title: Thyroid hormone-responsive miR-378 modulates cholesterol homeostasis by regulating hepatic bile acid synthesis

status: Public on Oct 29 2019

city: shanghai

first: chao

last: sun

state: shanghai

address: 320 Yueyang Road, Xuhui District, Shanghai, China

country: China

institute: Shanghai Institutes for Biological Sciences, University of Chinese Academy ofSciences

summary: An improved mechanistic understanding of the thyroid hormone (TH) action on bile acid (BA) synthetic pathway, the major route for cholesterol elimination, will facilitate the identification of novel therapeutic targets for hypercholesterolemia. Here, we show that hepatic miR-378 is positively regulated by TH. Transient overexpression of miR-378 in the liver of mice reduces the serum cholesterol levels, which is accompanied with an upregulation of key enzymes involved in the intrahepatic conversion of cholesterol to BAs. Importantly, transgenic mice with liver-specific and moderate overexpression of miR-378 also display a decrease in serum cholesterol levels accompanied with an enhanced BA synthesis and are resistant to diet-induced hypercholesterolemia. In contrast, mice lacking miR-378 exhibit an elevation of serum cholesterol levels accompanied with an impaired BA synthesis. Mechanistic studies reveal that hepatic miR-378 regulates BA synthesis and cholesterol homeostasis through its direct target gene MAFG, which is a transcriptional repressor of BA synthetic genes. We also show that miR-378 serves as an essential component in either incoherent or coherent feed-forward loop to confer robust and precise controls on BA synthesis in response to TH signalling. Together, we identify a previously undescribed miR-378-mediated mechanism underlying the cholesterol-lowering effect of TH. Our findings not only add a new dimension to our understanding the regulation of BA synthesis by TH, but also provide new therapeutic regimens to manage serum cholesterol levels

overall_design: There are two groups, Ad-Ctrl and Ad-378, one sample per group, and each sample is the pool of  livers of five mice treated the same.

first: Chao

last: Sun

first: Wei

last: Liu


title: Examing the m6A modification in control or METTL3 knockdown BGC823 cells

city: Shanghai

first: Ben

last: Yue

address: 160 Pujian Road

institute: Renji Hospital, School of Medicine, Shanghai Jiao Tong University

summary: To investigate the role of METTL3-mediated m6A modification, we performed m6A-sequencing to map the m6A modification in control or METTL3 knockdown BGC823 cells.

overall_design: Examing the m6A modification in gastric cancer cell (sh-NC and sh-METTL3)

first: S

middle: H

last: Yueben


title: Cellular response to hepatitis E virus (HEV) infection

status: Public on Oct 31 2019

city: Columbus

first: David

last: Brigstock

state: Ohio

address: 700 Children's Drive

country: USA

institute: Nationwide Children's Hospital

type: Expression profiling by high throughput sequencing

summary: What happens in cells infected with HEV is largely unknown. We used a recently established genotype 3 HEV cell culture system and profiled the host responses by RNA-seq.

overall_design: HepG2/C3A cells either inoculated with HEV (kernow C1 P6 strain) or not inoculated (mock) were cultured for 5 days. Total RNA were extracted and subjected RNA Seq. Differentially expressed genes between mock and infected groups were analyzed by DESeq2.

first: Xinlei

last: Li

first: Zongdi

last: Feng

first: Vijay

last: Nadella

first: James

last: Fitch


title: Identification of YAP-associated lncRNAs via RNA-binding protein immunoprecipitation sequencing (RIP-seq) experiments

city: Guangzhou

first: Wen

last: Ni

state: Guangdong

address: No. 135, Xingang Xi Road

institute: SUN YAT-SEN UNIVERSITY

summary: The analysis of the RNA-binding protein immunoprecipitation sequencing (RIP-seq) experiment is performed to identified YAP-specific binding lncRNAs.

overall_design: A RIP-seq assay for YAP-specific binding lncRNAs were performed and the anti-IgG group was performed as negative control.

first: Su

last: Yao


title: Effects of 2,3',4,4'5-Pentachlorobiphenyl Exposure during Pregnancy on Maturation of Offspring Oocytes in Mice

city: Nanjing

first: Wang

last: Haiquan

address: Hankou Road

institute: Nanjing University

summary: To investigate the effect of prenatal exposure of PCB118 on the maturation process of offspring mouse oocytes, we performed genome-wide transcriptome sequencing of mouse oocytes from each group,providing evidence for the effect of PCB118 exposure during pregnancy on the quality of offspring oocyte.

overall_design: The experiment included three groups of control group, low dose group and high dose group, and one sample was provided for each group.

first: Qi-Long

last: He

first: Hai-Quan

last: Wang


title: Cdk8 overexpression effect in heart

status: Public on Oct 30 2019

city: Iowa City

first: Long-Sheng

last: Song

state: IA

address: 285 Newton Rd

department: Internal Medicine

institute: University of Iowa

summary: Analysis of ventricular derived mRNA from cardiac specific Cdk8 overexpressing mice.  Results provide insight into the molecular mechanisms underlying dilated cardiomyopathy and heart failure.

overall_design: Methods: Ventricular samples (2 per group) from 21-day-old cardiac specific Cdk8 overexpressing versus wildtype male mice were used to generate polyA enriched stranded RNA libraries followed by RNAseq using the Illumina HiSeq platform.  Raw sequence reads were analyzed with BaseSpace (www.illumina.com) by aligning reads to the mus musculus mm10 genome using the TopHat Alignment app.  Transcripts were assembled and significant differentially expressed genes were determined with the Cufflinks Assembly and DE app using a false discovery rate <0.05. qRT–PCR validation was performed using SYBR Green assays

first: Chad

last: Grueter


title: Transcriptome analysis of different concentrations of benzyl isothiocyanate against Staphylococcus aureus

city: DaLian

first: Xiaoning

address: NO.1 Light-Industry Garden, Ganjingzi Borough

institute: Dalian Polytechnic University

summary: In this study, we monitored the transcriptional changes of S. aureus by RNA-seq analysis to better understand the effect of benzyl isothiocyanate (BITC) on the virulence inhibition of S. aureus and determined the bacteriostatic effect of BITC at subinhibitory concentrations. Our results revealed that compared with the control group (SAC), the BITC-treated experimental group (SAQ_BITC) had 708 differentially expressed genes (DEGs), of which 333 genes were downregulated and the capsular polysaccharide (cp) was significantly downregulated. Furthermore, we screened five of the most virulent factors of S. aureus, including the capsular polysaccharide biosynthesis protein (cp5D), capsular polysaccharide synthesis enzyme (cp8F), thermonuclease (nuc), clumping factor (clf) and protein A (spa).

overall_design: Analysis of genetic changes in S. aureus after BITC addition

first: Gongliang

last: Zhang


title: Epithelial EP4 plays an essential role in maintaining homeostasis in colon

city: Kyoto

first: Yoshihide

last: Matsumoto

state: Kyoto

address: Syogoinkawaramachi54 Sakyoku, Kyoto

country: Japan

institute: Kyoto University

summary: The EP4 receptor is known to mediate the protective effect of prostaglandin (PG) E2 in the gastrointestinal tract; however, the exact role of epithelial EP4 in intestinal pathophysiology remains unknown. We investigated the role of epithelial EP4 in maintaining colonic homeostasis by characterizing the intestinal epithelial cell-specific EP4 knockout (EP4 cKO) mice. We found a significant enrichment of genes involved in apoptosis-related pathways in the EP4 cKO colons. Moreover, inflammation-associated pathways were highly enriched and revealed more than half of the top 20 pathways related to immune response.

overall_design: Total pooled RNA isolated from 3 individual pools of control Villin-Cre and EP4 cKO colon tissues respectively was used for gene-expression analysis.

first: Yuki

last: Nakanishi

first: Akihisa

last: Fukuda

first: Hiroshi

last: Seno


title: RNA-seq of IPEC-J2 cells samples from different miRNA treatment groups

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

summary: RNA-seq of IPEC-J2 cells samples from different groups to search for miRNA effect on gene expression. Lentivirus of miRNA 133, and miRNA 143 were used to knock down (KD), or overexpress (OV) the two miRNAs. LV3NC is the control for knock down, Lv20NC is control for overexpression.  LV133 is the miRNA 133 knockdown, LV143 is the miRNA 133 knock down. OV143 is the miRNA 143 overexpression. miRNA 133 is no overexpression.

overall_design:
RNA-seq of IPEC-J2 cells samples from different groups to search for miRNA effect on gene expression:
Lentivirus of miRNA 133, and miRNA 143 were used to knock down (KD), or overexpress (OV) the two miRNAs. LV133 is the miRNA 133 knockdown, LV143 is the miRNA 133 knock down. OV143 is the miRNA 143 overexpression.
LV3NC is the control for knock down, Lv20NC is control for overexpression.

first: Bohui

last: Xiong

first: Cong

first: Hongfu


title: Establishing dose-strain specific transcriptomic changes in murine models of TCDD-induced toxicity

city: Toronto

first: Stephenie

last: Prokopec

state: Ontario

address: 661 University Avenue, Suite 510

country: Canada

institute: Ontario Institute for Cancer Research

summary: Environmental contaminants such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), are known to cause a wide range of toxicities. The consequences of acute exposure to TCDD in rodents, and to a lesser degree in humans, can range from mild chloracne to terminal illness, such as cancer. The aryl hydrocarbon receptor (AHR) plays a critical role in mediating the toxic effects of TCDD. However, the underlying mechanism of differential sensitivities to TCDD across organisms remain poorly understood, however differences in the AHR are known to play a role. To further investigate this, we profiled the transcriptomic responses in liver from TCDD sensitive or resistant mice, 19 hours following exposure to either 5 or 500 μg/kg TCDD. Analysis of transcriptomic profiles revealed several key findings: 1) TCDD sensitive C57BL/6 mice demonstrated an increased number of changes within the hepatic transcriptome than the TCDD resistant DBA/2 mice following exposure to low dose (5 μg/kg) TCDD, but this balanced out at the high dose (500 μg/kg), and the transcriptome from ratonized mice showed more changes than either C57BL/6 or DBA/2, regardless of dose; 2) mRNA abundance of the ‘AHR-core’ battery of genes was consistently perturbed in dioxin sensitive mice (C57BL/6 and rWT) in comparison to dioxin resistant mice (DBA/2), with Inmt showing significant changes in transcription only in the ratonized mouse liver and Cyp1a2 more response in non-transgenic mice (C57BL/6 and DBA/2); 3) a small subset of genes had significantly altered transcription in either the TCDD-resistant DBA/2 mouse liver (including Rpl18a, Mbd6, Onecut2 and Lipg) or the TCDD-sensitive cohorts (C57BL/6 and rWT; including Smcp, Acpp, Acot2 and Acot3). Overall, our results demonstrate considerable TCDD-induced transcriptomic differences between DBA/2 and C57BL/6 mouse lines.

overall_design: Adult male DBA/2 and C57BL/6 mice and transgenic rWT mice were treated by gavage with 0, 5, or 500 µg/kg TCDD dissolved in corn oil vehicle. Mice were euthanized 19 hours following treatment and liver tissue was harvested for analysis. RNA was isolated and the transcriptome for each animal assayed on separate  microarrays.

