title: Small RNA profiling from cultured cells and tissues derived from Parkinson's disease patient [small RNA-seq]

summary: High throughput sequencing of small RNAs (mature miRNA and piRNA/piRNA-like molecules) from control- and sporadic Parkinson´s disease patient derived fibroblasts (n=15), induced pluripotent stem cells (n=26) and differentiated midbrain neurons (n=10). In parallel, cingulate gyrus samples from eight control- and eight Parkinson´s disease patients obtained from the Netherlands Brain Bank were sequenced. We found significant differences between the groups in every cell type and in tissue.

overall_design:
Two-condition experiment in three cell types and brain tissue: Control- and Parkinson´s disease patient derived fibroblasts, induced pluripotent stem cells and differentiated neurons were compared. Fibroblast cell cultures were established from skin biopsies from six control patients and nine sporadic Parkinson´s disease patients and reprogrammed with the OSKM cocktail. Small RNA libraries were prepared with the  TrueSeq Small RNA kit (Illumina) and sequencing was performed on an Illumina HiSeq1000 instrument (1x50 bp). Differential expression analysis was performed comparing control- and Parkinson´s disease patient derived cells within each cell type (fibroblasts, induced pluripotent stem cells or neurons) with DESeq2.
Please note that Raw data is only available via dbGAP due to privacy concerns


title: The temporal expression of lncRNAs and mRNAs in the AOM/DSS induced primary colon cancer model

status: Public on Oct 12 2018

city: Chengdu

first: Hongxin

last: Deng

state: Sichuan

address: Ke-yuan Road 4, No. 1, Gao-peng Street

department: West China Hospital

country: China

institute: Sichuan University and Collaborative Innovation Center for Biotherapy

summary: Long noncoding RNAs (lncRNAs) have potential applications in clinical diagnosis and targeted cancer therapies. However, the expression profile of lncRNAs in colorectal cancer (CRC) initiation and progression is still unclear.In the present study, the expression profiles of lncRNAs and mRNAs were determined by microarray at specific tumor stages in an AOM/DSS-induced primary colon cancer model.

overall_design: A single AOM injection (10 mg/kg) is followed by three cycles of 2% DSS administration in the drinking water. The T0, T1, T2, and T3 samples indicated the time points of 0, 1, 2, and 10 weeks post-AOM injection. These differential expression genes (DEGs) exhibited a clear correlation with tumor progression.

first: Lei

last: Dai

first: Junshu

last: Li


title: AXL is a putative tumor suppressor and dormancy regulator in prostate cancer

status: Public on Oct 09 2018

city: Baltimore

first: Haley

middle: Dara

last: Axelrod

state: MD

address: 600 N. Wolfe St.

department: Urology

country: USA

institute: Johns Hopkins SOM

summary: To understand how AXL overexpression induces aggregation of prostate cancer cells, microarray analysis from prostate cancer cell lines was used to observe differences in gene expression of cells with high versus low aggregation potential upon AXL overexpression.

overall_design: C42B Tetracycline-On cells (Tet-Axl 1 and Tet-Axl 2) were cultured with doxycycline for 4 days, and then RNA was extracted and submitted for microarray analysis.

middle: D

first: Kenneth

middle: J

last: Pienta


title: RNA-seq of brain tissue from Parkinson's disease patients [coding exome RNA-seq]

status: Public on Oct 08 2018

city: Regensburg

first: Markus

last: Schulze

address: Franz-Josef-Strauss Allee 11

department: Neuropathology

country: Germany

institute: University Hospital Regensburg

type: Expression profiling by high throughput sequencing

summary: High throughput sequencing of coding exome RNA from cingylate gyrus brain tissue obtained from control- and Parkinson´s disease patients. In the Parkinson´s disease affected tissue, changes are present that are known to be related to the pathogenesis of neurodegenerative diseases.

overall_design:
Two-condition experiment: Cingulate gyrus from eight Control- and eight Parkinson´s disease patients. RNA was isolated from grey matter of the cingulate gyrus samples and libraries were prepared with the TrueSeq RNA Access Kit (Illumina) that is suitable for degraded RNA. Sequencing was performed on an Illumina HiSeq1000 instrument (1 x 50 bp)
Please note that Raw data is only available via dbGAP due to privacy concerns

last: Riemenschneider

first: Winkler

last: Jürgen

first: Winner

last: Beate


title: Global changes of gene expression inuced by MIR31HG knockdown

status: Public on Oct 07 2018

city: Beijing

first: Lingfei

last: Jia

address: 22 zhongguancun nandajie

department: Central lab

institute: Peking University of stomatology school and hospital

summary:
Human adipose-derived stem cells (hASCs) are a highly attractive source in bone tissue engineering.We found that MIR31HG significantly promote the osteogenic differentiation of hASCs. However, the underlying mechanisms still await investigations. Thus the alteration of gene expression induced by MIR31HG knockdown was investigated.
We used microarrays to detail the global programme of gene expression when MIR31HG was knocked down in hASCs and identified distinct classes of dn-regulated genes during this process.

overall_design: hASCs were transfected with shMIR31HG or the control vectors (shNC). Total RNA was isolated with Trizol from hASCs.

first: Yongsheng

last: Zhou


title: Monitoring the mating-type-driven transcriptomes of Aspergillus fumigatus

city: Erlangen

first: Sven

last: Krappmann

address: Wasserturmstr. 3/5

department: Institute for Microbiology

institute: FAU Erlangen-Nuernberg

summary: Sexual identity of the human pathogenic mold Aspergillus fumigatus is determined by the mating-type idiomorphs MAT1-1 and MAT1-2 residing at the MAT locus. Given that the MAT1 gene products are DNA binding master regulators that govern fruiting body formation, the MAT1-driven transcriptomes of A. fumigatus were monitored by conditional overexpression of either MAT1 gene followed by RNA-seq analyses.

overall_design: Overexpression (OE) of either mating-type factor was achieved by replacing the original promoter by a heterologous one (pxylP) that is conditionally active in the presence of xylose as sole carbon source. Strains were pre-grown in liquid cultures before shifting the fungal mycelia to inducing, xylose-containing culture medium. Two sets of strains were compared with the MAT1-1 and MAT1-2 wild-type (WT) progenitors D141 and Af293, respectively, serving as control samples that were compared to the recombinant OE strains AfS146 [pxylP::MAT1-1] and AfS147 [pxylP::MAT1-2], respectively. Two biological replicates per strain were generated, yielding eight samples that were evlauted a by case (OE) vs. control (WT) analysis for differentially expressed genes.

first: Yidong

last: Yu

first: Minou

last: Nowrousian


title: Comparative hepatic transcriptome analyses revealed possible pathogenic mechanisms of fasiglifam (TAK-875)-induced acute liver injury in mice

status: Public on Oct 10 2018

city: Nagoya-shi

first: Yuya

last: Urano

state: Aichi-ken

address: 65, Tsurumai-cho, Showa-ku

country: Japan

institute: Nagoya University

summary: Fasiglifam (TAK-875), a G protein-coupled receptor 40 (GPR40) agonist, was a drug candidate for type 2 diabetes. However, its development was terminated in phase 3 trials due to liver safety concerns. Although TAK-875 was reported to inhibit hepatobiliary transporters and disturb bile acid disposition, pathogenic mechanisms of TAK-875-induced liver injury are not fully understood. In this study, we sought to identify the mechanisms with a hepatic genome-wide transcriptomic analysis in a murine model. We demonstrated that, among the three GPR40 agonists, TAK-875, AMG-837 and TUG-770, only TAK-875 induced acute liver injury in mice. Transcriptome profiles of TAK-875-exposed liver was compared with those of non-hepatotoxic analogues AMG-837 and TUG-770 as negative controls and those of classical hepatotoxicants concanavalin A and carbon tetrachloride as positive controls. The comparative hepatic transcriptome analyses revealed the enrichment of genes involved in inflammation, endoplasmic reticulum (ER) stress, apoptosis, and hepatic lipid accumulation, suggesting that these events play pathophysiologic roles in the development of TAK-875-induced liver injury. These results were validated by quantitative PCR with significant changes in chemokines, danger signals, ER stress mediators, proapoptotic factors, and hepatic steatosis markers only in TAK-875-exposed liver. Pretreatment of TAK-875-administered mice with an ER stress inhibitor 4-phenylbutyric acid (4-PBA) alleviated the liver injury. Consistent with the in vivo study, pretreatment of HepG2 cells with 4-PBA significantly improved the decrease of cell viability induced by TAK-875. In conclusion, by a comprehensive transcriptomic analysis of GPR40 agonists, we found multiple possible processes that contribute to TAK-875-induced acute liver injury in mice.

overall_design: Liver samples were collected 24 hours after administration of each GPR40 agonist and vehicle. Total RNA was extracted from these liver samples and equal amount of RNA was pooled from 4 animals in each group.

first: Shingo

last: Oda

first: Koichi

last: Tsuneyama

first: Tsuyoshi

last: Yokoi


title: Role and function of Class III LitR, a photosensor homolog from Burkholderia multivorans ATCC 17616 in the regulation of folate production.

city: Fujisawa

first: Hideaki

last: Takano

state: KANAGAWA

address: 1866, Kameino

department: College of Bioresource Sciences

institute: Nihon University

summary: The LitR/CarH protein family is a adenosyl B12 (AdoB12)-dependent photoreceptor with DNA-binding activity and its homologs are widely distributed in the genome of diverged bacterial genera. Here, we studied a role and function of a LitR homolog from a Gram-negative soil bacteria Burkholderia multivorans, which has no AdoB12-binding domain. Transcriptome analysis revealed the existence of 19 light-induced genes (folE, cfa, litS, a Photolyase gene phrB2, cryB2) located in the flanking region of litR. Gene disruption of litR caused a constitutive expression of all light-inducible genes, while the mutation of the light-dependent expressed sigma factor litS abolished the transcription in cryB2, phrB2 operon and cfa operon, indicating that LitR and LitS play a central role in the light-inducible transcription. Gel-shift assay showed that a recombinant protein LitR specifically binds to the promoter region of litR and folE2 operon, and its ability was lowered by UV-A illumination. LitR absorbs maximally near 340 nm, and exhibited a photocyclic response and light-dependent subunit dissociation. Furthermore, the litR mutant produced a 20-fold high intracellular folate compared to the wild-type strain. Overall, the line of evidence suggest that Class III LitR light-dependently regulates the transcription of litR itself and folE2-litS operon, leading the production of folate, and then expressed RNA polymerase-LitS directs the transcription for phrB2 operon and cfa operon. Light-dependent characteristics suggests that Class III LitR in complex with a UV-A absorbing molecule has a novel light-sensing mechanism.

overall_design: Chromosomal RNA maps of wild-type cells cultured under the light conditions were compared with those of wild-type cells cultured under the dark conditions

first: Kenji

last: Ueda


title: RNA-seq, RRBS-seq and miRNA-seq study of Parkinson's disease patients

type: Methylation profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: RNA sequencing of red fruits of the Dongkui (DK) cultivar and the pink-white fruits of the Baidongkui (BDK) strain of Chinese bayberry

city: Fuzhou

first: Qihua

last: Lin

state: Fujian

address: No.102, Xiyuan Road,  Xindian Town, Jinan District

department: Tropical and subtropical fruit tree Research Laboratory

institute: Fruit Research Institute of Fujian Academy of Agricultural Sciences

summary: We have performed a transcriptome analysis of genes at three different ripening stages of the pink-white fruits and the ripe stage of the red fruits of Chinese bayberry. This analysis provided a total of 119,701 unigenes, of which 41.43% were annotated in the Nr database. Our results showed that the formation of the pink-white color in Chinese bayberry fruits depended on the anthocyanin metabolic pathway, regulated by MYB1. Downregulated expression of key anthocyanin biosynthetic pathway genes, such as UFGT, F3’H, and ANS at the late stage of fruits development compared with DK3 fruits resulted in the failure to form red fruits. Our findings shed light on the regulatory mechanisms and metabolic processes that control color development in the fruits of Chinese bayberry.

