title: Developing a clinically relevant ovarian cancer model incorporating surgical cytoreduction to evaluate treatment of micro-metastatic disease

status: Public on Apr 25 2020

city: Seattle

first: Kristin

middle: Gail

last: Anderson

address: 1100 Fairview Ave N

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

summary: Mouse models of ovarian cancer commonly involve tumor cell transfer into the peritoneal cavity to establish metastatic disease. However, once disease has become established and disseminated through the abdomen, surgical cytoreduction in mice is not feasible. We set out to develop an ovarian cancer model amenable to surgical cytoreduction to mimic clinical treatment paradigms.

overall_design: Late-stage primary and metastatic tumors isolated from 3 ID8-VEGF mice (tumor cells injected under the ovarian bursa) were analyzed.

first: Valentin

last: Voillet

first: Christopher

last: Morse

first: Raphael

last: Gottardo

first: Philip

last: Greenberg


title: Analysis of global gene expressions in initial infection of Mycobacterium avium subsp. paratuberculosis using epithelial cells-peripheral blood mononuclear cells culture passage model.

status: Public on Apr 29 2020

city: Seoul

first: Hong-Tae

last: Park

address: 1, Gwanak-ro

country: South Korea

institute: Seoul National University

type: Expression profiling by high throughput sequencing

summary:
Purpose: Understanding host-MAP interactions in initial stage of infection
Methods: Native MAP and MDBK processed (4h) MAP were infected to bovine PBMCs. Total RNA after 24h and 72h were harvested. RNA-Seq was performed using total RNA of each group.
Result: The gene expression patterns commonly activated in both groups suggest that Th17 activation is the main immunological response to MAP infection.

overall_design: in vitro epithelial cells-peripheral blood mononuclear cells (PBMCs) culture passage model to establish a host-MAP interaction during initial stage of infection.

first: Han-Sang

last: Yoo


title: microRNA profiles in KC (Kupffer cells) and MNCs (blood monocytes):

status: Public on May 19 2020

city: Moscow

first: Polina

last: Vishnyakova

address: Oparina 4

country: Russia

institute: National Medical Research Center for Obstetrics, Gynecology and Perinatology

summary: As a rule, mammalian organs contain a mixed population of macrophages from different sources of origin. It is assumed that the self-sustaining resident macrophages and the monocyte-derived transient macrophages differ by their functional properties and their roles in repair processes . The analysis of the functional features of different populations of macrophages is of significant practical importance, since macrophages are considered as therapeutic targets in various pathological conditions and as prospective basis for cell therapy products. The aim of this study was to compare microRNA profiles  of the two alternative macrophage species exemplified, respectively, by Kupffer cells of the liver and monocytes of the blood.

overall_design: In the study presented here, four samples of KC and four samples of MNC  was used to acquire microRNA profiles of a total of 577 mouse miRNA. For each sample, sorted cells from 5 mice were pooled.

first: Maria

last: Nikitina

first: Andrey

last: Elchaninov


title: Modular structure and function of the XIST RNP in X chromosome inactivation

status: Public on Apr 23 2020

city: Stanford

first: Zhipeng

last: Lu

state: CA

address: 269 Campus Drive

department: Department of Dermatology

country: USA

institute: Stanford University

summary: Long noncoding RNAs (lncRNAs) are an important class of transcripts that regulate gene expression on many levels, yet their mechanisms of action remain poorly understood. Previous studies have indicated that these RNAs can serve as modular scaffolds to recruit a variety of protein complexes and coordinate their distinct functions. XIST, a founding member of the lncRNA family, controls the inactivation of an entire X chromosome in placental mammals. Here we develop and integrate several orthogonal structure-interaction analysis methods to demonstrate that XIST RNA-protein complex folds into a modular architecture that is conserved in evolution. The discrete XIST RNA domains interact with distinct sets of effector proteins to orchestrate the X chromosome inactivation (XCI). The modular architecture plays an essential role, in addition to the sequence motifs, in determining the specificity of RBP binding and m6A modification. Together, this work builds a comprehensive structure-function model for the XIST RNA-protein complex, and establishes a paradigm for mechanistic studies of lncRNA functions.

overall_design: We used MeRIP-seq to determine the m6A modification pattern on mouse Xist after relocating the A-repeat region in the Xist architecture. Detailed method is as follows. Total mES RNA was subjected to one round of Poly(A)Purist MAG treatment to enrich for polyadenylated RNAs as per manufacturer’s instructions (Ambion). RNA was then fragmented to 100nt median sized fragments using RNA Fragmentation Reagents (Ambion) and subjected to one round of m6A immunoprecipitation. For immunoprecipitation of RNA, 5 ug of m6A antibody (Millipore) was coupled to 40 ul Protein A Dynabeads (Novex) in 100 ul 1X IPP Buffer (50mM Tris-HCl, pH 7.5; 150mM NaCl; 0.1% NP-40; 5mM EDTA) overnight at 4C. Beads were then washed twice in 1X IPP Buffer. Fragmented RNA was denatured at 70C for 2 min, cooled on ice, and bound to antibody-beads in 185 ul 1X IPP Buffer for 3h at 4C. Beads were then washed sequentially with (2x) 500 ul 1X IPP Buffer, (2x) 500 ul Low Salt Buffer (0.25X SSPE; 1mM EDTA; 0.05% Tween-20; 37.5mM NaCl), (2x) 500 ul High Salt Buffer (0.25X SSPE; 1mM EDTA; 0.05% Tween-20; 137.5mM NaCl), (1x) 500 ul TET Buffer (10mM Tris-HCl, pH 8.0; 1mM EDTA; 0.05% Tween-20). Beads were eluted with 50 ul RLT Buffer (Qiagen RNeasy Mini Kit) and incubated at 25C for 5 min, and recovered with RNeasy Mini Kit followed by concentrating with Zymo RNA Clean & Concentrator in 10 ul water. 10 ng of input RNA (before immunoprecipitation) and 10 ng of immunoprecipitated RNA were then used to prepare sequencing libraries using SMARTer Stranded RNA-Seq Kit - Pico Input Mammalian (Clontech #634411), as per manufacturer’s instructions. Sequencing libraries were pooled and sequenced on the Illumina MiSeq (files named *mar08* and *apr26*) and NextSeq (files named *jun24*).


title: Genome-wide characterization of Six1 binding in embryo and cochlea

status: Public on Apr 17 2020

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Otic ectoderm gives rise to almost all cell types of the inner ear; however, the mechanisms that link transcription factors, chromatin, lineage commitment and differentiation capacity are largely unknown. Here we show that Brg1 chromatin-remodeling factor is required for specifying neurosensory lineage in the otocyst and for inducing hair and supporting cell fates in the cochlear sensory epithelium. Brg1 interacts with the critical neurosensory-specific transcription factors Eya1/Six1, both of which simultaneously interact with BAF60a or BAF60c. Chromatin immunoprecipitation-sequencing (ChIP-seq) and ChIP assays demonstrate Brg1 association with discrete regulatory elements at the Eya1 and Six1 loci. Brg1-deficiency leads to markedly decreased Brg1 binding at these elements and loss of Eya1 and Six1 expression. Furthermore, ChIP-seq reveals Brg1-bound promoter-proximal and distal regions near genes essential for inner ear morphogenesis and cochlear sensory epithelium development. These findings uncover essential functions for chromatin-remodeling in the activation of neurosensory fates during inner ear development.

overall_design:
Six1 is a critical transcription factor for specifying cell fates in multiple organs and shares common DNA-binding sites with Six2/4/5. However, its molecular function in defining the specificity of Six1-DNA interactions and in instructing cell fates is poorly understood. We performed Six1 ChIP-seq analyses in E10.5 mouse embryos and E13.5 cochleae to map genome-wide CRMs through which Six1 and its interacting TFs function in a combinatorial fashion to control the network of gene regulation necessary for proper development. Genome-wide characterization has identified a robust set of Six1 targets in embryos and auditory sensory epithelium, including genes participating in Wnt/Notch/Shh/Fgf signaling pathways and regulators critical for auditory hair cell formation. Our data provide insights into how Six1 acts in multiple regulatory networks operating in distinct cell types at different stages.
Genome-wide Six1 binding feature was characterized in whole embryo and cochlea using ChIP-seq.

Please note that both Series and sample records have been updated on Dec 9th, 2020.

first: Jun

last: Li

first: Yong-Hwee

middle: E

last: Loh

first: Li

last: Shen

first: Pin-Xian

last: Xu


first: Eddie

department: Department of Neuroscience

summary: Six1 is a critical transcription factor for specifying cell fates in multiple organs and shares common DNA-binding sites with Six2/4/5. However, its molecular function in defining the specificity of Six1-DNA interactions and in instructing cell fates is poorly understood. We performed Six1 ChIP-seq analyses in E10.5 mouse embryos and E13.5 cochleae to map genome-wide CRMs through which Six1 and its interacting TFs function in a combinatorial fashion to control the network of gene regulation necessary for proper development. Genome-wide characterization has identified a robust set of Six1 targets in embryos and auditory sensory epithelium, including genes participating in Wnt/Notch/Shh/Fgf signaling pathways and regulators critical for auditory hair cell formation. Our data provide insights into how Six1 acts in multiple regulatory networks operating in distinct cell types at different stages.

overall_design: Genome-wide Six1 binding feature was characterized in whole embryo and cochlea using ChIP-seq.

first: Yong

last: Hwee

first: Shen


title: Profiling of miRNAs involved in liver carcinogenesis by age [HCC, sHCC]

status: Public on Jun 20 2020

city: Shinjyuku

first: Tomohiro

last: Umezu

state: Tokyo

address: 6-1-1 Shinjyuku

department: Department of Molecular Pathology

country: Japan

institute: Tokyo Medical University

summary:
Previous studies have identified several microRNAs (miRNAs) that may coordinate multiple pathways associated with age-related carcinogenesis. We compared hepatic miRNA expression patterns in chronic hepatitis (CH) and hepatocellular carcinoma (HCC) to elucidate age-related differences potentially underlying hepatocarcinogenesis.
2565 miRNAs in 97 liver tissues specimens were analyzed.

overall_design: Ninety-seven samples of HCC tumor tissue, with corresponding samples of surrounding tissue (hereafter referenced as sHCC) were collected by surgical resection.

