title: Elavl HITS-CLIP

status: Public on Sep 30 2019

city: New York

first: Robert

last: Darnell

state: New York

address: 1230 York Ave

country: USA

institute: Rockefeller University

summary: Mouse samples were subjected to HITS-CLIP to monitor Elavl binding

overall_design: Brain or cell line samples were UV-irradiated and subjected to Elavl HITS-CLIP (detailed desription in accompanying paper)

first: Christopher

last: Park

first: Claudia

last: Scheckel

middle: B


title: L.hongkongensis transcriptomes grown in media supplemented with or without malate

city: Hong Kong

first: Lifeng

last: Xiong

address: Pok Fu Lam

country: China

institute: the University of Hong Kong

type: Expression profiling by high throughput sequencing

summary: To better understand the malate-mediated metabolism and related regulatory profiles of L. hongkongensis, we compared the respective expression profiles of L. hongkongensis cells grown in modified M63 media supplemented with or without malate using high-throughput RNA-sequencing.

overall_design: We sequenced the Laribacter hongkongensis transcriptomes cultured in modified M63 minimal media, with or without malate addition, in both of wildtype and CRP mutant strains.

first: Patrick

middle: C

last: Woo


title: Transcriptional control of lung alveolar type 1 cell development and maintenance by NK Homeobox 2-1

status: Public on Sep 29 2019

city: Memphis

first: Danielle

middle: R.

last: Little

state: Tennessee

address: 262 Danny Thomas Pl Rm D2031

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Transcriptional control of lung alveolar type 1 cell development and maintenance by NK Homeobox 2-1 [RNA-Seq]

summary: The extraordinarily thin alveolar type 1 (AT1) cell constitutes nearly the entire gas exchange surface and allows passive diffusion of oxygen into the blood stream. Despite such an essential role, the transcriptional network controlling AT1 cells remains unclear. Using cell-specific knockout mouse models, genomic profiling, and three-dimensional imaging, we found that NK Homeobox 2-1 (NKX2-1) is expressed in AT1 cells and is required for the development and maintenance of AT1 cells. Without Nkx2-1, developing AT1 cells lose three defining features — molecular markers, expansive morphology, and cellular quiescence — leading to alveolar simplification and lethality. NKX2-1 is also cell-autonomously required for the same three defining features in mature AT1 cells. Intriguingly, Nkx2-1 mutant AT1 cells activate gastrointestinal genes and form dense microvilli-like structures apically. Single cell RNA-seq and whole lung ChIP-seq show NKX2-1 binding to 68% of genes that are downregulated upon Nkx2-1 deletion including 93% of known AT1 genes, but near-background binding to upregulated genes. Our results identify a key node in the AT1 cell transcriptional network and demonstrate remarkable plasticity of an otherwise terminally differentiated cell type.

overall_design: FACS-purified lung AT1 cells(P5) or whole lobes(P14) were obtained from control and mutant lungs, and analyzed to look for differences in gene expression.

first: Jichao

last: Chen


title: RNA-seq of healthy CD34+ HSPCs after co-culture with myelodyplastic syndrome patient-derived mesenchymal stromal cells

city: Singapore

first: Zhiyong

last: Poon

address: 20 College Road

country: Singapore

institute: Singapore General Hospital

summary: Cytopenia in at least one of the hematopoietic lineages (RBCs, WBCs or platelets) is a hallmark feature of MDS, indicating the lack of ability to support HSPC proliferation and the retention of their multilineage potential in the bone marrow. Here, wel investigate MDS-MSCs (with and without 5-azacitidine pre-treatment) as feeder layers for healthy CD34+ HSPCs. We performed RNA sequencing of co-cultured CD34+ HSPCs to compare their transcriptomic signatures after exposure to treated vs untreated MDS-MSCs.

overall_design: 5-azacitidine treated or MDS-MSCs were plated at a near confluent density of 2.0 × 104 cells/cm2 in DMEM with 10% FBS. 24 h later, healthy CD34+ HSPCs were seeded in contact with the MSC feeder layer at a density of 2.0 × 103 cells/cm2 in hematopoietic media and cultured for 14-21 days with replacement of media after 7 days. On the last day, CD34+ HSPCs were sorted for RNA extraction and subsequent sequencing.

first: Hwang

last: William


title: RNA sequencing of developing Mimulus seeds reveals conservation of three imprinted genes

status: Public on Sep 27 2019

city: Raleigh, NC

last: Franks

state: NC

address: Campus Box 7614

department: Plant & Microbial Biology Department

institute: NC State University

summary: The seeds of angiosperms are comprised of three main tissues--the seed coat, embryo, and endosperm--whose coordinated development will enable the next generation to disperse with sufficient maternal resources and germinate when conditions are favorable. We use high-throughput RNA sequencing technology to characterize the developmental dynamics of gene expression in whole seeds resulting from a compatible cross between two species of the Mimulus guttatus complex.We find that development in ovules and seeds involves the activation of the majority of annotated genes in M. guttatus (64-67%), and the differential expression over time of 6,691 genes, including 424 transcription factors. Most of the genes we detected (69%) were expressed at all stages, from ovules to heart-stage embryo seeds. We also detected and validated four genes exhibiting paternally-biased expression (MDB13, ATXR5, DnaJ and BGAL11). Intriguingly, three of our validated PEGs are have imprinted homologues in other plant species, suggesting that these proteins perform a shared role in endosperm development among distantly related plant taxa. Additionally, the overlap in gene expression profiles between stages of development suggests that most genes fulfill multiple developmental and biological roles. Future analyses should examine whether different regions of the seed (embryo, endosperm, and seed coat) have unique patterns of gene expression, and the extent to which spatial coordination and regulation of gene expression may play a role in regulating seed development.

sample_organism: Erythranthe pardalis x Erythranthe guttata

overall_design: Inbred lines of Mimulus guttatus (CSS4) and the selfing species Mimulus pardalis (SEC39) were grown in a chamber at 18-hour days, 21°C, 30% relative humidity.Total RNA was extracted from ovules and developing hybrid seeds from that had been removed from longitudinal-sectioned fruits. We sequenced a total of 20 samples, including 5 replicates of un-pollinated M. pardalis ovules and 3-5 replicates of M. pardalis x M. guttatus hybrid seeds collected at 2, 4, 6, and 8 DAP. Each replicate contained ~10-20 ovaries or fruits pooled from different plants.

first: Miguel

middle: A

last: Vergara

first: Elen

last: Oneal

first: Gonzalo

last: Villarino

first: Mario

last: Costa

first: Caitlyn

last: Roberts

first: Maria

last: De Luis Balaguer

first: Silvia

last: Coimbra

first: John

last: Willis


title: Loss of heterochromatin protein 1 (Hep1) in Fusarium graminearum leads to hypervirulence and mycotoxin overproduction during pathogenic growth.

city: Tulln/Donau

first: Stefan

last: Boedi

address: Konrad Lorenzstr. 24

country: Austria

institute: BOKU

summary: Upon axenic cultivation in presence of the mycotoxin inducing nitrogen source L- ornithine the HEP1 deletion mutant showed an altered secondary metabolite profile including reduced levels of deoxynivalenol (DON). This finding was contrasted with a 1.5 fold increased infection rate on the susceptible wheat cv. Remus which was accompanied by increased production of DON. Transcriptome analysis of the HEP1 deletion versus the PH-1 wildtype strain during pathogenic growth state as well as during saprophytic growth on dead (non-responding) wheat heads and axenic samples allows to distinguish gene response of the pathogen reacting on signals from the active, defending plant from those regulated by plant substrate effects or in vitro mimicked mycotoxin inducing conditions, providing insights into gene regulation underlying the observed hypervirulence.

overall_design: Three different growth conditions with two to three replicates

first: Harald

last: Berger

first: Thomas

last: Nussbaumer

first: Christian

middle: M

last: Sieber

first: Lena

last: Studt

first: Simone

last: Bachleitner

first: Martin

last: Münsterkötter

first: Wolfgang

last: Schweiger

first: Michael

last: Sulyok

first: Marc

last: Lemmens

first: Gerhard

last: Adam

first: Ulrich

last: Güldener

first: Joseph

last: Strauss


title: Mitofusin 2 is essential for oocyte and follicle development, and to maintain ovarian follicular reserve during reproductive aging [GV]

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

summary: We performed RNAseq analysis to determine the effect of MFN2 deletion on oocyte global gene expression profile. RNAseq revealed a total of 363 genes were significantly differentially expressed (p<0.05) in Mfn2-/- GV oocytes compared to WT (241 up-regulated and 122 down-regulated). Gene ontology (GO) analysis indicated significant over-representation of elements involved in regulation of embryonic development, cell death and survival, and cell morphology. Pathway analysis of top10 upregulated and downregulated annotated genes are listed. Our findings provide new insight into the role of MFN2 in the oocytes, and may help understand the potential mechanism of subfertility and reproductive aging associated with MFN2-deficiency.

overall_design: GV oocytes were collected from 8-week-old Mfn2-/- and WT mice (n=3 for each group) and 5 oocytes from each group were pooled for RNA sequencing analysis.

first: Man

last: Zhang

first: Emre

last: Seli


title: Expression data from S. aureus COL growing under acidic and alkaline conditions in biofilm or planktonic mode

city: Hull

first: Georgios

last: Efthimiou

address: Hardy Building, Cottingham Road

department: Biomedical and Forensic Sciences

country: United Kingdom

institute: University of Hull

summary:
Methicillin-resistant Staphylococcus aureus (MRSA) strains are important human pathogens and a significant health hazard for hospitals and the food industry. They are resistant to β-lactam antibiotics including methicillin and extremely difficult to treat. In this study, we show that the Staphylococcus aureus COL (MRSA) strain, with a known complete genome, can easily survive and grow under acidic and alkaline conditions (pH 5 and pH9, respectively), both planktonically and as a biofilm. Α microarray-based analysis of both planktonic and biofilm cells was performed under acidic and alkaline conditions showing that several genes are up- or down-regulated under different environmental conditions and growth modes. These genes were coding for transcription regulators, ion transporters, cell wall biosynthetic enzymes, autolytic enzymes, adhesion proteins and antibiotic resistance factors, most of which are associated with biofilm formation. These results will facilitate a better understanding of the physiological adjustments occurring in biofilm-associated S. aureus COL cells growing in acidic or alkaline environments, which will enable the development of new efficient treatment or disinfection strategies.
We used microarrays to detail the global programme of gene expression underlying growth of S. aureus COL growing under acidic and alkaline conditions in biofilm or planktonic mode and identified distinct classes of up-regulated genes during this process.

overall_design: We extracted total RNA from S. aureus COL growing under acidic and alkaline conditions in biofilm (24 h of culture) or planktonic mode (5 h of culture). The RNA samples were converted to cDNA and hybridised on Affymetrix arrays. The analysed data were used for identifying significantly differentially-expressed genes under these conditions.

last: Tsiamis

first: Milton

last: Typas

first: Katherine

last: Pappas


title: Transcriptomic analysis of follicular CD8 T cells in human secondary lymphoid organs in healthy donors and patients with common variable immunodeficiency

city: Prague

first: Adam

last: Klocperk

address: V Uvalu 84

department: Department of Immunology

country: Czech Republic

institute: University Hospital in Motol

summary: We performed a comparison of transcriptome between follicular CD8 T cells (CXCR5+CD8+CD3+) from 3 lymph nodes of patients with common variable immunodeficiency (CVID) and 3 tonsils of healthy donors, discovering 67 differentially expressed genes that show immunoregulatory potential of CVID follicular CD8 T cells.

