title: RNA-seq analysis of HSF1 knockout on LiCl treatment

status: Public on Aug 31 2020

city: HangZhou

first: Ping

last: Song

state: State...

address: 3 East Qingchun Road, Hangzhou, Zhejiang, China

country: China

institute: Zhejiang University School of Medicine

type: Expression profiling by high throughput sequencing

summary: Heat shock transcription factor 1(HSF1) is an important transcription factor which regulates the expression of a wide array of genes including heat shock proteins and oncogenes. Here, we report that HSF1 as a target of WNT/β-catenin signaling, regulates parts of target genes of WNT/β-catenin signaling. To explore the biological relevance of HSF1 activation to WNT/β-catenin signaling, we profiled gene expression of wild type mouse embryonic fibroblasts (WT MEF) and HSF1 knock out MEF (HSF1 KO MEF) before and after lithium chloride (LiCl) treatment which was a potent GSK3β inhibitor and increased the expression of β-catenin.

overall_design: Examination of transcription regulation with and without LiCl treatment at 20mM for 48 hours in WT MEF and HSF1 KO MEF

first: Lifeng

last: Feng

first: Liyuan

last: Zhu

first: Xian

last: Wang

first: Hongchuan

last: Jin


title: Plasma Level of Circular RNA hsa_circ_0000190 Correlates with Tumor Progression and Poor Treatment Response in Advanced Lung Cancers

city: Taipei

first: Pinghsing

last: Tsai

state: Taiwan

address: Rm. 825, 7F., No.322, Sec. 2, Shipai Rd., Beitou D

country: Taiwan

institute: Taipei Veterans General Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: Circular RNAs (circRNAs) were reported to play roles in cancers by targeting pro- and anti-oncogenic miRNAs. However, the mechanisms of circRNAs in lung cancer progression and their prognostic value of treatment response remain unclear. This study used next generation sequencing (NGS) to analyze the transcriptomes and circRNA profiles of 2 lung cancer cell lines (A549 and HCC827) and 1 normal lung cell line (BEAS-2B), and identified the highly overexpressed hsa_circ_0000190 and hsa_circ_000164 as potential biomarkers. By using highly sensitive RT-ddPCR method, these circRNAs were shown to be secreted by cell lines and were detected in human blood. We predicted the potential miRNA targets of the two circRNAs, and the further mRNA targets of these miRNAs. This NGS data allows us to compare the levels of predicted mRNAs to delineate potential involving mechanisms of the two circRNAs.

overall_design: mRNA and circRNA profiles of two lung cancer cell lines (A549 and HCC827) and 1 normal lung cell line (BEAS-2B) were generated by deep sequencing.

first: Ping-Hsing

first: Mong-Lien

first: Afeez

last: Ishola

first: Shih-Hwa

last: Chiou


title: Auxenochlorella protothecoides adapted to grow efficiently in low phosphate conditions display altered lipid profiles

city: Tucson

first: Seth

middle: Alan

last: Steichen

state: AZ

address: 1140 E South Campus Dr Room 425

department: Plant Sciences

country: USA

institute: University of Arizona School of Plant Sciences

summary: Renewable biodiesel produced by microalgae has great potential as a portable source of high-density energy that can replace certain traditional hydrocarbon sources. One limitation of scaling up algal cultivation to industrial levels is the availability of key macronutrients, particularly inorganic phosphorus (Pi), which is a finite and dwindling resource. Here, Auxenochlorella protothecoides was adapted to low Pi conditions through continuous cultivation in 100 times less Pi media for 285 days, or ~41 generations. The adapted populations demonstrated significantly higher growth rates than wild type (WT) cells in low Pi, with average maximum growth rates of 0.72 d-1 and 0.54 d-1, respectively in batch-culture experiments. Based on UPLC/MS analyses, the total lipid content of the adapting A. protothecoides populations showed a shift from their typical profile in nutrient replete media to the accumulation of non-phosphorus glycerolipids, with 306% MGDG and 189% SQDG, relative to WT at initial exposure, followed by a decline, and a steady increase until the final time point was reached. Transcriptome profiling by Illumina RNA-seq collected at 5 time points throughout the experiment, and results of the lipid analyses revealed a trend of increased transcript levels during the first ~11 generations of adaptation, followed by an overall decrease in gene expression after ~34 generations. The short-term changes in gene expression were associated with shifts in major metabolic pathways including carbon metabolism, oxidative phosphorylation, glycolysis, and gluconeogenesis. By comparison, certain transcripts showing decreased expression, reflected increased fatty acid turnover, and a stable decrease in photosynthesis-related gene expression. These results illustrate the utility of laboratory-directed evolution for the selection of microalgae populations with altered cultivation traits, revealing distinct phases of adaptation, based on expression profiles.  The results further demonstrate the use of metabolic engineering to select a microalga variant after only ~40 generations of growth in low-phosphate conditions that utilizes Pi more efficiently for growth than its wild type parent population and produces 1.22 times more biomass in batch growth experiments.

overall_design: mRNA levels for triplicate wild type cell populations (WT1, WT2, and WT3) compared to mRNA levels of triplicate cell populations grown in low phosphate media (LP1, LP4, and LP5) collected at four time points during adaptation over >41 generations.

middle: A

first: Judith

middle: K

last: Brown


title: KIAA1522 mediates resistance to cisplatin in lung adenocarcinoma cells

city: Shanghai

first: Boshi

address: No.800 Dongchuan Road

institute: Shanghai Cancer Institute

summary: KIAA1522 is aberrantly over-expressed and predicts the outcome of platinum-base chemotherapy. Down-regulation of KIAA1522 sensitizes lung adenocarcinoma cells to cisplatin. To evaluate the molecular mechanisms underlying KIAA1522-induced cisplatin resistance. The RNA sequencing assays were performed in KIAA1522-depleted 889 cells.

overall_design: The kiaa1522 gene was depleted through Cas9/sgRNA-mediated gene knockout in 889 cells.  The gene expression profiling in the control-sgRNA and kiaa1522-sgRNA expressed 889 cells were measured by RNA-seq and compared between groups. The differently expressed genes were then subjected to enrichment analyses to determine the KIAA1522-regulated signaling pathways.

first: Yizhen

last: Liu


title: A macrophage-specific lncRNA regulates apoptosis and atherosclerosis by tethering HuR in the nucleus

status: Public on Aug 29 2020

city: Valencia

first: Daniel

last: Perez-Cremades

state: Valencia

address: 15 Blasco Ibañez Avenue

department: Physiology Department

country: Spain

institute: University of Valencia

summary: We report the differentially expressed genes in BMDMs treated with MAARS or control gapmeRs.

overall_design: BMDMs were treated with MAARS or control gapmeRs and RNA-Seq analysis was performed after ribodepletion and standard library construction using Illumina HiSeq2500 V4 2x100 PE (Genewiz, South Plainfield, NJ).

first: Viorel

last: Simion

first: Haoyang

last: Zhou

first: Stefan

last: Haemmig

first: Jacob

middle: B

last: Pierce

first: Shanelle

last: Mendes

first: Yevgenia

last: Tesmenitsky

last: Pérez-Cremades

first: James

middle: F

last: Lee

first: Alex

last: Chen

first: Nicoletta

last: Ronda

first: Bianca

last: Papotti

first: Jarrod

last: Marto

first: Mark

middle: W

last: Feinberg


title: Acid resistance mechanism of Ochrobactrum intermedium M86 under artifical gastric fluid condition

status: Public on Aug 30 2020

city: Pune

first: Mahesh

last: Dharne

state: Maharashtra

address: Dr. Homi Bhabha Road

department: Biochemical Sciences

country: India

institute: CSIR National Chemical Laboratory

summary: Based on differential gene expression analysis acid response genes were identified. Urease gene cluster and ammonia producing genes were up-regulated in the acidic environment.

overall_design: Log phase cells were exposed to Luria Bertani medium (pH 7.0 and 3.7) and artificial gastric fluid medium (pH 3.87 and 2.9) for 15 mins and differential gene expression analysis was carried out using RNA-Seq

first: Kushal

last: Gohil


title: Glioma escape signature and clonal development under immune pressure

city: Hamburg

first: Krystian

middle: Daniel

last: Fita

address: Martinistrasse 52

department: Department of Neurosurgery

country: Germany

institute: University Medical Center Hamburg-Eppendorf

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

overall_design: Refer to individual Series


title: RGS2-mediated translational control drives cellular dormancy and resistance to ER-stress-induced apoptosis by inducing proteasome-mediated ATF4 degradation

city: Seoul

first: Ho-Young

address: Gwanak-ro 1

department: College of Pharmacy

country: South Korea

institute: Seoul National University

summary: Slow-cycling/dormant cancer cells (SCCs) are thought to cause cancer relapse, but the underlying biology remains obscure. A subpopulation of SCCs has been found even in rapidly growing tumors and cancer cell lines. To investigate the mechanism underlying cellular dormancy, we obtained SCCs from three NSCLC cell lines (H460, H1299, and SK-MES-1) and PDX tumor by using a cell proliferation-dependent fluorescent dye (CSFE).

overall_design: Three non-small cell lung cancer (NSCLC) cell lines (H460, H1299 and SK-MES-1) and two primary cell lines derived from different parts of NSCLC PDX tissue (PDX1-1, PDX1-2) were labelled with Carboxyfluorescein succinimidyl ester (CFSE) and then cultured for 7 days to distinguish active-cycling cells (ACCs, CFSElow) and dye remained slow-cycling cells (SCCs, CFSEhigh).  Cultured cells were sorted into CFSEhigh (upper, >90%) and CFSElow (lower, <10%) population by flow cytometry. Sorted cells were washed twice with PBS and then RNA was extracted using Trizol reagent (Qiagen). 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) with standard protocols. For deata process, Illumina Casava1.8 software used for basecalling. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2. Read count extraction and nomalization were performed using edgeR.

first: Jaebeom

last: Cho


title: Transcriptome profiling across five tissues of giant panda

city: Chengdu

first: Feng

last: Li

state: Sichuan

address: No.211, Huimin Road, Wenjiang District

institute: Sichuan Agricultural University

summary: Gene differential expression studies can serve to explore and understand the laws and 16 characteristics of animal life activities, and the difference in gene expression between different 17 animal tissues have been well demonstrated and studied. However, for the world-famous rare 18 and protected species giant panda (Ailuropoda melanoleuca), only the transcriptome of the blood 19 and spleen has been reported separately. Here, in order to explore the transcriptome differences 20 between the different tissues of the giant panda, transcriptome profiles of the heart, liver, spleen, 21 lung, and kidney from five captive giant pandas were constructed with Illumina HiSeq 2500 22 platform. The comparative analysis of the inter-tissue gene expression patterns was carried out 23 based on the generated RNA sequencing datasets. Analyses of Gene Ontology (GO) enrichment, 24 Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and protein-protein interaction 25 (PPI) network were performed according to the identified differentially expressed genes (DEGs). 26 We generated 194.52 GB clean base data from twenty-five sequencing libraries and identified 27 18,701 genes, including 3492 novel genes. With corrected p-value < 0.05 and |log2FoldChange| > 28 2, we finally obtained 921, 553, 574, 457, and 638 tissue-specific DEGs in the heart, liver, spleen, 29 lung, and kidney, respectively. In addition, we identified TTN, CAV3, LDB3, TRDN, and 30 ACTN2 in the heart; FGA, AHSG, and SERPINC1 in the liver; CD19, CD79B, and IL21R in the 31 spleen; NKX2-4 and SFTPB in the lung; GC and HRG in the kidney as hub genes in the PPI 32 network. The results of the analyses showed a similar gene expression pattern between the spleen 33 and lung. This study provided for the first time the heart, liver, lung, and kidney’s transcriptome 34 resources of the giant panda, and it provided a valuable resource for further genetic research or 35 other potential research.

overall_design: transcriptome profiles of the heart, liver, spleen, lung and kidney were obtained from 5 giant pandas, and differentially expressed genes, Gene Ontology (GO), and KEGG enrichment were analyzed.

first: Chengdong

last: Wang

first: Zhongxian

last: Xu

first: Desheng

first: Ying

first: Hemin

last: Zhang

first: Mingzhou

first: Linghua

last: Deng

first: Ming

last: Wei

first: Kai

last: Wu

first: Ruihong

last: Ning

first: Diyan

first: Mingyao

last: Yang

first: Mingwang

first: Qingyong

last: Ni

first: Bo

last: Zeng


title: DNA methylation - PRDM8 reveals aberrant DNA methylation in aging syndromes and is relevant for hematopoietic and neuronal differentiation.

