title: H3K27me3 deposition over sarcomeric and cytoskeletal promoters is required for cardiomyocyte cytokinesis and wound invasion during zebrafish heart regeneration [RNA-seq]

summary: We identify the global transcriptional changes that occur between homeostatic and proliferative cardiomyocytes in the zebrafish heart and uncover an essential role for H3K27me3 deposition in facilitating successful myocardial regeneration.  Specifically, we learned that cardiomyocyte proliferation is accompanied by downregulation of sarcomeric and cytoskeletal components and upregulation of the polycomb methylase Ezh2. Using ChIPseq, we demonstrate that this transcriptional repression is associated with deposition of new H3K27me3 modifications over the promoters. Using new genetic zebrafish lines that allow for inducible and cardiomyocyte-specific expression of a mutant form of histone 3 that is unable to be tri-methylated on lysine 27 (H3.3K27M), we discovered that addition of H3K27me3 marks is essential for cardiac regeneration in vivo. Earlier in the regenerative window, we found that H3.3K27M–expressing wound edge cardiomyocytes aberrantly maintain homeostatic levels of sarcomeric and actomyosin gene expression and show significant retention of sarcomere structure. While DNA replication occurs normally in these H3.3K27M cardiomyocytes, we observed significant increases in cardiomyocyte nucleation, a phenotype indicative of cytokinesis failures. In addition, nuclear density at the wound edge increases as new cardiomyocytes fail to colonize the injured area. Together, our study reveals that production of new cardiomyocytes and their infiltration into the injured region relies on H3K27me3-mediated sarcomeric and actomyosin cytoskeletal gene repression.

overall_design: Transcriptional profiling (RNA-seq) of regenerting versus uninjured FACS-purified cardiomyocytes from zebrafish ventricle apexes in triplicates


title: The C. elegans ortholog of human selenium binding protein 1 is a pro-aging factor protecting against selenite toxicity

status: Public on Sep 16 2019

city: Jena

first: Philipp

last: Koch

address: Beutenbergstraße 11

department: Core Facility Life Science Computing

country: Germany

institute: Leibniz Institute on Aging - Fritz Lipmann Institute

type: Expression profiling by high throughput sequencing

summary: Y37A1B.5, a SELENBP1 ortholog in C. elegans  modulates lifespan and stress resistance. Hence transcriptome profiling (RNA-seq) after depletion of  Y37A1B.5 via RNAi was performed, aiming to identify targets that would explain these effects.

overall_design: We compared RNAi treatment of Y37A1B.5 for five days to control vector treatment for five days in wildtype worms.

first: Karl

last: Köhnlein

first: Marco

last: Groth


title: Single cell sequencing of de-differentiated dermal adipocytes

city: Wuhan

first: Zhuzhen

last: Zhang

state: Hubei

address: 6015Shengke Building, College of life sciences, 299 Bayi Road, Wuchang

department: Biochemistry

country: China

institute: Wuhan University

summary:
Purpose: The goals of this study are to compare the de-differentiated dermal adipocytes with normal skin fibroblasts.
Methods: Library prepared followed by 10X Genomics standard protocol. Transcriptome was generated by high throughput sequencing.

overall_design: We previously derived a doxycycline-inducible (Tet-On) lineage-tracing model that allows for the indelible labeling of Adiponectin-expressing adipocytes (Adiponectin-rtTA; TRE-Cre; Rosa26RmT/mG; herein, Adipose Chaser mice). Prior to exposing animals to doxycycline, all cells express membrane tdTomato from the Rosa26 locus. Dermal adipose shows high plasticity. They display dynamic changes in volume and cell numbers in synchrony with hair cycling. But, no obvious apoptosis was reported during the recession of dermal adipose tissue. We set out to test the hypothesis that whether dermal adipose tissue undergo de-differentiation during the recession of dermal adipose tissue, and the difference between de-differentiated adipocytes and normal skin fibroblasts. Following the exposure to doxycycline-containing chow diet, Cre-mediated excision of the loxP-flanked tdTomato cassette occurs in Adiponectin-expressing (P28-P35) cells, and membrane-bound GFP (mGFP) expression is constitutively activated in adipocytes. Therefore, we labeled the pre-existing dermal adipocytes with GFP following doxycycline-containing chow diet during the second anagen when dermal fat have the most large volume. Next, we collected single cell suspension from skin at the pro-longed second telogen when dermal adipose tissue have most strong recession (P56-P63). FACS sorted CD31-CD45-Pdgfra+GFP- and CD31-CD45-Pdgfra+GFP+ cells were collected. CD31-CD45-Pdgfra+GFP- and CD31-CD45-Pdgfra+GFP+ cells were mixed together with the ratio of 1:1, approximately 7000 cells per group. To this end, we performed single cell RNA-sequencing of CD31-CD45-Pdgfra+GFP- and CD31-CD45-Pdgfra+GFP+ cells.

middle: E

last: Scherer

first: Mengle

last: Shao

first: Ashwani

last: Kumar


title: The circadian transcriptome of mouse CD8+ T cells

city: Montreal

first: Nicolas

last: Cermakian

state: QC

address: 6875 LaSalle blvd

department: Douglas Institute Research Centre

country: Canada

institute: McGill University

summary: To address the T cell-intrinsic rhythms underlying circadian variations of their functions, we analyzed gene expression rhythms in mouse CD8+ T cells. To do this, we entrained 8 weeks old male C57BL/6J mice for at least 2 weeks in a light:dark cycle, then put them in constant darkness (DD). Mice were sacrificed every 4 h over 48 h, on the second and third day in DD, and brachial, axillary and inguinal lymph nodes (LNs) were harvested. For each of the 12 time points, LNs from 6 mice were pooled. CD8+ T cells were isolated using EasySepTM mouse CD8a positive selection kit (STEMCELL technologies). The purity of the CD8 T cells was between 95.6 and 98.9% in all samples. Total RNA was extracted and RNA sequencing performed. Subsequent analysis aimed to identify transcript that show significant rhythmicity.

overall_design: CD8+ T cells from 8 weeks old male C57BL/6J mice sacrificed at 12 circadian times over 2 days in constant darkness

first: Nathalie

last: Labrecque

first: Chloé

middle: C

last: Nobis

first: Geneviève

last: Dubeau Laramée


title: Gill transcriptomic analysis in fast- and slow-growing individuals of the mussel Mytilus galloprovincialis reared under a daily air exposure regime

status: Public on Sep 15 2019

city: Leioa

first: Daniel

last: Prieto

address: Barrio Sarriena s/n

country: Spain

institute: University of the Basque Country

summary: Gill transcriptome of fast- and slow-growing mussels reared under continuous food supply was recently analysed in order to ascertain the differential gene expression underlying interindividual differences in growth rate. The present study aims to analyse the gene expression differences between fast- and slow-growing mussels submitted to an air exposure of 8 hours a day during the rearing period. Transcriptome will be also compared with their continuously submerged counterparts in order to analyse the effect of air exposure on the gene expression of fast- and slow-growing individuals.

overall_design: The gene expression in gill tissues of mussel (Mytilus galloprovincialis) specimens that were selected as fast- and slow-growers after rearing them for seven months in the laboratory under a daily air exposure regime was analysed. The gene expression was measured in 8 samples, representing 2 different experimental groups of the mussel Mytilus galloprovincialis. Thus, 4 samples per experimental groups were analysed. Each sample was a pool of 5 individuals.

first: Pablo

last: Markaide

first: Iñaki

last: Urrutxurtu

first: Enrique

last: Navarro

first: Sebastien

last: Artigaud

first: Elodie

last: Fleury

first: Irrintzi

last: Ibarrola

first: Miren

middle: B

last: Urrutia


title: Transcriptomic analysis of human extravillous trophoblast cells (HTR8/Svneo) cultured as 3D spheroids and 2D monolayers

city: Hamilton

first: Michael

last: Wong

state: Ontario

address: 1200 Main Street West, Health Sciences Building

institute: McMaster University

summary: The current objectives are to develop a 3D spheroid model that will allow us to better emulate placental invasion in vitro and to characterize the transcriptomic and functional outcomes.

overall_design: 200 ng of RNA was processed to assess 20,000+ genes using the Clarion S Human microarray (Thermo Fisher) and GeneChip™ 3000 instrument system (Thermo Fisher), all carried out at the SickKids TCAG Microarray facility. There are four biological replicates per group, and two groups in total (3D vs. 2D). Normalization and output file generation was performed with Affymetrix Gene Expression Console (Thermo) using the Robust Multi-Chip Analysis (RMA) algorithm [RMA-Gene-full].

middle: K

first: Mishquatul

last: Wahed

first: Sarah

middle: A

last: Shawky

first: Sandeep

last: Raha


title: The effect of talc on J774 cells

city: Providence

first: Alexey

middle: V

last: Fedulov

state: Rhode Island

address: 593 Eddy St.

department: RIH / Surgical Research

country: USA

institute: Alpert Medical School of Brown University

summary: The experiment tests the hypothesis that talc particles affect the trasncriptome of phagocytosing cells.

overall_design: Macrophages were plated and exposed to 10 µg/well of particles (talc (T) or titanium dioxide (Ti)) and 2 µg/mL of 17-β estradiol (E) or vehicle. After 24 hours of particle and estrogen treatment, the RNA was extracted through a RNeasy Mini Kit (Qiagen).

first: Loreilys

last: Mejías Rivera


title: Transcriptome sequencing of purified dermal adipocytes and inguinal adipocytes

first: Zhuzhen

last: Zhang

summary:
Purpose: The goals of this study are to compare the transcription difference between purified dermal adipocytes and inguinal adipocytes
Methods: Transcriptome of purified dermal adipocytes and inguinal adipocytes were generated by deep sequencing, using Illumina Hiseq 2500 v3 sequencing system.

overall_design: Dorsal skin and inguinal fat tissues from P30 (when there are more dermal fat) mice were harvested, and then digested the tissue to get pure mature adipocytes. RNA are extracted from the tissues for whole transcriptome RNA-seq

first: Philipp

last: Scherer


title: Genetic Evidence for Asymmetric Blocking of Higher-Order Chromatin Structure by CTCF/Cohesin

city: Shanghai

first: Jia

last: Shou

state: Shanghai

address: 800 Dongchuan Rd

department: Institute of Systems Biomedicine

institute: Shanghai Jiao Tong University

summary: The architectural protein CTCF binds to mammalian insulators genome wide with directionality and recruits cohesin to mediate oriented long-distance chromatin loops. In many cases, CTCF-binding sites (CBSs) are associated with distal enhancers and target promoters. It is generally thought that CTCF binding results in spatial contacts between distal enhancers and target promoters leading to activation of specific promoters. However, how CTCF orchestrates higher-order chromatin organization to regulate gene expression is not fully understood. Here we used CRISPR DNA-fragment editing to investigate the roles of CTCF in chromatin organization of the clustered protocadherin (Pcdh) genes, which is an ideal model system with repertoires of CBSs in variable promoters and super-enhancers. We found that the CBSs at chromatin domain boundary and even single CBSs could determine the orientation of long-distance chromatin looping. In addition, deletion or inversion of large regions containing tandem CBS arrays in mice demonstrated asymmetric influences on chromatin looping between super-enhancers and target promoters. These genetic data have important implications on the assembly mechanisms of higher-order chromatin structures.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: circularized chromosome conformation capture (4C) experiments

first: Yujia

last: Lu

first: Qiang

last: Wu


title: Introducing a new pre-clinical rat model of advanced NASH by combining carbon tetrachloride with high fat & cholesterol diet

