD) model. For this purpose, congenially labeled CD45.1 OT-I CD8+ Teff cells were transplanted to and activated in a lethally irradiated allogeneic CD45.2 host constitutively expressing their cognate antigen, the chicken ovalbumin protein. CD8+ Teff cells were retrieved from their respective organ environments by automated organ disintegration and MACS sorting, and compared with each other by whole genome gene expression profiling. Peripheral blood derived circulating CD8+ Teff cells were also analyzed, serving as circulating peripheral T effector cell controls

overall_design: Lethal acute graft versus host disease was induced in healthy 8-16 weeks old C57Bl/6 m-act OVA female mice (n=5-6) by allogeneic bone marrow transplantation. Recipient m-act OVA mice received total body irradiation and were transplanted with 3x10E+6 bone allogeneic marrow cells and 1.5x10E+7 splenocytes from 8-16 weeks old C57Bl/6  OT-I mice serving as donors. Graft OT-I CD8+ T cells were obtained from CD45.1 animals, while all other graft cells and recipients carried the CD45.2 allele. Four days after bone marrow transplantation grafted CD45.1 CD8+ OT-I T cells were recovered from the livers, lungs and small intestines of m-act OVA mice with full-fledged acute GVHD by MACS sorting of CD45.1+ cells, and subjected to whole genome gene expression profiling.

first: Barbara

last: Ersek

first: Peter

last: Pocza

first: Eszter

last: Sarzsinszky

first: Anett

last: Toth

first: Bence

last: Bagita

first: Hargita

last: Hegyesi

first: Andras

last: Falus

first: Geza

last: Safrany

first: Matolcsy

last: Andras

first: Edit

last: Buzas

first: Zoltan

last: Pos


title: Characterization of resident CD8+ Trm cell populations using whole-genome biomarker analysis

summary: This study seeks a better understanding of the functional differences between naturally acquired murine CD8+ T resident memory (Trm) cells of three distinct mucosal environments; the small intestine, the lung and the liver. CD8+ Trm cells of healthy young adult mice were retrieved from their respective organ environments by automated organ disintegration and MACS sorting, and compared with each other by whole genome gene expression profiling. Peripheral blood derived circulating CD8+ Tem cells were also analyzed, serving as nonresident peripheral memory T cell controls, in an attempt to identify common characteristics of resident mucosal CD8+ Trm subsets, as well.

overall_design: The livers, lungs, and small intestines of 8-16 weeks old healthy wild type C57Bl/6 mice were isolated to collect CD8+ T resident memory (Trm) cells by MACS cell sorting (n=5-6). Cirulating CD8+ T effector memory (Tem) cells were also collected from the peripheral blood by MACS sorting to serve as a reference, representing a circulating, nonresident CD8+ T memory T cell control. Finally, whole organ lysates were also collected as controls for possible parenchymal cell contamination of MACS sorted cells (n=3)


title: Comparative analysis of murine CD8+ resident memory and effector T cells in various organ environments

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

overall_design: Refer to individual Series


title: Recovery of the synaptic transmission genomic fabrics in the hypothalamic paraventricular nucleus of a rat model of autism treated with ACTH

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

summary: We profiled the whole transcriptomes of male and female rat hypothalamic paraventricular nuclei to determine the remodeling of the genomic fabrics responsible for the glutamatergic, GABAergic, dopaminergic, cholinergic and serotonergic transmission in epilepsy and recovery following treatment with ACTH. The rats were prenatally exposed (G15) to betamethasone followed by repeated adiministration of N-Methyl-D-Aspartic acid (NMDA) on postnatal days 12, 13 and 15 which triggered infantile spasms. Pups were treated with ATCH on days 13, 14 and 15 prior to NMDA administration to determine what effects the treatment had on transcriptome recovery. Our Genomic Fabric Paradigm (GFP) is proposed as a transformative research approach to enhance the understanding of the brain transcriptomic alterations in epileptic rats and recovery following various treatments. The genomic fabric of a particular synapse is the structured transcriptome associated with the most interconnected and stably expressed gene network responsible for that type of neurotransmission. GFP refines the description of functional pathways by selecting the most prominent genes and determining their networking.  Moreover, it quantifies the remodeling of functional pathways and their interplay in disease and recovery in response to a treatment. We found that priming with betamethasone had substantial consequences on the topology of the genomic fabrics of all kind of synaptic transmission and that NMDA-induced spasms strongly exacerbated the remodeling of these fabrics. ACTH treatment induced a moderate recovery of the normal synaptic transcriptomes.

overall_design: One tissue (P = hypothalamic paraventricular nucleus) x one prenatal exposures (B = betamethasone) x one condition for the betamethasone expossed rats (Y with autistic behavior) x one postnatal treatment (A = ACTH) x two sexes (M, F) . Biological replicates: 4 PBYAM, 4 PBYAF.

middle: A

first: Tamar

last: Chachua

first: Sanda

first: Jana

last: Velíšková

first: Libor

last: Velíšek


title: Synergistic cytotoxicity of renieramycin M and doxorubicin in MCF-7 breast cancer cells

city: Quezon City

first: Jortan

middle: Oste

last: Tun

state: National Capital Region

address: Velasquez Street

department: Marine Science Institute

country: Philippines

institute: University of the Philippines

summary:
Renieramycin M (RM) is a KCN-stabilized tetrahydroisoquinoline purified from the blue sponge Xestospongia sp., with nanomolar IC50s against several cancer cell lines. Our goal is to evaluate its combination effects with doxorubicin (DOX) in estrogen receptor positive MCF-7 breast cancer cells. MCF-7 cells were treated simultaneously or sequentially with various combination ratios of RM and DOX for 72 h. Cell viability was determined using the MTT assay. Synergism or antagonism was determined using curve-shift analysis, Combination Index method and isobologram analysis. Synergism was observed with pharmacologically achievable concentrations of DOX when administered simultaneously, but not sequentially. The IC95 of RM and DOX after combination were reduced by up to 4-fold and 8-fold, respectively. To gain insights on the mechanism of synergy, real-time profiling, cell cycle analysis, apoptosis assays, and transcriptome analysis were conducted. The combination treatment displayed similar profile with DNA-damaging agents and induced a greater and faster cell killing. The combination treatment also showed an increase in apoptosis. DOX induced S and G2/M arrest while RM did not induce significant changes in the cell cycle. DNA replication and repair genes were commonly downregulated by RM and DOX. p53 signaling and cell cycle checkpoints were regulated by DOX while ErbB/PI3K-Akt, integrin and focal adhesion signaling were regulated by RM upon combination. Genes involved in cytochrome C release and interferon gamma signaling were regulated specifically in the combination treatment. This study serves as basis for in vivo studies and provides a rationale for using RM in combination with other anticancer drugs.
We used microarray-based transcriptome profiling to gain insights to the mechanism of action of the individual drugs and the synergistic drug combination

overall_design: MCF-7 cells were treated with near IC50 concentrations of RM (6.25 nM), DOX (313 nM) and its combination (RM+DOX) for 60 h. Individual drug treatments and vehicle control were prepared in duplicates, while the combination treatment was prepared in triplicates.