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

type: Methylation profiling by genome tiling array

summary: Dyskeratosis congenita (DKC) and idiopathic aplastic anemia (AA) are bone marrow failure syndromes that share characteristics of premature aging with severe telomere attrition. In this study, we analyzed blood samples of 62 AA and 13 DKC patients to demonstrate that their epigenetic age predictions are overall increased, albeit not directly correlated with telomere length. Aberrant DNA methylation was observed in the gene PRDM8 in DKC and AA as well as in other diseases with premature aging phenotype, such as Down syndrome, Werner syndrome and Hutchinson-Gilford-Progeria syndrome. To gain further insight into the functional relevance of PRDM8 we generated induced pluripotent stem cells (iPSCs) with heterozygous and homozygous knockout. Loss of PRDM8 impaired hematopoietic and neuronal differentiation of iPSCs, but it did not impact on epigenetic age. Taken together, aberrant DNA methylation in PRDM8 provides a biomarker for bone marrow failure syndromes, which may contribute to the hematopoietic and neuronal phenotypes of premature aging syndromes.

overall_design: DNA from iPSC-derived neuronal cells was isolated after 10 days of neural differentiation. DNA was bisulfite converted and hybridized to the Illumina Infinium MethylationEPIC BeadChip.

first: Monika

last: Eipel

first: Olivia

last: Cypris

first: Julia

last: Franzen

first: Corinna

last: Rösseler

first: Joseph

middle: C

last: Kuo

first: Margherita

last: Vieri

first: Martin

last: Kirschner

first: Tim

middle: H

last: Brümmendorf

last: Zenke

first: Angelika

last: Lampert

first: Fabian

last: Beier


title: Next genereration sequencing reveals that CNAs associated with cyclin E overexpression tranlate into changes in transcriptional output.

city: La Jolla

first: William

last: Kim

state: California

address: 9500 Gilman Dr

institute: UCSD

summary: Transient cyclin E overexpression in human mammary epithelial cells leads to a distinct CNA signature. We carried out high throughput sequencing to determine if these CNAs translated into changes in transcription.

overall_design: RNA from 12 clones that survived transient cyclin E overexpression was subjected to high throughput sequencing.

first: Pablo

last: Tamayo

first: Servando

middle: G

last: Macias

first: Steven

middle: I

last: Reed

middle: J


title: Gliotoxin, identified from a screen of Aspergillus fumigatus metabolites, reverses HIV-1 latency via release of P-TEFb

city: Rotterdam

first: Robert-Jan

last: Palstra

address: Dr. Molewaterplein 40

department: Biochemistry

country: Netherlands

institute: ErasmusMC

summary: A leading pharmacological strategy towards HIV cure requires “shock” or activation of expression of the HIV genome in latently infected cells with Latency Reversal Agents (LRAs) followed by their subsequent clearance. As a source of bio-active molecules we used fungal secondary metabolites (extrolites) in a screen for novel LRAs. We used orthogonal mass spectrometry (MS) coupled to latency reversal bioassays, and identified gliotoxin (GTX) to potently reverse latency. GTX significantly induced  HIV-1 gene expression in latent ex vivo infected primary cells and in CD4+ T cells from all aviremic HIV-1+ participants. RNA sequencing identified 7SK RNA to be most significantly downregulated in independent donors upon GTX treatment of CD4+ T cells. GTX disrupted the 7SK snRNP complex causing release of P-TEFb, which induced phosphorylation of RNA Pol II CTD, and increased HIV transcription. Our data highlight the power of combining low throughput bioassays, mycology and orthogonal mass spectrometry as an approach to screen for and characterize novel LRAs.

overall_design: Ten million primary CD4+ T cells were stimulated with 20 nM gliotoxin or left unstimulated for 4 h. Experiment was performed in duplicate on cells isolated from two buffy coats from healthy donors

first: Mateusz

last: Stoszko

first: Wilfred

last: van IJcken

first: Tokameh

last: Mahmoudi


title: Gene expression - PRDM8 reveals aberrant DNA methylation in aging syndromes and is relevant for hematopoietic and neuronal differentiation.

first: Wolfgang

last: Wagner

overall_design: RNA from iPSC-derived neuronal cells was isolated after 27 days of neural differentiation and sequenced on a HiSeq2500 sequencer.

first: Monika

last: Eipel

first: Olivia

last: Cypris

last: Franzen


title: Epigenome analysis of normal and DNMT3L-overexpressing human neurons [array]

city: Shenyang

first: JIE

last: LU

state: Liaoning

address: 77 Puhe Road, Shenbei Xiqu

department: Human Anatomy

institute: China Medical University

summary: Genome wide DNA methylation profiling of cultured fetal human neurons infected with lentivirus carrying DNMT3L or ZsGreen genes for 4days. The Illumina Infinium 850k Human MethylationEPIC BeadChip was used to obtain DNA methylation profiles across approximately 850,000 CpGs in the infected cells. Samples included 3 control samples (ZsGreen) and 3 DNMT3L-overexpressing samples (DNMT3L).

overall_design: Bisulphite converted DNA from the 6 samples were hybridised to the Illumina Infinium 850k Human MethylationEPIC BeadChip.

first: Jie

last: Lu

first: Lin

last: Qin


title: PRDM8 reveals aberrant DNA methylation in aging syndromes and is relevant for hematopoietic and neuronal differentiation.


title: Transcriptomic sequencing of breast cancer

city: Wuhan

first: Chunjiang

last: He

state: Hubei

address: Donghu Road 185

institute: Wuhan University

summary: We did transcriptomic sequencing of blood samples from 6 breast cancer patients. Total RNA were extracted from peripheral blood and library were constructed for the illumina Xten sequencing. We did transcriptomic sequencing of adjacent normal tissues and cancer tissues from 6 breast cancer patients. Total RNA were extracted and library were constructed for the illumina Xten sequencing.

overall_design: Transcriptomic sequencing of blood samples from 6 breast cancer patients. Transcriptomic sequencing of adjacent normal tissues and cancer tissues from 6 breast cancer patients.

first: Xin

last: Dong

first: Lei

last: Wei


title: Hoxb1 LoF RNA-seq

city: MARSEILLE

first: Sonia

last: Stefanovic

address: 27 BD JEAN MOULIN

country: France

institute: INSERM U1251

summary: Transcriptomic profiling of second heart field progenitor cells deficient for Hoxb1 in mouse embryos.

overall_design: Microdissection of the second heart field region in E8.5 embryos.

first: Jean-Pierre

last: Devignes

first: Stéphane

last: Zaffran


title: Subpopulations second heart field RNA-seq

summary: Transcriptomic profiling of second heart field subpopulations FACS sorted

overall_design: Microdissection of the second heart field region in E9.5 embryos, digestion and cell sorting


title: HP1 are dispensable for liver development and functions but are essential to prevent liver tumorigenesis

city: montpellier

first: florence

last: cammas

address: 208 rue des apothicaires

institute: ircm

summary: Chromatin organization is known to play essential roles in cell identity and functions. Here, by hepatocyte-specific inactivation of all the genes encoding for HP1 proteins (HP1α, β and γ) within mice livers (HP1-TKO mice), we demonstrate that these proteins are dispensable for hepatocyte development, survival and functions and for liver development but are critical to prevent liver tumorigenesis. We further showed that the lack of HP1 leads to the loss of heterochromatin hallmarks and to the deregulation of many genes with liver-specific functions. Furthermore, HP1-TKO transcriptome is also characterized by a strong enrichment in genes encoding for members of the KRAB-ZFP family of transcriptional repressors and as a consequence by reactivation of several families of Endogenous Retrovirus (ERV) with some of them behaving either as enhancers or alternative promoters leading to deregulated expression of several genes in their vicinity.

overall_design: Examination of the liver transcriptome between mice controls and mice triple KO for the HP1 proteins (TKO)

first: Nehme

last: Saksouk

first: Shefqet

last: Hajdari

first: Marine

last: Pratlong

first: Aliki

last: Zavoriti

first: Célia

last: Barrachina

first: Céline

last: Graber

first: Amélie

last: Sarrazin

first: Nelly

last: Pirot

first: Jean-Yohan

last: Noël

first: Lakhdar

last: Khellaf

first: Eric

last: Fabbrizio

first: Florence

middle: M

last: Cammas


title: RNAseq of SEC23B wildtype (WT) and mutant (MUT) thyroid cell lines treated with Tunicamycin (Tunica, ER stress)

city: Cleveland

first: Charis

last: Eng

state: OH

address: 9500 Euclid Avenue

department: Genomic Medicine Institute

institute: Cleveland Clinic

summary: We report gene expression changes between SEC23B WT and MUT cells after treatment with Tunicamycin. The overall goal is to agnostically determine impacted signaling pathways in the wildtype and mutant settings.

overall_design: Stable non-malignant thyroid cell lines (Nthy-ori 3-1) were stably transduced to generate WT (Nthy-SEC23B-WT) and MUT (Nthy-SEC23B-V594G) cell lines. In these experiments, the cell lines were treated with Tunicamycin for 30 hours (hrs) or for 7 days prior to RNA extraction and downstream processing.

first: Lamis

last: Yehia


title: CHD7 functions upstream of the retinoic acid synthetase ALDH1A3 to regulate inner ear development

city: Ann Arbor

first: Donna

middle: M.

last: Martin

state: MI

address: 1150 W. Medical Ctr. Dr., 8220C MSRB III

department: Pediatrics and Communicable Diseases

institute: University of Michigan

summary: CHD7, an ATP-dependent chromatin remodeler, is disrupted in CHARGE syndrome, an autosomal dominant condition characterized by variably penetrant abnormalities in craniofacial, cardiac, and neuronal tissues.  The inner ear is uniquely sensitive to CHD7 levels and is the most commonly affected organ in individuals with CHARGE.  Interestingly, up- or down-regulation of retinoic acid (RA) signaling during embryogenesis leads to developmental defects similar to those in CHARGE syndrome, suggesting CHD7 and RA share target genes or signaling pathways. Here, we report that CHD7 and retinoic acid receptor (RAR) do not directly interact, and that RA induces rapid neuronal differentiation of human SH-SY5Y neuroblastoma cells without affecting CHD7 levels.  Instead, we provide evidence that CHD7 directly regulates expression of Aldh1a3, which encodes an RA synthetic enzyme, and that loss of Aldh1a3 partially rescues Chd7-mutant mouse inner ear defects, indicating that ALDH1A3 acts with CHD7 in a common genetic pathway to regulate inner ear development.

overall_design: poly(A) mRNA profiles of E10.5 Chd7+/+, Chd7Gt/+ and Chd7Gt/Gt mice were generated by deep sequencing, in duplicates, using Illumina HiSeq 2500.

first: Hui

last: Yao

first: Sophie

last: Hill

first: Jennifer

last: Skidmore

first: Ethan

middle: D

last: Sperry

first: Donald

middle: L

last: Swiderski

first: Gilson

last: Sanchez

first: Yehoash

last: Raphael

first: Peter

last: Scacheri

first: Shigeki

last: Iwase


title: SFP1 (RNA-seq)

city: Cambridge

first: Carl

last: de Boer

state: MA

address: 415 Main St

institute: The Broad Institute

summary: We measured global expression profiles in SFP1 deletion mutants and isogenic wild type strains during lag and log phase growth. To match the physiology of each species as well as minimize the effect on gene expression from differences in early growth rates, we profiled expression during log growth and lag after glucose repletion as previously described (Thompson et al., 2013).