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

summary: NASH is a severe form of NAFLD that can progress to cirrhosis and hepatocellular carcinoma and, its incidence has markedly increased in recent years. Current available animal models fail to reflect the whole spectrum of the disease. We herein designed a Barcelona NASH (BarNa) rat model using the combination of high fat & cholesterol diet with CCl4 inhalation for 10 weeks (NASH) or 24 weeks (NASH-CH). This model reflects the full spectrum of human NASH and present the main characteristics of the disease including: steatosis and metabolic syndrome, lipotoxicity, cellular death, inflammation, hepatic fibrosis and portal hypertension. Moreover, the molecular signature of the BarNa model shared the most important pathways involved in the pathophysiology of the human disease.

overall_design: We analyze the whole hepatic transcriptome of wistar rats from three different groups: control, NASH (10 weeks of CCl4+ HF&HCD) or NASH-CH (24 weeks of CCl4+ HF&HCD). N=6 each group.

first: R

last: Maeso-Diaz

first: J

middle: J

last: Gracia-Sancho


title: Coding and Non-coding gene expression signatures of endometrium from Polycystic Ovary Syndrome Patients

status: Public on Sep 13 2019

first: Jieying

last: Xu

address: 845 Lingshan Road

department: Renji Hospital, School of medicine

institute: Shanghai Jiao Tong university

summary: Polycystic ovary syndrome (PCOS), one of the most common endocrinal diseases among reproductive-aged women, is characterized by hyperandrogenemia, chronic oligo/anovulation and polycystic ovarian morphology. In this research, we presented microarrays to identify the differential expressed protein-coding genes and lncRNAs expression profile in the endometrium during the window of implantation between the PCOS and healthy subjects.

overall_design: The endometrium samples were collected during the window of implantation from normal and PCOS woman undergoing IVF or ICSI. RNA was extracted and hybridized to microarray screening of non-coding RNAs and mRNAs.

first: Jun

last: Zhao

first: Zi-Jiang

last: Chen

first: Yanzhi

last: Du


title: Transcriptome of amniotic fluid in vervet monkey

city: Pittsburgh

first: Anna

last: Jasinska

state: PA

address: 3550 Terrace Street

department: School of Medicine

institute: University of Pittsburgh

summary: Transcriptomic profiling is a crucial tool for understanding growth, development, behavior and predisposition to diseases and the development of health biomarkers. Here, we demonstrate the feasibility of transcriptomic assessment of cell-free fetal RNA in vervet monkey amniotic fluid supernatant (AFS).

overall_design: We conducted transcriptomic assessment of cell-free fetal RNA in vervet monkey amniotic fluid supernatant usign RNAseq

first: Dalar

last: Rostamian

first: Ashley

middle: T

last: Davis

first: Kylie

last: Kavanagh


title: An XRE-superfamily transcriptional regulator XrpA controls low pH tolerance of Serratia marcescens

city: WuXi

first: Changhao

last: Sun

address: LI lake avenue 1900

institute: Jiangnan University

summary: The acid tolerance of industrial strains is a significant challenge in the fermentation process. The bacterium Serratia marcescens is part of the Enterobacteriaceae family of eubacteria, which is a potential industrial microorganism. However, the molecular mechanism behind S. marcescens acid resistance is not properly understood. In this study, we screened for novel regulators that respond to acidic conditions by a Tn5G transposon insertion mutagenesis of S. marcescens and found mutations in a gene encoding for the HTH_XRE super-family regulatory protein member, here named xrpA. Using transcriptomics and further experiments, we showed that the xrpA disruption conferred pleiotropic phenotype changes, including highly decreased biomass, altered cell shape, H+-ATPase activity, and deficiency of cell membrane permeability and integrity, compared with those of the parent (JNB5-1) strain at low pH. These data revealed that the molecular mechanism by which xrpA affects acid resistance of S. marcescens is through positive regulation of cell membrane permeability, integrity, and H+-ATPase activity to maintain intracellular homeostasis at low pH. Finally, we constructed an acidic resistant strain JNB5-1/pSX1314 by overexpression of xrpA in S. marcescens and found that its ability to produce prodigiosin by fermentation increased by 21.74% compared with that of parent strain at pH4.0. These results indicated that xrpA regulates tolerance to low pH by transcriptional regulation of acid stress response genes to maintain cell membrane function in S. marcescens.

overall_design: Global transcription level of S. marcescens parent strain (JNB5-1) and mutant strant (SX1-25)

first: Xuewei

last: Pan


title: Integrative analysis from the epigenome to translatome uncovers patterns of dominant nuclear regulation during transient stress

city: La Jolla

first: Travis

middle: Andrew

last: Lee

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Background: The regulation of gene activity in response to energy availability is an universal phenomenon. When molecular oxygen is limited the production of ATP is inefficient and growth is curtailed. The plant Arabidopsis thaliana rapidly responds to oxygen deprivation (hypoxia) by elevating the abundance of ~50 hypoxia-responsive gene (HRG) transcripts that are prioritized for translation. Many other cellular mRNAs are sequestered in ribonucleoprotein complexes and not translated during hypoxia, including those encoding ribosomal proteins (RPs). Little is known of the effect of hypoxia on nuclear regulatory processes including histone modifications, chromatin accessibility, RNA polymerase II (RNAPII) engagement and nascent transcript production. Here we apply genomic technologies to evaluate epigenetic and transcriptional regulation in response to hypoxia.

Results: Hypoxia-induced dynamics in eight chromatin readouts were contrasted to the nuclear, polyadenylated and ribosome-associated mRNAs of Arabidopsis seedlings. This identified patterns of regulatory variation of gene cohorts including the HRGs and RPs. HRGs were characterized by increased chromatin accessibility in their promoters, as well as eviction of the Histone 2A.Z variant, elevation of Histone 3-lysine 9 acetylation, and engagement of RNAPII-Ser2P active in elongation. Following short term stress, over half of the HRGs promoters were bound by the Ethylene Responsive Factor group VII transcription factor, HYPOXIA-RESPONSIVE ERF 2 (HRE2), encoded by an HRG.  Prolonged stress maintained  RP transcription, accompanied by elevated Histone 3-lysine 14 acetylation (H3K14ac) and nuclear RNA retention. The stress-induced activation of genes associated with heat stress was distinct from the HRGs. These had high RNAPII-Ser2P engagement and nuclear accumulation after short term hypoxia without accumulation of higher levels of polyA RNA. These more progressively upregulated genes were enriched for cis-elements recognized by HEAT SHOCK FACTOR transcriptional activators and had more 5' biased histone marks on their gene bodies They had less H2A.Z eviction, Histone 3-lysine 4 trimethylation and H3K9ac than genes with promoters bound by HRE2 and coordinately upregulated from RNAPII-Ser2P engagement to translation. Genes associated with the circadian cycle, photosynthesis and development were also temporally regulated by hypoxia.

Conclusions: Hypoxic stress triggers dynamic epigenetic and transcriptional regulatory variations that differentiate rapid versus more progressive activation of stress-gene transcripts that are destined for translation. Growth-associated genes continue to be transcribed but their nascent transcripts are retained in the nucleus.

overall_design:
Examination of four histone modifications, one histone variant, chromatin accessibility, RNAP Ser2P association, nuclear RNA, poly(A)+ RNA, and TRAP-RNA in control and hypoxia stressed Arabidopsis seelings.  RNA-seq based data was performed in triplicate.  ChIP-seq and ATAC-seq data were performed in duplicate.  In total: 17 ChIP-seq, 4 ATAC-seq, 4 nRNA-seq, 4 poly(A)+ mRNA-seq, and 2 TRAP-seq datasets were generated

Condition - All initated at Zeitgeber time 16 (end of light cycle)
2h non-stress - 2NS - harvest after 2h darkness
2h hypoxic stress - 2HS - harvest after 2h darkness and hypoxia
9h non-stress - 9NS - harvest after 9h darkness
9h hypoxic stress - 9HS- harvest after 9h darkness and hypoxia
2h hypoxic stress + 1h reoxygenation - 1R - harvest after 2h darkness and hypoxia followed by 1h reoxygenation
2h hypoxic stress + 2h reoxygenation - 2R - harvest after 2h darkness and hypoxia followed by 2h reoxygenation
HRE2 ChIP- 2HS - harvest after 2h darkness and hypoxia

first: Julia

last: Bailey-Serres


title: Differential gene expression between human colon cancers and the adjacent nomral colon tissues.

city: Piscataway

first: Hong

last: Wang

state: NJ

address: 164 Frelinghuysen

department: Chemical Biology

institute: Rutgers the State Univesrity of New Jersey

summary: We reported the gene expression profiles of 9 human colon cancer samples and their matching adjacent normal tissues.

overall_design: Total RNA samples were extracted from 9 de-identified fresh frozen human colon cancer samples and their adjacent normal colon tissues.  RNA-sequencing were completed by BGI (US) using BGISEQ platform for Eukaryotic Transcriptomeresequencing.

first: Chung

middle: S

last: Yang


title: Gene expression profiles of mouse colitis epithelial tissues induced by DSS or DSS/PhIP

status: Public on Sep 14 2019

summary: We reported the gene expression profiles of hCYP1A mouse colitis epithelial tissues on Day 1, 3 and 7 after the treatment with DSS or DSS/PhIP for 5 days.

overall_design: Total RNA samples were extracted from mouse  colon epithelial tissues scripped from the colon of hCYP1A mice treated with 1.5% DSS in the drinking water for 5 days or control mice.  While one groups of mice, DSS-treated,  were treated with DSS only, the other groups, PhIP/DSS-treated were treated with dietary carcinogen PhIP a week before the DSS treatment.  RNA-sequencing were completed by BGI (US).


title: Regulation of stem cell property and drug resistance of cancer cells by targeting transcriptional machinery via inhibition of neddylation

city: Chongqing

first: Chuanming

last: Xie

state: Chongqing

address: 30 Gaotanyan Rd

department: Institute of Hepatobiliary Surgery

institute: Southwest Hospital

summary: MLN4924, also known as pevonedistat, is a small molecule inhibitor of NEDD8 activating enzyme (NAE), that inhibits the entire neddylation pathway. As the first-in-class neddylation inhibitor, MLN4924 is currently in Phase I/II clinical trials for anticancer application as a single agent or in combination with chemotherapeutic drugs. MLN4924 has shown impressive anticancer activity by inactivating Cullin-RING ligases (CRLs) to cause accumulation of tumor suppressor substrates.  Whether MLN4924 regulates the RNA expression by modulating the levels of transcription factor/repressor remain elusive.  In this study, we treated A549 lung cancer cells with MLN4924 at 0.25 or 0.5 µM for 8 or 24 hrs, respectively, followed by RNAseq analysis.  Here we found that MLN4924 significantly decreases the SOX2 mRNA level.  The mechanistic study revealed that MLN4924 inhibits FBXW2 E3 to cause MSX2 accumulation, which in turn transcriptionally represses SOX2, leading to suppression of stem cell property and sensitization of cancer cells to tamoxifen.

overall_design: Transcriptome analysis was performed in A549 cells after MLN4924 treatment for 8 or 24 hrs (6 groups, n=2 per group).

first: Chuan-Ming

first: Yi


title: Inducible degradation of Sros1 promotes IFN-γ-activated macrophage innate response by stabilizing STAT1 mRNA

city: Tianjin

first: Henan

last: XU

address: No.94 Weijin Road

department: immunology

institute: Nankai University

summary: To identify new target genes of miR-1, the affinity based purification experiments of mouse mRNAs using biotin-labeled miR-1 as probes was performed in peritoneal macorphages. Enriched RNAs and input samples were then subjected to RNA sequencing using an Illumina platform.