middle: O

first: Lilibeth

last: Salvador-Reyes

first: Michael

last: Velarde

first: Naoki

last: Saito

first: Khanit

last: Suwanborirux

first: Gisela

middle: P

last: Concepcion


title: Prenatal betamethasone remodels the genomic fabrics of the synaptic transmission in the rat hypothalamic paraventricular nucleis

summary: We profiled the whole transcriptomes of male and female rat hypothalamic paraventricular nuclei to determine the remodeling of the genomic fabrics responsible for the glutamatergic, GABAergic, dopaminergic, cholinergic and serotonergic transmission in rats prenatally exposed (G15) to betamethasone. Pups were treated with saline on days 13, 14 and 15. Our Genomic Fabric Paradigm (GFP) is proposed as a transformative research approach to enhance the understanding of the brain transcriptomic alterations in epileptic rats and recovery following various treatments. The genomic fabric of a particular synapse is the structured transcriptome associated with the most interconnected and stably expressed gene network responsible for that type of neurotransmission. GFP refines the description of functional pathways by selecting the most prominent genes and determining their networking.  Moreover, it quantifies the remodeling of functional pathways and their interplay in disease and recovery in response to a treatment. We found that priming with betamethasone had substantial consequences on the topology of the genomic fabrics of all kind of synaptic transmission.

overall_design: One tissue (hypothalamic paraventricular nucleus, P) x one prenatal exposures (B = betamethasone) x one condition (N =no spasms) x one postnatal treatment (S = saline) x two sexes (M,F) . Biological replicates: 4 PBNSM, 4 PBNSF.


title: Gene expression profile of human cancer associated hepatic stellate cells in HBV related hepatocellular carcinoma (HCC)

status: Public on Jan 03 2019

city: Shanghai

first: RUI

last: LIAO

state: Shanghai

address: Yixueyuan Road

department: Zhongshan hospital

institute: Fudan University

summary: We identified the genomic characteristics of peritumoral hepatic stellate cells (HSCs) in HBV related HCC. Expression levels of 17160 genes were compared between quiescent and activated HSCs and cancer associated myofibroblasts (CAMFs) from three independent samples per group. We find that among all significant changed genes (≥2-fold change and p<0.05), there were only 188 upregulated and 467 downregulated genes in peritumoral HSCs compared to intratumoral CAMFs. Compared with quiescent HSCs, the same patients-derived culture activated HSCs yielded as many as 1485 upregulated and 1471 downregulated genes. Between peritumoral HSCs/intratumoral CAMFs and culture-activated HSCs , there are 4479 and 3540 upregulated genes, and 3691 and 3380 downregulated genes, respectively. Between peritumoral HSCs/intratumoral CAMFs and quiescent phenotype HSCs, there are 1032 and 994 upregulated genes, and 1654 and 1188 downregulated genes, respectively.

overall_design: Examination of different gene expression in 4 cell phenotypes of hepatic stellate cells

first: Rui

last: Liao

first: Shuang-Jian

last: Qiu


title: Genomic Analysis of DNA Double-Strand Break Repair in Escherichia coli

city: Edinburgh

first: Benura

last: Azeroglu

address: Alexander Crum Brown Road

institute: University of Edinburgh

summary: Counting DNA reads using whole genome sequencing is providing new insight into DNA double-strand break repair (DSBR) in the model organism Escherichia coli. We describe the application of RecA chromatin immunoprecipitation coupled to genomic DNA sequencing (RecA-ChIP-seq) and marker frequency analysis (MFA) to analyse the genomic consequences of DSBR.

overall_design: RecA binding to the chromosome of two E. coli strains was analysed by RecA-ChIP.  Two biological repeats were carried out for each of the two strains. One strain experienced an induced DNA double strand break (DL4184) and one did not (DL4201).  Both strains were recombination proficient.

first: A

middle: M

last: Hasan

first: David

last: Leach


title: Gene expression signatures after immunisation with a range of live, inactivated and adjuvanted vaccines (BIOVACSAFE protocols 305A, 305B and 305C)

city: London

last: Lewis

address: Du Cane Road

department: ICRF

institute: Imperial College London

summary: The time course of whole blood gene expression was determined in healthy adult participants residing in an inpatient unit (CRC, University of Surrey, UK) to minimise background environmental variation, who were randomised into three protocols (305A, 305B and 305C) with study groups within each protocol (n = 20/21) receiving a single immunisation with a licensed vaccine or saline placebo control.

overall_design: Participants were randomised to receive one of the following vaccines: Protocol 305A: STAMARIL: subcutaneous live yellow fever vaccine given to yellow-fever seronegative participants; VARILRIX: subcutaneous live varicella zoster vaccine given to varicella zoster seropositive participants. Protocol 305B: ENGERIXB1: intramuscular alum-adjuvanted hepatitis B vaccine - priming dose given to hepatitis B naive participants; ENGERIXB3: intramuscular alum-adjuvanted hepatitis B vaccine  - second booster dose given to ENGERIXB1 participants at 6 months. Protocol 305C: AGRIPPAL: intramuscular seasonal influenza vaccine; FLUAD: intramuscular MF59C-adjuvanted seasonal influenza vaccine. PLACEBOAB1C : a control group distributed across the three protocols that received immunisation with 0.5 mL normal saline intramuscularly (protocols 305B and 305C) or subcutaneously (305A). PLACEBOB3  - control participants in protocol 305B also received a second intramuscular saline injection at 6 months to control the participants receiving ENGERIXB3. Participants were resident in an inpatient unit between days -1 and 5. Pre-immunisation baseline samples were drawn at 08:00H on days -1 and 0. Vaccines were administered at 08:00H on day 0, and further samples collected at 08:00H on days 1,2,3,4 and 5. Participants left the inpatient unit and returned on days 7, 14, 21 and 28 to have samples drawn. All samples were collected into PaxGene tubes.