overall_design: the BDK transcriptome at three different fruits ripening stages (55 d, 70 d, and 85 d after flowering) and the DK transcriptome at the ripe fruits stage (85 d after flowering).

first: Zehuang

last: Zhang

first: Qiuzhen

last: Zhong


title: Transcriptome profile in RAW264.7 cells in response to the polysaccharide from the roots of Actinidia eriantha (AEPS)

status: Public on Oct 05 2018

city: Hangzhou

first: Xiangfeng

last: Chen

state: Zhejiang

address: Yuhangtang Road

institute: Zhejiang University

summary: Recent studies have reported the activation of macrophages by the polysaccharide from the roots of Actinidia eriantha (AEPS). This study aims to explore the potential role of mRNAs and lncRNAs in AEPS-activated macrophages.

overall_design: Total RNA was prepared from RAW264.7 macrophage cells treated with or without AEPS (50 μg/ml) for 4 hours (n=3 replicates per condition).

first: Hong

middle: X

last: Sun

first: Xiang

middle: F

first: Jing

last: Du


title: Liver RNA microarray from female HDAC6–/–, HDAC9–/– mice

status: Public on Oct 04 2018

city: Philadelphia

first: Wayne

middle: W

last: Hancock

state: PA

address: 916B ARC, 3615 Civic Ctr Blvd

institute: CHOP/UPenn

summary: Whole livers from HDAC6, HDAC9 deficient and wild type C57BL/6 mice, age 8-12 weeks, gender: female. Wild type mice with or without high fat diet

overall_design: Whole livers from C57BL/6 mice with HDAC6 or HDAC9 deletion, and wild type control with or without high fat diet after weaning (3/group). RNA was isolated and subjected to Mouse430a; Affymetrix microarrays.

first: Ulf

middle: H

last: Beier

first: Tatiana

last: Akimova

first: Rongxiang

last: Han

first: Liqing

last: Wang


title: Gene expressions in Compound-treated vs. non-treated fibroblast of Leigh syndrome by DNA microarray analysis

city: Shimotsuke-shi

first: Akihiko

last: Miyauchi

state: Tochigi

address: 3311-1 Yakushiji

department: Pediatrics

institute: Jichi Medical University

summary: To overview compound-responsive genes in fibroblast, we performed microarray analysis of ~63,000 genes in compound-treated fibroblast of LSND3

overall_design: We treated the fibroblasts with 1μM compound, extracted RNAs from compound- and non-treated fibroblasts at 24 h after treatment, and compared the gene expression ratio between the two groups. Two duplicate experiments.

first: Hitoshi

last: Osaka


title: Control and Linc-AAM (a lincRNA associated with activated macrophages) knockdown RAW264.7 cells expression profiling under AEPS (the polysaccharide from the roots of Actinidia eriantha) stimulation

summary: To gain an understanding of Linc-AAM function, we performed transcriptome analysis with microarray using Linc-AAM kncockdown RAW264.7 cells or control cells with or without AEPS treatment

overall_design: We preformed our transcriptome microarray analysis (Agilent SurePrint G3  8 × 60 k Mouse Gene Expression Microarray) in Linc-AAM knockdown and Scramble knockdown RAW264.7 cells with or without AEPS (50 μg/mL) for 4 hours.

first: Hongxiang


title: Global transcriptional analysis of Campylobacter jejuni NCTC 11168 after inactivation of flagella biosynthesis regulator FlhF

status: Public on Oct 03 2018

city: Yangzhou

first: Fangzhe

last: Ren

state: Jiangsu

address: East Wenhui Road No.12

institute: Yangzhou university

summary: Campylobacter jejuni produces a single flagellum on one or both poles of the cell, the polar flagella not only confer the bacterium darting motility but also involved in its virulence and metabolic processes. FlhF is a lately defined flagella biosynthesis regulator, but how it regulates flagella assembly isn’t clear at present. Previous research had indicated FlhF was associated with gene expression, to understanding its role in flagella system and its correlation with C. jejuni virulence, the global gene expression profiles of C. jejuni NCTC 11168 after inactivation of FlhF was analyzed. Transcriptome analysis revealed that ten genes were significantly differentially expressed with 6 down-regulated and 4 up-regulated, these genes are involved in diverse cellular functions including bacterial chemotaxis, flagellar assembly and two-component system, significance analysis revealed that the pathway of flagellar assembly was remarkable affected. Further studies were focused on the flagella system, FlhF was found play a global role as 63% (41/65) of the flagella genes were down-regulated, it influences flagella gene transcription from the early stage, this effect persists during the synthesis process and has a remarkable impact on the late part. The results above expand our cognition of this regulator, and also helpful for comprehensively and systematically reveal its role in flagella system.

sample_organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

overall_design: Gene expression profiles of C. jejuni strains were measured after grown in MH broth for 20h. Three biological replicates for broth C. jejuni NCTC 11168 (WT) and flhF mutant.

first: Jinglin

last: Huang

first: Xin-an

last: Jiao


title: Ikarugamycin blocks the glycolysis in pancreatic cancer

status: Public on Oct 02 2018

city: Shanghai

first: Shuheng

last: Jiang

address: 800 Dongchuan Road

institute: Shanghai Cancer Institute

summary: Analysis of gene alterations in PANC-1 cells treated with different concentration of Ikarugamycin (Ika). A broad variety of biological activities of IKA has been reported, such as immune regulation, cytotoxic properties, anti-tumor effects and other pharmacological effects. This study provides insight into molecular basis of Ika in pancreatic cancer.

overall_design: Three 500 nM Ika-treated PANC-1 cells, three 1.5 μM Ika-treated PANC-1 cells and three untreated controls.

first: Jiang

last: Shuheng

first: Xu

last: Minjuan


title: β-cryptoxanthin enhanced peripheral leukocyte functions, and transcriptomes of the peripheral neutrophil and liver in Holstein cattle

city: Morioka

first: Keiichiro

last: Kizaki

state: Iwate

department: Vet. Med.

institute: Iwate University

summary: We investigated the effect of oral administration of β-CRX on its serum concentration, peripheral leukocyte functions, and transcriptomic dynamics of the peripheral neutrophil and liver tissue in Holstein cattle.

overall_design: β-CRX (0.2 mg/kgBW) was administrated orally on day 0, and blood samples were collected at 0 and 7 days after administration in Holstein heifers or steers.

first: Yo-Han

last: Kim


title: INDUCTION OF HUMAN MESENCHYMAL STEM CELLS FROM NEONATAL AND ADULT SOURCES BY A SMALL MOLECULE COCKTAIL

city: Thuwal

first: Gerardo

last: Ramos-Mandujano

department: Biological and Environmental Science and Engineering Division

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

summary: Human mesenchymal stem cells (MSCs) are good candidates for brain cell-replacement strategies and has been already used as adjuvant treatment in neurological disorders. MSCs can be obtained from many different sources, and the present study compares the neuronal potential transdifferentiation of MSCs from adult and neonatal sources with a protocol previously tested, consisting in a cocktail of six small molecules: I-BET151, CHIR99021, Forskolin, RepSox, Y-27632, and dbcAMP (ICFRYA). A neuronal morphology and the presence of cells positive to neuronal markers (TUJ-1 and MAP2) were considered attributes of neuronal induction. The present study showed marked differences between MSCs from different sources in response to the transdifferentiation protocol here used. These results may contribute to identifying the best source of MSCs for potential cell-replacement therapies.

overall_design: Mesenchymal stem cells (MSCs) from umbilical cord blood (UCB-MSCs) or bone marrow (BM-MSCs) were cultured in with neuronal induction medium plus six small molecules (I-BET151, CHIR99021, Forskolin, RepSox, Y-27632, and dbcAMP). UCB-MSCs and BM-MSCs cultured in mesenchymal medium were incluided as CONTROL.

first: Lorena

middle: V

last: Cortes-Medina

first: Herminia

last: Pasantes-Morales


title: Real-time quantitative PCR analysis of pro-inflammatory gene expression in Human embryonic kidney cells 293 (HEK293)

city: Galveston

first: Istvan

last: Boldogh

state: Texas

address: 301 UNIVERSITY BLVD.

department: Microbiology & Immunology

institute: UNIVERSITY OF TEXAS MEDICAL BRANCH

summary:
To assess the role of 8-oxoguanine DNA glycosylase 1 (OGG1) on TNF induced pro-inflammatory gene expression.
We used Qiagen Human Inflammatory Cytokines & Receptors PCR Array (PAHS-011Z) to quantitate inflammatory gene expression dependent on OGG1.

overall_design: Triplicate cultures of cells (n = 3; -/+OGG1 SiRNA, -/+ Negative control SiRNA) were TNF exposed for 30 minutes or no TNF exposed, RNAs were isolated, pooled, cDNA were synthesized using Superscript® III First Strand Synthesis System (Invitrogen), mixed with equal amounts of 2X iTaq Universal SYBR Green Supermix (Bio-Rad) and 20 μl of reaction mixture was added to each well of the PAHS-011Z array. The qRT-PCR was performed using an ABI PRISM® 7000 Sequence Detection System as recommended by SA Biosciences.

first: Leopoldo

last: Aguilera-Aguirre

first: Wenjing

last: Hao


title: The role of the Synechocystis sp. PCC 6803 homolog of the circadian clock output regulator RpaA in day-night transitions

status: Public on Oct 01 2018

city: Freiburg

first: Christin

last: Koebler

address: Schaenzlestrasse 1

department: Institute of Biology III

institute: University of Freiburg

summary: Like many other organisms, cyanobacteria exhibit rhythmic gene expression with a period length of 24 hours to adapt to daily environmental changes. In the model organism Synechococcus elongatus PCC 7942 the central oscillator consists of three proteins: KaiA, KaiB and KaiC and utilizes the histidine kinase SasA and its response regulator RpaA as output-signaling pathway. Synechocystis sp. PCC 6803 contains two additional homologs of the kaiB and kaiC genes. Here we demonstrate that RpaA interacts with the core oscillator KaiAB1C1 of Synechocystis sp. PCC 6803 via SasA, similar to Synechococcus elongatus PCC 7942. However, interaction with the additional Kai homologs was not detected, suggesting different signal transduction components for the clock homologs. Inactivation of rpaA in Synechocystis sp. PCC 6803, lead to reduced viability of the mutant in light-dark cycles that aggravated under mixotrophic growth conditions. Chemoheterotrophic growth in the dark was abolished completely. In accordance, transcriptomic data revealed that RpaA is involved in the regulation of genes related to CO2‑acclimation and carbon metabolism under diurnal light conditions. Further, our results indicate that RpaA functions in the posttranslational regulation of glycogen metabolism as well, and a potential link between the circadian clock and motility was identified.

overall_design: We performed whole-genome transcript profiling of an rpaA deletion mutant and Synechocystis sp. PCC 6803 WT in light-dark cycles. Samples were taken 5.5 hours after onset of light (5.5 h) or dark (17.5 h). Two independent experiments were performed for each timepoint.

