title: Gene analysis of ameloblasts in Sox21KO

city: SENDAI

first: Kan

last: Saito

state: Miyagi

address: 4-1 Seiryo-machi

department: Oral Health and Development Sciences

institute: Tohoku University

summary: Tooth and hair development starts from ectodermal invaginations. However, the determination of organ-specific cell fates is poorly understood. The transcription factor Sox21 is expressed in the epithelium of developing teeth. We discovered that disruption of Sox21 caused severe enamel hypoplasia and ectopic hair formation in the gingiva in Sox21 knockout incisors. We dissected tooth germ from P1 Sox21 KO and control incisors for microarray. In particular, several markers of ameloblast maturity, i.e. amelotin (Amtn), laminin α3 (Lama3), and kallikrein-related peptidase 4 (Klk4), were included among the downregulated molecules in Sox21 KO tooth germ, whereas the expression of Mmp20 and Amel was not changed. On the other hand, numerous keratin-related genes were upregulated in the Sox21 KO tooth germ and WT skin. As in the microarray results, the expression of dental epithelial stem cell marker Sox2, as well as keratin family and hair-related genes such as Lgr5, were increased in Sox21 KO dental epithelium. Taken together, these results reflected the perturbed differentiation of ameloblasts and a cell fate change in the Sox21 KO incisors.

overall_design: Microarray Analysis of Ameloblasts in the Sox21 KO Mouse Incisor ameloblasts and whole tooth germs were isolated from P0 wild-type (WT) and Sox21 KO mice. Labeled RNA samples were hybridized onto SurePrint G3 Mouse GE 8×60K microarrays.


title: Expression data from sorted hair follicle stem cells of control and Hes1 conditional knockout mice using K14-Cre at P70

status: Public on Dec 31 2019

city: Zhunan

first: Liang-Tung

last: Yang

state: Miaoli County

address: 35, Keyan Rd.

country: Taiwan

institute: National Health Research Institutes

summary:
Hes1 regulates hair follicle regenerative cycling
We used microarrays to profile the global gene expression of hair follicle stem cells in the telogen phase at P70 after depilation at P49. These microarray analysis were designed to identify the signaling networks regualting hair follicle stem cell behavior in the presence or absence of Hes1.

overall_design: 2 independent biologic replicates  (each pooled from 2 distinct mice) from control and Hes1 conditional knockout mice were FACS sorted for bulge stem cells (CD34+CD49f+)

first: Lin

last: Hsien-Yi

first: Yang

last: Liang-Tung


title: The Chromatin Remodelling Contributions of Snf2l in Cerebellar Granule Neuron Differentiation [ATAC-Seq]

city: Ottawa

first: David

last: Picketts

address: 501 Smyth Rd

country: Canada

institute: Ottawa Hospital Research Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Snf2l and the closely related protein, Snf2h, play a critical role in embryonic and post-natal brain development. Murine models lacking functional Snf2h or Snf2l point to complementary activities of these remodelers; Snf2h cKO mice present with a significantly reduced cerebellum, while Snf2l Ex6DEL cerebella are larger than their wild-type counterparts. Granule neuron progenitors (GNPs) isolated from Ex6DEL cerebella display delayed cell cycle exit and hindered terminal differentiation compared to wild-type littermates. Moreover, loss of Snf2l activity results in widespread transcriptome shifts which underlie the Ex6DEL GNP differentiation phenotype. In particular, key transcription factors (TFs) are differentially expressed without Snf2l remodelling activity. We confirm that ERK pathway activation is misregulated in Ex6DEL GNPs, possibly in response to elevated fibroblast growth factor 8 (Fgf8) expression in these cultures. We find that Snf2l activity maintains the chromatin landscape throughout GNP differentiation, as Ex6DEL cultures have a global increase in chromatin accessibility. We suggest that Snf2l-mediated chromatin condensation is responsible for proper regulation of gene expression programs in GNP differentiation.

overall_design: Assess modifications in chromatin accessibility upon loss of Snf2l activity (Ex6DEL)

first: Laura

middle: R

last: Goodwin

first: Matías

last: Alvarez-Saavedra

first: Stephen

last: Rennick

middle: J


title: Gene Expressions responsible for good response to Nivolumab treatment

status: Public on Dec 23 2019

city: Koto-ku,

first: Masashi

last: Kitazawa

state: Tokyo

country: Japan

institute: National of Institute of Advanced Industrial Science and Technology (AIST)

summary: Analysis of  gene expression in CD62Lhigh CD4+ T cells and CD62Llow CD4+ T cells from good responder (GR), intermediate responder (IR), and non-responder (NR).

overall_design: PBMC were obtained from two of each responder group; good responders, intermediate responders, and non-responders. CD4+ T cells were purified by negative selection using human CD4+ T cell isolation kits. CD4+ T cells were further separated into CD62Lhigh cells and CD62Llow cells by anti-CD62L mAb-coated microbeads and MACSTM system. We have invetigated the differences of gene expresion between CD62L high and low CD4+ Tcell from three kinds of patients groups.

first: Hiroshi

last: Kagamu

first: Katsuhisa

last: Horimoto


title: Inflammatory mediators regulate long non-coding RNA-PPTG1-1:1 in myeloid leukemia

city: Seoul

first: Marc

last: Diederich

address: Gwanak-ro, Gwanak-gu, 1

department: College of Pharmacy

country: South Korea

institute: Seoul National University

summary:
Analysis of the effect of TNFα on the expression of lncRNA during EPO or GM-CSF culture, in TF-1 cells at different time points.
The study attemps to determine the differents keys lncRNA Regulating response or regulated by TNFα during EPO induced differentiation or basal culture with GM-CSF.

overall_design: 4  experimental conditions at 4 different time points (0, 6, 24, 48 hours). Three biological replicates were done, including dye-swaps.

first: Sébastien

last: Chateauvieux

first: Anthoula

last: Gaigneaux

first: Marion

last: Orsini

first: Franck

last: Morceau

first: Mario

last: Dicato

first: Déborah

last: Gérard


title: Expression Signatures of Single Isolated Myofibers of Mouse Hindlimb.

status: Public on Dec 20 2019

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

summary: Skeletal muscles are composed by different myofiber types with a wide range of metabolic and functional properties. In the past years, biophysical analyses on isolated muscle fibers were extensively used to study the different contractile features of each myofiber type. To better clarify the complex mechanisms determining and regulating this heterogeneity, we applied genomic technologies at the level of single isolated myofibers. Fibers were prepared from soleus and EDL mouse muscles in order to obtain a comprehensive collection of fiber types classified according to myosin heavy chain (MyHC) isoforms. Transcriptomic analysis performed using microarray technology produced expression profiles of myofibers free from the background of non-contractile cell of the muscles. This permitted to identify a complete catalogue of genes differentially expressed among fiber types, mainly coding for metabolic enzymes, isoforms of the contractile proteins, and proteins involved in calcium homeostasis. Interestingly, myofibers transcriptionally grouped in 3 different transcriptional clusters, named transcriptional slow (tS), intermediate (tI), and fast(tF), mainly according to their metabolism and speed of contraction. This transcriptionally based myofibers grouping only partially fit with myofibers classification based on MyHC isoforms. In addition, using microarray data, we identified a limited set of transcriptional markers that can be used to unequivocally classify myofibers in one of the three clusters (tS, tI, or tF). This approach based on single cell analysis would allow a better description and comprehension of the adaptive transitions at transcriptional level occurring in myofibers under physiological and pathological conditions.

overall_design:
EDL and soleus mouse muscles were incubated with type I collagenase (Sigma-Aldrich) to dissociate intact myofibers that were separately collected under stereomicroscope. Isolated myofibers were divided in two parts: one was immersed in Laemmli buffer for fiber typing; the other was placed in TRIzol Reagent (Life Technologies) for RNA purification. Myofibers were classified according to their myosin heavy chain (MyHC) protein isoform in pure MyHC-1, -2A, -2X, -2B, and hybrid Hyb-2A/2X, and -2X/-2B (total: 6 myofiber types). We analyzed the transcription profiles of 10 single isolated myofibers (biological replicas) for each of the 6 patterns of MyHC isoform expression (total: 60 experiments). One-color hybridizations were performed on SurePrint G3 Mouse GE 8x60K Microarrays (Agilent Technologies).
Biological replicates of the same myofiber type were numbered from 1 to 10 and marked with the muscle of origin (S for soleus, and E for EDL) and the number of the animal.

first: Francesco

last: Chemello

first: Stefano

last: Cagnin

first: Pasqua

last: Cancellara

first: Paolo

last: Martini

first: Caterina

last: Millino

first: Beniamina

last: Pacchioni

first: Chiara

last: Romualdi

first: Carlo

last: Reggiani


title: Transcriptional changes induced by over-expression of miR-27a-3p in C2C12 myoblasts.

summary: Skeletal muscle has a central role in whole body metabolism with myofibers that represent its functional units. These are differentiated cells with different contraction power and metabolic traits. Faster contracting myofibers preferentially use glucose as substrate for energy production, while slower use lipids. Myofibers can plastically change phenotypic traits in response to pathophysiological stimuli. Since post-transcriptional mechanisms should administer the changes of these post-mitotic cells, we demonstrated that miR-27a-3p influences myofiber fuel availability and mitochondrial morphology. In vitro and in vivo experiments demonstrate that miR-27a-3p regulates glycogen utilization. We used microarrays to characterize the global changes in gene expression in C2C12 myoblasts due to over-expression of miR-27a-3p.

overall_design: C2C12 myoblasts were transfected with miR-27a-3p mimic or a scrambled sequence, as control. Transfection efficiency was estimated of about 60%. Transfection experiments were independently repeated in 6 replicates for miR-27a-3p mimic and 4 replicates for scrambled sequence. Results were evaluated after 72 hours of transfection.

first: Francesca

last: Grespi

first: Luca

last: Scorrano


title: Transcriptional changes induced by over-expression of miR-142-3p in C2C12 myoblasts.

summary: Skeletal muscle has a central role in whole body metabolism with myofibers that represent its functional units. These are differentiated cells with different contraction power and metabolic traits. Faster contracting myofibers preferentially use glucose as substrate for energy production, while slower use lipids. Myofibers can plastically change phenotypic traits in response to pathophysiological stimuli. Since post-transcriptional mechanisms should administer the changes of these post-mitotic cells, we demonstrated that miR-142-3p influences myofiber fuel availability and mitochondrial morphology. In vitro and in vivo experiments demonstrate that miR-142-3p regulates lipids utilization. We used microarrays to characterize the global changes in gene expression in C2C12 myoblasts due to over-expression of miR-142-3p.

overall_design: C2C12 myoblasts were transfected with miR-142-3p mimic or a scrambled sequence, as control. Transfection efficiency was estimated of about 60%. Transfection experiments were independently repeated in 6 replicates for miR-142-3p mimic and 4 replicates for scrambled sequence. Results were evaluated after 72 hours of transfection.


title: Expression Signatures of Single Isolated Myofibers of Mouse Hindlimb and miR-27a-3p or miR-142-3p overexpression in C2C12 myoblasts