first: January

last: Weiner

first: Jeroen

last: Maertzdorf


title: Genomic Analysis of DNA Double-Strand Break Repair in Escherichia coli (MFA profiles)

overall_design: Comparison of MFA profiles resulting from three different methods.  Two biological repeats were carried out for each of the for strains for all three methods. Two strains experienced an induced DNA double strand break (DL4184 and DL4243) and two did not (DL4201 and DL4257).  Two strains are wild-type for the ruvAB gene (DL4184 and DL4201) and two strains have the ruvAB gene deleted (DL4243 and DL4257). The analysis contains four re-analysed samples from GSE117541 (GSM3302820, GSM3302821, GSM3302824 and GSM3302825).


title: A Robust Auxin Response Network Controls Embryo and Suspensor Development through a bHLH Transcriptional Module

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Land plants can reproduce sexually by developing an embryo from a fertilized egg cell. However, embryos can also be formed from other cell types in many plant species. A key question is thus how embryo identity in plants is controlled, and how this process is modified during non-zygotic embryogenesis. The Arabidopsis zygote divides to produce an embryonic lineage and an extra-embryonic suspensor. Yet, normally quiescent suspensor cells can develop a second embryo when the initial embryo is damaged, or when response to the signaling molecule auxin is locally blocked. Here we have used auxin-dependent suspensor embryogenesis as a model to determine transcriptome changes during embryonic reprogramming. We find that reprogramming is complex and accompanied by large transcriptomic changes prior to anatomic changes. This analysis revealed a strong enrichment for genes encoding components of auxin homeostasis and response among misregulated genes. Strikingly, deregulation among multiple auxin-related gene families converged upon re-establishment of cellular auxin levels or response. This suggests a remarkable degree of feedback regulation to create resilience in auxin response during embryo development. Starting from the transcriptome of auxin-deregulated embryos, we identify an auxin-dependent bHLH transcription factor network that mediates the activity of this hormone in suppressing embryo development from the suspensor.

overall_design: Wild-type, bHLH49-mutant and bHLH49-overexpressing plants were grown for 4 days on MS, whereafter roots were harvested and total RNA was isolated.

first: Tatyana

last: Radoeva

first: Mark

middle: V

last: Boekschoten

middle: J

first: Dolf

last: Weijers


title: Endothelium muscle-specificity induction and fibroblast recruitment in engineered 3D human muscle environment for the study of fibrosis

status: Public on Jan 02 2019

city: Biella

first: Paola

last: Ostano

address: via Malta 3

institute: Fondazione Edo ed Elvo Tempia

summary: The integration of vascular structures into in vitro cultured tissues provides realistic models of complex tissue-vascular interactions. Despite the incidence and impact of muscle-wasting disorders, advanced in vitro systems are still far from recapitulating the environmental complexity of skeletal muscle. Our model comprises differentiated human muscle fibers enveloped by a sheath of human muscle-derived fibroblasts and supported by a vascular network with mural-like cells. We here demonstrated the induction of muscle-specific endothelium and the self-organization of endomysial muscle fibroblasts mediated by endothelial cells. We employed this model to mimic the fibrotic environment characterizing muscular dystrophies and to highlight key signatures of fibrosis which are neglected or underestimated in traditional 2D monocultures. Overall, this vascularized meso-scale cellular construct finely recapitulates the human skeletal muscle environment and provides an advanced solution for in vitro studies of muscle physiology and pathology.

overall_design: Microarray analysis were performed to compare the gene expression of primary endothelial cells extracted from muscle biopsies and endothelial cells from the 3D vascularized muscle model.

first: S

last: Bersini

first: M

last: Gilardi

first: G

last: Ugolini

first: V

last: Sansoni

last: Talò

last: Perego

last: Zanotti

last: Mora

last: Soncini

last: Vanoni

last: Moretti


title: Clonality analysis in breast tumour pairs using DNA methylation data

city: Gothenburg

first: Jana

last: Biermann

address: Medicinaregatan 1F

country: Sweden

institute: University of Gothenburg

type: Methylation profiling by genome tiling array

summary: Multiple tumours from the same patient were analysed for DNA methylation to assess tumour clonality. Seventy-four tumours corresponding to 37 patients were stratified into four groups based on the anatomic location of the multiple breast cancers (ipsilateral or bilateral) and time interval between the diagnoses (synchronous or metachronous). Ipsilateral was defined as tumours occurring in the same breast while bilateral was defined as the occurrence of tumours in both breasts. Metachronicity was defined as a time interval greater than six months between the diagnoses of the first and second tumours, while synchronicity specified that the two tumours occurred concurrently (BM: bilateral-metachronous; BS: bilateral-synchronous; IM: ipsilateral-metachronous; IS: ipsilateral-synchronous). A subset of 16 samples was randomly selected to represent each clinical group with four samples corresponding to two patients per group and analysed for DNA methylation using Illumina Infinium Human MethylationEPIC BeadChips.

overall_design: Genomic DNA was isolated from fresh-frozen tissue samples

first: Toshima

middle: Z

last: Parris

first: Szilárd

last: Nemes

first: Anna

last: Danielsson

first: Hanna

last: Engqvist

first: Elisabeth

last: Werner Rönnerman

first: Eva

last: Forssell-Aronsson

first: Anikó

last: Kovács

first: Per

last: Karlsson

first: Khalil

last: Helou


title: Clonal relatedness in tumour pairs of breast cancer patients

type: Genome variation profiling by genome tiling array


title: Transcriptome of discoid lupus erythematosus (DLE) skin

city: Boston

first: Julio

last: Mantero

state: MA

address: 72 E Concord St

department: Rheumatology

country: USA

institute: Boston University School of Medicine

summary: We used microarrays to explore  gene expression in the skin of DLE patients

overall_design: 7 patients with DLE had biopsies taken, RNA was isolated and purified from whole tissue and arrayed


title: A Group of SUVH Methyl-DNA Binding Proteins Regulate Expression of the DNA Demethylase ROS1 in Arabidopsis

first: Mingguang

last: Lei

address: No. 3888, Chenhua Road

country: China

institute: Shanghai Center for Plant Stress Biology

type: Methylation profiling by high throughput sequencing

summary: DNA methylation is typically regarded as a repressive epigenetic mark for gene expression. Genome-wide DNA methylation patterns in plants are dynamically regulated by the opposing activities of DNA methylation and demethylation reactions. In Arabidopsis, a DNA methylation monitoring sequence (MEMS) in the promoter of the DNA demethylase gene ROS1 functions as a methylstat that senses these opposing activities and regulates genome DNA methylation levels by adjusting ROS1 expression. How DNA methylation in the MEMS region promotes ROS1 expression is not known. Here, we show that several Su(var)3-9 homologs (SUVHs) can sense DNA methylation levels at the MEMS region and function redundantly to promote ROS1 expression. The SUVHs bind to the MEMS region, and the extent of binding is correlated with the methylation level of the MEMS. Mutations in the SUVHs lead to decreased ROS1 expression, causing DNA hypermethylation at more than one thousand genomic regions. Thus, the SUVHs function to mediate the activation of gene transcription by DNA methylation.

overall_design: Examination of methylation level in 4 genotype plants.

first: Xinlong

last: Xiao

first: Viswanathan

last: Satheesh


title: Genome-Wide Analyses Identify Filamin-A (FLNA) as a Novel Downstream Target for Insulin and IGF1 Action.