last: Köbler

first: Siri-Jasmin

last: Schultz

first: Dominik

last: Kopp

first: Karsten

last: Voigt

first: Annegret

last: Wilde


title: Comparison of PRPF4 knockdown in HEK293T cells compared to scrambled shRNA control

first: Tara

last: Davis

department: Biochemistry and Molecular Biology

institute: Drexel University College of Medicine

summary:
HEK293T cells transduced with two shRNAs from MISSION library (TRCN0000364755 and TRCN0000074769) using lentiviral delivery system. HEK293T cells transduced with scrambled shRNA, gifted from Dr. Mauricio Reginato. Sequence is 5′-CCTAAGGTTAAGTCGCCCTCGCTCTAGCGAGGGCGACTTAACCTT-3′. Primary contributions to creation of cell lines, preparation of RNA/cDNA for microarray, and validation of results were from Tara L Davis, S. RaElle Jackson, Beth Adams, Anh Trinh, Nicholas Fox, Jessica Kopenhaver, Alyson Hurlock, and Achraf Jardaly, all Drexel University College of Medicine, Philadephia PA, 19102. Hetty Rodriguez and John Tobias, affiliated with the Molecular Profiling Facility and Genomic Analysis Core Bioinformatics Group at the University of Pennsylvania, Philadelphia PA, performed Bioanalyzer and microarray expreriments and initial data processing.
pre-mRNA Processing Factor 4 (PRPF4) is a scaffolding protein, consisting of two N-terminal intrinsically disordered motifs and a C-terminal WD-40 domain. PRPF4 associates with the human spliceosome, the complex and dynamic machinery that removes intronic sequence from pre-messenger RNA (pre-mRNA). Although PRPF4 affects the ability of the spliceosome to assemble and catalyze splicing in vitro through de-stabilization of the tri-snRNP complex, little is known about what PRPF4 does to regulate transcription and splicing in vivo. To understand the function of PRPF4 in the nucleus, we knocked down PRPF4 in human cells. We characterized a set of alternative splicing and transcriptional events that are PRPF4-responsive. We used these splicing and transcriptional bioassays to show that PRPF4-responsive events are largely specific. The development of a bioassay for PRPF4 function can be used to answer fundamental questions about the role of spliceosomal proteins in regulating splicing and other nuclear functions.

overall_design: 3 replicates of PRPF4 knockdown cell lines in HEK293T cells, stably integrated, selected using puro, shRNAs TRCN0000364755 sequence 5'-CCGGCCACGAACTGTGTAGACATTGCTCGAGCAATGTCTACACAGTTCGTGGTTTTTG-3' and TRCN0000074769 sequence 5'-CCGGGCTCTCTCTAAGGAGCTGTTTCTCGAGAAACAGCTCCTTAGAGAGAGCTTTTTG-3'. 3 replicates of SCR control cell lines in HEK293T cells, stably integrated, selected using puro, sequence 5′-CCTAAGGTTAAGTCGCCCTCGCTCTAGCGAGGGCGACTTAACCTT-3′. Total RNA purified from ~1 million cells, cDNA converted using random hexamer primers, quantity measured using NanoDrop, quality quantified using BioAnaylzer). Affymatrix HTA2.0 array

middle: L

first: S

middle: R

last: Jackson

first: Beth

last: Adams

first: Anh

last: Trinh

first: Nicholas

last: Fox

first: Jessica

last: Kopenhaver

first: Alyson

last: Hurlock

first: Achraf

last: Jardaly

first: Hetty

last: Rodriguez

first: John

last: Tobias


title: Comparison of ZNF830 knockdown in HEK293T cells to scrambled shRNA control cells

summary:
HEK293T cells transduced with two shRNAs from MISSION library (TRCN0000180560 and TRCN0000148198) using lentiviral delivery system. HEK293T cells transduced with scrambled shRNA, gifted from Dr. Mauricio Reginato. Sequence is 5′-CCTAAGGTTAAGTCGCCCTCGCTCTAGCGAGGGCGACTTAACCTT-3′. Primary contributions to creation of cell lines, preparation of RNA/cDNA for microarray, and validation of results were from Tara L Davis, S. RaElle Jackson, Beth Adams, Anh Trinh, Jessica Kopenhaver, Alyson Hurlock, Angie Giang, and Purva Vaidya, all Drexel University College of Medicine, Philadephia PA, 19102. Hetty Rodriguez and John Tobias, affiliated with the Molecular Profiling Facility and Genomic Analysis Core Bioinformatics Group at the University of Pennsylvania, Philadelphia PA, performed Bioanalyzer and microarray expreriments and initial data processing.
Zinc Finger 830 (ZNF830) is a scaffolding protein, consisting of an N-terminal C2H2 zinc finger motif and a C-terminal domain of unknown function (DUF). ZNF830 associates with the human spliceosome, the complex and dynamic machinery that removes intronic sequence from pre-messenger RNA (pre-mRNA). Although ZNF830 knockdown in mice is lethal due to cell cycle defects, a common phenotype for regulators of alternative splicing, little is known about the targets of ZNF830 transcription and splicing regulation in human cells. To understand the function of ZNF830 in the nucleus, we knocked down ZNF830 in human cells. We characterized a set of alternative splicing and transcriptional events that are ZNF830-responsive. We used these splicing and transcriptional bioassays to show that ZNF830-responsive events are largely specific. The development of a bioassay for ZNF830 function can be used to answer fundamental questions about the role of spliceosomal proteins in regulating splicing and other nuclear functions.

overall_design: 3 replicates of ZNF830 knockdown cell lines in HEK293T cells, stably integrated, selected using puro, shRNAs TRCN0000180560 sequence 5'-CCGGGAGAATGCTGACAGCGATGATCTCGAGATCATCGCTGTCAGCATTCTCTTTTTTG-3' and TRCN0000148198 sequence 5'-CCGGGAAACGGATAGAATCTCCATTCTCGAGAATGGAGATTCTATCCGTTTCTTTTTTG-3'. 3 replicates of SCR control cell lines in HEK293T cells, stably integrated, selected using puro, sequence 5′-CCTAAGGTTAAGTCGCCCTCGCTCTAGCGAGGGCGACTTAACCTT-3′. Total RNA purified from ~1 million cells, cDNA converted using random hexamer primers, quantity measured using NanoDrop, quality quantified using BioAnaylzer). Affymatrix HTA2.0 array

first: Angie

last: Giang

first: Purva

last: Vaidya


title: mRNA sequencing analysis of transcripts from CA1 regions 90 minutes after Long-Term Potentiation was induced

city: NEW YORK

first: Chiara

last: Mariottini

state: NY

address: 1425 Madison Ave, Room 12-52

department: Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

summary:
Purpose: Study the differentially expressed genes in hippocampal rat CA1 regions 90 minutes after Long-Term Potentiation (LTP) was induced using field recordings
Methods: hippocampal rat CA1 region mRNA profiles of control (unstimulated) and 90 minutes after LTPwas induced (LTP 90) were generated by deep sequencing.  A pool of approximately 10 CA1 regions collected from at least 3 different animals were used. The seq library was prepared using TruSeq RNA Sample Prep Kit v2 protocol (Illumina, CA, USA).
For the RNA-Seq data analysis Tophat 2.0.13, bowtie 2.1.0 , samtool 0.1.7 and cufflinks 1.3.0  were used. The rn5-bowtie2 index was generated with the command 'bowtie2-build rn5.fa rn5'. The 'rn5.fa'-file was downloaded from the UCSC genome browser. The mm10-bowtie2 index was downloaded from http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml.  RefSeq geneTracks and GTF-files for the rn5 and mm10 genome assembly were downloaded from UCSC genome browser. Common gene ids in the GTF-files were matched to individual transcript_ids using the corresponding official symbols obtained from the geneTracks files.
Conclusions: Our study illustrates the nature of the different transcripts in acute rat hippocampal slices after LTP 90 minutes was induced using field electrophysiology and compares them with control, unstimulated slices. Thius allowed us to identify wich genes are modulated in the hippocampus in order to promote and sustain LTP.

overall_design: Hippocampal CA1 region mRNA profiles of Control and LTP 90 stimulated tissue were generated by deep sequencing using TruSeq RNA Sample Prep Kit v2 protocol (Illumina, CA, USA).

first: Jens

last: Hansen


title: A spatiotemporal DNA endoploidy map of the Arabidopsis root reveals roles for the endocycle in root development and stress adaptation

city: Ghent

first: Bert

last: De Rybel

address: Technologiepark 71

department: Center for Plant Systems Biology

country: Belgium

institute: VIB

summary: Somatic polyploidy caused by endoreplication is observed in arthropods, molluscs, and vertebrates, but is especially prominent in higher plants where it has been postulated to be essential for cell growth and fate maintenance. However, a comprehensive understanding of the physiological significance of plant endopolyploidy has remained elusive. Here, we modeled and experimentally verified a high-resolution DNA endoploidy map of the developing Arabidopsis thaliana root, revealing a remarkable spatiotemporal control of DNA endoploidy levels across tissues and a strong dependence on stress signals. Cellular and transcriptomic analysis revealed that inhibition of endoreplication onset alters the nuclear-to-cellular volume ratio and change in expression of cell wall modifying genes, correlated with the appearance of cell structural changes. Our data indicate that endopolyploidy might serve to coordinate cell expansion with structural stability, and that spatiotemporal endoreplication pattern changes may buffer for stress conditions, which may explain the widespread occurrence of the endocycle in plant species growing in extreme or variable environments.

overall_design: Two biological replicates of Col-0 were compared with three biological replicates of smr1

first: Rahul

last: Bhosale

first: Veronique

last: Boudolf

first: Fabiola

last: Cuevas

first: Thomas

last: Eekhout

first: Steven

last: Maere

first: Lieven

last: De Veylder


title: Transgenerational expression data from adult zebrafish exposed to low level TCDD

city: Gainesville

first: Tracie

last: Baker

state: FL

institute: University of Florida

summary:
Exposure to TCDD early in development produces reproductive abnormalities and decreased reproductive capacity in males in subsequent generations
We used microarrays to investigate the global programme of gene expression in testicular tissue and identified distinct multigenerational and transgenerational gene expression changes due to legacy TCDD exposure in males.

overall_design: Zebrafish were exposed to sublethal TCDD or vehicle (DMSO) during early development, males in the next two generations were analyzed for phenotypic and gene expression changes as adults. 5 TCDD and 5 Control males both the F1 and F2 generations.


title: acyltransferase brachypodium-arabidopsis-Impact of Brachypodium acyl-transferases

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

summary: ra15-03_oxpmt7-7 - acyltransferase brachypodium-arabidopsis - What biochemical function? What consequence on lignification when overexpressed in Arabidopsis thaliana? - Transcripts of Arabidopsis stem overexpressing an acyl transferase from Brachypodium are compared to wild type plants. The overexpression is under a specific promoter (C4H).

overall_design: 3 dye-swap - normal vs transgenic comparison.

first: Richard

last: Sibout

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Expression data of endoploidy-specific cells (with DNA content 2C, 4C, 8C and 16C)

state: Flanders

address: Technologiepark 927

department: VIB-UGent Center for Plant Systems Biology

institute: University of Ghent

summary:
Endocycle is an alternative cell cycle during which the DNA is replicated in the absence of cytokinesis, resulting in cellular endopolyploidy. The endocycle is frequenctly observed in plant species that grow under extreme conditions.  Thus, endopolyploidy has been postulated to be a mechanism facilitating adaptive growth.
We used microarrays to assess endoploidy-dependant gene expression profiles in Arabidopsis thaliana root and to understand how subpopulations of cells with different endoploidy contributes to plant growth under different environmental conditions

overall_design: Arabidopsis thaliana (pCO2:YFP-H2B , Col-0  ecotype) root cortical nucei were sorted by FACS based on YFP fluorescence and DNA content (2C, 4C, 8C and 16C), subjected to RNA extraction and Affymetrix ATH1 array hybridisation. Prior to hybridisation two consecutive rounds of RNA amplifications were performed using standard Affymetrix protocols for small samples. The amplified nuclear RNA of each DNA content class was used for microarray analysis.