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

overall_design: Refer to individual Series


title: ONECUT2 overexpression promotes RAS-driven lung adenocarcinoma progression

status: Public on Dec 27 2019

city: Shanghai

first: Qingyang

last: Ma

state: Xuhui

address: Yue Yang Road 320#

country: China

institute: Shanghai Institutes for Biological Sciences

type: Expression profiling by high throughput sequencing

summary: Aberrant differentiation, driven by activation of normally silent tissue-specific genes, results in a switch of cell identity and often leads to cancer progression. The underlying genetic and epigenetic events are largely unexplored. Here, we report ectopic activation of the hepatobiliary-, intestinal- and neural-specific gene one cut homeobox 2 (ONECUT2) in various subtypes of lung cancer. ONECUT2 expression was associated with poor prognosis of RAS-driven lung adenocarcinoma. ONECUT2 overexpression promoted the malignant growth and invasion of A549 lung cancer cells in vitro, as well as xenograft tumorigenesis and bone metastases of these cells in vivo. Integrative transcriptomics and epigenomics analyses suggested that ONECUT2 promoted the trans-differentiation of lung cancer cells by preferentially targeting and regulating the activity of bivalent chromatin domains through modulating Polycomb Repressive Complex 2 (PRC2) occupancy. Our findings demonstrate that ONECUT2 is a lineage-specific and context-dependent oncogene in lung adenocarcinoma and suggest that ONECUT2 is a potential therapeutic target for these tumors.

overall_design: We retrovirally transduced ONECUT2 or its mutant lacking DNA-binding domains into A549 cells to generate cells stably overexpressing HA-tagged ONECUT2 (A549-ONECUT2 cells) or ΔDBD mutant (A549-ONECUT2(ΔDBD) cells), respectively. We generated genome-wide expression profiles (RNA-seq) in A549-ONECUT2 cells and A549-ONECUT2(ΔDBD) cells. We also generated ChIP-seq from A549-ONECUT2 cells using HA antibody, as well as H3K4me3， H3K27me3 and EZH2 ChIP-seq from A549-ONECUT2 cells and A549-ONECUT2(ΔDBD) cells. To further investigate the involvement of PRC2 in epigenetic regulation of ONECUT2 transcription, we generated RNA-seq in A549 cells treated with EZH2 inhibitor (GSK126).

first: Landian

last: Hu

first: Xiangyin

last: Kong


title: Bonn Datasets of meta-analysis on AML classification

status: Public on Dec 18 2019

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)


title: Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair

city: Oxford

first: Tatjana

last: Sauka-Spengler

state: Oxfordshire

address: Radcliffe Department of Medicine

department: University of Oxford

country: United Kingdom

institute: MRC Weatherall Institute of Molecular Medicine

summary: Canonical roles for macrophages in mediating the fibrotic response after a heart attack (myocardial infarction) include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up-regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen-tagged transgenic zebrafish and splenic monocyte-derived macrophages from adult mouse GFPtpz-collagen donors, enhanced scar formation and induced fibrosis, respectively, via cell autonomous production of collagen.  In zebrafish, macrophage-specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo-injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts, and implicate macrophages as direct contributors to fibrosis during heart repair.

overall_design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury (ventricular resection and cryo-injury) at 3 different stages of regenerative process in the zebrafish heart.

first: Filipa

middle: C

last: Simões

first: Amy

last: Kenyon

first: Daria

last: Gavriouchkina

first: Michael

last: Weinberger

first: Eva

last: Masmanian

first: Sarah

last: Meyes

first: Paul

last: Riley


title: Genome wide browser of 5hmc abundance in MA9.3ITD cell with PBS or HHT treatment.

status: Public on Dec 19 2019

city: Monrovia

first: Jianjun

last: Chen

state: CA

department: Systems Biology

country: USA

institute: Beckman Research Institute of City of Hope

type: Methylation profiling by high throughput sequencing

summary: We propose a novel mechanism for HHT in treating acute myeloid leukemia with the 5hmC dysregulation involved.

overall_design: Examining the 5hmC abundance with or without HHT treatment in MA9.3ITD cell

first: Chenying

last: Li

first: Lei

last: Dong

first: Rui

last: Su

first: Chunxiao

last: Song


title: DNA methylation instability by BRAF-mediated TET silencing and lifestyle-exposure divides colon cancer pathways [3 cell lines]

city: Basel

first: Faiza

last: Noreen

address: Mattenstrasse 28

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

type: Methylation profiling by genome tiling array

summary: Promoter hypermethylation divides colon cancers into subtypes with and without a CpG island methylator phenotype (CIMP). Here, we performed genome-wide DNA methylation profiling of colonic normal and tumor tissues to dissect development of CpG hypermethylation in colon carcinogenesis. This identified age-environment related versus genetically driven CpG hypermethylation, the latter being associated with CIMP cancers. We found a strong association between BRAFV600E mutation and downregulation of the DNA demethylases TET1 and TET2. Expression of BRAFV600E in CIMP cancer cells suppressed TET1 transcription, which was sufficient to establish hypermethylation at CIMP genes promoters, including that of TET2. This phenotype was reverted by the BRAFV600E inhibitor vemurafenib. Thus, BRAFV600E, via impairment of cytosine de-methylation, is a genetic driver of CIMP in colon tumorigenesis.

overall_design: Bisulfite-converted DNA from three colon cancer cell lines were hybridised to the Illumina Infinium 450k Human Methylation BeadChip.

first: Kaspar

last: Truninger

first: Primo

last: Schär


title: DNA methylation instability by BRAF-mediated TET silencing and lifestyle-exposure divides colon cancer pathways [tumor, paired normal]

summary:
Promoter hypermethylation divides colon cancers into subtypes with and without a CpG island methylator phenotype (CIMP). Here, we performed genome-wide DNA methylation profiling of colonic normal and tumor tissues to dissect development of CpG hypermethylation in colon carcinogenesis. This identified age-environment related versus genetically driven CpG hypermethylation, the latter being associated with CIMP cancers. We found a strong association between BRAFV600E mutation and downregulation of the DNA demethylases TET1 and TET2. Expression of BRAFV600E in CIMP cancer cells suppressed TET1 transcription, which was sufficient to establish hypermethylation at CIMP genes promoters, including that of TET2. This phenotype was reverted by the BRAFV600E inhibitor vemurafenib. Thus, BRAFV600E, via impairment of cytosine de-methylation, is a genetic driver of CIMP in colon tumorigenesis.
Genome-wide DNA methylation profiling of adjacent non-tumor colon tissue and colon adenocarcinoma samples. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs. Samples included 8 colon cancer tissues and their associated healthy mucosa (CAM).

overall_design: Bisulfite-converted DNA from the 16 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2.


title: DNA methylation instability by BRAF-mediated TET silencing and lifestyle-exposure divides colon cancer pathways [Caco2 cell line]

overall_design: Caco2 cells stably expressing oncogenic BRAF (BRAFV600E) or GFP. Bisulfite-converted DNA were hybridised to the Illumina Infinium 450k Human Methylation BeadChip.


status: Public on Dec 16 2019

city: London

first: Trinidad

last: Montero

address: Charterhouse Square

department: Biochemical Pharmacology

institute: Whilliam Harvey Research Institute, Bart's and The London School of Medicine; Queen Mary University of London

summary: Gene expression profile of BMS-470539 on human synovial fibroblasts.

overall_design: Cells from 8 rheumatoid arthritis patients were cultured in vitro and treated either with the drug BMS-470539 or vehicle during 10 days.

last: Montero-Melendez

first: Mauro

last: Perretti

first: Christopher

middle: D

last: Buckley

first: Ai

last: Nagano

first: Andrew

last: Filler

first: Jason

last: Turner


title: DNA methylation instability by BRAF-mediated TET silencing and lifestyle-exposure divides colon cancer pathways

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Next Generation Sequencing Facilitates Quantitative Analysis of  Splenic Regulatory T cells Transcriptomes in Acute Myeloid Leukemia Mouse

status: Public on Dec 17 2019

city: Tianjin

first: Guo Guang

last: Zheng

state: Tianjin

address: Blood Hospital,288 Nanjing Road,Heping District

department: Institute of Hematology & Blood Hospital

institute: Chinese Academy of Medical Science& Peking Union  Medical College

summary: The goals of this study aim to reveal specific profiles of Treg cells in response to acute myeloid leukemia

overall_design: Comparion the Transcriptome of Treg cells from acute myeloid leukemia mice to that from normal mice

first: GuoGuang

first: Rong

last: Wang


title: RNA-sequencing of control and wy-14643 treated livers in wt and sirt6-hz mice

status: Public on Dec 15 2019

city: Ramat Gan

first: Tirza

middle: T

last: Doniger

state: Not US or Canada

address: Bar Ilan University

department: The Mina and Everard Faculty of Life Sciences

country: Israel

institute: Bar Ilan University

summary: wy-14643 activates PPARA to promote beta oxidation. SIRT6 is known to promote beta oxidation. Here we examine the effect of PPARA activation in SIRT6 heterozygote mice.

overall_design: Liver mRNA profiles of 1 year old wild type (WT) and SIRT6 heterozygote (SIRT6-HZ) livers orally gavaged with carboxymethyllcellulose control (CMC) or WY-14643 50mg/kg for 12 hours

first: Haim

middle: Y

last: Cohen


title: Human co-transcriptional splicing kinetics and coordination revealed by direct nascent RNA sequencing

status: Public on Dec 12 2019

city: Sherbrooke

first: Karine

last: Choquet

state: Québec

address: 3201 rue Jean-Mignault

department: Biochemistry and Functional Genomics

institute: Université de Sherbrooke

summary: Human genes have numerous exons that are differentially spliced within pre-mRNA. Understanding how multiple splicing events are coordinated across nascent transcripts requires quantitative analyses of transient RNA processing events in living cells. We developed nanopore analysis of CO-transcriptional Processing (nano-COP), in which nascent RNAs are directly sequenced through nanopores, exposing the dynamics and patterns of RNA splicing without biases introduced by amplification. nano-COP showed that in both human and Drosophila cells, co-transcriptional splicing occurs after RNA polymerase II transcribes several kilobases of pre-mRNA, suggesting that metazoan splicing transpires distally from the transcription machinery. Inhibition of the branch site recognition complex SF3B globally abolished co-transcriptional splicing in both species. Our findings revealed that splicing order does not strictly follow the order of transcription and is influenced by cis-regulatory elements. In human cells, introns with delayed splicing frequently neighbor alternative exons and are associated with RNA-binding factors. Moreover, neighboring introns in human cells tend to be spliced concurrently, implying that splicing occurs cooperatively. Thus, nano-COP unveils the organizational complexity of metazoan RNA processing.

sample_organism:
Drosophila melanogaster
Homo sapiens
synthetic construct

overall_design: Stringent purification of nascent RNA and sequencing with Illumina and Oxford Nanopore Technologies platforms. Direct RNA nanopore sequencing was performed on human K562 cells and Drosophila S2 cells.

first: Heather

middle: L

last: Drexler

first: L

middle: S

last: Churchman


title: Bone marrow-derived progenitors become decidual cells and are essential for implantation and pregnancy maintenance

status: Public on Dec 01 2019

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

summary: The pregnant decidua is infiltrated by many immune cells which are thought to originate in the bone marrow (BM) promoting pregnancy. In addition, BM-derived progenitor cells (BMDPCs) become non-hematopoietic endometrial cells. However, whether BMDPCs become non-immune decidual cells and their functional contribution to pregnancy were previously unknown. Here, we show that embryo implantation stimulates vast BMDPCs recruitment to decidua, where BMDPCs differentiate into non-hematopoietic stromal decidual cells. In addition, to determine the functional importance of BMDPCs to pregnancy, we used mice with endometrial stromal-specific defects precluding successful pregnancy. BM transplant (BMT) from wild-type (WT) into Hoxa11-/- mice, which lack decidualization, results in uterine transcriptional changes leading to stromal expansion, gland formation, and marked decidualization otherwise absent in Hoxa11-/- mice. By contrast, BMT from Hoxa11-/- into WT mice induces pregnancy loss. Importantly, in Hoxa11+/- mice, which have increased pregnancy losses, BMT from WT donors leads to normalized expression of numerous decidualization-related genes and rescue of pregnancy loss. Collectively, these findings reveal that BMDPCs have a novel non-hematopoietic physiologic contribution to decidual stroma, thereby playing indispensable roles in pregnancy establishment and maintenance.