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

institute: Tel Aviv University

summary:
Identification of filamin-A as a target for insulin and IGF1 action.
Insulin analogues have been developed to achieve further improvement in the therapy of diabetes. However, modifications introduced into the insulin molecule might enhance their affinity to the insulin-like growth factor-1 receptor (IGF1R). Most tumors, including endometrial cancers, express high levels of IGF1R. The present study was aimed at identifying the entire set of genes that are differentially activated by insulin glargine or detemir, in comparison to regular insulin and IGF1, in Type 1 and Type 2 endometrial cancer cell lines (ECC-1 and USPC-1, respectively). Global gene expression analyses demonstrated a ligand-dependent up-regulated expression of filamin-A (FLNA), a gene that encodes an actin filament cross-linking protein, in both endometrial cancer cell types. Silencing experiments linked to migration assays confirmed the role of FLNA in cell growth and motility. Our data suggest that the activation of distinct sets of genes by glargine may lead to stimulation of specific pathways or, alternatively, may provide additive effects, different from those classically induced by insulin. Given that metastasis is one of the major factors contributing to the aggressiveness of tumors, the identification of FLNA as a downstream target for insulin-like hormones may be of translational relevance in cancer research. Clinical studies in endometrial cancer may add further relevant information regarding the possible differential actions of insulin analogues with respect to native insulin.

overall_design: 20 Samples (arrays) were performed.

first: Daniel

last: Aizen

first: Rive

last: Sarfstein

first: Zvi

last: Laron

first: Ilan

last: Bruchim

first: Haim

last: Werner


title: Clonality analysis in breast tumour pairs using aCGH data

first: Jana

last: Biermann

summary: Multiple tumours from the same patient were analysed for copy number alterations to assess tumour clonality. Seventy-four tumours corresponding to 37 patients were stratified into four groups based on the anatomic location of the multiple breast cancers (ipsilateral or bilateral) and time interval between the diagnoses (synchronous or metachronous). Ipsilateral was defined as tumours occurring in the same breast while bilateral was defined as the occurrence of tumours in both breasts. Metachronicity was defined as a time interval greater than six months between the diagnoses of the first and second tumours, while synchronicity specified that the two tumours occurred concurrently (BM: bilateral-metachronous; BS: bilateral-synchronous; IM: ipsilateral-metachronous; IS: ipsilateral-synchronous).

first: Toshima

last: Parris

first: Szilárd

last: Nemes

first: Anna

last: Danielsson


title: Dual-center, dual-platform microRNA profiling identifies plasma biomarkers of adult temporal lobe epilepsy (Beaumont)

city: Dublin

first: Catherine

last: Mooney

address: Belfield

department: School of Computer Science

country: Ireland

institute: University College Dublin

summary:
There are no blood-based molecular biomarkers of temporal lobe epilepsy (TLE) to support clinical diagnosis. MicroRNAs are short noncoding RNAs with strong biomarker potential due to their cell-specific expression, mechanistic links to brain excitability, and stable and reliable detection in biofluids. Altered expression of circulating microRNAs has been reported in human epilepsy, but most studies collected samples from one clinical site, relied on a single platform for profiling or conducted minimal validation. We collected plasma samples from video-electroencephalogram-monitored adult TLE patients at epilepsy specialist centers in two different countries, performed genome-wide PCR-based and RNA sequencing during the discovery phase and validated in a large cohort of samples (>300 samples) that included patients with psychogenic non-epileptic seizures. After profiling, validation of the discovery cohort and validation in the larger patient groups we identified miR-27a-3p, miR-328-3p and miR-654-3p with strong TLE biomarker potential. Plasma levels of these microRNAs were regulated in the same direction in plasma from epileptic mice, and furthermore were not different to healthy controls in patients with psychogenic non-epileptic seizures. The biomarker potential was extended by determining microRNA copy number in plasma and we demonstrate rapid detection of these microRNAs using an electrochemical RNA microfluidic disk as a prototype point-of-care device. Investigation of the molecular transport mechanism in plasma determined analysis of all three microRNAs within the exosome-enriched provided highest diagnostic accuracy while levels of Argonaute-bound miR-328-3p selectively increased in patient samples collected after seizures. In situ hybridization revealed the presence of miR-27a-3p and miR-328-3p within neurons in human brain and bioinformatics analysis predicted targets linked to growth factor signaling and apoptosis. Taken together, this study extends evidence for the biomarker potential of circulating microRNAs for epilepsy diagnosis and mechanistic links to underlying pathomechanisms.
microRNA expression in the plasma of 16 patients with TLE, before and after seizure, and 16 controls was measured by TaqMan OpenArray Human MicroRNA Panel.

overall_design: microRNA expression in the plasma of 16 patients with epilepsy, before and after seizure, and 16 controls was measured by TaqMan OpenArray Human MicroRNA Panel.