first: Y

last: Murakami


title: An integrated multi-omics approach identifies the landscape of interferon-a-mediated responses of human pancreatic beta cells

status: Public on Apr 15 2020

city: Brussels

first: Maikel

middle: Luis

last: Colli

address: Route de Lennik, 808

department: Faculty of Medicine

country: Belgium

institute: Universite Libre de Bruxelles

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

overall_design: Refer to individual Series


title: The polymorphic PolyQ tail protein of the Mediator Complex, Med15, regulates variable response to stress

status: Public on Apr 06 2020

city: Morgantown

first: Amaury

last: Pupo

state: West Virginia

address: Life Sciences Building, PO Box 6057

department: Biology

institute: West Virginia University

summary: The Mediator is composed of multiple of proteins in the head, body, tail and CDK subunits conserved from yeast to humans. However, not all the components are required for transcription. Components of the tail subunit are not essential but to varying degrees are required for changes in transcription to stress. While some stresses are familiar such as heat, desiccation, and starvation, others are exotic yet elicit a physical stress response. MCHM is a hydrotrope that induces growth arrest in yeast. By exploiting genetic variation, specifically in Med15, between yeast strains, we found that Med15 with the polyQ expansion conferred MCHM sensitivity. This sensitivity was not from a loss of function as the reciprocal hemizygous hybrids were all sensitive, suggesting that there is an incompatibility between Mediator complexes from genetic divergent yeast strains. Transcriptomics from yeast expressing the incompatible Med15 changed expression in diverse pathways. Expansion of polyQ tracts in Med15 resulted in multiple isoforms which were mostly from likely post-translational modifications. Stability of Med15 was dependent on Ydj1, a chaperone and the incompatible Med15 allele was expressed at lower levels and less stable than the compatible Med15 allele. Med15 is tethered to the rest of the Mediator complex via Med2 and 3. Deletion of either Med2 or Med3 changes the Med15 isoform patterns in the in a similar manner whereas deletion of Med5, a distal component of the tail did not change the pattern. The med2 and 3 mutants are similarly sensitive to MCHM while med5 mutants are not. Differences between the Med15 alleles extend to responses to different stresses. Whereas the incompatible allele of Med15 improved growth to chemicals that produce free radicals, and the compatible allele of Med15 improved growth to reducing agents, caffeine, and hydroxyurea. This may reflect the positive and negative role that Med15 has in transcription.

overall_design: mRNA profiles of med15 knockout and mutants in a BY4741 background, in YPD or YM, treated or not with MCHM, in triplicate, using Illumina Miseq.

first: Jennifer

last: Gallagher

first: Casey

last: Nassif

first: Noor

last: Malik


title: Gene expression alternations in the offspring rat intestine from sitagliptin-treated dams

status: Public on Apr 10 2020

city: Beijing

first: Qian

last: Zhang

address: No. 1 Shuaifuyuan, Dongcheng District

country: China

institute: Peking Union Medical College Hospital

summary: More and more evidence shows that maternal overnutrition may increase the risk of diabetes in offspring. This study aimed to find out whether maternal early sitagliptin intervention improves glucose intolerance through gut target in offspring.

overall_design: We performed microarray analyses of offspring rat intestine from sitagliptin-treated dams

first: Xinhua

last: Xiao

first: Jia

last: Zheng

first: Ming

first: Miao

last: Yu

first: Fan

last: Ping

first: Zhixin

last: Wang

first: Cuijuan

last: Qi

first: Tong

first: Xiaojing


title: An integrated multi-omics approach identifies the landscape of interferon-a-mediated responses of human pancreatic beta cells [RNA-seq]

summary: Proinflammatory cytokines are important mediators of pancreatic beta cell dysfunction and demise in type 1 diabetes (T1D). We presently characterized human beta cell responses to IFNa by combining ATAC-seq, RNA-seq and proteomics assays. The initial beta cell response to IFNa was characterized by major chromatin remodeling, followed by marked changes in transcriptional and translational regulation. IFNa-induced changes in alternative splicing (AS) and first exon usage increased the diversity of transcripts expressed by beta cells. This, combined with changes observed on protein modification/degradation, ER stress and MHC class I, may significantly expand the peptide repertoire presented by beta cells to the immune system. On the other hand, beta cells up-regulated checkpoint proteins, such as PDL1 and HLA-E, that may protect them against the autoimmune assault. Data mining of the present multi-omics analysis led to the identification of two compound classes that revert IFNa effects on human beta cells and may be translated to clinical trials.

overall_design: RNA-sequencing of 5 independent experiments of the human beta cell line EndoC-BH1 cells exposed or not to intereron-alpha for 2, 8 and 24h.

first: Decio

middle: L

last: Eizirik


title: An integrated multi-omics approach identifies the landscape of interferon-a-mediated responses of human pancreatic beta cells [RNA-seq 2]

overall_design: RNA-sequencing of 6 independent experiments of the pancreatic human islets exposed or not to intereron-alpha for 2, 8 and 18h.


title: RNA sequencing of NT control cells, Traf3 KO, and Traf3/p100 double KO cells

status: Public on Mar 31 2020

city: Nashville

first: Maria

last: Fomicheva

state: TN

address: 465 21st Avenue S., U 3200 MRBIII, Dept. of Cell and Developmental Biology Vanderbilt University

department: Cell and Developmental Biology

institute: Vanderbilt University

summary: Loss of Traf3 caused a dramatic induction of innate immune response genes. Antigen presentation, interferon response genes and genes responsible for foreign DNA and RNA recognition were strongly upregulated by deletion of Traf3, but KO of p100 in Traf3 KO samples reversed the activation of these pathways. We did not detect any stimulation by Traf3 KO of those signaling pathways classically involved in proliferation, including PI3K/AKT, JNK, TGF-beta, WNT and Hippo

overall_design: We established a stable EpH4 line that expresses ES-FUCCI, which labels cells in G1/G0 with mCherry and cells in S/G2/M with mCitrine. We transduced EpH4-FUCCI mammary epithelial cell line with non-targeted (NT), Traf3, or Traf3 plus p100 sgRNA lentiviruses, and grew them to day 4 postconfluency. Then we sorted cells for G1/G0 phase (mCherry+) cells. This strategy eliminates indirect gene expression differences reflective of the larger fraction of cycling (mCitrine+) cells caused by loss of Traf3, but will not remove constitutive changes in gene expression. Two biological replicates of each cell line were processed for total RNA sequencing, and fastq files were analyzed using CLC Genomics Workbench. Differential gene expression was filtered for > 2-fold differences, FDR < 0.05.

first: Ian

middle: G

last: Macara


title: 10x single-cell RNAseq profiling of CD45+ melanoma-infiltrating leukocytes from APOE2 and APOE4 knock-in mice

status: Public on Mar 21 2020

city: Berlin

first: Benjamin

middle: N

last: Ostendorf

address: Augustenburger Platz 1

country: Germany

institute: Charité University Medicine

summary: APOE germline genotype modulates the tumor immune microenvironment. In APOE4 relative to APOE2 mice, there is shift towards an anti-tumor immune phenotype, with an increased ratio of immune effector to immunosuppressive cells.

overall_design: Examination of the immune tumor microenvironment of YUMM1.7 melanomas hosted by APOE2 versus APOE4 knock-in mice. CD45+ cells were sorted from dissociated melanomas and 10,000 cells each from 6 mice were pooled for each genotype.


title: PARIS analysis of mouse Xist RNA structure

first: Zhipeng

last: Lu

overall_design: Cells are crosslinked with AMT and RNA is extracted from cells by RNase digestion. Crosslinked RNA fragments are selected from total RNA by 2D gel electrophoresis. Purified crosslinked RNA duplexes are proximity ligated and crosslinking is reversed. Then the chimeric RNA molecules are converted into cDNA libraries for high-throughput sequencing.


title: RNAseq to profile transcriptomes in bone marrow-derived macrophages from TKO(mir-106a~363-/- mir-106b~25-/- mir-17~92flox/flox Lyz2-Cre) and WT(Lyz2-Cre) mice

status: Public on Mar 17 2020

first: Xiang

address: Tsinghuayuan Street

institute: Tsinghua University

summary: We performed the transcriptomic analysis of RNA-seq of BMDMs generated from WT and TKO mice to identify gene expression changes.

overall_design: BMDMs from WT and TKO mice were lysed. RNA was extracted, polyA enriched and prepared for sequencing libraries.


title: Distinctive regulatory architectures of ubiquitous, germline and somatic genes

status: Public on Mar 15 2020

city: Cambridge

first: Julie

last: Ahringer

address: Tennis Court Road

department: The Gurdon Institute

country: United Kingdom

institute: University of Cambridge

summary: Chromatin accessibility in Germline, Neurons, Muscle, Hypodermis and Intestine nuclei from young adult worms.

overall_design: ATAC-seq was used to profile chromatin accessibility in Germline, Neurons, Muscle, Hypodermis and Intestine nuclei from young adult worms.

first: Jacques

last: Serizay


summary: Nuclear long RNA-seq was used to profile gene expression in Germline, Neurons, Muscle, Hypodermis and Intestine nuclei from young adult worms.

overall_design: Gene expression in Germline, Neurons, Muscle, Hypodermis and Intestine nuclei from young adult worms.


title: An integrated multi-omics approach identifies the landscape of interferon-a-mediated responses of human pancreatic beta cells [ATAC-seq]

first: Maikel

last: Colli

overall_design: ATAC-sequencing of 4 independent experiments of the human beta cell line EndoC-BH1 cells exposed or not to intereron-alpha for 2 and 24h.


title: Cross-species analysis of melanoma enhancer logic using deep learning

status: Public on Apr 22 2020

city: Leuven

first: Stein

last: Aerts

address: O&N4 Herestraat 49 PO Box 602

institute: KU Leuven

summary: Here, we combine comparative regulatory genomics with machine learning to investigate enhancer logic in melanoma. Through epigenomics profiling of 26 melanoma cell lines across six species, we examine the conservation of the two main melanoma states and underlying master regulators. By training a deep neural network on topic models derived from the human lines, we were able to classify not only human melanoma enhancers, but also regulatory regions in the other species. The deep learning model revealed important genomic features (i.e. TF binding motifs) for the different melanoma states, how they co-occur within melanoma enhancers, and where they are placed with respect to the central enhancer nucleosome. This in-depth analysis of the melanoma enhancer code allowed us to propose a mechanistic model of TF binding in MEL melanoma enhancers. Finally, by exploiting the deep layers of our model, we are able to identify causal mutations for melanoma enhancer loss and gain through evolution, not only affecting enhancer accessibility but also activity.

sample_organism:
Danio rerio
Homo sapiens
Canis lupus familiaris
Equus caballus
Sus scrofa domesticus
Mus musculus

overall_design: (omni)ATAC-seq on melanoma cell lines across six species, as well as OmniATAC-seq on knock-down of transcription factors in the human melanoma cell line MM001

first: Liesbeth

last: Minnoye

first: Ibrahim

middle: I

last: Taskiran

first: Leonard

last: Zon

first: Song

last: Yang


title: TET1 and 5-hydroxymethylation preserve the stem cell state of mouse trophoblast

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

type: Methylation profiling by high throughput sequencing

summary: Analysis of 5mC and 5hmC and associated transcription in trophoblast stem cells cultured and differentiated at 20% and 5% oxygen, integrated with previously published datasets

overall_design: meDIP and hmeDIP was carried out to determine 5mC and 5hmC genomic distribution in tcontrol rophoblast stem cells and those lacking Tet1. hmeDIP and RNA-seq was also carried out in trophoblast stem cells cultured in 5% Oxygen to determine the effect of hypoxia on 5hmC and associated transcription

first: Claire

last: Senner

first: Stephanie

last: Chrysanthou

first: Sarah

last: Burge

first: Hai-Yan

last: Lin

first: Miguel

last: Branco

first: Myriam

last: Hemberger


title: VadR sRNA target identification

status: Public on Mar 10 2020

city: Jena

first: Kathrin

last: Fröhlich

state: Thuringia

address: Winzerlaer Straße 2

department: Fakultät für Biowissenschaften, Bacterial RNA Biology

institute: Friedrich-Schiller-Universität Jena

summary: In this study, we determined the target spectrum of the VadR sRNA via pulse-expression followed by RNA-sequencing.