first: Véronique

first: Gert

last: Van Isterdael

first: Georgina

last: Lambert


title: Ethylene-independent Promotion of Photomorphogenesis by Cytokinin Requires a Functional Cytokinin and Light Signaling Pathway.

city: Berlin

first: Henrik

last: Johansson

address: Albrecht-Thaer-Weg 6

institute: Freie Universität Berlin

summary: The transition of skotomorphogenesis to photomorphogenesis is induced by the perception of light and is characterized by the inhibition of hypocotyl elongation and opening of cotyledons. Although it is known that the plant hormone cytokinin, when applied in high concentrations, inhibits hypocotyl elongation in the dark-grown Arabidopsis plants, it is unclear to what extent this response is the result of cytokinin alone or cytokinin-induced ethylene production. We show that treatment of etiolated seedlings in presence of ethylene inhibitors (eg. AgNO3) or treatment of the ethylene-resistant mutant ein2, resulted in a significant inhibition of hypocotyl elongation. This indicates that cytokinin induced de-etiolation is largely independent of ethylene and suggests a close connection between the cytokinin two component system and the light singalling networks. We show that this cytokinin signal is mainly mediated through the cytokinin receptor ARIBIDOPSIS HISTIDIN KINASE 3 (AHK3) and the ARABIDOPSIS RESPONSE REGULATORS 1 (ARR1) in combination with ARR12. Interestingly, mutation of COP1, DET1 and CIN4/COP10 renders plants insensitive to cytokinin and these factors are indispensable for the transcriptional response during cytokinin induced de-etiolation which indicates that a functional light signaling pathway is essential for this cytokinin response. In addition, the cytokinin effect on hypocotyl elongation is highly dependent on the ambient light conditions where higher light intensities causes a switch in the response to CK from an inhibitor to a promoter of hypocotyl elongation.

overall_design: Investigation of the effect of 3 µM BA in presence of 10 µM AgNO3 on hypocotyl elongation in 4-days-old etiolated Arabidopsis seedlings, in triplicate, using RNA-seq analysis

first: Anne

last: Cortleven

first: Stephanie

last: Ehert

last: Schmuelling


title: The miRNA expression signatures in young and aging C57BL/6 mouse kidney

city: Dongguan

first: Shun

last: Xu

address: Xin Cheng Avenue 1#, Songshan Lake

institute: Guangdong Medical University

summary: To identify novel aging-related miRNAs, we initially established a physiological aging mouse model (20-month old male C57BL/6 mouse), compared with 2-month old male C57BL/6 mouse. Then, the Agilent miRNA microarray was performed to profile miRNA expression levels in kidney from 20-month old male C57BL/6 mouse (designated as Aging) and 2-month old male C57BL/6 mouse (designated as Young).

overall_design: The miRNA profile was measured in 2-month and 20-month old male C57BL/6.  Microarray assay was performed in triplicates, utilizing three independent sets of RNA preparations from each group (young or aging mouse).

first: Xinguang

last: Liu


title: The gene expression signatures in young and aging C57BL/6 mouse kidney

summary: To monitor the mRNA expression profiling in aging process, we initially established a physiological aging mouse model (20-month old male C57BL/6 mouse), compared with 2-month old male C57BL/6 mouse. Then, the Agilent mRNA microarray was performed to profile the gene expression levels in kidney from 20-month old male C57BL/6 mouse (designated as Aging) and 2-month old male C57BL/6 mouse (designated as Young).

overall_design: The gene expression profile was measured in 2-month and 20-month old male C57BL/6.  Microarray assay was performed in triplicates, utilizing three independent sets of RNA preparations from each group (young or aging mouse).


title: Cecum and liver gene expression profiles in response to dietary fibre

city: Aberdeen

first: Claus

last: Mayer

address: Greenburn Road

country: United Kingdom

institute: Biomathematics & Statistics Scotland

summary: To dentify cecal and liver gene expression changes associated with altered microbiota profiles and reduced weight gain in mice consuming a high-fat diet supplemented with the inulin, or with inulin esterified with propionate and butyrate.

overall_design: Male C57BL/6 mice, 12 weeks of age and 24-25 g in weight (Harlan, Bicester, UK), were acclimatised for 1 week to single housing on grid floors. Mice were randomly assigned to one of four dietary groups (n=12) and fed, either: 1. HFD (45% of energy from fat) (D12451) 2. LFD (low fat diet) (10% fat by energy) (D12450B) acting as a positive and negative controls respectively or the HFD where 10% of the carbohydrate by weight (5% corn starch, 5% cellulose) was replaced by inulin or 5% each of inulin propionate and inulin butyrate ester for 8 weeks.

first: Janice

last: Drew

first: Claus-Dieter


title: Gene expression signatures for human interleukin-6 (IL-6) treatment in human multiple myeloma (MM) cell lines.

city: Nagoya

first: Akinobu

last: Ota

state: Aichi

address: 1-1 Yazakokarimata

department: Food and Nutritional Environment

institute: Kinjo Gakuin University

summary: To investigate the effect of IL-6 on gene expression in IL-6-dependent MM cell lines, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to be associated with the cell proliferation of MM cells.  ANBL-6 and FLAM-76 cells were incubated for 48 h in the absense of IL-6, and then the cells were treated with IL-6 (10 ng/mL) for 0, 6, 12, and 24 h in vitro.

first: Ichiro

last: Hanamura


title: Hypertensive SHR vs WKY, RVLM, PVN, SON, NIL

city: Bristol

first: DAVID

last: MURPHY

state: AVON

address: Whitson Street

department: Medicine and Dentistry

institute: University of Bristol

summary: We have used Affymetrix microarray-driven gene profiling to comprehensively describe the expression of mRNAs in the brainstem and hypothalamus in the adult male spontaneously hypertensive rat (SHR) as compared to its normotensive parental Wistar-Kyoto (WKY) strain.

overall_design: Brain structures were dissected from hypertensive (SHR) and normotensive (WKY) strains of rat. For each structure, 10 independent Affymetrix Genechip 230 2.0 experiments were performed (5 SHR, 5 WKY), with each chip representing an independent biological replication (n=4 or n=5).


title: down/up regulation of nad biosynthesis in arabidopsis and role of l-aspartate oxidase-Down/up regulation of NAD biosynthesis in Arabidopsis : role of L-Aspartate oxidase

first: Stéphanie

last: Pateyron

summary: rs13_01_lao - down/up regulation of nad biosynthesis in arabidopsis and role of l-aspartate oxidase - Study of the biosynthesis of NAD in Arabidopsis. Involvment of L-Aspartate oxidase gene using T-DNA mutant (SAIL1145_B10) and overexpressor lines (promotor 35S, vector PCW162) at the same developmental stage (12 leaves)                                   - Study of the biosynthesis of NAD in Arabidopsis. Involvment of L-Aspartate oxidase gene using T-DNA mutant (SAIL1145_B10) and overexpressor lines (promotor 35S, vector PCW162) at the same developmental stage (12 leaves)

overall_design:
Study of the biosynthesis of NAD in Arabidopsis. Involvment of L-Aspartate oxidase gene using T-DNA mutant (SAIL1145_B10) and overexpressor lines (promotor 35S, vector PCW162) at the same developmental stage (12 leaves)
6 dye-swap - genotype comparaison

first: Bertrand

last: Gakière


title: Matrix mineralization controls gene expression in osteoblasts

status: Public on Sep 30 2018

first: Guenther

middle: HS

last: Richter

address: Augustenburger Platz 1

department: Department of Pediatrics, Division of Oncology and Hematology

institute: Charité - Universitätsmedizin Berlin

summary: Osteoblasts are adherent cells. Under physiological conditions they attach to mineralized and non-mineralized osseous surfaces. However, how exactly osteoblasts respond to these different osseous surfaces is largely unknown. Our hypothesis was that the state of matrix mineralization provides a functional signal to osteoblasts. To assess the osteoblast response to mineralized compared to demineralized osseous surfaces, we assessed the transcriptom.

overall_design: Porcine tibia was cut into 16 slices with 600 µm thickness each. 8 slices were demineralized with 0,5 M EDTA over 16 hrs, while the other 8 slices were left in their native condition. All slices were sterilized over 16 hrs, using 2% PAA (peracedic acid, Bioxal SA, Chalon-sur-Saône, France). MG-63 cells were seeded onto the osseous surfaces (200,000/cm²), followed by incubation of the samples for 72 hrs (37 °C, 5% CO2). After incubation, the adhesive cells were mechanically removed using a cell scraper.  For each surface (mineralized or demineralized), the 8 samples were randomly pooled in pairs, resulting in an n=4 per surface group. RNA was extracted in Trizol.

first: Oxana

last: Schmidt

first: Johannes

last: Wischmann

first: Rüdiger

last: von Eisenhart-Rothe

first: Philipp

last: Mayer-Kuckuk

first: Günther


title: VEGFC Upregulates Trans-Lymphatic Colorectal Cancer Metastasis in the Liver via Recruiting Bone Marrow Derived Cells

city: Fukuoka

first: Hiroyuki

last: Takahashi

address: 7-45-1 Nanakuma, Jonan-ku

department: Department of Regenerative Medicine and Transplantation

institute: Faculty of Medicine, Fukuoka University

summary: While colorectal cancer liver metastasis (CRCLM) is major cause of death of colorectal cancer, the mechanism of intrahepatic dissemination (trans-lymphatic metastasis) is not fully elucidated. Lymphangiogenesis can be the mechanism of the dissemination, but there are few evidences to prove it. In this study, we attempted to clarify the mechanism using syngeneic murine CRCLM model, especially focusing on vascular endothelial growth factor C (VEGFC), a promoter of lymphangiogenesis. We confirmed that 1) intrahepatic metastasis of CRCLM via lymphatic vessels was seen and lymphangiogenesis was upregulated in the CRCLM-bearing liver, 2) the degree of lymphangiogenesis and CRCLM was significantly correlated with the expression of VEGFC in colorectal cancer (CRC) cells and 3) macrophage inflammatory protein-1α (MIP-1α) was released from CRC cells under the stimulation of VEGFC and induced migration of immature bone marrow derived cells into the liver and differentiation into macrophage, which promoted dissemination of CRCLM. These findings suggest the possibility of therapeutic strategy targeting VEGFC / MIP-1α for diminishing CRCLM. In conclusion, VEGFC in CRC cells promoted trans-lymphatic metastasis of CRCLM by upregulation of lymphangiogenesis directly and indirectly via induction of macrophages derived from bone marrow cells.

overall_design: 4 samples: hepatic macrophage with treatment (n=2) and hepatic macrophage without treatment (n=2).

first: Takeshi

last: Itoh

first: Hitomi

last: Nishinakamura

first: Naoaki

last: Sakata

first: Gumpei

last: Yoshimatsu

first: Taisuke

last: Matsuoka

first: Hideaki

last: Yamada

first: Satoshi

last: Hirakawa

first: Suguru

last: Hasegawa

first: Shohta

last: Kodama


title: Non-coding RNA, RNY1 is essential for reprogramming process

city: Kyoto

last: Gojo

address: 465 Kajii-cho, Kamigyo-ku

institute: Kyoto Prefectural University of Medicine

summary: RNY1 is strongly expressed in cytoplasm during early iPS reprogramming phase (d0-3) but, underlying molecular mechanisms of RNY1 remain unknown during iPS reprogramming.