first: Rana

last: Raoof

first: Sebastian

last: Bauer

first: Hany

last: El Naggar

first: Niamh

last: Connolly

first: Gary

last: Brennan

first: Elizabeth

last: Brindley

first: Thomas

last: Hill

first: Hazel

last: McArdle

first: Elaine

last: Spain

first: Robert

last: Forster

first: Jochen

last: Prehn

first: Hajo

last: Hamer

first: Norman

last: Delanty

first: Felix

last: Rosenow

first: David

last: Henshall


title: Dual-center, dual-platform microRNA profiling identifies plasma biomarkers of adult temporal lobe epilepsy (Marburg)


title: Gene expression underlying differential adult hind leg morphogenesis in honeybee castes [worker_queen_prepupae]

city: Piracicaba

first: Ana

middle: Durvalina

last: Bomtorin

state: São Paulo

address: R Ajudante Albano 847

country: Brazil

institute: Universidade de Sao Paulo

summary: Along with differences in physiological and behavioral characteristics, workers and queens of Apis mellifera also differ in appendage morphology. Some appendage specializations in the hind legs of honeybee workers, which are highly specialized pollinators, deserve special attention. The hind tibia of the worker has an expanded bristle-free region used for carrying pollen and propolis, the corbicula. In queens, this structure is absent. Although these morphological differences have been well characterized, the genetic inputs triggering the development of this alternative morphology have remained unknown. Through microarray analysis, we detected 1,952 genes that are differentially expressed during worker versus queen hind leg development. The gene expression signatures of the two castes have similar patterns of genes controlling development. At the beginning of the last larval instar, Ultrabithorax (Ubx) activators are more strongly expressed than in prepupae and early pupae; at this time Ubx expression is approximately 25 times higher. Within the gene expression signature, we identified a cluster formed by genes in which Ubx, Twist and Zeste binding sites are over-represented. This cluster includes genes for which Drosophila orthologs are known to be bound by Ubx, as in the case of lola. We also tested the extent of Ubx mRNA processing during wing and leg development.

overall_design: RNA samples from pools of hind legs imaginal discs from female larvae and hind legs from white-eyed pupae of queens (Q_PP) and workers (W_PP) were hybridized in pairs and in dye-swaps (Cy3/Cy5), twice, then, combined in silico.

middle: D

first: Angel

middle: R

last: Barchuk

first: Zilá

middle: L

last: Simões


title: Gene expression underlying differential adult hind leg morphogenesis in honeybee castes [worker-queen_pupae]

overall_design: RNA samples from pools of hind legs imaginal discs from female larvae and hind legs from white-eyed pupae of queens and workers were hybridized in pairs and in dye-swaps (Cy3/Cy5), twice, then, combined in silico.


title: Gene expression underlying differential adult hind leg morphogenesis in honeybee castes [worker]


title: Gene expression underlying differential adult hind leg morphogenesis in honeybee castes [queen]


title: Gene expression underlying differential adult hind leg morphogenesis in honeybee castes [worker-queen_larvae]


title: LncRNA regulated by hnRNPAB in HCC cell lines

status: Public on Jan 01 2019

first: Yi

last: Yang

address: 180 Feng Lin Road

institute: Liver Cancer Institute, Zhongshan Hospital, Fudan University

summary: To reveal the HNRNPAB-regulated lncRNAs, we performed microarray analyses to screen differential lncRNAs in HCC cells after stable overexpression or knockdown of HNRNPAB. MHCC97H and HCCLM3 (HCC cell lines with high-metastatic potentials), PLC/PRF/5 and HepG2 (HCC cell lines with low-metastatic potentials) were used in this study. HepG2-control, HepG2-hnRNPAB, PLC/PRF/5-control, PLC/PRF/5-hnRNPAB, MHCC97H-control, MHCC97H-sh-hnRNPAB, HCCLM3-control, HCCLM3-sh-hnRNPAB were perpared with hU6-MCS-CBh-gcGFP-IRES-puromycin-shRNA-HNRNPAB/mock lentiviral and Ubi-MCS-SV40-EGFP-IRES-puromycin-HNRNPAB/mock cDNA lentiviral,respectively, each performed in triplicate.

overall_design: HepG2-control, HepG2-hnRNPAB, PLC/PRF/5-control, PLC/PRF/5-hnRNPAB, MHCC97H-control, MHCC97H-sh-hnRNPAB, HCCLM3-control, HCCLM3-sh-hnRNPAB were perpared and validated by qRT-PCR. Independent triplicate RNA samples in each cell was subjected to lncRNA microarrays.

first: Zhi

last: Dai


title: Effects of PVP/PEI coated Ag nanoparticles on dietarily exposed mussels Mytilus galloprovincialis at different seasons: a transcriptomic study.

city: Leioa

first: Nerea

last: Duroudier

address: Bº Sarriena s/n

institute: University of the Basque Country

summary: The present study tried to assess transcription level effects in the digestive gland of female mussels dietarily exposed to Ag NPs and to compare such transcription profiles in two different seasons, autumn and spring, since mussels are expected to be at a different gamete developmental stage (early and advanced gametogenic stage, respectively).

overall_design: Mussels Mytilus galloprovincialis were fed daily for 21 days with Isochrysis galbana microalgae previously exposed for 24 hours to a dose close to environmentally relevant concentrations of 1 µg Ag/L PVP/PEI coated 5 nm Ag NPs (in spring) and to a higher dose of 10 µg Ag/L of the same Ag NPs both in autumn and in spring. Then, after 1 and 21 days, RNA of mussels was hybridized in an 8x60K custom microarray containing 7806 identified genes.

first: Pablo

last: Markaide

first: Miren

last: Cajaraville

first: Eider

last: Bilbao


title: Gene expression underlying differential adult hind leg morphogenesis in honeybee castes

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

overall_design: Refer to individual Series


title: Analysis of miRNA profiles in mucinous ovarian cancer cells that silenced PRKRA.

city: Houston

first: Takeshi

last: Hisamatsu

state: Texas

address: 1515 Holcombe Boulevard

department: Gynecologic Oncology and Reproductive Medicine

institute: The University of Texas MD Anderson Cancer Center

summary: We compared miRNAs expression in mucinous ovarian cancer cell between treated with siPRKRA and contrl siRNA. We hypothesize that PRKRA regulates chemosensitivity in mucinous ovarian cancer. Therefore, we aim to idetify the PRKRA-mediated miRNA which regulate chemosensitivity in mucinous ovarian cancer.

overall_design: We analyzed human ovarian mucinous cancer cells by Nanostring, and validated microRNA profiles after silencing PRKRA.


title: The role of miRNA disregulation in the development of HIV associated polyneuropathy

city: Edmonton

first: William

middle: George

last: Branton

state: Alberta

address: 611 HMRC University of Alberta

department: Medicine

institute: University of Alberta

summary: We used microarrays to compare the expression of miRNAs in patient with HIV showing no neurological complications to those with HAND in the presence or absence of active HIV encephalitis

overall_design: Total RNA was extracted was extracted from serum samples from 69 patients using the miRNeasy serum/plasma kit, labelled and hybridized to Affymetrix miRNA 3.0 chips to assess specific changes in miRNA expression to provide clues to host genes with altered regulation in HIV associated DSP.