overall_design: mRNA profiles of V. cholerae ΔvadR strains carrying pBAD-ctr (empty vector control), pBAD-vadR (inducible sRNA expression vector). The bacteria were grown to exponential phase, expression of the sRNAs was induced by addition of L-arabinose, and RNA-samples were taken 10 minutes after induction. Three independent biological replicates for each condition are provided.

first: Nikolai

last: Peschek

first: Roman

last: Herzog

first: Praveen

middle: K

last: Singh

middle: S

first: Luise

last: Schröger

first: Fabian

last: Meyer

first: Marc

last: Bramkamp

first: Knut

last: Drescher

first: Kai

last: Papenfort


title: High density foci in  IDH1-mutated diffuse low-grade gliomas in adults

city: Tokyo

first: Nicolas

last: Leventoux

address: 35, Shinanomachi

department: Physiology

institute: Keio University

summary:
20% of patients affected with diffuse low-grade brain tumors have high cell density foci  harboring higher KI67 index and DNA alterations. These foci may represent tumor progression towards high-grade gliomas.
Here we performed transcriptome analysis of those foci vs adjacent tumoral tissues  dissected from formalin fixed and paraffin embedded blocks.

overall_design: We analyzed 8 diffuse low-grade gliomas (4 astrocytomas and 4 oligodendrogliomas) with Human Affymetrix 2.1ST chips.

first: Jean-Philippe

last: Hugnot

first: Valérie

last: Rigau

first: Hugues

last: Duffau


title: Single-cell mRNA sequencing of TAC-model mouse heart tissue

city: Durham

first: Li

last: Wang

address: 111 T.W. Alexander Dr

institute: NIH

summary: We studied the cell compositon of mouse heart by single-cell sequencing on TAC-model mice. Distint subgroups of cardiac muscle, fibroblast cell and endothelial cell were detected. We drawed a cell-cell interaction network using specific expressed ligands and receptors of cells. And we also observed the change of interaction and cell transformation with progress of the disease.

overall_design: Extract cells from left ventricle of mouse heart and conduct single-cell sequencing

first: Peng

last: Yu

first: Zongna

last: Ren

first: Zheng

last: Li


title: Deficiency of STING-signaling leads to neurogenic abnormalities and Autistic-Like Behaviors in the embryonic cortex [bulk RNA-seq]

status: Public on Mar 06 2020

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary:
Purpose: To gain  futher insight into how STING regulates the proliferative of neural progenitors ,RNA-seq was used to analyze the genome-wide changes resulting from the cerebral cortices of E13 STING conditional knock out mice and littermate wild-type.
Methods: Total RNA from E13 telencephalic tissue of wild-type(WT) and STINGf/f;Nestin-Cre mice was extracted. Specifically, Agilent 2100 Bioanalyze was used to quality controlled and quantified. then, total RNA was converted to cDNA and bound the library. RNA-sequencing analysis was used by the Illumina HiSeq 2500 platform in Annoroad Genomics
Results: Approximately  one thousand transcripts showed differential expression between the wild-type(WT) and STINGf/f;Nestin-Cre mice brain cortex, with a fold change ≥1.5 and p value <0.05.Geneontology analysis of the down or up-regulated genes showed obvious enrichment of biological processes related to brain development and cell fate commitment. These results reflected STING plays a role in cortex development.
Conclusions:  RNA-seq based transcriptome characterization would provide a overall understanding how STING gene contribute to brain cortical development.

overall_design: Total mRNA profiles of E13 wild type (WT) and STINGf/f;Nestin-Cre mice were generated by deep sequencing using Illumina HiSeq 2500.

first: Dongming

last: Zhang


title: Deficiency of STING-signaling leads to neurogenic abnormalities and Autistic-Like Behaviors in the embryonic cortex

overall_design: Refer to individual Series


title: Mendelian randomization identifies FLCN expression as a mediator of diabetic retinopathy

city: Chicago

first: Michael

last: Grassi

state: IL

address: 1855 West Taylor Street

department: Department of Ophthalmology and Visual Sciences

institute: University of Illinois at Chicago

summary: The goal of the study was to identify genes whose aberrant expression can contribute to diabetic retinopathy. We determined differential response in gene expression to high glucose in lymphoblastoid cell lines derived from matched type 1 diabetic individuals with and without retinopathy. Those genes exhibiting the largest difference in glucose response between diabetic subjects with and without retinopathy were assessed for association to diabetic retinopathy utilizing genotype data from a meta-genome-wide association study. All genetic variants associated with gene expression (expression QTLs; eQTLs) of the glucose response genes were tested for association with diabetic retinopathy. We detected an enrichment of the glucose response gene eQTLs among small association p-values for diabetic retinopathy. Among these, we identified FLCN as a susceptibility gene for diabetic retinopathy. Expression of FLCN in response to glucose is greater in individuals with diabetic retinopathy compared to diabetic individuals without retinopathy. Three large, independent cohorts of diabetic individuals revealed an enhanced association of FLCN eQTL to diabetic retinopathy. Mendelian randomization confirmed a direct positive effect of increased FLCN expression on retinopathy in diabetic individuals. Together, our studies integrating genetic association and gene expression implicate FLCN as a disease gene in diabetic retinopathy.

overall_design: We compared the differential response in gene expression to glucose for individuals with and without proliferative retinopathy. ‘Differential response’ in gene expression refers to gene expression comparisons that were determined by calculating the difference in response to glucose between groups. Specifically, we identified genes with a significant differential response in expression between diabetic individuals with and without proliferative diabetic retinopathy (RGpdr-ndr). We integrated these findings with results of a genome-wide association study meta-analysis of diabetic retinopathy and the results of a multi-tissue eQTL analysis to identify potential diabetic retinopathy susceptibility genes

first: Segun

last: Jung

first: Ana

middle: M

last: Sokovic


title: Architectural Mediator subunits are differentially essential for global transcription in yeast (ChIP-seq)

status: Public on Mar 05 2020

city: Bloomington

first: Gabriel

last: Zentner

state: IN

address: 915 E 3rd St

institute: Indiana University

summary: Mediator is a modular complex required for RNA polymerase II transcription in vivo. We show that Mediator destabilization via depletion of the main complex scaffold Med14 or the head module scaffold Med17 is lethal and results in global transcriptional downregulation, though Med17 destruction has a markedly greater negative effect. Depletion of Med14 or Med17 impairs pre-initiation complex (PIC) formation and/or stability to similar degrees, suggesting that the differential transcriptional effects of head module destabilization and overall dissociation of the complex are not due to different extents of defective PIC formation. Co-depletion of Med14 and Med17 reduced transcription and TFIIB promoter occupancy to similar degrees as Med17 loss alone, suggesting that the independent head module can weakly stimulate transcription in vivo, though not at a level that maintains viability. Collectively, our data suggest that the head is the major functional module of Mediator with respect to PIC function in vivo.

overall_design: ChIP-seq of PIC components with and without degradation of Mediator scaffold subunits

first: Jason

middle: P

last: Tourigny

first: Moustafa

last: Saleh


title: Single-Cell Transcriptomic Analysis Reveals Molecular Diversity of Human Oligodendrocyte Progenitor Cells

city: Baltimore

first: Xitiz

last: Chamling

state: MD

address: 400 N. Broadway

institute: Johns Hopkins University School of Medicine

summary: We performed single-cell-transcriptomic-analysis of developing human stem cell-derived oligodendrocyte-precursor-cells (hOPCs). We studied both a genome engineered hESC-reporter lines, containing an Identification-and-Purification tag expressed under control of the endogenous, OPC-specific, PDGFRa promoter, and an unmodified iPSC line, and performed time-course single-cell-RNA-sequencing of purified hOPCs. Our analysis uncovered transcriptional heterogeneity of PDGFRa+ hOPCs and identified regulatory genes and networks that control their differentiation and myelination competence. Pseudotime trajectory analysis suggested distinct trajectories for the development of oligodendrocytes vs astrocytes from the hOPCs. We also identified novel transcription factors and other genes that developing hOPCs potentially use to choose between oligodendrocyte vs astrocyte lineages. In addition, pathway enrichment analysis followed by pharmacological intervention of those pathways confirm that mTOR and cholesterol biosynthesis signaling pathways are involved in maturation of oligodendrocytes from hOPCs.

overall_design: hES-derived OPCs at four time-points spanning the in vitro differentiation process (day 77, 85, 89 and 104) were separately purified for their expression of PDGFRa, single cells were captured, and their transcriptome sequenced.

first: Donal

middle: J

last: Zack


title: RNA splicing factor Ybx1 maintains persistent Jak2-mutated neoplasms via Mknk1-ERK-signaling

status: Public on Mar 11 2020

city: Hannover

first: Florian

last: Perner

address: Carl-Neuberg-Str. 1

department: Hematology, Hemostasis, Oncology and Stem Cell Transplantation

institute: Hannover Medical School

summary: Measurement of DNA-binding of YBX1 in the HEL cell line (JAK2V617F mutated human cells)

overall_design: Using ChIP-seq we examinaed the chromatin occupancy of the multifunctional nucleic-acid binding protein YBX1 (YB-1) in the JAK2-V617F mutated human cells (HEL cell line).


title: RNA-sequencing from mouse embryonic spinal cord in the presence of FUS knockout or FUS NLS mutation delta14

city: London

first: Pietro

last: Fratta

address: Queen Square House

institute: University College London

summary: Mutations in the RNA-binding protein FUS cause amyotrophic lateral sclerosis (ALS), a devastating neurodegenerative disease in which the loss of motor neurons induces progressive weakness and death from respiratory failure, typically only 3-5 years after onset. FUS has been established to have a role in numerous aspects of RNA processing, including splicing. However, the impact of ALS-causative mutations on splicing has not been fully characterised, as most disease models have been based on FUS overexpression, which in itself alters its RNA processing functions. To overcome this, we and others have recently created knock-in models, and have generated high depth RNA-sequencing data on FUS mutants in parallel to FUS knockout

overall_design: Two transgenic mice lines - FUS delta 14 frameshift mutation (d14), and FUS knockout (KO) in an allelic series of wildtype, heterozygous and homozygous (WT, HET, HOM).

first: Jack

last: Humphrey


title: Transcriptomic profiling of dermatomyositis lesions.