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae
Nakaseomyces glabratus
Naumovozyma castellii
Saccharomyces paradoxus
Kluyveromyces lactis

overall_design: For each species, there are three replicates (A,B,C). Each Sfp1 mutant was compared to the corresponding WT at the corresponding time point (lag phase) or stage of log phase growth.

first: Toni

last: Delorey

first: Sara

last: Knaack

first: Sushmita

last: Roy


title: The roles of duplication and divergence in the evolution of a transcription factor

type: Genome binding/occupancy profiling by high throughput sequencing

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae
Nakaseomyces glabratus
Naumovozyma castellii
Saccharomyces paradoxus
Kluyveromyces lactis


title: Histone Demethylase KDM3A Functions As an Essential Factor for Epigenetic Control of Autophagy

city: Philadelphia

first: Kyoung Jae

last: Won

address: 3400 Civic Center Blvd

department: Genetics

institute: University of Pennsylvania

summary: Autophagy phenomenon is an essential mechanism to regulate cell homeostasis and is activated by various stresses such as nutrient starvation. It is well known that when autophagy is activated and how important components in the cytoplasm cause a series of reactions, but the regulatory mechanism of transcription in the nucleus is poorly known. Here, we identify that histone demethylase KDM3A plays a crucial role in the transcription of autophagy and lysosomal genes. Notably, KDM3A is increased in transcriptional levels in both glucose and amino acid starvation. Especially, transcriptional increase of histone demethylase in response to glucose starvation is dependent on AMP-activated protein kinase (AMPK). Furthermore, genome-wide analysis reveals that KDM3A acts as a co-activator in the expression of autophagy and lysosomal genes. Our finding of histone demethylase signaling cascade in nucleus, modulating histone demethylation signature is one of the predominant epigenetic event in autophagy activation, thereby providing the functional and mechanistic link between epigenetic control and transcriptional regulation of autophagy upon nutrient starvation.

overall_design: Gene expression profiling of WT and kdm3a KO MEFs  under nutrient rich condition or glucose starvation

first: Hyunkyung

last: Kim

first: Kyoung-Jae

first: Sung-Hee

last: Baek


title: Cigarette smoke induced changes in expression of small non-coding RNAs (15-100 bp in Mouse Lung Epithelial (MLE) 12 cells)

first: Anna

last: Blumental Perry

address: 10900 Euclid Ave.

institute: Case Western Reserve University

summary: This RNA sequencing aimed to verify mito-ncR-805 upregulation in CSE-treated cells, and determine its exact sequence in alveolar type-II cells.

overall_design: Examination of two biological replicates of untreated MLE12 cells, and two biological repliccates of MLE12 cells treated with 10% bubbled-through medium cigarette smoke extract (CSE)

first: Raul

last: Jobava

first: Alexander

last: Miron

first: Neil

last: Molyneaux

first: Maria

last: Hatzoglou

last: Blumental-Perry


title: Gene expression profiling data following TRIM8 knockdown in MCF-7 cells

first: Weixiang

last: He

address: Donghu Road

department: Urology

summary: Breast cancer (BC) is the most common female malignancies worldwide, and 70% of cases are estrogen receptor α (ERα) positive. In this study, we report that the E3 ubiquitin ligase TRIM8 acts as a novel regulator of ER signaling. TRIM8 is downregulated in BC and is associated with poor prognosis. In addition, the protein level of TRIM8 is negatively correlated with ERα expression. To investigate whether TRIM8 mediated estrogen signaling pathway, we generated a knockdown model of TRIM8 in human MCF7 cells.

overall_design: Gene expression profiling of MCF-7 cells were transfected with TRIM8 siRNA or control siRNA. Three biological replicates were used for each group.

first: Zelin

last: Tian


title: Next Generation Sequencing Facilitates Quantitative Analysis of Runx2fl/fl and Gli1-CreERT2;Runx2fl/fl Mouse Molar Transcriptomes

city: Los Angeles

first: Quan

last: Wen

state: Ca

address: 2250 Alcazar St. CSA 123

institute: University of Southern California

summary: Purpose: To study the function of Runx2 on mouse tooth root development. The goals of this study are to compare NGS-derived molar transcriptome profiling (RNA-seq)  bwtween Runx2fl/fl and Gli1-CreERT2;Runx2fl/fl mice to identify the potential downstream target of Runx2. Methods: molar mRNA profiles from PN7.5 Runx2fl/fl and Gli1-CreERT2;Runx2fl/fl mice (induction at PN3.5) were generated by deep sequencing, using Novaseq. Results: Using an optimized data analysis workflow, we mapped about 68 million sequence reads per sample to the mouse genome ( mm10) and identified  80,214 transcripts with Partek E/M workflow. 427 differentially regulated genes were identified (＞1.8-fold, p＜0.05), of which 219 were upregulated and 208 were downregulated.

overall_design: Methods: molar mRNA profiles from PN7.5 Runx2fl/fl and Gli1-CreERT2;Runx2fl/fl mice (induction at PN3.5) were generated by deep sequencing, using 2x50 sequencing with Novaseq, each group had 4 samples.

first: Yang

last: Chai


title: Characterization of gene expression patterns among human iPS cell-derived cardiomyocytes, iPS cells, fetal human heart tissue and adult human heart tissue

city: Fujisawa

first: Tadahiro

last: Shinozawa

address: Muraokahigashi 2chome

country: Japan

institute: Takeda pharmaceuticals

summary: Here we provide the gene expression patterns of human iPS cell-derived cardiomyocytes used in the motion field imaging assay, adult human heart tissues, fetal human heart tissue and iPS cells. These data provided the causal relationship between phenotype and function in the human iPS cell-derived cardiomyocytes.

overall_design: Comparison of transcriptome profiling among heart tissues and cells including human iPS cell-derived cardiomyocytes, iPS cells, fetal human heart tissue and adult human heart tissue.

first: Yoshiko

last: Okai

first: Toshikatsu

last: Matsui


title: TGF-β1 licensed murine mesenchymal stromal cells show superior therapeutic efficacy in modulating corneal allograft immune rejection in vivo

city: Galway

first: Aideen

last: Ryan

address: University Road

country: Ireland

institute: National University of Ireland, Galway

summary:
We report a novel licensing strategy to improve the immunosuppressive capacity of MSCs. Licensing murine MSCs with TGF-β1 (TGF-β MSC) significantly improved their ability to modulate both the phenotype and secretome of inflammatory bone marrow-derived macrophages and significantly increased the numbers of regulatory T lymphocytes (Tregs) following co-culture assays. These TGF-β MSC-expanded Tregs also expressed significantly higher levels of PD-L1 and CD73, indicating enhanced suppressive potential. Detailed analysis of T lymphocyte co-cultures revealed modulation of secreted factors, most notably, elevated prostaglandin E2 (PGE2). Furthermore, TGF-β MSCs could significantly prolong rejection-free survival (69.2% acceptance rate compared to 21.4% for un-licensed MSC treated recipients) in a murine corneal allograft model.
Mechanistic studies revealed that (i) therapeutic efficacy of TGF-β MSCs is Smad2/3-dependent; (ii) TGF-β MSC’s enhanced immunosuppressive capacity is contact-dependent and (iii) enhanced secretion of PGE2 (via prostaglandin EP4 receptor) by TGF-β MSCs is the predominant mediator of Treg expansion and T cell activation and is associated with corneal allograft survival. Collectively, we provide compelling evidence for the use of TGF-β1 licensing as an unconventional strategy for enhancing MSC immunosuppressive capacity.

overall_design: RNA sequencing of untreated murine mesenchyaml stromal cells (MSCs) (n=3) compared to TGF-β1 licensed MSCs (n=3)

first: Oliver

last: Treacy


title: Systems analysis of biliary atresia through integration of high-throughput biological data

first: Shankar

last: Subramaniam

state: CA

address: 9500 Gilman Drive

department: Bioengineering

summary: Biliary atresia (BA), blockage of the proper bile flow due to loss of extrahepatic bile ducts, is a rare, complex disease of the liver and the bile ducts with unknown etiology. Despite ongoing investigations to understand its complex pathogenesis, BA remains the most common cause of liver failure requiring liver transplantation in children. To elucidate underlying mechanisms, we analyzed the different types of high-throughput genomic and transcriptomic data collected from the blood and liver tissue samples of children suffering from BA. Through use of a novel integrative approach, we identified potential biomarkers and over-represented biological functions and pathways to derive a comprehensive network showing the dysfunctional mechanisms associated with BA. One of the pathways highlighted in the integrative network was hypoxia signaling. Perturbation with hypoxia inducible factor activator, dimethyloxalylglycine, induced the biliary defects of BA in a zebrafish model, serving as a validation for our studies. Our approach enables a systems-level understanding of human BA biology that is highlighted by the interaction between key biological functions such as fibrosis, inflammation, immunity, hypoxia, and development

overall_design: The pooled RNA libraries were prepared using Illumina’s mRNA Sequencing Sample Preparation kit (#RS-930-1001) from the explanted liver tissue samples of 6 BA patients and 6 normal pre-implant liver allografts. The pooled RNA libraries for the BA and the normal groups were sequenced on Genome Analyzer II with 36 bp paired-end at the Wistar Institute, Philadelphia. CASAVA software was used to generate a table of exon, gene, and splice counts in both BA and normal groups

first: Jun

last: Min

first: Mylarappa

last: Ningappa

first: Juhoon

last: So

first: Donghun

last: Shin

first: Rakeshi

last: Sindhi


title: Immunological fingerprint of 4CMenB recombinant antigens via protein microarray

status: Public on Aug 28 2020

city: Siena

first: Erika

last: Bartolini

state: Italy

address: Via Fiorentina 1

department: AIMB

country: Italy

institute: GSK Vaccines

summary: In this study, we describe the development and use of an ad hoc protein microarray to study the immune response induced by the three major 4CMenB antigenic components (fHbp, NHBA and NadA) in individual sera from vaccinated infants, adolescents and adults.

overall_design: A panel of  recombinant fragments of different length spanning the entire sequence of  fHbp, NHBA and NadA plus different full length fHbp, NHBA and NadA variants were printed in 8 or 16 replicated on a non-commercial Protein Microarray. All fragments were expressed in E. coli as either glutathione S-transferase-, His-tagged or TRX-fusions, purified from the cytoplasmic fraction as soluble forms. Human IgG (at 8 different concentration points) was distributed in each array copy as control. Sera were profiled for anti-Human IgG specific analysis of reactivity to the spotted proteins.

first: Marco

last: Bruttini


title: A conserved microRNA signature related to cellular transformation by the RAS oncogene (miRNA)