overall_design: Comparison of transcriptome between follicular CD8 T cells (CXCR5+CD8+CD3+) from 3 lymph nodes of patients with common variable immunodeficiency (CVID) and 3 tonsils of healthy donors.

first: Klaus

last: Warnatz


title: Mitofusin 2 is essential for oocyte and follicle development, and to maintain ovarian follicular reserve during reproductive aging


title: Actin cytoskeletal remodeling with protrusion formation is essential for heart regeneration in Hippo-deficient mice

status: Public on Sep 26 2019

city: Houston

first: Todd

middle: Ryan

last: Heallen

state: Texas

address: One Baylor Plaza

department: Molecular Physiology and Biophysics

institute: Baylor College of Medicine


title: Transcriptional control of lung alveolar type 1 cell development and maintenance by NK Homeobox 2-1 [scRNA-Seq]

first: Danielle

last: Little

overall_design: FACS-purified lung epithelial, immune, endothelial, and mesenchymal cells were processed through the Chromium Single Cell Gene Expression Solution Platform (10X Genomics)

first: Jichao

last: Chen


title: Mitofusin 2 is essential for oocyte and follicle development, and to maintain ovarian follicular reserve during reproductive aging [SFO]

summary: We performed RNAseq analysis to determine the effect of MFN2 deletion on oocyte global gene expression profile. RNAseq revealed a total of 1041 genes were significantly differentially expressed (p<0.05) in Mfn2-/- seceondary follicle enclosed oocytes (SFOs) compared to WT, with 510 up-regulated and 531 down-regulated genes. GO cluster analysis indicated significant over-representation of elements involved in regulation of cell death and survival, cellular development and cellular growth. Pathway analysis of top10 upregulated and downregulated annotated genes are listed. Our findings provide new insight into the role of MFN2 in the oocytes, and may help understand the potential mechanism of subfertility and reproductive aging associated with MFN2-deficiency.

overall_design: Secondary follicle-enclosed oocytes were collected from 8-week-old Mfn2-/- and WT mice (n=3 for each group) and 5 oocytes from each group were pooled for RNA sequencing analysis.


title: De novo transcriptome assembly and functional analyses on body tissues of Chrysodeixis includens larvae.

city: Davis

first: Joanna

middle: C.

last: Chiu

state: California

address: One shield Av

institute: University of California

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized genetic information from organisms that lack of gene sequencing data. Sequences of transcriptomic or genomic data of C. includens are no longer available to conduct relevant and applied studies to agriculture, such as, characterize biological process, screening for resistance and identification of new target genes. In this sense, we constructed a reference transcriptome of C. includens from head and body tissues of third instar larvae and we performed and analysis of gene expression functionality of transcripts between head and body.
Methods: Two replicates of pool 5 larvae (third instar) were dissected into two parts: head (enriched with neural tissue) and body (enriched with adipose and gut tissues). Paired-end libraries of head and body tissues, with an approximate average insert length of 300 bp, were sequenced on an Illumina HiSeq platform with 150 bp paired-end sequencing. Trimmed RNA-Seq reads from transcriptomes of head and body larvae were used for de novo assembly using de Bruijn graph-based assembler (Trinity). All contig sequences built on the reference transcriptome assembled were annotated using Blast2GO pipeline. For the expression analysis RNA-seq reads were mapped to the built reference transcriptome using TopHat and expression values of transcripts in FPKM (fragments per kilobase per million mapped reads) between head and body tissues were estimated on Cufflinks.
Results: The assembled transcriptome from reads of head and body tissues of C. includens larvae generated a fasta file format (136.2MB) containing 102,249 transcript sequences and 60,347 “genes”. The length distribution of transcripts was between a minimum of 200bp and a maximum of 37,230bp with an average of 1,005bp. As the RNA extraction of body included enriched tissues of tegument, gut, and hemolymph of third instar larvae, the transcripts were found to be involved on transmembrane transport, proteolysis, cation transport and many types of metabolic process. These biological processes in soybean looper were related to the cellular functionality of oxidoreductase, transmembrane transporter and serine-type endopeptidase activities and many types of binding functions. In the head tissue of C. includens we found most transcripts with gene ontology related to signal transduction. This biological process could be associated with the functionality of genes related to odorant binding, signaling receptor binding, DNA binding and other types of molecular binding. As we found, we suggest that these genes expressed only in the head tissue might be involved mainly in the detection of a signal and subsequent cascade expression of biological processes.
Conclusions: Our study represents the first detailed transcriptome of Chrysodeixis includens of different larvae tissues, with biologic replicates, generated by RNA-seq technology. Our results show that NGS offers a comprehensive and accurate sequencing data to species with reference genome not available. Also, RNA-seq data offer a global gene expression analysis between tissues and permit understand some biological process involved in insect physiology.

overall_design: Libraries of two replicates of pool 5 larvae (third instar) from head and body tissues were sequenced.

first: Frank

middle: G

last: Zalom

first: Jerson

middle: V

last: Guedes


title: FOXA1 Chromatin Binding is Regulated by LSD1-Mediated Demethylation

city: Boston

first: Changmeng

last: Cai

state: Massachusetts

address: 100 William T. Morrissey Blvd.

institute: University of Massachusetts Boston


title: DNA methylation in neutrophils from Juvenile Idiopathic Arthritis

status: Public on Sep 28 2019

first: Lisha

last: Zhu

state: TX

address: 7000 fannin st

institute: UT Health Science Center at Houston

type: Methylation profiling by high throughput sequencing

summary: In this study, we combined the MeDIP-Seq and MRE-Seq data of 6 ADU (active disease, untreated) and 5 HC (health control) samples to obtatin the differentially methylated regions (DMRs) between ADU and HC using the repMnM R package, and observed that those DMRs can successfully classify the two groups.

overall_design: 6 ADU (active disease, untreated) and 5 HC (health control) samples were carried out MeDIP-Seq and MRE-Seq by next-generation sequencing strategy

first: Kaiyu

first: Tao

last: Liu

first: James

middle: N

last: Jarvis


title: ChIP-seq in neutrophils from Juvenile Idiopathic Arthritis

summary: We used chromatin immunoprecipitation-sequencing to identify epigenetic marks associated with enhancer function (H3K4me1 and H3K27ac)  from two children with untreated active JIA (ADU) and three children who were undergoing therapy with methotrexate but whose disease still remained active (ADT).

overall_design: 2 ADU (active disease, untreated) and 3 ADT (active disease, treated) samples were carried out ChIP-Seq by next-generation sequencing strategy

last: Jiang


title: Glial and neuronal alpha synuclein induce unique transcriptional programs

first: Abby

last: Olsen

state: MA

address: 60 Fenwood Rd

department: Neurology

institute: Brigham and Women's Hospital

summary: We performed RNAseq using whole Drosophila heads after expressing human wild type alpha synuclein in either glia, neurons, or both types. We identified many upregulated genes when alpha synuclein was expresed in glia and many downregulated genes with it was expresed in neurons or both cell types.

overall_design: Human wild type alpha synuclein was expressed in Drosophila glia and/or neurons. For glia we used the UAS-GAL4 expression system and the pan-glial enhancer, Repo. For neurons we used the Q system and the pan-neuronal enhancer Synaptobrevin.

middle: L

first: Mel

last: Feany


title: Expression profile of adipose tissue microRNAs and of genes in the mTOR signalling network  following developmental high fat diet

city: Oslo

first: Nur

last: Duale

address: Lovisenbergg. 8, P.O.Box 4404 Nydalen,

department: Division of Climate and Environment Health

country: Norway

institute: Norwegian Institute of Public Health

summary: High fat diet (HFD) during early development may increase the susceptibility to metabolic diseases later in life. Adipose tissue is an important regulator of energy metabolism through secretion of endocrine and paracrine/autocrine factors. In the present study we first screened the expression profiles of about 500 miRNAs in visceral white adipose tissue (VAT) from mice fed a control diet (CD) and mice fed a matched HFD during three different life stages i) in utero (UT), ii) in utero and lactation (UL), iii) in utero until termination at age 23 weeks (WL). Fourteen differentially expressed miRNAs were identified and these miRNAs were used for prediction of targeted signalling pathways. In addition, analysis of high abundance miRNAs showed a marked downregulation of the miR-200 family members in the UT group. Subsequently, the transcript levels of 89 selected genes represented in the predicted signalling pathways were determined. Six genes (Deptor, Il6, Irs1, lep, Lpin1 and prkaa1) showed a significant differential expression due to HFD feeding compared to controls, and HFD treatment had significant effects on the WL-groups. The expression pattern of Deptor, Il6, Irs1, Lep genes showed a similar direction of change across all HFD treatment groups.  The differential expression of Irs1 and Deptor genes points to a persistent modification of the insulin receptor – mTOR signalling network. This finding is supported by increased serum insulin and IGF-1 levels and impaired glucose regulation in the HFD groups. This study shows that developmental HFD can lead to persistent changes in VAT miRNA expression levels that is associated with a modification of key signalling pathways regulating energy metabolism also in animals with normal BMI.dy we have screened over 500 miRNAs for differential expression in visceral white adipose tissue (vWAT) between mice fed a control diet (CD; 10% kcal from fat) and mice fed a matched high fat diet (HFD; 45% kcal from fat) during three different life stages i) in utero (UT), ii) in utero and lactation (UL), iii) in utero until termination (WL). All animals were sacrifices at an age of 23 weeks.

overall_design: Experimental design: In this study, male C57BL/6J wild-type mice were used. The mice were housed in air flow IVC racks (Innovive Inc., San Diego, CA, USA) in 100% PET plastic disposable cages on Nestpak Aspen 4HK bedding (Datesand Ltd., Manchester, UK) in a room with 12-h light/dark cycle, and controlled humidity (55 ± 5%) and temperature (20–24°C). Diet and municipal tap water were given ad libitum. The experiment reported in this paper was performed in conformity with the laws and regulations for animal experiments in Norway and was approved by the National Experimental Animal Board in Norway. The parental mice were fed a standard breeding diet (2018 Teklad Global 18% Protein Rodent Diet from Harlan Industries Inc., Indianapolis, IN, USA) before mating. The experimental litters were given diets of purified ingredients from Research Diets Inc. (New Brunswick, NJ, USA) in various life periods. The D12451 diet, containing 20%, 35%, and 45% of kcal from protein, carbohydrates, and fat, respectively, was used as a HFD. The D12450H diet, containing 20%, 70%, and 10% of kcal from protein, carbohydrates, and fat, respectively, was used as a matching control diet (CD). Mice were randomly assigned to the experimental groups and exposed to the CD (22 mice/17 litters) or the HFD during combinations of three periods of life; in utero, from mating via the dams (UT; 27mice/17litters); from mating to weaning (UL; 25 mice/19 litters); and from mating to termination at 23 weeks (WL; 23 mice/21 litters). For miRNA profiling following mice per group was used: CD (3 pooled samples from 12 mice); UT (3 pooled samples from 12 mice); UL (3 pooled samples from 12 mice) and WL (3 pooled samples from 12 mice).  Mice were sacrificed by cervical dislocation and epididymal fat pads were isolated, rapidly frozen on dry ice and kept at -80ºC until use.