first: Sandy

middle: S

last: Lee

middle: D

first: Ren

middle: X

last: Sun

first: Cindy

middle: Q

first: John

last: Watson

first: Raimo

last: Pohjanvirta

first: Paul

middle: C

last: Boutros


title: Long noncoding RNA Linc00673 which enhances cancer cells progression by sponging miR-515-5p to elevate expression of MARK4 in human breast cancer

city: Harbin

first: Jian

address: 600 Changjiang Road

institute: Northeast Agricultural University

summary: In the present study, Linc00673 displayed high expression in breast cancer tissues and was associated with poor prognosis of breast cancer patients. Importantly, Linc00673 depletion inhibited breast cancer cell proliferation by impairing cell cycle progression and apoptosis. Mechanically, RNA sequencing was performed to investigate the potential crosstalk between Linc00673 and its targets. We found that Linc00673 acted as a competing endogenous RNA by sponging miR-515-5p to regulate MARK4 expression which inhibits the Hippo signaling pathway to promote proliferation of breast cancer.

overall_design: mRNA profiles of MDA-MB-453 with Linc00673 knockdown and scramble were generated by deep sequencing. The sequence reads that passed quality filters were analyzed at the transcript

first: Kun

last: Qiao

first: Da

last: Pang


title: The Molecular Phenotype of Lupus Nephritis Histological Lesions

summary: Lupus nephritis (LN) is characterized by immune-complex deposition in kidney glomeruli and has been classified according to histological features, but has not been characterized on a molecular level. This study aimed to characterize the relationship between histological and molecular phenotypes in LN. Renal compartmental mRNA expression was measured in 54 kidney biopsy specimens from patients with LN and correlated to histological phenotypes. The top identified transcripts were compared to a separate longitudinal cohort of 36 patients with paired kidney biopsies obtained at the time of flare and at follow up. Unsupervised clustering based on mRNA abundance resulted in clear separation by renal compartment, but did not demonstrate a relationship with LN class based on the International Society of Nephrology/Renal Pathology Society (ISN/RPS) classification, or the NIH activity and chronicity indices. A strong interferon gene signature was observed in both cohorts. FN1, SPP1, and LGALS-3 correlated with disease activity in both cohorts. The relationship between mRNA expression and ISN/RPS classification is modest. However, correlation of mRNA expression with individual histologic lesions identifies transcripts that change with resolution of disease flare, and provide insights into the molecular pathways potentially responsible for pathologic kidney lesions. Combining molecular and pathologic kidney biopsy phenotype may hold promise to better classify disease and identify actionable treatment targets.

overall_design:
Kidney biopsy material was obtained from 54 patients undergoing a for-cause kidney biopsy at the Toronto General Hospital from January 2007 to December 2012. After written informed consent, a section of the clinical biopsy core was stored in RNA-later (Life Technologies, Carlsbad CA) at 4°C. After it was determined that this tissue was not required for clinical diagnosis, and the patient had agreed to banking the tissue, these cores were available for research per the University Health Network institutional protocol.

Please contact Dr. Reich (Heather.Reich@uhn.ca) for additional (clinical) information.

first: Salem

last: Almaani

first: Carmen

last: Avila-Casado

first: Joan

last: Wither

first: James

middle: W

last: Scholey

first: Valeria

last: Alberton

first: Ana

last: Malvar

first: Samir

last: Parikh

first: Brad

last: Rovin

first: Heather

middle: N

last: Reich


title: Distinct mRNA and Long Non-coding RNAs (lncRNAs)  Expression Profiles of Decidual Natural Killer Cells in Human Early Missed Abortion

status: Public on Oct 15 2020

first: Tong

last: Li

address: No.  910 Hengshan Rd

institute: International Peace Maternity & Child Health Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: Our present study analyzes decidual natural killer(dNK) cells expression profiles of the lncRNA and mRNA in missed abortional patients. A total of 276 mRNAs and 67 lncRNAs were identified to be significantly dysregulated in missed abortion (p<0.01). Subsequently, the potential function of dysregulated mRNAs and lncRNAs in missed abortion were explored through the bioinformatics method. In addition, the relationship between these dysregulated lncRNAs and mRNAs was revealed through constructing the lncRNA-mRNA interaction network. Our data showed that upregulated mRNAs were enriched in immune response and cytokine-cytokine receptor interaction while downregulated mRNAs were mainly related to cell adhesion and ECM-receptor interaction. Most importantly, several novel lncRNAs in dNKs, regulating core maternal-fetal interface activation-related mRNAs, were algorithmically predicted, indicating involvement of lncRNAs in  the pathogenesis in early missed abortion.Topology analysis of lncRNA-mRNA interaction network suggested that the network presented a small world property, which means that most of mRNAs in the network were regulated by relative small number of hub lncRNAs. This study paves the way of investigating pathogenesis of early human missed abortion and facilitating the development of novel missed abortion therapeutics targeting lncRNAs.

overall_design: RNA sequencing of dNK cells derived from three patients with missed abortion and the other three healthy control women undergoing elective abortions were performed to determine the expression profiles of mRNAs and lncRNAs with poly-A tails.

first: Xin-Zhu

first: Guang-Yong

last: Zheng

first: Tian-Tian

last: Yu

first: Yan-Yan

last: Guo

first: Wei-Hong

last: Zeng

first: Lin

last: Qiu

first: Xiao-Guo

first: Yu-Chen

first: He-Feng

last: Huang

first: Xin-Mei

last: Liu


title: Identification of N6-methyladenosine functions of YTHDF3 using MeRIP-seq analysis combined with transcription sequencing

first: Wen

last: Ni

summary: We performed methylated RNA immunoprecipitation followed by sequencing (MeRIP–seq) combined with transcription sequencing to clarify the mechanism underlined YTHDF3 in CRC

overall_design: More than 50 ug of total RNA is sufficient for followed RNA fragmentation and immunoprecipitation according to the manuscript of the Magna MeRIP™ m6A Kit (Merck, Darmstadt, Germany).

first: Su

last: Yao

first: Jianming


title: RNA-seq of two contrasting tomato genotypes in response to low nitrogen

city: Wuhan

first: Jianda

last: Shi

state: Hubei

address: Hube

institute: HZAU

summary: To excavate the underlying molecular processes that tomato affected by the low N supply ,we collected roots and leaves from two genotypes at two stages after low N treatment

overall_design: RNA-seq of tomato in low nitrogen

first: Yuan


title: Molecular profiling of stem cell-like female germ line cells in Drosophila delineates networks important for stemness and differentiation

city: Cologne

first: Andreas

last: Wodarz

address: Kerpener Str. 62, Building 37

department: Anatomy

country: Germany

institute: Uniklinik Cologne

summary: We characterize the transcriptome of germline stem cell (GSC)-like cells isolated from bag of marbles (bam) mutant Drosophila ovaries by next generation RNA sequencing (RNA-seq) and compare it to the transcriptome of germline cells isolated from wild type ovaries. We further refine this dataset by utilizing an RNA-immunoprecipitation strategy to identify transcripts bound to the master differentiation factor Bam.

overall_design: Transcriptomes of bam mutant and wild type (Vasa-GFP) ovaries were characterized and compared by paired-end mRNA sequencing, in triplicate. Further, transcripts bound to Bam-GFP were delineated by RNA-immunoprecipitation followed by mRNA sequencing, also in triplicate.


title: Effect of zinc chelation in Caco-2 cells

city: Tirupati

first: Guruprasad

middle: Ramarao

last: Medigeshi

state: Andhra Pradesh

address: Panguru (G.P.), Yerpedu Mandal

department: Biology

country: India

institute: Indian Institute of Science Education and Research Tirupati

summary:
To identify the molecular pathways that are perturbed due to transient zinc chelation
Zinc is known to regulate the functions of about 10% of the human proteome and a large number of physiological processes that are zinc dependent have been identified and characterized under conditions of zinc deficiency and supplementation. As zinc homeostasis is closely linked to the normal functioning of both prokaryotic and eukaryotic cells, many pathogens are directly or indirectly affected by perturbations in zinc homeostasis. Dengue virus (DENV), a mosquito-borne, positive-strand RNA virus from the family Flaviviridae, has emerged as one of the major public health concerns in India and recent estimates suggest that over 60 million people globally get infected with DENV every year. The crystal structures of NS5 protein of DENV and West Nile virus have identified zinc binding site in RdRp domain and propose an important structural role for zinc ions in polymerase activity. Therefore, we investigated whether perturbation in intracellular zinc pools influence dengue infection. We utilized N,N,N’,N’-tetrakis(2-pyridinylmethyl)-1,2-ethanediamine (TPEN), a zinc-specific chelator, to mimic zinc-deficiency in cell culture models of infection and investigated the effect of zinc depletion on DENV life-cycle.

overall_design: Caco-2 cells were treated with a zinc chelator, N,N,N’,N’-tetrakis(2-pyridinylmethyl)-1,2-ethanediamine (TPEN) for four hours and total RNA was isolated and used for RNA sequencing.


title: LX-2 cells pretreated with CM272 (400nM) or vehicle (0.01%DMSO)

city: Pamplona

first: Maite

middle: G

last: Fernandez-Barrena

address: Pio XII 55

country: Spain

institute: CIMA

summary: LX-2 cells were pretreated with CM272 (400nM) or vehicle (0.01%DMSO) for 24 hours followed by incubation of TGFβ1 (5ng/ml) for another 24 hours.

overall_design: 4 Samples

first: Matias

last: Avila

last: García


title: Identification of Atrial Fibrillation associated genes and functional non-coding variants

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

summary: Expression analysis of whole tissue and cardiomyocytes of fetal and adult atrial free wall

overall_design: RNA-seq on human atrial tissue

first: Antoinette

middle: F

last: van Ouwerkerk

middle: M


title: Quercetin attenuates atherosclerosis via modulating oxidized LDL-induced endothelial cellular senescence

city: JiNan

first: jiang

middle: yue

last: hua

address: Jingshi Road

department: Department of Cardiovascular

institute: Shandong University of Traditional Chinese Medicine

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

summary: We have employed transcriptome microarray expression profiling as a discovery platform to figure out the pharmacological mechanisms of quercetin against endothelial senescence induced by ox-LDL in vitro. Expression of RCHY1, EIF4E1B, IGFBP3, SERPINE1, BRAF, SLC5A11 from this signature was quantified in the same kind of samples by real-time PCR, confirming the change pattern.

overall_design: Human aortic endothelial cells (HAECs) treated with 50 μg/mL ox-LDL with/without 3 μmol/L quercetin  were analysed.

first: Yue-Hua

last: Jiang

first: Ling-Yu

first: Xiao

last: Li


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

city: Chicago

first: Jennie

last: Lin

address: 303 E Superior

institute: Northwestern University

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

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


title: Random forest-based modelling to detect novel biomarkers for prostate cancer progression

city: Heidelberg

first: Reka

last: Toth

address: Im Neuenheimer Feld 280

institute: DKFZ

type: Methylation profiling by genome tiling array

summary: The clinical course of prostate cancer (PCa) is highly variable, demanding an individualized approach to therapy and robust prognostic markers for treatment decisions. We here present a random forest-based classification model to predict aggressive behaviour of PCa. DNA methylation changes between PCa cases with good or poor prognosis (discovery cohort with n=78) were used as input. The model was validated with data from two independent PCa cohorts from ICGC and TCGA. Ranking of cancer progression-related DNA methylation changes allowed selection of candidate genes for additional validation by immunohistochemistry. We identified loss of ZIC2 protein expression as a promising novel prognostic biomarker for PCa in >12,000 tissue micro-array tumors. The prognostic value of ZIC2 proved to be independent from established clinico-pathological variables including Gleason, stage, nodal stage and PSA. In summary, we have developed a PCa classification model which either directly or via expression analyses of the identified top ranked candidate genes might help in decision making related to the treatment of prostate cancer patients.