overall_design: TIG-1 fibroblasts was infected using CytoTune-iPS 1.0 Sendai Reprogramming Kit. Cell were transfected siRNA for negative control or RNY1 gene, and harvested at d3 using TRIzol reagent and Directzol kit. We analyzed gene expression changing during early satege of iPS reprogramming.

first: Daisuke

last: Kami


title: miRNA analysis of iPS reprogramming in OSKM treated TIG-1 fibroblasts on day 0 and 3.

summary: We examined the miRNA in DDX6 antibody IP proteins during iPS reprogramming.

overall_design: The miRNAs contains in the DDX6 antibody-IP protein on days 0 and 3 using  nCounter system.


title: Profiles analysis reveals circRNAs involving zebrafish physiological development

city: Nanjing

first: Heng

last: Liu

address: No. 123 Tian Fei Xiang, Mo Chou Road

department: Department of Pediatrics

institute: Nanjing Maternity and Child Health Care Hospital

summary: Recent studies have found that known functions of circRNAs include sequestration of microRNAs or proteins, modulation of transcription and interference with splicing, and even translation to produce poly-peptides. The zebrafish model is also demonstrably similar to humans in many studies. In order to explore the changes in circRNAs during embryonic development, further to research the mechanism of action of circRNAs in development-related diseases. Zebrafish embryos at blastula period, gastrula period, segmentation period, throat stage and incubation period were collected. Illumina deep sequencing technology and CIRI algorithm were used to detecting circRNAs. Totally we identified 1028 circRNAs (junction reads ≥ 5 and p < 0.05). Considering that circRNAs function is related to host genes, then bioinformatics analysis revealed these differentially expressed host genes are involved in NOTCH signaling pathways, cardiovascular system development, retinal ganglion cell axon guidance and so on. Moreover, circRNAs can participate in biological regulation through miRNA sponges function. TargetScan and miRanda were used to predict 73 miRNAs binding to circRNAs such as miR-19b, miR-124 and so on, some miRNAs play important roles in embryogenesis. The peak expression of circRNAs is distributed at different time points, suggesting that it may be involved in embryogenesis at different stages. Our study provides a foundation for understanding the dynamic regulation of circRNA transcriptomes during embryogenesis and identifies novel key circRNAs that might control embryonic development in zebrafish model.

overall_design: circRNAs of five periods (blastula, gastrula, segmentation, throat and incubation) in zebrafish were detected by deep sequencing using Illumina HiSeq 2500.

first: Yin

last: Hu

first: Jing

last: Yin

first: Xiang-Yun

last: Yan

first: Wen-Juan

last: Chen

first: Xing-Yun

last: Wang

first: Zhang-Bin

last: Yu

first: Shu-Ping

last: Han


title: Molecular mechanisms and potential therapeutic drugs linking to cetuximab-induced reactions in human cells (HEK 293 cells)

city: Chiba

first: Yuki

last: Sawai

address: 1-8-1 Inohana,  Chuo-ku

department: Department of Oral Science

institute: Graduate School of Medicine, Chiba University

summary: To obtain differentially expressed genes associated with cetuximab induced cytotoxicity we analyzed RNA samples using whole genome microarray expression profiling as a discovery platform to identify genes . Two kinds of RNA samples were extracted from HaCaT and HEK 293 cell; without cetuximab and incubation for 24 hours with 1.63μM (fixed maintenance dose) cetuximab.

overall_design: Cetuximab induced cytotoxicity gene expression in HEK 293 cells was measured at 24 hours exposure to doses of 0 and 1.63 µM cetuximab.

first: Katsuhiro

last: Uzawa


title: Endometrial transcriptome changes in comparison of equine endometrium samples collected on Day 12 of pregnancy and Day 12 of the estrous cycle

city: Lindau

first: Stefan

middle: Michael

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

country: Switzerland

institute: University of Zurich

summary: Establishment and maintenance of pregnancy in equids is only partially understood. To provide new insights into early events of this process, we performed a systematic analysis of transcriptome changes in the endometrium at days 8 and 12 of pregnancy. Endometrial biopsy samples from pregnant and non-pregnant (Day 12) stages were taken from the same mares. Composition of the collected biopsy samples was analyzed using quantitative stereological techniques to determine proportions of surface and glandular epithelium and blood vessels. RNA-seq analysis was performed and differentially expressed genes were identified. The samples used for RNA-seq were already analyzed before by the use of Agilent microarrays (GSE21046).

overall_design: Messenger RNA profiles of equine endometrial biopsies collected on Day 12 of pregnancy and Day 12 of estrous cycle, respectively, from in total 4 healthy mares were generated by RNA-sequencing using Illumina Genome Analyzer IIx, one pregnant and one control (non-pregnant) sample were taken from every mare by random order

first: Maximiliane

last: Merkl


title: Reprogramming the CNS of the Proto-Vertebrate Ciona intestinalis Using Single-Cell Transcriptomics

status: Public on Sep 28 2018

city: Princeton

first: Chen

last: Cao

state: New Jersey

address: Icahn lab

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

summary: We applied single cell RNA seq with 10x genomics platform to study co-expression of both Ptf1a and Meis leading to the wholesale transformation of the entire CNS into Coronet cells.  Our study identify a cocktail of regulatory determinants for the efficient specification of Coronet cells.

overall_design: We injected Ptf1a>β2tubulin construct into Ciona oocytes, fertilized and let them developed into middle tailbud stage along with control. We also injected Ptf1a and Meis>β2tubulin construct into Ciona oocytes, fertilized and let them developed into late tailbud stage along with control. Embryos were dissociated into single cells and loaded into 10x platform for single cell RNA-seq. Reads are aligned to Ciona genome with Cell Ranger pipeline.

first: Kai


title: Cell type-specific endometrial transcriptome changes in comparison of equine endometrium samples collected on Day 12 of pregnancy and Day 12 of the estrous cycle

summary: The results of endometrial gene expression studies during the time of conceptus migration (Days 8 to 16) did not provide final conclusions on possible mechanisms of maternal recognition of pregnancy (MRP) in the mare. This finding called for the analysis of cell type-specific gene expression in the endometrium in response to the equine embryo, which could be the key for improved understanding of gene expression regulation in context of MRP. In a pilot study, we used laser capture microdissection (LCM) to collect samples of the luminal epithelium (LE), glandular epithelium (GE), and stroma from endometrial biopsies taken from five mares on Day 12 of pregnancy and Day 12 of the estrous cycle, respectively. RNA was isolated from the LCM samples in order to perform RNA sequencing. Data analysis showed that gene expression differences were greater between cell types than between pregnant and cyclic state. Differential gene expression between pregnant and cyclic state was mainly found in the LE but also in GE and stroma. The comparison with a previous RNA-Seq data set for whole biopsy samples derived from Day 12 of pregnancy revealed the specific origin of the observed gene expression differences. Furthermore, we found that a number of genes are specifically differentially expressed (DE) in only one cell type. Some genes not DE when looking at the whole biopsy were DE in one cell type and showed similar levels in the other cell types in comparison of pregnancy and cyclic stage. Overall, this study revealed new and important spatial information about endometrial gene expression during the phase of initial recognition of pregnancy in the mare. The results indicated induction of angiogenesis and blood vessel development by the presence of the conceptus, a specific spatial regulation of the immune system, spatial regulation of growth factors controlling cell differentiation and endometrial remodeling, and regulation of genes involved in production of prostaglandin (PG) precursors, PG transport, and PG receptors, specifically PTGFR in context of prevention of luteolysis. Furthermore, these results support our hypothesis of the existence of a specific response in different endometrial cell types in the mare and call for further studies.

overall_design: Messenger RNA profiles of laser capture microdissection samples (luminal epithelium, glandular epithelium, stroma) from equine endometrial biopsies collected on Day 12 of pregnancy and Day 12 of estrous cycle, respectively, from in total 6 healthy mares were generated by RNA-sequencing using Illumina HiSeq 2500

first: Iside

last: Scaravaggi


title: Microarray analysis of an synthetic a-synuclein induced cellular model

city: Guangzhou

first: Danyu

last: Lin

address: Yanjiang West Road 107

institute: Sun Yat-sen momerial hospital

summary: To uncover new disease-associated genes and their relevant mechanisms, we carried out a gene microarray analysis based on a Parkinson’s disease (PD) in vitro model induced by a-synuclein oligomers. The result do help to reveal the mRNA and lncRNA profile in a-syn induced cells and rotenone-stimulated cells.

overall_design: This cellular model of SY-SH5Y cells induced by 25 mmol/L a-synuclein oligomers or 10mmol/L rotenone has been confirmed to show the stable, transmissible neurotoxicity of a-synuclein, a typical PD pathological marker. And the microarray analysis was performed upon two distinct PD cellular model and normal contrl cell.

first: Enxiang

last: Tao


title: IQGAP1 serves a role in erlotinib-related purpuric dermatitis

city: Taipei

first: Yi-Shuan

last: Sheen

address: 7 Chun-Shan South Road

department: Dermatology

country: Taiwan

institute: Natioanl Taiwan University Hospital

summary: IQ Motif Containing GTPase Activating Protein 1 (IQGAP1) mediates erlotinib-related purpuric dermatitis.

overall_design: Three-condition experiment: HMEC-1 cells treated with erlotinib 0 uM vs. 0.1 uM vs. 1 uM.

first: Yi

middle: S


title: Molecular mechanisms and potential therapeutic drugs linking to cetuximab-induced reactions in human cells (HaCaT cells)

overall_design: Cetuximab induced cytotoxicity gene expression in HaCaT cells was measured at 24 hours exposure to doses of 0 and 1.63 µM cetuximab.


title: Expression data from mir-100 overexpression two TNBC cell lines

status: Public on Sep 27 2018

city: Shanghai

first: Lu

last: Deng

address: Dong'an Road

institute: USTC

summary:
Utilizing a tetracyclineinducible lentivirus to elevate expression of miR100 in human cells, we found that increasing miR100 levels  decreased the production of breast CSCs. This effect was correlated with an inhibition of cancer cell  proliferation in vitro and in mouse tumor xenografts.Furthermore, miR100 induction in breast CSCs immediately upon their  orthotopic implantation or intracardiac injection completely blocked tumor growth and metastasis formation. Then we wanted to indentify the target genes of mir100 in breast cancer cells.
We used microarrays to detail the changes of gene expression after mir100 overexpression in two TNBC cell lines and identified distinct classes of down-regulated genes during this process.

overall_design: SUM149 and MDA-MB-231 cells were transfected with Ptripz-mir100 plasmid utilizing lentivirus infection. Then these cells were selected with puromycin(5ug/ml) to get stable transfected cell lines for a week. Then the cells were treated with tetracycline for a week to induce mir100 overexpression. These cells were send to RNA extraction and hybridization on Affymetrix microarrays.

first: Suling

last: Liu


title: Transcriptome modulation by loss-of-YAP1/TAZ in SK-N-MC Ewing Sarcoma cells

city: Seville

first: Juan

last: Diaz-Martin

address: Av Manuel Siurot

country: Spain

institute: IBiS

summary: YAP1 (Yes-associated protein 1) and TAZ (transcriptional coactivator with PDZ-binding motif, or WWTR1) are nucleo-cytoplasmic shuttling proteins that can function in the nucleus as transcriptional coactivators. Here we sought to evaluate which genes are regulated by endogenous levels of YAP/TAZ. We compared SK-N-MC cells transfected with a control non-targeting siRNA with cells transfected with a mix of siRNA targeting both YAP and TAZ.