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

summary: The microarray experiment was employed to evaluate the gene expressions in skin lesions of dermatomyositis and healthy controls.

overall_design: To investigate the specific gene regulations in dermatomyositis, microarray profiling was performed on RNA extracted from paraffin embedded skin biopsy samples obtained from patients and healthy controls.

first: Joanne

last: Kahlenberg

middle: C


title: Transcriptomic genotype-dependent response of Arundo donax L. under salt stress.

status: Public on Feb 24 2020

city: Catania

first: Angela Roberta

last: Lo Piero

state: CT

address: Via S. Sofia 98

country: Italy

institute: University of Catania

summary: Arundo donax L. is one of the most promising bioenergy crop due to its high biomass yield and low irrigation requirement. The resistance to biotic and abiotic stress causes the high invasiveness of this plant, which can grow with very low management input (e.g., pesticides, fertilization, irrigation) even in marginal lands or in fields irrigated with waste or salty water. We report the leaf transcriptome sequencing, de novo assembly and annotation of a giant reed G34 genotype under salt stress. This genotype shows a different transcriptomic response to salinity compared to other A. donax genotypes. This finding was unexpected considering that the genetic variability of this species is supposed to be low due to its vegetative reproductive process.  This study aims to direct future efforts towards the A. donax genetic improvement.

overall_design: Examination of A. donax genotype (namely, G34) under one level of NaCl concentration (250 mM). The control sample is the G34 genotype under no NaCl addition. All the samples are in three biological replicates

first: A

last: Sicilia

first: G

last: Testa

first: D

middle: F

last: Santoro

first: S

last: Cosentino

middle: R


title: Pooled CRISPR screens in human intestinal organoids [ATAC-seq]

status: Public on Feb 26 2020

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

summary: We performed CRISPR screens on both a sub-library and a genome-wide scale in human intestinal organoids to discover cancer driver genes. We investigated the Wnt and the TGFB pathway and used both WT, APC-mutant and APC-TP53-mutant organoids.

overall_design:
To investigate how the identified SWI/SNF screening hits confer TGFB resistance, we assessed changes in chromatin accessibility upon ARID1A or SMARCA4 perturbation and TGFB treatment using ATAC-seq
Please note that each peak file was generated from both replicates and is linked to the corresponding rep1 sample records

first: Till

last: Ringel

first: Nina

last: Frey

first: Femke

last: Ringnalda

first: Sharan

last: Janjuah

first: Sarah

last: Cherkaoui

first: Stefan

last: Butz

first: Sumana

last: Srivatsa

first: Martin

last: Pirkl

first: Giancarlo

last: Russo

first: Lukas

last: Villiger

first: Gerhard

last: Rogler

first: Hans

last: Clevers

first: Niko

last: Beerenwinkel

first: Nicola

last: Zamboni

first: Tuncay

last: Baubec

first: Gerald

last: Schwank


title: ChIP-Seq and RNA-Seq analysis of the iron regulatory transcription factors in Cryptococcus neoformans in response to iron availability

status: Public on Feb 16 2020

city: Seoul

first: Yong-Joon

last: Cho

address: 1 Gwanak-ro, Gwanak-gu

institute: Seoul National University

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


title: Macrophage ATP citrate lyase deficiency stabilizes atherosclerotic plaques

status: Public on Feb 18 2020

city: Amsterdam

first: Menno

last: de Winther

address: Meibergdreef 9

department: Medical Biochemistry

country: Netherlands

institute: Academic Medical Center University of Amsterdam

summary: Macrophages represent a major immune cell population in atherosclerotic plaques and play central role in the progression of this lipid-driven chronic inflammatory disease. Targeting immunometabolism is proposed as a strategy to revert aberrant macrophage activation to improve disease outcome. Here, we show ATP citrate lyase (Acly) to be activated in inflammatory macrophages and human atherosclerotic plaques. We demonstrate that myeloid Acly deficiency induces a stable plaque phenotype characterized by increased collagen deposition and fibrous cap thickness, along with a smaller necrotic core. In-depth functional, lipidomic, and transcriptional characterization indicate deregulated fatty acid and cholesterol biosynthesis and reduced liver X receptor (LXR) activation within the macrophages in vitro. This results in macrophages that are more prone to undergo apoptosis, whilst presenting increased phagocytosis of apoptotic cells. Together, our results indicate that targeting macrophage metabolism improves atherosclerosis outcome and we reveal Acly as a promising therapeutic target to stabilize atherosclerotic plaques.

overall_design: RNA-seq of bone marrow-derived macrophages from female AclyM-WT and AclyM-KO mice.

first: Jeroen

last: Baardman

first: Sanne

last: Verberk

first: Saskia

last: van der Velden

first: Marion

last: Gijbels

first: Cindy

last: van Roomen

first: Judith

last: Sluimer

first: Jelle

last: Broos

first: Guillermo

last: Griffith

first: Koen

last: Prange

first: Michel

last: van Weeghel

first: Soufyan

last: Lakbir

first: Douwe

last: Molenaar

first: Elisa

last: Meinster

first: Annette

last: Neele

first: Gijs

last: Kooij

first: Helga

last: de Vries

first: Esther

last: Lutgens

first: Kathryn

last: Wellen

first: Jan

last: Van den Bossche


title: ChIP-Seq analysis of the iron regulatory transcription factors in Cryptococcus neoformans in response to iron availability

first: Yong-Joon

last: Cho

summary:
Purpose: Defining the regulatory role of the transcription factors, Cir1 and HapX, in C. neoformans.
Methods: Chromatin immunoprecipitation followed by high-throughput sequencing was performed using chromatin immunoprecipitated DNA from the strains Cir1-Flag and HapX-Flag grown in low- and high-iron condition.
Results: Cir1 and HapX bind to the promoter region of the genes involved in iron acquisition and metabolism in C. neoformans.

overall_design: The enriched binding peaks of Cir1 and HapX were compared with the input DNA (control).

first: Won

last: Jung

first: Eunsoo

last: Do

first: James

middle: W

last: Kronstad


title: Transcriptome analysis of the iron regulatory transcription factors in Cryptococcus neoformans in response to iron availability

summary:
Purpose: Understanding the iron-responsive regulatory networks in Cryptococcus neoformans.
Methods: The transcriptome profiles of the wild-type, cir1 mutant and hapX mutant were generated by RNA-seq using Illumina Hiseq, in triplicate. The transcriptome profiles of each mutant was compared with that of the wild-type strain.
Results: The iron-responsive transcription factors, Cir1 and HapX, are major regulators for iron acquisition and metabolism in C. neoformans.

overall_design: Transcriptome of each mutant vs. Transcriptome of the wild-type


title: Gene Expression Networks in the Drosophila Genetic Reference Panel

status: Public on Feb 28 2020

city: East Lansing

first: Wen

last: Huang

address: 474 S Shaw Ln, Anthony Hall 1205F

department: Animal Science

institute: Michigan State University

summary: A major challenge of modern biology is to understand how naturally occurring variation in DNA sequences affects complex organismal phenotypes through networks of intermediate molecular phenotypes. Here, we performed deep RNA sequencing of 200 Drosophila Genetic Reference Panel inbred lines with complete genome sequences and mapped expression quantitative trait loci for annotated genes, novel transcribed regions (most of which are long noncoding RNAs), transposable elements and microbial species. We identified host variants affecting expression of transposable elements independent of copy number and microbiome composition. We constructed sex-specific expression quantitative trait locus regulatory networks. These networks are enriched for novel transcribed regions and target genes in heterochromatin and euchromatic regions of reduced recombination and are associated with transposable element expression. This study uncovers novel genetic features that regulate natural genetic variation of gene expression and generates testable hypotheses for future functional analyses.

overall_design: We performed deep RNA sequencing of the Drosophila melanogaster Genetic Reference Panel (DGRP) of inbred lines with complete DNA sequences. We produced rRNA-depleted strand-specific total RNA-seq libraries for 200 DGRP lines. For each line, we collected two replicate pools of 3-5 day old mated flies, with 25 females and 30 males per line. cDNA libraries were prepared separately for each replicate and each sex, for a total of 800 RNA-seq samples (200 lines x 2 sexes x 2 replicates). All flies were reared in identical conditions and collected at the same time of day, using a strict randomized experimental design for sample collection.

first: Logan

last: Everett

first: Shanshan

last: Zhou

first: Mary

middle: A

last: Carbone

first: Richard

last: Lyman

first: Gunjan

last: Arya

first: Matthew

last: Geisz

first: Junwu

last: Ma

first: Fabio

last: Morgante

first: Genevieve

last: St. Armour

first: Lavanya

last: Turlapati

first: Robert

last: Anholt

first: Trudy

last: Mackay


title: Dysregulated lncRNA and mRNA expression in placenta accreta spectrum disorders

status: Public on Feb 14 2020

city: Foshan

first: Huishan

last: Zhang

address: No.11 Reminxi Road, Foshan, Guangdong,  China

institute: Foshan Institute of Fetal Medicine, Southern Medical University Afliated Maternal & Child Health Hospital of Foshan

summary: To find potential biomarkers and molecular mechanism for placenta accreta spectrum disorders , we identified the differently expressed patterns of lncRNAs and mRNAs in invasive placneta and adherent normal placenta tissues. The results provided a novel insight into the pathogenesis of placenta accreta spectrum disorders .

overall_design: In this study, we identified the differential expression profile of lncRNAs to identify novel targets of the further study of PAS. Five lncRNAs were chosen for qRT-PCR validation. To further identify the functions of dysregulated lncRNAs and corresponding mRNAs, we did function enrichment analysis, subgroup analysis and correlation analysis.

first: Zhengping

last: Liu


title: SINEUP long non-coding RNA acts via PTBP1 and HNRNPK to promote translational initiation assembly [eCLIP-seq]

status: Public on Feb 09 2020

city: Yokohama

first: Harshita

last: Sharma

state: Kanagawa

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

institute: RIKEN IMS

summary: We found novel functional long non-coding RNAs (lncRNAs) that contain a SINE element, and which up-regulate the translation of target mRNA, named SINEUPs. To investigate the network of translational regulation, we focused on the sub-cellular distribution of target mRNAs and SINEUP RNAs and SINEUP RNA binding proteins (RBPs). We identified PTBP1 and HNRNPK as essential RBPs. These proteins contributed to SINEUP RNA sub-cellular distribution and to assembly of translational initiation complexes, leading to enhancement of the target mRNA translation. To prove the SINEUP RBPs binding regions on SINEUP-GFP transcripts, we performed seCLIP; single-end enhanced crosslinking and immunoprecipitation assay to determine the specific binding sites of PTBP1 and HNRNPK on SINEUP-GFP RNA. These findings will promote a better understanding of the mechanisms on the fate of regulatory RNAs implicated in efficient protein translation.

overall_design: To identfy binding sites of PTBP1 and HNRNPK on SINEUP RNA by eCLIP analysis in HEK293T/17 cell.

first: Naoko

last: Toki

first: Ferdous-Ur

last: Rahman

last: Valentine

first: Hazuki

last: Takahashi

first: Silvia

last: Zucchelli

first: Stefano

last: Gustincich

first: Piero

last: Carninci


title: Deficiency of STING-signaling leads to neurogenic abnormalities and Autistic-Like Behaviors in the embryonic cortex [single-cell RNA-seq]

city: Beijing

first: Jianwei

last: Jiao

summary:
Purpose: To gain  futher insight into how STING causes abnormal cortical development in mice ,single cell RNA-seq was used to analyze the cell type changes resulting from the cerebral cortices of P0 STING conditional knock out mice and littermate wild-type.
Methods: Single cell isolation was prepared from P0 telencephalic tissue of wild-type(WT) and STINGf/f;Nestin-Cre mice. The fragmented cDNAs containing barcode and UMI sequences was built the library . Agilent 2100 Bioanalyze was used to quality controlled and quantified.Single cell RNA-sequencing analysis was used by the Illumina HiSeq 2500 platform in Annoroad Genomics
Results:  Clustering and labeling of these cells visualized on a t-SNE plot between the wild-type(WT) and STINGf/f;Nestin-Cre mice brain cortex
Conclusions:  Single cell RNA-seq data would provide a overall understanding of how STING gene influences cortical development in mice.