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

institute: Universitätsklinikum Düsseldorf

summary: The differential expression of microRNAs in Ras transformed epithelial cells of human and rat origin was investigated. Here we describe the group of miRNAs differentially expressed in two Ras transformed cell lines and defined  it as a  miRNA Ras signatures. We show that expression of these miRNAs are also affected in different primary tumors with high frequency of Ras mutation. We demonstate that introduction of different miRNAs lost during Ras transformation have big influence on cellular phenotype and mRNA expression. Importance of Ras pathway dependent transcription factors for miRNA regulation was shown as well. The complexity of miRNA – signal transduction pathways interactions and importance of miRNA regulation in Ras dependent malignant tumor formation is discussed.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: MiRNA microarrays were constructed using the NCODETM multi-species microarray probe set V1 (Invitrogen, CA, USA). Oligos were spotted at a concentration of 30µM on epoxy treated slides (Corning®, NY, USA) using the MicroGrid compact microarrayer (Genomic Solutions, Ann Arbor, USA) equipped with a MicroSpot 2500 quill pins. 100 ng of small RNA fraction were labelled using the NCODETM miRNA labeling system (Invitrogen, CA, USA) according to the manufacturer’s instructions.

first: Oleg

last: Chernitsa

first: Alexander

last: Gross


title: A conserved microRNA signature related to cellular transformation by the RAS oncogene (Affymetrix mRNA)

overall_design: Total RNA obtained from human embryonic kidney and rat ovarian surface epithelium cells, RAS transformed, mir22 mimicked, FRA1 silenced.

first: Alex


title: Expression profiling analysis of ELF3-knockdown (KD) and control human bile duct cells

status: Public on Aug 27 2020

city: Suita

first: Masami

last: Suzuki

state: Osaka

address: 2-2 Yamadaoka

institute: Osaka University

summary: An immortalized normal epithelial cell line of common bile duct origin (HBDEC2 cells) was established. An ELF3 gene knockdown clone was obtained using microRNA-155-based conditional RNA interference targeting the human ELF3 gene (5′-AGGTTCTGCTGGATCAGCT-3′) and EGFPmiR, targeting EGFP as a control (EGFP-miR; 5′-ACAAGCTGGTACAACTACA-3′).

overall_design: We performed a genome-wide expression profiling analysis of ELF3 KD cells and control cells.  Three independent samples were performed.

first: Shinichi

last: Yachida


title: Tri-4C: efficient and quantitative analysis of enhancer loops at hundred base pair resolution (ATAC-Seq)

city: Bronx

first: Yizhou

last: Zhu

state: NY

address: Price469 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

summary: Enhancer looping governs gene regulatory circuitry but is challenging to detect. Here we present Tri-4C, an ultrafine mapping method for distal chromatin contacts using triple restriction enzyme (RE) digestion. Tri-4C identifies enhancer loops that are undetectable by current single RE- based methods and reveals quantitative loop strengths in enhancer interaction networks underlying dynamic gene control. This multi-RE approach may be applied to general 3C-derived methods for accurate detection of enhancer loops.

overall_design:
Examination of enhancer landscape before and after IFNB1 induction IMR90 cells using ATAC seq.
Examination of enhancer landscape in H7-derived vascular smooth muscle cells using ATAC seq.

first: Yousin

last: Suh


title: EZH2 deficient T-cell acute lymphoblastic leukemia is sensitized to CHK1 inhibition through enhanced replication stress

city: London

first: Theresa

middle: Elizabeth

last: Leon

address: 72 Huntley St, Camden Town

department: Haematology

country: United Kingdom

institute: UCL Cancer Institute

summary: Loss-of-function mutations of EZH2, the enzymatic component of PRC2, are recurrently found in T-cell acute lymphoblastic leukemia (T-ALL) and have been associated with chemotherapy resistance and poor outcome. Using isogenic T-ALL cells, with and without CRISPR-induced EZH2-inactivating mutations, we performed a cell-based synthetic lethal drug screen. EZH2 deficient cells exhibited increased sensitivity to structurally diverse CHK1 inhibitors, an interaction that could be validated genetically. Notably, EZH2 deficient cells acquired a gene expression signature of immature T-ALL cells, with significant enrichment of MYC target genes. Mechanistically, EZH2 deficiency was associated with marked transcriptional upregulation of MYCN, increased replication stress, and enhanced dependency on CHK1 for cell survival. Furthermore, small molecule inhibition of CHK1 had efficacy in delaying tumor progression in isogenic EZH2 deficient, but not EZH2 wild-type T-ALL cells in vivo, suggesting there is an exploitable therapeutic window for CHK1 inhibitors in high risk EZH2 mutated T-ALL.

overall_design: Jurkat EZH2-WT (biological triplicates) versus Jurkat CRISPR/Cas9- edited -EZH2-KO1 (biological triplicates) and -EZH2-KO2 (biological triplicates) cell lines are analysed by RNA-seq

middle: E

last: León

first: Tanya

last: Rapoz-D’Silva

first: Cosetta

last: Bertoli

first: Sunniyat

last: Rahman

first: Michael

last: Magnussen

first: Brian

last: Philip

first: Nadine

last: Farah

first: Simon

last: Richardson

first: Sara

last: Ahrabi

first: Jose

last: Guerra-Assunção

first: Rajeev

last: Gupta

first: Elisabeth

last: Nacheva

first: Javier

last: Herrero

first: David

last: Linch

first: Robertus

last: de Bruin

first: Marc

middle: R

last: Mansour


title: Circular RNAs expression profiles and potential key molecules incompletely transected spinal cord injury.

city: ChangChun

first: Yuxin

last: Chang

address: 218 Ziqiang Street

institute: Jilin university

summary: Circular RNA is implicated in numerous diseases and conditions, including traumatic injury to the central nervoussystem. However, we know little regarding their role in completely transected spinal cord injury (SCI). Our studyused high-throughput sequencing to analyze circular RNA expression in rats after experimental completetransection of spinal cord. We found differential expression in 400 circular RNAs after SCI, with 249 significantlyup-regulated and 151 significantly down-regulated. We then selected five circular RNAs for qRT-PCR validation,and the results were in agreement with RNA sequencing. Additionally, we predicted the function of circular RNAin SCI through GO and KEGG analyses, as well as the construction of circRNA/microRNA interaction networks.Furthermore, we identified circular RNA chr9:1829226-1834212 and mRNA Hdac11 as key molecules after SCI.In conclusion, this study is the first to characterize circular RNA function in rats after completely transected SCI,through identifying their differential expression. Our results provide insight into the mechanism and therapeutictargets of SCI.

overall_design: Spinal cord circular RNA profiles of wild type and spinal cord injury(SCI) rats were generated by deep sequencing, in triplicate, using Illumina GAIIx.The latter group was subjected to surgery that completely transected the spinal cord, whereas the control was treated with laminectomy alone.


title: Tri-4C: efficient and quantitative analysis of enhancer loops at hundred base pair resolution (Tri-4C)

first: Yizhou

last: Zhu

overall_design:
Examination of long range chromatin interaction in IFNB1 locus in IMR90 cells.
Examination of long range chromatin interaction of ECAD9 in H7-derived vascular smooth muscle cells.
Examination of long range chromatin interaction of IMR90 using Tri-4C with alternative (CviAII) digestion.

The file "GSE119187_sample_viewpoints.xlsx" at the foot of this record includes the method (4C or Tri-4C) and the viewpoint sequence for each sample"

first: Yousin

last: Suh


title: Expression profiling analysis of ELF3-knockout (KO) and wild-type (WT)  human bile duct cells

first: Masami

last: Suzuki

summary: An immortalized normal epithelial cell line of common bile duct origin (HBDEC2 cells) was established. An ELF3 gene knockout clone was obtained using the CRISPR/Cas9-system.

overall_design: We performed a genome-wide expression profiling analysis of KO cells and WT cells.  Three independent samples were performed.

first: Shinichi

last: Yachida


title: Expression profiling analysis of an inducible ELF3-expressing and control human bile duct cells  [inducible ELF3]

summary: An immortalized normal epithelial cell line of common bile duct origin (HBDEC2 cells) was established. An inducible ELF3-expressing was generated by infection with the retrovial vector pRetroX-TetOne-Puro-ELF3-flag, expressing ELF3 fused to a flag-tag.

overall_design: We performed a genome-wide expression profiling analysis of an inducible ELF3-expressing cells and control cells.  Three independent samples were performed.


title: A conserved microRNA signature related to cellular transformation by the RAS oncogene

first: Wasco

last: Wruck

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

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

overall_design: Refer to individual Series


title: Transcriptional Profile of Microglia in Neurodegeneration

city: Palo Alto

first: Khoa

middle: Dinh

last: Nguyen

address: 3373 Hillview Ave

department: Pathology

institute: Stanford University

summary:
Purpose: RNASeq was used to identify transcriptional signature responsible for the metabolic reprogramming phenotype of microglia in neurodegenerative disease
Result: We identified Ppargc1a/Cebpb signaling pathway as a critical axis that controls microglial glycolytic transition during neurodegeneration

overall_design: Microglia from the midbrain region of animals with microglial Ppargc1a deficiency or controls were subjected to MPTP injections to induce neurodegeneration or treated with PBS as control. Total RNA from 3 microglia samples from each genotype/condition were isolated and used to prepare RNASeq library and analysis

first: Edgar

last: Engleman


title: Epigenetic profiling of hepatocyte, reprogrammed hepatocyte, and biliary cells

city: New York

first: Jinyang

last: Li

state: New York

address: 1230 York Ave

institute: The Rockefeller University

summary: ATAC-seq analysis of mouse hepatocyte, reprogrammed hepatocyte, and biliary cells

overall_design: Following DDC treatment of mice, hepatocyte, reprogrammed hepatocyte, and biliary cells were isolated from liver of mice for sample preparation.

first: Allyson

last: Merrell

first: Ben

last: Stanger


title: Expression profiling analysis ELF-deficient and ELF-expressing human bile duct cells


title: Transcriptomic analysis of peripheral blood mononuclear cells (PBMC) of patients with type 2 Diabetes Melittus(T2DM), Dyslipidemia (DL) and Periodontitis (P)

city: Campinas

first: Cristiane

middle: de Souza

last: Rocha

state: São Paulo

address: Av Tessália Vieira de Camargo, 126 Cidade Universitária "Zeferino Vaz"

department: Medical Genetics

country: Brazil

institute: Unicamp

summary:
We identified that PBMC of individuals simultaneously affected by a combination of T2DM, dyslipidemia and periodontitis, showed altered molecular profile mainly associated to inflammatory response, immune cell trafficking, and infectious disease pathways
Patients were divided into: T2DMpoorly-DL-P (n=5, Grupo 1), T2DMwell-DL-P (n=7, Grupo 2), DL-P (n=6, Grupo 3), P (n=6, Grupo 4) and Healthy (n=6, Control). T2DM poorly controlled = HbA1c ≥8.5%; T2DM well-controlled patients = HbA1c <7.0%

overall_design: PBMC were collected from 150 patients divided into 5 groups, the RNA was extracted using the Trizol® and purified by RNeasy Protection Mini Kit. It was used the GeneChip IVT Labeling Kit protocol and hybridized to U133 Plus 2.0 (Affymetrix)

first: Raquel

last: Scarel-Caminaga

first: Samia

last: Corbi

first: Claudia

last: Maurer-Morelli

first: Silvana

last: Orrico


title: Genome wide screening for binding target of ELF3 transcription factor in biliary epithrial cell line HBDEC2

address: Yamadaoka 2-2

summary:
ELF3, a member of E26 transformation-specific transcription factors, is inactivated in a range of cancers including biliary tract cancer. We performed chromatin immunoprecipitation followed by high-throughput DNA sequencing (ChIP-Seq) to identify direct ELF3 target genes. The number of uniquely mapped reads identified by ChIP-Seq was 109.9 M for the ELF3 binding site and 59.7 M for the control input DNA.
These read data were evaluated with MACS 1.4, and 13,960 peaks were identified throughout the genome with a false discovery rate (FDR) of < 0.1.