overall_design: SK-N-MC cells growing at 70-80% of confluency in standard growth conditions were transfected with the indicated siRNAs. The following day, growth medium was renewed and cells were incubated for 48 more hours, and then harvested for total RNA extraction. 4 independent biological replicates were plated, transfected and harvested in parallel for each siRNA transfection.

first: Laura

last: Romero-Perez


title: DUSP10 constrains innate IL-33-mediated cytokine production in ST2hi memory-type pathogenic Th2 cells

status: Public on Sep 23 2018

city: Chiba-city

first: Yusuke

last: ENDO

state: Chiba

address: 1-8-1 Inohana, Chuo-ku

department: Immunology

institute: Chiba University

summary: Memory CD4+ T helper (Th) cells are crucial for acquired immunity and protection from infectious microorganisms, and also drive pathogenesis of chronic inflammatory diseases, such as asthma.  ST2hi memory-type Th2 cells have been identified as a pathogenic subpopulation capable of directly inducing eosinophilic airway inflammation.  These ST2hi pathogenic Th2 cells produce large amounts of IL-5 upon stimulation via their TCR, but not in response to IL-33.  In contrast, IL-33 alone induces cytokine production in ST2+ group 2 innate lymphoid cells (ILC2).  We investigated the molecular mechanism that controls the innate function of IL-33-induced cytokine production, and identified a MAPK phosphatase Dusp10, as a key negative regulator of IL-33–induced cytokine production in Th2 cells.  We found that Dusp10 is expressed by ST2hi pathogenic Th2 cells but not by ILC2, and Dusp10 expression inhibits IL-33-induced cytokine production by preventing GATA3 activity through inhibition of p38 MAPK phosphorylation.  Strikingly, deletion of Dusp10 rendered ST2hi Th2 cells able to directly respond to IL-33 exposure and produce IL-5. Thus, DUSP10 constrains IL-33–induced cytokine production in ST2hi pathogenic Th2 cells by controlling p38-mediated GATA3 function.

overall_design: Functions of Dusp10, a family of dual specificity protein phosphatase, are assessed by RNA-seq.

first: Takeshi

last: Yamamoto

last: Endo

first: Atsushi

last: Onodera

first: Kiyoshi

last: Hirahara

first: Hikari

middle: K

last: Asou

first: Takahiro

last: Nakajima

first: Toshio

last: Kanno

first: Yasuo

last: Ouchi

first: Satoshi

last: Uematsu

first: Hiroshi

last: Nishimasu

first: Osamu

last: Nureki

first: Damon

last: Tumes

first: Naoki

last: Shimojo

first: Toshinori

last: Nakayama


title: miRNA expression signatures in chronic hepatitis B (CHB) treated with nucleos(t)ide analogues (NA)

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

institute: Sapporo Medical University

summary: Hepatitis B virus (HBV) infection is one of the major causes of hepatocellular carcinoma (HCC). Nucleos(t)ide analogue (NA) therapy is effective to reduce the HCC incidence, while it doesn’t completely prevent HCC. In this study, we explored the involvement of microRNA (miRNA) in the post-NA treatment HCC development. Chronic hepatitis B (CHB) patients who received NA treatment (n = 18) were divided into 2 groups: those who didn’t develop HCC during the follow-up period (non-HCC group) and those who developed HCC after treatment (HCC group). Liver specimens were obtained before and after NA therapy, and HCC tissues were also obtained from the HCC group patients. Normal liver tissues were also obtained from 4 liver hemangioma patients who underwent surgical resection. miRNA expression was analyzed using Agilent miRNA microarray V3.

overall_design: Total RNA was extracted from fresh frozen CHB or HCC specimens obtained from biopsy or surgical resections. Expression of 851 miRNAs was analyzed using Human miRNA Microarray V3 (Rel 12.0 G4470C; Agilent technologies, Santa Clara, CA, USA).

first: Hideki

last: Wakasugi


title: mRNA-seq of effects of food perception in C. elegans

status: Public on Sep 20 2018

city: Eugene

first: Amy

last: Webster

state: Oregon

address: Institute of Ecology and Evolution

institute: University of Oregon

summary: The quadruple mutant avr-14(vu47); glc-3(ok321) avr-15(vu227) glc-1(pk54) with avr-15 rescued with a myo-2 promoter for pharynx-specific expression (strain LRB269) was used. This allowed worms to perceive food but not eat it when the drug ivermectin is added.

overall_design: Larvae were collected for six conditions: ivermectin + food after 1hr, ivermectin + food after 24hr, ivermectin + no food 1 hr, ivermectin + no food 24hr, no ivermectin + no food 1hr, and no ivermectin + food 1 hr.

first: R

middle: E

last: Kaplan

first: A

last: Chitrakar

first: L

last: Baugh


title: RNA-seq analysis of hearts from control and cardiomyocyte-specific PRMT1-deficient mice

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

institute: University of Toyama

summary: We found that cardiomyocyte-specific PRMT1-deficient (PRMT1-cKO) mice showed dilated cardiomyopathy and aberrant cardiac alternative splicing. To identify novel cardiac splicing events, we performed a comprehensive analysis of gene expression changes in hearts of wildtype (WT) and PRMT1-cKO mice using RNA sequencing (RNA-Seq). To investigate differentially expressed genes (false discovery rate (FDR) p<0.05, fold change >2) between control and PRMT1-cKO mice, we performed pairwise comparisons of RNA-Seq data using the CLC Genomics Workbench software.

overall_design: Examination of mRNA profile and alternative splicing in control and PRMT1-cKO mice (n=2).

first: Kazuya

last: Murata

first: Jun

first: Akiyoshi

last: Fukamizu


title: In utero heat stress alters the offspring epigenome [methylation]

status: Public on Sep 05 2018

city: Madison

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

summary: Exposure to intrauterine heat stress during late gestation affects offspring performance into adulthood. However, underlying mechanistic links between thermal insult in fetal life and postnatal outcomes are not completely understood. Utilizing Reduced Representation Bisulfite Sequencing, this study evaluated DNA methylation of liver and mammary gland of bull calves and heifers that were gestated under maternal conditions of heat stress or cooling, i.e., in utero heat stressed (HT) vs. in utero cooled (CL). Liver samples from bull calves (CT = 5 and HT = 4) were collected at birth while mammary gland samples from heifers (CT = 3 and HT = 3) were collected during their first lactation.

overall_design: Nine bull calves and six heifers gestated under maternal conditions of heat stress (HT, dams had access to shade) or cooling (CL, dams had access to shade, fans and soakers) were used for this study. Both bull calves (HT = 4 and CL = 5) and heifers (HT = 3 and CL = 3) were exposed to the maternal treatment through the intrauterine environment during the last 6-7 weeks of fetal development. Liver samples were collect from bull calves inmediately after birth. Heifers were managed under identical conditions from birth through their first lactation and mammary gland samples were collected on day 21 of the first lactation, coinciding with the rising milk yield phase of the lactation cycle. Liver and mammary gland samples were subjected to DNA extraction and subsequent reduced representation bisulfite sequencing.

first: Jimena

last: Laporta

last: Peñagaicano


title: A molecular portrait of epithelial-mesenchymal plasticity in prostate cancer associated with clinical outcome.

status: Public on Sep 11 2018

city: Brisbane

first: Colleen

last: Nelson

state: Queensland

address: 199 Ipswich Road

department: Institute of Health and Biomedical Innovation; Vancouver Prostate Centre

country: Australia

institute: Queensland University of Technology; University of British Columbia

summary: The propensity of cancer cells to transition between epithelial and mesenchymal phenotypic states is considered to be critical in metastatic processes, cancer progression, and treatment resistance. To investigate a transient epithelial-mesenchymal transition (EMT) in prostate adenocarcinoma, LNCaP cells with inducible and reversible expression of SNAI1 or SNAI2 were generated. Cells were treated with doxycycline to induce a SNAI1- or SNAI2-mediated EMT for 5 days and then subsequently removed for 3, 5, and 20 days to allow for MET. LNCaP-iGFP cells were also generated for control purposes and were subjected to the same treatment regime.

overall_design: The dataset was derived from three independent repeats of all treatment groups except the GFP.MET.M20 group that only had two independent repeats.

first: Nataly

last: Stylianou

first: Melanie

last: Lehman

first: Chenwei

last: Wang

first: Atefeh

last: Taherian Fard

first: Anja

last: Rockstroh

first: Ladan

last: Fazli

first: Lidija

last: Jovanovic

first: Micheal

last: Ward

first: Martin

middle: C

last: Sadwoski

first: Abhishek

last: Kashyap

first: Ralph

last: Buttyan

last: Gleave

first: Thomas

last: Westbrook

first: Elizabeth

last: Williams

first: Jennifer

last: Gunter

first: Brett

middle: G

last: Hollier


title: Gene expression of osteosarcama cell line with vasculogenic mimicry phenotype

status: Public on Sep 15 2018

last: Yao

address: Shizi Street, Hongshan Road

institute: Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine

summary:
Vasculogenic mimicry has been generally accepted as a new form of tumor vascularization and regarded as an unfavorable prognostic factor in multiple aggressive malignancies. We previously reported the presence of vasculogenic mimicry in osteosarcoma patients. The mechanistic basis for osteosarcoma VM remains unclear.
We used microarrays to detail the global programme of gene expression between 143B cells and HOS cells exposed to Matrigel which showed greatly different vasculogenic mimicry formation potential and identified distinct classes of vasculogenic mimicry-realted genes during this process.

overall_design: Osteosarcoma cell lines 143B and HOS cultured in Matrigel after 24 hours were obtained for RNA extraction and hybridization on Affymetrix microarrays. There are duplicate samples for each cell line.

first: Ke

last: Ren

first: Chen

first: Jing

last: Zhou


title: Gene expression profiles in human iPS cells cultured by different four methods

status: Public on Sep 25 2018

city: Suita

first: Tomoki

last: Yamashita

state: Osaka

address: 1-6 Yamadaoka

department: Graduate School of Pharmaceutical Sciences

institute: Osaka University

summary: Hepatocyte-like cells differentiated from human iPS cells are expected to be utilized in pharmaceutical research and regenerative medicine. Recently, various culture methods for human iPS cell maintenance have been developed. However, it is not well known whether human iPS cell maintenance method affects hepatic differentiation potency. In this study, we cultured human iPS cells using four maintenance methods: ReproStem medium with feeder cells (mouse embryonic fibroblasts), AK02N medium with iMatrix-511 (E8 fragments of laminin511), Essential 8 medium with Vitronectin N (N-terminal domain of vitronectin), TeSR-E8 medium with Vitronectin XF (xeno-free vitronectin). Then, these human iPS cells were differentiated into the hepatocyte-like cells. Interestingly, the gene expression levels of definitive endoderm markers in the definitive endoderm cells generated from human iPS cells cultured with ReproStem or TeSR-E8 medium were higher than those in other groups. The gene expression level of foregut marker, HHEX, in the definitive endoderm cells generated from human iPS cells cultured with ReproStem medium was higher than that in other groups. Consistently, the expression levels of hepatocyte markers, albumin and urea secretion capacity, and CYP3A4 activity in the hepatocyte-like cells generated from human iPS cells cultured with ReproStem medium were higher than those in other groups. Our data indicated that the most suitable human iPS cell maintenance method for efficient hepatic differentiation was the on-feeder method which uses mouse embryonic fibroblasts, but not feeder-free methods. In conclusion, human iPS cell maintenance method largely affects hepatic differentiation potency.