overall_design: The study included 39 patients with good and 39 patients with bad prognosis prostate cancer patients. Sample selection was based on the following criteria: good prognosis is indicated by presence of organ confined disease (pT2) and lack of recurrence for at least 5 years. In contrast, bad prognosis is defined as systemic presence of metastatic disease, indicated by biochemical (PSA based) recurrence within 3 years and no response to local radiation therapy.

first: Heiko

last: Schiffmann

first: Claudia

last: Hube-Magg

first: Franziska

last: Büscheck

first: Doris

last: Höflmayer

first: Sören

last: Weidemann

first: Patrick

last: Lebok

first: Christoph

last: Fraune

first: Sarah

last: Minner

first: Guido

last: Sauter

last: Plass

first: Yassen

last: Assenov

first: Ronald

last: Simon

first: Jan

last: Meiners

first: Clarissa

last: Gerhäuser


title: Whole transcriptome sequencing of Treg with and without Mef2d, Mef2c, HDAC1, HDAC2 or Dyrk1 deletion

city: Philadelphia

first: Wayne

last: Hancock

state: PA

address: 916B ARC, 3615 Civic Ctr Blvd

institute: CHOP/UPenn

summary: Mef2d, Mef2c, HDAC1, HDAC2 and Dyrk1 are involved with Foxp3 Treg regulation. Conditional deletion of either gene in Foxp3 Treg (cre/loxP) was generated and RNA sequenced and analyzed via Novogene, Inc.

overall_design: Foxp3+ regulatory T cells from mice with or without a Foxp3-conditional Mef2d, Mef2c, HDAC1, HDAC2 or Dyrk1 deletion (Mef2d-fl/flFoxp3cre, Mef2c-fl/flFoxp3cre, HDAC1-fl/flFoxp3cre, HDAC2-fl/flFoxp3cre or Dyrk1-fl/flFoxp3YFPcre and Foxp3YFPcre mice) had RNA isolated. The RNA samples, with three independent biological replicates per group, were sent to NovoGene for mRNA sequencing using the Illuminia PE150 platform.

first: Eros

last: Di Giorgio

first: Liqing

last: Wang

first: Yan

last: Xiong

first: Rongxiang

last: Han

first: Ulf

last: Beier


title: Next Generation Sequencing Facilitates Quantitative Analysis of  Pseudomonas aeruginosa PAO1 Transcriptomes under AgNP and AgNR exposure

status: Public on Oct 18 2020

city: Brisbane

first: Jianhua

last: Guo

address: Research Road, Level 4 Gehrmann Building

department: Australian Centre for Water and Environmental Biotechnology

country: Australia

institute: University of Queensland

summary: The goals of this study are to use Next-generation sequencing (NGS)to detect bacterial mRNA profiles of  Pseudomonas aeruginosa PAO1 in response to 0, 1, 20 and 25 mg/L AgNPs or 0, 1,30 and 300 mg/L AgNRs for 2 h, using Illumina HiSeq 2500.The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp. The clean reads of each sample were aligned to the E. coli reference genome (NC_000913) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/). Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM, a normalized value generated from the frequency of detection and the length of a given gene.

overall_design: Bacterial mRNA profiles of Pseudomonas aeruginosa PAO1  in response to  0, 1, 20 and 25 mg/L AgNPs or 0, 1,30 and 300 mg/L AgNRs for 2 h, using Illumina HiSeq 2500

first: Ji

last: Lu


title: 2,3,7,8-tetrachlorodibenzo-p-dioxin modifies alternative splicing in mouse liver

first: Stephenie

last: Prokopec

summary: Alternative splicing is a co-transcriptional mechanism by including or excluding exons in different combinations, thereby expanding the diversity of protein isoforms of a single gene. Abnormalities in this process can result in deleterious effects to human health, and several xenobiotics are known to interfere with splicing regulation through multiple mechanisms. These changes could lead to human diseases such as cancer, neurological disorders, autoimmune diseases, and developmental disorders. 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is an environmental contaminant generated as a byproduct of various industrial activities. Exposure to this dioxin has been linked to a wide range of pathologies through the alteration of multiple cellular processes. However, the effects of TCDD exposure on alternative splicing have not yet been studied. Here, we investigate whether exposure to TCDD influenced hepatic alternative splicing in adult male C57BL/6J mice. We identified several genes whose alternative splicing of precursor messenger RNAs was modified following TCDD exposure. In particular, we demonstrated that alternative splicing of Cyp1a1, Ahrr, and Actn1 was significantly altered after TCDD treatment. These findings show that exposure to TCDD has an impact on alternative splicing, presumably  through binding to the aryl hydrocarbon receptor, and suggest a new avenue for AhR-mediated pathogenesis.

overall_design: Adult male C57BL/6 mice were treated by gavage with 0, 5, or 500 µg/kg TCDD dissolved in corn oil vehicle. Mice were euthanized 19 hours following treatment and liver tissue was harvested for analysis. RNA was isolated and the transcriptome for each animal assayed on separate  microarrays.

first: Ana

middle: B

last: Villaseñor –Altamirano

first: John

last: Watson

first: Cindy

last: Yao

first: Paul

last: Boutros

first: Raimo

last: Pohjanvirta

first: Jesús

last: Valdés-Flores

first: Guillermo

last: Elizondo


title: Concordance between gene expression in peripheral whole blood and colonic tissue in children with inflammatory bowel disease.

city: Boston

first: Jocelyn

middle: Anne

last: Silvester

state: Massachusetts

address: 300 Longwood Avenue

department: Gastroenterology

institute: Boston Children's Hospital

summary:
Presenting features of inflammatory bowel disease (IBD) are non-specific. We hypothesized that mRNA profiles could (1) identify genes and pathways involved in disease pathogenesis; (2) identify a molecular signature that differentiates IBD from other conditions; (3) provide insight into systemic and colon-specific dysregulation through study of the concordance of the gene expression.   Children (8-18 years) were prospectively recruited at the time of diagnostic colonoscopy for possible IBD. We used transcriptome-wide mRNA profiling to study gene expression in colon biopsies and paired whole blood samples. Using blood mRNA measurements, we fit a regression model for disease state prediction that was validated in an independent test set of adult subjects (GSE3365).   Results: Ninety-eight children were recruited [39 Crohn’s disease, 18 ulcerative colitis, 2 IBDU, 39 non-IBD]. There were 1,118 significantly differentially (IBD vs non-IBD) expressed genes in colon tissue, and 880 in blood. The direction of relative change in expression was concordant for 106/112 genes differentially expressed in both tissue types. The regression model from the blood mRNA measurements distinguished IBD vs non-IBD disease status in the independent test set with 80% accuracy using only 6 genes. The overlap of 5 immune and metabolic pathways in the two tissue types was significant (p<0.001).  Conclusions: Blood and colon tissue from patients with IBD share a common transcriptional profile dominated by immune and metabolic pathways. Our results suggest that peripheral blood expression levels of as few as 6 genes (IL7R, UBB, TXNIP, S100A8, ALAS2, and SLC2A3) may distinguish patients with IBD from non-IBD.
Ninety-eight children were recruited [39 Crohn’s disease, 18 ulcerative colitis, 2 IBDU, 39 non-IBD]. There were 1,118 significantly differentially (IBD vs non-IBD) expressed genes in colon tissue, and 880 in blood. The direction of relative change in expression was concordant for 106/112 genes differentially expressed in both tissue types. The regression model from the blood mRNA measurements distinguished IBD vs non-IBD disease status in the independent test set with 80% accuracy using only 6 genes. The overlap of 5 immune and metabolic pathways in the two tissue types was significant (p<0.001). Conclusions: Blood and colon tissue from patients with IBD share a common transcriptional profile dominated by immune and metabolic pathways. Our results suggest that peripheral blood expression levels of as few as 6 genes (IL7R, UBB, TXNIP, S100A8, ALAS2, and SLC2A3) may distinguish patients with IBD from non-IBD.

first: Nathan

middle: P

last: Palmer

first: I

last: Kohane

middle: A


title: Prenatal androgen exposure and transgenerational susceptibility to polycystic ovary syndrome

city: stockholm

first: yu

last: pei

address: Karolinska Vägen 6

country: Sweden

institute: karolinska institutet

summary: The effects of how obesity and elevated androgen levels in women with polycystic ovary syndrome (PCOS) affect their offspring are unclear. We found that daughters of PCOS mothers are more likely to be diagnosed with PCOS in a Swedish nationwide register-based cohort and a clinical case-control study from Chile. Further, female mice (F0) with PCOS-like traits induced by late gestation injection of dihydrotestosterone, with and without obesity, produced female F1–F3 offspring with a PCOS-like reproductive and metabolic phenotypes. Sequencing of single MII oocytes from F1–F3 offspring revealed common and unique altered gene expression across all generations. Notably, four genes were also differentially expressed in serum samples from daughters in the case-control study and unrelated women with PCOS. Our findings provide evidence of transgenerational effects in female offspring of PCOS mothers and identify possible candidate genes for the prediction of a PCOS phenotype in future generations.

overall_design: Transcriptomic profiles of mice MII oocytes across generations

first: Yu

last: Pei

first: Qiaolin

last: Deng

first: Elisabet

last: Stener-Victorin


title: Elucidation of the host transcriptomic response to bovine respiratory syncytial virus

city: Dunsany

first: Dayle

last: Johnston

state: Ireland

address: AGRIC

department: Animal and Bioscience Research Department

country: Ireland

institute: Teagasc

summary: Bovine respiratory disease (BRD) is the leading cause of morbidity and mortality in calves over one month of age. In a controlled challenge study in artificially-reared dairy calves, the influence of the host response to bovine respiratory syncytial virus (BRSV) was examined. Holstein-Friesian calves were either inoculated with BRSV (10^5/ml × 15 ml/animal) (n=12) or mock challenged with phosphate buffer saline (10ml/animal) (n=6). Calves were euthanised on day 7 post-challenge. Bronchial lymph nodes were collected; RNA was extracted and sequenced (75bp paired-end). Sequenced reads were adapter trimmed, quality assessed (FastQC) and aligned to the bovine genome (UMD 3.1) using STAR. Differential gene expression analysis was performed using EdgeR, and pathway and gene ontology analyses were carried out using g:Profiler, IPA and DAVID. There was a clear separation between BRSV challenged and control calves based on log2 fold gene expression changes, despite an observed mild clinical manifestation of the disease. There were 934 differentially expressed genes (DEG) (p < 0.05, FDR < 0.1, fold change > 2) between the BRSV challenged and control calves. Over-represented gene ontology terms, pathways and molecular functions, among the DEG, were associated with immune responses and defense responses to a virus.

overall_design: Bronchial lymph node tissues were collected for RNA-Seq analysis from 18 calves (12 BRSV challenged and 6 controls).