overall_design: Single cell isolation  of P0 wild type (WT) and STINGf/f;Nestin-Cre mice were generated by deep sequencing using Illumina HiSeq 2500.

first: Dongming


title: Macrophage GIT1 contributes to bone regeneration by regulating inflammatory response

status: Public on Feb 05 2020

city: Nanjing

first: Hao

address: 300 guangzhou road, gulou district, Nanjing, China

institute: The First Affiliated Hospital of Nanjing Medical University

summary: To investigate the altered gene expression levels in GIT1 CKO and control macrophages in response to LPS. Each group had a biological repeat (n=3). Results provide insight into the role of GIT1 in macrophages after treated with LPS.

overall_design: Three GIT1 CKO macrophages versus three GIT1 CWT macrophages

first: Shujie

last: Zhao


title: Epigenome analysis of Parkinson's disease and control samples from the Systema Genomics Parkinson's disease (SGPD) consortium

status: Public on Feb 17 2020

city: Brisbane

first: Jacob

last: Gratten

address: 37 Kent Street

department: Mater Research Institute

country: Australia

institute: University of Queensland

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation association analysis of Parkinson's disease and control samples. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in blood samples. Samples included 1001 Parkinson's disease cases and 973 controls.

overall_design: Bisulphite converted DNA from the 1974 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip. 85 samples failed QC and so were not included in the final dataset.


title: Molecular characterization of clonal human renal forming cells

status: Public on Feb 07 2020

city: Ramat-Gan

first: Tomer

last: Kalsiky

state: Israel

address: Ramat-Gan

country: Israel

institute: Bar-Ilan University

summary: The adult kidney replaces lost cells in-vivo via proliferation of cells functioning as committed clonal progenitors. Here we combined the generation of single cell derived clonal cultures from human adult kidney with transcriptomic analysis for molecular characterization of in-vitro clonal behavior at inception and after propagation. We discovered two types of clones; rapidly proliferating de-differentiated fibroblast-like (FL) originating from the proximal tubule and stably proliferating cuboidal epithelial-like (EL) originating from distal segments that efficiently propagate with one cell giving rise to 3.3*10(6) cells. Segment-specific clonal heterogeneity included molecular characteristics of cell-cycle, epithelial-mesenchymal transition (high NCAM1, Serpine1) and oxidative phosphorylation in FL-clones. In contrast, the more quiescent EL-clones harboring markers of mature kidney epithelia (high CD24, CDH1/E-cad, EpCAM) activate the BMP pathway.  Thus, the human adult kidney harbors progenitor cell function in which segment identity and the level of epithelial maturation dictate clonal behavior and sustained renal cell formation in culture.

overall_design: RNA-Sequencing of 9 hAK (human adult kidney) clones in early or late passage. Bulk hAK cultures were used as control

first: Itamar

last: Kanter


title: Impact of short and long-term electrically induced muscle exercise on gene signaling pathways, gene expression, and PGC1a methylation in men with spinal cord injury

status: Public on Jan 31 2020

city: Iowa City

first: Richard

last: Shields

address: 1-252 Medical Education Building

institute: The University of Iowa

summary: Exercise attenuates the development of chronic non-communicable diseases (NCDs). Gene signaling pathway analysis offers an opportunity to discover if electrically induced muscle exercise regulates key pathways among people living with spinal cord injury (SCI). We examined short-term and long-term durations of electrically induced skeletal muscle exercise on complex gene signaling pathways, specific gene regulation, and epigenetic tagging of PGC1a, a major transcription factor in skeletal muscle of men with SCI. After short or long-term electrically induced exercise training, participants underwent biopsies of the trained and untrained muscles. RNA was hybridized to an exon microarray and analyzed using a gene set enrichment analysis. We discovered that long-term exercise training regulated the Reactome gene sets for Metabolism (38 gene sets), Cell Cycle (36 gene sets), Disease (27 gene sets), Gene Expression and Transcription (22 gene sets), Organelle Biogenesis (4 gene sets), Cellular Response to Stimuli (8 gene sets), Immune System (8 gene sets), Vesicle Mediated Transport (4 gene sets), and Transport of Small Molecules (3 gene sets). Specific gene expression included: Oxidative catabolism of glucose including PDHB (p<0.001), PDHX (p<0.001), MPC1 (p<0.009), and MPC2 (p<0.007); Oxidative phosphorylation genes including SDHA (p<0.006), SDHB (p<0.001), NDUFB1 (p<0.002), NDUFA2 (p<0.001); Transcription Genes including PGC1α (p<0.030) and PRKAB2 (p<0.011); Hypertrophy gene MSTN (p<0.001); and the Myokine generating FNDC5 gene (p<0.008). Long-term electrically induced exercise de-methylated the major transcription factor, PGC1a. Taken together, these findings support that long term electrically induced muscle activity regulates key pathways associated with muscle health and systemic metabolism.

overall_design: We analyzed skeletal muscle using the Affymetrix Human Exon 1.0 ST platform. Array data was processed by Partek Genomic Suites.

first: Michael

last: Petrie

first: Arpit

first: Eric

middle: B

last: Taylor

first: Manish

last: Suneja


title: Repression of damaged and intact rDNA by the SUMO pathway

status: Public on Feb 01 2020

city: Ithaca

first: Yicheng

last: Luo

state: NY

address: 215 Tower Rd

department: Molecular Biology and Genetics

institute: Cornell University

type: Non-coding RNA profiling by high throughput sequencing

summary: Ribosomal RNAs (rRNAs) are essential components of the ribosome and are among the  most abundant macromolecules in the cell. To ensure high rRNA level, eukaryotic  genomes contain dozens to hundreds of rDNA genes, however, only a fraction of the rRNA  genes seems to be active, while others are transcriptionally silent. In Drosophila rDNA  units damaged by insertions of retrotransposons are repressed by an unknown  mechanism. Here, we established a new model to study regulation of rDNA expression  using molecularly marked rDNA transgenes. Using this model, we show that insertion of  any heterologous sequence into rDNA leads to transcriptional repression. We found that  SUMO (Small Ubiquitin-like Modifier) is required for efficient repression of damaged rDNA  units. Surprisingly, SUMO also controls expression of intact rDNA, demonstrating that a  single pathway is responsible for both selective repression of damaged units and silencing  of surplus rDNA.

overall_design: Transposons profiling by high throughput sequencing

first: Elena

last: Fefelova

first: Maria

last: Ninova

first: Yung-Chia

last: Chen

first: Alexei

last: Aravin


title: Methionine metabolism shapes T helper cell responses through regulation of epigenetic reprogramming [RNA-Seq]

status: Public on Feb 03 2020

city: Grand Rapids

first: Russell

last: Jones

state: Michigan

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

summary: Epigenetic modifications on DNA and histones regulate gene expression by modulating chromatin accessibility to transcription machinery. Chromatin-modifying enzymes are dependent on metabolic intermediates for chromatin remodeling, linking nutrient availability and cellular metabolism to the cellular epigenetic landscape. Here we identify methionine as a key nutrient affecting T cell epigenetic reprogramming in CD4+ T helper (Th) cells. Using metabolomic approaches, we showed that methionine is rapidly taken up by activated T cells and then serves as the major substrate for the biosynthesis of S-adenosyl-L-methionine (SAM), the universal methyl donor for cellular methyltransferases. Conversely, methionine restriction (MR) depletes intracellular SAM pools, reduces global histone H3K4 methylation (H3K4me3) in T cells, and reduces H3K4me3 levels at the promoter regions of key genes involved in CD4+ Th17 cell proliferation and cytokine production. Applied to the mouse model of multiple sclerosis (experimental autoimmune encephalomyelitis), dietary methionine restriction reduced the expansion of pathogenic Th17 cells in vivo, leading to reduced T cell-mediated neuroinflammation and disease onset. Overall our data identify methionine as a key nutritional factor that shapes T cell proliferation, differentiation, and function in part through regulation of histone methylation in T cells.

overall_design: RNA-seq of total mRNA from CD4+ Th17 cells cultured under control (200 uM) or methionine restriction (3 uM) conditions for 5 days

first: Dominic

last: Roy

first: Jocelyn


title: Chip-seq for MoAtf1

status: Public on Jan 29 2020

first: Zhengguang

last: Zhang

state: Jiangsu

address: No.1 Weigang, Nanjing Agricultural University

institute: Nanjing Agricultural University

summary: Chip-seq for MoAtf1 in M. oryzae, bZip transcription factor MoAtf1 was previous reported that involved in the full virulence of Magnaporthe oryzae. Here, we performed of MoAtf1 chip-seq assays to uncovered the regulation network

overall_design: MoAtf1-GFP binding with the whole promoters in M. oryzae

first: Xinyu

last: Liu


title: Structural and Functional Characterization of G Protein-Coupled Receptors with Deep Mutational Scanning

status: Public on Feb 06 2020

city: Los Angeles

first: Nathan

last: Lubock

email: nlubock@ucla.edu, nate@octant.bio

state: CA

address: 607 Charles E Young Drive

institute: UCLA

summary: In humans, the 813 G protein-coupled receptors (GPCRs) are responsible for transducing diverse chemical stimuli to alter cell state, and are the largest class of drug targets. Their myriad structural conformations and various modes of signaling make it challenging to understand their structure and function. Here we developed a platform to characterize large libraries of GPCR variants in human cell lines with a barcoded transcriptional reporter of G-protein signal transduction. We tested 7,800 of 7,828 possible single amino acid substitutions to the beta-2 adrenergic receptor (β2AR) at four concentrations of the agonist isoproterenol. We identified residues specifically important for β2AR signaling, mutations in the human population that are potentially loss of function, and residues that modulate basal activity. Using unsupervised learning, we resolve residues critical for signaling, including all major structural motifs and molecular interfaces. We also find a previously uncharacterized structural latch spanning the first two extracellular loops that is highly conserved across Class A GPCRs and is conformationally rigid in both the inactive and active states of the receptor. More broadly, by linking deep mutational scanning with engineered transcriptional reporters, we establish a generalizable method for exploring pharmacogenomics, structure and function across broad classes of drug receptors.

sample_organism:
Escherichia coli
Homo sapiens

platform_organism:
Escherichia coli
Homo sapiens

overall_design:
The overall design of this experiment is to test the functional  consequences of every amino acid substitution to the beta-2 adrenergic receptor (B2AR). This occurs in two stages that occurs roughly as follows (for more details, see Figure 1 of our bioRxiv preprint <https://www.biorxiv.org/content/10.1101/623108v3.full>). First, we use DNA microarray synthesis to generate a library of mutants at every position in the protein (think alanine scan, cysteine scan, aspartic acid scan, ...). We then clone these mutants into a plasmid backbone that's tagged with a  DNA barcode. We use NGS to associate each variant with its corresponding  barcode (this corresponds to the the Map_* and Eric_* fastq's that are  eventually processed into the NextSeq_MiSeq.map.csv.gz).
Second, the mapped library is integrated into human cell lines such that each cell only receives a single B2AR mutant - barcode pair. Activation of  the receptor by agonist incubation results in transcription of the mutant's  barcode, which we can detect with RNA-seq (the second set of fastq's  drug-*).

