title: Identification of potential biomarkers of response and resistance to programmed cell death-1 blockade in patients with advanced urothelial tumors

city: Madrid

first: Monica

last: Martinez-Fernandez

address: Avda Complutense 40

institute: CIEMAT

summary: We have performed an analysis of a small series of UC patients in order to analyze their characteristics and patterns of response and resistance to inmunotherapy

overall_design: Bladder FFPE samples from patients diagnosed with bladder cancer were studied by GeneChip Human Transcriptome array (HTA2.0) Arrays (Affymetrix, Santa Clara, CA). They were treated with pembrolizumab (MK-3475) and comparisons between responders and progressors were carried out.

first: Blanca

last: Homet Moreno

last: Dueñas

first: Mónica

last: Martínez-Fernández

first: Jesus

last: Paramio


title: Cycloheximide can distort measurements of mRNA levels and translation efficiency

status: Public on Mar 08 2019

city: San Francisco

first: Daniel

middle: A

last: Santos

state: CA

address: 1700 4th Street

department: Cellular and Molecular Pharmacology

country: USA

institute: UCSF

type: Expression profiling by high throughput sequencing

summary: Regulation of the efficiency with which an mRNA is translated into proteins represents a key mechanism for controlling gene expression. Such regulation impacts the number of actively translating ribosomes per mRNA molecule, referred to as translation efficiency (TE), which can be monitored using ribosome profiling and RNA-seq, or by evaluating the position of an mRNA in a polysome gradient. Here we show that in budding yeast, under nutrient limiting conditions, the commonly used translation inhibitor cycloheximide induces rapid transcriptional upregulation of hundreds of genes involved in ribosome biogenesis. Cycloheximide also prevents translation of these newly transcribed messages, leading to an apparent drop in TE of these genes under conditions that include key transitions of the yeast metabolic cycle, meiosis, and amino acid starvation; an effect which is abolished when cycloheximide pretreatment is omitted.  This response requires TORC1 signaling, and is modulated by the genetic background as well as the vehicle used to deliver the drug. The present work highlights an important caveat to the use of translation inhibitors when measuring TE, and will hopefully aid in future experimental design as well as interpretation of prior results

overall_design: Paired RNA-seq and ribosome profiling sequencing data for 28 yeast samples in various growth conditions, either with or without cycloheximide pretreatment

first: Lei

last: Shi

first: Benjamin

middle: P

last: Tu

first: Jonathan

middle: S

last: Weissman


title: Effect of Nudt7 overexpression on the global transcriptome of mouse liver in the fasted state

city: Morgantown

first: Roberta

last: Leonardi

state: WV

address: 1 Medical Center Drive

institute: West Virginia University

summary: RNAseq analysis was conducted to complement the targeted and untargeted metabolomics analysis of livers overexpressing the CoA-degrading enzyme Nudt7 or GFP (control). Lipid metabolism requires coenzyme A (CoA), which is found in multiple subcellular compartments including the peroxisomes.  In the liver, CoA levels are dynamically adjusted between the fed and fasted states.  The elevation in CoA levels that occurs during fasting is driven by increased synthesis but also correlates with decreased expression of Nudt7, the major CoA-degrading enzyme in the liver.  Nudt7 resides in the peroxisomes and we overexpressed this enzyme in mouse livers to determine its effect on the size and composition of the hepatic CoA pool in the fed and fasted states.  Nudt7 overexpression did not change total CoA levels but decreased the concentration of short-chain acyl-CoAs and choloyl-CoA in fasted livers, when endogenous Nudt7 activity was lowest.  The effect on these acyl-CoAs correlated with a significant decrease in the hepatic bile acid content and in the rate of peroxisomal fatty acid oxidation, as estimated by targeted and untargeted metabolomics, combined with the measurement of fatty acid oxidation in intact hepatocytes.  Identification of the CoA species and metabolic pathways affected the overexpression on Nudt7 in vivo supports the conclusion that the nutritionally-driven modulation of Nudt7 activity could contribute to the regulation of the peroxisomal CoA pool and peroxisomal lipid metabolism.

overall_design: Liver mRNA profiles of 4 mice injected with adeno-associated virus to overexpress Nudt7 and 4 mice injected with adeno-associated virus to overexpress GFP (control) were generated by RNAseq using Illumina HiSeq1500

first: Aniello

middle: M

last: Infante


title: Exosomal hsa-miR199a-3p promotes  proliferation and metastasis in  neuroblastoma

city: Shanghai

first: Haoyan

last: Chen

state: Shanghai

address: 145 Shandong Road

country: China

institute: Renji Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: To elucidate whether exosomal hsa-miR199a-3p plays a role in  neuroblastoma tumorigenesis, a miRNA-seq analysis on plasma exosomal miRNA from neuroblastoma patients and normal controls.

overall_design: miRNA-seq was performed in neuroblastoma patients and normal controls

first: Jing

last: Ma

first: Min

last: Xu

first: Minzhi

last: Yin

first: Jie

last: Hong

first: Yijin

last: Gao

first: Chenjie

last: Xie

first: Xi

last: Mo

first: Song

last: Gu

last: Shen


title: Comprehensive constitutional genetic and epigenetic characterization of Lynch-like individuals [FFPE]

status: Public on Mar 09 2019

city: L'Hospitalet de Llobregat

first: Estela

last: Damaso

state: Barcelona

address: Av.Gran Via de l'Hospitalet, 199-203

department: Hereditary Cancer Program

country: Spain

institute: Catalan Institute of Oncology (ICO)

type: Methylation profiling by genome tiling array

summary:
Background: In ~50% of Lynch syndrome (LS)-suspected patients (also called Lynch-like syndrome, LLS), the causal mechanism for cancer predisposition remains unknown. Our aim was to elucidate the constitutional basis of mismatch repair (MMR) deficiency in LLS patients throughout a comprehensive genetic and epigenetic analysis.
Methods: One hundred and fifteen LLS patients harboring MMR deficient tumors and no pathogenic germline MMR gene mutations were included in this study. Mutational analysis of 26 colorectal cancer associated genes was performed by using a customized multigene panel and massively parallel sequencing. Pathogenicity of MMR variants was assessed by mRNA analysis and multifactorial likelihood calculations. Genome-wide methylome analysis was perfomed by using the Infinium HumanMethylation450K BeadChip.
Results: The multigene panel analysis revealed the presence of two MMR gene truncating mutations not found in previous analysis. Of a total of 15 MMR variants of unknown significance identified, five - present in 6 unrelated individuals- were reclassified as pathogenic. In addition, 13 predicted deleterious variants in other CRC-predisposing genes (MSH3, MUTYH, POLD1, APC, EPCAM, BUB1, FAN1, EXO1 or PSM1) were found in 12 probands. Methylome analysis detected one constitutional MLH1 epimutation in an individual diagnosed with CRC at age 42, but no additional differentially methylated regions were identified in LLS compared to LS patients or healthy individuals.
Conclusions: In conclusion, the use of an ad-hoc designed gene panel combined with pathogenicity assessment of variants allows the identification of deleterious MMR mutations as well as new LLS candidate genes. Moreover, constitutional epimutations in non-LS-associated genes are not responsible for the MMR-deficient phenotype observed in LLS patients.

overall_design:
A total of 115 Caucasian Lynch-like syndrome patients harboring MMR deficient tumors MMR loss of expression and/or microsatellite instability (MSI) were analyzed by Infinium Human Methylation 450k Beadchip. From all included individuals, DNA from blood was collected. FFPE blocks of normal colorectal mucosa and colorectal cancer tissue were also included when available. The current subset includes only FFPE samples. Blood samples can be found in the other associated dataset from Damaso et al.
Clinical data abbreviations:
microsatellite instability (MSI+=Microsatellite Instabillity; MSS=Microsatellite stable; NP=Not performed; NV=Not Valuable)
BRAF status (WT=wildtype; NP=Not performed)

last: Dámaso

first: Maribel

last: González-Acosta

first: Gardenia

last: Vargas-Parra

first: Matilde

last: Navarro

first: Judith

last: Balmaña

first: Teresa

last: Ramon y Cajal

first: Noemí

last: Tuset

first: Bryony

last: Thompson

first: Fátima

last: Marín

first: Anna

last: Fernández

first: Carolina

last: Gómez

first: Àngela

last: Velasco

first: Ares

last: Solanes

first: Sílvia

last: Iglesias

first: Gisela

last: Urgel

first: Consol

last: López

first: Jesús

last: del Valle

first: Olga

last: Campos

first: Maria

last: Santacana

first: Xavier

last: Matias-Guiu

first: Conxi

last: Lázaro

first: Laura

last: Valle

first: Joan

last: Brunet

first: Marta

last: Pineda

first: Gabriel

last: Capellá


title: Gene epxression profiling in murine lymphoid-primed multipotent progenitor (LMPP) subpopulations

city: Yokohama

first: Tomohiko

last: Tamura

address: 3-9 Fukuura, Kanazawa-ku

department: Department of Immunology

country: Japan

institute: Yokohama City University

summary: To understand the mechanism underlying early DC specification

overall_design: LMPP subpopulations were isolated from IRF8-GFP knockin mice

first: Daisuke

last: Kurotaki

first: Akira

last: Nishiyama


title: Multiple myeloma cell lines expression profile of OTX015-treated cells compared to DMSO controls

city: Suzhou

first: Wenzhuo

last: Zhuang

state: Jiangsu

address: Ren Ai Road 199

department: Department of Cell Biology, School of Biology & Basic Medical Sciences

institute: Soochow University

summary: Several studies demonstrate that the bromodomain inhibitor OTX015 has preclinical antitumor activity in a variety of solid tumors and hematologic cancers. However, translation of these data to molecules suitable for clinical development has not yet to be accomplished in multiple myeloma (MM). Here, we identified genes and biologic processes that underpin the antimyeloma activity of OTX015 with global transcriptomics. OTX015 exerted strong antiproliferative effect and induced cell cycle arrest in vitro. Gene expression profiling showed that OTX015 targeted NF-κB, EGFR, cell cycle regulation, cancer proliferation signaling pathway. Gene expression signatures associated with different sensitivity to OTX015 were also identified. The data also showed that oral administration of OTX015 displayed significant antitumor activity in mice model of disseminated human myeloma. In addition, our study provided the first evidence and rationale that OTX015 could promoted osteoblast differentiation of mesenchymal stem cells (MSCs) and inhibited osteoclast formation and resorption in vivo experiments. Herein we expanded the mechanistic understanding of BET inhibitors OTX015 in MM. Our preclinical studies provided a strong rationale for extending the clinical testing of the novel antimyeloma agent OTX015 and revealed insights into biologic pathways required for myeloma cell proliferation.