overall_design: To de novo explore miR-1 target genes in peritnoeal macrophage cells, we performed a modified miRIP protocol  using biotin-labeled miR-1 as oligo nucleotide probes to in vivo affinity purify the genes using nucleic acid hybridization and use Illumina Next Generation Sequencing  assay to identify the associated RNAs.

first: Xuetao

last: CAO


title: Expression data from  wild-type and Robo2 homozygous kidneys

status: Public on Sep 12 2019

city: Beijing

first: Qinggang

last: Li

state: Outside the United States or Canada

address: 28 Fuxing Road,Haidian District

institute: Chinese PLA General Hospital

summary: We used microarrays to detail the global gene expression in tissues from  wild-type and Robo2 homozygous kidneys.

overall_design: Tissues from E17 wild-type and Robo2 homozygous kidneys were for RNA extraction and hybridization on Affymetrix microarrays.

first: Qinnggang


title: RNA sequencing for lncRNA, miRNA and mRNA expression analysis in human laryngeal cancer

city: Guangzhou

first: kexing

last: Lyu

state: Guangdong

address: 58 Zhongzhan Road II, Yuexiu Distict

department: Otorhinolaryngology

institute: Sun Yat-sen University

type: Non-coding RNA profiling by high throughput sequencing

summary: Accumulating evidence indicates that long noncoding RNAs can interact with microRNAs to regulate target mRNAs through competing interactions. However, this mechanism remains largely unexplored in laryngeal squamous cell carcinoma. In this study, transcriptome-wide RNA sequencing in 3 pairs of laryngeal squamous cell carcinoma tissues and adjacent normal tissues was performed to investigate the expression profiles of lncRNAs, miRNAs and mRNAs.

overall_design: 3 laryngeal squamous cell carcinoma tissues and 3 related adjacent normal tissues

first: Kexing

first: Yun

first: Wenbin

last: Lei

first: Yang

last: Xu


title: Identification of Key HIF-1α Target Genes that Regulate Adaptation to Hypoxic Conditions in Tibetan Chicken Embryos

first: Ying

last: Zhang

address: Haidian District, Yuanmingyuan West Road 2

institute: China Agricultural University

summary:
Background: Tibetan chicken, a unique plateau breed, has a suite of adaptive features that enable it to tolerate the high-altitude hypoxic environment. HIF‐1α (hypoxia inducible factor 1 subunit alpha) is a crucial mediator of the cellular response to hypoxia. HIF‐1α maintains oxygen homeostasis by inducing glycolysis, erythropoiesis, and angiogenesis; however, the target genes involved in adaptive responses to hypoxia in animals and birds of plateaus are still unclear.
Results: We used ChIP-seq to map HIF‐1α binding regions in chorioallantoic membrane (CAM) tissue of chicken embryos, and identified 752 HIF-1α target genes (TG), of which 112 were differentially expressed target genes (DTGs) between the two breeds. We found that eight genes (PTK2, GPNMB, CALD1, SLC25A1, SPRY2, NUPL2, RANBPL, and CBWD1) play important roles in hypoxic adaption by regulating blood vessel development, energy metabolism through angiogenesis, vascular smooth muscle contraction, and various hypoxia-related signaling pathways (including VEGF and MAPK) in Tibetan chickens during embryonic development.
Conclusions: This study enhances our understanding of the molecular mechanisms of hypoxic adaptation in Tibetan chickens and provides new insights into adaptation to hypoxia in humans and other species living at high altitude.

overall_design: Chorioallantoic membrane (CAM) of embryos profiles of 11-day-old Tibetan chickens (TCs) and Chahua chickens (CHs) were generated by deep sequencing, using Illumina HiSeq 2500 platform.

first: Hongliang

first: Bo

first: Yao

last: Ling

first: Hao


title: UMI-count modeling and differential expression analysis for single-cell RNA sequencing

city: Birmingham

first: Changde

last: Cheng

state: AL

address: 1824 6th Ave S, Wallace Tumor Institute 520A

department: Medicine

institute: University of Alabama at Birmingham

summary: Single cell RNA-seq of the human alveolar rhabdomyosarcoma cell line Rh41.

overall_design: Single cell RNA-seq of the human alveolar rhabdomyosarcoma cell line Rh41 using the 10x Genomics.

first: John

last: Easton

first: Xiang

last: Chen


title: Lgr5 and Col22a1 mark progenitor cells in the lineage toward juvenile articular chondrocytes

city: Pok Fu Lam

first: Peikai

address: Sassoon Road 5

department: Faculty of Medicine

country: Hong Kong

institute: The University of Hong Kong

summary: The synovial joint forms from a pool of progenitor cells in the interzone region of the future joint. Expression of Gdf5 and Wnt9a has been used to mark the earliest cellular processes in the formation of the interzone and the progenitor cells. However, progression and lineage specification toward the different tissues of the joint is not well understood. Here, by lineage tracing studies we identify a population of Lgr5+ interzone cells that contribute to the formation of cruciate ligaments, synovial membrane and articular chondrocytes of the joint. This is supported by single cell transcriptome analyses. Furthermore, we showed that Col22a1, a marker of early articular chondrocytes, co-expresses with Lgr5+ cells prior to cavitation as an important lineage marker specifying the progression towards articular chondrocytes. Lgr5+ cells contribute to the repair of a joint defect with the re-establishment of Col22a1 containing superficial layer.

overall_design: Knee joint and surrounding tissue was obtained from E14.5 Lgr5GPF/+  (https://www.jax.org/strain/008875) embryos and digested with enzyme for 10x genomics single cell analysis

first: Wilson

last: Chan

first: Yan

last: Lam

first: Danny


title: Myceliophthora thermophila Xyr1 is predominantly involved in xylan degradation and xylose catabolism

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

country: Netherlands

institute: Centre of fungal biodiversity

summary: The aim of this study is to investigate the role of the transcription factor Xyr1 in the regulation of cellulolytic and xylanolytic genes of the filamantous fungus  Myceliophthora thermophila

overall_design: Transcriptome data of wild type and xyr1 mutant of Myceliophthora thermophila grown on different carbon sources (glucose, xylose, arabinose and arabinoxylan) were compared

first: Ana

last: dos Santos Gomes

first: Evy

last: Battaglia

first: Daniel

last: Falkoski

first: Maira

middle: N

last: de Almeida

first: Caroline

last: Michielse

first: Nancy

last: Linares

first: Mao

last: Peng

first: Jaap

last: Visser

middle: P


title: Transcriptome-wide identification of splicing defects upon XAB2 knockdown

status: Public on Sep 23 2019

city: Dalian

first: Shuai

last: Hou

state: Liaoning

address: lvshun south road no.9

department: cancer stem cell institute

institute: Dalian Medical University

summary: We performed RNA-seq to determine the impact of XAB2 depletion on global splicing. The results show that XAB2 depletion using two different siRNAs led to a wide range of splicing defects, with more than 50% events were intron retention.

overall_design: HeLa cells were transfected with control or XAB2 siRNA for 48 h. Total RNA was then purified using TRIzol, treated with DNase I and Ribo-Zero rRNA Removal kit to generate sequencing libraries, and subjected to strand-specific paired-end RNA-seq analyses using Illumina Hiseq X Ten platform by Novogene company (China). We used junction usage model (JUM) program to identify XAB2-regulated differential alternative pre-mRNA splicing events.

first: Haixin

last: Lei


title: Transcriptomic analysis of induced sputum samples in severe asthma

city: New Lambton Heights

first: Katie

last: Baines

state: NSW

address: Lot 1 Kookaburra Circuit

department: Respiratory and Sleep Medicine

country: Australia

institute: University of Newcastle

summary: Gene expression profiles were generated from induced sputum samples in asthma and healthy controls. The study identified differential gene expression and pathways in severe asthma.

overall_design: Cross-sectional study investigating differential gene and pathway expression in severe asthma compared to non-severe asthma (controlled and uncontrolled) and healthy controls.

first: Katherine

first: Michael

last: Fricker

first: Vanessa

middle: M

last: McDonald

first: Jodie

middle: L

last: Simpson

first: Lisa

middle: G

last: Wood

first: Peter

last: Wark

first: Heather

last: Macdonald

first: Andrew

last: Reid

last: Gibson


title: Gene expression profiles in the PhIP/DSS-induced mouse colon tumors and the adjacent normal epithelium controls

first: Hong

last: Wang

summary: Differentially expressed genes in the PhIP/DSS-induced mouse colon tumors were identified through the mRNA expression profiles of the tumors and the matching controls using the mouse exonic evidence based oligonucleotide (MEEBO) microarray.

overall_design: The study includes 7 PhIP/DSS-induced colon tumors collected from 3 individual humanized CYP1A mice in order to identify the differentially expresssed genes in the tumors.

first: Chung

last: Yang


title: Analysis of differentially expressed genes between control and shTAK1 pancreatic cancer cells

city: Verona

first: Davide

last: Melisi

address: P.le LA Scuro 10

country: Italy

institute: University of Verona

summary: We compared gene expression profiles in Panc-1, AsPC1 and MDA-Panc28 pancreatic cancer cell lines stably expressing shControl or shTAK1 by microarray analysis in order to identify groups of genes associated with a specific signaling pathway or biological process

overall_design: Three pancreatic cancer cell lines stably expressing shControl (Panc-1 GFP, AsPC-1 GFP, MDA-Panc28 GFP) and three pancreatic cancer cell lines stably expressing shTAK1 (Panc-1 shTAK1, AsPC-1 shTAK1, MDA-Panc28 shTAK1) constructs. Total RNA was extracted from subconfluent cells using Trizol reagent.

first: Federica

last: Di Nicolantonio


title: A prostate cancer chromatin interaction map

city: Los Angeles

first: Suhn

last: Rhie

address: 1450 Biggy Street NRT 3504

department: Biochemistry and Molecular Medicine

institute: University of Southern California

summary:
A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome

Prostate cancer (PCa) is the leading cancer among men in the United States. To understand gene regulation in 3D, chromatin interactions in prostate cancer cell is measured using in situ Hi-C.
To better understand the impact of chromatin structure on regulation of the prostate cancer transcriptome, we developed high-resolution chromatin interaction maps in normal and prostate cancer cells using in situ Hi-C. By combining the in situ Hi-C data with active and repressive histone marks, CTCF binding sites, nucleosome-depleted regions, and transcriptome profiling, we identified topologically associating domains that changed in size and epigenetic states between normal and prostate cancer cells. Moreover, we identified normal and prostate cancer-specific enhancer-promoter loops and involved transcription factors. This creation of 3D epigenomic maps will enable a better understanding of prostate cancer biology and mechanisms of gene regulation.

overall_design:
Examination of prostate cancer epithelial cell 22Rv1 chromatin interactions using Hi-C
In situ Hi-C, ChIP-seq using active and repressive histone marks and CTCF binding sites, NOMe-seq for nucleosome-depleted regions, and RNA-seq for transcriptome profiling in prostate epithelial cells to characterize prostate cancer epigenomic transcriptome.