first: Bernadette

last: Earley

first: Matthew

middle: S

last: McCabe

first: Gordon

last: Blackshields

first: Kenneth

last: Lemon

first: Catherine

last: Duffy

first: Michael

last: McMenamy

first: S

middle: L

last: Cosby

first: JaeWoo

last: Kim

first: Jeremy

last: Taylor

first: Sinead

last: Waters


title: Genetically diverse uropathogenic Escherichia coli adopt a common transcriptional program in patients with urinary tract infections

city: Ann Arbor

first: Harry

last: Mobley

state: Michigan

address: 1150 W. Medical Center Drive

department: Microbiology and Immunology

institute: University of Michigan

summary: Uropathogenic Escherichia coli (UPEC) is the major causative agent of uncomplicated urinary tract infections (UTIs). A common virulence genotype of UPEC strains responsible for UTIs is yet to be defined, due to the large variation of virulence factors observed in UPEC strains. We hypothesized that studying UPEC functional responses in patients might reveal universal UPEC features that enable pathogenesis. Here we identify a transcriptional program shared by genetically diverse UPEC strains isolated from 14 patients during uncomplicated UTIs. Strikingly, this in vivo gene expression program is marked by upregulation of translational machinery, providing a mechanism for the rapid growth within the host. Our analysis indicates that switching to a more specialized catabolism and scavenging lifestyle in the host allows for the increased translational output. Our study identifies a common transcriptional program underlying UTIs and illuminates the molecular underpinnings that likely facilitate the fast growth rate of UPEC in infected patients.

overall_design: 14 UPEC mRNA profiles isolated directly from patient urine (collected into RNAprotect), and 14 UPEC mRNA profiles from in vitro cultures in filter-sterilized urine (mid-log phase)

first: Anna

last: Sintsova

first: Arwen

last: Frick-Cheng

first: Sara

last: Smith

first: Ali

last: Pirani

first: Evan

last: Snitkin


title: LncRNA-GAS5 negative regulation of YAP-target genes expression

city: Guangzhou

first: Wen

last: Ni

address: No. 135, Xingang Xi Road

institute: SUN YAT-SEN UNIVERSITY

summary: Analysis of RNA-seq-based differential expression after overexpression of GAS5 or knockdown of YAP revealed a highly significant overlap of common targets.

overall_design: LncRNA-seq of exogenous GAS5 or YAP-specific siRNA in CRC cells.

first: Su

last: Yao

first: Jianming

last: Li


title: MiR-29 Regulates de novo Lipogenesis in the Liver and Circulating Triglyceride Levels in a Sirt1-Dependent Manner

city: Ithica

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

summary: Systematic comparison of multiple models of diabetes / insulin resistance reveals miR-29 as a commonality among them, and further analysis reveals it as a key therapeutic target for insulin resistance.

sample_organism:
Macaca mulatta
Mus musculus
Rattus norvegicus

overall_design: Comparison of multiple models of diabetes at the small RNA-seq and RNA-seq level. Further sequencing analysis of miR-29 following perturbation using locked nucleic acids.

first: Matt

last: Kanke


title: Microarray analysis of Psm-induced transcriptome changes in the systemic leaves of Arabidopsis plants

city: Durham

first: Jian-Liang

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

summary: The goal of the microarray was to compare the bacterial pathogen Pseudomonas syringae pv. maculicola ES4326 (Psm)-induced transcriptome changes in the systemic leaves of the wild-type Col-0, lecrk-VI.2-2, and bak1-5 plants. Results showed that local Psm inoculation induced dramatic transcriptional changes in Col-0, with 564 and 151 genes up- and down-regulated at least twofold with a low q value (≤ 0.05), respectively. However, only 55 and 26 genes in lecrk-VI.2-2 and 221 and 121 genes in bak1-5 were up- and down-regulated, respectively.  The majority of the genes that were induced or suppressed twofold or more with a low q value (≤ 0.05) in Col-0 were induced or suppressed to a smaller extent in bak1-5 and the smallest extent in lecrk-VI.2-2. These results indicate that both lecrk-VI.2-2 and bak1-5 suppressed Psm-induced systemic signaling with the lecrk-VI.2-2 mutation having a stronger effect than bak1-5.

overall_design: Three replicates with systemic leaves from 12 plants per sample were collected at 48 hr after Psm inoculation of the local leaves. Systemic leaf tissues were collected as the control at 48 hr after the local leaves were treated with 10 mM MgCl2.  After extraction, RNA concentration was determined on a NanoDrop Spectrophotometer (Thermofisher Scientific, Waltham, MA) and sample quality was assessed using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Equal amount of RNA from the biological replicates were used for microarray analysis.

first: Chenggang

last: Wang

first: Xiaoen

last: Huang

first: Yanping

last: Zhang

first: Jian

first: Zhonglin

last: Mou


title: Identification of differentially expressed circRNA in gallbladder cancer compared with matched normal tissue

city: Los angeles

first: Xiangming

last: Ding

state: CA

address: 650 Charles E Young Dr S, Los Angeles, CA 90095

institute: UCLA

summary: We hypothesized that the circRNA will play an important role in the progresion of gallbladder cancer. To test this hypothesis, we collect the gallbladder cancer and matched normal tissue from 4 different patients and examined the circRNA expression in these 8 sampels through next generation sequencing.

overall_design: Examination of the circRNA exprerssion in 4 gallbladder cancer and matched normal tissue

first: Wang

last: shouhua


title: Formation of Friable Embryogenic Callus is Enhanced under Nitrate, Potassium and Phosphate Limited Condition in Cassava.

city: Yokohama

first: Motoaki

last: Seki

address: 1-7-22, Suehiro-cho, Tsurumi

institute: RIKEN CSRS

summary: Agrobacterium-mediated transformation is an important research tool and a practical tool for an improvement of cassava cultivar. The induction of friable embryogenic callus (FEC) is considered as a one of key step in cassava transformation. In this article, we optimized a media composition for improving the frequency of FEC induction and investigated about the physiological mechanism of FEC induction under optimized media condition using the transcriptome analysis. These results showed that changing to 10-folds lower media in comparison to MS media on nitrogen, potassium and phosphate contents and the use of excess vitamin B1 (changing from 0.1 mg/L to 10 mg/L) in addition to use of picrolam were necessary for leading to the effective induction to FEC and delaying the growth of non-FEC. An increase of transcripts concerning lipid metabolism, cell membrane and cell cuticle and a decrease of transcripts related to cell-wall modification process under long-term subculture were observed by microarray analysis, expecting that the nitrogen, potassium and phosphate limited condition and use of excess vitamin B1 provide the suitable condition for FEC induction through inhibition of excess cell proliferation and maintenance of fine FEC through formation of protective barriers in cell membranes. Our results will benefit as a one of significant techniques for cassava transformation, providing the more convenience transformation process using cassava genotypes and landrace adapted to the various field environments

overall_design: The friable embryogenic callus (FECs) were prepared in modified MS basal medium with 12mg/L piloram, 2% sucrose and 1.5% agarose (CIM-NPK) at 28ºC for 6 months (dark condition). The FECs were transferred to CIM-NPK or normal MS basal media with 12mg/L piloram, 2% sucrose and 1.5% agarose (CIM). The FECs were incubated for 1 month at 28ºC (dark condition). Total RNA was prepared from the incubated FECs and used for the microarray hybridization. Four replicative hybridization experiments were carried out using the independent biological samples.

first: Yoshinori

last: Utsumi

first: Chikako

first: Maho

last: Tanaka

first: Vu

middle: T

last: Ha

first: Satoshi

last: Takahashi

first: Akihiro

last: Matsui


title: Next generation sequencing facilitates quantitative analysis of MTAC-P (EGFR-TKI resistant cell line derived from PC9) with and without BCAT1 knockdown.

city: Shanghai

first: Yuetong

address: 320 Yue Yang Road, Room 713

department: Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences

institute: Chinese Academy of Sciences

summary: The goals of this study are to compare the different transcriptome signiture between MTAC-P cells with and without BCAT1 knockdown with NGS-derived retinal transcriptome profiling (RNA-seq).

overall_design: Total mRNA profiles of MTAC-P cells with and without BCAT1 knockdown were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Hongbin

last: Ji


title: Mouse gonadal transcriptome at 12.5dpc, 13.5dpc, 16.5dpc and 6dpp.

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

summary:
we employed RNA-Seq to examine transcriptome profiles of male and female mouse gonads at 12.5dpc, 13.5dpc, 16.5dpc and 6dpp.
Methods: Gonadal mRNA profiles of 12.5dpc,13.5dpc, 16.5dpc and 6dpp mice were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500. The cDNA library was constructed with a SMARTer® Ultra Low Input RNA for lllumina® Sequencing kit (Clontech Laboratories) and sequenced on an Illumina HiSeq 2500.After sequencing, clean reads were obtained by removing reads containing the adaptor sequences, reads with > 5% ambiguous bases, and low-quality reads, then mapped to the mouse genome (version: mm10_GRCm38) using TopHat software. Gene expression level was calculated using the fragments per kilobase per million mapped reads method.

overall_design: RNA sequencing was employed to examine transcriptome profiles of murine 4 female and 4 male gonads at developmental stages involving in sex differentiation, meiosis, and gametogenesis . Analysis of Differentially Expressed Genes (DEGs) was performed by the DESeq package in R language. Wayne analysis was then performed to screen sex-biased expressed genes. Genes were submitted to the databases of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) for enrichment analysis of the significant GO terms and KEGG pathways. The Series-Cluster analysis of expression profiles of DEGs was performed by using the STEM method. Weighted gene co-expression network analysis (WGCNA) was used to create a co-expression network. Alternatively spliced transcripts were identified by the software AS detector (ASD) using the Fisher’s exact test.

first: Zhuxia

last: Zheng


title: Compare gene expression difference between PC9 and MTAC-P

summary: To find different gene expression signature between PC9 cells and its resistant cell line established by mild-TKI treatment, we did microarray analyses.

overall_design: Each samples was duplicated


title: Chromatin remodeler INO80 is essential for cocaine craving during prolonged withdrawal

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Neuroadaptations in the nucleus accumbens (NAc) underlie cue-induced cocaine craving that intensifies (“incubates”) during withdrawal and contributes to persistent relapse vulnerability. Long-lasting gene changes govern perpetual behavioral abnormalities but the role of epigenetic plasticity in cocaine craving during prolonged withdrawal is poorly understood. Here we show that chromatin remodeler INO80 in the NAc mediates cocaine-induced, withdrawal-dependent plasticity and incubated cocaine craving.

overall_design: Cocaine or saline treatment, Nucleus Accumbens, Antibody: INO80

first: Craig

last: Werner

first: Jennifer

last: Martin

first: Andrew

last: Stewart

first: Ian

last: Maze

first: David

last: Dietz


title: Next generation sequencing facilitates quantitative analysis of PC9 and MTAC-P (EGFR-TKI resistant cell line derived from PC9)

last: Wang

summary: The goals of this study are to compare the different transcriptome signiture between PC9 and MTAC-P with NGS-derived retinal transcriptome profiling (RNA-seq).

overall_design: Total mRNA profiles of PC9 and MTAC-P cells were generated by deep sequencing, in triplicate, using Illumina GAIIx.