overall_design: OTX015 induced gene expression in multiple myeloma cell lines was measured at 72 hours after drug exposure

first: Bingzong

last: Li


title: Next Generation Sequencing Facilitates Quantitative Analysis of a circRNA, hsa_circ_0005505 regulated Transcriptomes in breast cancer cells (MDA-MB-231 lung metastatic cells LM2)

city: Nanjing

first: shouyu

last: wang

address: 22 Hankou Road

institute: Nanjing university medical school

summary:
Purpose: hsa_circ_0005505 stably knockdown cells (circ-sh1 and circ-sh2) and its corresponing control cells (con-sh) were constructed using its specific shRNAs. Next-generation sequencing (NGS) has used to examine hsa_circ_0005505 regulated transcripts.
Methods:  mRNA profiles of circsh1, circsh2 and con-sh were generated by deep sequencing using IlluminaI HiSeq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using SYBR Green assays
Results: We found 816 and 909 transcripts downregulated in circ-sh1 and circ-sh2 cells compared with con-sh cells, respectively. But 712 and 723 transcripts upregulated in circ-sh1 and circ-sh2 cells compared with con-sh cells, respectively. The differential expression with a fold change ≥1.5 and p value <0.05.
Conclusions: Our study represents the first detailed analysis of hsa_circ_0005505-regulated transcripts in breast cancer cells.

first: Shouyu

last: Wang


title: Cohesin-mediated genome architecture does not define replication timing domains

city: Norwich

first: Conrad

last: Nieduszynski

address: Norwich Research Park

country: United Kingdom

institute: Earlham Institute

overall_design: BrdU Repli-Seq samples from 4 Sphase bins of auxin treated (2H, 100µM)) and control HCT116 Scc1-mAID-mClover cells. BrdU Repli-Seq samples from synchronized auxin treated or control HCT116 Scc1-mAID-mClover cells at three time points post release from nocodazole.

first: Oldach

last: Phoebe

first: Nieduszynski

last: Conrad


title: Comprehensive constitutional genetic and epigenetic characterization of Lynch-like individuals

first: Estela

last: Damaso

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

overall_design: Refer to individual Series


title: Uterine transcriptome of hens laying hard or weak-shell eggs

status: Public on Mar 07 2019

city: Wuhan

first: Desheng

last: Qi

address: Shizishan Street No.1

department: College of Animal Nutrition and Feed Science

institute: Huazhong Agricultural University

summary: Our study investigated the differences of uterine transcriptome in laying hen holding a high or low breaking strength shell. The eggshell calcification periods are divided into three periods, namely initiation, growth and termination periods respectively. The large differences in the transcriptome proved that the initiation period of calcification determine eggshell strength.

overall_design: Examination of 3 eggshell calcification periods of hens laying hard or weak-shell respectively.

first: Jiacai

last: Zhang


title: Expression data from BEAS-2B cells II

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

summary:
BEAS-2B cells are human bronchial epithelial cells, and often used as a in vitro model for the detection of potential pulmonary toxicity of chemicals.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes after treated with chemical substance

overall_design: BEAS-2B cells were selected for RNA extraction and hybridization on Affymetrix microarrays. We tested the expression data of BEAB-2B cells treated with different sizes of silica nanoparticles suspended in DMEM or DMEM only as normal control.

first: Yang

first: Zhiwei

last: Sun


title: Aged blood impairs hippocampal neural precursor activity and activates microglia via brain endothelial cell VCAM1

city: Stanford

first: Michelle

middle: Berkeley

last: Chen

address: 318 Campus Drive

institute: Stanford

summary: Single cell RNAseq of Old (19 month) and Young (3 month) mouse brain endothelial cells isolated from hippocampi of C57BL6 males.

overall_design: Single cell RNAseq of murine brain endothelial cells.

middle: B

first: Hanadie

last: Yousef


title: Gene expression in minor salivary gland of female patients with primary Sjögren’s syndrome (pSS) and healthy volunteers

city: Ribeirão Preto

first: Eduardo M.

last: Rocha

state: SP

address: Av. Bandeirantes, 3900 - Vila Monte Alegre

department: Ophthalmology

country: Brazil

institute: University of São Paulo

summary: To study the difference of gene expression profile in minor salivary glands of female patients with primary Sjögren’s syndrome (pSS) and healthy volunteers

overall_design: Total mRNA was extracted from minor salivary glands of 8 female patients with primary Sjögren’s syndrome (pSS) and 6 healthy volunteers. Minor salivary glands of all 8 pSS patients showed low lymphocytic scores (focus score ≤ 2).

first: John

last: Chiorini

first: Y

middle: Q

last: Mo


title: Transcriptome-wide profiling of thyroid hormone-dependent gene expression in the mouse heart

first: Guo

middle: N

last: Huang

address: 555 Mission Bay Blvd S, CVRB 352V

department: Cardiovascular Research Institute

institute: University of California, San Francisco

summary: During the first weeks after birth, cardiomyocytes within the mouse heart progressively exit the cell cycle, binucleate, and lose regenerative capacity.  We have determined that postnatal day 14 (P14) mouse hearts incapable of responding to thryoid hormone signaling have enhanced proliferation, retain greater populations of mononucleated cardiomyocytes, and show increased regenerative ability. In this study, we perform transcriptome-wide analysis to identify gene networks regulating thryoid hormone-dependent exit of cardiomyocyte cell-cycle and loss of regenerative potential.

overall_design: Transgenic mice possessing cardiomyocyte-specific expression of Cre recombinase (Myh6-Cre) were bred with knock-in mice harboring an allele with Cre-dependent expression of a dominant negative mutant form of thryoid hormone receptor alpha (TRalphaAMI).  Three Myh6-Cre; TRalphaAMI pups and three TRalphaAMI littermate control pups were raised to postnatal day 14 (P14), total RNA was extracted from their hearts, and RNA-seq was performed to identify differentially expressed genes.


title: Sfp1 regulates yeast cell growth and division  through multiple promoter binding modes

city: GENEVA

first: Benjamin

last: Albert

address: 30, quai Ernest-Ansermet

department: Bimol

country: Switzerland

institute: University of Genevea

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Understanding how transcriptional programs help to coordinate cell growth and division is an important unresolved problem.  Here we report that the nutrient- and stress-regulated transcription factor Sfp1 is rate-limiting for expression of a large suite of genes involved in yeast cell growth, including ribosomal protein, ribosome biogenesis, and snoRNA genes.  Remarkably, the spectrum of Sfp1 transcription effects is concordant with a combination of chromatin immunoprecipitation and chromatin endogenous cleavage binding analyses, which together provide evidence for two distinct modes of Sfp1 promoter binding, one requiring a co-factor and the other a specific DNA-recognition motif.  In addition to growth-related genes, Sfp1 binds to and regulates the promoters of key G1/S regulon genes and that of MRS6, whose product regulates Sfp1 nuclear localization.  Our findings suggest that Sfp1 acts as a master regulator of cell growth and cell size by coordinating the expression of genes implicated in mass accumulation and cell division.

overall_design: Sfp1  occupancy as well as RNA Polymerase II binding was measured upon nuclear depletion or overexpression of Sfp1

first: David

last: Shore


title: Global subcutaneous white adipose tissue (scWAT) transcript data from fasted male BXD strains on chow or high fat diet

city: Lausanne

first: Johan

last: Auwerx

address: Station 15

department: SV IBI NCEM

institute: École Polytechnique Fédérale de Lausanne

summary:
Transcript data from subcutaneous white adipose tissue (scWAT) from fasted-state male BXD strains on chow or high fat diet
We used microarrays to compare the subcutaneous white adipose tissue (scWAT) expression differences across the BXD strain family and across two diverse diets

overall_design: 29-week-old male mice were fasted overnight (6pm-9am), anesthetized under isoflurane, and perfused. After about five minutes (towards the end of the tissue collection pipeline), subcutaneous white adipose tissue was weighed then snap-frozen in liquid nitrogen. Later, the tissue was taken from a -80 freezer for RNA extraction from all individuals. Each dietary and strain cohort consisted of ~5 animals which were prepared independently. These indendent RNA samples were then then pooled into single dietary and genetic cohorts (as shown here) evenly by µg RNA as measured by Nanodrop. These pools were cleaned up with RNEasy, then frozen again in -80. Samples were then shipped from Lausanne, Switzerland to Memphis, TN, where the Affymetrix arrays were run. Tissues were in the -80 freezer approximately 1-2 years before RNA was prepared. RNA (post pooling by cohort, but pre-RNEasy cleanup) were in the freezer approximately 2.5 years before microarrays were run.

first: Evan

middle: G

last: Williams

first: Hao

last: Li

first: Pooja

last: Jha


title: RNA-sequencing of fibrolamellar carcinoma (FLC) cell line treated with miR-375 mimic

city: Ithaca

first: Praveen

last: Sethupathy

state: NY

address: T7 006 Vet Research Tower

institute: Cornell University

summary: Fibrolamellar carcinoma (FLC) is a rare liver cancer. Expression of miR-375 is significantly lost in primary FLC tumors compared to non-malignant liver. Here, we treated a FLC cell line with miR-375 mimic or scramble control to determine the function of miR-375 in FLC.

overall_design: RNA expression profiles were generated by high throughput sequencing using the Illumina NextSeq500 platform

first: Timothy

last: Dinh

first: Matthew

last: Kanke


title: Binding of the pioneer factor FOXA1 is independent of hormonal signalling

city: Cambridge

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

institute: Cancer Research UK, Cambridge Institute

summary: We hormone deprived MCF-7 and ZR75-1 breast cancer cells for three days and treated them with vehicle (ethanol) or estrogen for 45 minutes. We then performed FOXA1 ChIP-seq and showed that the vast majority (>99%) of FOXA1 binding events are not affected by steroid conditions. A small number (<1%) of FOXA1 binding sites appear to be induced by estrogen, but these are not genuine de novo binding sites and represent ‘shadow’ binding sites that result from chromatin interactions at super-enhancer containing estrogen-regulated genomic regions. FOXA1 is therefore not regulated by estrogen and remains a bone fide therapeutic target that is entirely upstream of the ER complex.

overall_design: FOXA1 ChIPseq in hormone-deprived MCF-7 and ZR751 cells, treated with vehicle or estrogen for 45 minutes.

first: Silvia-Elena

last: Glont

first: Igor

last: Chernukhin


title: DNA methylation inhibition attenuates pressure overload-induced cardiac hypertrophy in rats

city: Singapore

first: Roger

last: Foo

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

type: Methylation profiling by high throughput sequencing

summary: Inhibitors of DNA methyl transferase (DNMT) might be useful for treating cardiac hypertrophy by preventing de novo methylation and reduced transcription of anti-hypertrophic genes. This approach had been tested, but without a detailed phenotypic and methylation analysis. Here, we subjected rats to pressure overload and treatment with the DNMT inhibitor N-phthalyl-L-tryptophan (RG108) and analysed DNA methylation by cardiomyocyte (CM)-specific reduced representation bisulphite sequencing (RRBS).