overall_design: The human iPS cell line, YOW-iPS was maintained by one of four different culture methods (Repro, AK02N, E8, and TeSR-E8 method). Repro, AK02N, E8, and TeSR-E8 were pooled from triplicate samples of one independent experiments, and then microarray analysis was performed.

first: Nobumasa

last: Matoba

first: Kazuo

last: Takayama

first: Fuminori

last: Sakurai

first: Hiroyuki

last: Mizuguchi


title: Most Sinorhizobium meliloti ECF-sigma factors perform accessory functions

city: Stanford

first: Melanie

last: Barnett

state: CA

address: 371 Jane Stanford Way

department: Biology

institute: Stanford University

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

platform_organism:
Sinorhizobium meliloti
Medicago truncatula

overall_design: Refer to individual Series


title: Overexpression of Sinorhizobium meliloti ECF sigma factors.

summary: We characterized transcriptomes for strains overexpressing each of the Sinorhizobium meliloti ECF sigma factors the via a plasmid-borne, melibiose-inducible promoter plasmid (PmelA; pCAP11: Pinedo et al. 2008 J Bacteriol 190:2947-2956) compared to control strains carrying the empty vector.

overall_design: To identify genes whose expression was dependent on each of the 11 ECF sigma factors (RpoE1-RpoE10 and FecI), we used strains overexpressing ECF sigma factors via the melibiose-inducible promoter (PmelA) plasmids.  Each plasmid was conjugated into S. meliloti wild type strain, CL150, an Rm1021-derived strain corrected for mutations in pstC and ecfR1 (Schlüter et al. 2013 BMC Genomics 14:156).  We employed three different control strains: CL150 pCAP11; CL101 pCAP11 (corrected only for ecfR1); and Rm1021 pCAP11.

first: Claus

last: Lang

first: Sharon

last: Long


title: The mRNA profiles of the macrophages with or without Trastuzumab-dependent tumor phagocytosis

status: Public on Sep 04 2018

first: Zhao

last: Jinghua

address: 107 Yanjiang West Road

institute: SunYat-Sen Memorial Hospital, SunYat-Sen University

summary: Therapeutic antibodies trigger antibody-dependent cellular cytotoxicity (ADCC) of cancer cells and also their antibody-dependent cellular phagocytosis (ADCP) by tumor-associated macrophages (TAMs). We report here our unexpected finding that TAMs that have undergone ADCP of tumor cells induced by therapeutic antibodies display immunosuppressive characteristics and inhibit the proliferation and tumoricidal effects of NK and tumor-specific CD8+ T cells in breast cancers and lymphomas. Mechanistically, we show that DNA released from the phagocytosed tumor cells after ADCP activates caspase 1 inflammasome, leading to IL-1β-mediated PD-L1 and IDO upregulation in these cells. Combined treatment with anti- HER2 antibody and inhibitors of PD-L1 and IDO increased the infiltration of NK and CD8+ T cells and enhanced anti- HER2 therapeutic efficacy in mouse models of HER2+ breast cancers. Furthermore, neo-adjuvant Trastuzumab therapy significantly increased PD-L1 and IDO expression in the TAMs of HER2+ breast cancer patients, which correlate with poor Trastuzumab response and reduced NK and CD8+ T cells in the tumors. Collectively, our findings unveil an unexpected role of ADCP induced by therapeutic antibodies in cancer immunosuppression, and suggest that antibody plus immune checkpoint blockade may provide synergistic therapeutic effects in cancer patients.

overall_design: HER2+ breast cancer cells pre-dyed by CellTtracker Deep Red Dye (Cat# C34565, Thermo Fisher) were co-cultured with macrophages pre-dyed by CellTracker CMFDA Dye (Cat# C7025, Thermo Fisher) with or without Trastuzumab (Roche). The ratio between tumor cells and macrophages was 1:5. After 24 hr, the cells were rigorously washed by PBS, digested by 10×TrypLE Selected Enzyme (Cat# A1217701, Gibco) diluted 5× in PBS with 1mM EDTA and sorted by CD14 Isolation Kit (Cat# 130-050-201, Miltenyi Biotec) to collect macrophages followed the instructions. we named untreated macrophages as Mɸ and macrophages pre-incubated with HER2+ tumor cells in the presence or absence of Trastuzumab as ADCP-Mɸs or TC-Mɸs respectively. Total RNA was extracted from macrophages with indicated treatments (5 x 106 cells) using the TRIzol Reagent (Cat#A33251, Thermo Fisher). The quality of extracted RNA was assessed using the NanoDrop ND-2000 spectrophotometer.

first: Jinghua

last: Zhao

first: Yue

last: Xing


title: Hrg1 promotes heme-iron recycling during erythrophagocytosis in zebrafish kidne

status: Public on Sep 03 2018

city: Bethesda

first: Michael

last: Krause

state: MD

address: Bld. 5, Rm B104, 5 Memorial Dr.

institute: NIH/NIDDK

summary: RNA-seq datasets on adult zebrafish kidneys and spleens, non-PHZ (phenylhydrazine) and PHZ treated, to compare the gene expression on Tü wild type and hrg1 knockout zebrafish.

overall_design: The kidney and Spleen from 5-6 months old adult zebrafish (Tü, hrg1 doulble knockout (DKO), both non-PHZ and PHZ-treated) were dissected out and flash-frozen in TRIzol for RNA extraction. Total of 24 samples with single-end 50 base reads were sequenced with HiSeq 2500 (Illumina); with triplicate libraries of spleens and kidneys.

first: Iqbal

last: Hamza


title: Single-cell analysis uncovers convergence of cell identities during axolotl limb regeneration

city: Heidelberg

first: Tobias

last: Gerber

address: Meyerhofstr. 1

department: Developmental Biology

institute: EMBL Heidelberg

summary: Amputation of the axolotl forelimb results in the formation of a blastema, a transient tissue where progenitor cells accumulate prior to limb regeneration. Connective tissue (CT) – skeleton, periskeleton, tendon, dermis, interstitial cells – contributes the vast majority of cells that populate the blastema, however it is unclear how individual CT cells may reprogram their fate in order to rebuild the tetrapod limb. Here we use a combination of Cre-loxP reporter lineage tracking and single-cell (sc) RNA-seq to molecularly track, for the first time, adult CT cell heterogeneity and its transition to a limb blastema state. We uncover a multi-phasic molecular program where CT cell types found in the uninjured adult limb revert to a relatively homogenous progenitor state that participates in inflammation and extracellular matrix disassembly prior to proliferation, establishment of positional information, and ultimately re-differentiation. While the early regeneration transcriptome states are unique to the blastema, the later stages recapitulate embryonic limb development. Notably, we do not find evidence of a pre-existing blastema-like precursor nor limb bud-like progenitors in the uninjured adult tissue. However, we find that distinct CT subpopulations in the adult limb differentially contribute to proximal and distal portions of the regenerated limb. Together, our data illuminates molecular and cellular reprogramming during complex organ regeneration in a vertebrate.

overall_design: Single-cell transcriptomics and reporter lineage tracking was used to deconstruct cell composition, reconstruct lineage relationships, and trace connective tissue reprogramming during axolotl limb regeneration.

first: Barbara

last: Treutlein


title: Gene expression in T cells from CD46-deficient patients and matcherd healthy controls

status: Public on Sep 14 2018

first: Mehdi

last: Pirooznia

address: 12 SOUTH DR

institute: National Institutes of Health

summary:
Recent data indicate that intracellularly activated and autocrine-functioning complement activation fragments - in conjunction with an NLRP3 inflammasome - is critical for normal human Th1 induction and contraction. More specifically, engagement of of the C3aR and CD46 by autocrine generated C3a and C3b, respectively, drives the metabolic reprogramming needed for IFN-gamma secrtion by human CD4+ T cells. It was not clear whether autocrine complement and/or the NLRP3 inflammasome are also needed for normal human cytotoxic CD8+ T cell (CTL) responses. During this study, we used CTLs isolated from patients with either CD46 deficiency or with NLRP3 hyperactivity to determine that CD46 is also required for normal IFN-gamma secretion as well as killing activity in CTLs, whilst a canonical NLRP3 inflammasome is not required for these key functions.
The  CD46-deficient patient utilized in this study has a mutation in the CD46 gene that leads to reduced cell surface CD46 expression and a dysfunction in Th1 induction. The patient suffers from episodes of atypical hemolytic uremic syndrome (aHUS) and  common variable immune deficiency (CVID) and recurrent infections.

overall_design: Total  CD8+ T cells of the patient and a sex- and age-matched healthy donor were isolated and activated for 6 hrs in vitro with immobilised antibodies to CD3 and CD3+CD46 in the presence of 25 U/ml IL-2. Toral RNA was isolated and gene array analyses pereformed as technical replicates of three.

first: Claudia

last: Kemper

first: Paul

last: Lavender


title: Transcriptome profiling of purified normal differentiated mesodermal cells (NDMCs) using Affymetrix Human Transcriptome Array 2.0

status: Public on Sep 01 2018

city: Darlinghurst

first: Timothy

middle: John

last: Peters

state: NSW

address: 384 Victoria St

institute: Garvan Institute of Medical Research

summary: To identify differential expression of transcripts in between NDMC depots, we performed global gene and transcript expression profiling of primary NDMC1 and NDMC2 using Affymetrix Human Transcriptome 2.0 expression arrays.

overall_design: Purified NDMC1 (n=3) and NDMC2 (n=3) were obtained during surgery for RNA extraction and hybridization on Affymetrix Human Transcriptome microarrays.

first: Hugh

last: French


title: Reovirus infection induces stabilization and up-regulation of cellular transcripts that encode regulators of TGF-beta signaling

status: Public on Aug 28 2018

city: minneapolis

first: Liang

last: Guo

state: MINNESOTA

address: 2001 6th Street SE

institute: University of Minnesota

summary: We utilized oligonucleotide microarrays to measure cellular mRNA decay rates in mock- or reovirus-infected murine L929 cells to determine if changes in host mRNA expression are a consequence of reovirus-induced alterations in cellular mRNA stability.

overall_design: Murine L929 cells were mock-infected or infected with reovirus strains clone87, clone8, and Dearing. At 19.5 h p.i., ongoing transcription was arrested by addition of actinomycin D and global mRNA expression levels were measured after 0, 45, 90 and 120 min of actinomycin D treatment using Affymetrix U74Av2 microarrays

first: Jennifer

middle: A

last: Smith

first: Michelle

last: Abelson

first: Irina

last: Vlasova-St. Louis

first: Leslie

last: Schiff

last: Bohjanen


title: Sinorhizobium meliloti root nodule bacterial transcriptomes for wild type and four mutant strains.

first: Melanie

middle: J

last: Barnett

summary: We characterized transcriptomes of Sinorhizobium meliloti root nodule bacteria with mutations in sigma factor genes.

overall_design: To identify genes whose expression was changed in S. meliloti root nodule bacteria deleted for various sigma factor genes, we inoculated Medicago truncatula host plants with four different deletion mutant strains (rpoE3-ecfR3; rpoE8-SMb20593; rpoH1; all ECF sigma factor genes) or CL150, a wild type strain corrected for mutations in pstC and ecfR1 (Schlüter et al. 2013 BMC Genomics 14:156). We used Custom Affymetrix GeneChips to profile S. meliloti nodule gene expression.