first: Eugene

last: Asahchop

first: Anand

last: Krishnan

first: Patricia

last: Chen

first: Douglas

last: Zochodne

first: B

last: Brew

first: M

last: Gill

first: Christopher

middle: N

last: Power


title: Comparative transcriptome analysis reveals genes regulating myogenesis and adipogenesis among different pig breeds

city: Taian

first: Yuding

last: Wang

address: No. 61, Daizong Street

institute: Shandong Agricultural University

summary: We performed transcriptome analysis of the longissimus dorsi muscle of four pig breeds (L, LDPL, DPL, DLDPL). This study provides a reference for exploring transcriptome regulation mechanisms affecting muscle growth and development in different pig breeds.

overall_design: Examination of  transcriptional variation among four different pig breeds.

first: Rongsheng

last: Zhu

first: Hongmei

last: Hu


title: Transcriptional changes associated with advancing stages of heart failure underlie atrial and ventricular arrhythmogenesis    underlie atrial and ventricular arrhythmogenesis

city: Philadelphia

first: Mariana

middle: Alejandra

last: Argenziano

state: Pennsylvania

address: 3615 Civic Center Blvd

department: Human Genetics

institute: Children's Hospital Of Philadelphia

summary: Heart failure (HF) is a leading cause of mortality and is associated with cardiac remodeling. Vulnerability to atrial fibrillation (AF) has been shown to be greater in the early stages of HF, whereas ventricular tachycardia/fibrillation develop during late stages. Here, we explore changes in gene expression that underlie the differential development of fibrosis and structural alterations that predispose to atrial and ventricular arrhythmias.

overall_design: RNA from canine right atria (RA) and right ventricle (RV) from controls and ventricular tachypaced to generate heart failure (HF) at early stages (2 weeks) and late stages (5 week)  was  isolated and gene expression was analysed by the Affymetrix (Canine_2 canFam2)  chip (triplicates)


title: Arsenopyrite (FeAsS) interacting Lysinibacillus sp. B2A1 transcriptome analysis

city: Tainan

first: Jiin-Shuh

last: Jean

address: 1st University Road

department: Department of Earth Science

country: Taiwan

institute: National Cheng Kung University

summary: RNA-seq based indentification of responsive and critical genes which might be involved in the arsenopyrite (FeAsS) weathering by Lysinibacillus sp. B2A1

overall_design: We used RNA-seq to elucidate the unique transcriptome profile of Lysinibacillus sp. B2A1 during its interaction with arsenopyrite (FeAsS) mineral, promoting arsenic mobilization and mineral weathering; No arsenic mineral exposure was used as a control.

first: Jagat

last: Rathod


title: Genes regulated by miR-328-3p in ovarian cancer cells

city: Columbus

first: Qi-En

state: OH

address: 420 W.12th Avenue

department: Radiation Oncology

institute: The Ohio State University

summary: To identify genes regulated by miR-328-3p, we transfected miR-328-3p mimics in ovarian cancer cell line OV2008, and compared the gene expression profiles between miR-328-3p mimics transfected and Negative Control miRNA-transfected cells.

overall_design: Negative control miRNA and miR-328-3p mimics were transfected into OV2008 cells separately for 3 days. Gene expression patterns in these cells were investigated

first: Amit

last: Srivastava


title: RNA-Seq mapping enabled quantitative analysis of gene expression differences between WT and rbm48 mutants in Zea mays (Maize).

city: Gainesville

middle: Bradley

last: Barbazuk

state: Florida

address: UF-CGRC Room 407 2033 Mowry Rd

institute: University of Florida

summary:
Purpose: The goals of this study are to compare NGS-derived transcriptomes (RNA-Seq) derived from rbm48 mutant and WT maize endosperm tissue. Homozygous rbm48 mutants exhibit a seed defect and are seedling lethal. Maize Rbm48 is homologouse to a human protein (rbm48) that is  thought o be invoilved in the splicing of minor (U12) introns.  This study characterizes DEGs between rbm48 alleles umu1 and umu2 and their WT counterparts and serves to identify U12 introns exhibiting retention as evidenced by RNA-seq read density within U12 introns in rbm49 mutants relative to WT controls.
Methods: Endosperm mRNA profiles from 16-18 days after pollination (DAP) normal and rbm48 kernels in the Zea mays W22 background were generated by deep RNA-Seq. Total RNA was prepared for 4 biological replicates of paired rbm48 and normal sibling pools.  4 total RNA samples of rbm48 umu1 and their WT controls, and 4 samples of rbm48 umu2 and their WT controls were obtained (16 total). Non strand specific Tru-Seq illumine libraries were constructed and sequenced on the Illumina HiSeq. The sequence reads that passed quality filters were aligned with GSNAP, read counts/gene were determined with the HTSeq-Count utility in the HTSeq package and DEG analysis performed with DESeq2.  Counts to U2 and U12 introns were also assessed and intron retention was assessed by measuring the Percent Splice Out (PSO) proportions for individual introns between mutant and WT samples. (PSO) calculations are based on the established methods for examining exon skip proportions (PSI).
Conclusions: Differential gene expression analysis of rbm48 identifies large-scale changes. Considering counts in introns, the major U2-type introns are largely unaffected with only 3-5% of introns in expressed genes have a ΔPSO >20%  By contrast, 65% and 53% of U12-type introns in rbm48-umu1 and rbm48-umu2, respectively, have a ΔPSO >20% suggesting more than half of U12-type introns are retained in rbm48 mutants. These RNA-Seq data help demonstrate that rbm48 plays a role in splicing U12 introns.

overall_design: Endosperm mRNA profiles from 16-18 days after pollination (DAP) normal and rbm48 kernels in the Zea mays W22 background were generated by deep RNA-Seq. Total RNA was prepared for 4 biological replicates of paired rbm48 and normal sibling pools (16 samples total). 2x100bp PE sequencing performed on an Illumina HiSeq2000.

middle: B

first: Andrew

last: Settles

first: Shailesh

last: Lal


title: High temperature transcriptomes of mutants in HDA9, PIF4 and Col-0 wild type of young Arabidopsis seedlings

city: Utrecht

first: Basten

last: Snoek

address: Padualaan

department: Mol. Plant. Physiology

institute: Utrecht University

summary: We determined the transcriptomes of hda9-1, pif4-2 and wild type Col-0 seedlings of 2 day old and 7 day old, at control and high temperature conditions (22oC vs 27oC), in short day (8h) photoperiod

overall_design: Pooled seedlings, grown on sterile MS-agar plates, harvested at dawn of day 3 after initiation of germination (2 day old) and of day 8 (7 day old), in 3 replicates per mutant of 3 pooled independent batches (>50 seedlings per batch), genotype and temperature environment in short day conditions.