overall_design: Rats were divided into 4 groups of n=12-16 each, subjected to sham or clip-based TAC surgery and treated daily with the non-nucleosidic, non-isoform specific DNMT inhibitor RG108 or solvent only. 4 weeks later, rats received cardiac MRI; heart weight and gene expression (qPCR) were quantified. For DNA methylation analysis, CM nuclei were isolated by magnetic cell separation with an antibody against PCM1, DNA was subjected to RRBS and data was analysed using R and IPA software (n=4 per group).

first: Justus

last: Stenzig


title: Next Generation Sequencing of Wild Type IFNG versus partial agonists in A549 cell line human transcriptomes

first: Juan

middle: Luis

last: Mendoza

address: 279 Campus Dr., Beckman Room B173

department: Molecular and Cellular Physiology

institute: Stanford University

summary:
Purpose: Next-generation sequencing (NGS) of human transcriptome of over 20,000 genes to compare gene expression of wild-type versus designed IFNG partial agonsits
Methods: A549 cells were treated with either wild-type IFNG or partial agonists for 48 hours. RNA was extracted and prepared for NGS on using Thermo Ampliseq human transriptome kit on an Ion S5 XL system (Thermo). Relative expression was determined from the data.
Results: Over 20,000 transcripts were matched to the human transcriptome to compare expression between protein treatments. We find genes that are stably expressed regardless of protein agonist treatment and other genes that have altered expression levels compared to wild-type.
Conclusions: Our study represents a comprehensive list of genes along with their sensitivity to IFNG induced signaling.

overall_design: RNA was extracted from two biological replicates in A549 cells after 48 hours of protein treatment, libraries prepared for and read on an Ion S5 XL system using the AmpliSeq human transcriptome kit.

first: J

middle: L

first: K

middle: C

last: Garcia


title: Jump-seq: Capture and amplify 5hmC Sites Whole Genome-Wide

city: Chicago

first: Yuwen

last: Liu

state: IL

address: 900 East 57th Street. KCDB building. Room 10250

department: Human Genetics

institute: University of Chicago

summary: We developed an efficient and precise method, which we name as Jump-seq, to capture and amplify 5hmC signal whole genome-wide, bridge the gap between base resolution (TAB-seq) and economic cost (hmC-seal).

overall_design: The principle is to label 5hmC by 6-N3-Glucose moiety and a hairpin DNA oligonucleotide carrying an alkyne group can be covalently connected to the azide-modified 5hmC via Huisgen cycloaddition (click) chemistry. The primer extension from the hairpin motif extends to the modified 5hmC site and will continue to “land” on the genomic DNA. 5hmC sites could be inferred from the DNA polymerase “landing” pattern at the 5-prime juncture.

first: Lulu

last: Hu

first: Shengtong

last: Han

first: Lei

last: Yang

first: Xiaolong

last: Cui

first: Yawei

last: Gao

first: Qing

last: Dai

first: Xingyu

last: Lu

first: Xiaochen

last: Kou

first: Yanhong

last: Zhao

first: Wenhui

last: Sheng

first: Shaorong

first: Xin

last: He

first: Chuan


title: The Set1 complex is dimeric and acts with Proof Only Jhd2 demethylation to convey symmetrical H3K4 trimethylation [ChIP-seq]

status: Public on Mar 06 2019

city: Dresden

first: Francis

last: Stewart

address: Tatzberg 47-49

country: Germany

institute: BIOTEChnology Center TU Dresden

summary: Epigenetic that deposit and/or propagate symmetry or asymmetry are not understood. Here we report that yeast Set1C/ COMPASS (complex of proteins associated with Set1) is dimeric and, consequently, symmetrically trimethylates histone 3 Lys4 (H3K4me3) on promoter nucleosomes. Mutation of the dimer interface to make Set1C monomeric abolished H3K4me3 on most promoters. The most active promoters, particularly those involved in the oxidative phase of the yeast metabolic cycle, displayed H3K4me2, which is normally excluded from active promoters, and a subset of these also displayed H3K4me3. In wild-type yeast, deletion of the sole H3K4 demethylase, Jhd2, has no effect. However, in monomeric Set1C yeast, Jhd2 deletion increased H3K4me3 levels on the H3K4me2 promoters. Notably, the association of Set1C with the elongating polymerase was not perturbed by monomerization. These results imply that symmetrical H3K4 methylation is an embedded consequence of Set1C dimerism and that Jhd2 demethylates asymmetric H3K4me3. Consequently, rather than methylation and demethylation acting in opposition as logic would suggest, a dimeric methyltransferase and monomeric demethylase cooperate to eliminate asymmetry and focus symmetrical H3K4me3 onto selected nucleosomes. This presents a new paradigm for the establishment of epigenetic detail.

overall_design: Examination of 3 different H3K4 modifications in Wt, three different sdc1 mutant, Jhd2 deletion, and double mutantion of sdc1 point mutant along with Jhd2 deletion by ChIP sequencing.

first: Rupam

last: Choudhury

first: Sukhdeep

last: Singh

first: Franics


title: Transcriptomes of  Tremella fuciformis and Annulohypoxylon stygium

city: wuhan

first: Dongmei

state: hubei

address: shi zi shan NO1 hubei

department: college of food science and technology

summary: In order to study the interaction between Tremella fuciformis and Annulohypoxylon stygium, the transcriptomes of individual T. fuciformis mycelia, T. fuciformis mycelia which interacted with A. stygium, dual mycelia of both, A. stygium mycelia which interacted with T. fuciformis and individual A. stygium mycelia were  obtained by RNA-seq

sample_organism:
Tremella fuciformis
Annulohypoxylon stygium

overall_design: Total mRNA of individual T. fuciformis mycelia, T. fuciformis mycelia which interacted with A. stygium, dual mycelia of both, A. stygium mycelia which interacted with T. fuciformis and individual A. stygium mycelia were generated by deep sequencing, using Illumina HiSeq 2000

first: Aimin

last: Ma


title: Genome-wide analysis of gene expression from islets of different sizes in response to in vivo serpin B13 mAB treatment

city: Rochester

first: Ching-Ho

last: Chang

address: 60 Crittenden Blvd, Apt 709

department: Biology

institute: U of Rochester

summary: By using oligonucleotide microarray-based technology as a tool for rapid mapping of unique differences in gene expression, we found that inhibiting serpin B13 in BALB/c mice treated with a mAb according to our protocol resulted in the upregulation of relatively few genes, including several Reg genes, which have been implicated in β-cell proliferation.

overall_design: BALB/c mice were intraperitoneally injected four times with 25 ug of serpin B13 mAb (clone: B29) or control mAb (IgG) (total dose of 100 ug) and sacrificed two weeks after the last injection.The islets were isolated and separated according to their diameter (<100 μM, 100~200 μM, and >200 μM). Total RNA was isolated from the islets. The results between serpin B13 mAb and control mAb were compared in the islets of different sizes.

first: Chi-Wen

last: Lo


title: The Set1 complex is dimeric and acts with Proof Only Jhd2 demethylation to convey symmetrical H3K4 trimethylation

relation:
SuperSeries of: GSE127840
SuperSeries of: GSE127841
SuperSeries of: GSE127842

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae


title: Altered expression of signaling pathways regulating neuronal excitability in hippocampal tissue of temporal lobe epilepsy patients with low and high seizure frequency

city: Tucson

first: Michael

last: Hammer

state: Arizona

address: 1657 E Helen St

institute: University of Arizona

summary: Despite recent advances in our understanding of synaptic transmission associated with epileptogenesis, the molecular mechanisms that control seizure frequency in patients with temporal lobe epilepsy (TLE) remain obscure. RNA-Seq was performed on hippocampal tissue resected from 12 medically intractable TLE patients with pre-surgery seizure frequencies ranging from 0.33 to 120 seizures per month. Differential expression (DE) analysis of individuals with low (LSF, mean= 4 seizure/month) versus high (HSF, mean= 60 seizures/month) seizure frequency identified 979 genes with ≥2-fold change in transcript abundance (FDR-adjusted p-value <0.05). Comparisons with post-mortem controls revealed a large number of downregulated genes in the HSF (1,676) versus LSF (399) groups. More than 50 signaling pathways were inferred to be deactivated or activated, with Signal Transduction as the central hub in the pathway network. While neuroinflammation pathways were activated in both groups, key neuronal system pathways were systematically deactivated in the HSF group, including calcium, CREB and Opioid signaling. We also infer that enhanced expression of a signaling cascade promoting synaptic downscaling may have played a key role in maintaining a higher seizure threshold in the LSF cohort. These results suggest that therapeutic approaches targeting synaptic scaling pathways may aid in the treatment of seizures in TLE.

overall_design: Investigation of alterations in hippocampal gene expression in temporal lobe epilepsy

first: Branden

last: Lau

middle: F


title: Expression data in the cerebral cortex of postnatal Dyrk1a+/+ and Dyrk1a+/- mice

city: Barcelona

first: Susana

last: de la Luna

address: Dr. Aiguader, 88

institute: Centre for Genomic Regulation

summary:
DYRK1A is a protein kinase with several roles in brain development. This kinase is involved in two intellectual disability syndromes: Down syndrome and DYRK1A haploinsufficiency syndrome. The Dyrk1a+/- mouse is a model for DYRK1A haploinsufficiency syndrome.
We used microarray to evaluate the impact of DYRK1A haploinsufficiency in the development of the cerebral cortex.

overall_design: Total RNA was prepared from the cerebral cortex of 4 Dyrk1a+/+ and 4 Dyrk1a+/- mice at both P0 and P7 for hybridization on Affymetrix Mouse GeneChip 430 2.0 Array.