first: AJ

last: Venkatakrishnan

first: Jeffrey

last: Wang

first: Alex

last: Tseng

first: Joseph

last: Paggi

first: Naomi

last: Latorraca

first: Daniel

last: Cancilla

first: Megan

last: Satyadi

first: Jessica

middle: E

last: Davis

first: M

last: Babu

first: Ron

middle: O

last: Dror

first: Sriram

last: Kosuri


title: Genome-wide maps of p53 binding sites in human embryonic stem cell H9 derived trilineage.

status: Public on Mar 03 2020

city: shenzhen

first: qian

last: he

state: guangdong

address: liuyibu ,luo hu region ,shen zhen city

institute: shenzhen poeple's hospital

summary: To determine the roles of IFI16-p53 interaction during H9-trilineage specification, we performed ChIP-seq to derive a genome-wide profile of p53-binding genes after IFI16 knockdown by shRNA-1865. p53 binding sites were mapped on Day 2 of trilineage induction.

overall_design: Examination of p53 peaks in 3 cell types after IFI16 knockdown.

first: Furong

last: Li


title: Gene expression profiling of lung epithelium: GENEBRO study

status: Public on Jan 08 2020

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: Our aim was to compare gene expression profiles of nasal and bronchial epithelium in a same individual, notably at the level of Th2 inflammation.

overall_design: Lung epithelium cells were collected by nasal and bronchial brushings in patients with asthma and allergic rhinitis, rhinitis alone, or healthy.

first: L

last: Chami

first: P

last: Barbry

first: N

last: Pons

first: K

first: A

last: Paquet


title: HCC prediction after clearance of HCV in chronic hepatitis C II

status: Public on Jan 24 2020

city: Kanagawa

first: Satoko

last: Takizawa

state: Kamakura

institute: Toray Industries, Inc.

summary:
We attempted to development prediction methods for hepatocellular carcinoma (HCC) in chronic hepatitis C patients who have been successfully treated by anti-viral therapy.
2565 miRNAs in 139 exosome specimens were analyzed.

overall_design: One hundred thirty-nine patients were enrolled and 99 patients had not developed HCC and 40 had developed HCC

first: Y

last: Murakami


title: Rapid and scalable profiling of nascent RNA with fastGRO

status: Public on Jan 17 2020

city: Edinburgh

first: Elisa

last: Barbieri

address: 5 Little France Drive

institute: University of Edinburgh

summary: We developed a new method to profile nascent RNA in mammalian cells. The new methodology is based on the incorporation of thio-UTP, an analog of UTP, during in vitro RNA Polymerase run-on.

overall_design: Profiling nascent RNA with in vitro RNA Polymerase run-on and 4SUTP incorporation.

first: Connor

last: Hill

first: Mathieu

last: Quesnel-Vallieres

first: Yoseph

last: Barash

first: Alessandro

last: Gardini


title: Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia: RNA-Seq Data

status: Public on Jan 01 2020

city: Oklahoma City

first: Michael

last: Stout

state: OK

address: 825 N.E. 13th Street

department: Aging and Metabolism

institute: Oklahoma Medical Research Foundation

summary: Studies of neuroepigenetic mechanisms in health and disease are hindered by a lack of approaches to analyze both the transcriptome and epigenome of specific cell types isolated from the complex milieu of the CNS. Cell isolation by cell surface markers is complicated by preparation artifacts, changes in markers with experimental conditions, and lack of specific markers. This study validates a Nuclear Tagging and Translating Ribosome Affinity Purification (NuTRAP) approach with tamoxifen (Tam) inducible cell-type specific cre recombination to allow the parallel interrogation of the epigenome and the transcriptome in astrocytes (Aldh1l1-creERT2) or microglia (Cx3cr1-creERT2). The recombined NuTRAP construct labels, in a cell-type specific manner, nuclei (RanGAP1) with biotin and mCherry, and the ribosomes (L10a) with EGFP, enabling INTACT isolation of DNA and TRAP isolation of RNA. Validation experiments by flow cytometry and imaging demonstrate cell-type specific induction of the NuTRAP construct. Transcriptomic studies demonstrate isolation of highly enriched RNA by TRAP and oxidative bisulfite studies of INTACT-isolated DNA demonstrate differential DNA modification patterns in microglia and astrocytes. LPS administration in Cx3cr1 NuTRAP mice demonstrates that microglia-specific transcriptome and epigenome changes are revealed that cannot be detected with tissue-level samples. These experiments demonstrate that the NuTRAP approach can be applied to CNS cell populations and that INTACT approaches can be used to study DNA modifications.  These results also provide an approach for generation and validation of NuTRAP neuroscience models crossed to any relevant cell-type specific cre line.

overall_design: 2 Cre/NuTRAP lines (Aldh1l1-cre/Ert2+; NuTRAP+ and Cx3cr1-cre/Ert2+; NuTRAP+); RNA isolated via TRAP methods- Input, Negative, and Positive fractions; 3 biological replicates for Aldh1l1-NuTRAP and 6 biological replicates for Cx3cr1-NuTRAP

first: Ana

last: Chucair-Elliott

first: Sarah

last: Ocanas

first: David

last: Stanford

first: Victor

last: Ansere

first: Kyla

last: Buettner

first: Hunter

last: Porter

first: Nicole

middle: L

last: Eliason

first: Amanda

last: Sharpe

last: Beckstead

first: Arlan

last: Richardson

first: Willard

last: Freeman


title: Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia: LPS Experiment RNA-Seq Data

overall_design: 1 Cre/NuTRAP lines (Cx3cr1-cre/Ert2+; NuTRAP+); 24 hrs after systemic LPS Challenge, RNA isolated from brain via TRAP methods- Input and Positive fractions; 4 PBS controls and 5 LPS experimental biological replicates


title: Genome-wide transcriptional changes triggered by water deficit on a drought-tolerant common bean cultivar

status: Public on Dec 31 2019

city: Tlaxcala

first: Josefat

last: Gregorio Jorge

state: Tlaxcala

address: Ex-Hacienda San Juan Molino Carretera Estatal Tecuexcomac-Tepetitla Km 1.5, Tlaxcala

department: Biotecnología Genómica

country: Mexico

institute: Instituto Politécnico Nacional

summary: Common bean (Phaseolus vulgaris L.) is a relevant crop cultivated over the world, largely in water insufficiency vulnerable areas. Since drought is the main environmental factor restraining worldwide crop production, efforts have been invested to amend drought tolerance in commercial common bean varieties. However, scarce molecular data are available for those cultivars of P. vulgaris with drought tolerance attributes. As a first approach, Pinto Saltillo (PS), Azufrado Higuera (AH), and Negro Jamapa Plus (NP) were assessed phenotypically and physiologically to determine the outcome in response to drought on these common bean cultivars. Based on this, a Next-generation sequencing approach was applied to PS, which was the most drought-tolerant cultivar to determine the molecular changes at the transcriptional level. The RNA-Seq analysis revealed that numerous PS genes are dynamically modulated by drought. In brief, 1005 differentially expressed genes (DEGs) were identified, from which 645 genes were up-regulated by drought stress, whereas 360 genes were down-regulated. Further analysis showed that the enriched categories of the up-regulated genes in response to drought fit to processes related to carbohydrate metabolism (polysaccharide metabolic processes), particularly genes encoding proteins located within the cell periphery (cell wall dynamics). In the case of down-regulated genes, heat shock-responsive genes, mainly associated with protein folding, chloroplast, and oxidation-reduction processes were identified. Our findings suggest that secondary cell wall (SCW) properties contribute to P. vulgaris L. drought tolerance through alleviation or mitigation of drought-induced osmotic disturbances, making cultivars more adaptable to such stress. Altogether, the knowledge derived from this study is significant for a forthcoming understanding of the molecular mechanisms involved in drought tolerance on common bean, especially for drought-tolerant cultivars such as PS.

overall_design: Assesment of the effect of drought on three common bean cultivars, with emphasis of molecular analysis for the Pinto Saltillo cultivar

first: Analilia

last: Arroyo-Becerra

last: Gregorio-Jorge

first: Miguel

last: Lopez-Villalobos


title: Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia: Whole Genome oxidative bisulfite sequencing data

overall_design: 2 Cre/NuTRAP lines (Aldh1l1-cre/Ert2+; NuTRAP+ and Cx3cr1-cre/Ert2+; NuTRAP+); Nuclei isolated via INTACT methods- Input, Negative, and Positive fractions; 4 biological replicates per cre line


title: Comparison of wild-type and Kdm7a mutan embryos

status: Public on Dec 23 2019

city: Tokyo

first: Yoshiki

last: Higashijima

address: 1-5-45 Yushima, Bunkyo

department: Medical Research Institute

institute: Tokyo Medical and Dental University

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

overall_design: Refer to individual Series


title: microRNA expression profile in vascular smooth muscle cells (VSMCs) after inducing calcification

city: Hwasun

first: Nakwon

last: Choe

state: Seoyang-ro 322

address: Baekseo-ro 160

department: Pharmacology

institute: Chonnam Univ. Med. Sch.

summary: Vascular calcification, the ectopic deposition of calcium in blood vessels, develops in association with various metabolic diseases and atherosclerosis. Because it often causes stiffness and remodeling of the blood vessels, vascular calcification increases morbidity and mortality. Both miRNA and mRNA microarrays (Series GSE74755) were performed with rat VSMCs and reciprocally regulated pairs of miRNA and mRNA were selected after bioinformatic analysis.

overall_design: Calcification was induced in rat aorta vascular smooth muscle cells with inorganic phosphate (Pi). Total RNA were extracted from the cells 3 and 6 days later. mRNA profile of the sample was compared with normal control.

first: Duk-Hwa

last: Kwon

first: Juhee

last: Ryu

first: Sera

last: Shin

first: Hosouk

last: Joung

first: Gwang-Hyeon

last: Eom

first: Youngkeun

last: Ahn

first: Woo-Jin

last: Park

first: Young-Kook

last: Kim

first: Hyun

last: Kook


title: Comparison of gene expression profiles between wild-type and Kdm7a mutan embryos

summary: Temporal and spatial colinear expression of Hox genes determines the specification of positional identities of the embryo. Post-translational modifications of histones contribute to transcriptional regulation, and are required for proper control of biological processes, including differentiation and development. Lysine demethylase 7A (Kdm7a) demethylates lysine 9 di-methylation of histone H3 (H3K9me2) and participates in transcriptional activation of developmental genes. However, the role of Kdm7a during mouse embryonic development remains to be elucidated. Here, we show that Kdm7a-/- mice exhibit anterior homeotic transformation of the axial skeleton (i.e. an increase in the number of presacral elements). Importantly, posterior Hox genes (caudally from Hox9) are specifically down-regulated in Kdm7a-/- embryos, which correlate with increased levels of H3K9me2. Taken together, these data suggest that Kdm7a is able to control transcription of posterior Hox genes, likely through its demethylating activity, and thereby regulating anterior-posterior development in mice.

overall_design: Total 12 samples were derived from [1] wild-type E9.5 embryos , [2] Kdm7a mutant E9.5 embryos, [3] wild-type E10.5 embryos, [4] Kdm7a mutant E10.5 embryos (n=3 for each condition).