overall_design:
Female Hoxa11 heterozygotes or wild type mice were given Hoxa11 knockout or wild type bone marrow transplants. After mating, uterine implantation sites were collected and total RNA was extracted on ED 5.5. 14 samples were sequenced by single-end next generation sequencing and differential transcriptome analysis.
Single cell RNA analysis of the E9.5 implantation site in mice using the same GFP BMT model to further establish the decidual stromal phenotype of GFP+ BMDC cell subsets.

first: Reshef

last: Tal

first: Shafiq

last: Shaikh

first: Pallavi

last: Pallavi

first: Aya

last: Lopez-Giraldez

first: Fang

last: Lyu

first: Yuan-yuan

last: Fang

first: Shruti

last: Chinchanikar

first: Ying

last: Liu

first: Harvey

last: Kliman

first: Myles

last: Alderman III

first: Nicola

last: Pluchino

first: Jehanzeb

last: Kayani

first: Ramanaiah

last: Mamillapalli

first: Diane

last: Krause

first: Hugh

last: Taylor


title: Mechanisms of RNA virus induced plant death

city: Norwich

first: Tamas

last: Dalmay

address: Earlham Road

department: School of Biological Sciences

institute: University of East Anglia

type: Non-coding RNA profiling by high throughput sequencing

summary: The changes of small RNA profile have been studied in tomato and wild tomato plants to understand the host reponse to the infection of a non-coding viral RNA infection.

sample_organism: Solanum lycopersicum x Solanum habrochaites

overall_design: Through comparing the response of tomato to necrogenic and non-necrogenic satRNA, the changes of small RNA profile gives the sRNAs that are correlated with the initiation of programmed cell death in tomato shoot apex. The difference in small RNA profiles in lethal host tomato and survival host S. habrochaitis underlines the sRNAs that may be involved in regulating plant death.

first: Ping

last: Xu

first: Irina

last: Mohorianu

first: Bidisha

last: Paul

first: Maria-Elena

last: Mannarelli

first: Marilyn

last: Roossinck

first: Hua

last: Wang


title: Viral determinants in H5N1 influenza A virus enable productive infection of HeLa cells

status: Public on Nov 21 2019

city: La Jolla

first: Max

last: Chang

address: 9500 Gilman Drive

institute: University of California, San Diego

summary: Influenza A virus (IAV) is a human respiratory pathogen that causes yearly global epidemics, and sporadic pandemics due to human adaptation of pathogenic strains. Efficient replication of IAV in different species is, in part, dictated by its ability to exploit the genetic environment of the host cell. To investigate IAV tropism in human cells, we evaluated the replication of IAV strains in a diverse subset of epithelial cell lines. HeLa cells were refractory to growth of human H1N1 and H3N2, and low pathogenic avian influenza (LPAIs) viruses. Interestingly, a human isolate of the highly pathogenic avian influenza (HPAI) virus H5N1 successfully propagated in HeLa cells to levels comparable to a human lung cell line. Heterokaryon cells generated by fusion of HeLa and permissive cells supported H1N1 growth, suggesting the absence of a host factor(s) required for replication of H1N1, but not H5N1, in HeLa cells. The absence of this factor(s) was mapped to reduced nuclear import, replication, and translation, and deficient viral budding. Using reassortant H1N1:H5N1 viruses, we found that the combined introduction of nucleoprotein (NP) and hemagglutinin (HA) from H5N1 was necessary and sufficient to enable H1N1 growth. Overall, this study suggests the absence of one or more cellular factors in HeLa cells that results in abortive replication of H1N1, H3N2, and LPAI viruses, but can be circumvented upon introduction of H5N1 NP and HA. Further understanding of the molecular basis of this restriction will provide important insights into virus-host interactions that underlie IAV pathogenesis and tropism.

overall_design: Comparison of gene expression in uninfected and influenza-infected A549 and HeLa cells.

first: Ariel

last: Rodriguez-Frandsen

first: Laura

last: Martin-Sancho

first: Anshu

middle: P

last: Gounder

first: Sumit

middle: K

last: Chanda


title: ChIP-seq for Gli1 and Gli2 in chondrosarcoma

city: Durham

first: Benjamin

last: Alman

state: NC

address: 200 Trent Drive, Orange Zone 5th floor

institute: Duke University

summary: Excessive Hedgehog signaling in chondrocytes is sufficient to cause formation of enchondroma-like lesions in mice which can progress to chondrosarcoma. To elucidate potential mechanisms through which activation of Hedgehog signaling contributes to cartilage tumor formation, we used chromatin immunoprecipitation and next generation sequencing to identify Gli1 and Gli2 target genes in primary human chondrosarcoma. In silico analyses were conducted to identify and characterize Gli1 and Gli2 binding regions, including de novo motif analysis, co-localization with additional transcription factors, distance to transcriptional start site, conservation between human and mouse, and supervised and unsupervised analyses of biological pathways and processes. Our results profile putative unique and overlapping target genes of Gli1 and Gli2 in chondrosarcoma.

overall_design: Cells were cultured from a primary chondrosarcoma obtained following surgery. Cells were divided into three groups and treated with Shh ligand to stimulate the Hedgehog signaling pathway. Following fixation, DNA was immunoprecipitated using antibodies against Gli1, Gli2, and IgG (negative control), and subjected to sequencing.

first: Shabana

middle: A

last: Ali

first: Ben

last: Niu

first: Kathy

last: Cheah


title: Netrin-1 signalling function in mouse pluripotent stem cells

status: Public on Dec 02 2019

city: Lyon

first: Fabrice

last: Lavial

address: 28 rue Laennec

country: France

institute: CRCL


title: Epithelial migration and non-adhesive periderm are required for digit separation during mammalian development

status: Public on Nov 26 2019

city: Irvine

first: Ghaidaa

last: Kashgari

address: 250 sprague Hall

institute: University of California Irvine

summary: GRHL3 is required for  epithelial morphogenesis and periderm function

overall_design: transcriptomic analysis of Grhl3-/- handpads compared to control embryos at E14.5

first: Bogi

last: Andersen


title: Early chromatin shaping predetermines multipotent vagal neural crest into neural, neuronal and mesenchymal lineages [scRNA-seq]

status: Public on Nov 27 2019

first: Tatjana

last: Sauka-Spengler

summary: The enteric nervous system (ENS) predominantly originates from vagal neural crest cells (VNC) that emerge from the caudal hindbrain, invade the foregut and populate the gastrointestinal tract. However, the gene regulatory network (GRN) orchestrating the early specification of VNC remains unknown. Using an EdnrB enhancer, we generated a comprehensive temporal map of the chromatin and transcriptional landscape of VNC in the avian model, revealing three VNC cell clusters (neural, neurogenic and mesenchymal), each predetermined epigenetically prior to neural tube delamination. We identify and functionally validate regulatory cores (Sox10/Tfap2B/SoxB/Hbox) mediating each programme and elucidate their combinatorial activities with other spatiotemporally-specific transcription factors (bHLH/NR). Our global deconstruction of the VNC-GRN in vivo sheds light on critical early regulatory mechanisms that may influence the divergent neural phenotypes in enteric neuropathies.

overall_design: Single neural crest cells isolated from HH18 avian embryo using FACS, single cell RNA-seq performed by 10X

first: Irving

last: Ling


title: Mycobacterium avium ssp. paratuberculosis Infection Induces an Immune Tolerance Phenotype in Primary Bovine Macrophages from Johne’s Disease Cows (Agriculture and Agri-Food Canada_N.Bissonnette_J000079)

status: Public on Dec 07 2019

first: Nathalie

last: Bissonnette

state: Quebec

address: 2000 rue College

department: Sherbrooke research center

institute: Agriculture and Agri-food Canada

summary: Mycobacterium avium ssp. paratuberculosis (MAP) is the causative agent of Johne’s disease (JD), which is also known as paratuberculosis, in ruminants. The mechanisms of JD pathogenesis are still unclear, but it is known that MAP subverts the host immune system for years by using macrophages as its primary reservoir. The effect of MAP infection on macrophages is often studied in healthy or experimentally infected cows, but reports on primary macrophages from naturally infected cows are lacking. In our study, the transcriptome of primary monocyte-derived macrophages challenged with live MAP was analyzed using next-generation sequencing (RNA‑seq). The gene expression signatures of macrophages from cows diagnosed as negative  or positive  for JD [JD(–) or JD(+), respectively] revealed differential host–pathogen interplay, highlighting long-term mechanisms established during mycobacterial disease. In JD(–) cows, a considerable number of genes (1,436) were differentially expressed at 8 h post-infection (hpi). Interestingly, while expected inflammatory immune response pathways were among the significant pathways, others related to Hepatic fibrosis/hepatic stellate cell activation, lipid homeostasis, such as the  LXR/RXR [liver X receptor/retinoid X receptor] activation, and autoimmune diseases such as atherosclerosis and rheumatoid arthritis were consistently among the top significant pathways. Unexpectedly, the macrophages from JD(+) cows did not present a clear response pattern to ex vivo MAP infection, neither during the early period nor at 24 hpi. Analyzing of the transcriptomic profile of the uninfected macrophages, revealed 868 genes that were differentially expressed in JD(+) versus JD(–) cows. The down-regulated genes particularly modified the general cell metabolism by down-regulating amino acid synthesis, cholesterol biosynthesis, and other energy production pathways while introducing a pro-fibrotic pattern associated with foam cells. These modifications show the apparent importance of the metabolic pathways hijacked by MAP to subvert the immune cells. Our findings support the hypothesis that MAP could induce a tolerant-like state in circulating peripheral blood monocytes when they are differentiating into macrophages, which could further promote the persistence. Similar to other mycobacteria and pathogen-associated molecular patterns, MAP could influence macrophage behavior in the long term. This report contributes to a better understanding of MAP control of immune cells and its mechanisms of survival.

overall_design: A total of 12 dairy cows were selected for RNA-seq analysis. Cows were assigned to one of the two groups (six biological replicates) according their Johne's disease (JD) status : JD negative [JD(–)] (n = 6) or JD positive [JD(+)] (n = 6) cows. Cows from the JD(+) group were identified A to F, and cows in the JD(–) group were assigned from G to L. For each cow, monocyte-derived macrophages were cultured and exposed ex vivo to MAP infection for 1h, 4h, 8h, or 24h or conserved as non-infected controls harvested at 4 or 24h).  The 72 libraries (2 controls + 4 infection time points per cow for 12 cows = 72 libraries) were sequenced.