Please note that processed data was generated from all replicates and is linked to the corresponding rep1 sample records (or to Series records).

last: Perez

first: Fides

middle: D

last: Lay

first: Shannon

last: Schreiner

first: Zhifei

last: Luo

first: Peggy

last: Farnham


title: Transcriptome profiles in the spleen of the Chinese giant salamander (Andrias davidianus) challenged with Citrobacter freundii

city: luoyang

first: Xiaochan

last: Gao

state: henan

address: kaiyuan street

institute: henan university of science and technology

summary: The Chinese giant salamander (Andrias davidianus) is one of the most important ecological breeding species with distinct characteristics and is cultured in many locations throughout China. In the present study, the transcriptome of A. davidianus spleen tissue, that had challenged with Citrobacter freundii, was analyzed using Illumina sequencing technology. The result was compared to a heathy control group. After assembly and annotation, 128,540 transcripts were generated with a median length of 349 bp. Comparative expression analysis indicated 1,995 differentially expressed genes (DEGs), 812 of which were up-regulated and 1,183 were down-regulated. Furthermore, DEGs were classified into three gene ontology categories, 535 of which were annotated to 237 KEGG pathways. Finally, six immune-related DEGs involved in the immune-related pathways were randomly selected for scrutinization. This work provides valuable data for an improved understanding the defense mechanisms of A. davidianus against bacterial pathogens at the transcriptional level.

overall_design: In this study, the transcriptome of A. davidianus spleen tissue, that had challenged with Citrobacter freundii, was analyzed using Illumina sequencing technology. The result was compared to a heathy control group.Each group contained three biological replicates sample.

first: Shuhui

last: Niu

first: Yong

last: Huang

first: Jianli

last: Xiong


title: Assessment of on- and off-target effects of dSpCas9-DNMT3A and dSpCas9-TET1 fusion proteins and the impact of modulating promoter strength on the specificity of CRISPR/dCas9-based epigenetic editing tools

city: Lyon

first: Zdenko

last: Herceg

address: 25 avenue Tony Garnier CS 90627

department: EGM

country: France

institute: IARC

summary:
Inferring causal relationship between epigenetic marks and gene expression requires molecular tools which can precisely modify specific genomic regions in a living cell. In this work, we present a comprehensive, modular and extensible CRISPR/dCas9-based molecular toolbox for targeted epigenetic modulation and direct gene regulation. It features a system for expression of orthogonal dCas9 proteins fused to catalytic domains of various effectors, and includes a multi-gRNA system for targeting dCas9 orthologs to up to six loci.
This part of the study aimed to determine the impact of promoter strength on modulating on- and off-target activity of dSpCas9-DNMT3A and dSpCas9-TET1 fusion proteins.   The dSpCas9-DNMT3A N-terminal fusion was used to target IL6ST with four sgRNAs, and the dSpCas9-TET1 N-terminal fusion was used to target MGAT3 with five gRNAs. For each locus, two types of constructs were used: i) construct having both the fusion protein and the selection marker (PuroR) under the same strong, constitutive CAG promoter; ii) the fusion construct under the weak EFS promoter, while maintaining efficient selection of transfected cells with PuroR under the strong SV40 promoter. Epigenome-wide profiling was conducted using the Illumina Infinium Human MethylationEPIC Beadchip arrays to assess on- and off-target activity of the fusion proteins in transfected HEK293 cells.

overall_design: Each transfection experiment consisted of one control (Mock transfected); dSpCas9-DNMT3A fusion protein with four sgRNAs targeting IL6ST under a strong, constitutive CAG promoter;  dSpCas9-DNMT3A fusion protein with four sgRNAs targeting IL6ST under the weak EFS promoter; dSpCas9-TET1 fusion protein with five gRNAs targeting MGAT3 under the CAG promoter; and dSpCas9-TET1 fusion protein with five gRNAs targeting MGAT3 under the weak EFS promoter. Two technical replicates for each of two biological replicates were analyzed for all experimental conditions.

first: Goran

last: Josipovic

first: Vanja

last: Tadic

first: Vladimir

last: Zanki

first: Marija

last: Klasic

first: Akram

last: Ghantous

first: Felicia

last: Chung

first: Josip

last: Madunic

first: Ivona

last: Be?eheli

first: Maria

last: Boškovic

first: Aleksandar

last: Vojta

first: Vlatka

last: Zoldoš


title: The Integrator complex cleaves many nascent mRNAs to attenuate transcription

city: Philadelphia

first: Jeremy

middle: E.

last: Wilusz

address: 363 Clinical Research Building, 415 Curie Boulevard

department: Department of Biochemistry & Biophysics

institute: University of Pennsylvania Perelman School of Medicine

summary: Cellular homeostasis requires transcriptional outputs to be coordinated, and many events post transcription initiation can dictate the levels and functions of mature transcripts. To systematically identify regulators of inducible gene expression, we performed high-throughput RNAi screening of the Drosophila Metallothionein A (MtnA) promoter. This revealed that the Integrator complex, which has a well-established role in 3' end processing of small nuclear RNAs (snRNAs), attenuates MtnA transcription during copper stress. Integrator complex subunit 11 (IntS11) endonucleolytically cleaves MtnA transcripts, resulting in premature transcription termination and degradation of the nascent RNAs by the RNA exosome, a complex also identified in the screen. Using RNA-seq, we then identified >400 additional Drosophila protein-coding genes whose expression increases upon Integrator depletion. We focused on a subset of these genes and confirmed that Integrator is bound to their 5' ends and negatively regulates their transcription via IntS11 endonuclease activity. Many non-catalytic Integrator subunits, which are largely dispensable for snRNA processing, also have regulatory roles at these protein-coding genes, possibly by controlling Integrator recruitment or RNA polymerase II dynamics. Altogether, our results suggest that attenuation via Integrator cleavage limits production of many full-length mRNAs, allowing precise control of transcription outputs.

overall_design: RNAseq experiments: 3 biological replicates were generated for Control (treated with B-galactosidase [Bgal] dsRNA for 3 days) and IntS9 depletion (treated with IntS9 dsRNA for 3 days) in DL1 cells. All samples were treated with 500 μM CuSO4 for the final 14 h.

first: Deirdre

last: Tatomer

first: Nathan

last: Elrod

first: Dongming

last: Liang

first: Mei-Sheng

last: Xiao

first: Jeffrey

middle: Z

last: Jiang

first: Michael

last: Jonathan

first: Kai-Lieh

first: Eric

last: Wagner

first: Sara

last: Cherry


title: Transcriptome profiling of rice G-alpha mutant and WT in response to nitrate treatment

city: New Delhi

first: Nandula

last: Raghuram

email: raghuram98@hotmail.com, ravipathak@aol.in, pathakster@gmail.com, navjyoti.chakraborty@gmail.com

state: Delhi

address: Dwarka, Sector -16C

department: School of Biotechnology

country: India

institute: Guru Gobind Singh Indraprastha University

summary: This study reports the genome-wide transcriptional profiling of the shoots of 1 month old Gα (RGA1) mutant and wild type rice plants grown in pots and treated with or without nitrate for 90 minutes after 2-days of N-free condition

overall_design: Agilent one-color experiment, organism: Oryza sativa, Agilent Custom Rice Whole Genome 8x60k Gene expression designed by Genotypic Technology Private Limited (AMADID:048014) ,,Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Annie

last: Jangam

first: N

first: Rupan

last: Virk


title: IL-1 inhibition in systemic sclerosis skin.

city: Boston

first: Julio

middle: C

last: Mantero

state: MA

address: 72 E Concord St

department: Rheumatology

institute: Boston University School of Medicine

summary:
IL-1 has been implicated in various fibrotic diseases. This randomized, Placebo-Controlled trial we examine the effect of il1-b inhibition on skin expression.
We used microarrays to explore  gene expression changes in the Rilonacept clinical trial

overall_design: Patients with diffuse cutaneous systemic sclerosis had biopsies taken prior and post treatment.

first: Robert

last: Lafyatis


title: Patient-derived xenograft models of non-small cell lung cancer for evaluating targeted drug sensitivity and resistance

city: Kanazawa

first: Hiro

last: Takahashi

state: Ishikawa

address: Kakuma-machi

country: Japan

institute: Kanazawa University

summary:
Background: Patient-derived xenograft (PDX) models are a useful tool in cancer biology research. However, the number of lung cancer PDXs is limited
Results: In the present study, we successfully established ten PDXs, including three adenocarcinoma (AD), six squamous cell carcinoma (SQ) and one large cell carcinoma (LA), from 30 patients with non-small cell lung cancer (NSCLC) (18 AD, 10 SQ, and 2 LA), mainly in SHO mice (Crlj:SHO-PrkdcscidHrhr). Histology of SQ, advanced clinical stage (III-IV), status of lymph node metastasis (N2-3), and maximum standardized uptake value (SUVmax) ≧10 when evaluated using a delayed 18F-fluoro-2-deoxy-D-glucose positron emission tomography (FDG-PET) scan, was associated with successful PDX establishment. Histological analyses revealed that PDXs showed a histology similar to that of patients’ surgically resected tumors (SRTs), while components of the microenvironments were replaced with murine cells after several passages. Next generation sequencing and microarray analyses demonstrated that after 2 to 6 passages, PDXs preserved the majority of the somatic mutations and mRNA expressions of the corresponding SRTs. Two out of three PDXs with AD histology had EGFR mutations (L858R or exon19 deletion) and were sensitive to EGFR tyrosine kinase inhibitors (EGFR-TKIs), such as gefitinib and osimertinib. Furthermore, in one of the two PDXs with an EGFR mutation, osimertinib resistance was induced that was associated with epithelial-to-mesenchymal transition.
Conclusions: This study presented ten serially transplantable PDXs of NSCLC in SHO mice and demonstrated the use of PDXs with an EGFR mutation for analyses of EGFR-TKI resistance.

overall_design: Lung cancer mRNA profiles of from six paired samples of PDXs and SRTs were generated by deep sequencing using Illumina HiSeq 2500.

first: Kenji

last: Kita

first: Seiji

last: Yano


title: Effects of ADAADi, an inhibitor of ATP-dependent chromatin remodeller, on human transcriptome

first: Rohini

last: Muthuswami

address: Room# 333, School of Life Sciences, JNU

department: School of Life Sciences

institute: Jawaharlal Nehru University

summary: Here we report the effects of Active DNA-dependent ATPase A Domain inhibitor (ADAADi) on human transcriptome

overall_design: HeLa cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin-amphotericin cocktail at 37°C in the presence of 5% CO 2 . Cells were treated with 5mM of ADAADi and incubated for 48 hours at which cells were harvested and total RNA was purified using Trizol (Sigma Aldrich, USA). Poly(A) mRNA was purified from total RNA using NEBNext® poly(A) mRNA magnetic isolation module (Catalog # E7490S), with certain optimization in the user protocol provided by the manufacturer. RNA-seq library was prepared using 100 ng purified poly(A) mRNA using NEBNext Ultra II RNA Library Prep Kit with certain optimization in the user protocol provided by the manufacturer.

first: R

last: Rakesh

first: Saddam

last: Hussain

first: Deepa

last: Bisht

first: Upasna

middle: B

last: Chanana


title: RNA-seq with knockdown ZBTB7A and NTC control

first: Changmeng

last: Cai

state: Massachusetts

address: 100 William T. Morrissey Blvd.

institute: University of Massachusetts Boston

summary: Zinc finger and BTB domain containing transcription repressor ZBTB7A has been recently reported as a tumor suppressor who plays important functions to prevent the progression of prostate cancer. However, the chromatin activity of ZBTB7A in prostate cancer cells remain unclear. In order to identify the cistrome and transcriptome of ZBTB7A, we performed ZBTB7A ChIP-seq in VCaP cells and RNA-seq in VCaP cells transfected with siRNA targeting ZBTB7A or non-targeting control, respectively (cells were grown in full serum). By using combined ChIP-seq and RNA-seq analyses in VCaP cells, we have precisely mapped the ZBTB7A binding sites and identified a subset of genes that are directly repressed by ZBTB7A. To study the chromatin interaction of ZBTB7A with androgen receptor (AR), we also performed ChIP-seq of ZBTB7A in VCaP cells stimulated with 10 nM DHT for 4 hours versus vehicle control (cells were hormone-depleted prior to DHT stimulation). Our results show that ZBTB7A binding is increased by androgen at AR and ZBTB7A overlapping sites.