title: Cohesin Members Stag1 and Stag2 Display Distinct Roles in Chromatin Accessibility and Topological Control of HSC Self-Renewal and Differentiation [RNA_LinNegBM]

first: Richard

last: Koche

institute: Memorial Sloan Kettering Cancer Center

summary: Transcriptional regulators, including the cohesin complex member STAG2, are recurrently mutated in cancer. The role of STAG2 in gene regulation, hematopoiesis, and tumor suppression remains unresolved. We show that Stag2 deletion in hematopoietic stem and progenitor cells (HSPCs) results in altered hematopoietic function, increased self-renewal, and impaired differentiation. Chromatin immunoprecipitation (ChIP) sequencing revealed that, although Stag2 and Stag1 bind a shared set of genomic loci, a component of Stag2 binding sites is unoccupied by Stag1, even in Stag2-deficient HSPCs. Although concurrent loss of Stag2 and Stag1 abrogated hematopoiesis, Stag2 loss alone decreased chromatin accessibility and transcription of lineage-specification genes, including Ebf1 and Pax5, leading to increased self-renewal and reduced HSPC commitment to the B cell lineage. Our data illustrate a role for Stag2 in transformation and transcriptional dysregulation distinct from its shared role with Stag1 in chromosomal segregation.

overall_design: RNA-seq of Stag2 KO and WT lineage depleted bone marrow

first: Aaron

middle: D

last: Viny

middle: P

first: Ross

last: Levine


title: Cohesin Members Stag1 and Stag2 Display Distinct Roles in Chromatin Accessibility and Topological Control of HSC Self-Renewal and Differentiation [ATAC_LinNegBM]

overall_design: ATAC-seq of Stag2 KO and WT lineage depleted bone marrow


title: Cohesin Members Stag1 and Stag2 Display Distinct Roles in Chromatin Accessibility and Topological Control of HSC Self-Renewal and Differentiation [ChIP_LinNeg_Stag1Stag2CTCF]

overall_design: ChIP-sequencing of Stag1, Stag2, Smc1a, Smc3, and CTCF in Stag2 wildtype and knockout cells


title: Expression Profiling-based Clustering of Healthy Subjects Recapitulates Classifications Defined by Clinical Observation in Chinese Medicine

city: Beijing

first: dan

last: liu

address: NO.1 Beichen West Road, Chaoyang District, Beijing

institute: Beijing Institute of Genomics, Chinese Academy of Sciences

summary:
Based on the theory of constitution of Traditional Chinese Medicine (TCM), healthy individuals can be grouped into distinctive types. the global gene expression signature for distinctive constitutions has not been sufficiently explored.
Here we examined gene expression profiles from 32 Chinese Han individuals with Yang/Yin deficiency (n=12 each) and Balanced constitutions (n=8).

overall_design: Venous blood (8ml) was obtained from each subject. We isolated the peripheral blood mononuclear cells (PBMCs) for extracting RNA.

first: Ruoxi

last: Yu

first: Dan


title: Cohesin Members Stag1 and Stag2 Display Distinct Roles in Chromatin Accessibility and Topological Control of HSC Self-Renewal and Differentiation [RNA_3populations_LSK_GMP_CFUE]

overall_design: RNA-seq of Stag2 KO and WT LSK, GMP, and CFU-E cells


title: Cohesin Members Stag1 and Stag2 Display Distinct Roles in Chromatin Accessibility and Topological Control of HSC Self-Renewal and Differentiation [ATAC_LSK_GMP_CFUE_Stag2KOWT]

overall_design: ATAC-seq of Stag2 KO and WT LSK, GMP, and CFU-E cells


title: ChIP-seq of embryonic muscle sample of two pig breeds

city: Guangzhou

first: Delin

last: Mo

address: Xingang Road

institute: Sun Yat-sen University

summary: ChIP-seq of embryonic muscle sample of Landrace and Wuzhishan pig breeds from embryonic day 35 and 28 dpc were conducted using H3K4me3 and H3K27me3 antibody.

overall_design: Examination of 2 different histone modifications in 2 pig breeds during two embryonic stages.

first: Xumeng

last: Zhang


title: Analysis of Notch2 conditional knockout (CKO) and wild type mouse hippocampal stem cells

city: Basel

first: Verdon

last: Taylor

address: Mattenstrasse 28

department: Biomedicine

country: Switzerland

institute: University of Basel

summary:
Regulated genes downsteam of Notch2
Methods: mRNA profiles of adult wild type and Notch2 CKO neural stem cells were generated by deep sequencing, in triplicate. Two libraries were generated for each RNA sample using Nextera XT DNA Library Preparation Kit (Illumina) and sequenced by SmartSeq2 kit (Illumina) on different days. Each sample was sequenced twice in two independent lanes on a Illumina HiSeq 2500. The sequence reads that passed quality filters were mapped to the mouse genome (GRCm38) by Bowtie2 and transcript identification and quantification were performed using HTSeq. qRT–PCR validation was performed using SYBR Green assays.
Results: This study identifies Notch2 regulated genes in neurogenic neural stem cells of the adult mouse hippocampus.


title: A novel deactivation factor of fibrogenic hepatic stellate cells induces regression of liver fibrosis in mice

city: Tokyo

first: Yasuhiro

last: Nakano

address: 1-5-45 Yushima

country: Japan

institute: Tokyo Medical and Dental University (TMDU)

summary: It has been reported that hepatic stellate cells (HSCs) differentiate from mesodermal-derived submesothelial cells during embryonic development, and that these cells express a common surface marker p75 neurotrophin receptor (p75NTR). We sorted p75NTR-expressing cells in embryonic liver at each developmental stage, and transcription profiles were analyzed using the DNA microarray.

overall_design: Liver tissues obtained from E11.5, E13.5, E14.5, and E17.5 fetuses or newborn mice (P1) were excised under a microscope and dissociated in 0.05% collagenase solution. The CD45(−)Ter119(−)p75NTR(+) cell fraction was obtained by FACS. Total RNA was prepared from isolated these cells and transcription profiles were analyzed using the DNA microarray. Hierarchical clustering of normalized signal intensities was performed using Euclidean distances and centroid linkage. Raw intensity values were normalized using the 75th percentile and transformed to log2 scale.

first: Akihide

last: Kamiya

first: Yutaka

last: Inagaki


title: Transcriptomic profile of circulating memory T cells in donors previously exposed to dengue virus

city: Seattle

first: Yuan

last: Tian

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

summary: Dengue virus is responsible for 400 million human infections each year . The characterization of exact molecular components of immune response associated may help design more effective therapeutic interventions. In this study, we aimed to characterize the immune signature of memory T cells associated with previous exposure to dengue virus. Transcriptomic profiling using RNA sequencing was performed on memory CD4 and CD8 T cells isolated from individuals with primary or secondary dengue infections from two endemic areas (Sri Lanka and Nicaragua), as well as from dengue negative healthy controls.

overall_design: RNA-sequencing of sorted memory CD4 and CD8 T cells from cryopreserved PBMC of 15 subjects with primary dengue infection, 30 subjects with secondary infection infection and 15 dengue virus negative healthy controls.

first: Daniela

last: Weiskopf

first: Patrick

last: O'Rourke

first: Gregory

last: Seumois

first: Zheng

last: Fu

first: Jason

last: Greenbaum

first: Bjoern

last: Peters

first: Pandurangan

last: Vijayanand

first: Alessandro

last: Sette


title: GntR-like regulator in the Archaeon Sulfolobus acidocaldarius

city: Gent

first: Laurentijn

last: Tilleman

address: Ottergemsesteenweg 460

country: Belgium

institute: Ghent University

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

overall_design: Refer to individual Series


title: Genome-wide interaction map of YtrA transcription factor in S. Acidocaldarius

summary: We report the characterization of GntR-like regulator in the Archaeon Sulfolobus acidocaldarius by looking at the genome wide interaction map of the protein in vivo

overall_design: examination of in vivo binding of YtrA protein

first: E

last: Peeter


title: Epigenetic safeguards are coordinately removed to reverse cell identity [5hmC Enrichment]

city: Madison

first: Rupa

last: Sridharan

state: WI

address: 330 N. Orchard Street

department: Wisconsin Institute for Discovery

institute: University of Wisconsin

summary: Epigenetic modifications operate in concert to maintain cell identity, yet   how these interconnected networks suppress alternative cell fates remains unknown.  Here we uncover a link between the removal of repressive histone H3K9 methylation and DNA methylation during the reprogramming of somatic cells to pluripotency. The H3K9me2 demethylase, Kdm3b, transcriptionally controls DNA demethylase Tet1 expression. Unexpectedly, in the absence of Kdm3b, loci that have to be DNA demethylated are trapped in an intermediate hydroxymethylated (5hmC) state and do not resolve to unmethylated cytosine. Ectopic 5hmC trapping precludes the chromatin association of master pluripotency factor, POU5F1, and pluripotent gene activation. Tet1 but not Tet2 is critical for this defining event in the reprogramming process. Taken together we uncover a mechanism of coordinated chromatin modification removal in disrupting cell identity.

overall_design: 5hmC Enrichment followed by sequencing during conversion of stalled intermediates to iPSCs

first: Khoa

last: Tran


title: Epigenetic safeguards are coordinately removed to reverse cell identity [RNA-Seq]

overall_design: RNA Sequencing of WT or Kdm3b KO stalled intermediates during the conversion to iPSCs .


title: Next generation sequencing facilitates transcriptome analyses of mock and NCCRP1 transfected esophageal squamous cell carcinoma cell line KYSE150 cells

city: tyuo-ku

first: noriko

last: nishi

state: Tokyo

address: 5-11 hakozaki 5F Yunibasaru Bldg

institute: Axiohelix Co. Ltd.

summary: We obtained transcriptome profiling (RNA-seq) of human esophageal squamous cell carcinoma cell line KYSE150 stabley transfected clones with pIRES2-EGFP vector or human NCCRP1-expression vector by using next generation sequencing.

overall_design: Comparison of expression pfofiles between KYSE150/Vector clones and KYSE150/NCCRP1 clones.

first: Fumika

last: Inazuka

first: Taeko

last: Dohi

first: Yuki

middle: I

last: Kawamura


title: Next generation sequencing facilitates transcriptome analyses of mock and RHCG transfected esophageal squamous cell carcinoma cell line KYSE30 cells

summary: We obtained transcriptome profiling (RNA-seq) of human esophageal squamous cell carcinoma cell line KYSE30 cells stabley transfected with pIRES2-EGFP vector or human RHCG-expression vector by using next generation sequencing.

overall_design: Comparison of expression pfofiles between KYSE30/Vector cells and KYSE30/RHCG cells.

first: Teruki

last: Hagiwara


title: Transcriptome Analysis of parietal cells isolated from high fat diet (HFD)-fed mice by using Next Generation Sequencing

summary: We obtained transcriptome profiling (RNA-seq) of H+/K+ ATPase positive parietal cells purified from gastric corpus of mice fed with HFD or control diet by using next generation sequencing.

overall_design: Comparison of expression profiles of murine parietal cells between HFD-fed and control mice.

last: Hirata


title: Expression analysis of wild-type Streptococcus pneumoniae PN4595-T23 and Vp1 deletion mutant

city: Pittsburgh

first: Rolando

middle: A.

last: Cuevas

state: Pennsylvania

address: 4400 Fifth Avenue, Mellon Institute, Room 217

department: Biological Sciences

institute: Carnegie Mellon University

summary: Investigation of differentially regulated genes in deletion of Vp1 compared to the wild-type. VP1 is a signaling peptide. Its characterization is described in Cuevas et al 2019 ADD TITLE AND REF

overall_design: A three chip study using RNA isolated from three separate wild-type cultures of Streptococcus pneumoniae PN4595-T23 and three separate cultures of VP1 mutant strain. Cultures were harvested at mid-log phase and used for RNA isolation and cDNA preparation and hybridized onto SpSGH array with custom designed probes. The SpSGH array covers the pneumococcal pangenome and a total of 1,930 genes were relevant for PN4595-T23. The design and validation of SpSGH array is described in Kadam et al 2015 Streptococcus pneumoniae Supragenome Hybridization Arrays for Profiling of Genetic Content and Gene Expression. Curr Protoc Microbiol. 2015; 36: 9D.4.1–9D.4.20.