first: Olivier

last: Ariel


title: Gene expression profile of FoxP3+ CD4+ follicular regulatory T cells

city: Birmingham

first: Jianmei

middle: Wu

last: Leavenworth

state: AL

address: 1600 6th Ave South

department: Neurosurgery, Microbiology

institute: University of Alabama at Birmingham

summary:
Follicular regulatory T cells (TFR) are a major cellular source of negative regulation of GC antibody responses. Blimp1 is expressed by the majority of TFR cells within B cell follicles during immune responses, as well as by other tissue-specific subsets of effector Treg (eTreg). However, the potential impact of FoxP3-specific Blimp1 deletion on TFR differentiation and suppressive activity has not been evaluated.
To better understand the role of Blimp1 in regulation of TFR differentiation and function, we profiled the differential gene expression in Blimp1-deficient TFR cells compared to WT control TFR cells.

overall_design: PD1+CXCR5+YFP+(FoxP3+)CD4+ TFR cells and CXCR5-YFP+(FoxP3+)CD4+ non-TFR cells were FACS-sorted from Prdm1fl/flFoxP3YFP-Cre (KO) and FoxP3YFP-Cre (WT) mice 7 days after immunization with NP-OVA in CFA. RNA was prepared, amplified, labeled and hybridized to Mouse Gene 2.0 ST Array (Affymetrix).

first: Harvey

last: Cantor


title: Silencing of Mu elements in maize involves distinct populations of small RNAs and distinct patterns of DNA methylation

status: Public on Nov 19 2019

city: West Lafayette

first: Meixia

last: Zhao

state: IN

address: 915 W State Steet

department: Agronomy

institute: Purdue University

summary: Epigenetic changes involve changes in gene expression that can be heritably transmitted to daughter cells in the absence of changes in DNA sequence.  Epigenetics has been implicated in phenomena as diverse as development, stress response and carcinogenesis. A significant challenge facing those interested in investigating epigenetic phenomena is determining causal relationships between DNA methylation, specific classes of small RNAs and associated changes in gene expression. Because they are the primary targets of epigenetic silencing in plants and, when active, are often targeted for de novo silencing, transposable elements (TEs) represent a valuable source of information about these relationships. We use a naturally occurring system in which a single TE can be heritably silenced by a single derivative of that TE. By using this system it is possible to unravel causal relationships between different size classes of small RNAs, patterns of DNA methylation and heritable silencing. Here, we show that the long terminal inverted repeats (TIRs) within Zea mays MuDR transposons are targeted by distinct classes of small RNAs during epigenetic silencing that are dependent on distinct silencing pathways. Further, these small RNAs target distinct regions of the TIRs, resulting in different patterns of cytosine methylation with different functional consequences with respect to epigenetic silencing and heritability of that silencing.

overall_design: Total of 10 samples with different genotypes associated with Mutator activity were sequenced.

first: Diane

last: Burgess

first: Hong

last: Li

first: Sang-Yeol

last: Kim

first: Damon

last: Lisch


title: Differential expression of rice root genes upon Rhodotorula treatment

status: Public on Nov 24 2019

city: Kolkata

first: Anindita

last: Seal

state: West Bengal

address: 35, Ballygunge Circular Road

department: Biotechnology

country: India

institute: University of Calcutta

summary: The experiments were performed to understand the molecular basis of plant growth promotion in rice by Rhodotorula mucilaginosa JGTA-S1, an endophytic yeast from Typha angustifolia.

overall_design: Three-week-old rice plant grown in untreated condition were supplemented with Rhodototorula cell suspension. Roots were harvested 0hr, 6hrs or 24hrs post treatment. Total RNA was isolated from those root tissue and used for microarray. 0 hr treated sample was considered here as Control.

first: C

last: Saha

first: A


title: Control of prostate tumour growth by the long non-coding RNA GHSROS (LNCaP)

status: Public on Nov 14 2019

city: Woolloongabba

first: Inge

last: Seim

state: Queensland

address: 37 Kent St

country: Australia

institute: Queensland University of Technology

summary: We overexpressed the long non-coding RNA GHSROS in the metastatic prostate cancer cell line LNCaP and subcutaneously injected the cells into NOD/SCID mice.

overall_design: Examination of LNCaP prostate cancer xenografts expressing the long non-coding RNA GHSROS


title: Genome-wide changes in OGT-deficient mouse liver tissue

status: Public on Nov 04 2019

city: New Haven

first: Xiaoyong

last: Yang

address: 375 Congress Ave

department: Comparative Medicine

summary: Over a billion people suffer from chronic liver diseases worldwide, which often leads to fibrosis and then cirrhosis. Treatments for fibrosis remain experimental, in part because no unifying mechanism has been identified that initiates liver fibrosis. O-linked β-N-acetylglucosamine (O-GlcNAc) transferase (OGT) plays a pro-survival role under stress in many tissues. Here we report that OGT protects against hepatocyte necroptosis and initiation of liver fibrosis. Decreased O-GlcNAc levels were seen in patients with alcoholic liver cirrhosis and in mice with ethanol-induced liver injury. Liver-specific O-GlcNAc transferase (OGT) knockout (OGT-LKO) mice progressed to liver fibrosis at 10 weeks of age. OGT-deficient hepatocytes underwent necroptosis. These findings identify OGT as a key suppressor of hepatocyte necroptosis and OGT-LKO mice may serve as an effective spontaneous genetic model of liver fibrosis.

overall_design: Total RNA was harvested from the liver tissue of 5-week-old OGT-deleted mice (n=4) and their control littermates (WT, n=5). Both genders were used for the study. Mice were fasted for 6 h before sacrifice.

first: Bichen

last: Zhang

first: Jin

middle: H

last: Nam

first: Dongjun

last: Chung


title: Nr4a1 suppresses cocaine-induced behavior via epigenetic regulation of homeostatic target genes.

status: Public on Dec 05 2019

city: Philadelphia

first: Song-Jun

last: Xu

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: Endogenous homeostatic mechanisms can restore normal neuronal function following cocaine-induced neuroadaptations. Such mechanisms may be exploited to develop novel therapies for cocaine addiction, but a molecular target has not yet been identified. Here we profiled mouse gene expression during early and late cocaine abstinence to identify putative regulators of neural homeostasis. Cocaine activated the transcription factor, Nr4a1, and its target gene, Cartpt, a key molecule involved in dopamine metabolism. Sustained activation of Cartpt at late abstinence was coupled with depletion of the repressive histone modification, H3K27me3, and enrichment of activating marks, H3K27ac and H3K4me3. Using both CRISPR-mediated and small molecule Nr4a1 activation, we demonstrate the direct causal role of Nr4a1 in sustained activation of Cartpt and in attenuation of cocaine-evoked behavior. Our findings provide evidence that targeting abstinence-induced homeostatic gene expression is a potential therapeutic target in cocaine addiction.

overall_design: mRNA profiles of mice undergo cocaine SA were generated by deep sequencing, in six replicates, using Hiseq 4000

first: Marco

last: Carpenter

first: Elizabeth

last: Heller


title: RNA expression profiles comparing primary and omental ovarian carcinoma samples

status: Public on Nov 08 2019

city: Kuopio

first: Minna

middle: U

last: Kaikkonen

department: A.I. Virtanen Institute, Department of Biotechnology and Molecular Medicine

country: Finland

institute: University of Eastern Finland

summary: RNA-Seq analysis was performed on primary and metastatic tumor samples from ten patients

overall_design: RNA-Seq

first: Hanna

last: Sallinen

first: Salla

last: Janhonen


title: Altered gene expression in liver and muscle of ADCK2(+/-) mouse

city: Sevilla

first: Daniel Jose

last: Moreno Fernandez-Ayala

address: Carretera de Utrera, Km. 1

country: Spain

institute: Universidad Pablo de Olavide

summary: Analysis of gene expression in both muscle and liver due to the lost of one copy of the gene ADCK2. Heterocygous mouse ADCK2(+/-) present an altered gene expression that explain the adult phenotype, including myopathy in muscle and steatosis and inflamation in liver.

overall_design: Total RNA obtained from isolated liver and gastronemius muscle of 3 year old mouse compared to control/wild type organs.

first: Daniel

last: Fernández-Ayala

first: Rafael

last: deCabo

first: Plácido

last: Navas


title: Affymetrix experiments for “Chronic repression by MAF1 supports futile RNA cycling as a mechanism for obesity resistance”

city: Lausanne

first: Nicolo

last: Riggi

state: VD

address: Bugnon 25

department: Département de Pathologie Expérimentale

institute: CHUV

summary: To determine how feeding and fasting might alter transcription, we analyzed liver mRNA from wild-type fasted (WT_F) or wild-type fasted and refed (WT_R) mice by gene expression arrays.

overall_design: Two conditions (fasted versus refed mice) in triplicates. Three mice were pooled for each replicate.

first: Nicolas

last: Bonhoure

first: Viviane

last: Praz

first: Ian

last: Willis

first: Nouria

last: Hernandez


title: Chronic repression by MAF1 supports futile RNA cycling as a mechanism for obesity resistance

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

overall_design: Refer to individual Series


title: Ribosome-profiling experiments for “Chronic repression by MAF1 supports futile RNA cycling as a mechanism for obesity resistance”

summary: To characterize the translation defects in Maf1-/- samples, we used ribosome profiling on three WT and three Maf1-/- fed livers. Each sample was spiked with a fixed amount of Drosophila S2 Schneider cell material as an internal control for sample-to-sample normalization, and to allow detection of global changes in translation.

overall_design: Two conditions (WT of Maf1 KO mice), three biological replicates per condition. For each sample, both Ribosome-protected fragments (RPFL) and total RNA fragments (TOTL) were sequenced.


title: ChIP-seq experiments for “Chronic repression by MAF1 supports futile RNA cycling as a mechanism for obesity resistance”

summary: To characterize the PolIII transcription changes in Maf1-/- samples, we perfomeded ChIP-seq on WT and Maf1-/- Mouse liver samples. Mice were either fasted during eight hours or fasted for four hours and then refed.

overall_design: Four conditions (WT_refed, WT_fasted, KO_refed KO_fasted), and two replicates per condition. One input per condition. All samples were spiked with 5% of human chromatin


title: Cucumber ovaries inhibited by dominant fruits still respond to pollination but display distinct metabolome and transcriptome profiles

status: Public on Nov 03 2019

city: Ramat Gan

first: Tirza

last: Doniger

institute: Bar Ilan University

summary: Cucurbits represent an attractive model to explore the dynamics of fruit set. Here we set out to characterize first fruit inhibition (FFI), i.e. the inhibitory effect of the first fruits on subsequent development of younger ovaries during pollination induced fruit set. After the first fertilized ovaries set fruit, younger ovaries fertilized above them on the main stem remained in a temporary state of inhibition. During this stage, the ovaries preserved their size and green color, and if the older fruits were removed within a one-week reversibility window, the inhibited ones set fruit. We compared the gene expression profiles of pollinated ovaries (committed to set fruits) with respect both to those affected by FFI and to non-pollinated ovaries (comitted to senescence). The three fates of the ovaries were characterized at 1 day post anthesis, compare to anthesis, by wide changes in gene expression, with several specific transcripts being up- or down-regulated in response to the presence (or absence) of pollination. Metabolic profiling was undertaken and integrated with the transcriptomic data in order to characterize early physiological changes that occur in post-anthesis ovaries in parthenocarpic and non-parthenocarpic genotypes.