overall_design:
First, we performed ChIP-seq analyses to identify ZBTB7A binding sites in VCaP prostate cancer cells, cultured in full serum. Second, we performed RNA-seq analyses to examine genes differentially regulated by ZBTB7A in VCaP cells transfected with siRNA against non-targeting control (siNTC), or ZBTB7A (siZBTB7A), cultured in full serum. Third, we also performed ChIP-seq analyses to identify ZBTB7A chromatin binding under the influence of androgen treatment in VCaP cells treated with or without 10 nM DHT for 4 hours, cultured in hormone-depleted serum.
This Series represents the RNA-seq dataset.

first: Dong

last: Han

first: Sujun

last: Chen


title: ZBTB7A ChIP-seq under different DHT level

overall_design:
First, we performed ChIP-seq analyses to identify ZBTB7A binding sites in VCaP prostate cancer cells, cultured in full serum. Second, we performed RNA-seq analyses to examine genes differentially regulated by ZBTB7A in VCaP cells transfected with siRNA against non-targeting control (siNTC), or ZBTB7A (siZBTB7A), cultured in full serum. Third, we also performed ChIP-seq analyses to identify ZBTB7A chromatin binding under the influence of androgen treatment in VCaP cells treated with or without 10 nM DHT for 4 hours, cultured in hormone-depleted serum.
This Series represents the ChIP-seq dataset.


title: Identification of ZBTB7A cistrome and transcriptome profiles in VCaP prostate cancer cells

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

overall_design: Refer to individual Series


title: RNA-seq of the lens transition zone in control vs Pea3-depleted mouse embryonic tissue

status: Public on Sep 11 2019

city: New york

first: Xin

last: Zhang

state: New york

department: Ophthalmology

institute: Columbia University

summary: The goal of the study is to find the transcriptional targets downstream of Pea3-mediated signaling during lens development. In order to look for the potential targets, we performed laser capture microdissection of the lens epithelial tissue at embryonic day E14.5 from control embryos as well as mutant embryos containing lens-specific deletion of Pea3 transcription factors. After tissue harvest, RNA was extracted. Conversion to cDNA as well as amplification was performed by Clontech SMART-seq v4 Ultra low input RNA kit, as well as cDNA library construction was performed using Nextera XT DNA library preparation kit by core facility at Columbia university prior to RNA sequencing. After preparation of cDNA library, each sample was sequenced using Illumina platform

overall_design: For this experiment, 3 control sample and 3 mutant sample were analysed.

first: Ankur

last: Garg

first: Xinm


title: Identification of ADAR3-bound targets in U87 cells

city: Santa Cruz

first: Todd

last: Lowe

address: 1156 High Street

department: Biomolecular Engineering and Bioinformatics

institute: University of California Santa Cruz

summary: We report transcripts bound by ADAR3 through RNA immunoprecipitation of U87 cells expressing 3X-FLAG tagged ADAR3 compard to control cells

overall_design: Determining transcripts enriched for ADAR3 binding by deep sequencing 3 biological replicates of RIP-RNA from U87 cells expressing ADAR3 and control cells and total RNA from the same cells

first: Eimile

last: Oakes

first: Aidan

last: Manning

first: Heather

last: Hundley


title: Mouse placental microRNA profiling upon zearalenone exposure

city: Athens

first: Christian

last: Andersen

state: Georgia

address: 501 D.W. Brooks Dr., Physiology and Pharmacology

department: Physiology and Pharmacology

institute: University of Georgia

summary: Mycoestrogens are derived from mold and can interfere with female reproduction. Mycoestrogen zearalenone (ZEA) is a common food contaminant in levels of ppb ~ low ppm. Previously we demonstrated disrupted mouse placental development by 40 ppm ZEA diet. MicroRNAs are sensitive to xenobiotics and have been implicated in placental physiology and pathology. We hypothesized that ZEA could dysregulate microRNA expression in the mouse placenta. Gestation day 13.5 (D13.5) placentas from young mice treated with 0 ppm (control), 4 ppm, and 40 ppm ZEA diets were analyzed for microRNA profiling using microRNA array. The top 20 most highly expressed microRNAs in the D13.5 control placentas are predicated to target genes involved in important signaling pathways that are critical for maternal-fetal communications, such as protein processing in endoplasmic reticulum, endocytosis, and regulation of actin cytoskeleton. Using criteria of Log2FC ≥ 1 and Log2FC ≤ -1 (linear 2 fold change (FC)), a false discovery rate adjusted p-value ≤ 0.05, and average reading > 100 (top 20% most abundant microRNAs), R package limma identified 8 differentially expressed miRNAs (mmu-miR-133b-5p, mmu-miR-7028-5p, mmu-miR-294-3p, mmu-miR-3970, mmu-miR-20b-5p, mmu-miR-7683-3p, mmu-miR-291b-3p, mmu-miR-369-3p) in the 40 ppm ZEA group that included all 4 differentially expressed miRNAs in the 4 ppm ZEA group. Some of these differentially expressed microRNAs have been shown in vitro to have important functions in placental growth and maternal-fetal transport. These data imply roles of placental microRNAs in regulating expression of genes critical for placental function in vivo and in sensing environmental contaminants.

overall_design: D13.5 placentas from mice fed 0 ppm (control), 4 ppm, or 40 ppm zearalenone (n=4/group) were used for the array.

first: Rong

last: Li

first: Xiaoqin

last: Ye


title: Expression data from Ctrl and Cko B10 cells in steady state and anti-CD40 stimulstion for 48 h.

city: Taipei City

first: Ying-Hsiu

last: Wang

address: No.161, Sec. 6, Minquan E. Rd., Neihu Dist.

country: Taiwan

institute: National Defense Medical Center

summary: Transcriptional repressor Prdm1/Blimp1 is known to play a key role in controlling B ells differentiation and regulating IL-10 production in regulatory T cells. B10 cells is the main IL-10 producing B cells in mouse spleen. We found that B10 cells and IL-10+ B cell levels are increased in Prdm1-deficient mice. Here, we compared the gene expression profiles of B10 cells from Prdm1-deficient mice (Cko) and its control littermate mice (Ctrl) in steady state and stimulated with anti-CD40 antibody for 48 h.

overall_design: To understand the genes involved in regulating the production of IL-10 by B10 cells, sorted B10 cells were stimulated with anti-CD40 for 48 hrs.

first: I-Ying

last: Lin

first: Kuo-I


title: Control of neural daughter cell proliferation by multi-level Notch/Su(H)/E(spl)HLH signaling. (PMID: 27070787)

city: St Lucia

first: Stefan

last: Thor

state: QLD

address: Otto Bldg (81) room 620

department: School of Biomedical Sciences

institute: University of Queensland

summary:
We expressed DamID and Flag-tagged versions of E(spl)HLH-m5, -m8 and Su(H), in Drosophila embryos and analyzed their DNA-binding by DamID-seq and ChIP-seq.
The Notch pathway controls proliferation during development and in adulthood, and is frequently affected in many disorders. However, the genetic sensitivity and multi-layered transcriptional properties of the Notch pathway has made its molecular decoding challenging. Here, we address the complexity of Notch signaling with respect to proliferation, using the developing Drosophila CNS as model. We find that a Notch/Su(H)/E(spl)-HLH cascade specifically controls daughter, but not progenitor proliferation. Additionally, we find that different E(spl)-HLH genes are required in different neuroblast lineages. The Notch/Su(H)/E(spl)-HLH cascade alters daughter proliferation by regulating four key cell cycle factors: Cyclin E, String/Cdc25, E2f and Dacapo (mammalian p21CIP1/p27KIP1/p57Kip2). ChIP and DamID analysis of Su(H) and E(spl)-HLH indicates direct transcriptional regulation of the cell cycle genes, and of the Notch pathway itself. These results point to a multi-level signaling model, and may help shed light on the dichotomous proliferative role of Notch signaling in many other systems.

overall_design: DamID-seq and ChIP-seq analysis of Drosophila melanogaster embryos, at developmental stage 9-16, expressing DamID and Flag-tagged versions of E(spl)HLH-m5, -m8 and Su(H)


title: Expression data from splenic IL-10 positive and IL-10 negative B cells of C57BL/6

summary: The mechanisms in regulating the development of IL-10 producing B cells are largely unknown. To clarify which transcription factor is critical for regulation of IL-10 producing B cells, we compared the gene expression profile of IL-10 positive B cells and IL-10 negative B cells. Transcriptional repressor Prdm1/Blimp1 is known to play a key role in controlling B ells differentiation. We show a dual role for Blimp-1 in IL-10 expression in IL-10 producing B cells and plasmablasts.

overall_design: To understand the genes involved in regulating the production of Il-10 by B cells, purified splenic B cells were stimulated with LPS or anti-CD40 for 48 hrs, followed by isolation of IL-10+ B cells and IL-10− B cells.


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type, genome-edited MTOR(G4448A)-p.C1483Y, and Torin1-treated Wild type Translatomics

city: Daejeon

first: JangKeun

last: Kim

state: YuseongGu

address: South Korea, Daejeon, Yuseonggu, Guseongdong KAIST E7 7108, Biomedical Research Center

department: Biomedical Science and Engineering Interdisciplinary Program

country: South Korea

institute: KAIST

summary: We performed rigorous ribosome profiling in genome-edited cell lines with human MTOR point mutations and Torin1 treated cell lines. By obtaining about 10 million bases of sequence cells, we generated genome-wide translatome and transcriptome data of genome-edited MTOR(G4448A)-p.C1483Y and Torin1 treated cell lines

overall_design: Examination of transcriptome and translatome in 3 cell types.

first: Jeong

middle: H

last: Lee


title: The lncRNA NEAT1_1 is seemingly dispensable for normal tissue homeostasis and cancer cell growth

city: Leuven

first: Florian

last: Rambow

address: Herestraat 49 box 912

country: Belgium

institute: VIB

summary: NEAT1 is one of the most studied lncRNAs, in part because its silencing in mice causes defects in mammary gland development and corpus luteum formation and protects them from skin cancer development. Moreover, depleting NEAT1 in established cancer cell lines reduces growth and sensitizes cells to DNA damaging agents. However, NEAT1 produces two isoforms and because the short isoform, NEAT1_1, completely overlaps the 5' part of the long NEAT1_2 isoform, the respective contributions of each of the isoforms to these phenotypes has remained unclear. Whereas NEAT1_1 is highly expressed in most tissues, NEAT1_2 is the central architectural component of paraspeckles, which are nuclear bodies that assemble in specific tissues and cells exposed to various forms of stress.  Using dual RNA-FISH to detect both NEAT1_1 outside of paraspeckles and NEAT1_2/NEAT1 inside this nuclear body, we report herein that NEAT1_1 levels are dynamically regulated during the cell cycle and targeted for degradation by the nuclear RNA exosome. Unexpectedly, however, cancer cells engineered to lack NEAT1_1, but not NEAT1_2, do not exhibit cell cycle defects. Moreover, Neat1_1-specific knockout mice do not exhibit the phenotypes observed in Neat1-deficient mice. We propose that NEAT1 functions are mainly, if not exclusively, attributable to NEAT1_2 and, by extension, to paraspeckles.