first: Natalia

last: Hiller


title: Identification of a novel role for FoxO3 isoform2 in osteoclastic inhibition

status: Public on Sep 25 2019

city: NEW YORK

first: Kazuki

last: Inoue

address: 535 E70TH STREET, S building 8th floor

institute: HOSPITAL FOR SPECIAL SURGERY

summary: We performed RNA-seq experiments, one with the WT control and Foxo3KO osteoclast precursors after RANKL stimulation to identify genes regulated by Foxo3 in osteoclast precursors.

overall_design: Bone marrow macrophages mRNA profiles of WT and Foxo3 KO mice were generated by deep sequencing using Illumina Hiseq4000.

first: Baohong

last: Zhao


title: Genome-wide CRISPR screen in standard growth conditions and stem cell conditions using primary low-passage KPf/fC pancreatic cancer cell lines

city: Glasgow

first: Neil

last: Robertson

state: Scotland

address: Switchback Road

department: Beatson Institute for Cancer Research

institute: University of Glasgow

summary:
Purpose: The goal of this study is to identify novel genes required for the survival and proliferation of pancreatic cancer cells in standard culture conditions and in stem cell conditions
Methods: Three independent primary pancreatic cancer cell lines were established from endstage Musashi2-reporter KPf/fC mice, and transduced with the genome-wide lentiCRISPR v2 library. Cells were grown under puromycin selection for 3 weeks (6 passages), then plated in non-adherent stem cell conditions in single-cell density for 1 week. Genomic DNA was isolated directly after library transduction, after selection in standard growth conditions, and after sphere growth in stem cell conditions. For sequencing, guide RNA's were amplified from total genomic DNA and barcoded for sequencing on an Illumina HiSeq2500 using V4 sequencing chemistry
Conclusions: Our study represents the first genome-wide CRISPR screen identifying genetic vulnerabilities of KPf/fC cells in stem cell conditions using 3 biologically unique primary cell lines.

overall_design: A multiplexed genome-wide CRISPR dropout screen was performed using primary KPf/fC cell lines in standard growth conditions and in stem cell conditions.

first: Nikki

middle: K

last: Lytle

first: Tannishtha

last: Reya


title: Epigenetic safeguards are coordinately removed to reverse cell identity


title: Transcriptome analyses of different region tissue of wheat grain endosperm

city: Zhengzhou

first: Dongyun

last: Ma

address: No.15 Longzihu College Park,Zhengzhou New District,Zhengzhou

institute: Henan Agricultural University

summary: The different parts of wheat grain endosperm at 25 days after anthesis were collected. Transcriptome analysis were conducted to investigate the differentially expressed transcript between inner and puter parts of endosperm. The study provide some useful information for understanding the protein gradient distribution in endosperm.

overall_design: mRNA profiles of 25-day after anthesis grain enposperm inner part and outer parts were generated by deep sequencing, in triplicate, using Illumina


title: Identification of root transcriptional responses to shoot illumination in Arabidopsis thaliana

city: Porto Alegre

first: Felipe

middle: dos Santos

last: Maraschin

state: RS

address: Av. Bento Goncalves 9500, Instituto de Biociencias - Departamento de Botânica - UFRGS, Prédio 43.423, sala 216

department: Botany

country: Brazil

institute: UFRGS

summary: This experiment aimed to investigate which genes are involved in the early photomorphogenic root development of dark grown roots when only the shoot was exposed to light.

overall_design: The samples consist of two biological replicates of total RNA extracted from primary roots from Arabidopsis Col-0 WT plants grown for 4 and 7 days in total darkness (4D and 7D samples) and grown roots in darkness and shoots in light (4LD and 7LD samples) to mimick the natural root growth environment.

last: dos Santos Maraschin


title: Transcriptome variations across species, organs and developmental stages

city: Lyon

first: Anamaria

last: Necsulea

address: 43 Bd. du 11 Novembre 1918

department: Laboratoire de Biométrie et Biologie Evolutive

country: France

institute: CNRS, Université Claude Bernard Lyon 1

type: Non-coding RNA profiling by high throughput sequencing

summary: We sequenced polyA-selected transcriptomes from three species (mouse, rat and chicken), four organs (brain, kidney, liver and testis) and five developmental stages (two embryonic stages, newborn, young adult and aged adult individuals). We analyzed gene expression pattern variations across species, organs and developmental stages for protein-coding and long non-coding RNA genes.

sample_organism:
Gallus gallus
Mus musculus
Rattus norvegicus

overall_design: Comparative transcriptomics analyses across species, organs and developmental stages

first: Fabrice

last: Darbellay


title: miRNA expression data from oral squamous cell carcinoma patients

city: Chang Sha

first: Hao

last: Pan

address: Xiangya NO.72

department: Department of Periodontics

institute: Xiangya Stomatological Hospital & School of Stomatology, Central South University

summary: Oral squamous cell carcinoma (OSCC) accounts for the high mortality rate and morbidity in head and neck cancer. Data for analysis were obtained from the microarray data of 6 OSCC tissues, tissues adjacent to cancer, and contralateral normal tissues.We used the affy package under the R environment to preprocess and normalize the original gene chip data.

overall_design: Data for analysis were obtained from the microarray data of 6 OSCC tissues, tissues adjacent to cancer, and contralateral normal tissues. We used the affy package under the R environment to preprocess and normalize the original gene chip data. Differentially expressed genes were obtained by pre-processing gene expression profile data to construct a weighted gene co-expression network and identify key gene modules.

first: Yuhong

last: Wang

first: Zhangui

last: Tang


title: Next Generation Sequencing Facilitates Quantitative Analysis of TFH2 cell Transcriptomes

city: Yokohama

first: Kosuke

last: Miyauchi

state: Kanagawa

address: 1-7-22 Suehiro-sho

institute: RIKEN Center for Integrative Medical Sciences

summary: Emergence of IgE antibodies that bind allergens with high affinity is highly correlated with the severity of anaphylaxis. However, the underlying molecular mechanisms by which high-affinity IgE is generated remain poorly understood. We discovered that IL-13-producing T follicular helper (TFH) cells, which we designated as TFH2 cells, are generated from conventional TH2 cells by antigen sensitization. TFH2 cells have a unique cytokine profile (IL-4+IL-5-IL-13+IL-21+) and co-express the TFH and TH2 master transcriptional regulators, BCL-6 and GATA3.

overall_design: Naïve CD4T, TH2, or TFH cells of  mice were sorted and analyzed the transcriptome using Illumina HiSeq1500.

first: Masato

last: Kubo


title: Gene expression from neonatal human fibroblasts and MV-derived iPSC clones

city: Rochester

first: Patricia

last: Devaux

state: Minnesota

address: 200 First St SW

institute: Mayo Clinic

type:
Expression profiling by array
Third-party reanalysis

summary:
Measles virus vector expressing the 4 reprogramming factors, OCT4, SOX2, KLF4 and cMYC was produced and used to derived iPSC from neonatal human fibroblasts (BJ).
We used microarrays to compare the global gene expression in the derived MV-iPSC and compare it to the parental human neonatal fibroblast (BJ) and human embryonic stem cell (GSM551202)

overall_design: Three MV-derived iPSC and BJ cells were selected for RNA extraction and hybridization on Affymetrix microarrays


title: Transcriptome changes of epithelial buds of mouse submandibular gland upon blebbistatin treatment

city: Seongnam

first: Jin Man

last: Kim

address: CHA BioComplex, Pangyoro 335

country: South Korea

institute: CHA University

summary: We performed RNA-seq for profiling genetic changes in mouse embryonic submandibular glands upon blebbistatin treatment.

overall_design: E13 mouse embryonic submandibular gland mRNA profiles of control and blebbistatin treated group were generated by deep sequencing, in triplicate.

first: Jin


title: Next generation sequencing to identify differentially expressed genes in the YtrASa overexpression strain

first: Laurentijn

last: Tilleman

summary: We report the regulon of a GntR-like regulator from the archaeon Sulfolobus acidocaldarius by looking at differentially expressed genes comparing a YtrASa overexpression strain with its isogenic wild ype

overall_design: next generation sequencing by coparing a YtrAsa overexpression strain with its isogenic wild type

first: E

last: Peeter


title: Prinary breast cancers and brain metastasis

city: Okayama

first: TAKAYUKI

last: IWAMOTO

address: 2-5-1 Shikata-cho, Kitaku

institute: Okayama university hospital

summary: Sixteen paired matched samples from primary breast cancers and brain metastases diagnosed between April 1, 2001 and December 31, 2012 were collected from 8 institutions. Brain metastases were identified based on magnetic resonance imaging and/or computed tomography findings. The clinical characteristics of all the patients were obtained from their medical records. This study was approved by the institutional review board of each participating institute (Tokai University School of Medicine; National Hospital Organization Osaka National Hospital; Kinki University School of Medicine; Niigata Cancer Center Hospital; Shizuoka General Hospital; Hokkaido Cancer Center; National Hospital Organization, Tokyo Medical Center; and Gunma Prefectural Cancer Center).    Matching primary breast cancers and brain metastases Formalin-Fixed Paraffin-Embedded (FFPE) specimens for gene expression analysis were collected into RNA. RNA from specimens was isolated, and quantity and quality of the each RNA was using an Agilent 2100 Bioanalyzer (Agilent Technologies). Genome-wide expression levels of transcripts were analyzed using the Affymetrix U133A gene chips (Affymetrix) according to the manufacture’s instructions.

overall_design: Retrospective study: Matching primary breast cancers and brain metastases from 16 patients.

first: Takayuki

last: Iwamoto


title: miRNA-Mediated Suppression of a Cardioprotective Cardiokine as a Novel Mechanism Exacerbating Post-MI Remodeling by Sleep Breathing Disorders [RNA-Seq]

city: beijing

first: hui

middle: yun

last: du

state: beijing

address: 2 Anzhen Rd, Chaoyang District, Beijing

department: the Beijing Institute of Heart, Lung, and Blood Vessel Diseases

institute: Beijing Anzhen Hospital, Capital Medical University

summary: This study provides the first evidence that MI+CIH upregulates miR-214-3p, suppresses cardiac CTRP9 expression, and exacerbates cardiac remodeling, suggesting that CTRP9 may be a novel therapeutic target against pathologic remodeling in MI patients with OSA

overall_design: Cardiac mRNA profiles of C57BL/6J mice in four different groups (Sham,MI, CIH, MI+CIH) were generated by deep sequencing, in triplicate.

first: Yunhui

last: Du

first: Xinliang


title: Role of CpxR in biofilm development: expression of key fimbrial, O-antigen and virulence operons of Salmonella Enteritidis

city: Saint Paul

first: Sinisa

last: Vidovic

state: MN

address: 1971 Commonwealth Avenue

institute: University of Minnesota

summary: We report our results of RNA-seq analysis on Salmonella Enteritidis biofilms and planktonic cells of the wild type and its cpxR mutant

sample_organism: Salmonella enterica subsp. enterica serovar Enteritidis

overall_design: RNA was isolated from biofilms and planktonic cells of the wild type Salmonella Enteritidis and S. Enteritidis cpxR mutant. Libraries were created using standard Illumina reagents and analyzed using a HiSeq 4000 PE100 Illumina.