overall_design: We  focused on the early changes that occur one day after anthesis in the gynoecious non-parthenocarpic line Elem Female. We compared anthesis day ovaries ready to be pollinated (coded "A") with 1 dpa pollinated ovaries ("F+1"), and non-pollinated ovaries ("S+1"). Inhibited ovaries ("f+1", see previous section) were sampled as well. In total, twelve cDNA preparations (triplicates of the above four developmental stages; only two replicate for f+1) were sequenced from individual ovaries. The samples were collected from 1 month old plants every day at 6-7 AM to minimize environmental and circadian effects. Same samples were used also for metabolome analysis.

first: Yulia

last: Shnaider

last: Perl-Treves


title: The histone variant H2A.Z in yeast is almost exclusively incorporated into the +1 nucleosome in the direction of transcription

status: Public on Oct 29 2019

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

summary: To investigate the incorporation dynamics of histone variant H2A.Z, we determined its genomic localization at single nucleosome resolution, as well as the localization of its chromatin remodelers Swr1 and Ino80. We find that Swr1 binding alone is a poor predictor of H2A.Z occupancy levels, and that normal Swr1 and Ino80 localization are actually dependent on H2A.Z. Additionally, we find that H2A.Z’s bimodal incorporation on either side of the NDR is not a general feature of TSS, but is specifically a marker for bidirectional transcription, such that the upstream flanking -1 H2A.Z-containing nucleosome is more appropriately considered as a +1 H2A.Z nucleosome for antisense transcription.

overall_design:
MNase-ChIP-seq data was produced to determine at single nucleotide resolution the genomic localization of the histone variant H2A.Z.
ChIP-seq was performed to determine the genomic localization of chromatin remodelers Ino80 and Swr1 both in the presence and absence of histone variant H2A.Z.
Smore-seq was performed with both ribo depletion and poly-A selection to map transcripts across the genome.

first: Dia

middle: N

last: Bagchi

first: Vishwanath


title: In vitro characterization of the human segmentation clock

status: Public on Oct 28 2019

city: Boston

middle: E

last: Wagner

state: MA

address: 200 Longwood Ave, Harvard Medical School, Systems Biology, Warren Alpert 536

institute: Harvard Medical School

summary: The segmental organization of the vertebral column is established early in embryogenesis when pairs of somites are rhythmically produced by the presomitic mesoderm (PSM). The tempo of somite formation is controlled by a molecular oscillator known as the segmentation clock. While this oscillator has been well-characterized in model organisms, whether a similar oscillator exists in humans remains unknown. Genetic analysis of patients with severe spine segmentation defects have implicated several human orthologs of cyclic genes associated with the mouse segmentation clock, suggesting that this oscillator might be conserved in humans. Here we show that in vitro-derived human as well as mouse PSM cells recapitulate oscillations of the segmentation clock. Human PSM cells oscillate twice slower than mouse cells (5-hours vs. 2.5 hours), but are similarly regulated by FGF, Wnt, Notch and YAP. Single cell RNA-sequencing reveals that mouse and human PSM cells in vitro follow a similar developmental trajectory to mouse PSM in vivo. Furthermore, we demonstrate that FGF signaling controls the phase and period of oscillations, expanding the role of this pathway beyond its classical interpretation in 'Clock and Wavefront' models. Overall, our work identifying the human segmentation clock represents an important breakthrough for human developmental biology.

overall_design: Single-cell mRNA sequencing of mouse E9.5 embryonic cells, mouse embryonic stem cells, and human iPSC in vitro cultures.

first: Margarete

last: Diaz-Cuadros

first: Christoph

last: Budjan

first: Olivier

last: Pourquié


title: Urine miRNA transcriptome of prostate cancer patients [Validation cohort]

status: Public on Oct 24 2019

city: Toronto

first: Jouhyun

last: Jeon

state: Ontario

address: 101 College Street

institute: Ontario Institute for Cancer Research

summary: Intra-individual stability of the urine miRNA transcriptome was examined by investigating longitudinal changes over time in a cohort of patients with localized prostate cancer. Using training and validation cohorts, urinary miRNA biomarkers are characterized and validated their utility to identify aggressive prostate cancer.

overall_design: miRNAs are isolated from urinary cell sediments. Discovery cohort is composed of 22 samples from 10 patients and used to measure intra-individual stability. Training cohort that are composed of urine samples from 49 low-risk prostate cancer patients and 50 high-risk prostate cancer patients are used to identify urine biomarker to predict cancer aggressivity and generate a predictive model. The predictive model is validated using an independent validation cohort with 29 low-risk and 15 high-risk (based on NCCN-risk, 11 high-risk based on GS-risk) prostate cancer patients. Control samples are used for data normalization.

first: Stanly

last: Liu

first: Bharati

last: Bapat

first: Paul

last: Boutros


title: Urine miRNA transcriptome of prostate cancer patients [Discovery cohort]


title: Reprogramming of bivalent chromatin states in NRAS-mutant melanoma suggests PRC2 inhibition as a therapeutic strategy

status: Public on Nov 07 2019

city: Houston

first: Kunal

last: Rai

address: 1801 East Rd

department: Genomic Medicine

institute: MD Anderson Cancer Center

summary: The dynamic evolution of chromatin state patterns during metastasis, their relationship with bona fide genetic drivers and therapeutic vulnerabilities are not completely understood. Combinatorial chromatin state profiling of 46 melanoma samples reveals an association of NRAS-mutants with bivalent H3K27me3 and Polycomb Repressive Complex 2. Reprogramming of bivalent domains during metastasis occurs on master transcription factors of a mesenchymal phenotype, including ZEB1, TWIST1 and CDH1. Resolution of bivalency using pharmacological inhibition of EZH2 decreases invasive capacity of melanoma cells and markedly reduces tumor burden in vivo, specifically in NRAS-mutants. Coincident with bivalent reprogramming the increased expression of pro-metastatic and melanocyte-specific cell identity genes are associated with exceptionally wide H3K4me3 domains, suggesting a role for this epigenetic element. Overall, we demonstrate that reprogramming of bivalent and broad domains represents key epigenetic alterations in metastatic melanoma, and that EZH2 plus MEK inhibition may provide a promising therapeutic strategy for NRAS-mutant melanoma patients.

overall_design: Comprehensive chromatin state profiling and analysis of metastatic melanoma by performing ChIP-sequencing of 6 core histone modifications. Chromatin profiling for H3K4me3 and H3K27me3 in NRAS-mutant MSTC and NRAS-mutant isogenic melanocytes.

first: Christopher

last: Terranova


title: RNASeq of mouse, human, and non-human primate primary dermal fibroblasts to poly(I:C) transfection

status: Public on Oct 20 2019

city: Princeton

first: Alexander

last: Ploss

state: NJ

address: Washington Road

department: Molecular Biology

institute: Princeton University

summary: Here, we performed RNA-Seq on mRNA isolated from primary dermal fibroblasts of human, mice and multiple non-human primate species transfected with polyinosinic-polycytidylic acid (polyI:C), a synthetic dsRNA analog that invokes a strong interferon-mediated response, or mock transfected.

sample_organism:
Saimiri sciureus
Macaca mulatta
Macaca nemestrina
Papio anubis
Gorilla gorilla
Pan paniscus
Pan troglodytes
Pongo abelii
Homo sapiens
Mus musculus

overall_design: For each of the ten species, primary fibroblasts were acquired from three donors. Cells from each donor were transfected in triplicate with 0.5 ug poly(I:C)/well in a six well plate (~0.05 ug/cm2) or mock-transfected (all transfection mixture components minus poly(I:C)) in triplicate. Thus, there were a total of 180 samples (10 species x 3 donors x 6 samples per donor).

first: Jenna

middle: M

last: Gaska

first: Lance

last: Parsons

first: Metodi

last: Balev

first: Anne

last: Cirincione

first: Wei

last: Wang

first: Robert

last: Schwartz


title: Urine miRNA transcriptome of prostate cancer patients [Training cohort]


title: bHLH transcription factor ATOH8 depletion effect on endothelial cells: loss-of-function model [LOF]

status: Public on Oct 17 2019

city: Tokyo

first: Masato

last: Morikawa

address: 2-21-1 Kaga, Itabashi-ku

department: Advanced Comprehensive Research Organization

institute: Teikyo University

summary: Analysis of human umbilical vein endothelial cells (HUVECs) depleted for the transcription factor ATOH8.

overall_design: ATOH8 was identified as a direct target gene of BMP-9/ALK-1/SMAD signaling in endothelial cells (ECs). In order to assess the function of transcription factor ATOH8 in ECs, HUVECs transfected with either siRNAs specific for ATOH8 or control siRNA were stimulated with 1 ng/ml BMP-9 for 24 h or left untreated.

first: Daizo

last: Koinuma

first: Hiroyuki

last: Aburatani

first: Kohei

last: Miyazono


title: SMAD1/5 binding pattern in human pulmonary arterial endothelial cells [ChIP-seq]

summary: We showed that the BMPRII/ALK-1/SMAD/ATOH8 axis protects against the development of pulmonary arterial hypertension (PAH). We have performed ChIP-seq analyses to reveal the function of both SMAD and ATOH8.

overall_design: SMAD1/5 ChIP-seq analyses were performed in human pulmonary arterial endothelial cells (HPAECs) treated with 1 ng/ml BMP-9 for 1.5 h (biological duplicate). FLAG ChIP-seq alalysis was performed in HPAEC stably expressing FLAG-ATOH8.

first: Carl-Henrik

last: Heldin


title: The analysis of the role of ALK-1/SMAD/ATOH8 axis in endothelial cells


title: The GNAS-R201C Mutation Associated with Clonal Hematopoiesis Maintains Mouse Long-Term Hematopoietic Stem Cell Potential

status: Public on Oct 08 2019

city: Saint Louis

first: Bo

last: Zhang

state: MO

address: 660 S. Euclid Avenue

department: Developmental Biology

institute: Washington University School of Medicine

summary: Gene expression analysis of mouse hematopoietic stem cells (HSCs) transduced with lentiviral vectors for control (GFP), GNAS wild-type, and GNAS-R201c mutant.

overall_design: Comparison of gene expression in HSCs over-expressing wild-type GNAS and GNAS-R201C mutation.

first: Grant

last: Challen


title: Urine miRNA transcriptome of prostate cancer patients

first: Jouhyun

last: Jeon

first: Stanly

last: Liu

first: Bharati

last: Bapat

first: Paul

last: Boutros


title: bHLH transcription factor ATOH8 overexpression effect on endothelial cells: gain-of-function model [GOF]

summary: Analysis of human umbilical vein endothelial cells (HUVECs) adenovirally expressing the transcription factor ATOH8.

overall_design: ATOH8 was identified as a direct target gene of BMP-9/ALK-1/SMAD signaling in endothelial cells (ECs). In order to assess the function of transcription factor ATOH8 in ECs, HUVECs were infected with either ATOH8 or control LacZ adenovirus for 72 h.


title: Microarray expression profiling in zebrafish rnaset2 mutant

city: Sheffield

first: Noemie

last: Hamilton

state: Great Britain

address: Western Bank

department: Department of Infection, Immunity and Cardiovascular Disease

institute: University of Sheffield

summary: RNASET2-deficient leukoencephalophathy is a severe leukodystrophy affecting children with psychomotor impairements in their forst year of life. We generated the first zebrafish model for a human leukodystrophy by targetting the ortholog rnaset2 gene using mutagenesis. This zebrafish mutant recapitulated the human clinical manisfestations and developed white matter defects detectable by MRI. Additionally, this zebrafish mutant identified this disease as a lysosomal storage disorders, with RNA accumulating in neurons. To understand how accumulation of RNA in neurons trigger white matter lesions, we undertook an unbiased approach and perfored microarray analysis. We identified differentially expressed genes in mutants and the immune system as a key pathway disregulated in the zebrafish rnaset2 mutant.