first: Lennard

middle: C

last: van der Woude

first: L

first: Marcel

last: van Verk

first: Martijn

last: van Zanten


title: Transcriptome Profiling of Bigelowiella natans in Response to Light Stress

city: Fredericton

first: Pattarasiri

last: Rangsrikitphoti

state: NB

address: 10 Bailey drive

institute: University of New Brunswick

summary: Bigelowiella natans is a marine chlorarachniophyte whose plastid was acquired secondarily via endosymbiosis with a green alga. Integrating a photosynthetic endosymbiont within the host metabolism on route to plastid evolution would require the acquisition of strategies for coping with changes in light intensity and modifications of host genes to appropriately respond to changes in photosynthetic metabolism. To investigate the transcriptional response to light intensity in chlorarachniophytes, we conducted an RNA-seq experiment to identify differentially-expressed genes following four-hour shift to high or very-low light.  A shift to high light altered the expression of over 2000 genes, many involved with photosynthesis, primary metabolism, and reactive-oxygen scavenging. These changes are related to an attempt to optimize photosynthesis and increase energy sinks for excess reductant, while minimizing photo-oxidative stress. A transfer to very-low light resulted in a lower photosynthetic performance and metabolic alteration, reflecting an energy-limited state. Genes located on the nucleomorph, the vestigial nucleus in the plastid, had few changes in expression in either light treatment, indicating this organelle has relinquished most transcriptional control to the nucleus. Overall, during plastid origin, both host and transferred endosymbiont genes evolved a harmonized transcriptional network to respond to a classic photosynthetic stress.

overall_design: 9 cDNA libraries were produced from RNA samples of 3 light condtions: very-low light (20 µmol quanta/m2/sec), low light (Reference, 60 µmol quanta/m2/sec), and high light (400 µmol quanta/m2/sec). Sampling done in triplicate. Libraries were prepared using the Illumina Truseq stranded mRNA library preparation kit.

first: Dion

middle: G

last: Durnford


title: Gene expression profile of the RAG2/pfp gene depletion on Spleen of mouse

city: Seoul

first: Yun-Jung

last: Choi

address: 120 Neungdon-ro,Gwangjib-gu

department: Animal biotechnology

country: South Korea

institute: KONKUK University

summary: It contains a disruption of the recombination activating gene 2 (RAG2)/pfp and fail to generate mature T or B or NK lymphocytes. (https://www.taconic.com)

overall_design: Gene expression profiling of spleen from Rag2/pfp_KO and wild-type mice.

first: Jin-Hoi

last: Kim


title: The methyltransferase HEN1 is required for microRNA and piRNA stability as well as larval metamorphosis in Nematostella vectensis

city: Plymouth, Devon

first: vengamanaidu

last: modepalli

address: The Laboratory,Citadel Hill

department: Cell and Molecular

country: United Kingdom

institute: Marine Biological Association of the UK

summary: Knockdown of Dicer and PIWI2 in Nematostella results in a developmental arrest. Small RNA sequencing revealed that the levels of both miRNAs and piRNAs drop dramatically in the morphant animals.

overall_design: Employ high throughput sequence of endogenous small RNAs

first: V

last: Modepalli

first: A

last: Fridrich

last: Maayan

first: Y

last: Moran


title: Trancriptomic and epigenetic analyses of mouse organoids expressing BrafV600E mutation [array]

city: BALTIMORE

first: hari

last: easwaran

state: MD

address: 1650 Orleans Street, CRB1, Room 530

department: Oncology

institute: Johns Hopkins University

summary: Abnormal promoter DNA hypermethylation arises early during tumorigenesis and yet its role in cancer initiation has remained underexplored. An important scenario for examining this is, BRAFV600E-mutant colon adenocarcinomas (COAD) which most often arise in the proximal colon and harbor extensive, abnormal gene promoter CpG-island methylation or the methylator phenotype (CIMP). How CIMP and BRAF-mutations specifically interact for COAD initiation has remained unclear. Using mouse colon-derived organoids, we show promoter hypermethylation spontaneously arises in wild type cells mimicking “aging like” phenotype. The silenced genes sufficiently activate the Wnt pathway, causing a stem–like state and profound differentiation block. This phenotype renders long-term cultured organoids to be rapidly susceptible to transformation by BRAFV600E with features of typical right-sided COAD. Our studies tightly link epigenetic abnormalities, suggested to arise with aging, to intestinal cell fate changes and define an “epi-driver” role for multiple abnormally silenced genes that predispose to BRAFV600E-driven colon tumorigenesis.

overall_design:
Cre-activable BrafV600E and wild type proximal colon organoids were derived from mice carrying heterozygous Cre-activable BrafV600E (termed Braf+/LSL). Lentiviral delivery of Cre with the lentiviral backbone alone serving as control (EV), is used to subsequently activate BrafV600E in the organoids. Expression and methylation analyses were done in organoids 5m after induction of oncogene, and in organoids selected to grow in medium without stem-cell niche factors (Base medium).
This Series represents the expression analysis.

first: Hari

last: Easwaran


title: Rotenone complex i mutants-Effect of the inhibition of the mitochondrial respiratory chain complex I (CI) on shoot initiation on protoplast-derived calli

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

summary: ra16-03_rotenone - rotenone_complex i mutants - How does inhibition of CI enhance organogenesis

overall_design: 14 dye-swap - gene knock out,genotype and ecotype comparison,time course

first: Pierre

last: Hilson

first: Alberto

last: Macho

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Gene expression profling of Mycobacterium tuberculosis H37Rv and H37RvΔdosSΔdosT in 0.2% glucose/acetate under aerobic/hypoxic conditions

city: New Delhi

first: Jaya

middle: Sivaswami

last: Tyagi

state: Delhi

address: Ansari Nagar

department: Biotechnology

country: India

institute: All India Institute of Medical Sciences

summary: The present study reports the gene expression data of Mycobacterium tuberculosis H37Rv and H37RvΔdosSΔdosT (DKO) grown on 0.2 % acetate/glucose under aerobic/hypoxic conditions. Acetate was reported to be present in granulomas of Mycobacterium tuberculosis infected guinea pigs which are also hypoxic. By exposing Mycobacterium tuberculosis H37Rv and H37RvΔdosSΔdosT to different combinations of granulomatous stresses (acetate/glucose and aerobic/hypoxic conditions) alongwith other experimental data, we were able to delineate a new signaling pathway that activates DevR (DosR) regulon through Acetyl phosphate. The presence of two pathways highlights the importance of targeting DevR and not DevS/DosT for intercepting DevRST signalling cascade.