first: Juan

middle: E

last: Abrahante


title: Oral dosing for antenatal corticosteroids in the rhesus macaque

city: Miami

first: Augusto

middle: F

last: Schmidt

address: 1611 NW 12th ave

institute: University of Miami Miller School of Medicine

summary:
Purpose: Evaluated the transcriptional effects of an effective oral dosing of antental corticosteroids using betamethasone-phophate compared to the clinical treatment with the combination drug betamethasone-phosphate+betamethasone-acetate for fetal lung maturation.
Methods: RNA-sequencing of the fetal hippocampus, liver and lung was done. Differential expression analysis was done using read counts.
Results: There were no significant differences between oral Beta-P and the clinical treatment in the fetal hippocampus. Small differences were detected in the fetal lung associated with cellular proliferation and in the fetal liver.
Conclusions: Oral betamethasone-phosphate is an effective oral treatment that does not cause toxic effect in the fetal brain despite the higher dose.

overall_design: Time-pregnant rhesus macaques received corticosteroid treatments or placebo 5 days prior to delivery at 80% gestation.

first: Matthew

middle: W

last: Kemp

first: Mark

last: Milad

first: Lisa

last: Miller

first: James

last: Bridges

first: Michael

last: Clarke

first: Paranthaman

middle: S

last: Kannan

first: Alan

middle: H

last: Jobe


title: Identification of drivers and therapeutic vulnerabilities in anti-androgen resistant prostate cancer cells

city: Leuven

first: Frank

last: Claessens

address: Herestraat 49, box 901

department: Cellular and Molecular Medicine

institute: KU Leuven

summary: Inhibition of the androgen receptor (AR) by anti-androgens is the standard treatment for castration resistant prostate cancer (CRPC), but it inevitably leads to the development of resistance. We generated two multi anti-androgen resistant cell-line models by treatment of LNCaP cells with enzalutamide (ResA) and RD-162 (ResB). Both cell-lines have an AR independent, non-neuroendocrine phenotype. To identify the resistance mechanisms we performed RNASeq analysis. To this end, the three cell-lines were plated in medium with 5% dextran-coated charcoal (DCC) treated FCS at a density of 1 million cells/well in 6-well plates. After 24 hours of steroid starvation the cells were treated with 10 nM of the androgen dihydrotestosterone (DHT), 10 µM of the anti-androgen enzalutamide, a combination of the two, or vehicle (DMSO) for 18 hours.

overall_design: Examination of the gene expression profile in LNCaP and the two LNCaP derived anti-androgen resistant cell-lines ResA and ResB in androgen-depleted conditions and in presence of DHT and enzalutamide.

first: Christine

last: Helsen

first: Stefan

last: Prekovic

first: Florian

last: Handle


title: Transcriptomic analysis of the effect of trastuzumab in human iPSC-CMs

city: Stanford

first: Lei

last: Tian

state: CA

address: 1215 Welch Rd

institute: Stanford's Postdoctoral Scholar programs

summary: We used human iPSC-CMs generated from healthy individuals and performed RNA-sequencing after 7 days of trastuzumab treatment to examine the mechanism associated with contraction dysfunction in iPSC-CMs after trastuzumab treatment. Transcriptome analysis revealed the key role of an altered energy metabolism pathway for cardiomyocytes in the disease pathogenesis.

overall_design: RNA profiling of 6 samples of trastuzumab- and no drug (control)-treated human iPSC-CMs

first: Tomoya

last: Kitani

first: Joseph

middle: C

last: Wu


title: The role of CRYBB2 in breast cancer

city: Baltimore

first: Saraswati

last: Sukumar

state: MD

address: 1650 Orleans St, CRB 1, Rm 132

department: Breast Cancer Program

institute: Johns Hopkins School of Medicine

summary: To study the function of CRYBB2, we overexpressed CRYBB2 in breast cancer cell lines using lentiviral vectors and investigated transcriptomic changes using Agilent 4x44K microarrays.

overall_design: DCIS.COM or MCF10AT1 cells were transduced with either control or CRYBB2 lentiviral vectors. RNA was extracted and sent for microarray analysis. Resulting files extracted using the Agilent Feature Extraction software were imported into R, quantile normalized, and ComBat batch correted.

first: Vanessa

last: Merino

first: Soonweng

last: Cho


title: DNA methylation and hydroxymethylation profiles reveal possible role of highly methylated TLR signaling on Fasciola gigantica excretory/secretory products (FgESPs) modulation of buffalo DCs

city: nanning

first: xuefang

last: mei

address: 100, Daxue Road, Xixiangtang Area, Nanning, China

institute: College of Animal Science and Technology, Guangxi University

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

overall_design: Refer to individual Series


title: Genetic determinants of venetoclax resistance

city: Cambridge

first: Candace

last: Patterson

address: 75 Ames St

institute: The Broad Institute

summary: Resistance to the first approved BCL-2 inhibitor venetoclax is emerging in lymphoid malignancies. The study aimed to identify the genetic determinants of such resistance. From genome-scale screens we determined the genes influencing the sensitivity to BCL-2 inhibition. The present set of data is related to expression changes (assessed by RNA sequencing) observed in the resistant OCI-Ly1 lymphoma cell line as well as those resulting from genetic perturbation (using CRISPR-Cas9) targeting the genes highlighted in our genome-scale screen.

overall_design:
Expression changes (RNA sequencing data) of 32 engineered OCI-Ly1 cell lines (duplicates for each): venetoclax resistant, parental and CRISPR-Cas9 manipulated cell lines with 2 different sgRNA per target (non-targeting sgRNA, ID3-KO, NFKBIA-KO, IKZF5-KO, OTUD5-KO, UBR5-KO, EP300-KO).
ATAC-seq of the ID3 OCI-Ly1 knockout (vs control) lines and of the OCI-Ly1-R vs OCI-Ly1-S (duplicates for each).

first: Romain

last: Guieze

first: Catherine

middle: J

first: Matthew

last: Lawlor

first: Christopher

last: Ott


title: The comparison of RNA expression between primary and CR cells

city: Tokyo

first: REI

last: MIMOTO

address: 3-25-8 Nishishinbashi, Minato-ku

department: Biochemistry

institute: The Jikei University School of Medicine

summary: We used microarrays to  identified the chracteristics of CR cells  that differ from primary tumor.

overall_design: We took the breast cancer tumor from primary site and generated CR cells. We obtained expression profiles from primary tumor  and CR cells.

first: Rei

last: Mimoto


title: DNA hydroxymethylation profiles reveal possible role of highly methylated TLR signaling on Fasciola gigantica excretory/secretory products (FgESPs) modulation of buffalo DCs [hMeDIP-seq]

summary:
Purpose: To investigate whether FgESP affects the hydroxylmethylation level of DCs
Methods: we have profiled the DNA hydroxymethylome by using hydroxymethylated DNA immunoprecipitation sequencing (h)MeDIP-Seq in the current study
Results: DNA hydroxymethylation profiles revealed significant changes in the 5-hydroxymethylcytosine (5hmC) levels in 360 genes when DCs were treated with FgESPs. These differentially expressed genes were highly enriched in pathways associated with immune function.
Conclusion: For the first time, our study provides a genome-wide mapping of DNA hydroxylmethylation for DCs that interacted with FgESPs.

overall_design: In the current study, we have profiled the DNA hydroxymethylome by using high-throughput sequencing. Total DNA was extracted from buffalo PBMC DCs that were treated with FgESP, which was followed byFgESPs, and then performed hydroxymethylated DNA immunoprecipitation sequencing (h)MeDIP-Seq.

first: Xuefang

last: Mei

first: Wei

last: Shi

first: Honglin

last: Luo

first: Weiyi

last: Huang


title: DNA methylation profiles reveal possible role of highly methylated TLR signaling on Fasciola gigantica excretory/secretory products (FgESPs) modulation of buffalo DCs [MeDIP-seq]

summary:
Purpose: To investigate whether FgESP affects the (hydroxyl)methylation level of DCs
Methods: we have profiled the DNA methylome  by using methylated DNA immunoprecipitation sequencing (MeDIP-Seq) in the current study
Results: DNA methylation and hydroxymethylation profiles revealed significant changes in the 5-methylcytosine (5-mC) levels in the promoter regions of 5432 genes and significant changes in the 5-hydroxymethylcytosine (5hmC) levels in 360 genes when DCs were treated with FgESPs. These differentially expressed genes were highly enriched in pathways associated with immune function. The characterizations of DCs were assessed using scanning and transmission electron microscopy (SEM/TEM) and quantitative reverse transcriptional PCR (qRT-PCR). Our results demonstrated that FgESPs could markedly suppress DC maturation by down-regulating the expression of membrane phenotypic markers, such as CD1a, MHC II. The functional enrichment analysis found hypermethylation of genes, especially in the NF-κB signaling pathway, and transcription was unchanged or low for the TLR2, TLR4, and IL-12 genes in DCs. Thus, we suggest a possible mechanism of FgESPs in suppressing TLR signaling pathway-dependent DC maturation and function. Moreover, there were 111 genes demonstrating changes in both 5-mC and 5-hmC levels, and 12 of which were enriched and interconnected in pathways associated with the inflammatory response. It is interesting to note that certain cancer-related pathways were indicated in our analysis, such as ‘pathways in cancer’.
Conclusion: For the first time, our study provides a genome-wide mapping of DNA (hydroxyl)methylation for DCs that interacted with FgESPs. Our study also suggests a possible immunoregulatory mechanism of FgESPs that acts by increasing DNA methylation levels on genes and pathways associated with TLR signaling.

overall_design: In the current study, we have profiled the DNA methylome and hydroxymethylome by using high-throughput sequencing. Total DNA was extracted from buffalo PBMC DCs that were treated with FgESP, which was followed byFgESPs, and then performed (hydroxy)methylated DNA immunoprecipitation sequencing [(h)MeDIP-Seq].


title: The effect of the fon2 and asp1 mutations on the expression profile in the inflorescence meristem

city: Bunkyo-ku

first: Chie

last: Suzuki

department: School of Science, Department of Biological Sciences

institute: The University of Tokyo

summary:
To determine the effect of the fon2 and asp1 mutations on meristem maintenance, we carried out microarray analysis using Rice (US) gene 1.0 ST array.
We analyzed gene expression profiles of the inflorescence meristems of WT, fon2-3, asp1-10, and fon2-3 asp1-fe.

overall_design: The inflorescence meristems at the In1~In2 stage including a few bracts were sampled.

first: Yukiko

last: Sugisawa

first: Hiro-Yuki

last: Hirano


title: tRNA profiling of MCF10A cells after H2O2 stress

city: New York

first: Doowon

last: Huh

state: New York

address: 1230 York Avenue

institute: Rockefeller University

summary: We report the changes in tRNA abundance as measured by tRNA profiling after cells have been exposed to oxidative stress by H2O2.

overall_design: MCF10A cells were exposed to H2O2 and then RNA was harvested 8 and 24 hours after treatment. These samples were compared to a non-treated control.

first: Sohail

last: Tavazoie


title: Ribosome profiling of MCF10A cells with tRNA-Tyr-GUA depletion by shRNA relative to shControl cells

summary: We report the changes in ribosome protected fragments  as measured by ribosome profiling in cells with or without depletion of tRNA-Tyr-GUA

overall_design: MCF10A cells with an shRNA against tRNA-Tyr-GUA or a control hairpin were subjected to ribosome profiling


title: RNA-sequencing of placenta during the second half of gestation in sows

city: chengdu

first: peng

last: wang

state: Sichuan province

address: No. 211, Huimin Road, Wenjiang District

department: Institute of Animal Nutrition

institute: Sichuan agricultural university

summary: Cholestasis of pregnancy endangers fetal and neonatal survival, however, the underlying mechanisms are largely undetermined. By RNA-sequencing analysis of developing placentas, we identified "bile acids secretion" and "complement and coagulation system" as the most affected KEGG pathway during late pregnancy. In "bile acids secretion" pathway, the downregulated placental carbonic anhydrase II (CA2) expression may in part account for the impaired placental bile acids transport in response to maternal cholestasis. In "complement and coagulation system", the activated placental C5a receptor 1(C5aR1) might provide further evidence for the potential correlation of serum C5a concentration and fetal death as previously observed in humans. Collectively, these results provide new explanation for impaired placental bile acids transport as pregnancy advances, and imply the potential role of "complement and coagulation system" activation in causing adverse fetal outcomes.