overall_design:
Gene expression profiles of rnaset2 zebrafish compared to WT sibling of whole embryos at 28hour post fertilisation, 3days post fertilisation and brain of 1 year old adults

***Please note that the original/unedited raw data files are unavailable and thus, not provided.

first: Noémie

first: Jutta

last: Gaertner


title: Esrrb plays an important role in maintaining self-renewal of trophoblast stem cells (TSCs) and reprogramming somatic cells to induced TSCs

status: Public on Oct 06 2019

city: Shanghai

first: Shaorong

last: Gao

address: Siping Road NO.1239

institute: Tongji University


title: Esrrb plays an important role in maintaining self-renewal of trophoblast stem cells (TSCs) and reprogramming somatic cells to induced TSCs [ChIP-Seq]

summary: Trophoblast stem cells (TSCs) are derived from the trophoectoderm of a blastocyst and can maintain self-renewal in vitro. Meanwhile, essential insights into the molecular mechanisms controlling placental developmental could be gained by using TSCs that can differentiate into the various placental trophoblast cell types in vitro. Esrrb is a transcription factor with pivotal roles in maintaining TSCs’ self-renewal, but the exact transcriptional networks that Esrrb involved in TSCs are largely unknown. In the present study, we elucidated the function of Esrrb during TSC self-renewal and differentiation. We demonstrate that precise levels of Essrb are critical for TSCs stemness maintenance and normal trophoblast differentiation, as Esrrb depletion results in down-regulation of the key TSC-specific transcription factors, consequently causing TSCs differentiation and forced expression of Esrrb can partially block TSCs differentiation in the absence of FGF4. This function of Esrrb is exerted by directly binding and activating a core set of TSC-specific target genes including Cdx2, Eomes, Sox2, Fgfr4 and BMP4. Furthermore, we investigate the role of Esrrb in reprogramming of mouse embryonic fibroblasts (MEFs) to induced TSCs (iTSCs). We show that Esrrb can facilitate the conversion of iTSCs from MEFs. Moreover, Esrrb can substitute for Eomes during this conversion process. Our findings provide a better understanding of the molecular mechanism of Esrrb in maintaining TSCs self-renewal and iTSCs reprogramming.

overall_design: We performed two or three independent IP reactions for each sample.

first: Haibo

first: Rui


title: Expression profiling of frozen primary and patient derived xenograft gastric cancer

status: Public on Oct 15 2019

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

institute: Candiolo Cancer Institute, University of Torino

first: Simona

last: Corso

first: Claudio

last: Isella

first: Silvia

last: Giordano


title: ATRX mutant neuroblastoma is sensitive to EZH2 inhibition via modulation of neuronal differentiation

city: New York

first: Emily

last: Bernstein

state: NY

address: 1470 Madison Avenue, 6th floor Rm 302

department: Oncological Sciences

institute: Mount Sinai School of Medicine

summary: We report on the characterization of ATRX in-frame fusion neuroblastoma and identify that ATRX IFF proteins re-locate from H3K9me3 enriched regions to active chromatin, such as the promoter of neural repressor REST. We further identify that REST is upregulated in ATRX IFF NB and that several neurogenesis and REST target genes are transcriptionally downregulated. Through ChIP-seq analysis, we observe that REST is bound to ATRX IFF Down genes, which have higher levels of H3K27me3. We further show that ATRX in-frame fusion neuroblastoma cells are sensitive to EZH2 inhibitors through de-repression of H3K27me3 bound neuronal function genes, includiing a subset of REST targets.

overall_design:
We examine the genomic occupancy of ATRX in one ATRX wild-type neuroblastoma cell line and two ATRX in-frame fusion neuroblastoma cell lines; REST in two ATRX in-frame fusion neuroblastoma cell lines; relevent histone modifications and the transcriptome of two ATRX wild-type neuroblastoma cell lines, two ATRX in-frame fusion neuroblastoma cell lines, and two ATRX in-frame fusion tumor sample. We further interrogate one ATRX wild-type and two ATRX in-frame fusion neuroblastoma cell lines for transcriptional changes upon EZH2 inhibition. Finally, we include here RNA-seq analysis of five ATRX wild-type neuroblastoma tumor samples, 5 MYCN-amplified neuroblastoma tumor samples, and 5 ATRX in-frame fusion and mutant tumor samples.

We also utilized RNA-seq analysis of SK-N-FI cells expressing MS2-NLS-control and MS2-NLS-ATRX-helicase as well as CHLA-90 control and REST knockdown cells.

first: Zulekha

last: Qadeer

first: David

last: Valle-Garcia

first: Lyra

last: Griffiths

first: Dan

last: Hasson

first: Michael

last: Dyer


title: Esrrb plays an important role in maintaining self-renewal of trophoblast stem cells (TSCs) and reprogramming somatic cells to induced TSCs [RNA-Seq]

overall_design: We performed two independent mRNA-seq replicates for each sample.


title: Spatial-temporal epigenetic landscape of mouse gastrula

status: Public on Oct 07 2019

city: Shanghai City

first: Naihe

last: Jing

address: Yueyang Road 320

institute: shanghai institute of biochemistry and cell biology

summary: Regionalized lineage progenitor cells emerged from the onset of gastrulation would facilitate mouse embryonic patterning and build a blueprint for future development. However, the molecular mechanism especially the epigentic mechanism underlying the formation and development of lineage restricted cells has not been fully unveiled. Here,we present a comprehensive landscape of H3K4me3, H3K4me1, H3K9ac, H3K27ac, H3K27me3 and DNA methylation pattern in mouse embryo from pre-streak stage to late-streak stage, and fully analyze the epigenetic mechansim driving the embryonic patterning of mouse gastrula

overall_design: To obtain a comprehensive epigenetic landscape of mouse gastrulation and the corresponding lineage development process, we have dissected mouse gastrula from pre-steak stage (E6.5) to late streak stage (E7.5)19 into extra-embryonic (ExE) and embryonic parts, and embryonic parts of E7.0 and E7.5 embryos will be further divided into sub-regions (A, P, AM) due to the emergence of embryo asymmetry.

first: Xianfa

last: Yang

first: Boqiang

last: Hu

first: Yu

last: Hou

first: Yunbo

last: Qiao

first: Fuchou

last: Tang

last: Jiang


title: Role of iron in the regulation of the epithelial-to-mesenchymal transition (RNA-seq)

status: Public on Oct 01 2019

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

institute: Institut Curie

summary: The biological process termed Epithelial-to-Mesenchymal Transition (EMT) plays a central role in cancer cell invasion, metastasis, self-renewal and resistance to therapy1,2. Here, we characterize using RNA sequencing  the mRNA levels changes occurring during EMT induced by epidermal growth factor in breast cancer MDA-MB-468 cells.  1. Nieto, M. A., Huang, R. Y., Jackson, R. A. & Thiery, J. P. EMT: 2016. Cell 166, 21–45 (2016). 2. Puisieux, A. & Brabletz, T. & Caramel, J. Oncogenic roles of EMT-inducing transcription factors. Nat. Cell Biol. 16, 488–494 (2014).

overall_design: Analyses of 6 samples: (i) untreated (ii) EGF 72h. Experiment was performed in 3 independent biological replicates

first: Fabien

last: Sindikubwabo

first: Sylvain

last: Baulande

first: Rodriguez

last: Raphael


title: Role of iron in the regulation of the epithelial-to-mesenchymal transition

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

overall_design: Refer to individual Series


title: Artificial reforestation has less diverse soil nitrogen-cycling genes than natural restoration

city: Beijing

first: Yun

last: Wang

address: Shuangqing Road 18th, Haidian District

institute: Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences

summary: Reforestation is effective in restoring ecosystem functions and enhancing ecosystem services of degraded land. The three most commonly employed reforestation methods of natural reforestation, artificial reforestation with native Masson pine (Pinus massoniana Lamb.), and introduced slash pine (Pinus elliottii Engelm.) plantations were equally successful in biomass yield in southern China. However, it is not known if soil ecosystem functions, such as nitrogen (N) cycling, are also successfully restored. Here, we employed a functional microarray to illustrate soil N cycling. The composition and interactions of N-cycling genes in soils varied significantly with reforestation method. Natural reforestation had more superior organization of N-cycling genes, and higher functional potential (abundance of ammonification, denitrification, assimilatory, and dissimilatory nitrate reduction to ammonium genes) in soils, providing molecular insight into the effects of reforestation.

sample_organism: Bacteria Archaea Fungi Viruses

platform_organism: Bacteria Archaea Fungi Viruses

overall_design: The diversity and interaction of nitrogen-cycling genes in the soils of three reforestation methods were studied. The three reforestation methods were naturally restored secondary forests (NRSF), artificial reforestation with native Masson pine (Pinus massoniana Lamb.) (ARMP), and introduced slash pine (Pinus elliottii Engelm.) plantations (ARSP). Each reforestation method included 15 replicates (plots) in red soil region in southern China. After DNA extraction and outlier (ARMP1, NRSF2, and NRSF7) checked, 14, 14, and 11 microarray replicates were obtained for ARSP, ARMP, and NRSF, respectively.

first: Hua

last: Zheng

first: Falin

last: Chen

first: Yunfeng

first: Jing

last: Zeng

first: Joy

last: Van Nostrand

first: Jizhong

last: Zhou

first: Zhiyun

last: Ouyang


title: Wild-type P53 proteolytic inactivation by asparagine endopeptidase promotes glioblastoma progression

first: Zhaoyuan

last: Fang

address: 320 Yueyang Road

institute: Chinese Academy of Sciences

summary: A comparison of expression changes between AEP RNAi and U87 control cell lines

overall_design: Total RNA was isolated from 3 control and 3 AEP RNAi U87 cell lines. RNA samples were prepared, amplified, Cy3 labeled, and hybridized onto Agilent SurePrint G3 platform in 8x60K format human gene expression microarrays (Agilent-072363, Agilent Technologies, Santa Clara, CA), following Agilent standard procedures and instructions. After array scanning and feature extraction (Feature Extraction software, Agilent Technologies), the raw signal data were processed, log transformed and quantile normalized (limma package).

first: Yingying

last: Lin

first: Zhongrun

last: Qian

first: Yifeng

last: Miao

first: Keman

last: Liao

first: Xi

last: Yang

first: Quanmin

last: Nie

first: Gang

first: Jianhua

last: Liu

first: Yiyi

last: Yu

first: Xiaohua

last: Zhang

first: Jiyao

first: Yongming

last: Qiu


title: Comparison of sRNA populations obtained using HD or standard Illumina adapters in S Lycopersicum (rdr6 mutant) without TAP treatment

city: Norwich

first: Tamas

last: Dalmay

address: Earlham Road

institute: University of East Anglia

summary: The sRNA population (sequence identity and distribution of abundances) in S Lycopersicum was assessed using High Definition (HD) [Sorefan et al 2012, Xu et al 2015] or standard Illumina adapters; the usage of HD adapters revealed a more diverse population of sRNAs (in particular, it revealed the presence of more unique 24mers)

overall_design: sRNA libraries from S Lycopersicum leafs were created using HD and standard Illumina adapters, without a TAP treatment; the resulting libraries were compared side by side.