first: Maria

last: Arbones

first: Elisa

last: Balducci

first: Ricardo

last: Gonzalo

first: Fatima

last: Nuñez

first: Rosa

last: Prieto

first: Alex

last: Sánchez


title: Wild-type and Math5-/- mouse dLGN (dorsolateral geniculate nucleus) at postnatal day time points

city: Blacksburg

first: Xiguang

last: Xu

state: VA

address: 1015 Life Science Circle

department: Department of Biomedical Sciences and Pathobiology

institute: Virginia Tech

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

overall_design: Refer to individual Series


title: Contrasting stage-dependent requirements during AML evolution identify EZH2 as a therapeutic target in AML

first: Brian

last: Huntly

address: Hills Road

department: Department of Haematology

institute: University of Cambridge

summary: Epigenetic regulators are commonly mutated in cancer. Activating mutations and overexpression of the lysine histone methyltransferase EZH2 occur in lymphoma and other malignancies, while loss-of-function mutations are found in myeloid malignancies. We study this apparent contradiction, examining the importance of cellular context for Ezh2 loss during the evolution of a single malignancy, Acute Myeloid Leukemia (AML). Remarkably, we observe diametrically opposite functions for Ezh2 at early and late stages during the evolution of leukemias generated by different AML-associated fusion-oncogenes. During disease maintenance we demonstrate that Ezh2 functions as an oncogene that may be therapeutically targeted. In contrast, Ezh2 acts as a tumour suppressor during AML induction and loss-of-function EZH2 mutations occur early in AML patient samples and confer a poor prognosis. Integrated genomic analysis demonstrates that different expression programmes are de-repressed during AML induction and maintenance following Ezh2 loss. During disease induction, Ezh2 loss de-represses a subset of bivalent promoters that resolve towards gene activation, inducing a feto-oncogene programme including genes such as Plag1, whose overexpression phenocopies Ezh2 loss to accelerate AML induction in mouse models. Our data highlight the importance of cellular context and phase of disease evolution for Ezh2 function. Moreover, we further identify EZH2 as a potential target in AML, whilst providing reassurance of the safety of this therapeutic strategy.

overall_design: ChIP-Seq analysis for histone modifications: Effect of Ezh2 knockout on H3K27me3, H3K4me3 and H3K27Ac modifications. RNA-Seq analysis: Effect of Ezh2 knockout on gene expression for normal lin- (lineage negative) murine BM HSPCs and in AML1-ETO9a/MLL-AF9 driven primary murine leukemias


title: Analysis of the polyA+ RNA of LPS-treated human CD14+ monocytes

city: Verona

first: Barbara

last: Mariotti

state: Verona

address: strada le grazie 8

department: Medicine

country: Italy

institute: University of Verona

summary: This study aims to investigate the profile and the role of lncRNAs in the IFN response initiated by TLR4 activation of primary human monocytes and their implication in the immune dysregulation present in SSc patients.

overall_design: PolyA+ RNA profiles of human primary CD14+ monocytes freshly isolated or treated with LPS (100 ng/mL) for 90min or 4h were generated by deep sequencing using Illumina HiSeq 2000.

first: Nicola

last: Tamasia

first: Flavia

last: Bazzoni

first: Marco

last: Cassatella


title: RNA-seq of Wild-type and Math5-/- mouse dLGN (dorsolateral geniculate nucleus) at postnatal day 3,  postnatal day 7, postnatal day 14 and postnatal day 23

summary: We performed transcriptome profiling for mouse dLGN (dorsolateral geniculate nucleus) tissues derived from P3, P7, P14 and P23 WT and Math5-/- mice.

overall_design: RNA-seq of mouse dLGN tissues from P3, P7, P14 and P23 WT and Math5-/- mice

first: Hehuang

last: Xie


title: iPSC-Derived Brain Endothelium Exhibits Stable, Long-Term Barrier Function in Perfused Hydrogel Scaffolds

city: Nashville

first: Ethan

last: Lippmann

state: TN

address: 2400 Highland Ave, Room 303

department: Chemical and Biomolecular Engineering

institute: Vanderbilt University

summary: We describe the construction a 3D blood-brain barrier model comprised of iPSC-derived brain endothelium cultured in channels within gelatin hydrogels. The iPSC-derived brain endothelium displays key features of the blood-brain barrier phenotype, including tight junction formation, efflux transporter activity, low paracellular permeability, and suppressed levels of transcytosis compared to non-blood-brain barrier endothelial controls. Collectively, this work provides the foundation for a fully human, biomimetic neurovascular model to study BBB in health and disease.

overall_design: iPSC-derived brain endothelium was cultured in 3D channels in gelatin hydrogels and analyzed for key signatures of blood-brain barrier phenotype. RNA-seq was used to assess changes in global gene expression signatures between endothelium cultured for one day under static conditions and fourteen days under perfused conditions.

first: Emma

middle: H

last: Neal

first: Shannon

last: Faley

first: Leon

last: Bellan


title: Histone modifications underlie monocyte dysregulation in Systemic Sclerosis patients, underlining the treatment potential of epigenetic targeting [RNA-seq]

city: Utrecht

first: Nila

middle: Hendrika

last: Servaas

address: Lundlaan 6

department: Laboratory for translational immunology

country: Netherlands

institute: UMC Utrecht

summary: Systemic sclerosis (SSc) is a chronic autoimmune disease that mainly affects the connective tissue. Monocytes have been shown to be an important cell type involved in the pathogenesis of SSc. By performing RNA-sequencing analysis on whole RNA isolated from peripheral blood CD14+ monocytes obtained from SSc patients, together with healthy controls matched for sex and age, obtained from the University Medical Center Utrecht (definite SSc cohort), and the University of Milan (non-fibrotic SSc cohort), we aimed to characterize the transcriptomic landscape of monocytes of patients with (pre-clinical) systemic sclerosis. Moreover, ChIPseq data was available for a part of the subjects included in the RNA-seq analysis and the correlation between the histone marks and gene expression was studied. The samples used in this study are part of the SYSCLASS cohort.

overall_design: Transcriptomic profiling was performed for two SSc cohorts. For the definite SSc cohort (Utrecht) total RNA from 9 heathy controls and 25 SSc patients were subjected to RNA-seq analysis. For the non-fibrotic SSc cohort (Milan) total RNA from 9 heathy controls and 30 pre-clinical SSc patients were subjected to RNA-seq analysis.

first: Maarten

last: van der Kroef

first: Marzia

last: Rossato

first: Timothy

middle: R

last: Radstake


title: Genome-wide maps of ISL1-binding site

city: beijing

first: guo

last: ting

address: 52 Fucheng Road, Haidian District

institute: Peking University Cancer Hospital & Institute, Beijing

summary: We report the high-throughput profiling of ISL1-binding sites in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide ISL1-binding maps of SGC7901 cells. This study provides a prediction of regulated genes by the ISL1.

overall_design: Examination of ISL1-binding sites in SGC7901 cell with overexpression ISL1.

first: Jiafu

last: Ji

first: Ting

last: Guo


title: The Set1 complex is dimeric and acts with Proof Only Jhd2 demethylation to convey symmetrical H3K4 trimethylation [Spike-in-ChIP-seq]

first: Francis

last: Stewart

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Quantitative examination of 3 different H3K4 modifications in Wt, three different sdc1 mutant, Jhd2 deletion, double mutantion of sdc1 point mutant along with Jhd2 deletion and set1 deletion mutant by ChIP sequencing. For quantifying changes in the methylation in different Saccharomyces cerevisiae cells we spiked in the ChIP with closely related Schizosaccharomyces pombe cells. The cells were mixed in a 2:1 ratio, respectively.

first: Rupam

last: Choudhury

first: Sukhdeep

last: Singh


title: Gene expression data of nasopharyngeal carcinoma (NPC) cell and Thiostrepton treatment

city: New Taipei City

first: Yu-Lun

last: Kuo

address: 7F-3, No.99, Sec. 1, Xintai 5th Rd., Xizhi Dist.

country: Taiwan

institute: BIOTOOLS

summary:
Thiostrepton, a natural antibiotic, has recently been shown to be a potential anticancer drug for certain cancers, but its study in nasopharyngeal carcinoma (NPC) is still limited. The aims of this study were to investigate the anticancer effect of thiostrepton on NPC cells and to explore its underlying mechanism. Our results showed that thiostrepton reduced NPC cell viability in a dose-dependent manner. Thiostrepton inhibited the migration and invasion of NPC cells in wound healing and cell invasion assays.
Thiostrepton effectively suppressed NPC cell proliferation, migration, and invasion, likely by several mechanisms. Thiostrepton may be a potential therapeutic agent for treating NPC in the future.

overall_design: Total RNA from NPC cells treated with or without 4 μM thiostrepton for 12 hours at 37°C was extracted using an illustra RNAspin Mini RNA isolation kit (GE Healthcare, Little Chalfont, UK) according to the manufacturer’s instructions. Amplification and biotinylation of the RNA and hybridization of the fragmented biotin-labeled cRNA with Affymetrix HG-U133 Plus 2.0 GeneChip microarrays.

first: Yen-Bin

last: Hsu

first: Ming-Chin

last: Lan

first: Chi-Ying

last: Huang


title: Single cell transcriptome analysis of TSCs differentiated TSCs, pTSCs and pTSCs isolated from blastoid

first: Nicolas

last: Rivron

state: Utrecht

address: Uppsalalaan 8

institute: Hubrecht Institute / Maastricht University

summary: We performed scRNA seq according to the CEL-seq2 protocol in order to define the equivalent developmental stages of TSCs

overall_design: Using FACS, we sorted single cells into 384 well plates  for TSCs derived in the Rossant lab. TSCs are cultured in Tx conditions. Differentiated TSCs have undergone differentiation after 6 days in culture without Fgf4, Tgfb nor heparin. pTSCs are culture din LT21 conditions. Blastoid single cells are isolated from harvested blastoids formed using pTS1 pTSCs.

first: Javier

last: Frias Aldeguer

first: Judith

last: Vivié

first: Anna

last: Alemany Arias

first: Niels

last: Geijsen

first: Clemens

last: van Blitterswijk


title: Mitochondrial genome encoded gene expression values from RNA sequencing data from multiple tissue types

city: London

first: Alan

last: Hodgkinson

address: The Strand

institute: King's College London

summary: We reprocessed 11,371 RNA-Seq libraries across 36 different tissue/cell types to generate expression values for 15 genes encoded in the mitochondrial genome.

overall_design: RNA sequencing reads were trimmed for adaptor sequences, terminal bases with nucleotide quality below 20 and poly(A) tails >4bp in length. We then mapped data to a reference genome (1000G GRCh37 reference, which contains the mitochondrial rCRS NC_012920.1) with STAR 2.51a, using two-pass mapping, and then then filter out non-properly paired and non-uniquely mapped reads. Parameters and filtering steps were designed to improve alignment to the mitochondrial genome. We then calculated transcripts per million (TPM) per gene, before log10 normalizing expression values and removing outlier values. A description of the full pipeline, methods and data can be found in "Nuclear Genetic Regulation of the Human Mitochondrial Transcriptome" by Ali et al (2019) [PMID: 30775970].