title: Gene expression of human pancreatic CAFs via Affymetrix

status: Public on Oct 28 2019

city: La Jolla

first: Paul

last: Insel

address: 9500 Gilman Drive

department: Pharmacology

institute: UC San Diego

summary:
Gene expression in low passage pancreatic Cancer-associated Fibroblasts (CAFs) was assayed via Affymetrix HG U133plus2.0 arrays
We used these array data to extract GPCR expression in human pancreatic CAFs, to compare with the same from RNA-seq and Taqman GPCR arrays

overall_design: Two replicates of low-passage pancreatic CAFs from patients with PDAC (Pancreatic Ductal Adenocarcinoma) were assayed via omics methods

first: Krishna

last: Sriram

first: Shu

middle: Z

last: Wiley


title: HDAC2-mediated miRNA profiling in acute myeloid leukemia

city: Napoli

first: Annamaria

last: Carissimo

address: via Castellino

country: Italy

institute: Tigem

summary: miRNA microarray expression analysis of human acute myeloid leukemia cell line (U937) after HDAC2 genetically and enzymatically defection

overall_design: 3 samples were analyzed in duplicates

first: Carmela

last: Dell'Aversana


title: Integrated transcriptomic and proteomic analysis of primary human umbilical vein endothelial cells

city: Baltimore

first: Akhilesh

last: Pandey

state: MARYLAND

address: 733 N Broadway

institute: Johns Hopkins School of Medicine

summary: Human umbilical vein endothelial cells (HUVECs) are a widely-used model system to study pathological and physiological processes associated with the cardiovascular system. An understanding of genes and proteins that are expressed in any cell type is a fundamental need which facilitates studies of molecular changes in disease states and response to various stimuli. In this study, we employed next generation sequencing and mass spectrometry to profile the transcriptome and proteome of primary HUVECs. Analysis of 145 million paired-end reads from next generation sequencing confirmed expression of 12,186 protein-coding genes (FPKM>0.1), 439 novel long non-coding RNAs and revealed 6,089 novel isoforms that were not annotated in GENCODE. A comparison of the transcripts against human gene expression data for 53 tissues catalogued by the Genotype-Tissue Expression (GTEx) project revealed a number of HUVEC-specific genes. Proteomics analysis identified 6,477 proteins including confirmation of N-termini for 1,091 proteins and isoforms for 149 proteins for which transcriptomic evidence was observed. Alternate translational start sites for seven proteins and alternate splicing in five proteins were also identified. A database search to specifically identify other post-translational modifications provided evidence for a number of modification sites on 117 proteins which included ubiquitylation, lysine acetylation and mono, di- and tri-methylation events. Based on the data from this study and a survey of other databases, we provide evidence for 11 “missing proteins,” which are proteins for which there was insufficient or no protein level evidence. Peptides supporting missing protein and novel events were validated by comparison of MS/MS fragmentation patterns with synthetic peptides. By creating a custom database of proteins containing sample-specific single amino acid variants (SAAV), we also identified 245 variant peptides derived from 207 expressed proteins. Overall, we believe that the integrated approach employed in this study is widely applicable to study any primary cell type for deeper molecular characterization.

overall_design: One set of RNA sample isolated from HUVECs was used in this study for mRNA enrichment by polyA tail capture using oligo-DT beads prior to heat-based fragmentation and elution of mRNA


title: Microarray gene expression from hepatitis B virus infection to hepatocellular carcinoma

city: Shang hai

first: Yi-yu

last: Lu

address: 1200 Cai Lun Road,Zhangjiang Hi-TechPark, Pudong New Area

institute: Research Center for Traditional Chinese Medicine Complexity System, Shanghai University of Traditional Chinese Medicine

summary: Background: The pathogenesis of hepatitis B virus (HBV)-caused hepatocellular carcinoma (HCC) is complex and not fully understood. In clinical, the effective prevention and treatment of HCC rely on the accurate diagnosis. We developed a biology network approach to investigate the potential mechanisms and biomarkers of each stages from HBV infection to HCC. Methods Global gene profiling of healthy individuals (HC), HBV carriers (HBVC), chronic hepatitis B patients (CHB), liver cirrhosis (LC) and HCC was analyzed by gene array. Differentially expressed genes (DEG) were found by RVM (Random variance model) corrective ANOVA and STC (Series Test of Cluster) analysis.

overall_design: peripheral blood mononuclear cells (PBMCs) from 3 healthy individuals (HC),3 HBV carriers (HBVC), 3 chronic hepatitis B patients (CHB), 3 liver cirrhosis (LC) and 3hepatocellular carcinoma (HCC) samples

first: Shi-Bing

last: Su


title: A high-throughput screen reveals SALL4-induced oxidative phosphorylation vulnerabilities in cancer

city: Singapore

first: Chan-Shuo

last: Wu

address: 14 Medical Drive, #12-01

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

summary: Transcription factors are important drivers of cancer but the development of therapeutics against these factors has had limited success. We developed a stringent high-throughput chemical genetic screening platform to identify compounds that target oncogene SALL4 dependency in liver cancer. The platform comprises SALL4 low- and high-expressing endogenous cell lines, and engineered SALL4-low isogenic lines overexpressing SALL4. We identified 4 oxidative phosphorylation (OXPHOS) inhibitors, from screening 21,575 natural product extracts, that selectively reduce SALL4-dependent cell viability. ATP synthase inhibitor Oligomycin suppresses SALL4-expressing cancer in culture and in vivo. When aberrantly overexpressed in cancer, SALL4 binds ~50% of OXPHOS and other mitochondrial genes, upregulating their expression. SALL4 upregulation also functionally increases OXPHOS. Our endogenous/isogenic transcription factor-screening platform reveals a therapeutically actionable OXPHOS vulnerability in SALL4-expressing cancer.

overall_design: RNA-seq was performed on SALL4 knockdown and SALL4 overexpression cell line models to identify alterations in gene expression.

first: Justin

last: Tan

first: Feng

last: Li

first: Joanna

last: Yeo

first: Kol

middle: J

last: Yong

first: Mahmoud

last: Bassal

first: Guo

middle: H

last: Ng

first: May

middle: Y

last: Lee

first: Chung

last: Leong

first: Hong

middle: K

first: Bee

last: Liu

first: Tim

last: Chan

first: Zi

first: Winston

first: Siyu

first: Kia

last: Low

first: Siming

last: Ma

first: Nikki

middle: R

last: Kong

first: Alicia

last: Stein

first: Matan

last: Thangavelu

first: Giridharan

last: Periyasamy

first: John

last: Asara

first: Yock

last: Dan

first: Huck

first: Yoganathan

last: Kanagasundaram

first: Siew

first: Wai

last: Tam

first: Li

last: Chai

first: Daniel

last: Tenen


title: Asymmetric down-regulation of tolerance to DNA damage at replication forks

city: Madrid

first: Rodrigo

last: Bermejo

address: Calle Ramiro de Maeztu 9

department: Center for Biological Research (CIB-CSIC)

institute: Spanish National Research Council (CSIC)

type: Genome binding/occupancy profiling by genome tiling array

summary:
The tolerance pathway allows bypassing deleterious lesions that block replicative DNA polymerases.
In eukaryotes tolerance is controlled by ubiquitylation of the DNA replication factor PCNA4.
Here, we show that PCNAK164-ubiquitin proteases (PCNA-DUBs) Ubp10 and Ubp12 localise to replication forks.
In particular, the main PCNA-DUB, Ubp10, associates primarily to nascent lagging strands.
We also found that cells deficient for PCNA deubiquitylation show both increased interaction of TLS polymerase ζ-associated Rev1 with lagging strands and Rad52-dependent template switching events.
This evidence reveals a fork-coupled layer of DDT regulation allowing strand-specific pathway choices.

overall_design:
Chip on chip analysis was carried out as described (Bermejo et al., 2011), employing anti-myc monoclonal antibody clone 4A6 (Millipore)
Labelled probes were hybridized to Affymetrix S.cerevisiae Tiling 1.0 (P/N 900645) arrays and processed with TAS software.

first: Vanesa

last: Álvarez

first: Camilla

last: Frattini

first: María

last: Sacristán

first: Alfonso

last: Gallego-Sánchez

first: Avelino

last: Bueno


title: Deep sequencing reveals the regulatory network of microRNA-transcription factor in paired normal and OSCC tissue suggesting a tumor suppress role of circadian clock gene RORα

city: Wuhan

first: Dong

last: Chen

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: The molecular interplay between miRNA and mRNA is critical for tumorigenesis, whereas it is not comprehensively profiled in OSCC. Here, we aimed to explore the potential network of miRNAs-mediated genes. Furthermore, the cooperative effect of miRNAs on RORα in tumor proliferation was elucidated. Four pairs of cancer and adjacent normal tissues were collected for high-throughput sequencing. The regulatory interactions between differentially expressed miRNAs and mRNAs were performed by bioinformatics analysis. Luciferase reporter assay and qRT-PCR assay were used to examine the effects of miRNAs on RORα. The CCK8 assay and mice xenografts assay were used to assess the role of RORα on OSCC proliferation in vitro and in vivo. Western blotting was used to detect the total and phosphorylated p53 protein level in cells with enforced or suppressed RORα expression.Differentially expressed mRNAs and miRNAs between paired OSCC and normal tissues were identified. The negative correlation networks between the up-regulated miRNA and down-regulated transcription factors (TFs) were determined. Five miRNAs (miR-503-5p, miR-450b-5p, miR-27a-3p, miR-181a-5p, miR-183-5p) were testified to directly target RORα, and resulted in a more stronger effect on RORα suppression by mixing together. In addition, RORα was detected to be generally decreased in 44 OSCC samples and significantly suppressed the proliferation of OSCC cells in vitro and in vivo. Attenuated RORα decreased p53 protein expression and suppressed p53 phosphorylation activity. The study revealed the possible miRNAs-mediated TFs network in OSCC and identified the cooperative miRNAs effect on RORα expression in OSCC proliferation.

overall_design: four pairs of cancer and adjacent normal epithelia specimens

first: Jiali

last: Zhang

first: Yi

first: Kejing

last: Wu


status: Public on Oct 27 2019

city: Beijing

first: Jian

last: Liu

address: Gong Ti  Nan Lu 8#

institute: Beijing Chao-Yang Hospital, Capital Medical University

summary:
MTA1, SOX4, EZH2 and TGF-β are all potent inducers of epithelial-mesenchymal transition (EMT) in cancer; however, the signaling relationship among these molecules in EMT is poorly understood. Here, we investigated the function of MTA1 in cancer cells and demonstrated that MTA1 overexpression efficiently activates EMT. This activation resulted in a significant increase in the migratory and invasive properties of three different cancer cell lines through a common mechanism involving SOX4 activation, screened from a gene expression profiling analysis. We showed that both SOX4 and MTA1 are induced by TGF-β and both are indispensable for TGF-β-mediated EMT. Further investigation identified that MTA1 acts upstream of SOX4 in the TGF-β pathway, emphasizing a TGF-β-MTA1-SOX4 signaling axis in EMT induction. The histone methyltransferase EZH2, a component of the polycomb (PcG) repressive complex 2 (PRC2), was identified as a critical responsive gene of the TGF-β-MTA1-SOX4 signaling in three different epithelial cancer cell lines, suggesting that this signaling acts broadly in cancer cells in vitro. The MTA1-SOX4-EZH2 signaling cascade was further verified in TCGA pan-cancer patient samples and in a colon cancer cDNA microarray, and activation of genes in this signaling pathway predicted an unfavorable prognosis in colon cancer patients. Collectively, our data uncover a SOX4-dependent EMT-inducing mechanism underlying MTA1-driven cancer metastasis and suggest a widespread TGF-β-MTA1-SOX4-EZH2 signaling axis that drives EMT in various cancers. We propose that this signaling may be used as a common therapeutic target to control epithelial cancer metastasis.
We used microarrays to detect MTA1-regulated genes in cancer cells.

overall_design: NCI-H446 control (NC) and MTA1-overexpressing (OE) cells were selected for RNA extraction and hybridization on Affymetrix microarrays.