overall_design: In order test whether NEAT1_1 modulates transcription we profiled the transcriptome of PAS KO and WT ctrl cells during G0 and G1/s phase by RNAseq

first: Carmen

last: Adriaens


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and FMCD mice Translatomics

summary: We performed rigorous ribosome profiling in FMCD mouse models with human MTOR point mutations. By obtaining about 10 million bases of sequence from FACS sorted mutation carrying cells in FMCD, we generated genome-wide translatome and transcriptome data of cortical neuron of FMCD.

overall_design: Examination of transcriptome and translatome in 3 mouse types.


title: Genome-wide analysis of gene expression modulated by anthracycline-based chemotherapy CHOEP in malignant T-cell lines

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

institute: IRCCS Ospedale San Raffaele

summary: Analysis of gene expression modulations induced by CHOEP treatment in malignant T-cell lines. The hypothesis tested in the present study was that the different sensitivity of malignant T-cell lines to CHOEP exposure can be explained by differentially expressed genes and pathways. Results provide evidence that a number of genes are  up- or down-regulated in response to CHOEP, suggesting the activation of pro-survival druggable pathways activated by chemotherapy.

overall_design: Total RNA obtained from cell lines treated with CHOEP for 24 hours compared to untreated control cells. For each cell line three biological replicates per experimental condition were analyzed.

first: Cristiana

last: Carniti

first: Loris

last: De Cecco


title: Single amino acid change underlies distinct roles of H2A.Z subtypes in human syndrome

city: Stanford

first: Rachel

last: Greenberg

state: CA

address: 265 Campus Drive

institute: Stanford University

summary: Craniofacial disorder Floating-Harbor Syndrome (FHS) is caused by heterozygous truncating mutations in SRCAP, a gene encoding a chromatin remodeler mediating incorporation of histone variant H2A.Z. Here, we demonstrate that FHS-associated mutations result in loss of SRCAP nuclear localization, alter neural crest gene programs in human in vitro models and Xenopus embryos, and cause craniofacial defects. These defects are mediated by one of two H2A.Z subtypes, H2A.Z.2, whose knockdown mimics and whose overexpression rescues the FHS phenotype. Selective rescue by H2A.Z.2 is conferred by one of the three amino acid differences between the H2A.Z subtypes, S38/T38. We further show that H2A.Z.1 and H2A.Z.2 genomic occupancy patterns are qualitatively similar, but quantitatively distinct, and that H2A.Z.2 incorporation at AT-rich enhancers and expression of their associated genes are both sensitized to SRCAP truncations. Altogether, our results illuminate the mechanism underlying a human syndrome and uncover selective functions of H2A.Z subtypes during development.

overall_design: Gene expression (RNA-seq) and histone binding of V5-tagged H2A.Z subtypes (ChIP-seq) were assayed in WT and FHS CNCCs derived from ESCs in biological and/or technical replicate.

first: Joanna

last: Wysocka


title: A Unique Epigenomic Landscape Defines Human Erythropoiesis

city: New Haven

first: Vince

last: Schulz

state: CT

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

type: Methylation profiling by high throughput sequencing


title: A peripheral blood gene expression signature diagnoses subclinical acute rejection [validation]

city: New York

first: Weijia

last: Zhang

state: NY

address: 1 Gustave L. Levy Pl

department: Renal

institute: Icahn School of Medicine at Mount Sinai

summary: Histological features of acute rejection can be detected in surveillance biopsies despite stable graft function and can negatively impact graft outcomes. However, routine surveillance biopsies for detection of subclinical rejection are not generally performed due to potential risks and costs associated with repeated biopsies. Noninvasive biomarkers are required to facilitate early detection of acute rejection and borderline changes. We examined the impact of histological abnormalities at 3-month in surveillance biopsies on graft outcomes in kidney transplant recipients from the prospective Genomics of Chronic Allograft Rejection (GoCAR) study. We then performed RNA sequencing on whole blood collected at the time of biopsy in 88 patients (22 vs. 66) to identify transcripts associated with histological abnormalities. Subjects with subclinical ACR or borderline ACR at 3 month (ACR-3) had higher risk of subsequent clinical acute rejection at 12 and 24 month (P < 0.05), more rapid functional decline (P < 0.05) and a decreased graft survival in adjusted cox analysis (P < 0.01) than patients with no abnormalities on 3-month biopsy. We then identified a 17-gene signature in peripheral blood that accurately diagnosed ACR-3. The gene set was then validated for diagnosis of ACR-3 using microarray data (N=65; 12 vs. 53; 26 overlapping with the RNAseq cohort).

overall_design: A microarray set (N=65) was used for validation of gene signatures associated with subclinical acute rejection.

first: Zhengzi

last: Yi

first: Barbara

last: Murphy


title: Real-time quantitative PCR analysis of mouse lungs after influenza A infection

city: Silver Spring

first: Hang

last: Xie

state: Maryland

address: 10993 New Hampshire Ave WO 52/72 Rm 1324

institute: US Food and Drug Administration, Center for Biologics Evaluation and Research

summary: Age-matched BALB/c female mice were implanted subcutaneously with slow release estradiol (E2) pellets (35 mg/pellet/mouse) or similar-sized placebo pellets .One week post-implantation, mice were infected intranasally with a sublethal dose of H5N1 A/Vietnam/1203/2004 vaccine reassortant bearing a monobasic HA cleavage site. Mouse lungs were harvested on day 1 post infection and total RNA was extracted using QIAgen RNeasy microarray tissue mini kit. A total of 100 µg high-quality RNA was reverse transcribed using RT2 Easy First Strand Kit (QIAgen). Resultant cDNA was used as the template along with Profiler™ PCR Array Mouse Signal Transduction PathwayFinder™ kit (QIAgen) to quantitate gene expression activated by E2 in response to H5N1 infection.

overall_design: qPCR lung gene expression profiling of estradiol (E2)- or placebo-pellet implanted mice on day 1 post-H5N1 infection as indicated in the summary. A total of 100 ng of high-quality RNA per mouse lung was subjected to gene expression profiling. The experiment was repeated twice with 2 mice per group per assay.

first: Courtney

last: Finch


title: A peripheral blood gene expression signature diagnoses subclinical acute rejection


title: Dual role of CSL (RBP-Jk) and NOTCH1 in cancer-associated fibroblast genome stability and expansion [RNA-seq]

city: Biella

first: Paola

last: Ostano

address: via Malta 3

institute: Fondazione Edo ed Elvo Tempia

summary: Genomic instability is a hallmark of cancer. Whether or not it also occurs in cancer-associated fibroblasts (CAFs) is a question of importance for the cancer/stromal cell co-evolution process. We find that DNA damage, telomere shortening and chromosome fusions occur at early times of CAF activation, as triggered by silencing of the CSL/RBP-J-κ gene in primary human dermal fibroblasts (HDFs) from multiple individuals. Similar alterations occur in skin Squamous Cell Carcinoma (SCC) - derived CAFs, in which CSL is down-modulated, versus HDFs from unaffected skin of the same patients. Mechanistically, CSL is part of a telomere protective complex with UPF1, KU70, and KU80 proteins, which fail to bind to telomeres in the absence of CSL. In CAFs, persistent genomic instability is associated with frequent amplification and overexpression of NOTCH1 gene, which is required to suppress DNA damage-induced ATM/P53 activation and growth arrest. These findings are of translational significance as, in an orthotopic model of skin SCC, genetic or pharmacological suppression of NOTCH1 activity suppresses cancer/stromal cell proliferation and expansion.

overall_design: RNA-Seq analysis was performed on two strains of HDFs infected with two different shRNAs against UPF1 in parallel with a control virus, and on one strain of HDFs infected in duplicate with two different shRNAs against CSL in parallel with a control virus.

first: Giulia

last: Bottoni

first: Gian

last: Dotto


title: Variant PRC2.1 and PRC2.2 co-operate to direct H3K27 methylations in ESCs [RNA-seq]

city: Dublin 2

first: Darren

middle: John

last: Fitzpatrick

state: Ireland

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

summary: Polycomb repressive complex 2 (PRC2) is composed of EED, SUZ12, and EZH1/2, and mediates mono-, di- and tri-methylation of Histone H3 at Lysine 27. While, two subcomplexes defined by their specific accessory proteins, termed PRC2.1 (Polycomb-like proteins 1-3, EPOP and PALI1/2) and PRC2.2 (AEBP2 and JARID2) exist, little is known about their differential functions. Here, we show that PRC2.1 and PRC2.2 share the majority of their target genes in mouse embryonic stem cells (ESCs). While loss of all three Polycomb-like proteins (PHF1, MTF2, PHF19) leads to eviction of EPOP and PALI1 from chromatin, PRC2.2 specific components are maintained together with SUZ12 and H3K27me3 at broad Polycomb domains. We show that PRC2.2 localises to PRC1 mediated H2AK119ub1 at these broad Polycomb domains to maintain H3K27me3, even in the absence of PRC2.1. Taken together, these data establish that PRC2.1 and PRC2.2 co-operate to direct H3K27me3, but have independent recruitment mechanisms.

overall_design: RNA seq analysis of Pcl1-3 WT and Pcl1-3 TKO  mouse embryonic stem cells and at three time points (Day 2, Day 4 and Day 8) during embryoid body differentiation (EB). 20 samples are included. Biological duplicates are present.

first: Evan

last: Healy

first: Marlena

last: Mucha

first: Eric

last: Conway

first: Guido

last: Van Mierlo

first: Marijke

last: Baltissen

first: Michiel

last: Vermeulen

first: Yoko

last: Koseki

first: Haruhiko

first: Adrian

last: Bracken


title: Expression data from tumor lungs after continuous vs. pulsatile selumetinib treatment in KRASG12C GEMM

first: Hyejin

last: Choi

address: 408 East 69th Street Z1525

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

summary:
KRAS is one of the driver oncogenes in non-small cell lung cancer (NSCLC), but remains refractory to current modalities of targeted pathway inhibition, which include inhibiting downstream kinase MEK to circumvent KRAS activation. Here, we show that pulsatile, rather than continuous, treatment with MEK inhibitors (MEKis) maintains T cell activation and better control tumor growth and survival.
We used microarrays to examine the MAPK signaling pathway suppression from tumor lungs of KRASG12C GEMM after continuous vs. pulsatile treatment of selumetinib.

overall_design: Tumor was induced by intranasal administration of adenoviral-Cre to KRASLSL-G12C/+ GEMM mice. Once the tumor size reached approximately 500 mm3 (at about 12 weeks after adenoviral inoculation), KRASG12C GEMM mice were treated with selumetinib continuously (daily for 3 weeks, 25mg/kg, BID) or pulsatilely (1 cycle: 1 week ON + 1 week OFF, total 3 cycles, 25mg/kg, BID) with their matched control (vehicles), since the treatments were not done at the same time. The mice were sacrificed after selumetinib treatment is completed.

first: Deng

last: Jiehui

first: Li

last: Shuai

first: Kwok

middle: K

last: Wong

first: Jedd

last: Wolchok

first: Taha

last: Merghoub


title: Transcriptional profiling of neurons in the midbrain of a Stard8-TRAP (ES2342) mouse line

status: Public on Sep 10 2019

first: Laura

last: Kus

address: 1230 York Avenue # 260

department: Heintz Laboratory

institute: The Rockefeller University

summary: TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain.  Using this technique we obtained RNA-Seq data from actively translating transcripts present in neurons in the thalamus of adult Stard8-EGFP/Rpl10a (ES2342) mice.

overall_design: TRAP-Seq of neurons in the midbrain of adult Stard8-EGFP/Rpl10a (ES2342) control mice.