overall_design: ELF3 ChIP-Seq was performed on ELF3 gene-knockout HBDEC2 cells with  ELF3 tet-ON system.

first: Mihoko

last: Saito-Adachi


title: YY1 Interacts with G quadruplex DNA to Regulate Gene Expression

city: Riverside

first: LIN

last: LI

address: 501 Big Springs Road, University of California at Riverside

department: Department of chemistry

institute: UC, riverside

summary: We systematically analyzed the alterations in mRNA transcriptome evoked by knockdown of YY1 with or without pyridostatin (PDS) treatment. Statistical analysis showed a strong correlation between PDS-regulated and YY1-regulated genes (Pearson r > 0.67), underscoring the role of YY1-G4 structure interaction in YY1-mediated gene regulation. Moreover, the RNA-Seq results revealed that YY1 can positively or negatively regulate the expression of genes through its interaction with G4 structures.

overall_design: Examination of gene expression after knockdown of YY1 with or without pyridostatin (PDS) treatment

first: Lin

first: Yinsheng

last: Wang


title: SFP1 (ChIP-seq)

first: Carl

last: de Boer

address: 415 Main St

summary: We set out to determine how Sfp1 binding targets evolved over time. We sampled our species of interest to include one pre-whole genome duplicaton (WGD) species containing SFP1A (K. lactis), one post-WGD species containing both SFP1 and SFP1PL (N. castellii), two post-WGD species containing only SFP1 (S. cerevisiae and S. paradoxus) and performed ChIP for each Sfp1 homolog in each species using an antibody that recognizes a conserved subdomain of Sfp1 common to both Sfp1, Sfp1a, and Sfp1pl. Because Sfp1pl was also present in N. castellii, a second antibody was used that is more specific to Sfp1pl (denoted as IP3). We also performed ChIP in SFP1 deletion mutants in each species tested, as a control."

sample_organism:
Saccharomyces cerevisiae
Naumovozyma castellii
Saccharomyces paradoxus
Kluyveromyces lactis

overall_design: Polyclonal antibodies were created (Bethyl, Inc) to bind a peptide from the conserved c-terminal portion of Sfp1 designated, αSfp1-1, while αSfp1-3 was raised to recognize was raised to bind specifically to the N. castellii Sfp1pl The ChIP protocol was performed as described by Lefrancois et al. in The Guide to Yeast Genetics (Weissman, Jonathan F., Guthrie, 2010); modifications noted below) with 2-3 replicates per sample. Strains were grown to optical densities (OD600) between 0.6 and 0.8 in 500 mL of BMW (Thompson et al., 2013). Fixation took place with 37% formaldehyde for 15 minutes at room temperature, with occasional shaking every 5 minutes. Samples were sheared on the Covaris E210 with the following settings: 20% / 8 intensity/ 200 cycles per burst in 1-minute cycles for 16 minutes. Sequencing libraries were prepared from the input and immunoprecipitated DNA and were sequenced on an Illumina HiSeq 2500 with 25 base pair, paired end reads. Reads were mapped to the reference genomes of each species (S288C R64 for S. cerevisiae, YGOB v7 Aug 2012 for K. lactis and N. castellii, and Scannell et al. for S. paradoxus (Scannell et al., 2011), using bowtie2.

first: Toni

last: Delorey

first: Sara

last: Knaack

first: Sushmita

last: Roy


title: The mammalian cap-specific m6Am RNA methyltransferase PCIF1 regulates transcript levels in mouse tissues

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

summary: The 5' end of eukaryotic mRNAs is protected by the m7G-cap structure. The transcription start site nucleotide is ribose methylated (Nm) in many eukaryotes, while an adenosine at this position is further methylated at the N6 position (m6A) by the mammalian Phosphorylated CTD-interacting Factor 1 (PCIF1) to generate m6Am. Here we show that while loss of cap-specific m6Am in mice does not affect viability or fertility, the Pcif1 mutants display reduced body-weight. Transcriptome analyses of mutant mouse tissues support a role for the cap-specific m6Am modification in stabilizing transcripts. In contrast, the Drosophila Pcif1 is catalytically-dead, but like its mammalian counterpart it retains the ability to associate with the Ser5-phosphorylated CTD of RNA pol II. Finally, we show that the Trypanosoma Pcif1 is an m6Am methylase that contributes to the N6,N6,2?-O-trimethyladenosine (m62Am) in the hypermethylated cap4 structure of Trypanosomatids. Thus, PCIF1 has evolved to function in catalytic and non-catalytic roles.

overall_design: RNA sequencing was used to identify gene expression differences between Pcif1-/- and Pcif1+/+  in mouse brain, spleen and testes.  To correlate the gene expression changes with loss of m6Am we used m6Am-Exo-Seq method to identify the m6Am transcripts in mouse testes.  Ribosome footprinting in mouse brain was used to search for effects on translation.

first: Radha

last: Pandey

first: Elena

last: Delfino

first: David

last: Homolka

first: Adriana

last: Roithova

first: Kuan-Ming

last: Chen

first: Lingyun

first: Giulia

last: Franco

first: Cathrine

middle: B

last: Vågbø

first: Emmanuel

last: Taillebourg

first: Marie-Odile

last: Fauvarque

middle: S


title: The effect of Kctd15 expression during early development in zebrafish [Dr_dev]

city: Bethesda

first: Matthew

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

summary: Examination of which genes are affected by loss of kctd15 expression during neural crest and larval development

overall_design: RNA was extracted from 1 somite and 25 hour embryos; 2, 5, 9, and 14 day larva

first: Alison

last: Heffer

first: Igor

last: Dawid


title: Effects of Fe(II) on anammox community activity and functional genes expression

city: Suzhou

first: Jing

last: Ding

address: No 1, Kerui Road

institute: Suzhou University of Science and Technology

summary: Four Fe(II) concentrations (0.03, 0.09, 0.12 & 0.75 mM) were tested to investigate the stimulation and inhibition effects of ferrous iron on anammox bacterial activity. RNAs were extracted from the cultures, and the synthesized cDNAs by reverse transcription were used to carry out GeoChip analysis, by which the functional communities and expression level differences in functional genes under different Fe(II) concentrations conditions were obtained, and the response of anammox bacteria to Fe(II) stimulation and inhibition are speculated.

sample_organism: anaerobic ammonium-oxidizing bacterium enrichment culture

overall_design: Enriched anammox culture was taken out from the parent reactor and used as inoculum. Then four Fe(II) concentrations (0.03, 0.09, 0.12 & 0.75 mM) were applied to four independent experimental cultures. RNAs  in 0.03, 0.09 and 0.12 mM Fe(II) cultures were isolated at the end of the experiments, while RNA in 0.75 mM Fe(II) culture was extracted after the inhibition occured. All of the RNAs were reversely transcribed into cDNAs, and then were used to do Geochip analysis.


title: Gene expression data in mouse liver following exposure to silver nanoparticles

city: Rensselaer

first: Sridar

middle: V

last: Chittur

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

summary:
We used microarrays to determine transcptional responses to silver nanoparticles (AgNPs) in the mouse liver following oral ingestion. Liver is a major target organ for AgNP accumulation after oral or intravenous exposure. Given that physicochemical properties of AgNPs such as surface coating may  influence transcriptional responses to exposure, we evaluated AgNPs with two different surface coatings such as citrate (cit) and polyvinylpirrolidone (PVP).
We identified common and unique mRNA and lncRNA expression profiles for cit-AgNPs and PVP-AgNPs. PVP-AgNPs induced a more robust transctiptional response characterized by a 2-fold higher number of differentially expressed mRNAs and lncRNAs.

overall_design: Mice were exposed to 20 nm AgNPs coated with citrate (cit-AgNPs) or polyvinylpyrrolidone (PVP-AgNPs) in aqueous solutions by oral gavage at  a dose of Ag of 4 mg/kg for 7 consecutive days, while mice that were exposed to water only served as controls. Livers were harvested for RNA extraction and hybridization on Affymetrix microarrays.

first: Ramune

last: Reliene

first: Sameera

last: Nallanthighal


title: Tri-4C: efficient and quantitative analysis of enhancer loops at hundred base pair resolution

first: Yizhou

last: Zhu


title: Apatite nanoparticle(sCA)-siTIMP1 delivery in NIH3T3

city: bunkyo

first: Masayo

last: Aoki

state: tokyo

address: 1-1-5 Sendagi

department: Plastic Surgery

institute: Nippon Medical School

summary:
Expression profiling of sCA-siRNA delivery in NIH3T3 cells (siControl vs. siTIMP1)
Goal was to determine the off target effects of sCA-siTIMP1 in NIH3T3 cells.

overall_design: Two-condition experiment, siControl vs. siTIMP1 transfected cells.


title: Comparison between PRRS and control in female and male pig amygdala in 22 day old pigs

city: Urbana

first: Sandra

last: Rodriguez Zas

state: IL - Illinois

address: 1207 W. Gregory Dr.

institute: University of Illinois at Urbana

summary: Maternal immune activation was conducted in pregnant gilt receiving either PRRS or control and measure gene expression at day 22 after birth in female and male pigs.

overall_design: RNA samples were obtained at day 22 after birth and were subjected to paired-end RNA sequencing


title: The effect of Kctd15 expression on the neural crest and sex organs in zebrafish [Dr_emb]

overall_design: RNA was extracted from 10 somite embryos, and adult ovary and testes tissue


title: Time-series transcript profiling analysis in stem base of rice crown rootless 1 mutant after ectopic expression induction by dexamethasone of the CRL1 gene

city: Montpellier

first: Pascal

last: Gantet

address: Avenue Agropolis

department: IRD

institute: Université Montpellier 2

summary:
Lateral Organ Boundary Domain (LBD) transcription factors are specific of plants and are involved in the control of development. One LBD clade is related to the control of root development (Coudert et al., 2013, Mol. Biol. Evol. 30, 569-572). Belonging to this clade, CROWN ROOTLESS 1 controls the initiation of crown roots in rice (Inukai Plant Cell, 17, 1387-1396, Liu et al., 2005, Plant J., 43, 47-56). The aim of this study was to identify the genes that are regulated by CRL1 in a time-dependant manner after its induction. A total of 1748 differentially expressed genes (DEG) were identified, 1034 of them upregulated, and 706 downregulated, and 14 both upregulated and downregulated at some point during the time series. Data analysis revealed three distinct phases in the time series that can represent three developemntal stage during crown root primordia formation.
Affymetrix microarrays were processed in the Microarray Core Facility “Transcriptome“ of the Institute in Regenerative Medicine and Biotherapy, CHU de Montpellier-INSERM-UM Montpellier, http://irmb.chu-montpellier.fr/ .