title: RNA sequencing of human mammary epithelial cells

city: Buffalo

first: AC

last: CHANG

address: Elm and Carlton

institute: RPCI

summary: Study of RNA expression changes in human mammary epithelial cells under TGFbeta1 induced epithelial mesenchymal transition

overall_design: RNA expression changes in MCF12A cells treated with TGFbeta1 or vehicle

first: Chun

last: Chang


title: Divergent effects of eRF3 and Upf1 on the expression of uORF carrying mRNAs and ribosome protein genes

city: Orsay

first: Olivier

last: Namy

address: Rue Gregor Mendel, bat 400

country: France

institute: CNRS, Université Paris-Sud

summary: In addition to its role in translation termination, eRF3 has been implicated in the nonsense-mediated mRNA decay (NMD) pathway through its interaction with Upf1. NMD is a RNA quality control mechanism, which detects and degrades aberrant mRNAs as well as some normal transcripts including those that harbor upstream open reading frames in their 5' leader sequence and long 3′ UTR. In this study, we used RNA-sequencing and ribosome profiling to perform a genome wide analysis of the effect of either eRF3 or Upf1 depletion in human cells. Our bioinformatics analyses allow to delineate the features of the transcripts controlled by eRF3 and Upf1 and to compare the effect of each of these factors on gene expression. We show that eRF3 and Upf1 have very different impact on the human transcriptome, only ~250 transcripts being targeted by both factors. We also show that in contrast to Upf1, eRF3a depletion globally derepressed the expression of mRNAs containing translated uORFs. Finally, we find that eRF3a and Upf1 have opposite effects on ribosome protein gene expression. Together, our results provide important elements for understanding the impact of translation termination and NMD on the human transcriptome and reveal novel determinants of ribosome biogenesis regulation.

overall_design: Examination of the translational consequences of the inactivation of the eRF3 and Upf1 in HCT-116

first: Affaf

last: Aliouat

first: Isabelle

last: Hatin

first: Pierre

last: Bertin

first: Vérène

last: Stierlé

first: Samia

last: Salhi

last: Jean-Jean


title: RNA-sequencing of primary human PASMCs and CFs for estimating GPCR expression

first: Paul

last: Insel

summary: RNA-seq was performed on primary human pulmonary arterial smooth muscle cells (PASMCs) and cardiac fibroblasts (CFs)

overall_design: Untreated cells at low passage were assayed via RNA-seq and GPCR expression was extracted

first: Krishna

last: Sriram


title: Doxorubicin response in diffuse large B-cell lymphoma cell lines varies with concentration, exposure duration, and level of intrinsic sensitivity

city: Aalborg

first: Julie

middle: Støve

last: Bødker

address: Sdr. Skovvej 15

department: Department of Heamatology

country: Denmark

institute: Aalborg University Hospital

summary: Although diffuse large B-cell lymphoma (DLBCL) is a very heterogeneous disease, patients are as standard treated with a combination of rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisolone (R-CHOP). Since approximately 40% of patients die due to refractory disease or relapse, enhanced knowledge about drug response mechanisms is required to improve treatment outcome. Therefore, this study assesses parameters that possibly influence doxorubicin response. Doxorubicin-induced impact on the number of living cells was evaluated for four human DLBCL cell lines, illustrating differences in intrinsic sensitivity levels. Six cell lines were subjected to gene expression profiling upon exposure to two distinct drug concentrations (0.00061 μg/mL and 2.5 μg/mL) for 2, 12, and 48 hours. Variation in gene expression compared to baseline was determined with a mixed-effects model, and gene ontology enrichment analysis was performed using the webtools GOrilla and REVIGO. Only few genes were differentially expressed after short exposure and/or exposure to the low concentration, suggesting lack of drug efficacy under these conditions. In contrast, 12-hour exposure to the high concentration induced several changes. In sensitive cell lines, doxorubicin affected the expression of genes involved in ncRNA metabolism, DNA repair, and cell cycle process mechanisms. In resistant cell lines, the expression of genes implicated in metabolic processes were altered. Thus, we observed a differential response rate to doxorubicin in distinct DLBCL cell lines and demonstrated that doxorubicin-induced alterations in gene expression and resulting ontologies vary with drug concentration, exposure duration, and intrinsic sensitivity level.

overall_design: Global gene expression data of DLBCL cell lines untreated or after 2, 12, and 48 hours of exposure to two distinct concentrations (0.00061 μg/mL and 2.5 μg/mL) of doxorubicin.

first: Sara

middle: C

last: Marques

first: Linn

last: Reinholdt

first: Alexander

last: Schmitz

first: Jacob

middle: G

last: Mikkelsen

first: Hans

middle: E

last: Johnsen

first: Martin

last: Bøgsted

first: Karen

last: Dybkær


title: Transcriptome analysis of B. subtilis cells during recovery from injury after high hydrostatic pressure treatment

status: Public on Oct 26 2019

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

summary: Vegetative cells of B. subtilis can recover from injury caused by high hydrostatic pressure (HHP) treatment at 250 MPa. DNA microarray analysis revealed that many ribosomal genes and translation relating factors (e.g. translation initiation factors) were induced during a growth-arrested phase after the HHP treatment. Expression of cold shock-responsive genes, whose products play key roles for efficient translation, and heat shock-responsive genes, whose product mediates the correct protein folding or degrades misfolded proteins, were also induced. In contrast, the expression of hpf, whose product (Hpf) is involved in ribosome inactivation through dimerization of 70S ribosomes, was repressed. Sucrose density gradient sedimentation analysis showed that ribosomes were dissociated in a pressure-dependent manner and then reconstructed during the growth-arrested phase. These results suggested that the translational machinery can be preferentially reconstructed in the HHP-injured cells. We also found that cell growth after HHP-induced injury was apparently inhibited by Mn2+ or Zn2+ supplemented to the recovery medium. Ribosome reconstruction in HHP-injured cells was significantly delayed in the presence of Mn2+ or Zn2+. Moreover, Zn2+ but not Mn2+ stimulated dimer formation of ribosomes in HHP-injured cells. This Zn2+-dependent accumulation of ribosome dimer was no longer observed in a Δhpf mutant lacking the functional Hpf. Furthermore, the growth recovery of the Δhpf mutant in the Zn2+-supplemented medium was faster than that of the parent strain. Thus, our results indicate that Zn2+ can prevent ribosome reconstruction by stimulating the Hpf-dependent ribosome dimerization, thereby inhibiting the growth recovery of the HHP-injured B. subtilis cells.

overall_design: The B. subtilis strain TI465 were grown in NaCl-free L medium (10 g tryptone, 5 g yeast extract, per liter) for 6 h at 37°C with vigorous shaking. Then, the culture was packed into a sterile polyethylene bag that was heat-sealed after exclusion of air bubbles and subjected to HHP treatment (250 MPa) using a Dr. CHEF (Kobe Steel, Kobe, Japan) at 25°C for 10 min as described previously (Inaoka, T., et al., Biosci Biotechnol Biochem 81 (2017) 1235-1240). The rate of increasing and decreasing of pressure was set at 200 MPa/min. The cells treated at 250 MPa were transferred into a recovery medium (NaCl-free L medium) and incubated at 37°C with vigorous shaking. Total RNAs were extracted from the cells incubated for 0 h (immediately after HHP treatment), 2 h (growth arrest phase), or 4 h (re-growing phase) and then subjected to DNA microarray analysis.

first: Nguyen

last: Huyen

first: Genki

last: Akanuma

first: Hoa

last: Tu

first: Keitarou

last: Kimura

first: Kazutaka

last: Yamamoto

first: Takashi

last: Inaoka


title: Selective translation mechanism through two paralogs of eukaryotic initiation factor 4A

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: 2-1, Hirosawa

department: Center for Pioneering Research

institute: RIKEN

summary: Eukaryotic initiation factor (eIF) 4A is a DEAD-box RNA-binding protein that plays a pivotal role in translation initiation. Although mammals have two eIF4A paralogs, eIF4A1 and eIF4A2, their redundancy has been long assumed because of high homology and their functional difference has been poorly understood. Here we show that eIF4A paralogs employ differential translation programs. Ribosome profiling of eIF4A1- and eIF4A2-knockout HEK293T cell lines revealed that translation efficiency changes were divergent across transcriptome and distinct group of mRNAs were regulated by each paralog. Our analysis indicates that eIF4A1 and eIF4A2 facilitate translation of specific mRNAs.

overall_design: Ribosome profiling and RNA-seq

first: Yuichi

last: Shichino

first: Mari

last: Mito


title: Expression data of mRNA from hearts of mice injected with ETX or PBS

city: Chongqing

first: Yu

last: Shi

state: Chongqing

address: 10 Changjiang Branch Road

department: Cardiology

institute: Military Medical University

summary:
ETX treatment promoted cardiomyocyte proliferation. To investigate the molecular mechanism, we performed microarray analysis to explore the molecular mechanism underlying the effect of ETX on cardiomyocyte proliferation.
In this study, we sought to determine if and how metabolic reprogramming regulates cardiomyocyte proliferation. In neonatal mice, blockade of glycolysis by inhibiting glucokinase reduced cardiomyocyte proliferation, while blockade of fatty acid oxidation by inhibiting carnitine palmitoyltransferase 1 (CPT1) delayed the cell cycle arrest in cardiomyocytes. ETX (Etomoxir) is an effective inhibitor of CPT1 which is the key enzyme of fatty acid oxidation,ETX induced cardiomyocyte proliferation and improved cardiac function post-MI in adult mice.

overall_design: The total RNA was extracted from P14 heart tissue after treatment with vehicle (PBS) or ETX for 1 week.Then, hybridizations for cartridge arrays were set up by using GeneChip® Hybridization, Wash and Stain Kit (Affymetrix). Finally, the probe arrays were washed, stained and scanned to generate the data.

first: Luxun

last: Tang

first: Qiao

last: Liao

first: Xuewei

last: Xia

first: Wenbin

last: Fu

first: Wei

last: Wang

first: Chunyu

last: Zeng


title: Differential gene expression in mouse tongues overexpressing ectopic Bmi-1

first: Kristian

last: Laursen

address: 1300 York Ave.

institute: Weill Cornell Medicine

summary: Ectopic Bmi-1 overexpression induces differential gene expression within normal tongue tissue of mice.

overall_design: ~6-week-old K14-rtTA Only and K14-rtTA; TREFLBmi-1 mice were treated with 2mg/mL Doxycycline over the course of 1 week. Gene expression analysis was performed on intact tongue tissue by RNA-seq.

first: Jocelin

middle: M

last: Kalish

first: Lorraine

last: Gudas


title: Ribo-depleted RNA-seq in KRasG12D; p53-null (KP) lung adenocarcinoma cells to measure gene expression changes upon the expression of a T6B-YFP fusion

city: Princeton

first: Yuri

last: Pritykin

state: NJ

address: 245 Carl Icahn Lab, Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

summary: The identification of miRNA targets by Ago2-CLIP methods has provided major insights into the biology of this important class of non-coding RNAs. However, these methods are technically challenging and not easily translated to an in vivo setting. To overcome these limitations and to facilitate the investigation of miRNA functions in mice, we have developed a method (HEAP) to map miRNA-mRNA binding sites. This method uses a novel mouse strain harboring a conditional Halo-Ago2 allele expressed from the Ago2 locus. By using a resin conjugated to the HaloTag ligand, Ago2-miRNA-mRNA complexes can be efficiently purified from cells and tissues expressing Halo-Ago2. We demonstrate the reproducibility and sensitivity of this method in embryonic stem cells, in embryos, in adult tissues and in autochthonous mouse models of cancers. These tools and datasets are valuable resources to the scientific community and will facilitate the characterization of miRNA functions under physiological and pathological conditions.

overall_design: Four independent clones of mouse KRasG12D; p53-null lung adenocarcinoma cells were engineered to express a wild-type or a mutant version of the T6B-YFP fusion protein.