overall_design: We perform RNA-seq on sow's placenta at day 60 of gestaion (G60), day 90 of gestaion (G90) and farrowing day (L0).RNA-seq was completed on an Illumina HiSeq 2000, paired-end 100bp reads.

first: Z

last: Fang

first: P

last: Wang


title: smRNA sequencing of MCF10A cells after H2O2 stress

summary: We report the changes in tRNA fragment abundance as measured by small RNA sequencing after cells have been exposed to oxidative stress by H2O2.

overall_design: MCF10A cells were exposed to H2O2 and then RNA was harvested 1 hour after treatment. These samples were compared to a non-treated control.


title: microRNA profiling of human pulmonary artery smooth muscle cells under hypoxia

city: Incheon

first: Hara

last: Kang

address: 119 Academy-ro

institute: Incheon National University

summary: Analysis of hypoxia-exposed human pulmonary artery smooth muscle cells to identify the commonly regulated microRNAs by hypoxia. Results provide insight into the regulatory mechanism of hypoxic responses in vascular smooth muscle cells.

overall_design: microRNA expression profiles of the human pulmonary artery smooth muscle cells after exposure to hypoxia by Illumina HiSeq 2000.


title: Oncogenic zinc finger protein ZNF322A promotes lung cancer stemness through transcriptionally suppressing c-Myc expression [ChIP-Seq]

city: Tainan

first: Yi-Ching

address: No.1, University Road, Tainan 70101, Taiwan, R. O. C.

department: Department of Pharmacology, College of Medicine

country: Taiwan

institute: National Cheng Kung University

summary: ZNF322A, a C2H2 zinc finger transcription factor, is an oncoprotein in lung cancer. However, the transcription mechanisms of ZNF322A in lung cancer stemness remain elusive. By integrating our chromatin immunoprecipitation-sequencing and RNA-sequencing datasets, we identified and validated transcriptional targets of ZNF322A, which significantly enriched in developmental processes. Indeed, overexpression of ZNF322A promoted self-renewal ability and increased stemness-related gene expressions in vitro and in vivo. Importantly, ZNF322A bound directly to c-Myc promoter to transcriptionally suppress c-Myc expression, which in turn increased mitochondrial oxidative phosphorylation, promoted cell motility and thus maintained lung cancer stemness properties. Clinically, ZNF322AHigh/c-MycLow expression profile was revealed as an independent factor for poor outcome of lung cancer patients. Our study provides first evidence that ZNF322A-centered transcriptome promotes lung tumorigenesis and ZNF322A acts as a transcription suppressor of c-Myc to maintain lung cancer stemness by shifting metabolism phenotype to oxidative phosphorylation.

overall_design: Genome-wide ZNF322A binding sites were identified via chromatin immunoprecipitation-sequencing analysis of vecoter control and HA-tagged ZNF322A overexpressing H460 lung cancer cells. ChIP-seq analyses were performed in duplicated samples using Applied Biosystems SOLiD system.

first: Jayu

last: Jen


title: Oncogenic zinc finger protein ZNF322A promotes lung cancer stemness through transcriptionally suppressing c-Myc expression


title: Human pulmonary artery smooth muscle cells under hypoxia


title: An adaptive stress-induced tRNA depletion response mediates codon-based gene repression and growth suppression


title: Deregulated pulmonary growth hormones after intrauterine smoke exposure

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

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

platform_organism:
Mus musculus
synthetic construct


title: Transcriptomic profiling of peripheral blood mononuclear cells from patients with Parkinson's disease and control subjects

city: Lille

first: Marie-Christine

last: Chartier-Harlin

address: 1 place de Verdun

institute: INSERM

summary: To get insight into systemic molecular events associated with Parkinson's disease (PD), an age-related neurodegenerative disorder, we compared gene expression patterns of peripheral blood mononuclear cells (PBMC) derived from elderly healhy controls and from PD patients.

overall_design: Transcriptomic profiling of patients with Parkinson's disease and control subjects. RNA were extracted from peripheral mononuclear blood cells and were hybridized on 4x44k Agilent expression microarrays.

first: M


title: Gene Expression Pathways Implicated in Posttraumatic Stress Disorder and Symptomatic Improvement

city: Bethesda

first: Heather

last: Rusch

address: 1 Cloister Court, Building 60

department: NINR

institute: NIH

summary: Military service members often return from deployment with a multiplicity of injuries, including mild traumatic brain injury, depression, and sleep disorders, which obsures diagnosis of PTSD symptoms and complicates treatment of PTSD. In order to understand the biological mechanisms underlying PTSD, gene expression profiles of military service members with and without PTSD were compared. Additionally, gene expression was examined based on intrusion symptoms, a distinct subtype of PTSD symptoms, and on improvement of PTSD symptoms at a three month follow up. RNA was extracted from blood samples and hybridized to the HG-U133_Plus_2 Affymetrix chip.

overall_design: Gene expression of subjects with PTSD (n=39) were compared to controls without PTSD (n=27) at baseline. Further analysis of gene expression for subjects with PTSD at follow-up was based on improvement or lack of improvement in PTSD symtpoms. 109 Samples (not all subjects had follow-up data) were analyzed in total.

first: Jessica

middle: M

last: Gill

first: Sijun

last: Yun


summary:
Background: In utero smoke exposure is a recognized risk factor for impaired lung function development and a significant risk factor for airway disease. Despite intensive anti-tobacco campaigns the prevalence of smoking pregnant women has remained high requiring additional strategies to protect the offspring’s lung. To achieve this goal, it is critical to understand the mechanisms how disease risks are established in early life.
Objective: To develop an animal model that recapitulates clinical findings in prenatally exposed children to allow the investigation of early molecular changes in the lung.
Methods: Pregnant mice were exposed to active smoking from gestational day (GD) 2.5 until caesarean section or spontaneous delivery. After careful maternal characterization, we monitored weight development, lung function, and airway remodeling in offspring. mRNA/miRNA arrays were performed in fetal lungs (GD18.5), followed by network analyses, qPCR and histone analyses.

overall_design: We performed mRNA expression microarray analysis on fetal (E18.5) lung tissue derived from mothers exposed to smoke or from untreated mothers.

first: Stefan

last: Dehmel

first: Petra

last: Nathan

first: Hagen

last: Scherb

first: Sabine

last: Bartel

first: Katrin

last: Milger

first: Gerrit

last: John

first: Ali

middle: A

last: Yildirim

first: Machteld

last: Hylkema

first: Martin

last: Irmler

first: Arthur

last: Penn

first: Bianca

last: Schaub

first: Oliver

last: Eickelberg

first: Susanne

last: Krauss-Etschmann


title: Gene expression changes in HSV-1 infected HeLa cells with knockdown of B2M

status: Public on Sep 24 2019

city: Beijing

first: Ziqiang

last: Wang

address: North Street of Zhongguancun, Haidian Distric

institute: Tsinghua University

summary: To understand the global effects of B2M knock-down on host gene expression, the RNA-seq study was carried out using HSV-1 infected HeLa cells transfected with B2M siRNAs (siB2M) or negative control siRNAs (siCTRL)

overall_design: HeLa cells were cultured in media and transfected with B2M siRNAs  (n=3) or negative control siRNAs (n=3) for 48 hours . Then, the cells were infected with HSV-1 at an MOI of 1 for 4 hours and were harvested for total RNA isolation.

first: Yaou

last: Zhang


title: Transcriptional profiling of human pulmonary artery smooth muscle cells under hypoxia

first: Hara

last: Kang

summary: Analysis of hypoxia-exposed human pulmonary artery smooth muscle cells to identify the commonly regulated genes by hypoxia. Results provide insight into the regulatory mechanism of hypoxic responses in vascular smooth muscle cells.

overall_design: mRNA expression profiles of the human pulmonary artery smooth muscle cells after exposure to hypoxia by Illumina HiSeq 2000.


title: Stag1 and Stag2 regulate cell fate decisions in hematopoiesis through non-redundant topological control [II]

first: Richard

last: Koche

institute: Memorial Sloan Kettering Cancer Center

summary: Transcriptional regulators, including the cohesin complex member STAG2, are recurrently mutated in cancer. The role of STAG2 in gene regulation, hematopoiesis, and tumor suppression remains unresolved. We show Stag2 deletion in hematopoietic stem/progenitor cells (HSPC) results in altered hematopoietic function, increased self-renewal, and impaired differentiation. ChIP-sequencing revealed that while Stag2 and Stag1 can bind the same loci, a component of Stag2 binding sites are unoccupied by Stag1 even in Stag2-deficient HSPCs. While concurrent loss of Stag2 and Stag1 abrogated hematopoiesis, Stag2 loss alone decreased chromatin accessibility and transcription of lineage-specification genes, including Ebf1 and Pax5, leading to blunted HSPC commitment to the B-cell lineage. Our data illustrate a role for Stag2 in transformation and transcriptional dysregulation distinct from its shared role with Stag1 in chromosomal segregation.

overall_design: Single-cell RNA sequencing was performed on 6 samples ( Lin-HSPC) from Stag2 KO (n=3) and WT (n=3) mice and were assayed for transcriptome-wide RNA-sequence.

first: Aaron

last: Viny

first: Vincent-Philippe

last: Lavallée

first: Ross

middle: L

last: Levine


title: Expresion data of Raw 264.7 cells treated with violacein

city: San Pedro

first: Alfonso

last: García-Piñeres

address: Ciudad Universitaria Rodrigo Facio

country: Costa Rica

institute: Universidad de Costa Rica

summary:
Violacein, an indole-derived purple-colored natural pigment isolated from Chromobacterium violaceum has shown multiple biological activities. In this study, we report that violacein activates murine macrophages through the up-regulation of TNF-α expression at non-cytotoxic concentrations (2 µmol/L). This was evaluated by measurement of TNF-α expression using real-time qRT-PCR. In addition, we obtained evidence of the molecular mechanism of activation by determining the mRNA expression pattern upon treatment with violacein.
Interestingly, the mRNA expression pattern also allowed us to observe that incubation with violacein caused activation of pathways related with an immune and inflammatory response. Together, our data indicate that violacein activates the TLR8 receptor signaling pathway, and in consequence induces production of inflammatory cytokines such as TNF-α, CCL3 and CCL4 and of negative regulators of TLR signaling such as AP20, IRG1, IκBα and IκBε. Finally, we studied the interaction of TLR8 with violacein in silico, and obtained evidence that violacein could bind to TLR8 in a similar fashion to imidazoquinoline compounds. Therefore, our results indicate that violacein could be a candidate to be applied in immune therapy.

overall_design: Raw 264.7 cells were treated with violacein (three positive controls) and other three samples with fresh medium (negative controls). After incubation,  total RNA extraction and  hybridization on Affymetrix microarrays was made.

first: Francisco

last: Venegas

first: Max

last: Chavarría

first: Juan

last: Araya

last: Garcia-Piñeres


title: Transcriptional Profiling of Werner Syndrome (WS) iPSC-derived MSC and the isogenic gene-edited controls

city: CUHK, Shatin

first: Hoi-Hung

last: Cheung

address: Rm.708A, LKS Integrated Biomedical Sciences Bldg.