title: Bacteroides thetaiotaomicron ameliorates colon inflammation in preclinical models of Crohn’s Disease [Bacteroides]

city: Aberdeen

first: Imke

last: Mulder

address: Cornhill Road

institute: 4D Pharma Research Ltd

summary:
Analysis of the Bacteroides thetaiotaomicron(BT)  transcriptome during co-culture with Caco-2 intestinal epithelial cells
To identify potential bacterial protein(s) involved in the anti-inflammatory effect of BT in colitis, BT was incubated with Caco-2 human intestinal epithelial cells for 2 hours, and bacterial gene expression was assessed on a Bacteroides thetaiotaomicron VPI-5482 specific microarray. Forty-three BT genes were up-regulated by five-fold or more and of these, twenty genes encoded hypothetical proteins.

overall_design: Caco-2 cells cultured in 35mm dishes were treated with flagellin of Salmonella enteritidis, phorbol-12-myristate-13-acetate or interleukin 1. BT was added at 109 CFU/mL and incubated for 2h. Bacterial culture was then removed and RNA was processed for hybridization to a Bacteroides thetaiotaomicron VPI-5482 specific microarray.


title: The Set1 complex is dimeric and acts with Proof Only Jhd2 demethylation to convey symmetrical H3K4 trimethylation [RNA-seq]

overall_design: Saccharomyces cerevisiae mRNA profile of exponentialy growing cells of wild type (WT),  three different Sdc1 deletion mutant, Jhd2 deletion mutant and strain with double mutation of sdc1 point mutation with Jhd2 deletion.


title: Derivation of functional oocytes from granulosa cells

city: Munich

first: Chenglei

last: Tian

address: Ingolstädter Landstraße 1

institute: Helmholtz Munich

summary: Limited oocyte and ovarian reserve in vivo or chemo-therapy leads to reproductive aging or premature aging and associated diseases including infertility. Excitingly, oocytes have been successfully derived from embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) by ectopic expression of transcription factors, showing great potential in fertility preservation or restoration. The accessible granulosa cells are a type of somatic cells that interact and evolve with oocyte development during folliculogenesis. Further, with stem cells-like property, granulosa cells are amenable to reprogramming to generate iPSCs and have been the first used for clone animals. These prompted us to explore the potential of granulosa cells in derivation of germ cells. Meanwhile, the strict genome fidelity required for germ cells inspired us to test reprograming by complete small chemicals, which avoids genetic manipulation, cell transfection and destruction of embryos. Here we show that somatic granulosa cells of adult mouse ovaries can be converted to germ cells and functional oocytes that reproduce fertile pups. We are able to consistently induce granulosa cells to pluripotent state (gPSCs) like ESCs in both developmental competence and molecular signatures. Notably, crotonic sodium-facilitated crotonylation is critical not only for pure small chemicals-based reprogramming of granulosa cells to gPSCs, but also confers the gPSCs with high germline capacity. Consequently, the gPSCs and the derived primordial germ-cell like cells hold longer telomeres and maintain high genomic stability which is critical for germ cells. Taken together, we efficiently generate high quality gPSCs and functional oocytes from adult granulosa cells by significantly improving chemical reprograming approach.

overall_design: We collected GCs, MEFs and 16D reprogramming cells (also called XEN-like cells) to do RNA-sequence experiment to analyze which cell type is more closely to XEN-like cells in transcriptome. We collected 28D reprogramming cells with or without crotonic acid to do RNA-sequence experiment to analyze how CA can promote gPSCs generation. We collected six gCiPS cell lines, GCs and ESCs to analyze different quality of gPSC cell lines in transcriptome. We collected ESCs, gPSC4, ESC-EpiLCs, gPSC4-EpiLCs, ESC-PGCLCs, gPSC4-PGCLCs and E12.5 PGCs to do RNA-sequence experiment to analyze the process of PGCLCs induction from ESCs or gPSCs.


title: Identification of genes and pathways regulated by epigenetic mechanisms in determining general intelligence (g) of inbred mice

city: Kobe

first: Pei-Chieng

last: Cha

state: Hyogo

address: 7-5-1 Kusunoki-chou, Chuo-ku

department: Division of Neurology/Molecular Brain Science

institute: Kobe University Graduate School of Medicine

summary: General intelligence (g) is a common core shared by cognitive tasks. To study epigenetic regulation of “g”, 41 inbred mice raised under similar environmental conditions were subjected to five behavioral tests. We used principal component analysis to analyze 11 parameters that measure performance and reflect cognition of mice. Microarray gene expression analysis by using hippocampal RNAs of the 5, 12, and 8 mice consistently classified as having high, medium, and low cognition, respectively, by PC1 score and IQ score identified 17 genes that showed at least 1.3-fold difference in expression between mice with high and low cognition (FDR<0.30). Two of these genes were down-regulated and 15 of these genes were up-regulated in the high cognitive mice. Subsequent pathway-based analysis further identified gene-sets (GS) enriched in high cognitive mice and GS enriched in low cognitive mice. A number of genes implicated in our study have been previously associated with cognitive impairments. Our findings provide insights into genes and pathways regulated by epigenetic mechanisms in determining “g” and may shed lights on various disorders that affect cognitive function.

overall_design: Male inbred mice of C57BL/6J Strain (10 week-old) were subjected to a comprehensive behavioral test battery consisting of general health and neurological screening, open field test, new social interaction test (Crawley’s version), Barnes circular maze test (BM), 8-arm radial maze test (RM), T-maze test (TM), light/dark transition test, elevated plus-maze test, hotplate, social interaction test (novel environment), tail suspension, rotarod, prepulse inhibition, Porsolt forced swimming test, cued and contextual fear conditioning (FZ), gait analysis and passive avoidance (PA) (tests were listed following the sequence the tests were being conducted). Five of the aforementioned tests, namely BM, RM, TM, FZ, and PA, measured memory and cognitive performance of mice. BM, RM, and TM tests were conducted when mice aged 10-11, 12-14, and 15-19 week-olds, respectively; whereas FZ and PA, which leave stronger impacts on mice, were conducted at later stage when mice were 33 and 37-38 week-olds, respectively. The raw data including those of other behavioral tests, which are not measuring cognitive performance of mice and therefore not described in this paper, are disclosed in mouse phenotype database (http://www.mouse-phenotype.org/) as “B6J” strain. General cognitive ability of the 39 mice with complete data on the 11 parameters of the five behavioral tests aforementioned was determined. Detailed procedures were described in our paper. Mice that were consistently ranked as having high, medium, and low cognition by both ranking systems were identified and were subjected to subsequent gene expression profiling analysis.  All behavioral testing procedures have been approved by Animal Care and Use Committee of Kyoto University Graduate School of Medicine, where the tests have been performed.

first: Kazuhiro

last: Kobayashi

first: Yuko

last: Ando

first: Keizo

last: Takao

first: Tsuyoshi

last: Miyakawa

first: Tatsushi

last: Toda


title: Histone modifications underlie monocyte dysregulation in Systemic Sclerosis patients, underlining the treatment potential of epigenetic targeting [ChIP-seq]

first: Nila

last: Servaas

summary: With H3K27ac and H3K4me3 chromatin immunoprecipitation we identified alterations in the chromatin landscape of patients with systemic sclerosis. RNAsequencing data was available for the majority of the subjects included for the ChIPseq analysis and the correlation between the histone marks and gene expression was studied. The samples used in this study are part of the SYSCLASS cohort.

overall_design: H3K27ac and H3K4me3 ChIP-sequencing of CD14+ monocytes derived from peripheral blood (PB) from healthy controls (HC) and limited and diffuse Systemic Sclerosis patients.

first: Maarten

last: van der Kroef

first: Tim

last: Radstake

first: Marzia

last: Rossato

first: Michal

last: Mokry

first: Monica

last: Castellucci


title: Histone modifications underlie monocyte dysregulation in Systemic Sclerosis patients, underlining the treatment potential of epigenetic targeting


title: FACT activity and histone H3-K56 acetylation promote optimal establishment of chromatin architecture independent of ongoing transcription in Saccharomyces cerevisiae [MNase-Seq]

city: Salt Lake City

last: Formosa

state: UT

address: 15 N Medical Dr East RM 4100

department: Biochemistry

institute: University of Utah School of Medicine

summary: FACT is a histone chaperone that can destabilize or assemble nucleosomes. Acetylation of histone H3-K56 weakens a histone:DNA contact that is central to FACT activity, suggesting that this modification could affect FACT functions. We tested this by asking how mutations of H3-K56 and FACT affect nucleosome structure, chromatin integrity, and transcription output. Mimics of unacetylated or permanently acetylated H3-K56 had different effects on FACT in vitro and in vivo as expected, but H3-K56 and FACT mutations caused surprisingly similar changes in transcription of individual genes. Notably, neither the changes in transcript levels nor the effects on nucleosome occupancy resulting from mutations conformed to the model that FACT is needed to overcome nucleosomal barriers during transcription initiation or elongation. Instead, the results suggest that both FACT and H3-K56ac are involved in establishing chromatin architecture prior to transcription and restoring it afterwards. They contribute to a process that optimizes transcription frequency, especially at conditionally expressed genes, and restores chromatin integrity after transcription, especially at the +1 nucleosome to block antisense transcription, but FACT appears to be less involved than expected in directly promoting transcription.

overall_design: 12 samples (3 replicates each of 4 yeast strains) were treated with MNase to digest linker DNA and the resulting resistant fragments representing nucleosomal DNA were sequenced to obtain a genome-wide map of nucleosomal occupancy and positioning

first: Laura

last: McCullough

first: Trang

last: Pham

first: Timothy

middle: J

last: Parnell

first: Mahesh

last: Chandrasekharan

first: David

last: Stillman


title: ISL1-binding site

first: guo

last: ting

overall_design: Refer to individual Series


title: GRO-sequencing identifies transcriptional regulators and ncRNAs important for iPSC to hepatocyte differentiation

city: Tampere

first: Leena

middle: Eloni

last: Viiri

address: Arvo Ylpön katu 34

country: Finland

institute: Tampere University

summary: Hepatocyte-like cells (HLCs) were differentiated from induced pluripotent stem cells (iPSCs) using two different protocols and the genome-wide transcriptomic profile of the iPSC, HLCs and primary human hepatocytes were compared using Global Run-On sequencing (GRO-seq). In addition to protein coding genes, GRO-seq enabled identification of noncoding RNA species including primary miRNAs and long non-coding RNAs (lncRNAs). Altogether, 29 hub miRNAs that could regulate ~3000 target mRNAs related to regulation of transcription, translation, protein metabolism and cell cycle were identified. Alternative transcription start site (TSS) usage between the cell types was detected for several miRNA clusters. Additionally, HLC differentiation included extensive changes in lncRNA expression, which exhibited strong co-regulation with the protein-coding gene expression. Analysis of the motifs within regulated TSSs, allowed identification of transcription factors that might drive the transcriptional changes during hepatocyte differentiation.