first: Xiaoyi

last: Li

first: Christina

last: Leslie

first: Andrea

last: Ventura


title: RNA-seq to measure gene expression changes caused by Dicer1 knockout in mouse embryonic stem cells (mESCs)

overall_design: Five Dicer1 knockout mESC clones and four wild-type clones were subjected to PolyA RNA-seq


title: Halo-enhanced Ago2 pulldown (HEAP) to identify miRNA targets in mouse embryonic stem cells (mESCs)

overall_design: HEAP libraries generated from mESCs


title: Differentially expressed genes after siRNA transfection in human cancer cell lines (SBC and T24)

status: Public on Oct 25 2019

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

institute: Chiba University

summary: To identify differentially expressed genes by anti cancer treatments (miRNA) in human cancer, several cell lines (lung cancer and bladder cancer) were subjected to Agilent whole genome microarrays.

overall_design: Human cell lines (SBC and T24) were treated with miRNAs (miR-30a-5p, miR-30a-3p, miR-34b-5p, miR34b-3p, miR-34c-5p, miR-34c-3p, miR-28-5p and miR-28-3p).

first: Yasutaka

last: Yamada


title: Autologous adipose-derived cells transiently moderate inflammation and fibrogenesis in early renal ischemia reperfusion injury

city: Glasgow

first: Rashida

last: Lathan

address: 126 University Avenue

department: Institute of Cardiovascular and Medical Sciences

country: United Kingdom

institute: University of Glasgow

summary: Adipose-derived regenerative cell (ADRC) heterogeneity and functionality in renal ischemia reperfusion injury

overall_design: Low depth single cell sequencing used as support flow cytometric analysis of ADRC hetereogeneity

first: Ryan

last: Ghita

first: Henry

last: Whalen

first: Rachanchai

last: Chawangwongsanukun

first: Dianne

last: Hillyard

first: Rhian

last: Touyz

first: Patrick

middle: B

last: Mark

first: Marc

last: Clancy


title: RNA-sequencing of mouse diabetic wounds treated with mast cell stabilizer MCS-01

city: Boston

first: Manoj

last: Bhasin

state: MA

address: 330 Brookline Avenue  RN 380E

institute: Beth Israel Deaconess Medical Center

summary: To investigate global changes in gene expression patterns following treatment with DSCG or MCS-01 we performed RNA-sequencing and nanostring profiling analyses on Day 10 wounds. Differential expression analysis on pre-MCS-01 samples compared to blank identified 649 significantly altered genes at p value <0.05 and absolute fold change >=2. Similarly, in post-MCS-01 samples 954 genes were differentially expressed, of which 566 were down- and 388 up-regulated. DCSG treatment resulted in differential expression of 91 genes. RT-qPCR corroborated increased expression of NFκB and STAT3 with post-MCS-01 treatment. In addition, we compared miRNA expression between MCS-01 samples and controls. Pre-treatment significantly altered expression of 11 miRNAs, while post-treatment altered expression of 28 miRNAs. RT-qPCR confirmed miR-34c upregulation, while significant inverse correlations were found between miR-34c and selected target genes Lef-1, Myb, and Mycn.

overall_design: Dorsal skin wound mRNA profiles of streptozotocin induced diabetic mice were generated by deep sequencing, in triplicate.

first: Theocharidis

last: Georgios


title: Transcriptome sequencing of Verticillium dahliae with different virulence

city: Shihezi

first: jin

last: li

state: Xinjiang

address: North Fourth Road

department: college of life science

institute: Shihezi university

summary: The V. dahliae could cause host obvious disease symptoms. Moreover, it was difficult to control, because of the rapidly genetic variation. Due to the rapidly genetic variation and complexity of the genetic background, the mechanism of pathogenicity differentiation of V. dahliae has still been unknown. To solve the problem, we isolated 24 strains of V. dahliae from a farmland of Shihezi city, Xinjiang province. Through ITS sequences and VCGs assay, the strains of SHZ-4, SHZ-5, and SHZ-9 had closer kinship. Moreover, the large difference was presented on the pathogenicity of SHZ-4, SHZ-5, and SHZ-9. Furthermore, a number of differentially expressed genes was identified through comparative transcriptome sequencing method and the genes were mainly centered on CWDEs and transport relative proteins. It was well understand that the CWDEs determined the source of nutrients of V. dahliae and the organic substance of host cell degraded by the CWDEs would induce the hyperosmosis of intercellular liquid. According to these, we proposed a hypothesis that the hyperosmosis induced the dehydration and death of host cell and contributed to absorb the nutrition for V. dahliae. The hyperosmosis promoting the nutrients scramble indicated that the V. dahliae could resist the hyperosmosis and the pathogenicity was positive associating with the tolerance. With regards to this, the sugar-induced-hyperosmotic resistance of the three V. dahliae isolates and cotton leaf tissue were analyzed through changing the sugar concentration. The result was entirely consistent with our hypothesis. It was firstly found that the pathogenicity of V. dahliae was relative to the resistance of sugar-induced-hyperosmosis, which could provide a new idea for cultivating a new varieties to resistant to the V. dahliae.

overall_design: Hypha mRNA profiles of three strains with different virulence were generated by deep sequencing, using Illumina Hiseq2500 PE125.

first: Jin

first: Juan

last: Pei


title: Dicer sequencing, whole genome methylation profiling and RNA sequencing analysis in basal cell carcinoma [methylation]

city: Bochum

first: Michael

last: Sand

state: NRW

address: Gudrunstr. 56

department: Depatment of Dermatology, Venereology and Allergology

institute: Ruhr-University Bochum

summary: Whole genome methylation profiling performed with Infinium MethylationEPIC BeadChips as well as RNA and smallRNA sequencing were performed in 5 sBCCs with the Illumina NextSeq500 next generation sequencing system.

overall_design: Basal cell carcinoma biopsy DNA methylation

first: Annabelle

last: Bromba

first: Daniel

first: Thilo

last: Gambichler

first: Schapoor

last: Hessam

first: Jürgen

last: Becker

first: Eggert

last: Stockfleth

first: Thomas

last: Meyer

first: Falk

last: Bechara


title: Dicer sequencing, whole genome methylation profiling and RNA sequencing analysis in basal cell carcinoma [RNA-seq]

summary: Dicer sequencing was performed on the Illumina MiSeq System in a total of 16 BCC samples (8 nodular BCCs / 8 sBCCs) and mapped against the human reference genome (hg19). Dicer sequencing was performed in all 16 BCC samples. Whole genome methylation profiling performed with Infinium MethylationEPIC BeadChips as well as RNA and smallRNA sequencing were performed in 5 sBCCs with the Illumina NextSeq500 next generation sequencing system. We identified a variety of Dicer mutations that could play a role in aberrant miRNA expression in BCC. The aforementioned RNA sequences should be further evaluated in functional studies towards their possible pathogenetic role in sBCC.

overall_design: Basal cell carcinoma biopsy, RNA sequencing


title: Splicing factors and chromatin organization enhance exon recognition by alleviating constraints generated by gene nucleotide composition bias

city: Lyon

first: jean-baptiste

last: claude

address: 46, allée d’Italie

institute: [CNRS/ENS Lyon/UCBL/HCL] Laboratoire de Biologie Moléculaire de la Cellule UMR5239

summary: To characterize the rules governing exon recognition during splicing, we analyzed RNA-seq datasets and identified ~4,000 GC-rich and ~5,000 AT-rich exons, labelled GC-exons and AT-exons, respectively whose inclusion depends on different sets of splicing factors. We show that a high GC-load is associated with predicted RNA secondary structures at 5'ss and that GC-exons are dependent on U1 snRNP-associated proteins. Meanwhile, a high AT-load is associated with a large number of decoy splicing-related signals upstream exons such as the number of branchpoints and SF1- or U2AF65-binding sites and AT-exons are dependent on U2 snRNP-associated proteins. Nucleotide composition bias also influences local chromatin organization. Since the GC content of exons correlates with that of their hosting-genes, -isochores and – topologically-associated domains, we propose that regional nucleotide composition bias leaves a footprint locally, at the exon level, inducing, during splicing, constraints that are alleviated by the local chromatin organization and specific splicing factors.

overall_design: Samples siFUS, siGL2, siHNRNPC, siHNRNPH1, siHNRNPK and siTRA2A-B were made together and are part of the same experiment (simplicates).  Samples siPP-1, siPP-2, siPP-3, siGL2-1, siGL2-2 and siGL2-3 were made together from different cell batchs and are part of the same experiment (triplicates).

first: Sébastien

last: LEMAIRE

first: Nicolas

last: FONTRODONA

first: Jean-Baptiste

last: CLAUDE

first: Hélène

last: POLVECHE

first: Fabien

last: AUBÉ

first: Laurent

last: MODOLO

first: Cyril

middle: F

last: BOURGEOIS

first: Franck

last: MORTREUX

first: Didier

last: AUBOEUF


title: Single cell RNA-seq identifies cell diversity in embryonic salivary glands [Single cell RNA-seq]

city: Bethesda

first: Rei

last: Sekiguchi

state: MD

address: 30 Convent Drive

institute: National Institute of Dental and Craniofacial Research

summary: Our single-cell and bulk transcriptome analyses revealed striking molecular heterogeneity in the mesenchymal cells of embryonic submandibular and parotid salivary glands during bud initiation, including distinct mesodermal and neural crest-derived molecular signatures that foreshadow later functions.

overall_design: Gene expression analyses of epithelial and mesenchymal cells in submandibular and parotid salivary glands.

first: Kenneth

last: Yamada


title: Single cell RNA-seq identifies cell diversity in embryonic salivary glands

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

overall_design: Refer to individual Series


title: Dicer sequencing, whole genome methylation profiling and RNA sequencing analysis in basal cell carcinoma

first: Michael

last: Sand


title: Single cell RNA-seq identifies cell diversity in embryonic salivary glands [Bulk RNA-seq]


title: Single-cell RNA sequencing of BCSCs

city: Hangzhou

first: sen

last: ye

state: Zhejiang

address: 866 Yuhangtang Rd, Hangzhou, Zhejiang Province, P.R. China

institute: Zhejiang University


title: BCSCsSETD4 and BCSCsGFP


title: Dicer sequencing, whole genome methylation profiling and RNA sequencing analysis in basal cell carcinoma [Dicer sequencing]

overall_design: Dicer sequencing

first: Annabelle

last: Bromba

first: Daniel

first: Thilo

last: Gambichler

first: Schapoor

last: Hessam

first: Jürgen

last: C. Becker

first: Eggert

last: Stockfleth


title: ChIP-SEQ of H4K20me3 in  BCSCsSETD4 and BCSCsGFP

summary: We report the ChIP-SEQ results of H4K20me3 in BCSCsSETD4 and BCSCsGFP. To explore epigenetic regulation by H4K20me3 in BCSC quiescence, we performed chromatin immunoprecipitation sequencing (ChIP-seq) using BCSCsSETD4 and BCSCsGFP. Quiescent BCSCsSETD4 showed marked enrichment of H4K20me3 modifications relative to BCSCsGFP.

overall_design: Examination of the ChIP-SEQ results of H4K20me3 in BCSCsSETD4 and BCSCsGFP.

first: Sen

last: Ye

first: Yan-Fu

last: Ding

first: Qian

last: Zhu

first: Xiao-Li

last: Liu

first: Wen-Huan

last: Jia

first: Sun-Li

last: Cai

first: Xue-Ting

last: Huang

first: Yao-Shun

last: Yang

first: Jin-Shu

first: Sheng-Nan

first: Guo-Ping

first: Yue-Hong

last: Wang

first: Jiao-Jiao

last: Zhou

first: Yi-Ding

last: Chen

first: Wei-Jun


title: The list of differential gene expression between BCSCs, qBCSC and activated qBCSCs

first: sen

last: ye

summary: We report the whole transcriptome of BCSCs, qBCSCs, and activated qBCSCs.