overall_design: Agilent one-color experiment; Organism: Mycobacterium tuberculosis; Agilent Custom Mycobacterium tuberculosis Whole Genome Array 8 x 15k designed by University of Delhi South Campus Microarray Centre (UDSCMAC, AMADID: G2509F_034585); Labeling kit: Low Input Quick Amp WT labeling kit (Agilent Technologies G4140-90042)

first: Saurabh

last: Sharma

first: Priyanka

last: Kumari

first: Atul

last: Vashist

first: Malobi

last: Nandi

first: Chanchal

last: Kumar

middle: S


title: Gene expression profile of the RAG2/pfp gene depletion on Thymus of mouse

first: Yun-Jung

last: Choi

overall_design: Gene expression profiling of thymus from Rag2/pfp_KO and wild-type mice.

first: Jin-Hoi

last: Kim


title: Effect of cinacalcet HCL on gene expression in mouse kidney

first: R. Todd

last: Alexander

department: Paediatrics

country: Canada

institute: The University of Alberta

summary: In order to identify renal pathways regulated by activation of the calcium sensing receptor (CaSR) we performed a microarray on RNA isolated from kidneys of mice not treated or treated with conacalcet HCL

overall_design: 12 week male Mice fed standard chow or cinacalcet HCL (1mg/g body weight) for 5 days were euthanized and whole kidney extracted and then snap frozen. Total RNA was then isolated by Trizol exctration and an Agilent mouse 8 x 60K chip run for expression

first: R

middle: T


title: Gene expression profile of the RAG2/pfp gene depletion on LN of mouse

overall_design: Gene expression profiling of lymph node from Rag2/pfp_KO and wild-type mice.


title: Gene expression profile of the RAG2/pfp gene depletion on mouse spleen, lymph node (LN), and thymus

overall_design: Refer to individual Series


title: Promoter distortion and opening in the RNA polymerase II cleft

city: Göttingen

first: Christian

last: Dienemann

address: Am Faßberg 11

country: Germany

institute: MPI Göttingen

summary: Transcription initiation complexes

overall_design: Examination of the effect Ssl2 anchor away strains in S. cerevisiae on transcription

first: Patrick

last: Cramer


title: Allele specific effects of a Drosophila hybrid incompatibility gene

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

summary: Using Drosophila SL2 cells we induced overxpression of the HMR protein and generated genome-wide binding profiles by performing ChIP-Seq with anti-HMR antibody.

overall_design: Analysis of HMR binding at the genome upon induced overxpression in Drosophila SL2 cells

first: Andrea

last: Lukacs


title: Dynamic rewiring of transcription factor networks during smooth muscle cell phenotypic modulation (ChIP-Seq data sets)

first: Charles

middle: Yang

last: Lin

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: Phenotypic modulation of smooth muscle cells (SMC) is a hallmark of vascular disease and a classic cell state transformation mediated by convergent signal-integration in the nucleus. Here, using PDGF-mediated SMC activation, we describe for the first time the dynamic active chromatin response and global transcriptional remodeling of cell state. We find that PDGF stimulation drives global transcriptional amplification and anabolism concurrent with increased proliferation and motility. Kinetic gene expression and Brd4 chromatin co-activator occupancy analysis reveals transcription factor (TF) directed enhancer re-wiring shaped by an immediate-early (Jun/Fos) response followed by increased nuclear hormone receptor transcriptional signaling that is Rev-erbdependent. Interdicting signaling between enhancers and transcription via Brd4 inhibition halts canonical cellular features of PDGF stimulation, and in vivo Brd4 inhibition potently abrogates vascular injury responses. These data provide a global map of TF-directed chromatin remodeling during SMC phenotypic modulation and elucidate key therapeutic mechanisms of transcriptional inhibition in vascular disease.

overall_design: ChIP-Seq in rat aortic smooth muscle cells (RASMC) for Brd4, H3k27ac, and RNA PolII

first: Priti

last: Anand

first: Rachel

middle: A

last: Hirsch

middle: Y

first: Saptarsi

middle: M

last: Haldar


title: Dynamic rewiring of transcription factor networks during smooth muscle cell phenotypic modulation (RNA-Seq data sets)

overall_design: RNA-Seq in rat aortic smooth muscle cells (RASMC)


title: Dynamic rewiring of transcription factor networks during smooth muscle cell phenotypic modulation (ChIP-Rx data sets)

overall_design: ChIP-Rx in rat aortic smooth muscle cells (RASMC) for H3K27ac and input control


title: Dynamic rewiring of transcription factor networks during smooth muscle cell phenotypic modulation

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


title: Dynamic rewiring of transcription factor networks during smooth muscle cell phenotypic modulation (ATAC-Seq data sets)

overall_design: ATAC-Seq in rat aortic smooth muscle cells


title: Gene expression after human SW982 cells treated with anlotinib by a microarray profiling (Affymetrix)

city: Shanghai

first: Wenxi

last: Yu

state: N/A = Not Applicable

address: No.600, Yishan Road, Xuhui District, 200233 Shanghai, People's Republic of China

institute: Department of Oncology, Affiliated Sixth People's Hospital, Shanghai Jiaotong University

summary:
Anlotinib could significantly suppresses synovial sarcoma proliferation in PDTX model and cell lines.
To identify potential anlotinib targets in synovial sarcoma, we performed a microarray profiling (Affymetrix) in human SW982 cells treated with anlotinib.

overall_design:
Human synovial sarcoma SW982 cells were treated with anlotib, and a microarray profiling (Affymetrix) was conducted to investigate the potential gene expression change.
contributor: Jikai Com.Ltd


title: Gene expression after human SW982 cells treated with GINS1 knockdown by a microarray profiling (Affymetrix)

summary:
In vivo and vitro study, GINS1 was proven to act as an oncogene in proliferation of synovial sarcoma
Affymetrix GeneChip was used to describe an overview of GINS1 potential biological function through GINS1 knockdown in SW982 cells.

overall_design:
Human synovial sarcoma SW982 cells were treated with or without GINS1 knockout, and a microarray profiling (Affymetrix) was conducted to investigate the potential gene expression change.
contributor: Jikai Com.Ltd