overall_design: 3 iPSC cell lines were used and as a reference primary human hepatocytes (PHHs) from 2 donors (Hu8209, male, Caucasian, 50 years and Hu8132, female, Caucasian, 57 years)

middle: E

first: Tommi

last: Rantapero

first: Mostafa

last: Kiamehr

first: Mikko

last: Oittinen

first: Keijo

first: Henri

last: Niskanen

first: Matti

last: Nykter

first: Minna

middle: U

last: Kaikkonen

first: Katriina

last: Aalto-Setälä


title: Next generation sequening on control salivary submandibular glands versus glands from mice with an epithelial deletion in SOX10 via the Cre-Flox system

city: Ann Arbor

first: Isabelle

last: Lombaert

state: MI

address: 2800 Plymouth Rd

institute: University of Michigan

summary: We report sequencing data on fetal mouse submandibular glands (SMGs) where SOX10 was deleted in the epithelia. By obtaining embryonic day 16 (E16) SMGs, we compared control glands with glands where SOX10 was deleted in the epithelial compartment. We found that loss of SOX10 resulted in smaller glands, which had reduced expression of genes related to the initiation of acinar, myoepithelial and intercalated duct cells.

overall_design: Examination of gene expression in 2 different glands.


title: The immediate impact of exoribonucleolysis on nuclear RNA processing, turnover and transcriptional control revealed by rapid depletion of DIS3, EXOSC10 or XRN2 from human cells

city: Exeter

first: Steven

last: West

state: Devon

address: Stocker Rd

department: Living Systems Institute

institute: University of Exeter

summary: Cell-based studies of human ribonucleases traditionally relies on methods that deplete proteins slowly.  To assess their immediate roles in nuclear RNA biology, we engineered cells where the 3’->5’ exoribonucleases of the exosome complex, Dis3 and EXOSC10, can be eliminated within 60 minutes.  Loss of Dis3 has the greatest impact, causing thousands of enhancer RNAs, intragenic transcripts, promoter upstream transcripts (PROMPTs) and products of premature cleavage and polyadenylation (PCPA) to accumulate.  Interestingly, EXOSC10 only targets these substrates when Dis3 is absent, which is explained by its rapid mis-localization to the nucleoplasm following Dis3 loss.  Direct detection of EXOSC10 substrates revealed a more specific role in trimming of short 3’ extensions on ribosomal and small nucleolar RNAs.  Finally, the 5’-3’ exoribonuclease, Xrn2, has little activity on exosome substrates, but promotes termination following PCPA.  Interestingly, Xrn2 is not rate limiting for PROMPT termination providing a distinction between sense and anti-sense transcriptional regulation.

overall_design: Nuclear RNA-seq was performed on an auxin-inducible degron (AID) tagged cell lines in treated with or without auxin inducing rapid depletion of EXOSC10 or DIS3 protein. HCT116 cells also ectopically express TIR1 from a sleeping beauty transposon integrated cassette. AID incorporated proteins contain in-frame insertion of AID tag, P2A cleavage site, antibiotic resistance marker and SV40 polyA site. Two repair templates expressing different antibiotic resistance markers (neomycin and hygromycin) were used to ensure biallelic intersion of the repair cassette using CRISPR/Cas9. We also performed individual nucleotide cross-linking and immunoprecipitation (iCLIP) on a catalytic mutant of EXOSC10 (D313N), in order to complement a previous iCLIP experiment using EXOSC10 WT. We reasoned that by using a catalytic mutant  of EXOSC10 we would be able to stabilize interactions between the exoribonuclease and it global RNA substrates. In the process we identified 30nt footprints of iCLIP density downstream of pre-rRNAs and pre-snoRNAs exclusively seen in EXOSC10 CAT CLIP profiles.

first: Lee

last: Davidson

last: Francis

first: Ross

middle: A

last: Cordiner

first: Joshua

middle: D

last: Eaton

first: Chris

last: Estell

first: Sara

last: Macias

first: Javier

last: Caceres

first: Steve


title: WGBS (Whole Genome Bisulfite Sequencing) of Wild-type and Math5-/- mouse dLGN (dorsolateral geniculate nucleus) at postnatal day 6 and postnatal day 23

first: Xiguang

last: Xu

summary: We performed methylome profiling for mouse dLGN tissues derived from P6 and P23 WT and Math5-/- mice.

overall_design: WGBS of mouse dLGN tissue from P6 and P23 WT and Math5-/- mice.

first: Hehuang

last: Xie


title: Bacteroides thetaiotaomicron ameliorates colon inflammation in preclinical models of Crohn’s Disease

first: Imke

last: Mulder

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

sample_organism:
Mus musculus
Bacteroides thetaiotaomicron VPI-5482


title: Gene expression and epigenetic alterations in human hepatocytes treated with low doses of chemical carcinogens

status: Public on Mar 05 2019

city: Jefferson

first: Volodymyr

last: Tryndyak

address: 3900 NCTR Rd

department: Division of Biochemical Toxicology

institute: US-FDA National Center for Toxicological Research

summary: The increasing number of man-made chemicals in the environment that may pose a carcinogenic risk emphasizes the need for the development of reliable time- and cost-effective approaches for carcinogen detection.  To address this issue, we have investigated the utility of human hepatocytes for the in vitro identification of genotoxic and non-genotoxic carcinogens.  Induced pluripotent stem cell (iPSC)-derived human hepatocytes were treated with the genotoxic carcinogens aflatoxin B1 (AFB1) and benzo[a]pyrene (B[a]P) and with the non-genotoxic liver carcinogen methapyrilene at non-cytotoxic concentrations for 7 days, and transcriptomic profile was examined. 1569 (892 protein-coding and 677 non-coding), 1693 (922 protein-coding and 771 non-coding), and 2061 (1462 protein-coding and 599 non-coding) differentially expressed genes were detected in cells treated with AFB1, B[a]P, and methapyrilene, respectively.  Additionally, we examined the toxicogenomics response to AFB1, B[a]P, and methapyrilene exposure in human HepaRG cells and demonstrated that carcinogens had a less prominent effect on the cellular transcriptome as compared to that in human iPSC-derived hepatocytes.  Overall, the results demonstrate that the prime non-genotoxic effect of exposure to carcinogens, regardless of their mode of action, in short-term in vitro testing is a profound global transcriptome response, indicating a greater value of toxicogenomics for rapid carcinogen screening in vitro.

overall_design: iPSC-derived human hepatocytes (on the 4th day after seeding) were treated with 0.2 µM AFB1 or AFB2, 1 µM B[a]P or B[e]P, or 20 µM methapyrilene for 7 consecutive days.

first: Frederick

last: Beland

first: Igor

middle: P

last: Pogribny


title: Bacteroides thetaiotaomicron ameliorates colon inflammation in preclinical models of Crohn’s Disease [mouse colon]

summary:
Analysis of the gut transcriptome as affected by treatment with Bacteroides thetaiotaomicron in a mouse model of IBD
Here, we report analysis of the gut transcriptome in IL10KO mice after treatment with Bacteroides thetaiotaomicron (BT). Comparative transcriptome analysis of ascending colon tissue of IL10KO and IL10KO/BT-treated mice showed differential expression of a wide range of genes associated with inflammatory responses between the two treatment groups. Expression of proinflammatory genes and genes involved in pathogen recognition was particularly lower in IL10KO/BT mice.

overall_design: IL10KO mice were dosed with BT 3 times a week from weaning at 3 weeks old, for a total period of 13-14 weeks. Control IL10KO mice were dosed with culture medium alone.


title: Exosome release is regulated by mTORC1 via a Rab27A-dependent mechanism

city: guangzhou

first: zou

middle: wen

last: chong

state: guangdong

address: Sha Tai ROAD

department: Department of Cell Biology

institute: Southern Medical University

summary: Exosomes are small membrane-bound vesicles released into extracellular spaces by many types of cells. These nanovesicles carry proteins, mRNA and miRNA and are involved in cell waste management and intercellular communication. In the present study we show that exosome release, which leads to net loss of cellular membrane and protein content, is negatively regulated by mechanistic target of rapamycin complex 1 (mTORC1). We find that in cells and animal models exosome release is inhibited by sustained activation of mTORC1, leading to intracellular accumulation of CD63-positive exosome precursors. Inhibition of mTORC1 by rapamycin or nutrient and growth factor deprivation stimulates exosome release, which occurs concomitantly with autophagy. The drug-stimulated release is blocked by siRNA-mediated downregulation of small GTPase Rab27A. Analysis of the cargo content in exosomes released from rapamycin treated cells reveals that inhibition of mTORC1 does not alter its protein and miRNA profiles. These observations demonstrate that exosome release, like autophagy, is negatively regulated by mTORC1 in response to changes in nutrient and growth factor conditions

overall_design: Examination of 2 different microRNA expressions on rapamycin (Rapa) or mock treated (Ctrl) cells

first: Wenchong

last: Zou

first: Xiaochun

last: Bai


title: FACT activity and histone H3-K56 acetylation promote optimal establishment of chromatin architecture independent of ongoing transcription in Saccharomyces cerevisiae

first: Tim

last: Formosa


title: Expression profiling of PBMCs from VA-ECLS patients

status: Public on Mar 04 2019

city: Grand Rapids

first: Eric

last: Kort

address: 333 Bostwick NE

institute: Van Andel Research Institute

summary: We profiled RNA expression by means of single cell RNA-Seq from a total of ~60,000 cells from 38 patients undergoing VA-ECMO due to acute heart failure (including acute exacerbation of chronic failure). Samples were taken at the time of initiation of ECMO (mean +/- 79 minutes from cannulation).

overall_design:
Survival analysis, 30 day survival, with cross sectional analysis of gene expression at start of VA-ECLS
Submitters plan to submit raw files to dbGaP to protect patient sequence privacy

first: Stefan

last: Jovinge


title: Dynamic imbalance between cancer cell subpopulations induced by Transforming Growth Factor Beta (TGF-β) is associated with a DNA methylome switch [expression array]

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

summary: Distinct subpopulations of neoplastic cells within tumors, including hepatocellular carcinoma (HCC), display pronounced ability to initiate new tumors and induce metastasis. Recent evidence suggests that signals from transforming growth factor beta (TGF-β) may increase the survival of these so called tumor initiating cells leading to poor HCC prognosis. However, how TGF-β establishes and modifies the key features of these cell subpopulations is not fully understood.  In the present report we describe the differential DNA methylome of CD133-negative and CD133-expressing liver cancer cells. Next, we show that TGF-β is able to increase the proportion of CD133+ cells in liver cancer cell lines in a way that is stable and persistent across cell division. This process is associated with stable genome-wide changes in DNA methylation that persist through cell division. Differential methylation in response to TGF-β is under-represented at promoter CpG islands and enriched at gene bodies, including a locus in the body of the de novo DNA methyl-transferase DNMT3B gene. Moreover, phenotypic changes induced by TGF-β, including the induction of CD133, are impaired by siRNA silencing of de novo DNA methyl-transferases.  Our study reveals a self-perpetuating crosstalk between TGF-β signaling and the DNA methylation machinery, which can be relevant in the establishment of cellular phenotypes. This is the first indication of the ability of TGF-β to induce genome-wide changes in DNA methylation, resulting in a stable change in the proportion of liver cancer cell subpopulations.