first: Erika

last: Andrade

last: Schmidt

first: Nathaniel

last: Heintz


title: Striatum transcriptome analysis of Shank3 knock-out/heterozygous mice

city: Seoul

first: Kihoon

last: Han

address: 73, Inchon-ro, Seongbuk-gu

department: Neuroscience

institute: Korea University College of Medicine

summary: Shank3 is a core excitatory postsynaptic protein expressed in multiple brain regions including the medial prefrontal cortex, striatum, and hippocampus. Shank3 knock-out mice display autism-like behaviors and synaptic dysfunction. To understand molecular mechanisms underlying the behavioral and synaptic changes, we performed transcriptome (RNA-sequencing) analysis of the striatum tissues from 10 to 12-week-old wild-type and Shank3 knock-out/heterozygous mice.

overall_design: Striatum transcriptome of 10 to 12-week-old wild-type and Shank3 knock-out/heterozygous mice

first: Yeunkum

last: Lee

first: Hyojin

last: Kang


title: Mycobacterial cord factor reprograms the macrophage response to IFN-gamma towards enhanced inflammation yet impaired antigen presentation and expression of Gbp1

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

institute: Uniklinikum Erlangen

summary:
Mycobacteria can survive and persist in macrophages despite triggering multiple pattern recognition receptors and strong T cell-derived IFN-gamma production. The mycobacterial cord factor trehalose-6,6-dimycolate binds the C-type lectin receptor Mincle and induces inflammatory gene expression through the Syk-Card9 pathway. It is well established that TDM and IFN-gamma synergize to induce expression of iNOS. However, the cord factor may also act to down-regulate IFN-gamma-induced responses and contribute to mycobacterial immune evasion.
Here, we have investigated the cross-regulation of the macrophage transcriptome by IFN-gamma and by TDM, as well as its synthetic analog TDB. For genome-wide expression profiling, bone marrow derived macrophages (BMMs) from female C57BL/6 mice aged 6 to 8 weeks were used for stimulation.

overall_design: BMMs from female C57BL/6 mice aged 6 to 8 weeks were used in stimulation experiments; three independent replicates of each stimulation were performed.

first: Alexandra

last: Huber

first: Roland

last: Lang

first: Arif

last: Ekici


title: Transcriptome analysis reveals malignant and hypoxic signature of glioblastoma

city: Chongqing

first: bao

last: liu

address: 30 Gaotanyan street

department: Institute of Medicine and Hygienic Equipment for High Altitude Region

institute: 3rd Military Medical University

summary:
Purpose:Glioblastoma (GBM) is the most common primary brain tumor in adults with poor prognosis and short medial survival after therapy. we have utilized U87-MG cell line as a human GBM cell model and human brain HEB cell line as non-neoplastic brain cell cultured in normoxia and 1% O2 hypoxia for transcriptional profiling to gain further insight into the molecular underpinnings that maintained the properties of GBM andclarify the molecular mechanism of hypoxia resistance of GBM.
Methods:We have utilized U87-MG cell line as a human GBM cell model and human brain HEB cell line as non-neoplastic brain cell cultured in normoxia and 1% O2 hypoxia for transcriptional profiling. And  validating the analysis results with specimens of GBM patients.
Results: Firstly, the resulting data set revealed previously unknown proteins, including AKR1B1, MT2A, UBC, EEF1A1 and MTRNR2l2 in U87-MG cells, which promoted GBM characters through MAPK pathway. Meanwhile, we found that toll-like pathway was a new avenue mediating the function of inflammatory response in GBM. Furthermore, The results suggested that cytokine TGF-β1 and HIFs’ targeted genes, including HMOX1 and STC1 could be regard as hypoxic markers for GBM.
Conclusion:Taken together, our study identified new potential biomarkers and illustrated the genes associated with inflammation in GBM. More importantly, the unique pattern to hypoxia implied new insight for the GBM research of hypoxia resistance and recurrence in future.

overall_design: Glioblastoma (GBM) is the most common primary brain tumor in adults with poor prognosis and short medial survival after therapy. To gain further insight into the molecular underpinnings that maintained the properties of GBM, we have utilized U87-MG cell line as a human GBM cell model and human brain HEB cell line as non-neoplastic brain cell cultured in normoxia and 1% O2 hypoxia for transcriptional profiling. Firstly, the resulting data set revealed previously unknown proteins, including AKR1B1, MT2A, UBC, EEF1A1 and MTRNR2l2 in U87-MG cells, which promoted GBM characters through MAPK pathway. Meanwhile, we found that toll-like pathway was a new avenue mediating the function of inflammatory response in GBM. Furthermore, to clarify the molecular mechanism of hypoxia resistance of GBM, we evaluated the difference of transcriptional profiling between U87-MG and HEB cells under hypoxia, and validated with specimens of GBM patients. The results suggested that cytokine TGF-β1 and HIFs’ targeted genes, including HMOX1 and STC1 could be regard as hypoxic markers for GBM. Taken together, our study identified new potential biomarkers and illustrated the genes associated with inflammation in GBM. More importantly, the unique pattern to hypoxia implied new insight for the GBM research of hypoxia resistance and recurrence in future.

first: Yixing

last: Gao

first: Bao

last: Liu

first: Erlong

last: Zhang

first: Kai

last: Zhou

first: Wu

last: Gang

first: Mianfu

last: Cao

first: Haibo

last: Wu

first: You-hong

last: Cui

first: Xia

first: Xin-dong

first: Yan

last: Wang

first: Yuqi

first: Xiu-wu

last: Bian


title: A peripheral blood gene expression signature diagnoses subclinical acute rejection [discovery]

first: Weijia

summary: Histological features of acute rejection can be detected in surveillance biopsies despite stable graft function and can negatively impact graft outcomes. However, routine surveillance biopsies for detection of subclinical rejection are not generally performed due to potential risks and costs associated with repeated biopsies. Noninvasive biomarkers are required to facilitate early detection of acute rejection and borderline changes. We examined the impact of histological abnormalities at 3-month in surveillance biopsies on graft outcomes in kidney transplant recipients from the prospective Genomics of Chronic Allograft Rejection (GoCAR) study. We then performed RNA sequencing on whole blood collected at the time of biopsy in 88 patients (22 vs. 66) to identify transcripts associated with histological abnormalities. Subjects with subclinical ACR or borderline ACR at 3 month (ACR-3) had higher risk of subsequent clinical acute rejection at 12 and 24 month (P < 0.05), more rapid functional decline (P < 0.05) and a decreased graft survival in adjusted cox analysis (P < 0.01) than patients with no abnormalities on 3-month biopsy. We then identified a 17-gene signature in peripheral blood that accurately diagnosed ACR-3.

overall_design: The transcriptomic profiles of discovery set (N=88) was used for identification of gene signatures associated with subclinical acute rejection.

first: Zhengzi

last: Yi

first: Barbara

last: Murphy


title: RNA-seq analysis of Ehrlichia muris infection induced murine splenic and hepatic memory B cells subsets.

city: Pittsburgh

first: Mark

last: Shlomchik

state: PA

address: The Assembly, 5051 Centre Avenue

department: Department of Immunology

institute: University of Pittsburgh

summary: Purpose: The goal of this study is to complare the transcitpional profiles of freshly isolated, murine splenic and hepatic memory B cells (B220+ CD73+) sorted as CD11b, CD11c double negative and CD11b, CD11c double positive cell populations induced by Ehrlichia muris infection.

overall_design: Methods: For mRNA sequencing analysis, B220 positive, CD73 positive MBCs were sorted as CD11b, CD11c double negative and CD11b, CD11c double positive. After the sort, the cells were spun down and washed with PBS and re-suspended in RLT+1% beta-mercaptoethanol. RNA was prepared with RNAeasy microplus kits from Qiagen, according to recommended protocol. cDNA libraries were constructed using SMARTer low input kit for mRNA seq. Samples were sequenced using Illumina NextSeq 500 with 75 bp paired-end reads and aligned to the mm10 genome using the STAR aligner ((Dobin et al., 2013). The number of uniquely aligned reads ranged from 22 to 32 million. Gene-level counts were determined using featureCounts (Liao et al., 2014), and raw counts were quantile normalized to each other for differential expression using the voom method (Law et al., 2014) in the limma R package (Ritchie et al., 2015) The presence of certain liver-specific transcripts indicated unavoidable liver cell contamination in the liver sample; to prevent this from confounding our analysis, differential expression was performed only on genes, which were having at least 30 counts in the all liver and spleen samples. All gene-set enrichments were preformed using the rankSumTestWithCorrelation function in limma, which explicitly corrects for correlation among genes in the gene set being interrogated.

first: Nikita

last: Trivedi

first: Shuchi

last: Smita

first: Maria

last: Chikina

middle: J


title: Variant PRC2.1 and PRC2.2 co-operate to direct H3K27 methylations in ESCs [ChIP-seq]

first: Darren

last: Fitzpatrick

sample_organism:
Drosophila melanogaster
Homo sapiens
Mus musculus

overall_design: Quantitative ChIP-Rx analysis of Pcl1-3 WT and Pcl1-3 TKO mouse embryonic stem cells. ChIPs for certain histone modification include a 1.67% spike in of Drosophila chromatin (S2 cell line). ChIPs for PRC2 components and H2AK119ub1 include a 10% spike in of human chromatin (NT2 cell line). 19 samples are included

first: Evan

last: Healy

first: Marlena

last: Mucha

first: Eric

last: Conway

first: Guido

last: Van Mierlo

first: Marijke

last: Baltissen

first: Michiel

last: Vermeulen

first: Yoko

last: Koseki

first: Haruhiko

first: Adrian

last: Bracken


title: Single-cell transcriptome analysis reveals gene signatures associated with T-cell persistence following adoptive cell therapy

city: Bethesda

first: Li

last: Jia

state: MD

address: 10 Clinic center

institute: NCI/NIH

summary:
A patient (4095) with metastatic colorectal cancer was treated with polyclonal tumor infiltrating lymphocytes (TILs) targeting the KRAS(G12D) hotspot mutation. Three dominant clonotypes  specifically recognizing KRAS(G12D) epitopes were identified, but we found that only two clonotypes persisted 40 days after TIL treatment. Because of these findings, in this study, we utilized a 10X system to perform single-cell TCR/transcriptome analysis for the TILs isolated from this patient, together with 4 additional TILs isolated from 4 patients (4007, 4069, 4071, 4081) treated within 5-month window. In addition, we performed single-cell TCR/transcriptome analysis on Patient 4095's peripheral blood lymphocytes (PBL) day 12 or day 40 after TIL treatment.
   We also utilized a low-throughput Fluidigm C1 system to perform single-cell RNA-Seq on TIL4095. Please use accession number GSE136610 to find the dataset.