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: WS iPSC (iWS780) is a WRN-null iPSC line derived from AG00780 fibroblast. This iPSC line showed normal 46,XY karyotype. iWS780 was gene-edited by CRIPSR/Cas9 to correct the WRN point mutation. Two clones (C21 & C24) were characterized and showed expression of wild-type WRN protein after gene editing. The iPSC lines (isogenic) were subsequently differentiated into mesenchymal stem cells (MSC). RNA-seq was performed on these MSC.

overall_design: WRN-mutant iPSC line was gene-corrected and differentiated to MSC. Transcriptional profiling was performed on the MSC.

first: Wai-Yee

last: Chan


title: Pharmacological Induction of a Progenitor State for the Efficient Expansion of Primary Human Hepatocytes

city: Lausanne

first: Evarist

last: Planet

state: Vaud

address: Route Cantonale

institute: EPFL

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

overall_design: Refer to individual Series


title: Polysome profiling quantified by RNA sequencing in ERα knockdown and control BM67 cells

city: Solna

first: Ola

last: Larsson

address: Tomtebodavägen 23A

country: Sweden

institute: Karolinska Institute

summary: Estrogen receptor alpha (ERα) activity is associated with increased cancer cell proliferation. Studies aiming to understand the impact of ERα on cancer-associated phenotypes have largely been limited to its transcriptional activity. Herein, we demonstrate that ERα coordinates its transcriptional output with selective modulation of mRNA translation. Importantly, translational perturbations caused by depletion of ERα largely manifest as "translational offsetting" of the transcriptome, whereby amounts of translated mRNAs and corresponding protein levels are maintained constant despite changes in mRNA abundance. Transcripts whose levels, but not polysome-association, are reduced following ERα depletion lack features which limit translation efficiency including structured 5'UTRs and miRNA target sites. In contrast, mRNAs induced upon ERα depletion whose polysome-association remains unaltered are enriched in codons requiring U34-modified tRNAs for efficient decoding. Consistently, ERα regulates levels of U34-modifying enzymes and thereby controls levels of U34-modified tRNAs. These findings unravel a hitherto unprecedented mechanism of ERα-dependent orchestration of transcriptional and translational programs that may be a pervasive mechanism of proteome maintenance in hormone-dependent cancers.

overall_design: Polysome profiling was performed on 4 replicates of ERα knockdown and control BM67 cells. Total input mRNA and polysome-associated mRNA (mRNA associated with > 3 ribosomes) were quantified using RNA sequencing.

first: Julie

last: Lorent

first: Eric

last: Kusnadi

first: Vincent

last: van Hoef

last: Rebello

first: Matthew

last: Leibovitch

first: Johannes

last: Ristau

first: Shan

last: Chen

first: Mitchell

middle: G

last: Lawrence

first: Krzysztof

last: Szkop

first: Baila

last: Samreen

first: Preetika

last: Balanathan

first: Francesca

last: Rapino

first: Pierre

last: Close

first: Patricia

last: Bukczynska

first: Karin

last: Scharmann

first: Itsuhiro

last: Takizawa

first: Gail

last: Risbridger

first: Luke

last: Selth

first: Sebastian

last: Leidel

first: Qishan

last: Lin

first: Ivan

last: Topisirovic

first: Luc

last: Furic


title: Small RNA sequencing in ERα knockdown and control BM67 cells

first: Ola

last: Larsson

overall_design: Small RNA sequencing was performed on 3 replicates of ERα knockdown and control BM67 cells.

first: Julie

last: Lorent

first: Eric

last: Kusnadi

first: Vincent

last: van Hoef

first: Richard

last: Rebello

first: Matthew

last: Leibovitch

first: Johannes

last: Ristau

middle: P


title: HITS-CLIP of SSB from MDA-231 cells

first: Doowon

last: Huh

country: USA

summary: We report the CLIP binding interactions from the RNA binding protein SSB

overall_design: MDA-231 cells were used to identify RNA binding interactions from SSB

first: Sohail

last: Tavazoie


title: Oncogenic zinc finger protein ZNF322A promotes lung cancer stemness through transcriptionally suppressing c-Myc expression [RNA-Seq]

first: Yi-Ching

last: Wang

overall_design: mRNA profiles of A549 lung cancer cells treated with control or si-ZNF322A oligo were generated by RNA-sequencing

first: Jayu

last: Jen


title: Translational offsetting as a mode of estrogen receptor alpha-dependent regulation of gene expression


title: NanoCAGE in ERα knockdown BM67 cells

overall_design: nanoCAGE sequencing of cytosolic mRNA from shERα BM67 cells was performed on 3 biological replicates. Each biological replicate was prepared with 2 barcodes.

first: Shan

last: Chen

first: Mitchell

last: Lawrence

first: Krzysztof

last: Szkop

first: Baila

last: Samreen

first: Preetika

last: Balanathan

first: Francesca

last: Rapino

first: Pierre

last: Close

first: Patricia

last: Bukczynska

first: Karin

last: Scharmann

first: Itsuhiro

last: Takizawa

first: Gail

last: Risbridger


title: Polysome profiling quantified by DNA-microarrays in ERα knockdown and control BM67 cells

first: Ola

last: Larsson

overall_design: Polysome profiling was performed on 3 replicates of ERα knockdown and control BM67 cells. Total input mRNA and polysome-associated mRNA (mRNA associated with > 3 ribosomes) were quantified using Affymetrix Mouse Gene 1.1 ST Array.

first: Julie

last: Lorent

first: Eric

last: Kusnadi

first: Vincent

last: van Hoef

first: Richard

last: Rebello

first: Matthew

last: Leibovitch

first: Luke

last: Selth

first: Sebastian

last: Leidel

first: Qishan

last: Lin

first: Ivan

last: Topisirovic

first: Luc

last: Furic


title: Cardiac profiling of Yap-bound chromatin in neonatal Salvador mutant mice

city: Houston

first: Todd

middle: Ryan

last: Heallen

state: Texas

address: One Baylor Plaza

department: Molecular Physiology and Biophysics

institute: Baylor College of Medicine

summary: In this study, we identified chromatin regions bound by YAP, a major effector of the Hippo tumor suppressor pathway. To disrupt Hippo signaling in the mouse heart, we inactivated the single mammalian Salv ortholog using a Salv conditional null allele and and tamoxifen inducible Myh6-cre/Esr1 allele, Cre activity was induced with 4 consecutive intraperitoneal (i.p.) or subcutaneous injections of tamoxifen from P7-P10.

overall_design: Genomic DNA from P8-stage and P12-stage hearts were used for Yap ChIP-seq.

middle: R

first: Min

last: Zhang


title: Coordinated regulation of pre-mRNA splicing by the SFPS-RRC1 complex to promote photomorphogenesis in Arabidopsis

city: Austin

first: Enamul

last: Huq

state: TX

address: 205 West 24th

department: IB

institute: University of Texas at Austin

summary: We report the application of illumina high throughput RNA sequencing for rrc1-3 mutants in both light and dark conditions(three replicates under each condition) in Arabidopsis.  By obtaining over 100 million reads (150bp paired_end) for each rRNA depleted lib, we compared the transcriptome profile between rrc1-3 mutant and Col-0 wild type light and dark conditions. We find that genome wide spliciing activities are general defective in rrc1-3 mutant comparing to Col-0 wild type, which indicates the importance of post-transcriptional processing on gene expression regulation. In addition, the sequencing data also indicates light signal probably regulates both splicing cascade and transcriptional cascade to control the downstream gene expression.

overall_design: Examination of splicing profile in rrc1-3 mutants, comparing with Col-0 wild type under both light and dark conditions.

first: Ruijiao

last: Xin

first: Praveen

last: Kumar Kathare


title: Copper Regulation of HIF-1 Transcription Activity

city: Chengdu

first: Zhijuan

last: Wu

state: Sichuan

address: Keyuan Road 4, Gaopeng avenue

department: Sichuan University West China Hospital

country: China

institute: Regenerative Medicine Research Center


title: Copper Regulation of HIF-1 Transcription Activity [ChIP-seq]

summary: Copper (Cu) regulates hypoxia-inducible factor-1 (HIF-1) transcription activity by affecting the selectivity of HIF-1α targeting to the promoters of the affected genes. Here, we made an effort to provide a comprehensive understanding of Cu regulation of the selectivity of HIF-1α targeting across genome. We used tetraethylenepentamine (TEPA), a Cu selective chelator, to reduce Cu content in the cells. In hypoxia, we conducted chromatin immunoprecipitation combined with massively parallel DNA sequencing (ChIP-seq) to globally map the binding sites of HIF-1α, Pol Ⅱ (RNA polymeraseⅡ) and histone H3K27ac. We also performed RNA-sequencing (RNA-seq) in EA.hy926 cells under hypoxia (1% O2) with or without Cu depression to determine the profile of mRNA expression. Our analyses identified 3197 HIF-1α binding sites under hypoxia. Cu depression by TEPA reduced 1820 binding sites from the 3197, but induced additional 274 new binding sites. We analyzed these binding sites in the promoter and putative enhancer regions, coupled with their mRNA expression profiles, and found 281 Cu-dependent and 10 Cu-independent HIF-1α target genes. We found that the core bases “GGAA” and “TTCC” constituted the critical motifs for the binding sites of Cu-dependent genes. This study thus revealed that Cu, by affecting the binding of HIF-1α to the critical motifs in the promoter and putative enhancer regions of HIF-1 regulated genes, leads to the selectivity of HIF-1 regulated expression of Cu-dependent genes.

overall_design: Analysis of DNA-binding profiling of HIF-1α, Pol Ⅱ and H3K27ac in TEPA treated and -untreated cells. .

first: Wenjing


title: Differential expression of microRNAs and their target genes in Dilated Cardiomyopathy

city: Ji'nan

first: Huang

last: Guangyong

address: Cultural West Road,No.44

institute: Shandong University

summary: We aimed to identify aberrantly expressed microRNA and mRNA expression profiles of dilated cardiomyopathy (DCM) and explore their potential functions, 10 DCM blood samples and paired healthy control blood samples underwent RNA-sequence.

overall_design: A prospective case-control study was designed to identify the changes in expression of microRNA and mRNA, 10 DCM blood samples and paired healthy control blood samples underwent RNA-sequence, using Illumina HiSeq 4000.

first: Guangyong

last: Huang


title: Therapeutic targeting of the pre-metastatic stage in human brain metastasis

city: Toronto

first: Igor

last: Jurisica

state: Ontario

address: 60 Leonard Avenue

department: Krembil Research Institute

country: Canada

institute: University Health Network

summary: We have used our established brain metastasis initiating cell (BMIC) models and gene expression analyses to characterize pre-metastasis in human lung-to-brain metastases.

overall_design: We utilized early passage Brain Metastasis cell lines derived from primary patient samples of lung-to-brain metastases in our work, as these samples are enriched for brain metastasis initiating cells (BMICs) that have already successfully completed the metastatic process. Previous work in our lab successfully established preclinical models of lung-to-brain BM(Nolte, et al., 2013; Singh, et al., 2017). Briefly, we injected mice through three different injection routes: a) intracranial (ICr), b) intrathoracic injections (IT), and c) intracardiac injections (ICa), where we were able to replicate the pre-metastatic and macro-metastatic stages from IT and ICa injections respectively(Singh, et al., 2017). Here, we have further isolated and characterized BMICs at each metastatic stage.  BMIC lines transduced with GFP were injected into our BM models and were shown to reform tumors at each stage of the metastatic cascade, from primary lung (LT) and secondary brain (BT) tumor formation to the pre-metastatic (BMIT) and macro-metastasis (BMIC) stages of tumor growth. BMICs were isolated from BT, BMIT, and BMIC tumors and minimally cultured. RNA was extracted from these cells and submitted for RNA seq analysis.