first: Nao

last: Nagai

first: Yasuharu

last: Kanki


title: A cell atlas of the adult Drosophila midgut

status: Public on Dec 19 2019

city: Boston

first: Rory

last: Kirchner

state: MA

address: 677 Huntington Ave

department: Department of Biostatistics

institute: Harvard T.H. Chan School of Public Health

summary: Drosophila guts were dissociated to single cells as previously described (Dutta et al., 2015) with a few modifications. Guts were dissected from 7-day old adult esg-sfGFP/+, pros- Gal4>RFP/+ females. After pulling out the gut, the crop and midgut/hindgut junction (where the Malpighian tubules branch out of the gut) and Malpighian tubules were removed. Five flies at a time were dissected and immediately transferred into cold PBS containing 1% BSA to avoid exposing the midgut tissue to room temperature for a long period of time. Once 40 guts were dissected, they were transferred to a dissection plate and chopped into small pieces using a razor blade. These small fragments were immediately transferred to an eppendorf tube containing 400 ul of 1 mg/ml elastase/PBS solution (Sigma E0258) and incubated on a shaker at 27 ̊C for 30 min. 1% of BSA in PBS (final concentration) was used to stop the digestion reaction and prevent cells from aggregating. The cell suspension was passed through 100 um and then a 40 um cell strainer and loaded on the top of Optiprep with density gradient 1.12 g/ml. Viable cells were isolated from the top layer of the sample after centrifugation at 800xg for 20 min. Cell viability and number were assessed by 0.4% trypan blue and hemocytometer.

overall_design: inDrop and 10x single-cell RNA-sequencing of 10605 cells from the Drosophila midgut

first: Ruei-Jiun

last: Hung

first: Yanhui

last: Hu

first: Fangge

last: Li

first: Chiwei

last: Xu

first: Aram

last: Comjean

first: Sudhir

middle: G

last: Tattikota

first: Wei

last: Song

first: Shannan

middle: H

last: Sui

first: Norbert

last: Perrimon


title: Comparison of genome-wide distribution of histone modifications (H3K4me3, H3K9me2, H3K27me2, and H3K27me3) between wild-type and Kdm7a mutant embryos

first: Yoshiki

last: Higashijima

overall_design: Total 46 ChIP-seq samples include [1] input for each experiment,  [2] ChIP samples for histone marks H3K4me3, H3K9me2, H3K27me2, and H3K27me3.


title: microRNA expression profile in renal tissues of  rats with doxorubicin nephropathy by Mongolian medicine Narenmandula

status: Public on Dec 14 2019

city: Tongliao

first: Xiulan

last: Wang

state: Inner Mongolia

address: HuoLinhe

department: Affiliated Hospital

institute: Inner Mongolia University For The Nationlities

summary:
Objective: Detection and analysis of Mongolian medicine Narenmandula the kernel full of adriamycin nephrosis rats kidney tissue expression of miRNA.
Methods: The biological information of the differentially expressed miRNA between the normal group, the model group and the Mongolian medicine Narenmandula group was studied by Affymetrix miRNA chip detection.
Results: The biological information of miRNA expression in kidney tissues of rats with doxorubicin nephropathy was analyzed by detection, which laid a foundation for further elucidating the multi-target regulatory role of Mongolian medicine Narenmandula in renal function protection and provided data.
The biological information of miRNA expression in renal tissues of doxorubicin rats was detected and analyzed using Affymetrix miRNA chip detection technology, which laid a foundation for further elucidating the multi-target regulation effect of the renal function protection and provided data of Mongolian medicine Narenmandula .

overall_design: The rats were divided into three groups, namely normal group, model group and Mongolian medicine Narenmandula group ,containing 15 samples, the kidney tissue, through the tail vein injection adriamycin mold.


title: Gene expression profile of gastric organoids p53 KO and KD

status: Public on Dec 10 2019

first: Chunyang

last: Bao

address: 415 Brookline Avenue

institute: Dana-Farber Cancer Institute

summary: Gastric organoids were manipulated to knockout p53

overall_design: Examination of mRNA expression in gastric organoids with or without p53

first: Nilay

last: Sethi

first: Osamu

last: Kikuchi

first: Adam

last: Bass


title: Gene expression profiles of active and restricted R/G-HIV+ primary human fetal astrocytes

status: Public on Dec 18 2019

city: Fort WORTH

first: Kathleen

last: Borgmann

state: TX

address: 3500 Camp Bowie Blvd

department: Pharmacology and Neuroscience

institute: University of North Texas Health Science Center

summary: The gene expression patterns of astrocyte harboring active vs restricted LTRs were similar, and that the active population demonstrated more widespread and robust changes.

overall_design: Infection of astrocytes with VSVG pseudotyped Red/Green-HIV-1 wildtype and integrase (D116A) mutant.  Astrocytes were sorted into latent (R+/G-), active (R+/G+), D116A (R-/G-) and untreated two weeks post-infection.  RNA was isolated and sequenced in three separate donors.

first: Venkata

middle: V

last: Edara


title: mRNA-seq of wild-type(N2), hlh-11 knock-out(KO) and hlh-11 over-expression(OE) worms

status: Public on Nov 23 2019

city: beijing

first: Yi

state: beijing

address: peking univerity, haidian district

institute: PKU

summary:
Purpose: Comparing the transcriptome of wild-type(N2), hlh-11 knock-out and hlh-11 over-expression worms to identify genes with differential expression.
Methods: For each condition, two replicates were examined. For each sample, approximately 2,000 synchronized young adult worms were collected and resuspended in TRIzon Reagent (CW0580, CWBIO). Total RNA was isolated by chloroform extraction, followed by isopropanol precipitation. Sequencing was performed using HiSeq2500. The clean reads were aligned to WBcel235 genomes with TopHat2. Gene differential expression was analyzed using DEseq2. A threshold of p < 0.05 was set to determine differentially expressed genes. Induction (KO_up or OE_up) or suppression (KO_down or OE_down) of genes were obtained through comparing gene expressions in hlh-11 KO or OE worms to wild-type N2.
Results: >86% reads were uniquely mapped. 2637 genes were significantly up regulated and 2845 genes were significantly down regulated in hlh-11 knock-out worms compared to wild-type. 107 genes were significantly up regulated and 237 genes were significantly down regulated in hlh-11 over-expression worms compared to wild-type.
Conclusions: This study revealed the genes transcriptionally regulated by hlh-11.

overall_design: mRNA-seq of yong adult wild-type(N2), hlh-11 knock-out and hlh-11 over-expression worms, two replicates, using HiSeq2500 (Illumina, San Diego, CA)

first: Ying

last: Liu


title: Surviving climate change – the role of acclimatization in reef-building corals

status: Public on Dec 05 2019

city: University Park

first: Iliana

last: Baums

state: PA

address: 212 Mueller Laboratory, Penn State University

department: Biology

institute: The Pennsylvania State University


title: UV Stress Regulates Differential Associations of Brd4 and P-TEFb with Chromatin and Modulates Transcription by Brd4 Acting as either Activator or Repressor

status: Public on Dec 01 2019

city: Guangzhou

first: Lihui

last: Lin

state: Guangdong

address: No.190, Kaiyuan Street

department: Stem cell

institute: Guangzhou Institutes Of Biomedicine and Health Chinese Academy Of Science

summary:
Purpose: The goal of this study is to investigate the role of Brd4 in UV-regulated genome-wide gene expression.
Methods: RNA samples from control and Brd4-depleted cells at 0, 0.5 and 2 hr after UV treatment were analyzed using RNA-sequencing (RNA-seq).
Results: Signals higher or lower than >1-fold by log2 were regarded as significant and analyzed further. And only either unregulated or downregulated genes in Brd4-depleted cells compared with control cells at the same time point (0, 0.5 or 2 hr) after UV treatment were analyzed. Indeed, a transcriptome analysis indicated that UV-upregulated genes are positively affected by the Brd4 level.

overall_design: Examination of the dynamic associations between chromatin and Brd4/P-TEFb and Brd4-mediated gene regulation after UV stress.

first: Hongjie

last: Yao


title: circRNA expression in NPRA-/- and NPRA+/+ myocardium tissues

status: Public on Nov 22 2019

city: 西安

first: Jun

last: Yu

state: Shaanxi

address: North of Wei 32nd Road, and east of Xitai Road, High-tech Zone

department: Clinical Experimental Center

institute: Xi'an International Medical Center Hospital

summary: To build a circRNA-miRNA-mRNA network in the condition of NPRA deletion in the heart, we used circRNA microArray analysis form Arraystar to examine the expression of circRNAs in NPRA-/- and NPRA+/+ myocardium tissues.

overall_design: Myocardium tissue from cardiac-specific NPRA-deficient mice and normal mice, then perform circRNAs chips by Arraystar Mouse circRNA Array V2 (8x15K, Arraystar).

first: Shen

last: Xi


title: The gut microbiome protects genetically predisposed mice against leukemia

status: Public on Oct 30 2019

city: Salamanca

first: Isidro

last: Sánchez García

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

country: Spain

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

summary:
We used microarrays to investigate gene expression changes in leukemic cells from Pax5+/- mice treated with antibiotics.
Precursor B cell acute lymphoblastic leukemia (pB-ALL), the most common type of childhood leukemia, is frequently characterized by the cooperation of a genetic predisposition acquired in utero and secondary oncogenic events taking place only in a fraction of predisposed children after birth. Although predisposition can be detected at birth, it is currently unknown which factors determine the development of overt leukemia in genetic carriers and how this can be potentially prevented. Experimental studies have shown that infectious stimuli promote disease onset in genetically predisposed mice. Here, we analyzed the impact of the microbiome on leukemogenesis in a mouse model (Pax5+/- mice) that faithfully mimicks genetic predisposition and leukemogenesis of human pB-ALL related to the synergy of genetic predisposition and exposure to a natural infectious environment. Employing 16S rRNA sequencing and machine learning we can accurately predict a distinct gut microbiome which is determined by a specific constitutional genetic variant. Deprivation of the gut microbiome by antibiotic treatment enhanced pB-ALL development in Pax5+/- predisposed (63% vs. 22%) but not in wildtype mice (0%). This finding was observed in the presence but also -to a lesser extent- in the absence of a natural, infectious environment (48%). The composition of the gut microbiome constitutes a biomarker signature and allows to identify specifically those Pax5+/- mice that developed leukemia. This indicates that the gut microbiome can be used to identify carriers at risk to develop leukemia and to reduce this risk by early-life interventions.

overall_design: Bone marrow leukemic cells from Pax5+/- mice treated with antibiotics (n=9) compared with bone marrow proB and preB cells from 4 WT mice. Only the Pax5+/- mice were treated with antibiotics.