first: Ping

last: Xu

first: Irina

last: Mohorianu


title: Comparison of mRNA-seq quantification from libraries obtained using either HD or standard Illumina adapters in A thaliana, in wildtype and DCL1 mutants

summary: One method of directional cloning of fragmented mRNA is based on single strand RNA ligation, for which ligation bias occurrs if the adapters have single sequences. The sequencing bias affects the mRNA quantification and subsequently the differential expression analysis. High definition (HD) adapters [Sorefan et al 2012, Xu et al 2015] can be used to diminish the cloning bias during library construction. HD adapters and standard illumina adapters were used to construct mRNA-seq libraries for a side by side comparison.

overall_design: same RNA samples (wild type and dcl1 mutants) were used to generate mRNA-seq libraries created using HD and standard illumina adapters.

first: Martina

last: Billmeier

first: Rachel

middle: R

last: Pilcher


title: Effect of PROTAC-mediated BRD4 degradation in acute myeloid leukemia [OCI-AML3]

first: Zhiqiang

last: Wang

state: Texas

address: 7455 Fannin St.

department: Lymphoma and Myeloma

institute: University of Texas MD Anderson Cancer Center

summary:
BRD4, a member of the BET family of histone readers, binds to acetylated lysine of histone H3 and promotes assembly of super-enhancer complexes that drive expression of key oncogenes in acute myeloid leukemia (AML) and other cancers. ARV-825 is a proteolysis-targeting chimera (PROTAC) that targets BRD4 for CRBN-mediated ubiquitination and degradation. We treated the AML cell line OCI-AML3, as well as primary tumor cells from a case of AML, with ARV-825 in vitro.
At low concentrations, ARV-825 caused profound and sustained reduction in BRD4 protein levels. This caused reduction in transcription of key genes including MYC, anti-apoptotic BCL2 and BCLXL, PIM1, and CD44. Downstream effects included loss of CXCR4 surface expression and mitochondrial respiration; increased reactive oxygen species; toxicity to AML cells in vitro; and efficacy vs. OCI-AML3 cells in a mouse model of AML.

overall_design: OCI-AML3 cells (10 nM) and primary AML cells (50 nM) were cultured in triplicate or duplicate, respectively, with ARV-825 or DMSO control. After 24 hr, cells were harvested for gene expression analysis.

first: Sujan

last: Piya

first: Hong

last: Mu

first: R

last: Davis

first: Michael

last: Andreeff

first: Gautam

last: Borthakur


title: Effect of PROTAC-mediated BRD4 degradation on bone marrow-derived mesenchymal stromal cells [BM-MSCs]

summary:
BRD4, a member of the BET family of histone readers, binds to acetylated lysine of histone H3 and promotes assembly of super-enhancer complexes that drive expression of key oncogenes in acute myeloid leukemia (AML) and other cancers. ARV-825 is a proteolysis-targeting chimera (PROTAC) that targets BRD4 for CRBN-mediated ubiquitination and degradation. BM-MSCs are an important element of the bone marrow microenvironment of AML. To understand how targeting BRD4 in BM-MSCs may contribute to the overall effect on AML of targeting BRD4, we treated BM-MSCs from two normal donors with ARV-825 in vitro.
Treatment of BM-MSC monocultures with ARV-825 for 24 hr caused extensive changes in gene expression, highly uniform between triplicates. Although the cultures from the two normal donors showed different profiles, their changes with ARV-825 were highly similar. These changes implicated effects on oxidative stress, osteogenic differentiation, retinoid metabolism, F-actin polymerization, CXCL12, and proliferation.

overall_design: BM-MSCs were prepared from BM aspirates of normal donors as previously described (PMID: 24599548). BM-MSC from each donor were incubated for 24 hr in triplicate with either DMSO control or 25 nM ARV-825, a concentration similar to the 50 nM used to treated AML cells in monocultures. ARV-825 treatment did not affect the number or viability of BM-MSCs at 24 hr, although there was a slight relative decrease in cell number at 72 hr. Western blotting showed marked reductions in BRD4 and MYC protein levels at 24 hr.


title: Effect of PROTAC-mediated BRD4 degradation in acute myeloid leukemia


title: microRNA expression data from mouse primary stomach tissues

status: Public on Sep 28 2019

city: Seoul

first: Jun Won

last: Park

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Veterinary Pathology

institute: Seoul National University

summary:
We investigated microRNA expression profiles of gastric cancer tissues from Pdx-1-Cre;Cdh1F/+;Trp53F/F;Smad4F/F mice (pChePS_GC) and normal gastric epithelium (NGE) from Pdx1-1-Cre-negative mice.
We used microarrays to detail the global microRNA expression underlying gastric carcinogenesis and identified distinct classes of up and down-regulated microRNAs during this process.

overall_design: We collected gastric cancer tissues from Pdx-1-Cre;Cdh1F/+;Trp53F/F;Smad4F/F mice (pChePS_GC) and normal gastric epithelium (NGE) from Pdx1-1-Cre-negative mice.

first: Hark

last: Kim

first: Dae


title: Gene and microRNA expression data from mouse primary stomach tissues

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

platform_organism:
Mus musculus
synthetic construct


title: Gene expression data from mouse primary stomach tissues

summary:
We investigated gene expression profiles of gastric cancer tissues from Pdx-1-Cre;Cdh1F/+;Trp53F/F;Smad4F/F mice (pChePS_GC), gastric cancer tissues from Pdx-1-Cre;Cdh1F/F;Trp53F/F mice (pCP_GC), and normal gastric epithelium (NGE) from Pdx1-1-Cre-negative mice.
We used microarrays to detail the global programme of gene expression underlying gastric carcinogenesis and identified distinct classes of up and down-regulated genes during this process.

overall_design: We collected gastric cancer tissues from Pdx-1-Cre;Cdh1F/+;Trp53F/F;Smad4F/F mice (pChePS_GC), gastric cancer tissues from Pdx-1-Cre;Cdh1F/F;Trp53F/F mice (pCP_GC), and normal gastric epithelium (NGE) from Pdx1-1-Cre-negative mice.


title: Combination effect of G-TPP and LXR623 on stem cell like glioma cells

status: Public on Sep 25 2019

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: We performed microarray analysis in order to evaluate the combination effect of the mitochondrial matrix chaperone inhibitor gamitrinib-triphenylphosphonium (G-TPP) and Liver X receptor agonist LXR623 on gene expression in stem cell like glioma cells (NCH644).

overall_design: NCH644 cells were treated with 1 µM of G-TPP, 5 µM of LXR623, both treatments, or neither treatment, in 0.1% DMSO. After 24 hours treatment, total RNA was isolated and analyzed.

first: Chiaki

last: Ishida

first: Markus

last: Siegelin


title: mRNA and miRNA expression of HeLa cancer stem cells and non-cancer stem cells

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.


title: miRNA expression of HeLa cancer stem cells and non-cancer stem cells

summary: miRNA and mRNA expression of  HeLa cancer stem cells and non-cancer stem cells

overall_design: Comparison of the miRNA expression profiles between HeLa CSC and nonCSC

first: Keisuke

last: Tamari

first: Hideshi

last: Ishii


title: mRNA expression of HeLa cancer stem cells and non-cancer stem cells

overall_design: Comparison of the mRNA expression profiles between HeLa CSC and nonCSC


title: Effects of pioglitazone and beta-naphtoflavone on human primary trophoblasts

city: Kuopio

first: Jaana

last: Rysae

address: Yliopistonranta 1C

department: School of Pharmacy

institute: University of Eastern Finland

summary: Effects of pioglitazone and beta-naphtoflavone treatmend for 72 hours on human primary trophoblasts were investigated. 0.25% DMSO was a control.

overall_design: 12 samples, 3 controls, 3 beta-naphtoflavone and 6 pioglitazone treated samples

last: Rysä

first: Markku

last: Pasanen

first: Pasi

last: Huuskonen


title: Expression data from Prostate Cancer xenograft with CtBP1 control or depleted generated in mice with metabolic syndrome

status: Public on Sep 21 2019

city: Buenos Aires

first: Adriana

last: De Siervi

state: Buenos Aires

address: Vuelta de Obligado 2490

department: Instituto de Biología y Medicina Experimental

country: Argentina

institute: CONICET

summary:
Prostate cancer (PCa) is the most common cancer among men. Metabolic syndrome (MeS) is associated with increased PCa aggressiveness and recurrence. We propose C-terminal binding protein 1 (CTBP1), a transcripcional co-repressor, as a molecular link between these two conditions. CTBP1 depletion decreased PCa growth in MeS mice. The aim of this study was to investigate the molecular mechanisms that explain the link between MeS and PCa mediated by CTBP1. We  found that CTBP1 repressed several mRNAs and miRNAs including Chloride Channel Accessory 2 (CLCA2) in prostate xenografts developed in MeS animals. CTBP1 bound to CLCA2 promoter and repressed its transcription and promoter activity in PCa cell lines. Furthermore, we found that CTBP1 formed a repressor complex with ZEB1, EP300 and HDACs that modulates the CLCA2 promoter activity. CLCA2 promoted PCa cell adhesion inhibiting Epithelial-Mesenchymal Transition (EMT) and activating CTNNB1 together with epithelial markers (CDH1) induction, and mesenchymal markers (SNAI2 and TWIST1) repression. Moreover, CLCA2 depletion in PCa cells injected s.c. in MeS mice increased the Circulating Tumor Cells (CTCs) foci compared to control. A miRNA expression microarray from PCa xenografts developed in MeS mice, showed 21 miRNAs modulated by CtBP1 involved in angiogenesis, extracellular matrix organization, focal adhesion and adherents junctions, among others. We found that miR-196b-5p directly targets CLCA2 by cloning CLCA2 3'UTR and performing reporter assays. Altogether, we identified a new molecular mechanism for PCa and MeS link based on CLCA2 repression by CTBP1 and miR-196b-5p molecules that might act as key factors in the progression onset of this disease.
We used microarrays to identified the miRNAs regulated by CtBP1 in a Metabolic Syndrome model

overall_design: The mice were fed a high fat diet for 12 weeks, then injected with PC3 control or CTBP1 depleting cells. After 6 weeks the xenografts were processed, total RNA was obtained and hybridized to miRNA 4.0 Affymetrix array

first: Juliana

last: Porretti

first: Guillermo

last: Dalton

first: Cintia

last: Massillo

first: Georgina

last: Scalise

first: Paula

last: Farré

first: Paola

last: De Luca


title: Role of iron in the regulation of the epithelial-to-mesenchymal transition (ChIP-seq)

first: Nicolas

last: Servant

summary: The biological process termed Epithelial-to-Mesenchymal Transition (EMT) plays a central role in cancer cell invasion, metastasis, self-renewal and resistance to therapy. Here, we characterize using chromatin immunoprecipitation and Next Generation Sequencing  the genome-wide H3K9me2 distribution occurring during EMT induced by epidermal growth factor in breast cancer MDA-MB-468 cells.

overall_design: Analysis of 9 samples:  (i)Input DNA to normalize samples; (ii) H3K9me2 Immunoprecipitated in untreated cells and (iii) H3K9me2 immunoprecipitated in EGF-treated cells. Experiment was performed in 3 independent biological replicates.