first: Mohini

last: Singh

first: Chitra

last: Venugopal

first: Minomi

last: Subapanditha

first: Maleeha

last: Qazi

first: David

last: Bakhshinyan

first: Parvez

last: Vora

first: Naresh

last: Murty

first: Sheila

middle: K

last: . Singh

first: Tomas

last: Tokar


title: TCF12 promotes the tumorigenesis and metastasis of hepatocellular carcinoma via upregulation of CXCR4 expression [ChIP-seq]

status: Public on Sep 23 2019

city: Shanghai

first: Jing

last: Yang

address: 25/Ln 2000 Xietu Road

institute: Shanghai Cancer Institute, Renji Hospital

summary: Stable ectopic TCF12 expression or knockdown in HCC cell lines was established by lentiviral infection. Then, MTT, colony formation, migration, invasion and HUVEC tube formation assays as well as an orthotopic xenograft model were used to investigate the biologic function of TCF12 in HCC cells in vitro and in vivo. Subsequently, RNA-Seq analysis was utilized to explore the target gene regulated by TCF12. RT-qPCR, western blotting, a dual-luciferase reporter assay, Ch-IP and functional rescue experiments were used to confirm the target gene regulated by TCF12. Finally, RT-qPCR, western blot and immunohistochemical (IHC) staining were performed to detect the expression level of TCF12 and to analyze the correlation of TCF12 with downstream genes as well as the clinical significance of TCF12 in human primary HCC.Our functional studies revealed that stable overexpression of TCF12 in human HCC cells enhanced cell proliferation, migration and invasion in vitro and in vivo, whereas knockdown of TCF12 showed opposing effects. Mechanistically, CXCR4 was a downstream target of TCF12, and TCF12 directly bound to the CXCR4 promoter to regulate its expression. Moreover, CXCR4, with its ligand CXCL12, played a critical role in tumor progression induced by TCF12 via activation of the MAPK/ERK and PI3K/AKT signaling pathways. Clinically, IHC analysis revealed that TCF12 was significantly associated with poor survival of HCC patients and that TCF12 expression was closely correlated with CXCR4 expression in primary HCC tissues. Our findings are the first to indicate that TCF12 could promote the tumorigenesis and progression of HCC mainly by upregulating CXCR4 expression and is a prognostic indicator for patients with HCC.

overall_design: Identification of TCF12 binding sites in Hep3B cells

first: Lili

last: Zhang


title: Stag1 and Stag2 regulate cell fate decisions in hematopoiesis through non-redundant topological control [I]

city: New York

first: Richard

last: Koche

summary: Transcriptional regulators, including the cohesin complex member STAG2, are recurrently mutated in cancer. The role of STAG2 in gene regulation, hematopoiesis, and tumor suppression remains unresolved. We show Stag2 deletion in hematopoietic stem/progenitor cells (HSPC) results in altered hematopoietic function, increased self-renewal, and impaired differentiation. ChIP-sequencing revealed that while Stag2 and Stag1 bind a shared set of genomic loci, a component of Stag2 binding sites are unoccupied by Stag1 even in Stag2-deficient HSPCs. While concurrent loss of Stag2 and Stag1 abrogated hematopoiesis, Stag2 loss alone decreased chromatin accessibility and transcription of lineage-specification genes, including Ebf1 and Pax5, leading to increased self-renewal and reduced HSPC commitment to the B-cell lineage. Our data illustrate a role for Stag2 in transformation and transcriptional dysregulation distinct from its shared role with Stag1 in chromosomal segregation.

overall_design: ChIP-sequencing of PU.1 in Stag2 wildtype and knockout cells derived from murine bone marrow and spleen

first: Aaron

middle: D

last: Viny

first: Ross

last: Levine


title: Copper Regulation of HIF-1 Transcription Activity [RNA-seq]

first: Zhijuan

last: Wu

overall_design: Analysis of mRNA profiles in TEPA treated and -untreated cells. .

first: Wenjing


title: Compared the gene expression profiles between the PTL-Her2-CAR-T cells and Her2-CAR-T cells isolated from tumor tissues

city: Guangzhou

first: Lijuan

last: Lu

address: 74 Zhongshan 2nd Rd

institute: Sun Yat-sen University

summary: To further development of different gene expression between the PTL-Her2-CAR-T cells (knockdown of PD-1, Tim-3, Lag-3 by shRNA-clusters in Her2-CAR-T cells)  and Her2-CAR-T cells,  we have employed whole genome microarray expression profiling as a discovery platform.

overall_design: SKOV3-bearing NSG mice were injected with various CAR-T cells via tail. At 28 days after CAR-T-cells infusion, mice were euthanized and tumor tissues were resected. The tumor was divided and tumor infiltrating CAR-T cells were separated for RNA-seq.

first: Fan

last: Zou


title: TCF12 promotes the tumorigenesis and metastasis of hepatocellular carcinoma via upregulation of CXCR4 expression

overall_design: the transcriptome of Hep3B-NC and Hep3B-shTCF12-2 cells was examined by RNA-Seq analysis.


title: Subclonal cooperation drives metastasis through modulating local and systemic immune microenvironments

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Bulk RNA-Seq: Gene expression analysis of stromal and tumor fractions of primary and metastatic lesions of polyclonal and monoclonal origin. Primary tumor control samples consist of monoclonal Thy1.1 (no replicates), monoclonal parental (no replicates), monoclonal IL11 (duplicate), monoclonal FIGF (duplicate), and monoclonal CFP (duplicate). Primary polyclonal tumor samples consist of separated Thy 1.1 (duplicate), CFP (no replicates), IL11 (triplicate), and FIGF (triplicate). Metastatic tumor samples consist of monoclonal CFP (duplicate), monoclonal IL11 (quadruplicate), monoclonal FIGF (quadruplicate), monoclonal Thy1.1 (duplicate), and polyclonal samples (duplicate). Metastatic stromal fractions consist of monoclonal CFP (duplicate), monoclonal FIGF (quadruplicate), monoclonal IL11 (quadruplicate), monoclonal parental (duplicate), monoclonal Thy1.1 (duplicate), and polyclonal samples (triplicate). Primary stromal  samples consist of monoclonal CFP (duplicate), monoclonal FIGF (duplicate), monoclonal IL11 (duplicate), monoclonal parental (no replicates), monoclonal Thy1.1 (duplicate), and polyclonal samples (triplicate). Further stromal controls consisted of a single fatpad sample and lung sample.     Single cell RNA-Seq: Blood, tumors and lungs were isolated from test groups (DOX+ and DOX-) and tumor-naÃ¯ve animals. Samples were pooled across 3 animals per group, and CD45+populations were FACS-sorted. Two thousand single cells were targeted for each sample.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Gene expression analysis of IL11RA and PLXDC sorted fractions from lungs of tumor-bearing mice. Tumor cells were induced to overexpress IL11/FIGF with DOX diet given to the animals.

first: Michalina

last: Janiszewska

first: Doris

last: Tabassum

first: Zafira

last: Castrano

first: Simona

last: Cristea

first: Kimiyo

middle: N

last: Yamamoto

first: Natalie

last: Kingston

first: Katherine

last: Murphy

first: Shaokun

last: Shu

first: Nicholas

last: Harper

first: Carlos

last: Gil Del Alcazar

first: Maša

last: Alečković

first: Muhammad

last: Ekram

first: Ofir

last: Cohen

first: Minsuk

last: Kwak

first: Yuanbo

last: Qin

first: Tyler

last: Laszewski

first: Adrienne

last: Luoma

first: Andriy

last: Marusyk

first: Kai

last: Wucherpfennig

first: Nikhil

last: Wagle

first: Rong

last: Fan

first: Franziska

last: Michor

first: Sandra

last: McAllister


title: Developmental plasticity of epithelial stem cells in tooth and taste bud renewal

city: London

first: Paul

middle: T.

last: Sharpe

state: Please select one below:

address: Guy's hospitial

department: Centre for Craniofacial and Regenerative Biology

country: United Kingdom

institute: King's College London

summary: In Cichlids, replacement teeth (RT) share a continuous band of epithelium with adjacent taste buds (TB) and both organs co-express stem cell factors in subsets of label-retaining cells. In the mouse and other mammals, the tongue inter molar eminence (IE) oral papillae of Follistatin (Fat, BMP antagonist) mutants exhibited dysmorphic invagination. By using NGS-derived transcriptome profiling (RNAseq) analysis, we compared differential gene expression in the mouse tongue tissue in Follistatin (Fst) mutants mice with the wild type controls. Our results demonstrated ectopic expression of dental markers in tongue IE indicating that vertebrate oral epithelium retains inherent plasticity to form tooth and taste-like cell types mediated by BMP, therefore revealed under appreciated epithelial cell populations with promising potential in bioengineering and dental therapeutics.

overall_design: Total RNA was extracted from mouse IE tissue at E17.5 in triplicate from Follistatin mutants and wild type mice. The mRNA profiles were generated by deep sequencing using Illumina Hiseq platform and the sequence reads that passed the quality filters were aligned with mouse mm10 reference genome by Partek workflows with default parameters. Aligned reads were annotated and normalized and differential gene expression was identify by GSA. Data analysis with BWA workflows revealed a number of potential differential tooth genes related to BMP signaling pathway that ectopically expressed in the tongue IE suggesting an evolutionary and developmental lineages of cells that function in oral organ systems may provide clues to their manipulation in regenerative medicine.

first: Ryan

last: Bloomquist

first: Teresa

middle: E

last: Fowler

first: Zhengwen

last: An

first: Tian

last: Yu

first: Kawther

last: Abdileh

first: Gareth

last: Fraser

middle: T

first: J

last: Streelman


title: Differential expression profiles of extracellular vesicle-coupled miRNA in follicular fluid of cows at different metabolic status

city: Bonn

first: Tsige

last: Hailay

address: Endenicher Allee 15

department: Animal Breeding and Husbandry

institute: University of Bonn

summary: This study was performed to discover the association between postpartum during negative energy balance and the expression of extracellular vesicle-coupled microRNAs signatures in follicular fluid of large follicle in dairy cows. For this, next-generation sequencing to total RNA miRNA was performed.

overall_design: Collected of follicular fluid was performed from both postpartum cows and heifers using an ovum pick-up technique from large follicles. Follicular fluid from postpartum cows was collected from week 5-10 of postpartum in weekly bases. Follicular fluid from heifers was collected for continuous 5 weeks. Prior to pooling of samples, the energy balance statuses of individual postpartum cows were assessed using three criteria: blood serum metabolite analysis, body weight curves, and overall energy balance based on dry matter intake. Based on these three criteria’s, animals were grouped in to three phenotypes namely: Transient cows (TCs) (n=20), Always Negative cows (ANCs) (n=5) and Always positive cows (APCs) (n=5). Follicular fluid samples from cystic ovaries and blood contamination are discarded from the analysis. Follicular fluid samples from TCs at week 5 and 6 (n=11) and at week 9 and 10 (n=7) were separately pooled to create three biological replicates. Follicular fluid collected from ANCs (n=2) and APCs (n=2) at week 5 and 6 were pooled to generate two biological replicate per group of cows. For heifers, follicular fluid recovered from eight heifers was also pooled to generate three biological replicates after the analysis of their metabolites and all was at positive energy balance.

first: T

first: M

last: Hoelker

last: Poirier

first: S

last: Gebremedhn

first: F

last: Rings

last: Saeed Zidane

first: D

last: Salilew-Wondium

first: C

last: Dauben

first: E

last: Tholen

last: Neuhoff

first: K

last: Schellander

last: Tesfaye