overall_design: We transformed the crl1 mutant with a construction allowing the control of CRL1 expression by exogenous dexamethasone (DXC line) and with an empty construction as a control (DX line). Transcriptome profiling were conducted  in both lines each 3 hours from 0 to 45 hour after dexamethasone addition (hours after induction : hai). After 5 hours dexamethasome was removed by renewing the liquid culture media. 3 independent experiments were carried out (rep1 to rep3)

first: J

last: Lavarenne

first: P


title: YY1 regulates DNA-DNA interaction

first: LIN

last: LI

summary: The DNA Guanine quadruplexes (G4) plays important roles in multiple cellular processes, including regulation of DNA replication, transcription and genome stability. Here, we show that Yin Yang-1 (YY1), a ubiquitously expressed and multifunctional transcription factor, can bind with G4 structures directly. Fluorescence anisotropy experiments shows that YY1 binds towards G4 structures with Kd in low nanomolar range (<100 nM) through the C terminal zinc finger domains. ChIP-seq results show that 81% of the YY1 ChIP-seq peaks contain G4 forming sequences, which is highly overlapped with the G4 ChIP-seq peaks. YY1 facilitate the DNA-DNA interaction through its binding with G4 structures in vivo and in vitro, which can be disturbed by G4 stabilizer treatment. In all, our studies identify a novel G4 structure binding protein-YY1, and reveal that G4 structure functions in DNA-DNA interaction.

overall_design: We performed the ChIPseq and HiChIP for YY1 with or without PDS or TMPYP4 treatment. At least two replicates were done for each experiments.

first: Lin

last: Li

first: Yinsheng

last: Wang


title: Dysregulation of p53-RBM25-mediated circAMOTL1L biogenesis contributes to prostate cancer progression (Agilent circRNA data set)

city: Shijiazhuang

first: Zhan

last: Yang

state: Hebei

address: 215 Heping W Rd

institute: The Second Hospital of Hebei Medical University

summary: To explore the molecular mechanisms underlying circRNA role in prostate carcinogenesis and progression of PCa, we first used circular RNA microarrays to acquire circRNA profiles in PCa tissues. Five pairs of samples were taken from the two different areas, i.e., high-grade PCa (Gleason>8) and low-grade PCa (Gleason< 6), within the same PCa sample

overall_design: Microarray hybridization analysis of circRNA expression in five pairs of PCa samples with areas of high grade disease (Gleason>8) or areas of low grade (Gleason<6) was performed according to the manufacturer’s protocol (Arraystar, Inc., Rockville, MD, USA).

first: Xiao-lu


title: Dysregulation of p53-RBM25-mediated circAMOTL1L biogenesis contributes to prostate cancer progression (RNA-seq data set)

summary: To clarify the effect of p53 on RBP gene expression, we knocked out p53 gene in PC3 cells to generate p53 knockout stable cell line (p53-/- PC3 cells) and examined the expression of the known RBP genes by RNA sequencing.

overall_design: 4 sample with 2 control and 2 p53 knockout in PC3 cell line


title: Dysregulation of p53-RBM25-mediated circAMOTL1L biogenesis contributes to prostate cancer progression

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

overall_design: Refer to individual Series


title: Identification of transcriptional alterations that distinguish sensitive from insensitive neuronal populations in a genetic model of Parkinson’s disease.

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: Loss-of-function mutations in the parkin gene can cause early onset Parkinson’s disease, a movement disorder resulting from the selective degeneration of dopaminergic neurons in the basal ganglia. Analogously, movement deficits and loss of a subset of dopaminergic neurons are observed in Drosophila melanogaster homozygous for null mutations in parkin. Parkin is an E3 ubiquitin ligase that functions with the mitochondrial localized serine/threonine kinase PINK1 in a pathway required to maintain mitochondrial integrity. We previously established that the PINK1/Parkin pathway functions in Drosophila dopaminergic and cholinergic neurons to maintain mitochondrial membrane potential. However, the mechanisms through which the PINK/Parkin pathway selectively impacts dopaminergic neuron survival remains unclear, as do the mechanisms that lead to the selective vulnerability of dopaminergic neurons in Parkinson’s disease. Because the transcriptome of a cell determines its identity we hypothesized that knowledge of the transcriptional alterations that occur in dopaminergic neurons isolated from parkin null Drosophila would provide insight into the mystery of selective vulnerability in Parkinson's disease. Results: To test our hypothesis we measured the transcriptome of dopaminergic and cholinergic neurons isolated from isogenic heterozygous and homozygous parkin null mutants using a novel flow cytometry-based method we developed. Computational analysis and experimental confirmation demonstrate that our method allows for the successful expression analysis of defined neural subsets from the Drosophila brain. In addition, our dataset implicates iron handling and dopamine signaling as being significantly dysregulated in parkin null dopaminergic neurons. Conclusions: Our flow cytometry-based method allows for the isolation and microarray analysis of neuronal subsets from the adult Drosophila brain. Our microarray analyses implicate iron handling and dopamine metabolism as contributing factors in the etiology of parkin-associated early onset Parkinson’s disease. Here we provide a novel dataset that may serve as a foundation for subsequent functional analyses of the pathways underlying neuronal selective vulnerability in Parkinson's disease.

overall_design: Three replicates of 115 dopaminergic neurons or cholinergic neurons for mutant and control parkin null animals (a total of 12 samples).

first: Jonathon

last: Burman

first: Ramkmar

last: Hariharan


title: Brd4-bound enhancers drive cell intrinsic sex differences in glioblastoma [ChIP-Seq]

status: Public on Aug 26 2020

city: St. Louis

first: Zongtai

last: Qi

state: Missouri

address: 4515 Mckinley Ave

institute: Washington University in St Louis

summary: We report the application of ChIP-seq for high-throughput profiling of histone mark H3K27ac in male and female mouse glioblastoma.

overall_design: Examination of histone mark H3K27ac in DMSO-treated male and femal mouse astrocytes and JQ1 treated ones.

first: Najla

last: Kfoury

first: Jason

last: Gertz


title: The Ndr/LATS kinase Cbk1 regulates a specific subset of Ace2 functions and suppresses the hyphae-to-yeast transition in Candida albicans

city: Iowa City

first: Damian

last: Krysan

state: IA

address: 25 South Grand, 2040 ML

department: Division of Pediatrics & Infectious Disease

institute: University of Iowa Hospitals and Clinics

summary: The Regulation of Ace2 and Morphogenesis (RAM) pathway is an important regulatory network in the human fungal pathogen Candida albicans. The RAM pathway’s two most well-studied components, the NDR/Lats kinase Cbk1 and its putative substrate, the transcription factor Ace2, have a wide range of phenotypes and functions. It is not clear, however, which of these functions are specifically due to the phosphorylation of Ace2 by Cbk1. To address this question, we first compared the transcriptional profiles of CBK1 and ACE2 deletion mutants. This analysis indicates that, of the large number of genes whose expression is affected by deletion of CBK1 and ACE2, only 5.5% of those genes are concordantly regulated. Our data also suggest that Ace2 directly or indirectly represses a large set of genes during hyphal morphogenesis. Second, we generated strains containing ACE2 alleles with alanine mutations at the Cbk1 phosphorylation sites. Phenotypic and transcriptional analysis of these ace2 mutants indicates that, as in Saccharomyces cerevisiae, Cbk1 regulation is important for daughter cell localization of Ace2 and cell separation during yeast phase growth. In contrast, Cbk1 phosphorylation of Ace2 plays a minor role in C. albicans yeast-to-hyphae transition. We have, however, discovered a new function for the Cbk1-Ace2 axis. Specifically, Cbk1 phosphorylation of Ace2 prevents the hyphae-to-yeast transition. To our knowledge, this is one of the first regulators of the C. albicans hyphae-to-yeast transition to be described. Finally, we present an integrated model for the role of Cbk1 in the regulation of hyphal morphogenesis in C. albicans.

overall_design: Candida albicans mRNA expression was compared between wild-type or ace2∆∆ mutant cells in two different growth conditions and mRNA expression in wild-type compared to cbk1∆∆ mutant cells in a single growth condition. Within each comparison, wild-type cells represented baseline expression and each strain had 3 biological replicates.

first: Rohan

last: Wakade

first: Laura

middle: C

last: Ristow

first: Mark

middle: A

last: Stamnes

first: Anuj

last: Kumar


title: The pregnane X receptor drives sexually dimorphic hepatic changes in lipid and xenobiotic metabolism in response to gut microbiota in mice

city: Toulouse

first: Sandrine

last: Ellero-Simatos

address: 180 chemin de Tournefeuille

institute: INRAe

summary: The gut microbiota-intestine-liver relationship is emerging as an important factor in multiple hepatic pathologies, but the hepatic sensors and effectors of microbial signals are not well defined. By comparing publicly available liver transcriptomics data from conventional vs. germ-free mice, we identified pregnane X receptor (PXR, NR1I2) transcriptional activity as strongly affected by the absence of gut microbes. Microbiota depletion in Pxr+/+ vs Pxr-/- C57Bl6/J mice revealed that most microbiota-sensitive genes were PXR-dependent in the liver in males, but not in females. Pathway enrichment analysis revealed that microbiota-PXR interaction controlled fatty-acid and xenobiotic metabolism. Antibiotic treatment reduced liver triglyceride content and hampered xenobiotic metabolism in livers from Pxr+/+ but not Pxr-/- male mice. These findings identify PXR as a hepatic effector of sexually dimorphic responses to microbiota-derived signals and reveal a potential new mechanism for unexpected drug-drug or food-drug interactions.

overall_design: Littermate Pxr+/+ and Pxr-/- male and female C57Bl6/J adult mice were treated or not with broad-spectrum antibiotics (ATB) in drinking water for 2 weeks to deplete the gut microbiota. 8 groups were compared: Pxr+/+ Control males, Pxr+/+ ATB males, Pxr-/- Control males, Pxr-/- ATB males, Pxr+/+ Control females, Pxr+/+ ATB females, Pxr-/- Control females, Pxr-/- ATB females.. Transcriptomic data were generated for 6 mice per group (3 per cage).

first: Sharon

last: Barretto

first: Claire

last: Naylies

first: Yannick

last: Lippi


title: Brd4-bound enhancers drive cell intrinsic sex differences in glioblastoma [RNA-Seq]

summary: We report the application of RNA-seq for high-throughput profiling of transcriptom in male and female mouse glioblastoma.

overall_design: Transcriptom profiles of DMSO-treated male and femal mouse astrocytes, JQ1 treated male and femal mouse astrocytes and CPI-treated male and femal mouse astrocytes.


title: Deep RNA-sequencing of the RPE Reveals a Suppressed Innate Immune Response and Activation of Dedifferentiation Pathway in Response to Chronic Smoking

first: Matthew

last: Brooks

summary: Cigarette smoking is the strongest environmental risk factor for developing age-related macular degeneration (AMD), the most common cause of blindness among the elderly in western societies. Despite intensive study, the full impact of smoking on the retinal pigment epithelium (RPE), a central cell type involved in AMD pathobiology, remains unknown. The relative contribution of the known dysfunctional pathways to AMD, at what stage they are most pathogenic, or whether other processes are relevant, is poorly understood, and furthermore, whether they are activated by smoking, is unknown. We performed global RNA-sequencing of the RPE from C57BL/6J mice exposed to chronic cigarette smoke or air for 6 months to identify potential pathogenic and cytoprotective pathways. The RPE transcriptome induced by chronic cigarette smoking exhibited a mixed response of marked suppression of the innate immune response that included the antiviral response with type I and II interferons concurrent with upregulation of cell differentiation and morphogenic gene clusters, suggesting an attempt by the RPE to maintain its differentiated state despite smoke-induced injury. Given that mice exposed to chronic smoke develop early features of AMD, these novel findings are potentially relevant to the transition from aging to AMD.