overall_design: Single-cell TCR/transcriptome analysis on tumor infiltrating lymphocytes (TILs) and peripheral blood lymphocytes (PBL) was perform on a 10X Chromium instrument using single-cell VDJ kits

first: Yong-Chen

last: Lu


title: Whole transcriptome sequencing of Treg with and without Rcor1 deletion

city: Philadelphia

first: Wayne

middle: W

last: Hancock

address: 916B ARC, 3615 Civic Ctr Blvd

institute: CHOP/UPenn

summary: Foxp3+ T-regulatory (Treg) cells have well established roles in maintaining immune homeostasis and tolerance, but the contributions of several large multiprotein complexes that regulate gene expression remain unexplored in Tregs. We analyzed the role in Tregs of the evolutionarily conserved CoREST complex that consists of a scaffolding protein, Rcor1 or Rcor2, plus Hdac1, Hdac2 and Lsd1 enzymes. We found Rcor1, Rcor2 and Lsd1 were physically associated with Foxp3, and that mice with conditional deletion of Rcor1 in Foxp3+ Treg cells had decreased proportions of Tregs in their peripheral lymphoid tissues, and increased Treg expression of IL-2 and IFN-g compared to WT cells. In vivo, compared with WT mice, mice with conditional deletion of Rcor1 in their Tregs had reduced suppression of homeostatic proliferation, inability to maintain long-term allograft survival despite costimulation blockade, and enhanced antitumor immunity in syngeneic models. Comparable findings were seen in WT mice treated with a CoREST inhibitor. Our data point to the potential for therapeutic modulation of Treg functions by pharmacologic targeting of enzymatic components of the CoREST complex, and contribute to an understanding of the biochemical and molecular mechanisms by which Foxp3 represses large gene sets and maintains the unique properties of this key immune cell type.

overall_design: Foxp3+ regulatory T cells from mice with or without a Foxp3-conditional Rcor1 deletion (Rcor1fl/flFoxp3YFPcre and Foxp3YFPcre mice) had RNA isolated. The RNA samples, with three independent biological replicates per group, were sent to NovoGene for mRNA sequencing using the Illuminia PE150 platform.

first: Yan

last: Xiong

first: Liqing

last: Wang

first: Rongxiang

last: Han

first: Ulf

last: Beier


title: MicroRNA differential expression in skin and oral mucosal epithelium

city: Chicago

first: Xiaofeng

last: Zhou

state: Illinois

address: 801 S Paulina Street

institute: University of Illinois at Chicago

summary: While skin and oral mucosa share many morphological similarities, oral mucosal wounds heal more rapidly than skin wounds. Epithelial cells from oral mucosa exhibit increased migratory and proliferative capacities when compared to cells from skin, suggesting that the improved repair of mucosa may involve intrinsic differences in epithelial cells. This is an exploratory experiment to define the differential microRNA expression of baseline unwounded skin and oral mucosa epithelium.

overall_design: Microarray-based microRNA profiling were performed on pooled total RNA samples isolated from paired skin and oral mucosa specimens of mouse (n=3) were profiled .

first: Lin

last: Chen

first: Zujian

first: Luisa

middle: A

last: DiPietro


title: Transcriptional profiling of neurons in the midbrain of a Lhx5-TRAP (DT154) mouse line

first: Laura

last: Kus

summary: TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain.  Using this technique we obtained RNA-Seq data from actively translating transcripts present in neurons in the midbrain of adult Lhx5-EGFP/Rpl10a (DT154) mice.

overall_design: TRAP-Seq of neurons in the midbrain of adult Lhx5-EGFP/Rpl10a (DT154) control mice.

first: Jim

last: Li

first: Nathaniel

last: Heintz


title: Transcriptional profiling of neurons in the hypothalamus of a Lhx5-TRAP (DT154) mouse line

summary: TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain.  Using this technique we obtained RNA-Seq data from actively translating transcripts present in neurons in the hypothalamus of adult Lhx5-EGFP/Rpl10a (DT154) mice.

overall_design: TRAP-Seq of neurons in the hypothalamus of adult Lhx5-EGFP/Rpl10a (DT154) control mice.


title: Analysis of gene expression in the lung of influenza virus infected C57BL/6 mice

city: Beijing

first: jing

last: ouyang

address: NO.1 Beichen West Road, Chaoyang District

institute: Institute of microbiology, Chinese Academy of Sciences

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

summary: We employ cDNA microarry(Agilent Mouse lncRNA (4*180K,Design ID:049801) ) to detect the differential expression of mRNAs and lncRNAs in the lung of mice infected with or without A/WSN/33 influenza virus. Microarry analysis revealed that 2092 mRNAs and 1640 lncRNAs differentially expressed in the lung of IAV infected mice compared to control,including 1399 mRNAs and 1052 lncRNAs upregulated, 693 mRNAs and 588 lncRNAs downregulatded. Our finding indicates that thousands of genes are involved in and may play critical roles in the influenza virus-host interactions.

overall_design: C57BL/6 mice were infected intranasally with A/WSN/33 influenza virus (PFU= 5×104) or PBS for 24 hours.Then the gene expression in the lung of mice was analysed by using microarray. Each group included three repeats.

first: Jilong

first: Jing

last: Ouyang

first: Biao

first: Ruoxiang

last: Yan

first: Song


title: Spontaneous Superimposed Preeclampsia: Chronology and Expression Unveiled by Temporal Transcriptomic Analysis

city: Jackson

first: Kenji

last: Maeda

state: MS

address: 2500 North State Street

department: Pharmacology & Toxicology

institute: University of Mississippi Medical Center

summary: Preeclampsia (PE), a multifactorial pregnancy-specific syndrome accounting for up to 8% of pregnancy complications, is a leading cause of maternal and fetal morbidity and mortality and PE is also associated with long-term risk of hypertension and stroke for both the mother and fetus. Currently, the only “cure” is delivery of the baby and placenta, largely because the pathogenesis of preeclampsia is not yet fully understood. Preeclampsia is associated with impaired vascular remodeling at the maternal-fetal interface and placental insufficiency; however, the specific factors that contribute to this impairment have not been identified. To identify potential contributing pathways, we examined temporal transcriptomic changes occurring within the uterus, uterine implantation sites, and placentae from the Dahl salt-sensitive (Dahl S) rat model of superimposed preeclampsia compared to Sprague Dawley (SD) rats. We hypothesized that the Dahl S maternal-fetal interface would exhibit a unique temporal transcriptomic profile unveiling novel biomarkers, therapeutic targets, and mechanistic pathways regarding the development of PE. Our initial study focused on evaluation of genes previously linked to the development PE from using real time quantitative PCR (RT qPCR) and total RNA was isolated from uterus (day 0), uterine implantation sites (days 7, 10, 14), and placenta (days 14 and 20). Subsequently, an unbiased transcriptome analysis was performed at each time point using whole genome microarray to identify novel factors involved in PE. 624, 332, 185 , and 366 genes were found to be differentially expressed on days 0, 7, 10 and 14 respectively, with a Reactome Pathway enrichment for “Fatty acid metabolism, Metabolism of water-soluble vitamins and cofactors, Metabolism, Synthesis of substrates in N-glucan biosynthesis on Day 7”; ”Glycerophospholipid biosynthesis, Phospholipid metabolism, and Metabolism of lipids on Day 10”; and “Metabolism of lipids, Phospholipid metabolism, degradation of the extracellular matrix, Fatty acid metabolism, and Collagen degradation on Day 14” in the Dahl S rat vs. SD. Our data revealed numerous pathways that may play a role in the pathophysiology of spontaneous superimposed PE and allow for further investigation of novel therapeutic targets and biomarker development.

overall_design: Whole genome transcript analysis was performed using Affymetrix platform on rat uterine tissue, uterine implantation sites, or placental tissue.

first: Jennifer

last: Sasser


title: RNA-Seq analysis of human Tr1, Tregs and IL10neg cells

city: Vancouver

first: Megan

last: Levings

address: 950 West 28th Ave

institute: University of British Columbia

summary: To determine the differentially expressed genes between these subsets and identify the core human in vivo differentiated Tr1 cell gene signature

overall_design: Human Tr1 and IL-10 neg cells were sorted using an IL-10capture assay following 16h CD3/CD28 bead activation, matched Tregs were sorted from unstimulated cells then activated by CD3/CD28 beads for 16h.  Samples are from 3 donors from 3 independent experiments (HIF037, HIF038 and HIF039).

first: M

first: L

last: Cook


title: Chromatin architecture as a checkpoint for NASH-associated liver injury

city: Ann Arbor

first: Jiandie

last: Lin

state: MI

address: 210 Washtenaw Ave

department: Cell & Developmental Biology, Life Science Institute

institute: University of Michigan

summary: Nonalcoholic steatohepatitis (NASH) is a progressive liver disease that is characterized by liver injury, inflammation and fibrosis. NASH pathogenesis is linked to reprogramming of chromatin landscape in the liver that predisposes hepatocytes to stress-induced tissue injury. However, the molecular nature of the putative checkpoint that maintains chromatin architecture and preserves hepatocyte health remains elusive. Here we show that heterogeneous nuclear ribonucleoprotein U (hnRNPU), a nuclear matrix protein that governs chromatin architecture and gene transcription, is a critical factor that couples chromatin disruption to NASH pathogenesis. RNA-seq and ChIP-seq studies revealed an extensive overlap between hnRNPU occupancy and altered gene expression during NASH. Hepatocyte-specific inactivation of hnRNPU disrupted liver chromatin accessibility, activated the molecular signature of NASH and sensitized mice to diet-induced NASH pathogenesis. Mechanistically, hnRNPU deficiency stimulated the expression of a truncated isoform of TrkB that promotes inflammatory signaling in hepatocytes and stress-induced cell death. These findings illustrate a novel mechanism through which disruptions of chromatin architecture drive the emergence of disease-specific signaling patterns that promote liver injury and exacerbate NASH pathogenesis.

overall_design: 6 biological replicates were analyzied in each group for ATAC-seq (control vs liver specific knockout); 2 control and 3 liver specific knockout samples were used in RNA-seq

first: Tongyu

last: Liu

last: Xiong


title: Effect of AMI-5 on mouse pancreas differentiation

city: Dresden

first: Anthony

last: Gavalas

address: Fetscherstr. 105

institute: TU Dresden

summary: Mouse embryonic pancreata at 14.5 dpc were cultured for two day in air to liquide interface cultures in the absence (control) or presence of 10 uM AMI-5, a protein methyltransferase inhibitor

overall_design: Three control samples and three treated were used for RNA preparation and RNA Sequencing

first: Ioannis

last: Serafimidis

first: Mathias

last: Lesche


title: Methylation profiling and machine learning distinguishes primary lung squamous cell carcinomas from head and neck metastases

city: München

first: Philipp

last: Jurmeister

address: Thalkirchner Straße 36

department: Institute of Pathology

institute: Ludwig Maximilians University Hospital Munich

summary: Head and neck squamous cell carcinoma (HNSC) patients are at risk of suffering from both pulmonary metastases or a second squamous cell carcinoma of the lung (LUSC). Differentiating pulmonary metastases from primary lung cancers is of high clinical importance, but not possible in most cases with current diagnostics. To address this, we performed DNA methylation profiling of primary tumors and trained three different machine learning methods to distinguish metastatic HNSC from primary LUSC. We developed an artificial neural network that correctly classi- fied 96.4% of the cases in a validation cohort of 279 patients with HNSC and LUSC as well as normal lung controls, outperforming support vector machines (95.7%) and random forests (87.8%). Prediction accuracies of more than 99% were achieved for 92.1% (neural network), 90% (support vector machine), and 43% (random forest) of these cases by applying thresholds to the resulting probability scores and excluding samples with low confidence. As independent clinical validation of the approach, we analyzed a series of 51 patients with a history of HNSC and a second lung tumor, demonstrating the correct classifications based on clinicopathological properties. In summary, our approach may facilitate the reliable diagnostic differentiation of pulmonary metastases of HNSC from primary LUSC to guide therapeutic decisions.

overall_design: A total of 51 samples of patients with a history of head squamous cell carcinoma (HNSC) and a synchronous or metachronous lung tumor were characterized using the Illumina Infinium MethylationEPIC BeadChip, including 31 pulmonary metastases of HNSC and 20 primary lung squamous cell carcinomas.

first: Michael

last: Bockmayr

first: David

last: Capper

first: Frederik

last: Klauschen