overall_design: Total RNA obtained from HepG2 and Huh7 liver cancer cell lines after 8 days of exposure to transforming growth factor beta (TGFb).


title: Decipherment of transcriptional aneuploidy response patterns of monosomic alien addition lines (MAALs) in a restituted Brassica rapa

city: Wuhan P.R. China

first: Bin

last: Zhu

address: No.1,Shizishan Street · Hongshan District · Wuhan · Hubei Province · 430070 · P.R.China

department: College of Plant Science and Technology

institute: Huazhong Agricultural University

summary: Herein, we performed high-throughput technology to detect gene expression alterations of a whole set of nine Brassica rapa-oleracea monosonic alien addition lines (MAALs, C1-C9) in comparison of parental restituted B. rapa (RBR). Both MAALs and RBR obtained previously are in the background of natural B. napus genotype “Oro”. We found that, compared to diploid RBR, all the MAALs showed various degree of dysregulated expression genes resulting from cis-effect and more prevailing trans-effect. And trans-effect on gene expression in MAALs likely was increasing with the homology between recipient A genome and additional C chromosome instead of genes content of extra C chromosome. Totally, 10 trans-effect dysregulated expression genes mainly involved in the function of transporter activity were observed in all pairwise comparisons. Strikingly, highly expressed gene was more prone to down-regulated and opposite situation was observed for low expressed genes in all pairwise comparisons, suggesting this is a common character in transcriptional patterns response to aneuploidy.

overall_design: The newly expanded third leaves without petioles from six plants of each genotype were collected and immediately stored in liquid nitrogen for RNA extraction. Three samples with three replicates were sequenced via  Illumina HiSeqTM 3000.

first: Qi

last: Pan

first: Pan

last: Zeng

first: Bowei

last: Cai

first: Xianhong

last: Ge

first: Zaiyun

last: Li


title: RNAseq analysis of glomerular transcriptome of wild-type vs. Podocyte Cosmc knockout

city: Boston

first: Johannes

last: Schlondorff

state: MA

address: 99 Brookline Ave, RN304B

department: Nephrology

institute: Beth Israel Deaconess Medical Center

summary: Cosmc is an obligate chaperone for C1GalT1 T transferase necessary for generating mature mucin-type O-glycans.  Animals lacking Cosmc in glomerular podocytes develop proteinuria, glomerulosclerosis and progressive renal failure.  This study was designed to examine transcriptome differences in 1 month male animals with and without podocyte Cosmc, a time point when proteinuria is established but glomerular architecture is still relatively intact.

overall_design: Glomeruli were isolated by Dynabead perfusion technique from 1 month old control(n=5) and Podo-Cre; CosmcY/flox(n=4) male animals.  RNA was isolation using Rneasy Plus Mini kit (Qiagen).  Samples were sent to GeneWiz for polyA-based mRNA enrichment, cDNA synthesis, RNA-seq library preparation and sequencing on an Illumina HiSeq.  Paired end 2x150 bp reads were obtained.  Bioinformatic analysis was performed through GeneWiz

middle: S


title: The oncoprotein NUP98-HOXD13 (NHD13) induces thymocyte self-renewal via Lmo2/Lyl1

city: Clayton

first: Wei

last: Shi

state: Victoria

address: Wellington Rd

country: Australia

institute: Monash University

summary: T-cell Acute Lymphoblastic Leukaemia (T-ALL) can be classified into a number of subfamilies, including those that overexpress TAL1/LMO, TLX1/3 and HOXA transcription factors. Whilst it has been previously shown in mouse models that TAL1/LMO transcription factors induce thymocyte self-renewal, whether this is the case for other transcription factor subclasses is currently unknown. To address this, we have studied vav-Nup98-HoxD13-transgenic (NHD13-Tg) mice, a model of HOXA-driven T-ALL, which overexpress HOXA transcription factors throughout haematopoiesis and display features of myelodysplastic syndrome in the bone marrow along with T-cell developmental abnormalities in the thymus and subsequent development of T-ALL in approximately 15% of mice. Thymocytes from preleukemic NHD13-Tg mice could engraft long-term in serial transplantation assays, demonstrating that NHD13-Tg thymocytes have acquired self-renewal capacity. Transcriptome analysis showed that NHD13-Tg thymocytes exhibited a Stem Cell like transcriptional program which closely resembled that of Lmo2 transgenic thymocytes, including Lmo2 itself and the critical Lmo2 cofactor Lyl1, suggesting a common mechanism of thymocyte self-renewal in these models. To determine whether Lmo2/Lyl1 are required for NHD13-induced thymocyte self-renewal, NHD13-Tg mice were crossed with Lyl1 knockout mice to generate NHD13-Tg mice lacking Lyl1. This showed that Lyl1 is essential for expression of the stem cell-like gene expression program in NHD13-Tg thymocytes and for thymocyte self-renewal. Surprisingly however, absence of Lyl1 accelerated the onset of T-ALL in NHD13-Tg mice. These studies demonstrate that Lyl1 is essential for self-renewal of NHD13-Tg thymocytes, suggesting that Lmo2 and Lyl1 may mediate thymocyte self-renewal induced by a variety of T-cell oncogenes. However, whilst Lyl1-induced thymocyte self-renewal is essential for Lmo2-driven T-cell leukemia, NHD13 can also promote T-ALL via an alternative pathway.

overall_design: Total RNA obtained from sorted CD4-CD8 double-negative thymocytes

first: Benjamin

last: Shields

first: Matthew

last: McCormack


title: Genome-wide stress responses to copper and arsenic in a field population of Daphnia.

city: Gent

first: Jana

last: Asselman

address: Coupure Links 653 (Building F, 2nd floor)

country: Belgium

institute: Ghent University

summary: Over the past decade, significant advances have been made to unravel molecular mechanisms of stress response in different ecotoxicological model species. Within this study, we focus on population level transcriptomic responses of a natural population of Daphnia magna Straus, (1820), to heavy metals. We aim to characterize the population level transcriptomic responses, which include standing genetic variation, and improve our understanding on how populations respond to environmental stress at a molecular level. We studied population level responses to two heavy metals, copper and arsenic, and their binary mixture across time. Transcriptomic patterns identified significantly regulated gene families and genes at the population level including cuticle proteins and resilins. Furthermore, some of these differentially regulated gene families, such as cuticle proteins, were also significantly enriched for genetic variations including SNPs and MNPs. In general, genetic variation was observed in specific gene families, many of which are known to be involved in stress response. Overall, our results indicate that molecular stress responses can be identified within natural populations and that linking molecular mechanisms with genetic variation at the population level could contribute significantly to adverse outcome frameworks.

overall_design: We exposed a field population of daphnia to copper, arsenic and a mixture of copper and arsenic and extracted RNA at different time points

first: Ilias

last: Semmouri

first: Craig

last: Jackson

first: Nathan

last: Keith

first: Filip

last: Van Nieuwerburgh

first: Dieter

last: Deforce

first: Joseph

last: Shaw

first: Karel

last: De Schamphelaere


title: Dynamic imbalance between cancer cell subpopulations induced by Transforming Growth Factor Beta (TGF-β) is associated with a DNA methylome switch

first: Hector

last: Hernandez-Vargas


title: Effects of Polybrominated Diphenyl Ether (PBDE) Mixture on estrogen receptor positive (ER+) patient-derived tumor xenograft (PDX) model

city: Duarte

first: Noriko

last: Kanaya

address: 1500 East Duarte

department: Cancer Biology

institute: Beckman Research Institute at City of Hope

summary: ER+ PDX (COH-SC31) were exposed to PBDE mixture for 1 weeks. RNA-sequencing analysis was performed to evalaute the gene expression changes.

overall_design: RNA-Seq gene expression was compared between control (DMSO, dimethyl sulfoxide) and treatment with mixture of PBDEs.

first: Shiuan

last: Chen


title: FACT activity and histone H3-K56 acetylation promote optimal establishment of chromatin architecture independent of ongoing transcription in Saccharomyces cerevisiae [RNA-Seq]

first: Tim

last: Formosa

overall_design: 24 samples (3 replicates each of 8 yeast strains) were RNA-Seq profiled.

first: Laura

last: McCullough

first: Trang

last: Pham

first: Timothy

last: Parnell

first: Mahesh

middle: B

last: Chandrasekharan

first: David

last: Stillman


title: Effect of Polybrominated diphenyl ethers (PBDEs) on gene expression of MCF7 cells

summary: RNA sequence analysis showed that PBDE47 had estrogenic activity through cell cycle regulation, and PBDE100 and PBDE153 had anti-estrogenic activity throguth ER and AhR cross talk.

overall_design: MCF7 expression was compared with control (DMSO, dimethyl sulfoxide), a known estrogen agonist (PPT, propyl pyrazole),  a combination of PPT and MPP (methyl piperidino pyrazole, a known estrogen antagonist to counteract the effect of PPT treatment), and 3 types of PBDEs.  PBDE47 was treated without any other compounds (with the expectation that it is an estrogen agonist), while PBDE100 and PBDE153 were treated along with PPT (so that expected estrogen antagonists could counteract the PPT treatment).


title: Dynamic imbalance between cancer cell subpopulations induced by Transforming Growth Factor Beta (TGF-β) is associated with a DNA methylome switch [methylation]

summary: Distinct subpopulations of neoplastic cells within tumors, including hepatocellular carcinoma (HCC), display pronounced ability to initiate new tumors and induce metastasis. Recent evidence suggests that signals from transforming growth factor beta (TGF-β) may increase the survival of these so called tumor initiating cells leading to poor HCC prognosis. However, how TGF-β establishes and modifies the key features of these cell subpopulations is not fully understood. In the present report we describe the differential DNA methylome of CD133-negative and CD133-expressing liver cancer cells. Next, we show that TGF-β is able to increase the proportion of CD133+ cells in liver cancer cell lines in a way that is stable and persistent across cell division. This process is associated with stable genome-wide changes in DNA methylation that persist through cell division. Differential methylation in response to TGF-β is under-represented at promoter CpG islands and enriched at gene bodies, including a locus in the body of the de novo DNA methyl-transferase DNMT3B gene. Moreover, phenotypic changes induced by TGF-β, including the induction of CD133, are impaired by siRNA silencing of de novo DNA methyl-transferases.  Our study reveals a self-perpetuating crosstalk between TGF-β signaling and the DNA methylation machinery, which can be relevant in the establishment of cellular phenotypes. This is the first indication of the ability of TGF-β to induce genome-wide changes in DNA methylation, resulting in a stable change in the proportion of liver cancer cell subpopulations.