overall_design: PolyA RNA from RPE/choroid using triplicate biological replicates for filtered air or smoking exposure were sequenced. Note: one filtered air replicate was eliminated from analysis for excessive neural retina tissue contamination.

first: Lei

last: Wang

first: Koray

last: Kaya

first: Sujung

last: Jun

first: Jie

first: Ying

last: Xin

first: Jiang

last: Qian

first: Anand

last: Swaroop

middle: T

last: Handa


title: Whole transcriptome sequencing of bovine mammary epithelial subpopulations

city: Grugliasco

first: Eugenio

last: Martignani

state: TO

address: Largo Braccini 2

department: Veterinary Science

institute: University of Torino

summary: The bovine mammary gland has a heterogeneous epithelial population which comprises terminally differentiated luminal and myoepithelial cells but also bipotent or lineage restricted progenitors and adult stem cells. The aim of our study was to use a novel surface marker (P-Cadherin) to characterize different mammary subpopulation, to sort adult stem cells with better enrichment and to perform whole RNA-seq among sorted population to identify biological processes or molecular functions associated gene enrichment. We found that only the CD49fhigh/PCadherinneg was enriched for adult mammary stem cells, while in other fractions we could detect luminal progenitors. Analysis of functional enrichments showed that in the stem cell compartment proliferation associated genes were downregulated, while genes relating to adhesion to ECM and to other neighboring cells were upregulated.

overall_design: Bovine mammary cells were collected at the slaughter house from 3 animals. Isolated mammary epithelial cells of each animal were sorted into 4 fraction according to their expression of CD49f and P-Cadherin. RNA was extracted from cells for each fraction and sequence using Illumina TruSeq with a depth/coverage of 30M reads per sample. Data from the 3 animals were then used as replicates to identify differentially expressed genes among the 4 mammary subpopulations.

first: Martignani

last: Eugenio

first: Ala

last: Ugo

first: Sheehy

last: Paul

first: Thomson

last: Peter

first: Baratta

last: Mario


title: Gene expression profiling in diptoindonesin G-treated MDA-MB-231 cells

city: Nanjing

first: Minmin

last: Fan

state: Jiangsu

address: 138 Xianlin Avenue

institute: Nanjing University of Chinese Medicine

summary: To understand the role of diptoindonesin G in the regulation of differentiation of breast cancer cells, the gene expression profile of MDA-MB-231 cells treated with diptoindonesin G was analyzed using Hiseq deep sequencing.

overall_design: MDA-MB-231 cells were treated with or without diptoindonesin G for 24 h. Three replicates were performed in every independent experiment.

first: Jingwei

last: Chen

first: Yan

last: Shen


title: Transcriptome reprogramming via Tob2-promoted global mRNA turnover

city: Houston

first: Ann-Bin

last: Shyu

state: Texas

address: 6431 Fannin Street, Rm 6.200

institute: The University of Texas Health Science Center at Houston

summary: We found that multilayered phosphorylation of human Tob2 modulates its PABP-binding ability to change global deadenylation and mRNA turnover, which in turn reprograms transcriptome to influence cell proliferation.

overall_design: Bromouridine-metabolic labeling pulse-chase RIP-seq approach was combined with time-course experiments to monitor mRNA decay across the transcriptome upon induced expression of human Tob2. Vector only was used as controls.

first: Chyi-Ying


title: Identify genome-wide binding sites of GFI1 in NB4 cells

city: Shanghai

first: Yun

last: Tan

state: Shanghai

address: Room 1109, Building 11, 197 Ruijin Er Rd

department: Shanghai Institute of Hematology

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

summary: Abarrent transcriptional regulation is one of hallmarks of leukemia. GFI1 is a transcriptional regulator with context-dependent roles in hematopoiesis and leukemogenesis. Reduced or loss of GFI1 expression has been reported in myeloid malignancies, while high GFI1 expression has been observed in AML1-ETO-positive acute myeloid leukemia (AML) and acute lymphoid leukemia, but without clear roles defined for GFI1 in APL pathogenesis. We here performed ChIP-seq analysis using antibodies against GFI1 and identified genome-wide binding site of GFI1 in NB4 cells.

overall_design: Examination of binding sites for GFI1 in NB4 cells.

first: Kankan

last: Wang


title: A genome-wide view of transcriptional responses during Aphis glycines Matsumura infestation in soybean

first: Yao

last: Luming

address: DongChun Rd

department: Plant science

institute: Shanghai Jiao Tong University

summary: Soybean aphid is one of the major limiting factors for soybean production. However, the mechanism for aphid resistance in soybean is remain enigmatic, very little information is available about the different mechanisms between antibiosis and antixenosis genotypes. Here we dissected aphid infestation into three stages and used genome-wide gene expression profiling to investigate the underlying aphid-plant interaction mechanisms. Approximately 990 million raw reads in total were obtained, the high expression correlation in each genotype between infestation and non-infestation indicated that the response to aphid was controlled by a small subset of important genes. Moreover, plant response to aphid infestation was more rapid in resistant genotypes. Among the differentially expressed genes (DEGs), a total of 901 transcription factor (TF) genes categorized to 40 families were identified with distinct expression patterns, of which AP2/ERF, MYB and WRKY families were proposed to playing dominated roles. Gene expression profiling demonstrated that these genes had either similar or distinct expression patterns in genotypes. Besides, JA-responsive pathway was domination in aphid-soybean interaction compared to SA pathway, which was not involved plant response to aphid in susceptible and antixenotic genotypes but played an important role in antibiosis one. Throughout, callose were deposited in all genotypes but it was more rapidly and efficiently in antibiotic one. However, reactive oxygen species were not involved in response to aphid attack in resistant genotypes during aphid infestation. Our study helps uncover important genes associated with aphid-attack response in antibiosis and antixenotic genotypes of soybean.

overall_design: mRNA profiles of aphid-susceptible, antibiotic and antixenotic soybean genotypes in 24h, 48h and 96h after infestation generated using Illumina HiSeq 4000 platform, in triplicate

first: Luming

last: Yao

first: Biao

first: Yina

last: Jiang


title: Deep transcriptomic analysis reveals the dynamic developmental progression during early development of channel catfish (Ictalurus punctatus)

city: Auburn University

first: Xu

state: AL

address: 273 CASIC Building, Auburn Research Park, 559 Devall Dr

department: Pathobiology, College of Veterinary Medicine

institute: Auburn University

summary: Seven early developmental stages in channel catfish, Ictalurus punctatus, were selected for transcriptome sequencing and analysis, Differential expression analysis and WGCNA approach was applied. The genes that play vital roles in embryogenesis and regulation of early development in channel catfish were detected.  Our work reveals new insights for exploring the underlying mechanisms of channel catfish early development.

overall_design: Profile of transcriptome-wide gene expression levels in seven early development stages of channel catfish

first: Xiaoli

last: Ma

first: Rex

last: Dunham


title: Obesity and Race Alter Gene Expression in Skin

city: New York

first: James

last: Krueger

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

summary: We studied differences in epithelial thickness by histology and gene expression by Affymetrix gene arrays and PCR in the skin/fat of 10 obese (BMI 35-50) and 10 normal weight (BMI 18.5-26.9) postmenopausal women paired by age and race

overall_design: Skin and fat biopsies were collected from 20 subjects  (10 obese, 10 normal wight). Biopsies were evaluated by immunohistochemical staining, and gene expression profiling with Affymetrix U133 2.0Plus arrays and RT-PCR.

first: Peter

last: Holt

middle: G

first: Sandra

last: Garcet


title: Next Generation Sequencing Facilitates Quantitative Analysis of HHSteCs and HHSteC treated rhCYGB [HSC]

status: Public on Aug 25 2020

city: Osaka

first: Le

middle: Thi Thanh

last: Thuy

address: 1-4-3 Asahimachi, Abeno-ku, Osaka 545-8585, Japan

department: Department of Hepatology

institute: Osaka City University, Graduate School of Medicine

summary:
Purpose: Hepatic stellate cells (HSCs) plays an important role in liver fibrosis. Recombinant human Cytoglobin (rhCYGB) can inhibit the activation of HSCs. The goal of this study is to investigate the rhCYGB targeted signalling pathways regulating the activation of HSCs.
Method: mRNA profiles of HHSteCs control and HHSteCs treated with rhCYGB (80 µg/ml, for 48 hour) were generated by deep sequencing.
Results: The RNA-seq data  confirmed that extracellular matrix-encoding genes and fibrosis-related genes  were down-regulated by the His-CYGB treatment. The top of up-regulated genes following His-CYGB treatment were interferon (IFN)-stimulated genes (ISGs), implying IFN signaling in His-CYGB treatment.

overall_design: mRNA profiles of HHSteCs with or without rhCYGB treatment

first: Norifumi

last: Kawada

first: Ninh

middle: Q

last: Dat


title: Next Generation Sequencing Facilitates Quantitative Analysis of Control and rhCYGB treated liver transcriptomes [TAA]

summary:
Purpose: The goal of this study is to investigate the effect of recombinant human Cytoglobin (rhCYGB) on liver fibrosis induced by TAA in mice.
Method: mRNA profiles of liver tissues from TAA-control mice and TAA-rhCYGB treated mice were generated by deep sequencing.
Results: The RNA-seq data confirmed that extracellular matrix-encoding genes and fibrosis-related genes were down-regulated by the rhCYGB treatment.

overall_design: mRNA profiles of liver tissues with or without rhCYGB treatment


title: Next Generation Sequencing Facilitates Quantitative Analysis of Control and rhCYGB treated liver transcriptomes  [DDC]

summary:
Purpose: The goal of this study is to investigate the effect of recombinant human Cytoglobin (rhCYGB) on liver fibrosis induced by DDC diet in mice.
Method: mRNA profiles of liver tissue of DDC-control mice and  liver tissue of DDC-rhCYGB treated mice treated were generated by deep sequencing.
Results: The RNA-seq data  confirmed that extracellular matrix-encoding genes and fibrosis-related genes  were down-regulated by the His-CYGB treatment.


title: Impact Of Oil Spill To Human Lung Health – Next Generation Sequencing And Mouse Model Based Analysis

city: New Orleans

first: Yao-Zhong

last: Liu

state: LA

address: 1440 Canal Street, Suite 1610

department: Biostatistics and Data Science

institute: Tulane University School of Public Health and Tropical Medicine

summary: This project addresses the question of impact of oil spills on lung health. Specifically the project will address the general hypothesis, which is upon oil/dispersant respiratory exposure there will be a higher carcinogenic potential of lung tissue.

overall_design: Wild-type C57BL/6 (B6) mice were exposed to  BP crude oil, dispersant Corexit 9500, dispersant Corexit 9527, oil + 9527, oil + 9500 and saline (as control) using intratracheal instillation method for 2 weeks. Each treatment (exposure) group contains 3 female and 3 male mice. Treatment of male and female mice were performed separately.

first: Gilbert

middle: F

last: Morris


title: KLRG1+ Memory CD8 T cells Combine Properties of Short-lived Effectors and Long-lived Memory

city: Minneapolis

first: Todd

middle: P

last: Knutson

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

summary: CD8 effector T cells with a CD127hi KLRG1- phenotype are considered precursors to the long-lived memory pool, while KLRG1+ CD127low cells are viewed as short-lived effectors. Nevertheless, we and others have shown that a KLRG1+ CD127low population persists into the memory phase and that these T cells (termed long-lived effector cells or LLEC) display robust protective function during acute re-challenge with bacteria or viruses. Whether these T cells represent a true memory population or are instead a remnant effector cell population that failed to undergo initial contraction has remained unclear. Here, we show that LLEC from mice express a distinct phenotypic and transcriptional signature that shares characteristics of both early effectors and long-lived memory cells. Furthermore, we find that LLEC are exclusively derived from day 12 KLRG1+ effector cells. Our work challenges the concept that the KLRG1+ CD127low population is dominated by short-lived cells and shows that KLRG1 downregulation is not a prerequisite to become a long-lived protective memory T cell.