first: Carolina

last: Vicente-Dueñas

first: Stefan

last: Janssen

first: Marina

last: Oldenburg

first: Franziska

last: Auer

first: Inés

last: González-Herrero

first: Ana

last: Casado-García

first: Javier

last: Raboso-Gallego

first: Daniel

last: Hein

first: Katharina

last: Gössling

first: Diego

last: Alonso-López

last: De Las Rivas

first: Francisco

last: Criado

first: María

last: Cenador

first: Julia

last: Hauer

first: Ute

last: Fischer

last: Sanchez-Garcia

first: Arndt

last: Borkhardt


title: WNT activated cells are the origin of regrowth of colorectal cancer organoids after irradiation

status: Public on Nov 07 2019

city: Kyoto

first: Masahiro

last: Inoue

state: Kyoto

address: Med-Pharm Collaboration Bldg 503, Shimoadachi-cho 46, Sakyou-ku, Kyoto, 606-8304, Japan

institute: Kyoto Univ Graduate School of Medicine

summary: Regeneration capacity of intestinal epithelial cells are highly dependent on the status of stemness. In the homeostasis, only a small subset of stem cells is responsible for the turnover of the intestinal epithelium. However, at the injury, such as caused by radiation, intestinal epithelial cells show substantial plasticity for regeneration. Most of the colorectal cancers (CRCs) are differentiated adenocarcinoma, which maintain the expression of both stemness and differentiation markers, suggesting an existence of a similar regeneration system as in normal cells, although the role of such fluctuation of stemness in regeneration of cancer after irradiation is not well understood. In the present study, we first examined the effect of radiation on growth, stemness and differentiation using organoids derived from differentiated CRC. Both proliferation and stemness markers were once drastically decreased after sub-lethal dose of irradiation, meanwhile differentiation markers remained. After the static phase, regrowth foci consisting of proliferating cells with expression of the stem cell markers reappeared. We applied the foci formation to a radio-sensitivity assay in CRC organoids. Radio-sensitivity, the ability of foci formation, differed among the examined lines, and correlated well with the in vivo radiation sensitivity. The radio-sensitivity decreased after mechanical disruption of the organoids, which we have reported to increase the stemness of CRC organoids in a WNT dependent manner. Pre-treatment of organoids with histone deacetylase inhibitors increased radiation sensitivity, accompanied with suppressed expression of WNT target genes, and WNT inhibitors increased radio-sensitivity, suggesting that not all but some of the cancer cells with high WNT activity at the timing of radiation is the origin of the foci formation. The radiation sensitivity assay using CRC organoids established in the present study would provide a novel platform to evaluate the radiosensitizers against differentiated adenocarcinoma of CRC.

overall_design: One sample for each condition. Control; DMSO treated or TSA treated, without irradiation. Time course; 0h, 24h, 48h


title: Comparative Analysis of the Transcriptome of Latent Autoimmune Diabetes (LADA) Patients from Eastern China

status: Public on Sep 21 2019

city: Haining

first: Jian

last: Liu

state: Zhejiang

address: 718 East Haizhou Rd.

department: Zhejiang University - University of Edinburgh Institute

institute: Zhejiang University

summary: We did the transcriptome analysis of peripheral blood mononuclear cells of LADA patients and healthy controls

overall_design: RNA-seq analyses were conducted on peripheral blood mononuclear cells of LADA patients and healthy controls

first: Yuqiao

last: Ji

first: Dongmei

last: Jiang

first: Xiaolong

last: Chen

first: Tian

last: Xia

first: Zhujun

last: Yin

first: Lei

last: Li

first: Hao

last: Jin

first: Hongmei

first: Mingzhong

last: Sun


title: Molecular genetics and transcriptomes of Oryzias mekongensis (Adrianichthyidae: Beloniformes) from the northeast Thailand

status: Public on Dec 27 2019

city: Bangkok

first: Arin

last: Ngamniyom

address: 114 Sukumvit 23

department: Major in Environment, Faculty of Environmental Culture and Eco-tourism

country: Thailand

institute: Srinakharinwirot University

summary: Oryzias mekongensis de novo transcriptome

overall_design: We report the transcriptome sequencing of Oryzias mekongensis by deep sequencing using Illumina HiSeq 2500


title: Knocking out a negative regulator of photosynthesis 1 (NRP1) increases rice leaf photosynthesis and biomass production in the field

status: Public on Oct 15 2019

city: Shanghai

first: Faming

address: 320 Yue Yang Road

department: CAS-MPG Partner Institute for Computational Biology

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

summary: Improving photosynthesis is a major approach to increase crop yield potential. Here we report a negative transcription factor of photosynthesis, which can be manipulated to increase rice photosynthesis and plant biomass in the field. This transcription factor named negative regulator of photosynthesis 1 (NRP1) (Os07g0471900) which was identified through a co-expression analysis using rice leaf RNA sequencing (RNA-seq) data. The NRP1 showed significantly negative correlation with the expression of many genes involved in photosynthesis. Knocking out NPR1 led to greater photosynthesis and increased biomass in the field, while overexpression of NRP1 decreased photosynthesis and biomass. Transcriptomic data analysis shows that NRP1 can negatively regulate the expression of photosynthetic genes. Protein transactivation experiments show that NRP1 is a transcription activator, implying that NRP1 may indirectly regulate photosynthesis gene expression through an unknown regulator. This study shows that combination of bioinformatics analysis with transgenic testing can be used to identify new regulators to improve photosynthetic efficiency in crops.

overall_design: For gene expression profiling, we took the leaf samples at the early heading stage. 3 replications of the top second leaves for WT, the OE lines (OE-2, OE-3, OE-4) and the CRISPR lines (C-13, C-14, C-16) were harvested in the field at about 9:00 a.m.

first: Guangyong

last: Zheng

first: Xinguang

last: Zhu


title: The SUMO ligase Su(var)2-10 induces co-transcriptional repression of piRNA targets

city: Pasadena

first: Maria

last: Ninova

address: 1200 E California Blvd

department: Division of Biology and Biological Engineering

institute: Calfironia Institute of Technology

summary: In Drosophila, Piwi-induced transcriptional repression is associated with the establishment of repressive chromatin marks by the histone methyltrasferase SetDB1, however how the Piwi/piRNA complex recruits this effector to chromatin targets is poorly understood. We identified a new player in piRNA-guided transcriptional silencing encoded by the Su(var)2-10 gene. Su(var)2-10 is required for transcriptional silencing and deposition of repressive chromatin marks on transposons and it physically associates with the Piwi/piRNA target recognition complex. Recruitment of Su(var)2-10 to a target locus in a piRNA-independent fashion induces transcriptional repression and deposition of the H3K9 trimethyl mark by the histone methyltransferase dSetDB1/Eggless. Su(var)2-10 belongs to a conserved family of proteins that function as SUMO E3 ligases and we found that the SUMO pathway is essential for the repressive function of Su(var)2-10 and for transcriptional repression of transposons. Together, our data identifies Su(var)2-10 as an essential component of the piRNA-induced transcriptional silencing pathway that links the target recognition complex to the silencing effector and reveals a novel role of SUMO modification in the piRNA-induced repression.

overall_design: Gene expression and genome occupancy profiling by high throughput sequencing

first: Katalin

last: Fejes Tóth

first: Alexei

last: Aravin

first: Yung-Chia

first: Alicia

middle: K

last: Rogers

first: Yicheng

last: Luo

first: Baira

last: Godneeva


title: Human lymphoma cells: BLS type vs. conventional diffuse large B-cell lymphoma (DLBCL)

status: Public on Aug 29 2019

city: Tainan

first: Kung-Chao

last: Chang

address: 138 Sheng-Li Road

department: Department of Pathology

country: Taiwan

institute: National Cheng Kung University Hospital

summary: mRNA profiling of BLS type DLBCL cells comparing with conventional DLBCL cells. The former were sorted from bone marrow and the latter were isolated from pleural effusions by using magnetic microbeads coated with anti-CD20 antibody after loaded onto a column. The goal was to determine the global genes upregulated in BLS type DLBCL.

overall_design: Two-condition experiment, BLS type vs.conventional DLBCL cells. Only one sample in each group due to limited tumor cells.


title: A low DNA methylation epigenotype in squamous cell lung cancer and its association with idiopathic pulmonary fibrosis and poorer prognosis

status: Public on Oct 26 2019

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

summary: Comprehensive DNA methylation analysis in clinical samples of lung squamous cell carcinoma with or without tidiopathic pulmonary fibrosis. Infinium HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across 485,577 CpG sites. Samples included 20 lung squamous cell carcinoma with or without tidiopathic pulmonary fibrosis and 13 surrounding lung samples.

overall_design: Bisulphite converted DNA from the 33 clinical samples underwent Infinium HumanMethylation450 BeadChip analysis.

first: Atsushi

last: Hata

first: Takahiro

last: Nakajima

first: Keisuke

last: Matsusaka

first: Ichiro

last: Yoshino

last: Kaneda


title: Effect of high glucose on transcriptomic expression of cholangiocarcinoma cells

city: Muang Khon Kaen

first: Charupong

last: Saengboonmee

state: Khon Kaen

address: 123 Moo 16, Mittraphap Highway

department: Department of Biochemistry, Faculty of Medicine

institute: Khon Kaen University

summary: This project was aimed to study the transciptomic profiles of cholangiocarcinoma cells cultured in different concentration of glucose. The established human cholangiocarcinoma cell line; KKU-213, and highly metastatic subline; KKU-213L5, were used. KKU-213 were cultured in either Dulbecco Modified Eagle's Medium (DMEM) with normal (5.6 mM) or high glucose (25 mM) and labeled as KKU-213NG or KKU-213HG according to thier cuture medium and KKU-213L5 was cultured in high glucose DMEM medium. The RNA from all conditions (KKU-213NG, KKU-213HG and KKU-213L5) were then extracted and quality-controlled. Qualified RNA were subjected to sequenced and transcriptomics were processed for the abundance of genes expresed in each condition. The differentially expressed genes were then selected for furhter study to figure out the interaction between them and also the candidate genes that might be a promising target for the treatment of cholangiocarcinoma patients who also have diabetes mellitus.

overall_design: Comparative transcritptomic expression between cholangiocarcinoma cell lines cultured in normal or high glucose medium.

first: Marie-Claude

last: Gingras

first: Wunchana

last: Seubwai

first: Sopit

last: Wongkham

first: Kyle

last: Covington

first: Richard

last: Gibbs

first: Chaisiri

first: Oliver

last: Hampton

first: Kazuo

last: Umezawa

first: Chatchai

last: Phoomak


title: Nucleome Dynamics during Retinal Development[Hi-C_Mm]

status: Public on Sep 05 2019

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

summary: The nuclei of rod photoreceptors in mice and other nocturnal species have an unusual inverted chromatin structure with centrally located heterochromatin that helps to focus light and improve photosensitivity. To gain a deeper understanding of this unique nuclear organization of rod photoreceptors, we have carried out Hi-C on retina at 3 stages of development and on purified rod photoreceptors. Predicted looping interactions from the Hi-C data were validated with fluorescent in situ hybridization (FISH). We discovered that a subset of genes important for retinal development, cancer and stress response in the retina are localized to the facultative heterochromatin domain in a developmental stage– and cell type–specific manner.  We used machine learning to develop an algorithm based on our chromatin Hidden Markov Modeling (chromHMM) of retinal development to predict heterochromatin domains and study their dynamics during retinogenesis. FISH data for 264 genomic loci were used to train and validate the algorithm.  These integrated data (https://pecan.stjude.cloud/retinalnucleome) were used to identify a developmental stage- and cell type-specific core regulatory circuit super-enhancer (CRC-SE) upstream of the Vsx2 gene that is required for bipolar neuron expression. Deletion of the Vsx2 CRC-SE in mice led to the loss of bipolar neurons in the retina.

overall_design: Examination of chromatin interaction profiles in 5 cell types

first: Issam

last: Aldiri

first: Michael

last: Dyer