first: Claus

last: Lang

first: Sharon

last: Long


title: Genome-wide expression profiling of human prostate stromal cells in response to multiple chemotherapeutic agents

status: Public on Aug 31 2018

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

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

summary: The DNA damage secretory program (DDSP) provoked by the side effects of genotoxic therapeutics results in senescence associated secretory phenotype (SASP) and fuels advanced pathologies particularly cancer resistance. However, the complete mechanism underlying SASP development in the tumor microenvironment (TME) remains unclear. We treated PSC27, a primary normal human prostate stromal cell line, with two distinct groups of chemotherapeutic drugs that are either genotoxic or not, and determined the key molecules and their associated pathways responsible for development of a typical SASP phenotype under DNA damage conditions.

overall_design: ArrayStar human LncRNA Microarray v3.0 (8 x 60K, ArrayStar, Rockville, MD) was used to profile expression of PSC27 cells treated with various chemotherapeutic agents to induce cell damage in vitro. Total RNA was isolated and amplified prior to hybridization in a one-color experiment. There were totally seven samples analyzed, each composed of three biological replicates, including controls and experimental groups.

first: Boyi

last: Zhang


title: Transcriptome profiling of Normal and Cancerous Prostate Cells using Affymetrix Human Transcriptome Array 2.0

summary: To identify aberrant expression of transcripts in prostate cancer, we performed global gene and transcript expression profiling of normal prostate epithelial cells (PrEC) and the prostate cancer cell line LNCaP using Affymetrix Human Transcriptome 2.0 expression arrays.

overall_design: LNCaP and PrEC cells (n=1) were cultured for RNA extraction and hybridization on Affymetrix Human Transcriptome microarrays.

first: Helen

last: Speirs

first: Jenny

middle: Z

last: Song

first: Clare

last: Stirzaker

first: Susan

last: Clark


title: In utero heat stress alters the offspring epigenome

status: Public on Aug 30 2018

first: Francisco

last: Peñagaricano

summary: Exposure to intrauterine heat stress during late gestation affects offspring performance into adulthood. However, underlying mechanistic links between thermal insult in fetal life and postnatal outcomes are not completely understood. Utilizing RNA Sequencing, this study characterized the mammary gland transcriptome of heifers that were gestated under maternal conditions of heat stress or cooling, i.e., in utero heat stressed (HT) vs. in utero cooled (CL). Mammary tissues were collected from three HT and three CL heifers during their first lactation.

overall_design: Six heifers (all born in 2014) gestated under maternal conditions of heat stress (HT, dams had access to shade) or cooling (CL, dams had access to shade, fans and soakers) were used for this study. These six heifers (HT = 3 and CL = 3) were exposed to the maternal treatment through the intrauterine environment during the last 6-7 weeks of fetal development. All the heifers were managed under identical conditions from birth through their first lactation in summer 2016. Mammary gland biopsies were collected on day 21 of the first lactation, coinciding with the rising milk yield phase of the lactation cycle. Mammary tissue samples were subjected to RNA extraction, library generation, and subsequent sequencing.

first: Jimena

last: Laporta


title: Expression data from Low Temperature Plasma-treated primary prostate cultures

status: Public on Aug 27 2018

city: York

first: John

last: Packer

state: North Yorkshire

address: Wentworth Way

institute: Mr

summary:
Prostate basal epithelial cultures generated from patient normal and cancer tissue were treated with LTP for 3 minutes and RNA harvested at 2hrs post-LTP.
Microarrays were used to analyze whole transcriptome changes between untreated and LTP-treated prostate cells.

overall_design: Six primary prostate culture (two Gleason 9 cancer samples, and two Gleason 7 with matched Normal tissue samples from the same patient) were grown in culture and treated with LTP. 2hrs after treatment, RNA was harvested from LTP-treated and untreated cells. RNA was then submitted for microarray analysis and comparison was generated between the two conditions for each primary prostate culture.

first: Alasdair

last: Droop


title: Genome-wide maps of H3K27ac and H2A.Zac in HeLa K cells after depletion of PWWP2A by siRNA-mediated knockdown.

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Our study investigates changes in acetylation levels on H3K27 and H2A.Z after PWWP2A depletion as measured by ChIP-seq.

overall_design: In this study we examined two different histone modifications in HeLa K cells after siRNA-mediated depletion of PWWP2A as measured by ChIP-seq.

first: Stephanie

last: Link

first: Sandra

last: Hake


title: Sequencing of DNA from the biotinylated chromatin from HeLa S3 clonal cell line

status: Public on Aug 24 2018

city: Astana

first: Pavel

last: Tarlykov

address: 13/5, Kurgalzhynskoye Road

country: Kazakhstan

institute: National Center for Biotechnology

summary: Sequencing shows that macroH2A1-emerin interaction occurs in lamina-associated domains on a genome-wide scale. We decided to verify that the biotinylated signal is indeed enriched in the chromatin domains positioned at the nuclear periphery. In this regard, we purified the biotinylated chromatin from HeLa S3 clonal cell line stably coexpressing BirA-emerin and BAP-macro-H2A1 using proximity utilizing biotinylation native chromatin immunoprecipitation (PUB-nChIP). Instead of analysing the protein fraction, we isolated DNA from the biotinylated chromatin pull down and performed high throughput sequencing in order to get insight into the genome wide distribution of the isolated DNA. Importantly, PUB-nChIP-seq of the DNA purified from HeLa S3 clonal cell line stably coexpressing BirA-emerin and BAP-macro-H2A1 showed high levels of enrichment at the lamina associated domains, which were identified previously in HeLa cells using anti-Lamin B1 and anti-Lamin A chIP-seq (Lund et al., 2015). The enrichment of BirA-emerin labelled BAP-macro-H2A at LADs is visibly clear at both the chromosome level and at individual LADs. To test if this enrichment was significant, the genome was divided into 100kb windows and monte carlo simulation using 10,000 iterations was performed to examine if probes overlapping LADs were significantly different to the genomic average. For both replicates, at both LMNA and LMNB1 LADs, the enrichment of biotinylated BAP-macroH2A1 observed was significant relative to the genome wide average.

overall_design: Total (nonbiotinylated) and biotinylated chromatin from Hela S3 cell line stably coexpressing BirA-emerin and BAP-macroH2A1 fusion proteins was isolated. The chromatin was digested with Mnase. Input DNA from the total chromatin was isolated and  sequenced. For library construction, the DNA fragments (100 ng) were converted to blunt ends by end repair using Ion Xpress Plus Fragment Library Kit (Thermo Fisher Scientific) and ligated to Ion Xpress Barcode Adapters.

first: Lee

last: Siggens


title: A Protein-Protein Interaction Underlies the Molecular Basis for Substrate Recognition by an Adenosine to Inosine RNA Editing Enzyme

status: Public on Aug 23 2018

city: Santa Cruz

first: Todd

last: Lowe

address: 1156 High Street

department: Biomolecular Engineering and Bioinformatics

institute: University of California Santa Cruz

summary: We report an unbiased analysis of ADR-2 binding across the C. elegans transcriptome, which indicates that ADR-1 is required for ADR-2 to stably bind a majority of target mRNAs in vivo. By obtaining 30-50 million reads from immunoprecipitated RNA and input samples from wild type and adr-2(-) strains, we identified 1235  ADR-2 bound targets in wild-type worms. Comparing these ADR-2 bound targets with a list of all known edited targets in C. elegans, we determined ~65% of them are edited. Additionally sequencing reads from an ADR-2 RIP assay performed in the adr-1(-) strain were used to determine that the majority of ADR-2 targets (80%) have significantly reduced binding by ADR-2 in the absence of adr-1.

overall_design: ADR-2 RIP-seq in WT, adr-2(-) and adr-1(-) was performed in duplicates, using Illumina NextSeq500 along with RNA-seq of input lysates from the above three strains.

first: Suba

last: Rajendren

first: Aidan

last: Manning


title: Identification of early biological changes in palmitate-treated isolated human islets

status: Public on Aug 19 2018

city: Uppsala

first: Ernest

last: Sargsyan

address: Husargatan 3

country: Sweden

institute: Uppsala University

summary:
Background: Long-term exposure to elevated levels of free fatty acids (FFAs) is deleterious for beta-cell function and may contribute to development of type 2 diabetes mellitus (T2DM). Whereas mechanisms of impaired glucose-stimulated insulin secretion (GSIS) in FFA-treated beta-cells have been intensively studied, biological events preceding the secretory failure, when GSIS is accentuated, are poorly investigated. To identify these early events, we performed genome-wide analysis of gene expression in isolated human islets exposed to fatty acid palmitate for different time periods.
Results: Palmitate-treated human islets showed decline in beta-cell function starting from day two. Affymetrix Human Transcriptome Array 2.0 identified 903 differentially expressed genes (DEGs). Mapping of the genes onto pathways using KEGG pathway enrichment analysis predicted four islet biology-related pathways enriched prior but not after the decline of islet function and three pathways enriched both prior and after the decline of islet function. DEGs from these pathways were analyzed at the transcript level. The results propose that in palmitate-treated human islets, at early time points, protective events, including up-regulation of metallothioneins, tRNA synthetases and fatty acid-metabolising proteins, dominate over deleterious events, including inhibition of fatty acid detoxification enzymes, which contributes to the enhanced GSIS. After prolonged exposure of islets to palmitate, the protective events are outweighed by the deleterious events, which leads to impaired GSIS.
Conclusions: The study identifies temporal order between different cellular events, which either promote or protect from beta-cell failure. The sequence of these events should be considered when developing strategies for prevention and treatment of the disease.

overall_design: In total, 5 experiments/repetitions were done. Each experiment includes 1 control and 5 treatment conditions (culture at 0,5 mM palmitate for 4 hours, 12 hours, 1 day, 2 days or 7 days). As a result, we have 30 samples in total.

first: Jing

last: Cen

first: Kirsten

last: Roomp

first: Reinhard

last: Schneider

first: Peter

last: Bergsten


title: Genome-wide transcriptome analysis of regulatory T cells induced by Sox12

status: Public on Aug 16 2018

city: Chiba

first: Shigeru

last: Tanaka

address: 1-8-1 Inohana

department: Allergy and Clinical Immunology

institute: Chiba University

summary: We analyzed RNA-seq of regulatory T cells recovered from DSS-colitis mice. We also transduced Sox12 gene into CD4 T cells and analyzed transcriptome.

overall_design:
Two separate experiments:
1. RNA were purified from regulatory T cells from non-treat mice or mice drinking 3% DSS water.
2. RNA were purified from CD4 T cells transduced with either mock vector or Sox12 vector.

first: Suto

last: Akira

first: Hiroshi

last: Nakajima


title: Next Generation Sequencing Facilitates Quantitative Analysis during avian leukosis virus, subgroup J-induced tumorigenesis in chickens

status: Public on Aug 21 2018

city: Yangzhou

first: Lingling

last: Qiu

address: 88 South University Ave.

department: College of Animal Science and Technology

institute: Yangzhou University

summary: We generated ribominus RNA sequencing data from three normal chicken spleen tissues and three ALV-J-infected chicken spleen tissues. We examined the expression of mRNAs in the spleens of 20-week-old chickens infected with ALV-J and uninfected chickens. 1723 mRNAs in the spleen  showed differentially expressed between the uninfected and infected groups with a fold change ≥ 2 and P value < 0.05. Altered expression of several genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering, enrichment analysis of differentially expressed genes uncovered several tumor-associated or immune-related genes that may contribute to ALV-J-induced tumorigenesis in chicken.

overall_design: Three normal chicken spleen tissues and three ALV-J-infected chicken spleen tissues

first: Guobin

last: Chang

first: Zhiteng

last: Li