overall_design: This study includes 15 samples (5 groups in triplicate) analyzed by bulk RNA sequencing. These samples consist of various splenic memory CD8 T cell subsets collected from mice 90 days post infection and analyzed. The study also includes 2 single cell RNA sequencing samples taken at day 12 and day 60 post infection. The study also includes 2 samples (no sample replicates) of splenic memory CD8 T cells captured at 12 or 60 days post infection and analyzed as a large population of single cells using scRNAseq methods.

first: Kristin

last: Renkema

first: Matthew

last: Huggins

first: Henrique

last: Borges da Silva

first: Christy

middle: M

last: Henzler

first: Sara

last: Hamilton


title: The transcriptome of WT and fun30 mutant

first: Yan

last: Zhu

address: 2005, Songhu Road

department: Biochemistry

institute: Fudan University, School of life sciences

summary: Chromatin remodeling factors utilize ATP hydrolysis to modulate chromatin dynamics, and the Fun30-subfamily members in yeast and animals are a class of well-studied remodelers implicated in diverse biological processes. However, the molecular activity of plant Fun30 orthologues and their functions in plant growth still remain obscure yet. Compared with yeast and animal orthologues, Arabidopsis Fun30 possesses conserved ATP-dependent nucleosome sliding activity but loses the CUE domain functioning as protein adapter in evolution. Fun30 gene shows a tissue-specific expression pattern in vegetative meristems and various vascular tissues, and is functionally implicated in transcriptional repression of a large number of responsive genes under uninduced conditions. We focused on the interconnected phytohormones SA/JA pathways, and proved the Fun30 recruitment and changes of local nucleosome occupancy within chromatin regions of several key signaling and effector genes in each pathway. Besides SUVR2 involved in RdDM pathway, Fun30 also interacts with non-catalytic subunits of histone deacetylase complex, and Fun30-binding proteins exert in vitro TSA-inhibited histone deacetylase activity. In fun30 mutant, we detected increased H3 acetylation level within local chromatin regions of Fun30 target genes in vivo. Intriguingly, Fun30 transcription is severely inhibited by SA treatment, which thus releases its repression on SA-induced gene during the activation of the downstream SA pathway. Meanwhile, basal transcription level and JA-induced activation of key transcription factor MYC2 gene, as well as the consequent susceptibility to necrotrophic pathogen Botrytis cinerea, are abnormally increased in Fun30-deficient plants.

overall_design:
To find out the differentially expressed genes in fun30 mutant.
RNA was extracted from 12-day-old seedlings of WT and fun30 mutant.

first: Zhu

last: Yan


first: Ann-Bin

last: Shyu

overall_design: Bromouridine-metabolic labeling pulse-chase RIP-seq approach was combined with time-course experiments to monitor mRNA decay across the transcriptome upon induced expression of a phosphomimetic mutant (S254D) of Tob2.

first: Chyi-Ying

last: Chen


title: High-throughput sequencing of OS cells treated with activated compound B5.

city: Wen Zhou

first: zhi guo

last: liu

address: Wenzhou medical university of  higher education park  chashan town

institute: Wenzhou Medical University

summary: The high-throughput sequencing technology was performed after the treatment of human osteosarcoma cells U2OS and MG63 with the active compound B5 designed and synthesized by ourselves, to explore the expression of genes related to cell adhesion, migration and invasion of human osteosarcoma cells U2OS and MG63 after the treatment of the active compound Changes to explore the effect of active compounds on the motility of osteosarcoma cells.

overall_design: Human osteosarcoma cells U2OS and MG63 was treated with active compound B5 at the concentration of 10μM for 48 hours.

first: Zhiguo

first: Xiaojing


title: Nitrogen-reponsive transcriptome of a mutant strain of Nostoc sp. PCC 7120 lacking nsiR3 (ΔnsiR3)

city: Freiburg im Breisgau

first: Manuel

last: Brenes-Álvarez

address: Schänzlestraße 1

department: Genetics and Experimental Bioinformatics

institute: University of Freiburg

summary: In order to identify possible RNAs regulated by small RNA NsiR3 we have analyzed the responses to nitrogen removal in a mutant lacking nsiR3 (ΔnsiR3). RNA samples were isolated from cells growing in the presence of combined nitrogen (ammonium) or after 8 h of nitrogen deprivation.

overall_design: Nitrogen deprivation-induced expression in Nostoc sp. PCC 7120 (ΔnsiR3 strain) was measured in cells subjected to nitrogen deprivation for 0 and 8 hours. Two different experiments were performed for each time-point.

first: Isidro

last: Álvarez-Escribano

first: Elvira

last: Olmedo-Verd

first: Jens

last: Georg

first: Wolfgang

last: Hess

first: Agustín

last: Vioque

first: Alicia

last: Muro-Pastor


title: Inhibition of Gli2 suppresses tumorigenicity in glioblastoma stem cells derived from a de novo murine brain cancer model [Agilent-028005]

city: Kyoto city

first: Seisuke

last: Tanigawa

state: Kyoto

address: 465 Kajii-cho,Kawaramachi-Hirokoji

department: Neurosurgery

institute: Kyoto prefectural university of medicine

summary: Prognosis of glioblastoma remains poor despite a great deal of research. In glioblastoma, the existence of glioblastoma stem cells (GSCs) has been shown, which are responsible for tumorigenesis, invasive capacity, and therapy resistance. One of cancer stem cell markers, Leucine-rich repeat-containing G-protein coupled receptor (Lgr5) plays a role in maintenance of GSCs, however, properties of the Lgr5 positive GSCs have not been fully understood. We applied the Sleeping-Beauty transposon-induced glioblastoma model to the Lgr5-GFP transgenic mice and sorted the GFP-positive cells from the neurosphere cultures derived from the mouse glioblastoma tissues. We found that the GFP-positive GSCs exhibited higher expression of Gli2 using a global gene expression analysis.

overall_design: To test the effect of suppression of Gli2 on the gene expression, murine GSC was tranducted with lentiviral non-target (control) or Gli2 shRNA. Gli2-knockdown GSCs were compared to control cells.

first: Mitsugu

last: Fujita

first: Chiami

last: Moyama

first: Shota

last: Ando

first: Hiromi

last: Ii

first: Yasushi

last: Kojima

first: Teruaki

last: Fujishita

first: Masahiro

last: Aoki

first: Hayato

last: Takeuchi

first: Takumi

last: Yamanaka

first: Yoshinobu

last: Takahashi

first: Naoya

last: Hashimoto

first: Susumu

last: Nakata


title: Host-pathogen interactions between Xanthomonas fragariae and its host Fragaria × ananassa investigated with a dual RNA-seq analysis

city: Wädenswil

first: Joël

last: Pothier

address: Einsiedlerstrasse 31

department: Institute of Natural Resource Sciences

institute: Zurich University of Applied Sciences (ZHAW)

summary: Strawberry is economically important and widely grown but susceptible to a large variety of phytopathogenic organisms. Among them, Xanthomonas fragariae is a quarantine bacterial pathogen threatening strawberry productions by causing angular leaf spots. Using whole transcriptome sequencing, gene expression of both plant and bacteria in planta was analyzed at two time points, 12- and 29-days post inoculation, in order to compare pathogen and host response between the stages of early visible and of well-developed symptoms. Among 28’588 known genes in strawberry and 4’046 known genes in X. fragariae expressed at both time points, a total of 361 plant and 144 bacterial genes were significantly differentially expressed, respectively. The identified higher expressed genes in the plants were pathogen-associated molecular pattern receptors and pathogenesis related thaumatin encoding genes, whereas the more expressed early genes were related to chloroplast metabolism as well as photosynthesis related coding genes. Most of X. fragariae genes involved in host interactions, recognitions and pathogenesis, were lower expressed at late-phase infection. This study gives a first insight on the interaction of X. fragariae with its host. The strawberry plant changed its metabolism consistently with the progression of infection.

overall_design: This dual RNA-seq experiment captures expression data from strawberry leaves (Fragaria × ananassa variety Elsanta) challenged by the angular leaf spot disease responsible bacterium Xanthomonas fragariae PD885(T) after 12- and 29- days post inoculation by spraying foliar part of the plants. Three replicates per time point were sequenced but two outlier replicates were retained after reproducibility control using a principal component analysis.

first: Michael

last: Gétaz

first: Joanna

last: Puławska

first: Theo

last: Smits


title: Attenuated lymphocyte activation leads to the development of immunotolerance on bovine fetuses persistently infected with BVDV

city: New Haven

first: Hanah

last: Georges

state: Connecticut

address: 333 Cedar St

institute: Yale University

summary:
Fetal spleens were collected at days 82 and 97 of gestation following maternal infection with BVDV on day 75 of gestation.
A microarray was performed on RNA -> cDNA of the splenic samples. Treatment groups consist of Controls (non-infected) and PI (persistently infected).

overall_design: Day 82 fetuses represent th fetal immune system before BVDV crosses the placenta while day 97 fetuses represent the fetal immune system days after BVDV infects the fetus. Control fetuses were from dams innoculated with MEM media and PI fetuses are from dams innoculated with BVDV on day 75 of gestation. Both day groups have 4 animals in the control treatment group. Day 82 PI n = 3 and day 97 PI n = 4.

first: Georges

last: Hanah

first: Hansen

last: Thomas


title: Compartment-specific transcriptomics of ozone-exposed murine lungs reveal sex- and cell type- associated perturbations relevant to mucoinflammatory lung diseases

city: Raleigh

first: Yogesh

last: Saini

state: NC

address: 1060 William Moore Dr

department: Biomedical Sciences

institute: North Carolina State University

summary: Ozone is known to cause lung injury and resident cells of the respiratory tract, i.e., epithelial cells and macrophages, respond to inhaled ozone in a variety of ways that affect their survival, morphology, and functioning. However, complete understanding of sex-associated and cell type-specific gene expression changes in response to ozone exposure is still limited. Through transcriptome profiling, we aimed to analyze gene expression alterations and biological pathways enrichment in three distinct cell type-enriched compartments of ozone-exposed murine lungs. We chronically exposed adult males and females to 0.8ppm ozone or filtered air.  RNA-Seq was performed on airway epithelium-enriched airways, parenchyma, and purified airspace macrophages. Differential gene expression and biological pathway analyses were performed and supported by cellular and immunohistochemical analyses. While majority of differentially expressed genes (DEGs) in ozone-exposed versus air-exposed groups were common between both sexes, sex-specific DEGs were also identified in all the three tissue compartments. As compared to ozone-exposed males, ozone-exposed females had significant alterations in gene expression in three compartments. Pathways relevant to cell division and DNA repair were enriched in the ozone-exposed airways indicating ozone-induced airway injury and repair which was further supported by immunohistochemical analyses. In addition to cell division and DNA repair pathways, inflammatory pathways were also enriched within the parenchyma supporting contribution by both epithelial and immune cells. Finally, immune response and cytokine-cytokine receptor interactions were enriched in macrophages, indicating ozone-induced macrophage activation. Lastly, our analyses also revealed the overall upregulation of mucoinflammation and mucous cell metaplasia-associated pathways.