overall_design: Bisulphite converted DNA from 24 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip


title: ChIP-seq from gastrocnemius medialis (ENCSR903SJC)

status: Public on Mar 03 2019

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
ChIP-seq on human gastrocnemius medialis

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Identification of atheroprone shear stress responsive regulatory elements in endothelial cells

city: Leipzig

first: Olga

last: Bondareva

state: Saxony

address: Philipp-Rosenthal-Straße 27

department: HI-MAG

institute: Helmholtz Zentrum München

summary: While variations in gene transcription networks in models of atherosclerosis have been reported, the underlying changes in the chromatin landscape induced by pro-atherogenic stimuli remain elusive. In the present study, we report changes in chromatin regulatory elements that mediate transcriptional control upon the application of oscillatory shear stress of ±3 dyn/cm2 in primary cultured human umbilical vein endothelial cells (HUVECs) at 6 h time point of oscillatory shear stress stimulation compared to static condition.

overall_design: H3K27ac ChIP-Seq and total RNA-Seq profiles of HUVEC under oscillatory and static conditions were generated by paired-end sequencing using Illumina NextSeq 500 System.

first: Hans

last: Schnittler


title: Polybrominated diphenyl ethers (PBDEs)

overall_design: Refer to individual Series


title: Inflammatory Mediator Expression Associated With Antibody Response Induced by Live Attenuated vs Inactivated Influenza Virus Vaccine in Children.

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh

summary:
The reasons for differences in vaccine effectiveness between live attenuated influenza vaccine (LAIV) and inactivated influenza vaccine (IIV) are not clea
Blood samples were obtained before vaccination and at days 7 and 21 postvaccination with 2015-2016 quadrivalent IIV or LAIV. Serologic response to the vaccine was measured by hemagglutination inhibition assay.
Targeted RNA sequencing and serum cytokine analysis were performed. Paired analyses were used to determine gene expression and were compared between IIV and LAIV recipients.

overall_design: Targeted transcriptomic analysis of blood samples from patients before vaccination and at days 7 and 21 post vaccination

first: John

last: Alcorn

first: Richard

last: Zimmerman


title: Aged blood impairs hippocampal neural precursor activity and activates microglia via brain endothelial cell VCAM1

city: Palo Alto

first: Liana

middle: Nicole

last: Bonanno

state: California

address: 3801 Miranda Ave, Bldg 100 Rm D3-111

department: Neurology

institute: Stanford University

summary: RNAseq of Old (19 month) vs Yound (3 month) mouse brain endothelial cells

overall_design: Old and Young brain endothelial cells were isolated from cortex and hippocampus of C57Bl/6 mice

first: Hanadie

last: Yousef

first: Ramesh

middle: V

last: Nair

first: Tony

last: Wyss-Coray


title: ChIP-seq from HEK293 (ENCSR776MDR)

summary:
eGFP-ZNF577 ChIP-seq on human HEK293 cells.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from K562 (ENCSR621ATC)

summary:
ZNF184 ChIP-seq on human K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from subcutaneous adipose tissue (ENCSR498VPN)

summary:
ChIP-seq on human adipose tissue

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from HepG2 (ENCSR210HBN)

summary:
Chip-Seq on HepG2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from suprapubic skin (ENCSR491PTJ)

summary:
Chip-Seq on suprapubic skin

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Differentially regulated miRNAs following murine femoral artery injury

city: Hannover

first: Daniel

last: Sedding

address: Carl-Neubergstr. 1

department: Cardiology

institute: Hannover Medical School

summary:
We performed wire-induced injuries in 12 week old C57BL/6J mice. Dilation of the femoral artery was performed by inserting a straight spring wire (0.38 mm diameter) for 10 mm towards the iliac artery, as described previously (Sedding D, Daniel JM, Muhl L, Hersemeyer K, Brunsch H, Kemkes-Matthes B, Braun-Dullaeus RC, Tillmanns H, Weimer T, Preissner KT, Kanse SM. The g534e polymorphism of the gene encoding the factor vii-activating protease is associated with cardiovascular risk due to increased neointima formation. The Journal of experimental medicine. 2006;203:2801-2807).
Mice were sacrificed and perfused with phosphate buffered saline via the left ventricle. Femoral arteries were excised at 10 and 21 days after injury, snap-frozen and miRNA was isolated by phenol-chloroform extraction following the purelink

overall_design: Each sample consisted of 3 femoral arteries to increase RNA yield. Two samples per timepoint were assembled and the corresponding uninjured femoral arteries were used as controls.


title: Serological autoantibody profiling of type 1 diabetes  by protein arrays.

city: Tempe

first: Xiaofang

last: Bian

address: 1001 S. McAllister Ave.

institute: Arizona State University

summary: The study was aimed to identify novel autoantibody(AAB) biomarkers for Type 1 diabetes.

overall_design: The immunoreactivity was compared between 74 T1D cases and 75 healthy controls against ~750 human proteins that printed duplicate on microscopic slides.

first: Shane

last: Miersch

first: Sahar

last: Sibani


title: ChIP-seq from K562 (ENCSR497VFH)

summary:
ZNF639 ChIP-seq on human K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from K562 (ENCSR494UQJ)

summary:
NR3C1 ChIP-seq on human K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from sigmoid colon (ENCSR481ZPB)

summary:
Chip-Seq on -human (fragmentation date:Mon Sep 19 2016 00:00:00 GMT-0500 (CDT)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from HepG2 (ENCSR485OYR)


title: Gene expression signatures of innate lymphoid cells from human blood

city: Zurich

first: Ge

last: Tan

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

institute: University of Zurich

summary: We aimed to determine the characteristic of 3 different ILC subsets (ILC1, 2 and 3) isolated from human blood.

overall_design: mRNA profile of ILC1, ILC2 and ILC3

first: Shuo

last: Li

first: Cezmi

last: Akdis


title: ChIP-seq from prostate gland (ENCSR467YGK)

first: ENCODE

last: DCC

summary:
Chip-Seq on -human (fragmentation date:Sun Oct 30 2016 23:00:00 GMT-0600 (CST)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from suprapubic skin (ENCSR467CRM)

summary:
Chip-Seq on -human (fragmentation date:Mon Sep 12 2016 00:00:00 GMT-0500 (CDT)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from suprapubic skin (ENCSR464CSO)


title: ChIP-seq from K562 (ENCSR474CVP)

summary:
TRIM28 ChIP-seq on human K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from right atrium auricular region (ENCSR457JBY)

summary:
ChIP-seq on human right atrium auricular region

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from esophagus muscularis mucosa (ENCSR442ZTI)

summary:
Chip-Seq on muscle layer of esophagus

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from K562 (ENCSR996ESX)

summary:
NFRKB ChIP-seq on human K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from sigmoid colon (ENCSR978LQC)

summary:
Chip-Seq on sigmoid colon

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from suprapubic skin (ENCSR972HZL)


title: ChIP-seq from HEK293 (ENCSR993DED)

summary:
eGFP-ZNF214 ChIP-seq on human HEK293 cells.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from K562 (ENCSR986CDX)

summary:
NEUROD1 ChIP-seq on human K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from GM12878 (ENCSR437GBJ)

summary:
NFATC3 ChIP-seq on human GM12878

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from upper lobe of left lung (ENCSR986QAR)

summary:
Chip-Seq on upper lobe of left lung

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from RWPE2 (ENCSR987PNT)

summary:
H3K27ac ChIP-seq on human RWPE2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from K562 (ENCSR439OCL)

summary:
ZNF407 ChIP-seq on human K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from vagina (ENCSR475KZM)


title: ChIP-seq from K562 (ENCSR431XGJ)

summary:
PYGO2 ChIP-seq on human K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from spleen (ENCSR959UQA)

summary:
Chip-Seq on spleen

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from prostate gland (ENCSR442CIF)

summary:
Chip-Seq on prostate

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from GM12878 (ENCSR961PPA)

summary:
ATF2 ChIP-seq on human GM12878

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from K562 (ENCSR953DVM)

summary:
E2F8 ChIP-seq on human K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from spleen (ENCSR950CUQ)


title: ChIP-seq from K562 (ENCSR426URK)

summary:
AFF1 ChIP-seq on human K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from breast epithelium (ENCSR951JUP)

summary:
Chip-Seq on -human (fragmentation date:Fri Nov 11 2016 00:00:00 GMT-0600 (CST)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from K562 (ENCSR949NVY)

summary:
ZNF639 ChIP-seq on human K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from MCF-7 (ENCSR423RTK)

summary:
GATA3 ChIP-seq on human MCF-7

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from MCF-7 (ENCSR419ODQ)

summary:
ZNF507 ChIP-seq on human MCF-7

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from esophagus muscularis mucosa (ENCSR936JHB)

summary:
Chip-Seq on muscle layer of esophagus

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from breast epithelium (ENCSR939FGB)

summary:
Chip-Seq on mammary gland

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from spleen (ENCSR936XMR)

summary:
Chip-Seq on -human (fragmentation date:Thu Nov 10 2016 00:00:00 GMT-0600 (CST)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from suprapubic skin (ENCSR411EGZ)

summary:
ChIP-seq on human suprapubic skin

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from HEK293 (ENCSR946ZLI)

summary:
eGFP-KLF13 ChIP-seq on human HEK293 cells.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from HepG2 (ENCSR412ZDC)

summary:
Chip-Seq on HepG2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from HepG2 (ENCSR404JRP)

summary:
Reverse crosslink control Chip-Seq on HepG2 human (fragmentation date 8-22-2013)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from bipolar neuron (ENCSR418KUS)

summary:
Chip-Seq on biopolar spindle neuron

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from prostate gland (ENCSR404VWY)


title: ChIP-seq from sigmoid colon (ENCSR403USE)

summary:
Chip-Seq on sigmoid colon

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from RWPE2 (ENCSR394DWD)

summary:
ChIP-seq on human RWPE2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from MCF-7 (ENCSR402JAC)

summary:
ZNF574 ChIP-seq on human MCF-7

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from MCF-7 (ENCSR934JDG)

summary:
CLOCK ChIP-seq on human MCF-7

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from K562 (ENCSR928KOR)

summary:
GMEB1 ChIP-seq on human K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ChIP-seq from sigmoid colon (ENCSR920FID)