overall_design: Examination of the differential gene expression between BCSCs, qBCSCs, and activated qBCSCs.


title: Dicer sequencing, whole genome methylation profiling and RNA sequencing analysis in basal cell carcinoma [small RNA-seq]

first: Michael

last: Sand

overall_design: Basal cell carcinoma biopsy, small RNA sequencing

first: Annabelle

last: Bromba

first: Daniel

first: Thilo

first: Schapoor

first: Jürgen

last: Becker

first: Eggert

first: Thomas

last: Meyer

first: Falk

last: Bechara


title: Single cell RNAseq of adoptively transferred Tregs in rhesus macaques

status: Public on Oct 24 2019

city: Pittsburgh

first: Warren

middle: David

last: Shlomchik

state: PA

address: 3550 Terrace Street

department: Medicine

institute: University of Pittsburgh

summary: Animal R.401 was infused with ex-vivo expanded T-regulatory cells.  After adoptive transfer, PBMC were obtained and stained with surface antibodies.  Single cell libraries from sorted populations were generated using a UMI-based droplet-partitioning platform (10X Genomics) and sequenced using a NextSeq 500 (Illumina).  Resulting reads were processed using Cellranger software (10X Genomics) and downstream analysis was performed using Monocle6,7 using a negative binomial model of distribution with fixed variance.

overall_design: Time-course

first: Scott

last: Furlan


title: Licochalcone A suppresses the proliferation of sarcoma HT-1080 cells, as a selective R132C mutant IDH1 inhibitor

city: Shanghai

first: Cheng

last: Luo

state: Shanghai

address: No. 555 Zuchongzhi Road

institute: Shanghai Institute of Materia Medica

summary: IDH1 mutations are closely related to the development and progression of various human cancers, such as glioblastoma, sarcoma, and acute myeloid leukemia. By screening dozens of reported natural compounds using both wild-type and mutant IDH1 enzymatic assays, we discovered Licochalcone A is a selective inhibitor to the R132C-mutant IDH1 with an IC50 value of 5.176 μM, and inhibits the proliferation of HT1080 cells with an IC50 value of 10.75 μM. Suggested by the molecular docking results, Licochalcone A might occupy the allosteric pocket between the two monomers of IDH1 homodimer, and the R132H mutation was unfavorable for the binding of Licochalcone A with the IDH1 protein, as compared to the R132C mutation. Revealed by the RNA-Seq data analysis, the Cell Cycle pathway was the most over-represented pathway for HT1080 cells treated with Licochalcone A. Consistent with these results, Licochalcone A induced apoptosis and cell cycle arrest of HT1080 cells, while it showed minimal effect against the proliferation of normal RCTEC cells. The discovery of Licochalcone A as a mutation-selective IDH1 inhibitor can serve as a promising starting point for the development of mutation-selective anti-tumor lead compounds that target IDH1.

overall_design: The RNA-Seq data was collected for HT-1080 cells after the treatment of Licochalcone A

first: Chujiao

last: Hu

first: Lei

last: Tang

first: Hao

last: Zhang


title: Single-cell RNA sequencing of BCSCs from solid tumors taken from NOD/SCID mice

summary: We report the single-cell transcriptome of breast cancer stem cells (BCSCs) from solid tumors taken from NOD/SCID mice.

overall_design: Examination of the heterogeneous and molecular signitures of BCSCs from solid tumors taken from NOD/SCID mice.

first: Sen

last: Ye

first: Yan-Fu

last: Ding

first: Qian

last: Zhu

first: Xiao-Li

last: Liu

first: Wen-Huan

last: Jia

first: Sun-Li

last: Cai

first: Xue-Ting

last: Huang

first: Yao-Shun

first: Jin-Shu

first: Sheng-Nan

first: Guo-Ping

first: Yue-Hong

first: Jiao-Jiao

first: Yi-Ding

first: Wei-Jun


title: Single-cell RNA sequencing of BCSCs from MCF7 cell lines

first: sen

last: ye

summary: We report the single-cell transcriptome of breast cancer stem cells (BCSCs) from MCF7 cell lines.

overall_design: Examination of the heterogeneous and molecular signatures of BCSCs.

last: Yang

last: Wang

last: Zhou

last: Chen


title: The list of differential gene expression between BCSCsSETD4 and BCSCsGFP

summary: We report the whole transcriptome of BCSCsSETD4 and BCSCsGFP

overall_design: Examination of the differential gene expression between BCSCsSETD4 and BCSCsGFP.


title: Targeting Glioblastoma Stem Cells through Disruption of the Circadian Clock

city: San Diego

first: Jeremy

last: Rich

address: 9500 Gilman Drive #0695

institute: University of California, San Diego


title: Targeting Glioblastoma Stem Cells through Disruption of the Circadian Clock [RNA-Seq]

summary: Glioblastomas are highly lethal cancers, containing self-renewing glioblastoma stem cells (GSCs). Here, we show that GSCs, differentiated glioblastoma cells (DGCs), and normal brain cultures all displayed robust circadian rhythms, yet GSCs alone displayed exquisite dependence on core clock transcription factors, BMAL1 and CLOCK, for optimal cell growth. Downregulation of BMAL1 or CLOCK in GSCs induced cell cycle arrest and apoptosis. Chromatin immunoprecipitation revealed BMAL1 preferentially bound at metabolic genes in GSCs, associated with differences in active chromatin regions compared to NSCs. Targeting BMAL1 or CLOCK attenuated mitochondrial metabolic function and reduced expression of the tricarboxylic acid (TCA) cycle enzymes. Small molecule agonists of two independent BMAL1::CLOCK negative regulators, the Cryptochromes and REV-ERBs, downregulated stem cell factors and reduced GSC growth. Combination of Cryptochrome and REV-ERB agonists induced synergistic anti-tumor efficacy. Collectively, GSCs coopt circadian regulators beyond canonical circadian circuitry to promote stemness maintenance and metabolism, offering novel therapeutic paradigms.

overall_design: RNA-seq from patient derived glioblastoma stem cell specimens following treatment with a non-targeting shRNA and an shRNA targeting BMAL1

first: Zhen

last: Dong

first: Guoxin

first: Meng

last: Qu

first: Ryan

last: Gimple

first: Qiulian

last: Wu

first: Zhixin

last: Qiu

first: Briana

last: Prager

first: Xiuxing

first: Leo

last: Kim

first: Andrew

last: Morton

first: Deobrat

last: Dixit

first: Wenchao

first: Haidong

first: Bin

last: Li

first: Zhe

first: Shideng

last: Bao

first: Stephen

last: Mack

first: Lukas

last: Chavez

first: Steve

last: Kay


title: Silver nanocolloids affects glycosylation in medaka fish to cause embryonic malformation.

city: Itakura

first: Shosaku

last: Kashiwada

state: Gunma

address: 1-1-1 Izumino

department: Department of Life Sciences

institute: Toyo University

summary: We observed silver nanocolloids (SNCs) exposure to medaka embryo induced morphological deformities like shortened body and undeveloped head and eyes, and our gene expression analysis using medaka oligo DNA microarray suggested that glycan/glycosylation genes, such as gns and alg2, might be the targets of SNCs' toxicity.  Validation studies of gns and alg2 gene expressions by qPCR showed stage-dependent and altered mRNA expression patterns, and their altered expressions were more severe in earlier stages of embryogenesis.  A result from structural analysis of glycan revealed that stage 11 was the most sensitive stage to SNCs exposure, and stress seemed to be imposed upon endplasmic reticulum (ER) by SNCs.  In fact, qPCR analysis of ER mannosidase demonstrated that N-glycan synthesis in ER was inhibited by SNCs.  Overall, this study revealed that SNCs exposure caused embryonic malformations through disruption of glycan biosynthetic pathway in ER.

overall_design: Silver content of the purified silver nanocolloids which we used in our experiment contained approximately 15-20% ionic silver and 80-85% particle silver.  Mean particle diameter of SNCs was about 28.4 ± 8.5 nm.  For the DNA microarray gene expression analysis, each of the three sets of fifteen medaka embryos at stage 21 were exposed to 5 mL of 0.05 mg/L SNCs (dissolved in dH2O) solution in embryo-rearing medium at pH7.0 in 6-well plate at 25℃ in the dark for 48 hours (the test solutions were renewed every 24 hours).  No-exposure (control) experiment was also carried out in the same way except that the SNCs solution was replaced by 5 mL of dH2O.

first: Kashiwada

last: Shosaku

first: Shimizu

last: Kaori

first: Kagami

last: Yoshihiro


title: Targeting Glioblastoma Stem Cells through Disruption of the Circadian Clock [ChIP-Seq]

first: Jeremy

last: Rich

overall_design: BMAL1 ChIP-sequencing was performed on two glioma stem cell and two normal neural stem cell samples. Two replicates were performed for each sample

first: Zhen

last: Dong

first: Guoxin

last: Zhang

first: Meng

last: Qu

first: Ryan

first: Qiulian

first: Zhixin

first: Briana

last: Wang

last: Zhou

last: Huang

last: Zhu


title: An evolutionary recent IFN-IL-6-CEBP axis is linked to monocyte expansion and tuberculosis severity in humans.

city: Florianopolis

first: Edgar

middle: Ernesto

last: Gonzalez Kozlova

state: Santa Catarina

address: Corrego Grande s/n

department: Farmacologia

country: Brazil

institute: Universidade Federal de Santa Catarina

summary: Monocyte counts are increased during human tuberculosis (TB) but it has not been determined whether Mycobacterium tuberculosis (Mtb) directly regulates myeloid commitment. We demonstrated that exposure to Mtb directs primary human CD34+ cells to differentiate into monocytes/macrophages. In vitro myeloid conversion did not require type I or type II IFN signaling. In contrast, Mtb enhanced IL-6 responses by CD34+ cell cultures and IL-6R neutralization inhibited myeloid differentiation and decreased mycobacterial growth in vitro. Integrated systems biology analysis of transcriptomic, proteomic and genomic data of large data sets of healthy controls and TB patients established the existence of a myeloid IL-6/IL6R/CEBP gene module associated with disease severity. Furthermore, genetic and functional analysis revealed the IL6/IL6R/CEBP gene module has undergone recent evolutionary selection, including Neanderthal introgression and human pathogen adaptation, connected to systemic monocyte counts. These results suggest Mtb co-opts an evolutionary recent IFN-IL6-CEBP feed-forward loop, increasing myeloid differentiation linked to severe TB in humans.

overall_design: Time course analysis of Mycobacterium tuberculosis infection in purified cord blood CD34+ cells.

first: Murilo

last: Delgobo

first: Daniel

last: Mendes

last: Kozlova

first: Edroaldo

last: Rocha

first: Gabriela

last: Rodrigues-Luiz

first: Lucas

last: Mascarin

first: Greicy

last: Dias

middle: O

last: Patricio

first: Tim

last: Dierckx

first: Maíra

last: Bicca

first: Gaëlle

last: Bretton

first: Yonne

last: Tenório de Menezes

first: Márick

last: Starick

first: Darcita

last: Rovaris

first: Joanita

last: Del Moral

middle: S

last: Mansur

first: Johan

last: Van Weyenbergh

first: André

last: Báfica