first: Fabien

last: Sindikubwabo

first: Sylvain

last: Baulande

first: Rodriguez

last: Raphael


title: FOXG1 and DDX5 control PRKAR2B expression via miR200 in a mouse model of atypical Rett-syndrome

status: Public on Sep 22 2019

city: Göttingen

first: Gaurav

last: Jain

state: Lower Saxony

address: Von-Siebold-Str. 3a, Office no: 2.212

institute: The German Center for Neurodegenerative Diseases (German: Deutsches Zentrum für Neurodegenerative Erkrankungen DZNE)

summary: Rett syndrome is a complex neurodevelopmental disorder that is mainly caused by mutations in MECP2. However, mutations in FOXG1 cause a less frequent non-congenital form called atypical Rett syndrome. FOXG1 is a key transcription factor implicated in forebrain development, where it maintains the balance between progenitor proliferation and neuronal differentiation. Using quantitative proteomics and genome-wide small RNA sequencing, we identified that FOXG1 interacts with the ATP-dependent RNA helicase, DDX5/p68 and controls the biogenesis of miRNAs. Both, FOXG1 and DDX5 bind to the miR200b/a/429 primary transcript and associate with the microprocessor complex, whereby DDX5 recruits FOXG1 to DROSHA. In vivo and in vitro experiments show that both FOXG1 and DDX5 are necessary for effective maturation of miR200b/a/429. RNAseq analyses of Foxg1-heterozygote hippocampi and miR200b/a/429 overexpressing Neuro-2a cells revealed that the cAMP-dependent protein kinase type II-beta regulatory subunit (PRKAR2B) is a target of miR200 in neural cells. Since it is known that PRKAR2B inhibits postsynaptic functions by attenuating protein kinase A (PKA) activity, increased PRKAR2B levels may contribute to neuronal dysfunctions in FOXG1 Rett syndrome.

overall_design: FOXG1-DDX5 complex controls miR200 biogenesis

first: Stefan

last: Weise

first: Ganeshkumar

last: Arumugam

first: Tanja

last: Vogel

first: Andre

last: Fischer

first: Farahnaz

last: Sananbenesi


title: Identification of thiostrepton as a pharmacological approach to rescue misfolded alpha-sarcoglycan mutant proteins from degradation

status: Public on Sep 19 2019

city: Corbeil-Essonnes

first: MARGOT

last: JARRIGE

address: 28, Rue Henri Desbruères

institute: I-Stem/INSERM U861

summary: Limb-girdle muscular dystrophies type 2D (LGMD2D) are characterized by a progressive proximal muscle weakness. LGMD2D is due to mutations in the gene encoding α sarcoglycan (-SG), a dystrophin-associated glycoprotein playing a key role in the maintenance of sarcolemma integrity in striated muscles. Here, we report the development of a new in vitro high-throughput screening assay that allows monitoring the proper localization of the most prevalent mutant form of -SG (R77C substitution). Using this assay, we screened a library of 2560 FDA-approved drugs and bioactive compounds and identified thiostrepton, a cyclic antibiotic, as a potential drug to repurpose for LGMD2D treatment. Characterization of thiostrepton effect revealed a positive impact on R77C--SG and other missense mutant proteins (R34H, I124T, V247M) localization in fibroblasts overexpressing these proteins. Finally, further investigations of the molecular mechanisms of action of the compound revealed an inhibition of the chymotrypsin-like activity of the proteasome 24h following thiostrepton treatment and a synergic effect with bortezomib, a FDA-approved proteasome inhibitor. This study reports the first in vitro model of LGMD2D compatible with high throughput screening and propose a new therapeutical option for LGMD2D caused by missense mutations of -SG.

overall_design: Identification of Thiostrepton as a pharmacological approach to rescue misfolded alpha-sarcoglycan mutant proteins from degradation


title: Gene Expression Profiling of Whole Blood: A Comparative Assessment of RNA-Stabilizing Collection Methods

status: Public on Sep 20 2019

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

summary: Peripheral Blood gene expression is widely used in the discovery of biomarkers and development of therapeutics. Recently, a spate of commercial blood collection and preservation systems have been introduced with proprietary variations that may differentially impact the transcriptomic profiles. Comparative analysis of these collection platforms will help optimize protocols to detect, identify, and reproducibly validate true biological variance among subjects. In the current study, we tested two recently introduced whole blood collection methods, RNAgard® and PAXgene™ RNA, in addition to the traditional method of peripheral blood mononuclear cells (PBMCs) separated from whole blood and preserved in Trizol reagent. Study results revealed striking differences in the transcriptomic profiles from the three different methods that imply ex vivo changes in gene expression occurred during the blood collection, preservation, and mRNA extraction processes. When comparing the ability of the three preservation methods to accurately capture individuals’ expression differences, RNAgard® outperformed PAXgene™ RNA, and both showed significantly better individual separation of transcriptomic profiles than PBMCs. Hence, our study recommends using a single blood collection platform, and strongly cautions against combining methods during the course of a defined study.

overall_design: Peripheral blood was collected from eight healthy volunteers. Three comparitive groups for each subject, namely, blood preserved in PAXgene™ RNA tube, RNAgard® Blood Tube and CPT tube. Biological replicates (per subject): 3 RNAgard® Blood Tubes, 2 PAXgene™ RNA tubes and 3 CPT tubes (reference group).

first: Duncan

last: Donohue

first: Seshamalini

last: Srinivasan

first: Stacy

last: Ann-Miller

first: Rasha

last: Hammamieh

first: Marti

last: Jett


title: Expression data from piperlongumine treated bladder cancer T24 cells

city: Wuhan

first: Di

last: Liu

state: Hubei

address: 1277 Jiefang Road

department: Department of Urology

institute: Union Hospital

summary:
Piperlongumine (PL), a natural alkaloid isolated from longer pepper plants, is recently found to be a potent selective anti-cancer compound. To further explore the therapeutic spectrum and molecular mechanisms of PL, we tested its anti-cancer effects in bladder cancer, the fifth most common and aggressive cancer worldwide.
We used microarrays to detail the profile of miRNA expression underlying piperlongumine treatment and identified distinct classes of regulated microRNA during this process.

overall_design: T24 cells treated with PL or control  were selected  for RNA extraction and hybridization on Affymetrix microarrays. We sought to reveal that PL exerted anticancer effects via miRNA regulation and their target genes involving in anticancer drug efficacy or resistant.

first: XinYao

last: Qiu


title: Role for the Transcriptional Activator ZRF1 in Breast Cancer Progression and Endocrine Resistance

status: Public on Sep 24 2019

city: Mainz

first: Sergi

last: Sayols

address: Ackermannweg 4

institute: Institute of Molecular Biology, Mainz

summary: RNAseq analysis upon KD of ZRF1 to prove that depletion of ZRF1 results in the acquisition of metastatic behavior and drug resistance via misregulation of cell death and cell survival related pathways in MCF7 cells.

overall_design: Control and shZRF1 MCF7 cells are grown as organoids in suspension culture during 7 days. Total RNA extracted from these organoids are seqeunced to find out which biological processes are impaired in ZRF1 depleted conditions.

first: Richly

last: Holger

first: Kaymak

last: Aysegul


title: Comparison of microRNA expression profiles in soft palate muscle of patients with OSAHS and chronic tonsillitis.

city: Xi'an

first: Jin

last: Hou

state: Shaanxi

address: 157 Xiwu Road

department: Otolaryngology- Head and Neck Department

institute: The Second Affiliated Hospital of Xi'an Jiaotong University

summary: The expression profile of miRNAs in soft palate muscle of patients with OSAHS (obstructive sleep apnea/hypopnea syndrome) and chronic tonsillitis was examined using miRNA microarray analysis. Combining with the following real time PCR and bioinformatics analysis, the physiological importance of the miRNA-autophagy interconnection  is far more likely to be elucidated.

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Cytomegalovirus
Lymphocryptovirus
Rhadinovirus
JC polyomavirus
Human immunodeficiency virus 1
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: In the study presented here, four samples from soft palate muscle of patients with OSAHS and four samples from patients with chronic tonsillitis. These samples  were used to acquire expression profiles of all human miRNAs annotated in miRBase 18.0

first: Min

last: Xu


title: Comparison of stem cell like glioma cells (NCH644 and NCH690) and their differentiated cells

status: Public on Sep 18 2019

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

summary: Microarray analysis was performed to compare gene expression between stem cell like glioma cells and their differentiated cells.

overall_design: Two human stem cell like glioma cells (NCH644 and NCH690) were differentiated and RNA samples of stem cell like cells and their differentiated cells were analyzed. Total RNA of differentiated cells were obtained after 7 passages.

first: Chiaki

last: Ishida

first: Markus

last: Siegelin


title: Expression data of U87 MG glioblastoma cells with vehicle or with 30nM Panobinostat treatment for 3 weeks

summary:
Low dose of HDAC inhibitor (Panobinostat) treatment causes U87 cells to become resistant to the drug.
Gene expression of the resistant cell line is altered comparing to the vehicle control.

overall_design: U87 glioblastoma cells cultured in control and 30nM panobinostat for 3 weeks were harvested for RNA extraction and hybridization on Affymetrix microarrays.

first: Yiru

last: Zhang


title: MEK and GSK3β inhibition drives ES cells into a naive pluripotent state irrespective of their global methylation status

city: Edinburgh

first: John

middle: Paterson

last: Thomson

address: Crewe Road

department: MRC Human Genetics Unit

institute: University of Edinburgh

summary: We carry out methyl DNA immunoprecipitation (meDIP), hydroxymethyl DNA immunoprecipitaion (hmeDIP) and H3K27me3 chromatin imminoprecipitation (ChIP) prior to sequencing on the Ion Proton semiconductor sequencing platform to report on the genome-wide epigenetic patterns in J1 mESC and mutant mESCs (hyper active DNMT3b/3l or DNMT1/3a/3b triple knock out)  grown under serum conditions or in 2i meadia for 14 days

overall_design: Genome-wide patterns were generate on the Ion Proton P1 sequencer.

first: Ruchi

last: Shukla

first: Heidi

last: Mjoseng

first: Angie

last: Fawkes

first: Richard

last: Clark

first: Lee

last: Murphy

last: Meehan


title: Lipid signaling during neuronal degeneration in KA-treated mice

status: Public on Sep 23 2019

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

institute: IBENS

summary: Lipid homeostasis is dysregulated in several forms of neurodegeneration. Here we examined changes in sterols, neutral lipids and transcripts that control their homeostasis during the neuronal death induced in the CA1 region of mouse hippocampus by focal kainic acid (KA) injection. We defined changes in the lipid economy of neurons and glial cells by staining for neutral lipids and for free cholesterol. Lipid droplets filled with neutral lipids were induced in microglia at ~24 hrs after KA-treatment. At 2-4 days after injection, filipin staining revealed punctate deposits of free cholesterol in neuronal somata. These changes were correlated with alterations in cellular organelles observed in electron microscopy and transcriptomic changes obtained with RNA-seq of tissue from the CA1 region. Mitochondria, the innate inflammatory response and lipids. Lipid droplet transcriptome. Cholesterol economy. Lipids and phagocytosis.

overall_design: Comparaison of mouse hippocampus CA1 area transcriptome at 6 hours, 1, 2, 4, 6 and 12 days after injection of Kainate or NaCl.

first: Farah

last: Chali

first: Serge

last: Marty

first: Giampaolo

last: Milior

first: Mélanie

last: Morin-Brureau

first: Caroline

last: Le Duigou

first: Corinne

last: Blugeon

first: Laurent

last: Jourdren

first: Etienne

last: Savary

last: Miles